tag:blogger.com,1999:blog-4962634673003702642024-03-14T07:21:40.364+00:00The Y.O.R.F.The York Open Reading FrameCathttp://www.blogger.com/profile/08645968914831610862noreply@blogger.comBlogger44125tag:blogger.com,1999:blog-496263467300370264.post-4168756627888288092012-07-09T11:09:00.001+01:002012-07-09T11:21:54.294+01:00TOPLESS across plant evolution<span style="float: left; padding: 5px;"><a href="http://www.researchblogging.org"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border:0;"/></a></span>Although plants and animals became multicellular organisms independently they use many of the same mechanisms to control the complex feat of going from one cell to trillion. Both need to produce organs (arms or leaves) and their embryos need to decide what is top and bottom (head vs feet or shoot vs root). After a round of random mutagenesis (Long et al., 2002; Long et al., 2006), identified a mutant, which at elevated temperatures had the human equivalent of two heads, one of them being where its legs/feet should be. This doubled rooted phenotype was caused by a mutation in a transcriptional co-repressors then named <i>TOPLESS</i> due to the lack of a ‘top’ (shoot) in the mutant plant. The proteins encoded by the <i>TOPLESS</i> gene in plants has related co-repressors in animals. Their job is to regulated which genes are turned off. But they do no bind DNA directly and have no innate specificity for particular genes. Specificity is achieved through transcription factors binding target genes and recruiting co-repressors, which mediates the repression of these genes. It is still not fully understood why the mutation in TOPLESS causes the double rooted phenotype as the TOPLESS protein is involved in many processes including regulating stem cell number and flowering time (Causier et al., 2012a). However, it probably involves the plant hormone auxin. This hormone has a role in nearly every aspect of plant development, including top-bottom (apical-basal) patterning. It has been shown TOPLESS is used by regulators of auxin-dependent gene expression (Aux/IAA proteins) to turn of genes (Szemenyei et al., 2008).<br />
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We decided to ask when TOPLESS become involved with auxin during the evolution of plants. The above work was done in the model flowering plant <i>Arabidopsis thaliana</i>. The first flowering plants emerged during the time of the dinosaurs (about 150 million years ago) but plants first appeared on land about half a billion years ago! One of these early groups of land plants resembled modern day mosses. Taking living mosses like the lab model <i>Physcomitrella patens</i>, we can ask if the same mechanisms controlling growth existed in the last common ancestor of mosses and flowering plants, which existed about half a billion years ago.<br />
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Using a technique called yeast-two hybrid we can detect if two proteins physically interact. We took the two moss TOPLESS proteins and three Aux/IAA proteins and tested their interaction. As expected, both TOPLESS proteins interacted with all three Aux/IAA proteins (Causier et al., 2012b). Previous work has shown A. thaliana TOPLESS interacts with Aux/IAA proteins by using their LxLxL motif in domain 1 (where L is Leucine and x is any amino acid). Moss TOPLESS proteins have an LxLxPP (P is Proline) instead and might be the functional equivalent (Paponov et al., 2009). We mutated the second L of the LxLxPP motif and found no interaction between TOPLESS proteins and Aux/IAA proteins (Causier et al., 2012b).<br />
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Previously, it was shown some auxin response factors (ARF proteins) from <i>A. thaliana</i> interact with TOPLESS (Causier et al., 2012a). These are not the ARFs involved with the ‘classical’ auxin signalling. These are repressors and little is know about them. This work suggests they may act as repressors thanks to the actions of TOPLESS. We investigated if these interactions were also conserved in moss. Although not all repressive ARFs in moss interacted with TOPLESS, two did (Causier et al., 2012b). These are form the ARF10/16/17 family.<br />
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Together, these data show that TOPLESS has been involved with auxin signalling components for the last 500 million years since the origins of land plants. Perhaps these interactions pre-date land plants? But we have shown using simple lab techniques we can try to answer fundamental questions about how the regulation of gene expression has evolved.<br />
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<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Plant+physiology&rft_id=info%3Apmid%2F22065421&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=The+TOPLESS+interactome%3A+a+framework+for+gene+repression+in+Arabidopsis.&rft.issn=0032-0889&rft.date=2012&rft.volume=158&rft.issue=1&rft.spage=423&rft.epage=38&rft.artnum=&rft.au=Causier+B&rft.au=Ashworth+M&rft.au=Guo+W&rft.au=Davies+B&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Causier B, Ashworth M, Guo W, & Davies B (2012). The TOPLESS interactome: a framework for gene repression in Arabidopsis. <span style="font-style: italic;">Plant physiology, 158</span> (1), 423-38 PMID: <a rev="review" href="http://www.ncbi.nlm.nih.gov/pubmed/22065421">22065421</a></span><br />
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<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Plant+signaling+%26+behavior&rft_id=info%3Apmid%2F22476455&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=TOPLESS+co-repressor+interactions+and+their+evolutionary+conservation+in+plants.&rft.issn=1559-2316&rft.date=2012&rft.volume=7&rft.issue=3&rft.spage=&rft.epage=&rft.artnum=&rft.au=Causier+B&rft.au=Lloyd+J&rft.au=Stevens+L&rft.au=Davies+B&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Causier B, Lloyd J, Stevens L, & Davies B (2012). TOPLESS co-repressor interactions and their evolutionary conservation in plants. <span style="font-style: italic;">Plant signaling & behavior, 7</span> (3) PMID: <a rev="review" href="http://www.ncbi.nlm.nih.gov/pubmed/22476455">22476455</a></span><br />
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<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Science+%28New+York%2C+N.Y.%29&rft_id=info%3Apmid%2F16763149&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=TOPLESS+regulates+apical+embryonic+fate+in+Arabidopsis.&rft.issn=0036-8075&rft.date=2006&rft.volume=312&rft.issue=5779&rft.spage=1520&rft.epage=3&rft.artnum=&rft.au=Long+JA&rft.au=Ohno+C&rft.au=Smith+ZR&rft.au=Meyerowitz+EM&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Long JA, Ohno C, Smith ZR, & Meyerowitz EM (2006). TOPLESS regulates apical embryonic fate in Arabidopsis. <span style="font-style: italic;">Science (New York, N.Y.), 312</span> (5779), 1520-3 PMID: <a rev="review" href="http://www.ncbi.nlm.nih.gov/pubmed/16763149">16763149</a></span><br />
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<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Development+%28Cambridge%2C+England%29&rft_id=info%3Apmid%2F12050130&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Transformation+of+shoots+into+roots+in+Arabidopsis+embryos+mutant+at+the+TOPLESS+locus.&rft.issn=0950-1991&rft.date=2002&rft.volume=129&rft.issue=12&rft.spage=2797&rft.epage=806&rft.artnum=&rft.au=Long+JA&rft.au=Woody+S&rft.au=Poethig+S&rft.au=Meyerowitz+EM&rft.au=Barton+MK&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Long JA, Woody S, Poethig S, Meyerowitz EM, & Barton MK (2002). Transformation of shoots into roots in Arabidopsis embryos mutant at the TOPLESS locus. <span style="font-style: italic;">Development (Cambridge, England), 129</span> (12), 2797-806 PMID: <a rev="review" href="http://www.ncbi.nlm.nih.gov/pubmed/12050130">12050130</a></span><br />
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<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=BMC+evolutionary+biology&rft_id=info%3Apmid%2F19493348&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=The+evolution+of+nuclear+auxin+signalling.&rft.issn=&rft.date=2009&rft.volume=9&rft.issue=&rft.spage=126&rft.epage=&rft.artnum=&rft.au=Paponov+IA&rft.au=Teale+W&rft.au=Lang+D&rft.au=Paponov+M&rft.au=Reski+R&rft.au=Rensing+SA&rft.au=Palme+K&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Paponov IA, Teale W, Lang D, Paponov M, Reski R, Rensing SA, & Palme K (2009). The evolution of nuclear auxin signalling. <span style="font-style: italic;">BMC evolutionary biology, 9</span> PMID: <a rev="review" href="http://www.ncbi.nlm.nih.gov/pubmed/19493348">19493348</a></span><br />
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<span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Science+%28New+York%2C+N.Y.%29&rft_id=info%3Apmid%2F18258861&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=TOPLESS+mediates+auxin-dependent+transcriptional+repression+during+Arabidopsis+embryogenesis.&rft.issn=0036-8075&rft.date=2008&rft.volume=319&rft.issue=5868&rft.spage=1384&rft.epage=6&rft.artnum=&rft.au=Szemenyei+H&rft.au=Hannon+M&rft.au=Long+JA&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Szemenyei H, Hannon M, & Long JA (2008). TOPLESS mediates auxin-dependent transcriptional repression during Arabidopsis embryogenesis. <span style="font-style: italic;">Science (New York, N.Y.), 319</span> (5868), 1384-6 PMID: <a rev="review" href="http://www.ncbi.nlm.nih.gov/pubmed/18258861">18258861</a></span>James Lloydhttp://www.blogger.com/profile/08219295648051788360noreply@blogger.com6tag:blogger.com,1999:blog-496263467300370264.post-58086138942016629332010-02-18T17:43:00.010+00:002010-02-28T18:07:04.764+00:00Of moss and me<span style="float: left; padding: 5px;"><a href="http://www.researchblogging.org"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border:0;"/></a></span>I recently had a look through some new papers published on moss (Physcomitrella patens) and found one published in Cell titled ‘Transcriptional control of gene expression by microRNAs’ [1]. This didn’t seem to fit the same pattern of a lot of moss papers I have read (ie in less high impact journals). This paper shows how useful moss is for studying gene expression using reverse genetics (so hopefully my PhD wont be a failure). <br /><br />I think it is important to study important biological problems, such as RNA silencing and epigenetics, in a diverse range of organisms. I take this title from a short review published in Nature Medicine recently (as well as the Steinberg book) by Sir David Baulcombe (who holds a prestigious chair at Cambridge). He wrote about what we have learnt by studying things in plants (eg discovery of transposons) and their importance as a model, using his own research into RNA silencing and epigenetics as the main example [2]. I think this new moss paper goes some way to support this, but also to show the importance of this particular organism. My choice to work with Physcomitrella was because I wanted to stay in the plant world but wanted to work with something where I could knock out specific genes by homologous recombination and was simple to grow. Physcomitrella can be grown on simple agar media plates and joins the few species where genes can be knocked out. <br /><br />Khraiwesh et al (2010) looked at what happened when you knocked out two Dicer-like (DCL) proteins in moss [1]. Dicer proteins in animals and plants cut long dsRNA to make small RNAs loaded onto Argonaute proteins (producing the effector complex). This effector complex is what causes the target mRNA to be cut or repress its translation. When PpDCL1a was knocked out you see a lack of microRNAs (miRNAs) being produced and the plant is restricted to its first developmental stage only. Not surprising. Strangely, when you knocked out PpDCL1b get production of miRNAs but not cleavage of the targets. It has been shown in animals, but not other plants, Dicer proteins can sometimes be used to help a small RNA in the effector complex to cut the target, as well as in miRNA or siRNA biogenesis. Very interestingly they found these targets had a lower level of expression in the mutant plants. If cleavage is not reducing the mRNA levels then what? The answer to this as many other odd questions in biology is epigenetics. Well DNA methylation at least. siRNAs have been shown to cause gene silencing but not much evidence for miRNAs doing this before. The authors went onto show the ratio of miRNA to mRNA target is critical. If you only have a little miRNA compared to mRNA target you get cleavage. If you have lots of miRNA to target mRNA it causes DNA methylation and silencing. But the methylation was only seen in the knockout so why should we care?<br /><br />Finally they end the paper by showing ratio of miRNA to target mRNA is important in an endogenous gene involved with a hormone response. The plant hormone ABA mediates drought response and abiotic stress. In moss, when ABA treated you get a decrease in a transcription factor response gene. This is a target of a natural miRNA. This down-regulation is due to an increase in miRNA expression, changing the effect from cleaving the transcription factor’s mRNA to targeting its promoter for methylation and silencing expression. This study shows that miRNAs have the potential to cause DNA methylation, which had not yet been show, as well as suggesting a mechanism for it. Future studies can now go on to show the relevance of this in other systems from yeast to flies to mammals. <br /><br />I end by simply saying MOSS ROCKS.<br /><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Cell&rft_id=info%3Adoi%2F10.1016%2Fj.cell.2009.12.023&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Transcriptional+Control+of+Gene+Expression+by+MicroRNAs&rft.issn=00928674&rft.date=2010&rft.volume=140&rft.issue=1&rft.spage=111&rft.epage=122&rft.artnum=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867409015700&rft.au=Khraiwesh%2C+B.&rft.au=Arif%2C+M.&rft.au=Seumel%2C+G.&rft.au=Ossowski%2C+S.&rft.au=Weigel%2C+D.&rft.au=Reski%2C+R.&rft.au=Frank%2C+W.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Khraiwesh, B., Arif, M., Seumel, G., Ossowski, S., Weigel, D., Reski, R., & Frank, W. (2010). Transcriptional Control of Gene Expression by MicroRNAs <span style="font-style: italic;">Cell, 140</span> (1), 111-122 DOI: <a rev="review" href="http://dx.doi.org/10.1016/j.cell.2009.12.023">10.1016/j.cell.2009.12.023</a></span><br /><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Nature+Medicine&rft_id=info%3Adoi%2F10.1038%2Fnm1008-1046&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Of+maize+and+men%2C+or+peas+and+people%3A+case+histories+to+justify+plants+and+other+model+systems&rft.issn=1078-8956&rft.date=2008&rft.volume=14&rft.issue=10&rft.spage=1046&rft.epage=1049&rft.artnum=http%3A%2F%2Fwww.nature.com%2Fdoifinder%2F10.1038%2Fnm1008-1046&rft.au=Baulcombe%2C+D.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Baulcombe, D. (2008). Of maize and men, or peas and people: case histories to justify plants and other model systems <span style="font-style: italic;">Nature Medicine, 14</span> (10), 1046-1049 DOI: <a rev="review" href="http://dx.doi.org/10.1038/nm1008-1046">10.1038/nm1008-1046</a></span>James Lloydhttp://www.blogger.com/profile/08219295648051788360noreply@blogger.com4tag:blogger.com,1999:blog-496263467300370264.post-75730241266494801502009-11-04T00:02:00.001+00:002009-11-04T00:02:42.343+00:00Freedom of speech within scienceNot so much research but a rant. As you may have heard the chief advisor to the government about drugs policy Prof Nutt was told to resign recently after he gave a lecture stating his views on cannabis classification in the UK and how the government (former Home Secretary Jackie Smith) did not listen to their advice on the matter and increased its classification and punishment for taking it. I do not care about the drug’s classification to be honest. I don’t take it and never have but the current Home Secretary (Alan Johnson, tipped to be future Labour leader, among a couple of others) has had a disagreement with the scientist and dismissed him after he gave a lecture stating his opinion. The reason given was he had crossed the boundary between science and politics. What? A scientist who is an unpaid advisor states his opinion based on evidence then states the government didn’t listen to them when deciding policy is crossing the line?! It sounds like he was starting a debate, using his freedom of speech to discuss topics. The government has decided no, if you don’t agree with us and you are helping us then sod off. Whether you agree with Prof Nutt or not I don’t think it matters. What matters is whether advisors are allowed to criticise the government’s policy when they are not listened to. They believe not. Alan Johnson said: ‘he was not dismissed because of the work of the council but because of his failure to recognise that... his role is to advise rather than criticise’. My PM Gordon Brown said: ‘Prof Nutt had repeatedly undermined Labour's drug message.’ I think it is ridiculous to suggest a scientist cannot talk about such things in public and suggests to me the government is being hypersensitive over these matters. Perhaps because they cannot handle anymore bad press and people going against them. After all the chances of them winning the next election are slim to none. <br /><br />So far Lord Drayson (a businessman) who determines science policy in the government’s Business department and coordinates with the research councils was strongly against this when he first heard it. Lord Winston FRS, a respected scientist in the public eye and Labour peer, is against the dismissal and Prof John Beddington FRS (who recently recovered an honorary degree from York University in the Summer 2009 graduation ceremony) has spoken the most sense on the matter (http://news.bbc.co.uk/1/hi/sci/tech/8340318.stm). He is the chief advisor to the government on all things sciencey. He points out most scientific committees do not have a problem with the government. This is reassuring but and the send of an email the Home Secretary (with no background what so ever in science) has dismissed an advisor and caused two to quit in sympathy because they don’t think they can work with a government that a) doesn’t listen to them and b) forces out the head of the committee for no good reason. I think this is unacceptable from the government hence I have written to the Home Secretary and feel I should email my local MP as well. Hopefully my next post will contain more science and less ranting. It’s being planned, just need to get some pretty photos.James Lloydhttp://www.blogger.com/profile/08219295648051788360noreply@blogger.com3tag:blogger.com,1999:blog-496263467300370264.post-15958964814336667352009-10-12T13:13:00.003+01:002009-10-12T13:25:09.081+01:00Ig Nobels 2009For a few years now that I have been following the Ig Nobels as they are awarded. To continue the tradition, here is a post with the list of this year's winners:
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<br />VETERINARY MEDICINE PRIZE
<br />Catherine Douglas and Peter Rowlinson of Newcastle University, Newcastle-Upon-Tyne, UK, for showing that <strong>cows who have names give more milk than cows that are nameless</strong>.
<br /><span style="font-size:85%;">"</span><a href="http://www.ingentaconnect.com/content/berg/anthroz/2009/00000022/00000001/art00006"><span style="font-size:85%;">Exploring Stock Managers' Perceptions of the Human-Animal Relationship on Dairy Farms and an Association with Milk Production</span></a><span style="font-size:85%;">," </span><a href="http://www.ncl.ac.uk/afrd/staff/profile/catherine.douglas"><span style="font-size:85%;">Catherine Bertenshaw [Douglas]</span></a><span style="font-size:85%;"> and </span><a href="http://www.ncl.ac.uk/afrd/staff/profile/peter.rowlinson"><span style="font-size:85%;">Peter Rowlinson</span></a><span style="font-size:85%;">, Anthrozoos, vol. 22, no. 1, March 2009, pp. 59-69.</span>
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<br />PEACE PRIZE
<br /><a href="http://www.virtopsy.com/index.php?option=com_content&view=article&id=24&Itemid=3"><span style="color:#000000;">Stephan Bolliger</span></a><span style="color:#000000;">, </span><a href="http://www.virtopsy.com/index.php?option=com_jresearch&view=member&task=show&id=3&Itemid=3"><span style="color:#000000;">Steffen Ross</span></a><span style="color:#000000;">, Lars Oesterhelweg, </span><a href="http://www.virtopsy.com/index.php?option=com_jresearch&view=member&task=show&id=1&Itemid=3"><span style="color:#000000;">Michael Thali</span></a><span style="color:#000000;"> </span>and Beat Kneubuehl of the University of Bern, Switzerland, <strong>for determining — by experiment — whether it is better to be smashed over the head with a full bottle of beer or with an empty bottle</strong>.
<br /><span style="font-size:85%;">"</span><a href="http://dx.doi.org/10.1016/j.jflm.2008.07.013"><span style="font-size:85%;">Are Full or Empty Beer Bottles Sturdier and Does Their Fracture-Threshold Suffice to Break the Human Skull?</span></a><span style="font-size:85%;">" Stephan A. Bolliger, Steffen Ross, Lars Oesterhelweg, Michael J. Thali and Beat P. Kneubuehl, Journal of Forensic and Legal Medicine, vol. 16, no. 3, April 2009, pp. 138-42.</span>
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<br />ECONOMICS PRIZE
<br />The directors, executives, and auditors of four <a href="http://www.vanityfair.com/politics/features/2009/04/iceland200904"><span style="color:#000000;">Icelandic banks</span></a> — Kaupthing Bank, Landsbanki, Glitnir Bank, and Central Bank of Iceland — <strong>for demonstrating that tiny banks can be rapidly transformed into huge banks, and vice versa — and for demonstrating that similar things can be done to an entire national economy.</strong>
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<br /></strong>CHEMISTRY PRIZE
<br /></strong><a href="http://www.javiermorales.com.mx/"><span style="color:#000000;">Javier Morales</span></a><span style="color:#000000;">, </span><a href="http://www.fata.unam.mx:8080/paginapersonal.jsp?l=2&a=19"><span style="color:#000000;">Miguel Apátiga</span></a><span style="color:#000000;">, and Victor M. Castaño of Universidad Nacional Autónoma de</span> México, <strong>for creating diamonds from liquid — specifically from tequila</strong>.
<br /><span style="font-size:85%;">"</span><a href="http://arxiv.org/ftp/arxiv/papers/0806/0806.1485.pdf"><span style="font-size:85%;">Growth of Diamond Films from Tequila</span></a><span style="font-size:85%;">," Javier Morales, Miguel Apatiga and Victor M. Castano, 2008, arXiv:0806.1485.</span>
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<br />MEDICINE PRIZE
<br />Donald L. Unger, of Thousand Oaks, California, USA, <strong>for investigating a possible cause of arthritis of the fingers, by diligently cracking the knuckles of his left hand — but never cracking the knuckles of his right hand — every day for more than sixty (60) years</strong>.
<br /><span style="font-size:85%;">"</span><a href="http://www3.interscience.wiley.com/journal/86510619/abstract?CRETRY=1&SRETRY=0"><span style="font-size:85%;">Does Knuckle Cracking Lead to Arthritis of the Fingers?</span></a><span style="font-size:85%;">", Donald L. Unger, Arthritis and Rheumatism, vol. 41, no. 5, 1998, pp. 949-50. </span>
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<br />PHYSICS PRIZE
<br /><a href="http://asweb.artsci.uc.edu/collegedepts/anthro/fac_staff/profile_details.aspx?ePID=MjQyMzU0"><span style="color:#000000;">Katherine K. Whitcome</span></a><span style="color:#000000;"> of the University of Cincinnati, USA, </span><a href="http://www.fas.harvard.edu/~skeleton/danlhome.html"><span style="color:#000000;">Daniel E. Lieberman</span></a><span style="color:#000000;"> of Harvard University, USA, and </span><a href="http://uts.cc.utexas.edu/~lshapiro/"><span style="color:#000000;">Liza J. Shapiro</span></a><span style="color:#000000;"> of the University of Texas, USA, <strong>for analytically determining why pregnant women don't tip over.</strong></span>
<br /><span style="font-size:85%;">"</span><a href="http://www.nature.com/nature/journal/v450/n7172/abs/nature06342.html"><span style="font-size:85%;">Fetal Load and the Evolution of Lumbar Lordosis in Bipedal Hominins</span></a><span style="font-size:85%;">," Katherine K. Whitcome, Liza J. Shapiro & Daniel E. Lieberman, Nature, vol. 450, 1075-1078 (December 13, 2007). DOI:10.1038/nature06342.</span>
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<br />LITERATURE PRIZE
<br />Ireland's police service <span style="color:#000000;">(</span><a href="http://www.garda.ie/"><span style="color:#000000;">An Garda Siochana</span></a>), <strong>for writing and presenting more than fifty traffic tickets to the most frequent driving offender in the country — </strong><a href="http://images.google.com/images?hl=en&safe=off&um=1&sa=1&q=" aq="'f&oq=" aqi="&start="><strong>Prawo Jazdy</strong></a><strong> — whose name in Polish means "Driving License".</strong>
<br />
<br />PUBLIC HEALTH PRIZE
<br />Elena N. Bodnar, Raphael C. Lee, and Sandra Marijan of Chicago, Illinois, USA, <strong>for inventing a brassiere that, in an emergency, can be quickly converted into a pair of protective face masks, one for the brassiere wearer and one to be given to some needy bystander</strong>.
<br /><span style="font-size:85%;">U.S. patent # 7255627, granted August 14, 2007 for a “</span><a href="http://www.google.com/patents?id=z_WAAAAAEBAJ&dq=7255627"><span style="font-size:85%;">Garment Device Convertible to One or More Facemasks</span></a><span style="font-size:85%;">.”</span>
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<br />MATHEMATICS PRIZE
<br /><a href="http://www.gideongono.com/"><span style="color:#000000;">Gideon Gono</span></a><span style="color:#000000;">, governor of Zimbabwe’s </span><a href="http://www.rbz.co.zw/"><span style="color:#000000;">Reserve Bank</span></a><span style="color:#000000;">, <strong>for giving</strong></span><strong> people a simple, everyday way to cope with a wide range of numbers — from very small to very big — by having his bank print </strong><a href="http://shop.ebay.com/i.html?_nkw=zimbabwe+bank+notes&_sacat=0&_trksid=p3286.m270.l1313&_dmpt=Paper_Money&_odkw=zimbabwe+currency&_osacat=0"><strong>bank notes</strong></a><strong> with denominations ranging from one cent ($.01) to one hundred trillion dollars ($100,000,000,000,000)</strong>.
<br /><a href="http://www.amazon.com/Zimbabwes-Economy-Extraordinary-Measures-Challenges/dp/0797436790/ref=sr_1_1?ie=UTF8&qid=1254603508&sr=1-1-fkmr0"><span style="font-size:85%;">Zimbabwe's Casino Economy — Extraordinary Measures for Extraordinary Challenges</span></a><span style="font-size:85%;">, Gideon Gono, ZPH Publishers, Harare, 2008, ISBN 978-079-743-679-4.
<br /></span>
<br />BIOLOGY PRIZE:
<br />Fumiaki Taguchi, Song Guofu, and Zhang Guanglei of Kitasato University Graduate School of Medical Sciences in Sagamihara, Japan, <strong>for demonstrating that kitchen refuse can be reduced more than 90% in mass by using bacteria extracted from the feces of giant pandas.</strong>
<br /><span style="font-size:85%;">"</span><a href="http://dx.doi.org/10.1016/S1389-1723(01)80326-1"><span style="font-size:85%;">Microbial Treatment of Kitchen Refuse With Enzyme-Producing Thermophilic Bacteria From Giant Panda Feces</span></a><span style="font-size:85%;">," Fumiaki Taguchia, Song Guofua, and Zhang Guanglei, Seibutsu-kogaku Kaishi, vol. 79, no 12, 2001, pp. 463-9. [and abstracted in Journal of Bioscience and Bioengineering, vol. 92, no. 6, 2001, p. 602.]</span>
<br />Cathttp://www.blogger.com/profile/08645968914831610862noreply@blogger.com2tag:blogger.com,1999:blog-496263467300370264.post-62775612663269313972009-09-06T18:26:00.007+01:002009-09-06T18:46:41.376+01:00Looking for some science on swine flu<div style="text-align: justify;">As a medical association in Spain has recently communicated to the press, more than anything there seems to be an epidemic of fear going on. As I am currently living in Portugal, I do not know what the situation is in other countries, but I can tell you how the situation is here. Every news bulletin starts with more news about the flu, even though no one has died here yet. It then finishes with a previously recorded warning on how one should wash hands frequently and keep 1m away from other people while talking to them, quite an ordeal in a country where the common greeting is a couple of kisses in the cheek. In addition, we have ambulances going around with the paramedics dressed as in the photo, right out of films like ‘Outbreak’. Now, most people seem to assume that because I have just graduated with a Biology degree that I should know everything there is to know about the current flu. Besides the generic question ‘So, what do you think about this flu thing?’, I have had some more specific questions, from ‘I heard that it is impossible for this combination of genes to happen in nature, surely this must have been created by evil scientists with corporative interests?’ to ‘This virus is called H1N1, the 1918 pandemic virus was also H1N1, are we all going to die of Spanish flu?’. I try to explain people that at uni we are taught how to get informed about things, rather than becoming specialist on every single biological problems; and that frankly I am so fed up of hearing about this flu that I couldn’t be bothered to look it up. However, I think the hysteria might be affecting me, probably because I’ve just read the book Blindness (if you have read it/watched the film you will know why). So I decided to interrupt my holidays-away-from-science to read a bit about this topic, and thought I would tell you some of my findings.<br /></div><div style="text-align: justify;"><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgv9idICn90k14_fVmfrqufOsG5rELkNl1QnxHx7Wk5Q2RbISu91pYD8T1Km88cj3R4HMMisXGKtl9gKIWCoARevYqbGQH0nF4jtjDt7XUxOwihq_EQNYzV1Vl_y4EX7NsDL9oaf2K9EX4/s1600-h/paramedics.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 320px; height: 236px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgv9idICn90k14_fVmfrqufOsG5rELkNl1QnxHx7Wk5Q2RbISu91pYD8T1Km88cj3R4HMMisXGKtl9gKIWCoARevYqbGQH0nF4jtjDt7XUxOwihq_EQNYzV1Vl_y4EX7NsDL9oaf2K9EX4/s320/paramedics.jpg" alt="" id="BLOGGER_PHOTO_ID_5378412046287376754" border="0" /></a><br />My first port of call was the website of the World Health Organisation, usually a reliable source for information. I was pleasantly surprised by the lack of over-dramatic information. There is of course a whole section dedicated to this flu, right in the home page, but the answers given in the FAQs seem quite sensible. It tells us that 2009 A(H1N1) is spread as the normal flu, and that the current worries as based on the fact that being a virus which never circulated in humans before, there is no, or very little, immunity. In addition, as stated in their website, the virus is spreading fast in young people (10-45), from a majority of mild cases to some serious illnesses, the majority of which in patients with underlying conditions. The recommendations of the WHO are to take pain killers and drink loads of fluids if you have the flu. And only contact the medical services if you have serious symptoms like shortness of breath, or if the fever lasts for longer than 3 days. Quite unlike what recently happened in Portugal. When a man who had travelled to Britain was diagnosed with this flu, he saw his house invaded by doctors who quickly took him away to a hospital and confined the whole family to their house. Without telling them what to do or when they could leave.<br /><br />Anyway, I then thought it would be a good idea to read some information from journals, a bit more scientific and hopefully less dramatic source of news. However, as you know, I am currently unable to access most papers, as I am in between universities and am yet to be provided with a username in my new institution. So what follows is based on a couple of papers I could access, and is by no means comprehensive.<br /><br />As an introduction, some information from the Virology handouts we were given last October. Influenza viruses are RNA viruses that have a segmented genome (8 segments/genome). The glycoprotein spikes, haemagglutinin (HA) and neuraminidase (NA) are important in the entrance of the virus in the host cells. There are 15 known HA and 9 NA serotypes, and their combination provides the name that we see for the viruses such as H1N1. Birds and pigs are important reservoirs for genetic and antigenically diversity and reassortment in these viruses. In particular pigs, as their cells can be infected by both avian and human influenza viruses, making them nice ‘mixing pots’.<br /><br />In July this year Garten et al., published a paper in Science in which they characterised the 2009 A(H1N1) virus both antigenically and genetically. They start the paper by giving a small introduction on the influenza pandemics of the last century, and how we got from those to the current 2009 A(H1N1). Then it goes on to characterise the actual viruses. The closest ancestral gene for each of the eight segments seems to have a swine origin, although having originally come from avians and sometimes humans in different occasions. This is quite interesting, as swine influenza viruses had not, until now, caused much disease or been incredibly good at human-human transmission. As the authors point out, this virus probably had been circulating for a while in pigs, unnoticed due to lack of monitoring.<br /><br />Analysis of the virus genome showed that none of the molecular signatures of increased transmissibility or virulence of A(H1N1) viruses can be found in this strain, and that functionally important receptor binding sites on HA do not differ from classic swine influenza viruses. No markers were also found that indicate adaptation to the human host or features of previous pandemic virus. The main important difference seems to be a genetic marker for resistance to adamantine antivirals, but the virus still seems to be sensitive to the other type of antivirals, the neuraminidase inhibitors. So, this study concludes, we must be worried about this virus firstly because we don’t really know what makes it good at replicating in humans, and secondly because it has a genetic composition not seen before, so we don’t really know what to expect.<br /><br />I then went on to read a couple of papers regarding studies done in mammal models such as ferrets (apparently classic models for influenza studies) and mice.<br /><br />The first study was published in Science also in July, by Maines et al. This post is becoming quite long already, so I’ll just summarise their results (based on 3 independently isolated 2009 A(H1N1) viruses as compared with a seasonal influenza strain). They basically inoculated 106 p.f.u in ferrets and monitored different indicators such as body weight, viral titres, direct and indirect transmissibility, etc. The main conclusion from the study was that 2009 A(H1N1) caused higher morbidity (weight loss, etc, depending on which virus isolate), showed, unlike seasonal flu, high viral titres in the lower respiratory tract or the intestine, but that it was less efficient at indirect transmission (putting healthy ferrets in cages near to inoculated animals).<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZIc38sTmTJHM7K4hWGr_0L_XkIQ9A4DjXxHQIquzeIKt9QiB7pTJ6_wPNqDGEpulL751DLCXnh2GMvQiYDTdVQLOnpVVxzcBQ90bbERe8Dmsae5m9evFpqiYSaD2n41cYTQFZ-RUQytU/s1600-h/swine+flu.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 319px; height: 320px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEjZIc38sTmTJHM7K4hWGr_0L_XkIQ9A4DjXxHQIquzeIKt9QiB7pTJ6_wPNqDGEpulL751DLCXnh2GMvQiYDTdVQLOnpVVxzcBQ90bbERe8Dmsae5m9evFpqiYSaD2n41cYTQFZ-RUQytU/s320/swine+flu.jpg" alt="" id="BLOGGER_PHOTO_ID_5378408930037024994" border="0" /></a><br />The second animal study I looked at was published online by Nature, in what they call a ‘near final version’. They also used virus isolated from infected humans, though not all of which were the same as in the Science paper. They studied the effect of these viruses in mice, macaques, ferrets and pigs, though not all of the virus isolates seem to have been used in all of the experiments. They also looked at more indicators, such as pro-inflammatory cytokines, lung pathology, etc. In ferrets the results were similar to those of the Science paper, except that this time indirect transmission was successful. In mice and macaques, the 2009 A(H1N1) virus seems to be worse than the seasonal virus (at least one of the isolates that they seem to mostly use throughout, CA04) although according with which criteria varies with the model. The inoculated pigs were asymptomatic, explaining why the virus had not been noticed before in this animal.<br /><br />So, what are the conclusions I could get, overall, from these three studies? Overall it seems that the 2009 A(H1N1) virus is worse than the seasonal influenza viruses in mammalian models. However, how much worse is probably hard to say. I am not familiar at all with viral studies, so it is hard for me to critically analyse these studies, but it seems to me that in most cases the n numbers were quite small (n=3 in some cases in the Nature study), but this is perhaps not surprising, as they must have been quite quick studies, considering the current need to understand this new virus. And, as it is probably the case in most animal studies in general, I reckon the doses used were probably much higher than what humans would be exposed to in the real world. In addition, there is always the question on how well do these animal models really reflect what happens in humans.<br /><br />In any case, it seems that so far these studies indicate that 2009 A(H1N1) is, in these models, worse than seasonal flu. Whether it is as bad as some of the pandemics that have been affecting us in the last 100 years it is unknown. The other worry is of course that the virus might evolve into something much more dangerous. Though all the virus isolates obtained so far tend to be quite similar, 5 minor genome variants have already been detected. Restricting the spread of the virus, even if it is not so bad right now, might be a good way of preventing it from acquiring any more deadly features. Whether this data justifies the measures being taken by most government, that is really, as PHD comics puts it so well, beyong the scope of my area of study. I will leave that to those who study the spread of pandemics and know of population health. I think we have had enough speculation for one disease.<br /><br /></div><span style="padding: 5px; float: left;"><a href="http://www.researchblogging.org/"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border: 0pt none ;" /></a></span><br /><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Science+%28New+York%2C+N.Y.%29&rft_id=info%3Apmid%2F19465683&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Antigenic+and+genetic+characteristics+of+swine-origin+2009+A%28H1N1%29+influenza+viruses+circulating+in+humans.&rft.issn=0036-8075&rft.date=2009&rft.volume=325&rft.issue=5937&rft.spage=197&rft.epage=201&rft.artnum=&rft.au=Garten+RJ&rft.au=Davis+CT&rft.au=Russell+CA&rft.au=Shu+B&rft.au=Lindstrom+S&rft.au=Balish+A&rft.au=Sessions+WM&rft.au=Xu+X&rft.au=Skepner+E&rft.au=Deyde+V&rft.au=Okomo-Adhiambo+M&rft.au=Gubareva+L&rft.au=Barnes+J&rft.au=Smith+CB&rft.au=Emery+SL&rft.au=Hillman+MJ&rft.au=Rivailler+P&rft.au=Smagala+J&rft.au=de+Graaf+M&rft.au=Burke+DF&rft.au=Fouchier+RA&rft.au=Pappas+C&rft.au=Alpuche-Aranda+CM&rft.au=L%C3%B3pez-Gatell+H&rft.au=Olivera+H&rft.au=L%C3%B3pez+I&rft.au=Myers+CA&rft.au=Faix+D&rft.au=Blair+PJ&rft.au=Yu+C&rft.au=Keene+KM&rft.au=Dotson+PD+Jr&rft.au=Boxrud+D&rft.au=Sambol+AR&rft.au=Abid+SH&rft.au=St+George+K&rft.au=Bannerman+T&rft.au=Moore+AL&rft.au=Stringer+DJ&rft.au=Blevins+P&rft.au=Demmler-Harrison+GJ&rft.au=Ginsberg+M&rft.au=Kriner+P&rft.au=Waterman+S&rft.au=Smole+S&rft.au=Guevara+HF&rft.au=Belongia+EA&rft.au=Clark+PA&rft.au=Beatrice+ST&rft.au=Donis+R&rft.au=Katz+J&rft.au=Finelli+L&rft.au=Bridges+CB&rft.au=Shaw+M&rft.au=Jernigan+DB&rft.au=Uyeki+TM&rft.au=Smith+DJ&rft.au=Klimov+AI&rft.au=Cox+NJ&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology"><br /><br /></span><div style="text-align: justify;"><span style="font-size:85%;"><br /><br /></span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Science&rft_id=info%3Adoi%2F10.1126%2Fscience.1176225&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Antigenic+and+Genetic+Characteristics+of+Swine-Origin+2009+A%28H1N1%29+Influenza+Viruses+Circulating+in+Humans&rft.issn=0036-8075&rft.date=2009&rft.volume=325&rft.issue=5937&rft.spage=197&rft.epage=201&rft.artnum=http%3A%2F%2Fwww.sciencemag.org%2Fcgi%2Fdoi%2F10.1126%2Fscience.1176225&rft.au=Garten%2C+R.&rft.au=Davis%2C+C.&rft.au=Russell%2C+C.&rft.au=Shu%2C+B.&rft.au=Lindstrom%2C+S.&rft.au=Balish%2C+A.&rft.au=Sessions%2C+W.&rft.au=Xu%2C+X.&rft.au=Skepner%2C+E.&rft.au=Deyde%2C+V.&rft.au=Okomo-Adhiambo%2C+M.&rft.au=Gubareva%2C+L.&rft.au=Barnes%2C+J.&rft.au=Smith%2C+C.&rft.au=Emery%2C+S.&rft.au=Hillman%2C+M.&rft.au=Rivailler%2C+P.&rft.au=Smagala%2C+J.&rft.au=de+Graaf%2C+M.&rft.au=Burke%2C+D.&rft.au=Fouchier%2C+R.&rft.au=Pappas%2C+C.&rft.au=Alpuche-Aranda%2C+C.&rft.au=Lopez-Gatell%2C+H.&rft.au=Olivera%2C+H.&rft.au=Lopez%2C+I.&rft.au=Myers%2C+C.&rft.au=Faix%2C+D.&rft.au=Blair%2C+P.&rft.au=Yu%2C+C.&rft.au=Keene%2C+K.&rft.au=Dotson%2C+P.&rft.au=Boxrud%2C+D.&rft.au=Sambol%2C+A.&rft.au=Abid%2C+S.&rft.au=St.+George%2C+K.&rft.au=Bannerman%2C+T.&rft.au=Moore%2C+A.&rft.au=Stringer%2C+D.&rft.au=Blevins%2C+P.&rft.au=Demmler-Harrison%2C+G.&rft.au=Ginsberg%2C+M.&rft.au=Kriner%2C+P.&rft.au=Waterman%2C+S.&rft.au=Smole%2C+S.&rft.au=Guevara%2C+H.&rft.au=Belongia%2C+E.&rft.au=Clark%2C+P.&rft.au=Beatrice%2C+S.&rft.au=Donis%2C+R.&rft.au=Katz%2C+J.&rft.au=Finelli%2C+L.&rft.au=Bridges%2C+C.&rft.au=Shaw%2C+M.&rft.au=Jernigan%2C+D.&rft.au=Uyeki%2C+T.&rft.au=Smith%2C+D.&rft.au=Klimov%2C+A.&rft.au=Cox%2C+N.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology" style="font-size:85%;">Garten, R., Davis, C., Russell, C., Shu, B., Lindstrom, S., Balish, A., Sessions, W., Xu, X., Skepner, E., Deyde, V., Okomo-Adhiambo, M., Gubareva, L., Barnes, J., Smith, C., Emery, S., Hillman, M., Rivailler, P., Smagala, J., de Graaf, M., Burke, D., Fouchier, R., Pappas, C., Alpuche-Aranda, C., Lopez-Gatell, H., Olivera, H., Lopez, I., Myers, C., Faix, D., Blair, P., Yu, C., Keene, K., Dotson, P., Boxrud, D., Sambol, A., Abid, S., St. George, K., Bannerman, T., Moore, A., Stringer, D., Blevins, P., Demmler-Harrison, G., Ginsberg, M., Kriner, P., Waterman, S., Smole, S., Guevara, H., Belongia, E., Clark, P., Beatrice, S., Donis, R., Katz, J., Finelli, L., Bridges, C., Shaw, M., Jernigan, D., Uyeki, T., Smith, D., Klimov, A., & Cox, N. (2009). Antigenic and Genetic Characteristics of Swine-Origin 2009 A(H1N1) Influenza Viruses Circulating in Humans <span style="font-style: italic;">Science, 325</span> (5937), 197-201 DOI: <a rev="review" href="http://dx.doi.org/10.1126/science.1176225">10.1126/science.1176225</a></span><span style="font-size:85%;"><br /><br /></span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Science+%28New+York%2C+N.Y.%29&rft_id=info%3Apmid%2F19574347&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Transmission+and+pathogenesis+of+swine-origin+2009+A%28H1N1%29+influenza+viruses+in+ferrets+and+mice.&rft.issn=0036-8075&rft.date=2009&rft.volume=325&rft.issue=5939&rft.spage=484&rft.epage=7&rft.artnum=&rft.au=Maines+TR&rft.au=Jayaraman+A&rft.au=Belser+JA&rft.au=Wadford+DA&rft.au=Pappas+C&rft.au=Zeng+H&rft.au=Gustin+KM&rft.au=Pearce+MB&rft.au=Viswanathan+K&rft.au=Shriver+ZH&rft.au=Raman+R&rft.au=Cox+NJ&rft.au=Sasisekharan+R&rft.au=Katz+JM&rft.au=Tumpey+TM&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology" style="font-size:85%;">Maines TR, Jayaraman A, Belser JA, Wadford DA, Pappas C, Zeng H, Gustin KM, Pearce MB, Viswanathan K, Shriver ZH, Raman R, Cox NJ, Sasisekharan R, Katz JM, & Tumpey TM (2009). Transmission and pathogenesis of swine-origin 2009 A(H1N1) influenza viruses in ferrets and mice. <span style="font-style: italic;">Science (New York, N.Y.), 325</span> (5939), 484-7 PMID: <a rev="review" href="http://www.ncbi.nlm.nih.gov/pubmed/19574347">19574347</a></span><span style="font-size:85%;"><br /><br /></span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Nature&rft_id=info%3Adoi%2F10.1038%2Fnature08260&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=In+vitro+and+in+vivo+characterization+of+new+swine-origin+H1N1+influenza+viruses&rft.issn=0028-0836&rft.date=2009&rft.volume=&rft.issue=&rft.spage=&rft.epage=&rft.artnum=http%3A%2F%2Fwww.nature.com%2Fdoifinder%2F10.1038%2Fnature08260&rft.au=Itoh%2C+Y.&rft.au=Shinya%2C+K.&rft.au=Kiso%2C+M.&rft.au=Watanabe%2C+T.&rft.au=Sakoda%2C+Y.&rft.au=Hatta%2C+M.&rft.au=Muramoto%2C+Y.&rft.au=Tamura%2C+D.&rft.au=Sakai-Tagawa%2C+Y.&rft.au=Noda%2C+T.&rft.au=Sakabe%2C+S.&rft.au=Imai%2C+M.&rft.au=Hatta%2C+Y.&rft.au=Watanabe%2C+S.&rft.au=Li%2C+C.&rft.au=Yamada%2C+S.&rft.au=Fujii%2C+K.&rft.au=Murakami%2C+S.&rft.au=Imai%2C+H.&rft.au=Kakugawa%2C+S.&rft.au=Ito%2C+M.&rft.au=Takano%2C+R.&rft.au=Iwatsuki-Horimoto%2C+K.&rft.au=Shimojima%2C+M.&rft.au=Horimoto%2C+T.&rft.au=Goto%2C+H.&rft.au=Takahashi%2C+K.&rft.au=Makino%2C+A.&rft.au=Ishigaki%2C+H.&rft.au=Nakayama%2C+M.&rft.au=Okamatsu%2C+M.&rft.au=Takahashi%2C+K.&rft.au=Warshauer%2C+D.&rft.au=Shult%2C+P.&rft.au=Saito%2C+R.&rft.au=Suzuki%2C+H.&rft.au=Furuta%2C+Y.&rft.au=Yamashita%2C+M.&rft.au=Mitamura%2C+K.&rft.au=Nakano%2C+K.&rft.au=Nakamura%2C+M.&rft.au=Brockman-Schneider%2C+R.&rft.au=Mitamura%2C+H.&rft.au=Yamazaki%2C+M.&rft.au=Sugaya%2C+N.&rft.au=Suresh%2C+M.&rft.au=Ozawa%2C+M.&rft.au=Neumann%2C+G.&rft.au=Gern%2C+J.&rft.au=Kida%2C+H.&rft.au=Ogasawara%2C+K.&rft.au=Kawaoka%2C+Y.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology" style="font-size:85%;">Itoh, Y., Shinya, K., Kiso, M., Watanabe, T., Sakoda, Y., Hatta, M., Muramoto, Y., Tamura, D., Sakai-Tagawa, Y., Noda, T., Sakabe, S., Imai, M., Hatta, Y., Watanabe, S., Li, C., Yamada, S., Fujii, K., Murakami, S., Imai, H., Kakugawa, S., Ito, M., Takano, R., Iwatsuki-Horimoto, K., Shimojima, M., Horimoto, T., Goto, H., Takahashi, K., Makino, A., Ishigaki, H., Nakayama, M., Okamatsu, M., Takahashi, K., Warshauer, D., Shult, P., Saito, R., Suzuki, H., Furuta, Y., Yamashita, M., Mitamura, K., Nakano, K., Nakamura, M., Brockman-Schneider, R., Mitamura, H., Yamazaki, M., Sugaya, N., Suresh, M., Ozawa, M., Neumann, G., Gern, J., Kida, H., Ogasawara, K., & Kawaoka, Y. (2009). In vitro and in vivo characterization of new swine-origin H1N1 influenza viruses <span style="font-style: italic;">Nature</span> DOI: <a rev="review" href="http://dx.doi.org/10.1038/nature08260">10.1038/nature08260</a></span></div>Cathttp://www.blogger.com/profile/08645968914831610862noreply@blogger.com7tag:blogger.com,1999:blog-496263467300370264.post-986382287359195702009-08-16T05:38:00.011+01:002009-08-16T14:54:48.091+01:00Investigating the Smallest Bacterial Genome<span style="padding: 5px; float: left;font-family:arial;font-size:85%;" ><a href="http://www.researchblogging.org/"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border: 0pt none ;" /></a></span><span style="font-size:100%;"><span style="font-family:arial;">During the first two terms of my final year at university I took on a dry project based on bacterial genetics. In retrospect this was quite a cheap move since it avoids so many of the problems involved in normal lab work, but in my defence it was the project that interested me most and I really wanted some computing experience before making PhD applications.</span> <span style="font-family:arial;">My work was based on bacterial endosymbionts of insects, which have been of recent interest due to their extremely small genomes. Bacteria in these symbiotic relationships are given a protected, nutrient-rich environment and in return they allow insects to survive on unbalanced diets by synthesising scarce biomolecules.</span>
<br />
<br /><span style="font-family:arial;">Primary endosymbiotic bacteria live their entire lives inside insects and are vertically transmitted from generation to generation, a process that leads to coevolution between the bacteria and the insect. One of the results of this coevolution was major changes to the original bacterial genome, which contained many genes that are essential for free-living bacteria but are unnecessary for life within an insect. Consequently, common features of endosymbiotic genomes compared to those of free-living bacteria are severe gene loss, genome compaction and skewing of GC content.
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<br /></span></span><div style="text-align: center;"><span style="font-size:100%;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0ME_PeYy5QXmvlhb1jfJZC34wikoymIF_lDOalzNi9Fc07-tJ2q3jnwUUKCOa-7Xrp_Fau40uICjD3aLUlFGAcqTm8Eqxdvy2sMKvk8hNI704Un4MfthnRheRDhWLkODVrXKbMaDZAXI/s1600-h/YORF1.bmp"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 320px; height: 236px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj0ME_PeYy5QXmvlhb1jfJZC34wikoymIF_lDOalzNi9Fc07-tJ2q3jnwUUKCOa-7Xrp_Fau40uICjD3aLUlFGAcqTm8Eqxdvy2sMKvk8hNI704Un4MfthnRheRDhWLkODVrXKbMaDZAXI/s320/YORF1.bmp" alt="" id="BLOGGER_PHOTO_ID_5370555356348365042" border="0" /></a>
<br /></span><meta equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 11"><meta name="Originator" content="Microsoft Word 11"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5CJoe%5CLOCALS%7E1%5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml"><!--[if gte mso 9]><xml> <w:worddocument> <w:view>Normal</w:View> <w:zoom>0</w:Zoom> <w:punctuationkerning/> <w:validateagainstschemas/> <w:saveifxmlinvalid>false</w:SaveIfXMLInvalid> <w:ignoremixedcontent>false</w:IgnoreMixedContent> <w:alwaysshowplaceholdertext>false</w:AlwaysShowPlaceholderText> <w:compatibility> <w:breakwrappedtables/> <w:snaptogridincell/> <w:wraptextwithpunct/> <w:useasianbreakrules/> <w:dontgrowautofit/> </w:Compatibility> <w:browserlevel>MicrosoftInternetExplorer4</w:BrowserLevel> </w:WordDocument> </xml><![endif]--><!--[if gte mso 9]><xml> <w:latentstyles deflockedstate="false" latentstylecount="156"> </w:LatentStyles> </xml><![endif]--><style> <!-- /* Font Definitions */ @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4; mso-font-charset:0; mso-generic-font-family:swiss; mso-font-pitch:variable; mso-font-signature:-1610611985 1073750139 0 0 159 0;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman"; mso-ansi-language:EN-US; mso-fareast-language:EN-US;} @page Section1 {size:612.0pt 792.0pt; margin:72.0pt 90.0pt 72.0pt 90.0pt; mso-header-margin:36.0pt; mso-footer-margin:36.0pt; mso-paper-source:0;} div.Section1 {page:Section1;} --> </style><!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;} </style> <![endif]--><span style=";font-family:Calibri;font-size:100%;" lang="EN-US" >Electron micrograph showing bacteriocytes taken from <i style="">P. venusta
<br /></i></span><meta equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 11"><meta name="Originator" content="Microsoft Word 11"><link rel="File-List" href="file:///C:%5CDOCUME%7E1%5CJoe%5CLOCALS%7E1%5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml"><!--[if gte mso 9]><xml> <w:worddocument> <w:view>Normal</w:View> <w:zoom>0</w:Zoom> <w:punctuationkerning/> <w:validateagainstschemas/> <w:saveifxmlinvalid>false</w:SaveIfXMLInvalid> <w:ignoremixedcontent>false</w:IgnoreMixedContent> <w:alwaysshowplaceholdertext>false</w:AlwaysShowPlaceholderText> <w:compatibility> <w:breakwrappedtables/> <w:snaptogridincell/> <w:wraptextwithpunct/> <w:useasianbreakrules/> <w:dontgrowautofit/> </w:Compatibility> <w:browserlevel>MicrosoftInternetExplorer4</w:BrowserLevel> </w:WordDocument> </xml><![endif]--><!--[if gte mso 9]><xml> <w:latentstyles deflockedstate="false" latentstylecount="156"> </w:LatentStyles> </xml><![endif]--><style> <!-- /* Font Definitions */ @font-face {font-family:Calibri; panose-1:2 15 5 2 2 2 4 3 2 4; mso-font-charset:0; mso-generic-font-family:swiss; mso-font-pitch:variable; mso-font-signature:-1610611985 1073750139 0 0 159 0;} /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman"; mso-ansi-language:EN-US; mso-fareast-language:EN-US;} @page Section1 {size:612.0pt 792.0pt; margin:72.0pt 90.0pt 72.0pt 90.0pt; mso-header-margin:36.0pt; mso-footer-margin:36.0pt; mso-paper-source:0;} div.Section1 {page:Section1;} --> </style><!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Table Normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;} </style> <![endif]--> <p class="MsoNormal"><span style=";font-family:Calibri;font-size:100%;" lang="EN-US" ><span style="font-size:85%;">1 – Bacteriocyte; 2 – <i style="">C. ruddii</i>; 3 – Unidentified electron-dense mass</span><o:p></o:p></span></p><span style="font-size:100%;">
<br /></span></div><span style="font-size:100%;"> </span><span style="font-size:100%;"><span style="font-family:arial;">
<br />My project focused on </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >Carsonella ruddii</span><span style="font-size:100%;"><span style="font-family:arial;">, the only bacterial endosymbiont of the psyllid, </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >Pachypsylla venusta</span><span style="font-size:100%;"><span style="font-family:arial;">. It was hailed as the smallest bacterial genome chracterised when it was sequenced in 2006 and still holds that record. Its genome contains only 182 ORFs, less than 3% intergenic DNA and has a GC content of 16.5%. The bacteria appears to be provided with many nutrients by its host and its metabolism has been reduced to a few pathways: ATP synthesis, a section of the pentose phosphate pathway and biosynthesis of certain amino acids.</span> <span style="font-family:arial;">
<br />
<br />The early stages of my project involved a reannotation of the </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii</span><span style="font-size:100%;"><span style="font-family:arial;"> genome followed by a sequence-based functional analysis of its metabolic enzymes. Using the enzymes deemed functional in this analysis I built an updated model of the </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii</span><span style="font-size:100%;"><span style="font-family:arial;"> metabolism which could be divided into six pathways involved in amino acid biosynthesis, five of which were incomplete. The only fully intact pathway led to the production of isoleucine and valine. These are both essential amino acids for insects and are severely under-represented in the adult psyllid diet.</span>
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<br /><span style="font-family:arial;">Four of the incomplete amino acid pathways were missing only one reaction and the conservation of the rest of each of the pathways suggested that they might still be functional in </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii</span><span style="font-size:100%;"><span style="font-family:arial;">. The ‘missing’ reactions might occur spontaneously under some conditions or could be catalysed by unidentified enzymes. For three of these four missing reactions I found an example in the literature of a different bacterial endosymbiont which had lost that reaction but had retained the rest of the pathway. This seemed to suggest that the enzymes catalysing these reactions might be expendable and subject to loss during genome reduction in endosymbionts. Based on this and some other evidence from similar situations in endosymbionts I predicted that these pathways are probably functional in </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii</span><span style="font-size:100%;"><span style="font-family:arial;"> and that its main role symbiotic role is to provide the psyllid with essential amino acids.</span>
<br />
<br /><span style="font-family:arial;">The fourth of these incomplete pathways was the most interesting because I was unable to locate another endosymbiont which was missing the same reaction. The reaction was catalysed by the product of a gene, </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >AS</span><span style=";font-family:arial;font-size:100%;" >, which was present on the </span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddi</span><span style=";font-family:arial;font-size:100%;" ><span style="font-style: italic;">i</span> genome but which I had labelled as a pseudogene during functional analysis. Although it’s difficult to conclusively say that an enzyme is inactive solely by sequence analysis, multiple alignments showed that this copy of </span><span style="font-style: italic;font-family:arial;font-size:100%;" >AS</span><span style=";font-family:arial;font-size:100%;" > was extensively degraded and was missing both of its key catalytic residues as well as its substrate binding residues. However, later in the project when I was scanning an EST set taken from the insect host of </span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii</span><span style=";font-family:arial;font-size:100%;" > I located another copy of AS which also had bacterial origin but which was not present on the </span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii</span><span style=";font-family:arial;font-size:100%;" > genome. Sequence analysis showed that this version of </span><span style="font-style: italic;font-family:arial;font-size:100%;" >AS</span><span style="font-size:100%;"><span style="font-family:arial;"> seemed to be active and could potentially fill the gap in the pathway.</span> <span style="font-family:arial;">
<br />
<br />Where did this copy of </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >AS</span><span style="font-size:100%;"><span style="font-family:arial;"> originate from? It aligned well with the version of </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >AS</span><span style="font-size:100%;"><span style="font-family:arial;"> from </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >P.</span><span style="font-size:100%;"> </span><span style="font-style: italic;font-family:arial;font-size:100%;" >aeruginosa</span><span style="font-size:100%;"><span style="font-family:arial;"> and appeared to have a bacterial origin but was not found on the </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii</span><span style="font-size:100%;"><span style="font-family:arial;"> genome or the psyllid mitochondrial genome, both of which have been sequenced. Several lines of evidence ruled out the presence of a second bacterial endosymbiont in this symbiosis and since no plasmids had been reported during DNA sequencing of </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii</span><span style="font-size:100%;"><span style="font-family:arial;"> the source of this sequence appeared to be the nuclear genome of </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >P. venusta</span><span style="font-size:100%;"><span style="font-family:arial;"> itself.</span> <span style="font-family:arial;">The presence of this bacterial sequence in the eukaryotic genome suggests that LGT may have taken place between a bacterial genome and the insect nuclear genome. This would be one explanation for the fact that </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii</span><span style="font-size:100%;"><span style="font-family:arial;"> has only 182 ORFs, which is significantly lower than the predicted minimal bacterial genome. However, it is also possible that C. ruddii uses mitochondrial proteins to survive and so LGT is not the only explanation for the low ORF count.</span> <span style="font-family:arial;">
<br />
<br />This was my favourite line of investigation during my project but the symbiosis between </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii</span><span style="font-size:100%;"><span style="font-family:arial;"> and </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >P. venusta</span><span style="font-size:100%;"><span style="font-family:arial;"> had many more interesting features that I read about over the year. One of the questions I got in my viva was whether </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii</span><span style="font-size:100%;"><span style="font-family:arial;"> should be labelled as a bacterium or an organelle. I think this question is only really important when considering a minimal bacterial genome and if </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii</span><span style="font-size:100%;"><span style="font-family:arial;"> does turn out to be importing essential proteins from elsewhere then I think that the label organelle is definitely more appropriate. However, the definition of an organelle doesn't seem to be well-established and so whether or not </span></span><span style="font-style: italic;font-family:arial;font-size:100%;" >C. ruddii </span><span style="font-size:100%;"><span style="font-family:arial;">really does have the smallest bacterial genome is a matter of opinion.
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<br /></span></span><span style=";font-family:arial;font-size:100%;" class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Science+%28New+York%2C+N.Y.%29&rft_id=info%3Apmid%2F17038615&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=The+160-kilobase+genome+of+the+bacterial+endosymbiont+Carsonella.&rft.issn=0036-8075&rft.date=2006&rft.volume=314&rft.issue=5797&rft.spage=267&rft.epage=&rft.artnum=&rft.au=Nakabachi+A&rft.au=Yamashita+A&rft.au=Toh+H&rft.au=Ishikawa+H&rft.au=Dunbar+HE&rft.au=Moran+NA&rft.au=Hattori+M&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology" >
<br />Nakabachi A, Yamashita A, Toh H, Ishikawa H, Dunbar HE, Moran NA, & Hattori M (2006). The 160-kilobase genome of the bacterial endosymbiont Carsonella. <span style="font-style: italic;">Science (New York, N.Y.), 314</span> (5797) PMID: <a rev="review" href="http://www.ncbi.nlm.nih.gov/pubmed/17038615">17038615</a></span><span style=";font-family:arial;font-size:100%;" > </span><span style=";font-family:arial;font-size:100%;" class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Microbiology+and+Molecular+Biology+Reviews&rft_id=info%3Adoi%2F10.1128%2FMMBR.68.3.518-537.2004&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Determination+of+the+Core+of+a+Minimal+Bacterial+Gene+Set&rft.issn=1092-2172&rft.date=2004&rft.volume=68&rft.issue=3&rft.spage=518&rft.epage=537&rft.artnum=http%3A%2F%2Fmmbr.asm.org%2Fcgi%2Fdoi%2F10.1128%2FMMBR.68.3.518-537.2004&rft.au=Gil%2C+R.&rft.au=Silva%2C+F.&rft.au=Pereto%2C+J.&rft.au=Moya%2C+A.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology" >
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<br />Gil, R., Silva, F., Pereto, J., & Moya, A. (2004). Determination of the Core of a Minimal Bacterial Gene Set <span style="font-style: italic;">Microbiology and Molecular Biology Reviews, 68</span> (3), 518-537 DOI: <a rev="review" href="http://dx.doi.org/10.1128/MMBR.68.3.518-537.2004">10.1128/MMBR.68.3.518-537.2004</a></span><span style=";font-family:arial;font-size:100%;" > </span><span style=";font-family:arial;font-size:100%;" class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Proceedings+of+the+National+Academy+of+Sciences&rft_id=info%3Adoi%2F10.1073%2Fpnas.0510013103&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Essential+genes+of+a+minimal+bacterium&rft.issn=0027-8424&rft.date=2006&rft.volume=103&rft.issue=2&rft.spage=425&rft.epage=430&rft.artnum=http%3A%2F%2Fwww.pnas.org%2Fcgi%2Fdoi%2F10.1073%2Fpnas.0510013103&rft.au=Glass%2C+J.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology" >
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<br />Glass, J. (2006). Essential genes of a minimal bacterium <span style="font-style: italic;">Proceedings of the National Academy of Sciences, 103</span> (2), 425-430 DOI: <a rev="review" href="http://dx.doi.org/10.1073/pnas.0510013103">10.1073/pnas.0510013103</a></span><span style="font-size:100%;">
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<br /></span><span style=";font-family:arial;font-size:100%;" class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Applied+and+Environmental+Microbiology&rft_id=info%3Adoi%2F10.1128%2FAEM.66.7.2898-2905.2000&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Cospeciation+of+Psyllids+and+Their+Primary+Prokaryotic+Endosymbionts&rft.issn=0099-2240&rft.date=2000&rft.volume=66&rft.issue=7&rft.spage=2898&rft.epage=2905&rft.artnum=http%3A%2F%2Faem.asm.org%2Fcgi%2Fdoi%2F10.1128%2FAEM.66.7.2898-2905.2000&rft.au=Thao%2C+M.&rft.au=Moran%2C+N.&rft.au=Abbot%2C+P.&rft.au=Brennan%2C+E.&rft.au=Burckhardt%2C+D.&rft.au=Baumann%2C+P.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology" >Thao, M., Moran, N., Abbot, P., Brennan, E., Burckhardt, D., & Baumann, P. (2000). Cospeciation of Psyllids and Their Primary Prokaryotic Endosymbionts <span style="font-style: italic;">Applied and Environmental Microbiology, 66</span> (7), 2898-2905 DOI: <a rev="review" href="http://dx.doi.org/10.1128/AEM.66.7.2898-2905.2000">10.1128/AEM.66.7.2898-2905.2000</a></span><span style="font-size:100%;">
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<br />Joseph Boylehttp://www.blogger.com/profile/16489640800322311480noreply@blogger.com7tag:blogger.com,1999:blog-496263467300370264.post-9216108300211106822009-07-15T13:31:00.008+01:002009-07-15T14:13:16.890+01:00Non-B DNA structures and disease<span style="padding: 5px; float: left;"><a href="http://www.researchblogging.org/"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border: 0pt none ;" /></a></span>
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<br /><div style="text-align: justify;">People seem to have started contributing actively to the blog again so I thought it was my turn to try again. And this is an achievement, as facing any science, in particular anything written by me about it, would have been impossible a month ago.
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<br />I decided to keep things simple for this one and just give a short introduction on the theme of non-B DNA structures and how they influence disease, the topic of my open essay.
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<br />When we think about DNA, we think about its B-DNA structure, the one that Watson and Crick described in that famous Nature paper more than 50 years ago, i.e. a right-handed double helix, 20Å diameter, in which the base pairs are almost perpendicular to the axis of the helix, 10.5bps per turn. Although most DNA will be in this structure, it can also form other structures, the so called non-B DNA structures. Some of these are shown in the figure. These alternative structures have a few common characteristics: firstly, whether or not a structure is formed, and which specific structure, seems to be sequence dependent, as it often involves formation of new pairings of bases. Secondly, most of these structures are in higher energetic state than normal B-DNA, for example, because they require the separation and reformation of hydrogen bonds. Overall, therefore, DNA with a favourable sequence tends to remain in its B-DNA form, requiring events such as DNA replication, transcription or protein binding to be transiently converted to these unusual structures. Sequences with propensity to form unusual structures are quite common in the human genome, and it seems that in some cases they are necessary for the normal functioning of the cell. However, they have also been implicated in disease, and this is what I’ll be focusing till the end of this post.
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<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxMI-XdOnvdtdCuyC_4R-yVcOb1P1G1Jmkr5iEiX3FaJBiI-R7bVJXgUdHdOR-3IVSzYTKuYyz9bXh6NEh2VopQ-V54GopZ2yITUgY6AloPJSAi6EaToQOT1LUbrYqATTBcprUsFFEqpo/s1600-h/non-B+DNA+structures.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 283px; height: 320px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgxMI-XdOnvdtdCuyC_4R-yVcOb1P1G1Jmkr5iEiX3FaJBiI-R7bVJXgUdHdOR-3IVSzYTKuYyz9bXh6NEh2VopQ-V54GopZ2yITUgY6AloPJSAi6EaToQOT1LUbrYqATTBcprUsFFEqpo/s320/non-B+DNA+structures.jpg" alt="" id="BLOGGER_PHOTO_ID_5358668279384683474" border="0" /></a>
<br /><div style="text-align: justify;">There is a considerable list of diseases thought to involve, as part of their pathology, the formation of non-B DNA structures, but the mechanisms by which this is though to happen can vary. For example, certain sequences/structures have been thought to cause genomic instability, e.g. by causing chromosomal rearrangements due to the propensity of these structures to promote double strand breaks. Another interesting form of genomic instability associated with these unusual structures is repeat expansion, implicated in motor diseases such as Huntington’s disease. Non-B DNA structures, namely Z-DNA, have also been associated with viral infections.
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<br />Now, there isn’t really enough space here to talk about everything, so I’m going to give one examples of a situation in which a non-B DNA structure is though to be involved in disease. Friedreich ataxia (FRDA) is a disease caused by the expansion of GAA•TTC tracts in intron 1 of a gene encoding the protein frataxin, essential for mitochondrial function. In this disease, repeat expansion is associated with loss of protein expression. One of the current models by which frataxin production is thought to be reduced in expanded GAA•TTC repeats is based on their ability to form triplexes (an alternative model suggests that epigenetic changes may also be important). Duplex opening within the repeated region, due to the passage of RNA polymerase, is thought to allow one of the separated single strands to form Hoogsteen hydrogen bonds with the purine strand of a B-DNA duplex within the same repeated sequence. This leads to the formation of a 3-stranded helix. Its formation on the non-template GAA strand in frataxin probably interferes with RNA polymerase progression. The free template strand is then thought to base pair with the newly synthesised RNA transcript, forming stable RNA/DNA dimers and preventing further transcription.
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<br />Now, this is only a model, for a specific type of structure within the context of a specific disease. And although different sequences have been shown to form these unusual structures, and these structures to be somehow associated with specific diseases, to neatly demonstrate how exactly one influences the other seems to be quite hard. This is particularly difficult because different groups often use different model organisms or protocols, leading to sometimes contradictory results. Overall, although I liked writing about this topic, since I had never considered how the structure of DNA could have an impact on disease, I got the feeling that a lot of work still needs to be done before convincing evidence is given for how exactly these structures impact on our wellbeing, and what sort of therapeutics can be developed from this knowledge.
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<br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimHBYMpOsfXdKsSe_cJbMBuaheObWkmtJB8tBO6O6GDLL_bCr-WRWqhygZ_ITnq9Hoe98h3vwYTgUj011LuqPpAAK8vRNoovjQLe7MAK3A2iXpycwPYBiL46f0QMh2MzWM2EaOvLRlnWc/s1600-h/frataxin.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 252px; height: 164px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEimHBYMpOsfXdKsSe_cJbMBuaheObWkmtJB8tBO6O6GDLL_bCr-WRWqhygZ_ITnq9Hoe98h3vwYTgUj011LuqPpAAK8vRNoovjQLe7MAK3A2iXpycwPYBiL46f0QMh2MzWM2EaOvLRlnWc/s320/frataxin.jpg" alt="" id="BLOGGER_PHOTO_ID_5358664426370088754" border="0" /></a>
<br /><meta equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 11"><meta name="Originator" content="Microsoft Word 11"><div style="text-align: center;"><link rel="File-List" href="file:///C:%5CUsers%5CCCVICE%7E1%5CAppData%5CLocal%5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml"><!--[if gte mso 9]><xml> <w:worddocument> <w:view>Normal</w:View> <w:zoom>0</w:Zoom> <w:punctuationkerning/> <w:validateagainstschemas/> <w:saveifxmlinvalid>false</w:SaveIfXMLInvalid> <w:ignoremixedcontent>false</w:IgnoreMixedContent> <w:alwaysshowplaceholdertext>false</w:AlwaysShowPlaceholderText> <w:compatibility> <w:breakwrappedtables/> <w:snaptogridincell/> <w:wraptextwithpunct/> <w:useasianbreakrules/> <w:dontgrowautofit/> <w:usefelayout/> </w:Compatibility> <w:browserlevel>MicrosoftInternetExplorer4</w:BrowserLevel> </w:WordDocument> </xml><![endif]--><!--[if gte mso 9]><xml> <w:latentstyles deflockedstate="false" latentstylecount="156"> </w:LatentStyles> </xml><![endif]--><style> <!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman"; mso-fareast-language:EN-GB;} @page Section1 {size:612.0pt 792.0pt; margin:72.0pt 90.0pt 72.0pt 90.0pt; mso-header-margin:36.0pt; mso-footer-margin:36.0pt; mso-paper-source:0;} div.Section1 {page:Section1;} --> </style><!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabela normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;} </style> <![endif]--><span style=";font-family:Arial;font-size:11;" >Red, GAA repeat strand; blue, GTT complementary strand; orange, RNA transcript; yellow, RNA polymerase. 1, Intramolecular triplex; 2, Stalled RNA polymerase; 3, DNA/RNA hybrid</span>
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<br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Biochimie&rft_id=info%3Adoi%2F10.1016%2Fj.biochi.2007.12.005&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Targeting+the+gene+in+Friedreich+ataxia&rft.issn=03009084&rft.date=2008&rft.volume=90&rft.issue=8&rft.spage=1131&rft.epage=1139&rft.artnum=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0300908407003434&rft.au=Hebert%2C+M.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Hebert, M. (2008). Targeting the gene in Friedreich ataxia <span style="font-style: italic;">Biochimie, 90</span> (8), 1131-1139 DOI: <a rev="review" href="http://dx.doi.org/10.1016/j.biochi.2007.12.005">10.1016/j.biochi.2007.12.005</a></span>
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<br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Journal+of+Biological+Chemistry&rft_id=info%3Adoi%2F10.1074%2Fjbc.R400028200&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Non-B+DNA+Conformations%2C+Genomic+Rearrangements%2C+and+Human+Disease&rft.issn=0021-9258&rft.date=2004&rft.volume=279&rft.issue=46&rft.spage=47411&rft.epage=47414&rft.artnum=http%3A%2F%2Fwww.jbc.org%2Fcgi%2Fdoi%2F10.1074%2Fjbc.R400028200&rft.au=Bacolla%2C+A.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Bacolla, A. (2004). Non-B DNA Conformations, Genomic Rearrangements, and Human Disease <span style="font-style: italic;">Journal of Biological Chemistry, 279</span> (46), 47411-47414 DOI: <a rev="review" href="http://dx.doi.org/10.1074/jbc.R400028200">10.1074/jbc.R400028200</a></span>
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<br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Trends+in+Biochemical+Sciences&rft_id=info%3Adoi%2F10.1016%2Fj.tibs.2007.04.003&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Non-B+DNA+conformations%2C+mutagenesis+and+disease&rft.issn=09680004&rft.date=2007&rft.volume=32&rft.issue=6&rft.spage=271&rft.epage=278&rft.artnum=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0968000407000916&rft.au=WELLS%2C+R.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">WELLS, R. (2007). Non-B DNA conformations, mutagenesis and disease <span style="font-style: italic;">Trends in Biochemical Sciences, 32</span> (6), 271-278 DOI: <a rev="review" href="http://dx.doi.org/10.1016/j.tibs.2007.04.003">10.1016/j.tibs.2007.04.003</a></span>
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<br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Molecular+Carcinogenesis&rft_id=info%3Adoi%2F10.1002%2Fmc.20508&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Models+for+chromosomal+replication-independent+non-B+DNA+structure-induced+genetic+instability&rft.issn=08991987&rft.date=2009&rft.volume=48&rft.issue=4&rft.spage=286&rft.epage=298&rft.artnum=http%3A%2F%2Fdoi.wiley.com%2F10.1002%2Fmc.20508&rft.au=Wang%2C+G.&rft.au=Vasquez%2C+K.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Wang, G., & Vasquez, K. (2009). Models for chromosomal replication-independent non-B DNA structure-induced genetic instability <span style="font-style: italic;">Molecular Carcinogenesis, 48</span> (4), 286-298 DOI: <a rev="review" href="http://dx.doi.org/10.1002/mc.20508">10.1002/mc.20508</a></span>Cathttp://www.blogger.com/profile/08645968914831610862noreply@blogger.com2tag:blogger.com,1999:blog-496263467300370264.post-10063377509157865942009-06-29T16:11:00.000+01:002009-06-29T16:13:04.180+01:00Learning how to tell time with cyanobacteriaMost living things can innately tell the time. If you take a person and put them into continuous darkness for months by themselves they will follow a sleep-wake cycle of about 24-25 hours (as well as going a little mad). Circadian rhythms allow life to predict the raising and setting of the sun to allow us to change our gene expression metabolism and behaviour with the changing of the day. Predicting changes in temperatures and light levels are very important. Circadian clocks have three important features. First of all they are free-running at about 24 hours (in constant conditions like light or darkness they will keep going at ~24 hours). Secondly they are temperature compasatory meaning that changes in temperature do not greatly affect the clock. Finally they must be able to be reset by environmental inputs. The changes of the seasons mean days get longer or shorter so to accurately predict the raising of the sun your clock must be reset. Plus for those who fly great distances we must reset according to the new environment and sadly suffer from jet lag while we are slowly adjusting (Johnson et al., 2008). <br /><br />These clocks have evolved independently multiple times. In animals, plants, some fungi and recently discovered in cyanobacteria (Johnson et al., 2008). It was once thought because prokaryotes divide so raplidly that a 24 hour rhythm would be useless to them but that is not the case (Johnson et al., 1996). A great deal has been learnt about rhythms in bacteria but there are still many unanswered questions. The fact circadian clocks have evolved multiple times shows it offers a great advantage to those that posses one but was no present in the last common ancestor of life. Changing behaviour to only occur at a specific time of day is a great advantage to organisms, plants to photosynthesize and animals to look for food at the right times (Bell-Pedersen et al., 2005). <br /><br />Cyanobacteria also rely on the sun for energy so predicting when the sun will rise allows them to start synthesising photosystem proteins before the sun raises while not producing them all night or waiting for the sun to raise. It has been shown when you make a mixed culture of bacteria with a mutant clock (no rhythmic changes in gene expression) and wild-type then wild-type will soon outcompete the mutants. Those that have a different length period (eg 16 hours rather than 24 hours) will always lose to wild-type in 24 hour day conditions but wild-type will lose in conditions that match the internal clock of these mutants (Yan et al., 1998). Interestingly in cyanobacteria the whole genome shows rhythmic expression! (Liu et al., 1995) This is in contrast to most organisms that control 15%-35% of their genome in a circadian dependant manner (McDonald and Rosbach, 2001; Correa et al., 2003; Michael and McClung, 2003). This is controlled by the supercoiled state of the whole genome! (Smith and Williams, 2006) I eagerly await the paper that explains how this achieved. <br /><br />What is rather fascinating about this system is the oscillator. In most organisms gene expression is negatively regulated by its product in a way it cycles its levels over 24 hours and controls output (Bell-Pedersen et al., 2005). In cyanobacteria, this is not the case. Rhythmic expression of clock proteins occur but they do not repress there own synthesis. Also an in vitro oscillator can be setup. In the test tube the clock protein KiaC will cycle through different phosphorylation states if with KaiA, KaiB and ATP. In the organism this forms the post-translational oscillator (Nakajima et al., 2005). This is temperature compensatory and this is built into the ATPase activity of KaiC (Terauchi et al., 2007). It has been shown even when locked in one phosphorylation state you get a weak rhythm so a transcriptional-translational feedback loop as in eukaryotes is needed for a robust system (Kitayama et al., 2008) posing the question of whether this occurs in eukaryotes. <br /><br />And to finish off I will add one final oddity about the circadian rhythms of cyanobacteria. Instead of using a photoreceptor to sense light inputs like other organisms they read the state of the metabolism. When light is high photosynthesis is occurring and the redox state of the cell changes and is seen as an input to reset the clock (Ivleva et al., 2005). <br /><br />References<br /><br />*Of importance<br />**Truly significant<br /><br />Bell-Pedersen, D., Cassone, V.M., Earnest, D.J., Golden, S.S., Hardin, P.E., Thomas, T.L. and Zoran, M.J. (2005) Circadian rhythms from multiple oscillators: Lessons from diverse organisms. Nature Reviews Genetics, 6, 544-556.<br /><br />Correa, A., Lewis, A.Z., Greene, A.V., March, I.J., Gomer, R.H. and Bell-Pedersen, D. (2003) Multiple oscillators regulate circadian gene expression in Neurospora. Proceedings of the National Academy of Sciences of the United States of America, 100, 13597-13602.<br /><br />Ivleva, N.B., Bramlett, M.R., Lindahl, P.A. and Golden, S.S. (2005) LdpA: a component of the circadian clock senses redox state of the cell. Embo Journal, 24, 1202-1210.<br /><br />Johnson, C.H., Golden, S.S., Ishiura, M. and Kondo, T. (1996) Circadian clocks in prokaryotes. Molecular Microbiology, 21, 5-11.<br /><br />Johnson, C.H., Mori, T. and Xu, Y. (2008) A Cyanobacterial Circadian Clockwork. Current Biology, 18, R816-R825.<br /><br />**Kitayama, Y., Nishiwaki, T., Terauchi, K. and Kondo, T. (2008) Dual KaiC-based oscillations constitute the circadian system of cyanobacteria. Genes & Development, 22, 1513-1521.<br /><br />Liu, Y., Tsinoremas, N.F., Johnson, C.H., Lebedeva, N.V., Golden, S.S., Ishiura, M. and Kondo, T. (1995) Circadian Orchestration of Gene-Expression in Cyanobacteria. Genes & Development, 9, 1469-1478.<br /><br />McDonald, M.J. and Rosbach, M. (2001) Microarray analysis and organization of circadian gene expression Drosophila. Cell, 107, 567-578.<br /><br />Michael, T.P. and McClung, C.R. (2003) Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis. Plant Physiology, 132, 629-639.<br /><br />*Nakajima, M., Imai, K., Ito, H., Nishiwaki, T., Murayama, Y., Iwasaki, H., Oyarna, T. and Kondo, T. (2005) Reconstitution of circadian oscillation of cyanobacterial KaiC phosphorylation in vitro. Science, 308, 414-415.<br /><br />Smith, R.M. and Williams, S.B. (2006) Circadian rhythms in gene transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus. Proceedings of the National Academy of Sciences of the United States of America, 103, 8564-8569.<br /><br />Terauchi, K., Kitayama, Y., Nishiwaki, T., Miwa, K., Murayama, Y., Oyama, T. and Kondo, T. (2007) ATPase activity of KaiC determines the basic timing for circadian clock of cyanobacteria. Proceedings of the National Academy of Sciences of the United States of America, 104, 16377-16381.<br /><br />Yan, O.Y., Andersson, C.R., Kondo, T., Golden, S.S. and Johnson, C.H. (1998) Resonating circadian clocks enhance fitness in cyanobacteria. Proceedings of the National Academy of Sciences of the United States of America, 95, 8660-8664.James Lloydhttp://www.blogger.com/profile/08219295648051788360noreply@blogger.com4tag:blogger.com,1999:blog-496263467300370264.post-18343438184270324232009-06-25T03:36:00.022+01:002009-07-02T17:32:37.576+01:00The Life and Death of Elysia Chlorotica<a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg8Q2A34s1BvAR36tHr4nruvzXW-w2yb1QVDm5qOtpChIofRToh1p6l3Iyx3joVSCf1WJBRHMw6lP9fPfGqusN5vsiumNGtJRpYCtSNE11xNsQxDZL74rBI5gR1NC4iwz_wpaWB1XlP7Xc/s1600-h/Uncurled.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 196px; height: 237px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEg8Q2A34s1BvAR36tHr4nruvzXW-w2yb1QVDm5qOtpChIofRToh1p6l3Iyx3joVSCf1WJBRHMw6lP9fPfGqusN5vsiumNGtJRpYCtSNE11xNsQxDZL74rBI5gR1NC4iwz_wpaWB1XlP7Xc/s320/Uncurled.jpg" alt="" id="BLOGGER_PHOTO_ID_5351090427347776594" border="0" /></a><meta name="GENERATOR" content="OpenOffice.org 3.0 (Win32)"><style type="text/css"> <!-- @page { margin: 2cm } P { margin-bottom: 0.21cm } --</style>Since the end of university I’ve had some trouble letting go of science as a constant occupation. Fortunately I was given the chance to post here about an old journal club presentation rather than go cold turkey, so here is a short piece on one of the most interesting organisms I’ve read about. <p style="margin-bottom: 0cm;">The picture on the left is of a sea slug of the genus <i>Elysia</i> which has evolved to blend in with its surroundings by looking almost exactly like a small leaf. The green colour that makes this camouflage so convincing is produced when the slug feeds on algae and steals their chloroplasts, subsequently storing them throughout its body. The use of chloroplast pigments to produce a leaf colour is common among sea slugs but the subject of this post is exceptional among the rest of its family. While in the majority of sea slugs the chloroplasts stop working within days or weeks of incorporation, those taken up by <i>Elysia chlorotica</i> can remain stable and active within the slug for at least ten months. As a result the slug is a rare example of a photosynthetic animal and it can survive without food for a long time, as long as it has light and carbon dioxide.</p> <p style="margin-bottom: 0cm;"><i>E. chlorotica</i> has coevolved with a specific species of algae named <i>Vaucheria litorea</i>, which is a source of food and chloroplasts for the slug. The metamorphosis of <i>E. chlorotica</i> larvae into their slug form takes place only if the larvae are attached to filaments of <i>V. litorea</i> and in the absence of this algal species the larvae will die. Immediately after metamorphosis the slugs feed on the algae to which they are attached and take up their chloroplasts, incorporating them into their branched digestive tract. </p><p style="margin-bottom: 0cm;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhIItl5Y3eyJcl9C-Bou4HB6riXLt-jS3MPDZR3RTM2n30KPo9DC6HpVbnJ6y5_dVJoKYyZeTH6cqX5-wIhbE1UbLBt-vSrlp5oHB5VarpDdXaydHM6DQFhmUVtSuWZRhcPyaXhAc6VTG8/s1600-h/Curled.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 320px; height: 225px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhIItl5Y3eyJcl9C-Bou4HB6riXLt-jS3MPDZR3RTM2n30KPo9DC6HpVbnJ6y5_dVJoKYyZeTH6cqX5-wIhbE1UbLBt-vSrlp5oHB5VarpDdXaydHM6DQFhmUVtSuWZRhcPyaXhAc6VTG8/s320/Curled.jpg" alt="" id="BLOGGER_PHOTO_ID_5351096858572509922" border="0" /></a></p> <p style="margin-bottom: 0cm;">As mentioned previously, most species of sea slug lose their chloroplast functions soon after obtaining them from algae. This is expected to be because the majority of genes required for chloroplast survival and function are encoded on the algal nucleus. Since animals do not have genes involved in chloroplast maintenance the question of how <i>E. chlorotica</i> manages to sustain its stolen plastids was investigated by several labs. In a recent study, the chloroplast genome of <i>V. litorea</i> was sequenced to determine whether it had greater genetic autonomy than previously sequenced chloroplasts, however, the chloroplast genome was found to be largely normal and was missing many genes essential for photosynthesis.
<br /></p> <p style="margin-bottom: 0cm;">One of these missing genes, <i>psbO</i>, encodes a component of photosystem II which is vulnerable to damage during photosynthesis and needs to be regularly resynthesised for chloroplast function. Rumpho <i>et al.</i> were able to amplify the whole of this gene from sea slug DNA using primers based on seqeuence databases. The amplified sequence was shown to correspond exactly to the version of <i>psbO </i>from <i>V. litorea</i>, indicating that lateral gene transfer had taken place between the algae and the slug. The same sequence could be amplified from sea slug eggs which had not yet encountered algae, confirming that the sequence had entered the <i>E. chlorotica</i> germline. The authors behind this study speculate that all of the other genes needed for chloroplast survival and function have also been transferred to the slug germline, explaining the unique ability of <i>E. chlorotica</i> to maintain its chloroplasts for its entire life. So it seems that the sea slugs have stolen both DNA and organelles from algae, which is quite an achievement.
<br /></p> <p style="margin-bottom: 0cm;">Another interesting property of <i>E. chlorotica</i> is that its generations are separated from each other. Whether slugs are collected in the lab or monitored in their natural environment, the entire adult population undergoes a synchronous death every year after they have laid their eggs. Pierce <i>et al. </i>observed that viral particles could be seen in the cytoplasm and nuclei of slugs just before their mass death and suggested that they may be responsible for the mortalities. The morphology of the viruses and the presence of reverse transcriptase activity suggest that they are retroviruses and, since the particles were found even under controlled laboratory conditions, it is likely that the virus is encoded on the genome of the sea slug. The group who made this observation suggested that the viruses may respond to annual environmental changes and kill the sea slugs in the spring, though this hypothesis has not been tested so far. </p> <p style="margin-bottom: 0cm;">Unfortunately, the last paper I found on research into the viruses within the sea slugs was in 1999 and so research into this interesting aspect of the organism may not be ongoing. However I'm hoping to find some more about it in the future.</p><p style="margin-bottom: 0cm;">
<br /><span style="float: left; padding: 5px;"><a href="http://www.researchblogging.org"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border:0;"/></a></span>
<br /></p><p style="margin-bottom: 0cm;"><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=PLANT+PHYSIOLOGY&rft_id=info%3Adoi%2F10.1104%2Fpp.123.1.29&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Solar-Powered+Sea+Slugs.+Mollusc%2FAlgal+Chloroplast+Symbiosis&rft.issn=15322548&rft.date=2000&rft.volume=123&rft.issue=1&rft.spage=29&rft.epage=38&rft.artnum=http%3A%2F%2Fwww.plantphysiol.org%2Fcgi%2Fdoi%2F10.1104%2Fpp.123.1.29&rft.au=Rumpho%2C+M.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Rumpho, M. (2000). Solar-Powered Sea Slugs. Mollusc/Algal Chloroplast Symbiosis <span style="font-style: italic;">PLANT PHYSIOLOGY, 123</span> (1), 29-38 DOI: <a rev="review" href="http://dx.doi.org/10.1104/pp.123.1.29">10.1104/pp.123.1.29</a></span>
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<br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Biological+Bulletin&rft_id=info%3Adoi%2F10.2307%2F1542990&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Annual+Viral+Expression+in+a+Sea+Slug+Population%3A+Life+Cycle+Control+and+Symbiotic+Chloroplast+Maintenance&rft.issn=00063185&rft.date=1999&rft.volume=197&rft.issue=1&rft.spage=1&rft.epage=0&rft.artnum=http%3A%2F%2Fwww.jstor.org%2Fstable%2F1542990%3Forigin%3Dcrossref&rft.au=Pierce%2C+S.&rft.au=Maugel%2C+T.&rft.au=Rumpho%2C+M.&rft.au=Hanten%2C+J.&rft.au=Mondy%2C+W.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Pierce, S., Maugel, T., Rumpho, M., Hanten, J., & Mondy, W. (1999). Annual Viral Expression in a Sea Slug Population: Life Cycle Control and Symbiotic Chloroplast Maintenance <span style="font-style: italic;">Biological Bulletin, 197</span> (1) DOI: <a rev="review" href="http://dx.doi.org/10.2307/1542990">10.2307/1542990</a></span>
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<br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Biological+Bulletin&rft_id=info%3Adoi%2F10.2307%2F1543594&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Horizontal+Transfer+of+Functional+Nuclear+Genes+between+Multicellular+Organisms&rft.issn=00063185&rft.date=2003&rft.volume=204&rft.issue=3&rft.spage=237&rft.epage=0&rft.artnum=http%3A%2F%2Fwww.jstor.org%2Fstable%2F1543594%3Forigin%3Dcrossref&rft.au=Pierce%2C+S.&rft.au=Massey%2C+S.&rft.au=Hanten%2C+J.&rft.au=Curtis%2C+N.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Pierce, S., Massey, S., Hanten, J., & Curtis, N. (2003). Horizontal Transfer of Functional Nuclear Genes between Multicellular Organisms <span style="font-style: italic;">Biological Bulletin, 204</span> (3) DOI: <a rev="review" href="http://dx.doi.org/10.2307/1543594">10.2307/1543594</a></span>
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<br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Proceedings+of+the+National+Academy+of+Sciences&rft_id=info%3Adoi%2F10.1073%2Fpnas.0804968105&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=From+the+Cover%3A+Horizontal+gene+transfer+of+the+algal+nuclear+gene+psbO+to+the+photosynthetic+sea+slug+Elysia+chlorotica&rft.issn=0027-8424&rft.date=2008&rft.volume=105&rft.issue=46&rft.spage=17867&rft.epage=17871&rft.artnum=http%3A%2F%2Fwww.pnas.org%2Fcgi%2Fdoi%2F10.1073%2Fpnas.0804968105&rft.au=Rumpho%2C+M.&rft.au=Worful%2C+J.&rft.au=Lee%2C+J.&rft.au=Kannan%2C+K.&rft.au=Tyler%2C+M.&rft.au=Bhattacharya%2C+D.&rft.au=Moustafa%2C+A.&rft.au=Manhart%2C+J.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Rumpho, M., Worful, J., Lee, J., Kannan, K., Tyler, M., Bhattacharya, D., Moustafa, A., & Manhart, J. (2008). From the Cover: Horizontal gene transfer of the algal nuclear gene psbO to the photosynthetic sea slug Elysia chlorotica <span style="font-style: italic;">Proceedings of the National Academy of Sciences, 105</span> (46), 17867-17871 DOI: <a rev="review" href="http://dx.doi.org/10.1073/pnas.0804968105">10.1073/pnas.0804968105</a></span> </p> Joseph Boylehttp://www.blogger.com/profile/16489640800322311480noreply@blogger.com2tag:blogger.com,1999:blog-496263467300370264.post-58815383751915924092009-05-01T14:50:00.003+01:002009-05-07T08:00:25.087+01:00Flu flu go away, come again another day (when I don't have exams)Right I should be revising for those finals but with my arm hurting I am using it as an excuse not to write practice essays today and typing doesn't put as much strain on it (I think). <br /><br />So Swine flu/Mexican flu/H1N1 flu has brought Mexico to a halt and scared the rest of the world into a panic. Big mouth Vice-president Biden of the USA has done it again saying he wouldn't trust travelling etc. fair point but you are trying to calm the masses as a leader. From what is humble virologist wannabe can see is this new hybrid strain made from genes of avian, swine and human flu is doing is spreading very quickly among people. For some reason it has killed lots in Mexico (allegedly) but only causing mild cases elsewhere. Today however the researcher at Mill Hill have suggested this strain is not very deadly. This paints a rather paradoxical picture. We see many deaths in Mexico from a fast spreading flu. Yes the world should be worried and has done the right thing by preparing for the worse. But we have only seen mild cases in most people outside Mexico and its genome suggests it is only mild. It doesnt have the make-up that causes cytokine storm that kills young people (like Spanish flu did). That is one thing not to worry about (right now). Plus it only infects cells near the top of the respiratory track so doesn't cause infections deep in the lungs, making it easy to spread but not as deadly as some. <br /><br />So two things need to be thought about 1) why has it killed so many people in Mexico? and 2) what shall we call it? I am not going to tackle the first but I have some thought. The second I think should be Mexican flu. Swine flu is hurting the pig farming industry (some countries have banned pork imports!) while H1N1 is just rubbish. Loads of flu strains are called H1N1. Some seasonal flu is H1N1 and Spanish flu of 1919 was H1N1!!! I personally think the H and N naming system is out dated and inaccurate. It is not the H and N proteins that make a virus what is is per se but the many other changes with them. <br /><br />Closing thought though, Flu has a high mutation rate with its RNA genome (no where near HIV but still more than what we would like) so changes may occur soon that could be game changers. <br /><br />http://news.bbc.co.uk/1/hi/health/8028371.stmJames Lloydhttp://www.blogger.com/profile/08219295648051788360noreply@blogger.com0tag:blogger.com,1999:blog-496263467300370264.post-38172233869831662572009-04-07T21:06:00.012+01:002009-04-12T01:14:08.548+01:00When a bit more fat is not that bad<span style="float: left; padding: 5px;"><a href="http://www.researchblogging.org"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border:0;"/></a></span><br /><br />Nothing is as simple as it looks in Biology. We can’t even rely on gene or protein sequences to tell us what is going to happen. At the chromosomal level, the new field of epigenetics is showing how the nucleotide sequence does not define everything. At protein level we have to consider post-translational modifications. My final year project, now at the final write up stages, concentrated on an aspect of Trypanosoma brucei molecular biology which I very pompously described as a potential drug target and the cure for African sleeping disease. This bit was probably ‘paper talk’ though. In any case, the project focused on protein palmitoylation.<br /><br />Palmitoylation is part of a group of several lipid modifications that can occur in proteins. Examples include N-myristoylation, prenylation and GPI-anchors. N-myristoylation is the reason why I thought it was not pushing it to much to say that we can kill parasites by targeting these modifications. N-myristoylation corresponds to the co-translational addition of myristate to an N-terminus glycine, and is catalyzed by N-myristoyltransferases (NMT). It so happens that NMTs were shown to be essential for parasite viability, and several antifungal NMT inhibitors apparently work on reducing NMT activity in T.brucei as well(1).<br /><br />But back to palmitoylation, the post-translational addition of palmitic acid to a cysteine residue (reviewed in 2 and 3). It can occur in any place in the protein, and so far no consensus palmitoylation motif has been identified. Often it occurs in an N-terminus cysteine, just next to a myristoylation site. These proteins are said to be dually acylated. Palmitoylation can also happen in close proximity to prenylation sites. Palmitoylation can perform many functions in the cell, the most obvious being protein tethering to membranes and cellular localization. It has also been shown to interfere with protein-protein interactions and even with protein degradation. For example, the yeast SNARE Tgl1, when is not palmitoylated, can interact with the ubiquitin ligase Tul1(4).<br /><br />Those paying attention (or still reading) will think that it is a bit strange that palmitoylation can regulate protein degradation like that. In fact, most of these lipid modifications, N-myristoylation for example, last for the life time of the protein. Well, palmitoylation is characterized by a unique feature: it is reversible. This means that it can determine processes that other lipidations cannot. Dynamic trafficking of proteins of proteins, for example. This is the case of Ras protein, which through an deacylation/reacylation cycle is able to exchange between the plasma membrane and the Golgi apparatus (5). Reversibility can also be important for signalling. Regulator of G-protein signalling 2 (RGS2) was shown to increase or decrease its GTPase-activating ability depending on which of its cysteine residues are palmitoylated(6).<br /><br />The process of palmitoylation in itself is catalyzed by the enzymes palmitoyl-acyltransferases (PATs). These were pretty hard to identify, apparently. Not only they were difficult to purify, but the reaction itself can occur spontaneously with biological significance(7), which made many sceptic on whether these enzymes existed at all. However, they were identified, first in yeast, now in mammals and in my dear T.brucei.<br /><br />And what was supposed to be a short post if already long enough. I finish by adding that my project was about finding proteins that were palmitoylated and that would change their localization in the absence of this modification, in an attempt to identify substrates for RNAi PAT studies in T.brucei. I must say that the project was not particularly successful, but I developed the important skill of writing long discussions based on few results, which I bet will come handy in the future.<br /><br />I now challenge Mel to continue in this post-translational modification topic and tell us about his project on glycosylation.<br /> <br /><br />References:<br /><br />1. <span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Journal+of+Biological+Chemistry&rft_id=info%3Adoi%2F10.1074%2Fjbc.M211391200&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Myristoyl-CoA%3AProtein+N-Myristoyltransferase%2C+an+Essential+Enzyme+and+Potential+Drug+Target+in+Kinetoplastid+Parasites&rft.issn=00219258&rft.date=2002&rft.volume=278&rft.issue=9&rft.spage=7206&rft.epage=7214&rft.artnum=http%3A%2F%2Fwww.jbc.org%2Fcgi%2Fdoi%2F10.1074%2Fjbc.M211391200&rft.au=Price%2C+H.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Price, H. (2002). Myristoyl-CoA:Protein N-Myristoyltransferase, an Essential Enzyme and Potential Drug Target in Kinetoplastid Parasites <span style="font-style: italic;">Journal of Biological Chemistry, 278</span> (9), 7206-7214 DOI: <a rev="review" href="http://dx.doi.org/10.1074/jbc.M211391200">10.1074/jbc.M211391200</a></span><br /><br />2. Nadolski MJ, Linder ME. Protein lipidation. FEBS J 2007;274:5202-10.<br /><br />3. Greaves J, Chamberlain LH. Palmitoylation-dependent protein sorting. J Cell Biol 2007;176:249-54.<br /><br />4. Valdez-Taubas J, Pelham H. Swf1-dependent palmitoylation of the SNARE Tlg1 prevents its ubiquitination and degradation. EMBO J 2005;24:2524-32.<br /><br />5. Rocks O, Peyker A, Kahms M, et al. An acylation cycle regulates localization and activity of palmitoylated Ras isoforms. Science 2005;307:1746-52.<br /><br />6. Ni J, Qu L, Yang H, et al. Palmitoylation and its effect on the GTPase-activating activity and conformation of RGS2. Int J Biochem Cell Biol 2006;38:2209-18.<br /><br />7. Kummel D, Heinemann U, Veit M. Unique self-palmitoylation activity of the transport protein particle component Bet3: a mechanism required for protein stability. Proc Natl Acad Sci U S A 2006;103:12701-6.Cathttp://www.blogger.com/profile/08645968914831610862noreply@blogger.com5tag:blogger.com,1999:blog-496263467300370264.post-68308399882466658802009-03-31T13:03:00.001+01:002009-03-31T13:03:49.170+01:00Faith of a different sortSo having finals upon us should be no excuse to stop the advancement of scientific and philosophical thought on here. So when I wandered into town today to do a favour for my dad (30 min walk for me, 3 hour drive for him) I saw a stall with a sign talking about truth. I still have no idea what a truth is so I thought I would have a look at what truths they were talking about. It was a stall full of Jehovah’s witnesses and I was very nice and polite before you say anything! I always am to there face. Being nasty and telling them, ‘you are probably was wrong as you can be’ doesn’t help win them over to your cause! Richard Dawkins QED. But over our chat I mentioned I supported evolution and was an atheist. But they suggested trusting some of the gaps in evolution had an explanation needed faith. This is an interesting one. It doesn’t but it requires something. I know very little physics and geology. If someone was to question the age of the earth in front of me I would have to turn around I say ‘I don’t know how they worked it out and don’t understand the sciences behind it’ so is it faith in these people I have in other scientists? Probably. But is it bad or wrong for me. I think it is a different sort of faith. First of all it is not blind absolute trust. I know I can easily be wrong about many things (it doesn’t happen often enough though) and I know other can be. <br /><br />We all need to have this kind of faith to get through life. We cannot know everything so we need to trust others or ‘the system’. Imagine a friend offers you a life in there car but you have never seen them drive before in your life. You don’t know if they are good or bad or will get you killed or not. But you get in anyway. Perhaps because you are so lazy you don’t care if you could die as long as it gets you there faster like me. Or because you have faith that having passed a driving test and having belief in there abilities means you can trust them. It is like knowing peer reviewing produces mostly good knowledge and the author is confident in the results even if you don’t understand the experiments or the maths used to analyse it. This evidence based faith is not a bad thing but needs use to take the results with a large pinch of results. It is not perfect. Sometimes someone who you think would be a good driver turns out not to be while taking a ‘fact’ at face value because you trust the scientist you get it from could mean you are wrong but sometimes we need to take these ‘leaps of faith’. Just know that is what you are doing when you do. <br /><br />Agree or not?James Lloydhttp://www.blogger.com/profile/08219295648051788360noreply@blogger.com6tag:blogger.com,1999:blog-496263467300370264.post-12667370907765160332009-02-16T04:14:00.009+00:002009-02-16T11:02:00.446+00:00Drosophila: Virgins, balancers and jump-outs<div style="text-align: justify;"><span style="font-size:85%;"><span style="font-family:georgia;">A wise man once said that the sooner you find your model organism, the better. Ignoring the fact that the wise man I am quoting is actually me, I think I generally agree with him. This year I am working on an exciting project which extensively uses the model organism Drosophila melanogaster, geneticists’ favourite little invertebrate. In the 15 short weeks I have been working with flies, I have learned a gr</span></span><span style="font-size:85%;"><span style="font-family:georgia;">eat deal from these wonderful creatures and experienced emotions from adoration to amusement to frustrated rage in my dealings with them.</span></span><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www-tc.pbs.org/wgbh/nova/allfours/images/gene-fruitfly-l.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer; width: 138px; height: 146px;" src="http://www-tc.pbs.org/wgbh/nova/allfours/images/gene-fruitfly-l.jpg" alt="" border="0" /></a><span style="font-size:85%;"><span style="font-family:georgia;">Briefly, this is your average everyday “fruit fly” (even though a more appropriate name would be “vinegar fly”) with the complete package of a head, a thorax with 2 wings and 6 legs, an abdomen, and everything else that makes flies flies. I will spare you the tediously detailed anatomy and physiology lecture and will instead jump s</span></span><span style="font-size:85%;"><span style="font-family:georgia;">traigh</span></span><span style="font-size:85%;"><span style="font-family:georgia;">t to the cool stuff that interests us geneticists and you readers of genetics blogs.</span></span><br /><br /><span style="font-size:85%;"><span style="font-family:georgia;">One of the most interesting things about Drosophila is in fact the people that use them in research. These people are commonly known as “fly pushers”, since they do in fact spend a lot of their time pushing flies around under a microscope using an old half-mangled paintbrush. One thing that you will inevitably hear about once you start hanging out with fly pushers is how interested they are in virgin females. Flies, that is. You see, since experiments in fly genetics involve crossing male flies from one line to female flies of another in order to obtain progeny of the required genotype, one must ensure that the females have not already been fertilised by males before picked out and crossed to a different line. Collecting </span></span><span style="font-size:85%;"><span style="font-family:georgia;">virgins involves looking for flies that have a dark spot in their abdomen called the meconium, which is visible for 2-3 hours from eclosion (i.e. emergence of the adult from the pupa). Females will not be receptive</span></span><span style="font-size:85%;"><span style="font-family:georgia;"> to males for up to 8 hours from eclosion so any fly that has a meconium can be safely considered a virgin. The most efficient way to collect virgins is to empty a vial of eclosing flies in the morning, selecting females with visible meconium, and returning in the evening. Any females in that vial will be virgins even if the meconium isn’t visible, since less than 8 hours will have passed since your last collection. Much like the world we live in these days, virgins can be rather hard to find, so if you ever hear a scientist worrying about the fact that they need as many virgins </span></span><span style="font-size:85%;"><span style="font-family:georgia;">as possible, you now have an idea of what they are talking about.</span></span><br /><br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhi25wvrvY_5KMBMlsqvLGCDNNdTYI1-8PfToMS0Vi5twiee-bP1VzftDfcrZZSRnAwVM-cY0ykPpumEjuG9IuKuqh1aJoN6zKATTvcYIB_q9stKbTvSsZYta7mzR3eYsPFXAa7INbQGzRL/s1600-h/meconium.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 233px; height: 320px;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEhi25wvrvY_5KMBMlsqvLGCDNNdTYI1-8PfToMS0Vi5twiee-bP1VzftDfcrZZSRnAwVM-cY0ykPpumEjuG9IuKuqh1aJoN6zKATTvcYIB_q9stKbTvSsZYta7mzR3eYsPFXAa7INbQGzRL/s320/meconium.jpg" alt="" id="BLOGGER_PHOTO_ID_5303246409814300098" border="0" /></a><br /><br /><span style="font-size:85%;"><span style="font-family:georgia;">N</span></span><span style="font-size:85%;"><span style="font-family:georgia;">ow let’s delve into some actual genetics. One of the multitude of reasons Drosophila are an excellent test tube for genetic experimentation is something called a “balancer chromosome”. A line of flies carrying a recessive lethal mutation can be maintained by tracking the mutation using dominant markers, or by “balancing” it over a different lethal mutation on its homologous chromosome. This way each chromosome “rescues” the mutation the other is carrying. However, if recombination takes place between these chromosomes, it is likely that you will then have one chromosome carrying both mutations over a wild type chromosome, which will quickly take over the stock and the mutations will be lost. You could always outcross males every generation (there is no recombination in male Drosophila) but that would be very laborious. In order to get around this problem, fly geneticists initially discovered and subsequently intentionally generated balancer chromosomes. </span></span><span style="font-size:85%;"><span style="font-family:georgia;">These are full chromosomes </span></span><span style="font-size:85%;"><span style="font-family:georgia;">which </span></span><span style="font-size:85%;"><span style="font-family:georgia;">contain multiple inversions (essentially all the genes are still th</span></span><span style="font-size:85%;"><span style="font-family:georgia;">ere and intact, but their order is jumbled up) in order to suppress recombination with its </span></span><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://www.exploratorium.edu/imaging_station/gal_media/drosophila/fly_curly/fly_curly_cat.jpg"><img style="margin: 0pt 0pt 10px 10px; float: right; cursor: pointer; width: 160px; height: 120px;" src="http://www.exploratorium.edu/imaging_station/gal_media/drosophila/fly_curly/fly_curly_cat.jpg" alt="" border="0" /></a><span style="font-size:85%;"><span style="font-family:georgia;">homologous chromosome and make any gametes with </span></span><span style="font-size:85%;"><span style="font-family:georgia;">recombined chromosomes non-viable due to aneuploidy. </span></span><span style="font-size:85%;"><span style="font-family:georgia;">They also carry some dominant visible markers such as Cy (curly wings), Tb (tubby), Sb (stubble) and others, and some recessive lethal markers, meaning that they can never go homozygous.</span></span><br /><br /><span style="font-size:85%;"><span style="font-family:georgia;">So, to illustrate this, if you have a recessive lethal mutation on chromosome 2 (let’s now call that chromosome “Yorf”), in order to establish a line that will self-perpetuate and not need constant attention, all you need to do is cross it to a line that carries a balancer second chromosome, for example the chromosome CyO. You will now have a line whose flies will always have the same genotype, i.e. Yorf/CyO. As the Yorf/CyO flies interbreed, any Yorf/Yorf progeny will not survive because the mutation will be lethal, and any CyO/CyO flies will also not survive because of the recessive lethal marker that CyO carries. There will also never be any recombination between the Yorf and CyO chromosomes because of the multiple inversions in CyO that prevent homologous pairing. Wonderful, isn’t it?</span></span><br /><br /><span style="font-size:85%;"><span style="font-family:georgia;">Another great thing about Drosophila is insertional mutagenesis. P-elements are transposons, short stretches of DNA which, in the presence of transposase and absence of inhibitor, are excised from the genome and reinserted randomly into another site. Some P-elements are rendered inactive by having the transposase gene deleted. This temporarily immobilises the transposon, until that fly is crossed to a fly carrying an active transposase gene. In the progeny, the P-element will jump out, and if it inserts into the coding sequence of a gene, it can disrupt its function. A mutagenesis screen can then be carried out and the insertion locus can be mapped using standard complementation or cytological mapping. There is however an application of P-element mutagenesis that has accelerated Drosophila genetics in recent years.</span></span><br /><br /><span style="font-size:85%;"><span style="font-family:georgia;">The targeted gene knock-out system developed in mice is an excellent way to study the role of single genes, but the long generation time and ethical concerns make the mouse a rather cumbersome model organism. An analogous targeted gene disruption tool has been developed in Drosophila, taking advantage of a property of P-element transposition. When a P-element is transposed, its excision from the genome can sometimes be imprecise, taking some of its flanking DNA along with it, thus causing a deletion in that gene. Since an extensive library of mapped P-element inserts already exists (in over half the fly genome), a line carrying a P-element insert in a particular gene can be obtained and the P-element “jumped out” by crossing to a transposase line. In the cases where the jump-out has been imprecise, the result will effectively be a targeted gene knock-out.</span></span><br /><br /><span style="font-size:85%;"><span style="font-family:georgia;">This is, of course, only scratching the surface of the range of genetic tools that Drosophila offers. The best way to understand fly genetics is to try some crosses on paper yourself. Some quite amazing things can be achieved within a few weeks’ time simply by performing a series of crosses and studying the progeny. The waiting time is still a little too long for impatient people like myself, but careful time planning can ensure that you always have some flies to play with and are never stuck staring at a pupa, waiting for the damn fly to emerge.</span></span></div><span style="font-size:85%;"> </span>Menelaos Symeonideshttp://www.blogger.com/profile/05361581879935604330noreply@blogger.com2tag:blogger.com,1999:blog-496263467300370264.post-14878539360817721762009-01-22T13:30:00.001+00:002009-01-31T00:44:38.654+00:00Meaning out of nonsenseImagine you are a eukaryotic cell. You have many genes and make many mRNAs. One problems is mutated genes, pseudogenes and mistakes by RNAPII all make mRNAs which contain Premature Stop Codons (PTC). These then make truncated proteins which could be toxic to the cell. Eukaryotes have evolved a mechanism to recognise these and degrade them. I guess prokaryotes do not have an analogous system (that I know of) because the half-life of these mRNAs are minutes long not hours long like most eukaryotic mRNAs. Eg the average mRNA half-life in Arabidopsis is between 4-6 hours and is very variable between mRNAs. Personally I am not convinced this is an important enough reason to have a quality control check mechanism. The system I am referring to is called Nonsense-Mediated mRNA Decay (NMD). Mediators of it have been found in the early branching Giardia and is conserved between fungi/animals to plants. A PTC is recognised as wrong rather than a correct stop codon at the end of a ORF during the first round of translation by the ribosome. When the ribosome reaches a stop codon it has two choices, terminate correctly or stall and cell effectors of NMD to take it away for degradation by whatever nucleases that cell uses. It was first found in yeast and the mutants were called upf1-3 (for up-frame shift 1-3) and these yeast grow fairly normally but have increased levels of transcripts with stop codons. Raises the question why did it evolve if not very important when you KO it. In C. elegance SMG1-7 were identified having genital defects. Strangely, these were involved NMD with SMG2-4 corresponding to UPF1-3. Homologues of most of these proteins are found in many other eukaryotes. UPF1 is generally phosphorylated when ribosome stalling takes place and condemns it to degradation. Interestingly, it is a DEAD box RNA helicase (SF2 I believe).<br /><br />The two questions I find interesting is 1) how do organisms tell the difference between a PTC and normal stop codon and 2) how this can be used to regulated gene expression in cell signalling. You may ask ‘James, you charismatic stallion, how can something degrading useless mRNAs be useful or regulated for controlling gene expression’ and I would reply ‘wait and read the rest of this post you $#£!&%’. The first question is rather interesting as different organisms do different things. Yeast and invertebrates such as C. elegance and the fly pushers Drosphilia use something called the 3’ faux model. Something in the 3’ end allows normal termination when the stop codon is here but NMD starts when the stop codon (PTC) is distant from the 3’ end. It has been found the distance from the poly-A tail and therefore the Poly-A Binding Protein (PABP) determines this. When a long 3’ UTR is present the mRNA is degraded. When PABP is tethered close to the stop codon termination occurs normally. This also works in plants and mammals. However, another mechanism also works in both of them. When an introns is spliced out an Exon-Junction Complex (EJC) is left behind and if a EJC is found near a stop codon by the ribosome NMD starts. Why this operates in both plants and mammals but not yeast and invertebrates is curious. Did both mechanisms operate in the last common ancestor of plants and animals and has been lost a few times in the fungi and animal kingdoms or is it convergent evolution? I hope to better understand that.<br /><br /><br />Another and perhaps more important question is what is NMD role in plants and animals. Does it provide another function other than keeping toxic protein levels low? Short answers, yes. It affect development in C. elegance and embryo lethality in mice. Clearly it plays a role in animal development. In yeast the cells senesce sooner in upf1-3 mutants because telomeres shorten. In mammals, amino acid deletion causes problems for the ribosome and NMD is down regulated and genes for amino acids biosynthesis are up-regulated so more amino acids will be made. In Arabidopsis, when upf-1 is completely KO we see embryo lethality but Knock-down alleles see some developmental phenotypes (such as in the flowers) and altered stress responses.<br /><br />I will finished up now but feel free to ask questions. I have just finished writing a 4-page grant proposal on this. Just to piss Mel off, I will say this. I didn’t do any reading for this. This was all from memory when I got home. No PDF files were opened – not one!James Lloydhttp://www.blogger.com/profile/08219295648051788360noreply@blogger.com3tag:blogger.com,1999:blog-496263467300370264.post-58254892037879811422009-01-01T02:24:00.009+00:002009-01-01T03:23:12.978+00:00Arch nemesisEvidence is the cornerstone of science. It is what allows scientists to reject or accept hypotheses, and a robust piece of evidence can force the staunchest defender of a theory to completely reject it. People tend to like evidence when it supports their "beliefs", and dislike it when it refutes them, but scientists have no choice, they need to be apathetic and disinterested towards any results, so as to avoid introducing bias. However, scientists are also (rumoured to be) people, and the tendency to like or dislike a piece of evidence can be quite hard to resist.<br /><br />How could a scientist maintain an interest in their research while avoiding interest in the data generated from it? It seems almost self-contradictory. What goals do scientists usually have when carrying out research? For a scientist working at a pharmaceutical company (assuming they wanted to keep their job), this goal would be to get a drug on the market. For a graduate student, the goal could be to find something surprising or revolutionary in order to jump-start their career. For a hardened senior professor, it could be to prove their own hypotheses right and boost their reputation (and maybe get in line for a Nobel prize?). All these goals are fundamentally selfish, and you would be hard pressed to find pure altruism in even the "most moral" scientist (whatever that means...). Perhaps that's because scientists tend to be ambitious, competitive animals, and that's a selfish motivator in itself, but I would say it's because people's goals tend to be selfish in nature.<br /><br />These selfish goals scientists have certainly pose the most danger in making them introduce bias into their data. However, the drive that these goals give to scientists is what has led to so many historical discoveries. I'm sure some discoveries had altruistic motives but let's just say Watson and Crick weren't really thinking about saving humanity from terrible doom. Not to paint a sad picture of scientists, but sometimes the only thing that scientists get up for in the morning is the tiny chance that today's experiment will get them even slightly closer to achieving their goal.<br /><br />I think that scientists manage to minimize the danger of introducing bias by finding the one person on Earth they most disagree with and establishing an intimate, life-long professional relationship with them, manifested mostly through heckling at conferences and angry e-mail exchanges. This works much more efficiently in academia than in industry, because industry scientists are usually either unwilling or not allowed to talk to outsiders about anything they do. Academics are also secretive to a certain extent in order to avoid being scooped, but the spirit of collaboration and criticism is much stronger. This kind of mutually abusive relationship is what every scientist needs, and I personally can't wait to meet my arch nemesis!<br /><br />P.S. Happy 2009!Menelaos Symeonideshttp://www.blogger.com/profile/05361581879935604330noreply@blogger.com3tag:blogger.com,1999:blog-496263467300370264.post-2378672193476275672008-10-17T13:17:00.011+01:002009-04-11T17:08:27.849+01:00Kinetoplastid DNA<span lang="EN-GB" style="font-family:Arial;"><span style="padding: 5px; float: left;"><a href="http://www.researchblogging.org/"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border: 0pt none ;" /></a></span>It seems to be that time of the year in which we post about something to do with our posts, as these are the topics we are supposed to be reading about now. Therefore, a post on parasites. That’s where the connection with my project finishes, but anyway.<o:p></o:p></span><div style="text-align: justify;"> </div><p style="text-align: justify;" class="MsoNormal"><span lang="EN-GB" style="font-family:Arial;">As you might know, tryponosomatids are organisms from the family Troponosomatidae, which include some pretty nasty unicellular</span><span lang="EN-GB" style="font-family:Arial;"> parasites such as <i style="">Tr</i></span><span lang="EN-GB" style="font-family:Arial;"><i style="">ypanosoma brucei</i>, causer for African sleeping disease, and <i style="">Leishmania</i>, causer of leishmaniasis. As other higher eukaryotes, these parasites are characterised by two genomes: a nuclear g</span><span lang="EN-GB" style="font-family:Arial;">enome and a mitochondrion genome, 10-30% of all the cell DNA, situated in the kinetoplast (the name given to the mitochondrion in these organisms). </span></p><p style="text-align: justify;" class="MsoNormal"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtKmuD61acFVcy8rni9ZCNb0CSqxzaCV4u0Ogdtl9DX1AW47_CMpq5OwXeA6aZlgv58YxRFH1XD2-toy3cl24GK6IHVh-YNZb-LZwBuTn2TAEi9ckEF3FblUXX0K5iH8IBsifmNtPu2IA/s1600-h/fig+1.bmp"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgtKmuD61acFVcy8rni9ZCNb0CSqxzaCV4u0Ogdtl9DX1AW47_CMpq5OwXeA6aZlgv58YxRFH1XD2-toy3cl24GK6IHVh-YNZb-LZwBuTn2TAEi9ckEF3FblUXX0K5iH8IBsifmNtPu2IA/s320/fig+1.bmp" alt="" id="BLOGGER_PHOTO_ID_5258098177114680866" border="0" /></a></p><p style="text-align: center;" class="MsoNormal"><span style="font-weight: bold;font-size:85%;" >Fig.1 </span><span style="font-size:85%;">A- Schematic minicircle organization. B- <span style="font-style: italic;">in </span></span><span style="font-size:85%;"><span style="font-style: italic;">vivo</span> network organization, seen sideways.<br /></span></p><p style="text-align: center;" class="MsoNormal"><span style="font-size:85%;">(Adapted from reference 1)</span><br /></p><div style="text-align: justify;"> </div><p style="text-align: justify;" class="MsoNormal"><span lang="EN-GB" style="font-family:Arial;">So far nothing extraordinary. Things get interesting, when one looks at the structure of the kinetoplast DNA (kDNA) in these species. The kDNA is constituted by thousands of small DNA circles, the minicircles, and a few dozen of large DNA circles, the maxicircles. These are interlocked, as in a chain mail of medieval armour. Each circle is interlocked with 3 other neighbouring circles. The minicircles and max</span><span lang="EN-GB" style="font-family:Arial;">icircles are stretched into a disk-shaped structure, situated near to the flagellar basal body (Fig.</span><span lang="EN-GB" style="font-family:Arial;">1). The maxicircles are those more similar to normal mitochondrion genome. They include rRNAs and genes encoding proteins associated with the respiratory processes that takes place in this organelle. <span style=""> </span>However, the maxicircles mRNA requires extensive </span><span lang="EN-GB" style="font-family:Arial;">editing, namely the introduction or deletion of uridylate. The minicircles encode the guide RNAs used as templates for this editing. Since there are many types of editing required, as well as maxicircles with different sequences, there is the need for the thousand minicircles with different sequences. Seems a bit of a wasteful system, but what do I know!</span></p><div style="text-align: justify;"> </div><p style="text-align: justify;" class="MsoNormal"><span lang="EN-GB" style="font-family:Arial;">More interesting is to think of the replication process. The minicircles must stop being interlocked, replicated, interlocked again, and in the end originate two new networks of thousands of minicircles that separate into the two new daughter cells. Let us look at the differ</span><span lang="EN-GB" style="font-family:Arial;">ent steps, following an individual minicircle (Fig.2):</span></p><p style="text-align: justify;" class="MsoNormal"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiC6TvYSMK8agNCPATjgAQNRSEzB4MF79tvEM572kp2F-kGfh5SyU1CzqeuKP2t-wXvRm_-dULHkxV6mHBm6IuKRzBXzsFpMBzma5rrWfVvWtczBBdHZMnx62P-dQ5kR-r5zqkJPCh_8bY/s1600-h/Fig.2.bmp"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiC6TvYSMK8agNCPATjgAQNRSEzB4MF79tvEM572kp2F-kGfh5SyU1CzqeuKP2t-wXvRm_-dULHkxV6mHBm6IuKRzBXzsFpMBzma5rrWfVvWtczBBdHZMnx62P-dQ5kR-r5zqkJPCh_8bY/s400/Fig.2.bmp" alt="" id="BLOGGER_PHOTO_ID_5258099217401487522" border="0" /></a></p><div style="text-align: justify;"> </div><p style="text-align: center;" class="MsoNormal"><span lang="EN-GB" style="font-family:Arial;"><span style="font-size:85%;"><span style="font-weight: bold;">Fig.2</span> kDNA replication model. (From reference 2)</span><br /></span></p><p style="text-align: justify;" class="MsoNormal"><span lang="EN-GB" style="font-family:Arial;">1- A minicircle must first be released from the network into the so-called kinetoflagellar zone (KTZ), where several proteins involved in the process exist. Here the unidirectional replication of the circle occurs, although the details of this process are not well known.<o:p></o:p></span></p><div style="text-align: justify;"> </div><p style="text-align: justify;" class="MsoNormal"><span lang="EN-GB" style="font-family:Arial;"><span style=""> </span>2- The two daughter minicircles move to opposite ant</span><span lang="EN-GB" style="font-family:Arial;">ipodal sites of the circle, where there are two protein assemblies. Here a variety of reactions occur: the RNA primers are removed, the gaps between <st1:city st="on"><st1:place st="on">Okazaki</st1:place></st1:city> fragments are filled by DNA pol, and nick as sealed by DNA ligase. An important characteristic, however, is that the minicircles maintain at least one gap in their structure. This is thought to be a self-check feature of this system, as a way to guarantee that no minicircle is replicated twice.</span></p><div style="text-align: justify;"> </div><p style="text-align: justify;" class="MsoNormal"><span lang="EN-GB" style="font-family:Arial;">3- Minicircles are attached by topoisomerase II to the network periphery adjacent to the antipodal sites.<o:p></o:p></span></p><div style="text-align: justify;"> </div><p style="text-align: justify;" class="MsoNormal"><span lang="EN-GB" style="font-family:Arial;">The way the minicircles are attached to the disk varies with the species of trypanosomatid. In <i style="">T.brucei</i>, for example, the minicircles accumulate at the network poles. In <i style="">T.cruzi, </i>and <i style="">C.fasciculata</i>, the minicircles seem to be uniformly attached around the periphery of the disk, creating a ring of new minicircles, of increased thickness. How this uniform attachment is done is not certain, but it is though that either the antipodal protein complexes or the disk itself must rotate! (Fig.3)</span></p><p style="text-align: justify;" class="MsoNormal"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWI8yCGpt0pwkXlu9BpdCw_kZtnW8USIHfw8_jMWpZ-h9JZOvIQPmWPbrBbH-7FH_D-5VcjYv7kPYuWRGVezJ6X8Tu7FaflmscA1gwQOuLlN0TLl_8fd19MDjOCy5jOF40ar0VZB8csHk/s1600-h/Fig.3.bmp"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgWI8yCGpt0pwkXlu9BpdCw_kZtnW8USIHfw8_jMWpZ-h9JZOvIQPmWPbrBbH-7FH_D-5VcjYv7kPYuWRGVezJ6X8Tu7FaflmscA1gwQOuLlN0TLl_8fd19MDjOCy5jOF40ar0VZB8csHk/s400/Fig.3.bmp" alt="" id="BLOGGER_PHOTO_ID_5258099908572795522" border="0" /></a></p><p style="text-align: center;" class="MsoNormal"><span style="font-size:85%;"><span style="font-weight: bold;">Fig.3</span> Replication in <span style="font-style: italic;">C.fasciculata</span>. New minicircles have been labelled with fluorescent nucleotides. The arrangement of the new minicircles around the periphery of the disk is obvious (from reference 2).</span></p><p style="text-align: center;" class="MsoNormal"><span style="font-size:85%;"></span><br /></p><div style="text-align: justify;"> </div><p style="text-align: justify;" class="MsoNormal"><span lang="EN-GB" style="font-family:Arial;">4- Regardless of the method, new minicircles are attached to the disk, and the valence must increase to 4 to 6 attachments per minicircle, in order to ensure twice as many minicircles in the same space (the mitochondrion membrane has not doubled at this point). When the space increases, topoisomerase II ensures that valence returns to 3.<o:p></o:p></span></p><div style="text-align: justify;"> </div><p style="text-align: justify;" class="MsoNormal"><span lang="EN-GB" style="font-family:Arial;">5- Finally, the nicks are repaired and the network splits into 2, although how exactly this division occurs is not well known. Most importantly, it is not known for sure how to guarantee that the two daughter networks have the exactly same minicircles. Considering their importance in maxicircle mRNA editing, the loss of one minicircle could have dramatic consequences.<o:p> </o:p></span></p><div style="text-align: justify;"> </div><p style="text-align: justify;" class="MsoNormal"><span lang="EN-GB" style="font-family:Arial;">There is much to be explained in this process, namely identify exactly how the minicircles are moved to the different antipodal sites, or the details of individual minicircle replication, but such understanding will require the identification of the proteins involved. Considering the complexity of the process, many must be involved, but only a few have been identified so far. <o:p></o:p></span></p><div style="text-align: justify;"> </div><p style="text-align: justify;" class="MsoNormal"><span lang="EN-GB" style="font-family:Arial;">This is probably not life-changing research, but it is surely interesting. It is important to remind ourselves once in a while that though we learn the textbook pathways and processes, Nature seems to like using hundreds of alternatives. Just to make scientists lives harder, I assume!</span></p><span style="font-weight: bold;font-family:arial;" ></span><span style="font-family:arial;"><br /><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Trends+in+Parasitology&rft_id=info%3Adoi%2F10.1016%2Fj.pt.2005.06.008&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Fellowship+of+the+rings%3A+the+replication+of+kinetoplast+DNA&rft.issn=14714922&rft.date=2005&rft.volume=21&rft.issue=8&rft.spage=363&rft.epage=369&rft.artnum=http%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS1471492205001698&rft.au=Liu%2C+B.&rft.au=Liu%2C+Y.&rft.au=Motyka%2C+S.&rft.au=Agbo%2C+E.&rft.au=Englund%2C+P.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Liu, B., Liu, Y., Motyka, S., Agbo, E., & Englund, P. (2005). Fellowship of the rings: the replication of kinetoplast DNA <span style="font-style: italic;">Trends in Parasitology, 21</span> (8), 363-369 DOI: <a rev="review" href="http://dx.doi.org/10.1016/j.pt.2005.06.008">10.1016/j.pt.2005.06.008</a></span><br /><br />(2) Smith D. and Parsons M. (1996). Molecular Biology of Parasitic Protozoa, <span style="font-style: italic;">Kinetoplast DNA: Structure and Replication, </span>Oxford University Press, USA<br /></span><p style="text-align: justify; font-family: arial;" class="MsoNormal"></p>Cathttp://www.blogger.com/profile/08645968914831610862noreply@blogger.com2tag:blogger.com,1999:blog-496263467300370264.post-41544112770871279572008-10-12T21:54:00.005+01:002009-01-31T00:41:55.740+00:00Apical dominance, MAX and my projectOne of the most important things the plant hormone auxin does is play an important role in is apical dominance. This is where the Shoot Apical Meristem (SAM), the growing part of the above ground half of the plant, produces a signal that inhibits growth from other auxiliary meristems. The SAM and auxiliary meristems contain the plant’s ‘stem cells’ and generate new leaves, stems and flowers. They both have the same ability to generate new organs. When the plant grows and leaves emerge from the meristem, an auxiliary meristem is left behind with the leaf, which may or may not grow out, just above where the leaf meets the stem. For years it was known auxin from the SAM inhibited their outgrowth. Auxin is produced in the SAM and moved down the plant and when it is stopped, the auxiliary meristem can grow out. The best person to tell you this is a gardener. When pruning, they remove the SAM on a plant, like a rose bush, to allow dormant growing parts of the plant grow out and make it bushier. It is also a pain for, let’s say for example, tobacco farmers. They ‘top’ tobacco plants so it does not grow up and make the leaves fatter. However, this stops auxin travelling down the stem and auxiliary meristems grow out. The addition of unpleasant chemicals is used to solve this problem.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6IJZ7td2itqB98lmcG7ZZ2tLretr2WS4-62ugHLDxL-rF0d1Mngw169ZE0QNjmCAxx3tflZ6sVlieZu3BnoAqNOJRgrdFc7oczeiJTkPcc3OoIuTK43OlL3VNv0plnmafg7ht98OCFqc/s1600-h/Node+and+SAM.jpg"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEj6IJZ7td2itqB98lmcG7ZZ2tLretr2WS4-62ugHLDxL-rF0d1Mngw169ZE0QNjmCAxx3tflZ6sVlieZu3BnoAqNOJRgrdFc7oczeiJTkPcc3OoIuTK43OlL3VNv0plnmafg7ht98OCFqc/s320/Node+and+SAM.jpg" alt="" id="BLOGGER_PHOTO_ID_5256374304344223314" border="0" /></a><br /><br />Auxin does not travel up into the auxiliary meristem, so how does auxin inhibit bud outgrowth? A second signal must be involved. This ‘second messenger’ is not an easy thing to understand. It turns out to be a complex interplay of plant hormones that I will try to explain now control bud outgrowth. I will start by explaining the players involved. The hormone cytokinin (Ck) often plays the opposite role to auxin in plant grow. When it is applied to an auxiliary meristem it will grow out. Ck is generated both in the roots and locally in the stem but it is unclear which is more relevant to shoot branching (I think it varies from species to species). The auxin signalling pathway does regulate Ck synthesis but this is not the whole story. Auxin signalling pathway mutants do show some increase in shoot branching but it is lower than those affected by mutations in MAX genes (see below) and the effects of these are additive to auxin signalling.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEif9593a-NPdMK_zbhnqpHTQilb9WTZdnUpzMTaA6VSkUBbn2xUNX2C5Aw014v4XN_K2oIDsbQBcu76ORU3c2pYEACvFckXe7gyETXF9wZFa-xIoCHkxS_oFFf0_Ly8n3Dop-maquOYBxQ/s1600-h/WT+vs+max4.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEif9593a-NPdMK_zbhnqpHTQilb9WTZdnUpzMTaA6VSkUBbn2xUNX2C5Aw014v4XN_K2oIDsbQBcu76ORU3c2pYEACvFckXe7gyETXF9wZFa-xIoCHkxS_oFFf0_Ly8n3Dop-maquOYBxQ/s320/WT+vs+max4.jpg" alt="" id="BLOGGER_PHOTO_ID_5256374680381581362" border="0" /></a><br />Mutant screens reviled the MAX genes. max mutants have increased shoot branching. To cut a long story short, the MAX pathway does not produce the inhibitory signal but helps auxin regulate shoot-branching. MAX3 and 4 produce enzymes that alter a caratinoid. MAX1 is a P450 that acts downstream of MAX3 and 4 and alters the chemical further, producing the MAX-dependent hormone (more on the identity below). MAX2 does not produce the graft-transmissible signal but helps perceives the MAX-dependent hormone. In fact, it is an F-box protein like TIR1 from my post on auxin signalling. However, I think it is unlikely to bind the MAX-dependent hormone directly as TIR1 does auxin. I suppose this cannot be looked at until the hormone has been characterised better. MAX2 is also involved with leaf senescence and some features of light perception but its roles in these are not very well understood either.<br /><br />The Leyser lab has been working on finding the identity of the MAX-dependent hormone but two papers published in the same September issue of Nature (just after my subscription ended!) suggest the identity in pea and rice. Ottoline has just written a short review on them (below). They found a chemical, called strigolactones, was involved. Previously shown to be involved with germination, formation of mycorrhiza with fungi and growth of parasitic plants, now it appears they are a key regulator of shoot branching. The exact identity of the biological active strigolactone is still yet to be found.<br /><br />The MAX pathway’s mode of action is through limiting auxin transport. This work was published with a PhD student at York as the lead author in the Leyser lab (he was a very well known blue coat). Auxin is transported from the SAM to the roots. To move in and out of cells, auxin needs proteins to transport it. One important class are the PIN proteins. They can become localised to a particular part in a plant cell, such as the basal side, to ensure auxin only moves in one direction. This is very important in creating a vascular system in the plant. First of all, auxin is made by the auxiliary meristems but it is their ability to transport auxin out that allows them to grow out. It is best to imagine the auxin transport network as roads. Auxin (the cars) leaves the SAM and moves down the stem via PIN proteins (lanes on a motor way). In a normal plant, not all lanes are open. So auxin from the SAM fills most of the PIN proteins and only a little auxin from the buds can enter, letting some grow out. max mutants have an increase transport capacity because more PIN proteins are present. This is like opening extra lanes on a motor way so auxin from all the buds can enter and move freely, letting them grow out! Integrating the actions of all hormones leads to something like this: auxin moves down the plant and its movement down is limited by the MAX-dependent hormone from the roots. This limits the amount of auxin auxiliary merisetems can transport out, so large amounts of auxin accumulate in these buds. This (somehow) inhibits Ck production to limit growth of the bud. The integration of multiple hormones has been described as the brain of plants.<br /><br />The reason max mutants and auxin signalling double mutants have an additive effect is because auxin works both through its classical signalling pathway but also through auxin transport. This is where, for me, things get confusing. How does auxin in the bud know not to be exported and form vascular tissue to connect to the main flow in the stem? This has been a long standing question, not for shoot branching but for the formation of a vascular network, yet there is no answer (or good one at least).<br /><br />My final year project is in the Leyser lab, for what I hope are obvious reasons now. They have done lots of great work. A modifier of the max1 phenotype was found in a mutants screen and mapped to a location on chromosome 1. My job is to widdle the candidate genes down from around 20 to one! I don’t want to give too much away about the project on here but the mutation alters the max1 phenotype and has its own slight developmental phenotype. Hopefully understanding it will help in the long term goal of understanding plant development. I doubt it will have a direct role synthesis or degradation of the MAX-dependent hormone but I believe it will affect downstream events. I hope this has been enlighting.<br /><br />Here is a very good review and explains these things better than I can do by someone in the Leyser lab:<br />http://www.ncbi.nlm.nih.gov/pubmed/17728300?ordinalpos=4&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum<br /><br />Here is an ahead of print short review on the identity of the MAX-dependent hormone by Ottoline:<br />http://www.ncbi.nlm.nih.gov/pubmed/18804430?ordinalpos=1&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSumJames Lloydhttp://www.blogger.com/profile/08219295648051788360noreply@blogger.com2tag:blogger.com,1999:blog-496263467300370264.post-58834233479812831102008-10-03T15:06:00.007+01:002009-01-31T00:43:55.230+00:00IgNobels 2008<div style="text-align: center;"><span style="font-weight: bold;font-family:georgia;font-size:100%;" >'For achievements that first make people LAUGH and then make them THINK'</span></div><div style="text-align: center;"> </div> <div style="text-align: justify;"><span style=";font-family:georgia;font-size:100%;" ><br />As I seem to be spending all my holidays memorizing hard words in english (Melly will know what I mean) I actually haven't had the time to read anything 'scientific' like you guys. I had, however, time to have a look to what Nature regards as, and I agree, 'the highlight of the scientific calendar'. Yes, my friends, the Ig Nobels are out again. As you will remember, I wrote a post last year when I realized that these amazing prizes existed, and have been eagerly waiting for this year's winners. So, below, enjoy the list of the IgNobel winners 2008!</span> </div><div style="text-align: justify;"> </div><span style="font-weight: bold;font-family:georgia;font-size:100%;" ><br />NUTRITION</span><span style="font-size:100%;"><br /></span><div style="text-align: justify;"><span style=";font-family:georgia;font-size:100%;" >Massimiliano Zampini of the University of Trento, Italy and <a style="color: rgb(0, 0, 0);" href="http://www.neuroscience.ox.ac.uk/directory/charles-spence"><span style="" lang="EN-GB">Charles Spence </span></a></span><span style=";font-family:";font-size:100%;" lang="EN-GB"><span style="font-family:georgia;">of </span><st1:place style="font-family: georgia;" st="on"><st1:city st="on">OxfordUniversity</st1:city>,<st1:country-region st="on">UK</st1:country-region></st1:place><span style="font-family:georgia;">, for </span><span style="font-weight: bold; font-style: italic;font-family:georgia;" >electronically modifying the sound of a potato chip to make the person chewing the chip believe it to be crisper and fresher than it really is.</span></span><span style="font-size:100%;"> </span><br /></div><span style="font-size:100%;"><br /></span><span style="font-size:100%;"></span><div style="text-align: justify;"><span style=";font-family:";font-size:100%;" lang="EN-GB"> <!--[if !supportLineBreakNewLine]--></span> <span style=";font-family:";font-size:100%;" lang="EN-GB"><span style="font-weight: bold;font-family:georgia;" >PEACE</span></span><span style="font-size:100%;"><br /></span><span style=";font-family:";font-size:100%;" lang="EN-GB"><span style="font-family:georgia;">The Swiss Federal Ethics Committee on Non-Human Biotechnology (ECNH) and the citizens of Switzerland </span><span style="font-weight: bold; font-style: italic;"><span style="font-family:georgia;">for adopting the legal principle that plants have dignity. </span></span></span><span style="font-size:100%;"><br /></span> <span style="font-size:100%;"><br /></span></div><span style=";font-family:georgia;font-size:100%;" lang="EN-GB"><span style="font-weight: bold;">ARCHEOLOGY</span></span><span style="font-size:100%;"> </span><span style=";font-family:";font-size:100%;" lang="EN-GB"> <!--[if !supportLineBreakNewLine]--></span><span style=";font-family:georgia;font-size:100%;" lang="EN-GB"><a href="http://sistemas.usp.br/atena/atnCurriculoLattesMostrar?codpes=321422"><span style="" lang="EN-GB">Astolfo G. Mello Araujo </span></a>and José Carlos Marcelino of Universidade de São Paulo, Brazil, f<span style="font-weight: bold; font-style: italic;">or measuring how the course of history, or at least the contents of an archaeological dig site, can be scrambled by the actions of a live armadillo.</span></span> <span style=";font-family:";font-size:100%;" lang="EN-GB"> <!--[if !supportLineBreakNewLine]--></span> <span style=";font-family:";font-size:100%;" lang="EN-GB"> <!--[endif]--></span><span style="font-weight: bold;font-size:100%;" ><br /><br />BIOLOGY</span><span style="font-size:100%;"> </span><span style=";font-family:georgia;font-size:100%;" lang="EN-GB">Marie-Christine Cadiergues, Christel Joubert,, and Michel Franc of Ecole Nationale Veterinaire de Toulouse, France <span style="font-weight: bold; font-style: italic;">for discovering that the fleas that live on a dog can jump higher than the fleas that live on a cat.</span></span><span style="font-size:100%;"> </span><span style=";font-family:";font-size:100%;" lang="EN-GB"> <!--[if !supportLineBreakNewLine]--></span><span style="font-size:100%;"><br /></span><span style="font-size:100%;"><br /></span><div style="text-align: justify;"><span style=";font-family:georgia;font-size:100%;" ><span style="font-weight: bold;">MEDICINE</span></span><span style="font-size:100%;"><br /></span><span style=";font-family:georgia;font-size:100%;" ><a href="http://www.predictablyirrational.com/"><span style="" lang="EN-GB">Dan Ariely </span></a></span><span style=";font-family:";font-size:100%;" lang="EN-GB"><span style="font-family:georgia;">of </span><st1:place style="font-family: georgia;" st="on"><st1:city st="on">Duke University</st1:city>, <st1:country-region st="on">USA</st1:country-region></st1:place><span style="font-family:georgia;">, </span><span style="font-weight: bold; font-style: italic;font-family:georgia;" >for demonstrating that high-priced fake medicine is more effective than low-priced fake medicine. </span><span style="font-family:georgia;">(a study on placebo effects)</span></span><span style="font-size:100%;"> </span><span style=";font-family:";font-size:100%;" lang="EN-GB"> <!--[if !supportLineBreakNewLine]--></span> <span style=";font-family:";font-size:100%;" lang="EN-GB"> <!--[endif]--></span><span style="font-weight: bold;font-family:georgia;font-size:100%;" ><br /><br />COGNITIVE SCIENCE</span><span style="font-size:100%;"> </span><span style=";font-family:georgia;font-size:100%;" >Toshiyuki Nakagaki of Hokkaido University, Japan, Hiroyasu Yamada of Nagoya, Japan, Ryo Kobayashi of Hiroshima University, Atsushi Tero of Presto JST, Akio Ishiguro of Tohoku University, and <a href="http://www.staff.u-szeged.hu/%7Eatoth/index.html"><span style="" lang="EN-GB">Ágotá Tóth </span></a></span><span style=";font-family:";font-size:100%;" lang="EN-GB"><span style="font-family:georgia;">of the University of Szeged, Hungary,</span><span style="font-weight: bold; font-style: italic;font-family:georgia;" > for discovering that slime molds can solve puzzles.</span></span> <span style=";font-family:";font-size:100%;" lang="EN-GB"> <!--[if !supportLineBreakNewLine]--></span> <span style=";font-family:";font-size:100%;" lang="EN-GB"> <!--[endif]--></span><span style="font-weight: bold;font-family:georgia;font-size:100%;" ><br /><br />ECONOMICS</span><span style="font-size:100%;"><br /></span><span style=";font-family:georgia;font-size:100%;" ><a href="http://www.unm.edu/%7Epsych/faculty/sm_gmiller.html"><span style="" lang="EN-GB">Geoffrey Miller</span></a></span><span style=";font-family:";font-size:100%;" lang="EN-GB"><span style="font-family:georgia;">, Joshua Tybur and Brent Jordan of the </span><st1:placetype style="font-family: georgia;" st="on">University</st1:placetype><span style="font-family:georgia;"> of </span><st1:placename style="font-family: georgia;" st="on">New Mexico</st1:placename><span style="font-family:georgia;">, </span><st1:country-region style="font-family: georgia;" st="on"><st1:place st="on">USA</st1:place></st1:country-region><span style="font-family:georgia;">, f</span><span style="font-weight: bold; font-style: italic;font-family:georgia;" >or discovering that a professional lap dancer's ovulatory cycle affects her tip earnings.</span></span><span style="font-size:100%;"> </span><span style=";font-family:";font-size:100%;" lang="EN-GB"> <!--[if !supportLineBreakNewLine]--></span> <span style=";font-family:";font-size:100%;" lang="EN-GB"> <!--[endif]--></span><span style="font-weight: bold;font-family:georgia;font-size:100%;" ><br /><br />PHYSICS</span><span style="font-size:100%;"> </span><span style=";font-family:georgia;font-size:100%;" lang="EN-GB">Dorian Raymer of the Ocean Observatories Initiative at Scripps Institution of Oceanography, <st1:country-region st="on">USA</st1:country-region>, and <a href="http://physics.ucsd.edu/%7Edes/"><span style="" lang="EN-GB">Douglas Smith </span></a>of the <st1:placetype st="on">University</st1:placetype> of <st1:placename st="on">California</st1:placename>, <st1:place st="on"><st1:city st="on">San Diego</st1:city>, <st1:country-region st="on">USA</st1:country-region></st1:place>, <span style="font-weight: bold; font-style: italic;">for proving mathematically that heaps of string or hair or almost anything else will inevitably tangle themselves up in knots.</span></span><br /><br /><span style="font-weight: bold;font-family:georgia;font-size:100%;" >CHEMISTRY</span><span style=";font-family:georgia;font-size:100%;" > </span> <span style=";font-family:georgia;font-size:100%;" >Sharee A. Umpierre of the University of Puerto Rico, Joseph A. Hill of The Fertility Centers of New England (USA), <a href="http://www.bumc.bu.edu/Dept/Content.aspx?DepartmentID=59&PageID=13021"><span style="" lang="EN-GB">Deborah J. Anderson </span></a></span><span style=";font-family:";font-size:100%;" lang="EN-GB"><span style="font-family:georgia;">of Boston University School of Medicine and Harvard Medical School (USA), </span><span style="font-weight: bold; font-style: italic;font-family:georgia;" >for discovering that Coca-Cola is an effective spermicide</span><span style="font-family:georgia;">, and to Chuang-Ye Hong of Taipei Medical University (Taiwan), C.C. Shieh, P. Wu, and B.N. Chiang (all of Taiwan)</span><span style="font-weight: bold; font-style: italic;font-family:georgia;" > for discovering that it is not.</span></span><br /><br /><span style=";font-family:";font-size:100%;" lang="EN-GB"><!--[if !supportLineBreakNewLine]--></span> <span style=";font-family:";font-size:100%;" lang="EN-GB"> <!--[endif]--></span><span style="font-weight: bold;font-family:georgia;font-size:100%;" >LITERATURE</span><span style="font-size:100%;"><br /></span><span style=";font-family:georgia;font-size:100%;" ><a href="http://www.cass.city.ac.uk/faculty/d.sims/"><span style="" lang="EN-GB">David Sims </span></a></span><span style=";font-family:";font-size:100%;" lang="EN-GB"><span style="font-family:georgia;">of </span><st1:place style="font-family: georgia;" st="on"><st1:placename st="on">Cass</st1:placename> <st1:placename st="on">Business</st1:placename> <st1:placetype st="on">School</st1:placetype></st1:place><span style="font-family:georgia;">. </span><st1:place style="font-family: georgia;" st="on"><st1:city st="on">London</st1:city>, <st1:country-region st="on">UK</st1:country-region></st1:place><span style="font-family:georgia;">, </span><span style="font-weight: bold; font-style: italic;font-family:georgia;" >for his lovingly written study "You Bastard: A Narrative Exploration of the Experience of Indignation within Organizations."</span></span><span style="font-size:100%;"> </span><span style=";font-family:";font-size:12;" lang="EN-GB"> <!--[if !supportLineBreakNewLine]--></span> <span style=";font-family:";font-size:12;" lang="EN-GB"> <!--[endif]--></span><br /><br />Hehe, as usual, delicious to read... For more information on the Ig Nobels or this year's ceremony (I actually don't know yet what's this year's topic. Last year it was chicken and involved dressing proper Nobel laureates in egg outfits), see the link below<br /><br />http://improbable.com/ig/winners/#ig2008<br /><br /></div><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEho6T5mAdNDBgkwoPENvHIZuo7zbfleieXHcw1LhyphenhyphenE3DyapvXvFiUXdCj65IfXyMUgMgRn1GIu5Lyya3VR2nbttssQxfAEn_m5rfA4svRFrgUjVftjM5xlpxGWcjhbaRP142VBWhuh4CEU/s1600-h/297_sword_swallow.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEho6T5mAdNDBgkwoPENvHIZuo7zbfleieXHcw1LhyphenhyphenE3DyapvXvFiUXdCj65IfXyMUgMgRn1GIu5Lyya3VR2nbttssQxfAEn_m5rfA4svRFrgUjVftjM5xlpxGWcjhbaRP142VBWhuh4CEU/s320/297_sword_swallow.jpg" alt="" id="BLOGGER_PHOTO_ID_5252934357056153186" border="0" /></a><div style="text-align: center;"><span style="font-size:85%;">One of last year's winners, Dan Meyer demonstrates his skills, after winning the 2007 IgNobel for medicine in collaboration with Brian Witcombe, for their study on sword swallowing and its side-effects</span><br /></div>Cathttp://www.blogger.com/profile/08645968914831610862noreply@blogger.com2tag:blogger.com,1999:blog-496263467300370264.post-84271059640505640712008-10-03T14:43:00.003+01:002009-01-31T00:41:15.792+00:00The wonders of auxinI am a complete sell out. I have worked for a plant biotech company and getting funding from Gatsby (a charity with a goal, alone with others, is to get scientists interesting in plants). These people have been very nice by helping me pay rent, buy DVDs and science magazines as well as sending me to Mexico for a conference. Therefore, I thought I should give something back by educating my friends in a bit of plant biology. Don’t worry faint hearted, I will keep it nice and molecular as that is the way I like it.<br /><br />After returning from my Mexico trip I realised a few things, English seems to be spoken by everyone, don’t eat food from Mexico City airport and auxin is a fascinating plant hormone and virtually everyone in the plant community agrees. Most talks there were on auxin biosynthesis, receptor function and structure, its control of shoot branching and transport around the plant. However, I do not recall all of it. Or hardy any of it as I was jet lagged with little prior knowledge of plant hormones (plus it has been over a year since the conference).<br /><br />Auxin was the most interesting of all the plant signalling molecules. It has been studied for over 100 years and only today we are starting to understand how it controls plant development and cell biology. Auxin is a small molecule made from an amino acid and its most biologically active for is called IAA. Auxin controls cell elongation and division, and can promote these or stop them depending on the tissue type auxin enters. Auxin causes lateral root growth and patterns the vascular system of plants. Auxin starts shaping the plant in the embryo. What is interesting is how it regulates many of these things.<br /><br />It controls gene expression by activating Auxin Response Factors (ARFs). This is done by destabilizing proteins called Aux/IAAs. Genes activated by the addition of auxin contain Auxin Response Elements (ARE) which an ARF binds to. When no auxin is present, an ARF is bound to an ARE but it is diamerized with an Aux/IAA, which represses transcription of this gene. When auxin enters the cell, it gets ride of this Aux/IAA and the ARF diamerizes with another ARF. This causes transcription of the auxin regulated gene. How does auxin cause breakdown of Aux/IAA? (I thought I would sound more intelligent if I asked a lot of questions) Auxin doesn’t have a nice receptor at the cell membrane that activates a second message or a phosphorylation pathway, no that would be to simple. In 2005 Ottoline Leyser and Stefan Kepinski (then post-doc, now lecturer at Leeds) published in Nature that TIR1 was an auxin receptor. tir1 mutants had been known to be deficient in auxin signalling for a long time but not thought to be a mutation in the receptor. TIR1 is an F-box protein, which are not famous for being receptors (until now). Normally they simply act as an E3 ubiqutin (Ub) ligase, meaning they take Ub from one protein and add it to another creating a poly-ubiquitin tag that sends a protein for degradation by the 26S proteasome. Ubiqutination and targeting to the proteasome is found animals and fungi and plays an important role in signalling, including regulation of the cell cycle! TIR1 adds Ub to the Aux/IAA when auxin enters the cell. It was assumed that auxin was perceived by some other protein in the cell and caused some modification of the Aux/IAA or TIR1 to cause this to happen, probably by phosphorylation. Now we know that auxin binds toTIR1 and acts as a molecular glue, bridging the gap between TIR1 and Aux/IAA so it can be broken down. I think this is a brilliant method. I am glad to see plants are being original and creating cool new signalling pathways instead of being just like boring old animals and fungi that love there MAPK so much they should just go along and marry it. Please see my simplified diagram of the auxin signalling pathway, it is not perfect, but who is......except maybe Colombo. But then how does auxin have very different effects on different cell types. This appears to be because different tissues expresses different ARFs and Aux/IAAs and these turn on different genes but little is known right now.<br /><br /><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgb2gVXHuVk7pJkJ3ofIIukhR7UWHrGW7hNp1oEZBmw5diPpBEBHNdJEOZQVE6pjgjvXKL9Vj566vaKmYFHlbIWo7jfHTRdyFgubbSaL0dySuk2lHq7GRAqgN1pUksU_Q7d1PW-vJtQ9zE/s1600-h/aux+signalling.JPG"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEgb2gVXHuVk7pJkJ3ofIIukhR7UWHrGW7hNp1oEZBmw5diPpBEBHNdJEOZQVE6pjgjvXKL9Vj566vaKmYFHlbIWo7jfHTRdyFgubbSaL0dySuk2lHq7GRAqgN1pUksU_Q7d1PW-vJtQ9zE/s320/aux+signalling.JPG" alt="" id="BLOGGER_PHOTO_ID_5252923567614143298" border="0" /></a><br /><br />One final thing, is TIR1 the only receptor? A good question indeed. Like I said earlier, I like asking questions to make me sound smart. Other F-box proteins appear to do the same job. The same only story of redundancy. However, this style of signalling cannot explain all the effects auxin has on plants. Some auxin responses occur very quickly after auxin addition. These happen so quickly, it is unlikely proteolysis followed by transcription and translation of effectors can account for them. Things like guard cell outward K+ current up, increased cytoplasm calcium, cell wall acidification starts (to help increase cell wall expansion) and elongation growth. How can we explain auxin’s influence over these physiological changes? There is debate and investigation over what causes these things. Some are caused by changes in membrane potential and perhaps Auxin Binding Protein 1 (ABP1) has some control over some changes but I am not convinced and other features are unrelated to this. After auxin addition MAP kinase activity increase but this is unrelated to both TIR1 and ABP1. There are still a lot of unanswered questions.<br /><br />Here is a short, concise review by Ottoline’s old post-doc (now at Leeds), which I found yesterday and does a far better job of introducing people to this that I have!<br />The anatomy of auxin perception<br />http://www.ncbi.nlm.nih.gov/pubmed/17876776?ordinalpos=57&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_DefaultReportPanel.Pubmed_RVDocSum<br /><br />Another one talking a more detailed look at auxin receptors and the debate around them. I have not read it fully, sadly.<br />Receptors for auxin: will it all end in TIRs?<br />http://www.ncbi.nlm.nih.gov/sites/entrez?db=pubmed&cmd=search&term=Receptors+for+auxin%3A+will+it+all+end+in+TIRs%3F<br /><br />I have not referenced here for two reasons. First, I can’t be bothered and secondly, a lot of this is from conferences or meetings I have been to. I hope you enjoyed this little rant from the plant person.James Lloydhttp://www.blogger.com/profile/08219295648051788360noreply@blogger.com4tag:blogger.com,1999:blog-496263467300370264.post-45469249802649573682008-10-01T16:55:00.009+01:002009-03-03T21:42:57.568+00:00Rats at a rave<span style="font-size:85%;"><span style="font-family:georgia;"><span style="float: left; padding: 5px;"><a href="http://www.researchblogging.org"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border:0;" /></a></span>The illegal recreational drug ecstasy, also known as X, or MDMA (an abbreviation of its chemical formula), is popular in the rave scene and is used to induce euphoria and enhance the experience of dancing and loud music. The drug is considered relatively safe by the average raver due to its short term effects, despite having received publicity for various dangers identified by scientific research.<br /></span> <span style="font-family:georgia;"><br /></span></span><div style="text-align: center;"><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://ecstasy-addiction.org/img/ecstasy_pill2_group.jpg"><img style="margin: 0px auto 10px; display: block; text-align: center; cursor: pointer; width: 224px; height: 226px;" src="http://ecstasy-addiction.org/img/ecstasy_pill2_group.jpg" alt="" border="0" /></a><span style="font-size:78%;">Ecstasy pills</span><br /></div><br /><span style="font-size:85%;"><span style="font-family:georgia;">The most widely known (undesired) effect of the drug is overexertion and sweating, leading to the ecstasy user drinking large amounts of water and being in danger of hyponatremia (the depletion of solutes from the blood plasma), which can eventually lead to cerebral edema. The drug has also been known for causing “holes in the brain”, Parkinsonian tremors, and permanent brain damage from single use, however these claims have been discredited* and retracted from the literature (1). Some research has shown that the drug may not be as toxic as once thought when used in moderation, but that does not address whether environmental effects could change the action of the drug and potentially make it more dangerous than a “traditional” toxicity study might suggest.</span><br /><br /></span><a onblur="try {parent.deselectBloggerImageGracefully();} catch(e) {}" href="http://usversusthem.files.wordpress.com/2007/08/rat.jpg"><img style="margin: 0pt 0pt 10px 10px; float: right; cursor: pointer; width: 173px; height: 173px;" src="http://usversusthem.files.wordpress.com/2007/08/rat.jpg" alt="" border="0" /></a><span style="font-size:85%;"><span style="font-family:georgia;">R</span></span><span style="font-size:85%;"><span style="font-family:georgia;">esearch conducted in Italy and published in 2006 (2) has shown that not only does the drug enhance the rave experience for the user, but this works both ways, with the loud music physically enhancing the effect of the drug. Rats were given various doses of MDMA and treated to a surely exciting 4 hours of white noise at 95 dB (the loudest level permissible in Italian night clubs) while electrocortical activity in their brains was monitored by electroencephalography. Controls were conducted with rats treated with saline instead of MDMA, as well as both treatments without sound. ECoG monitoring was repeated over 5 days without administration of the drug or sound in order to study long term effects. The ECoG “spectrum power” was taken to be indicative of higher neural function in rats.</span> <span style="font-family:georgia;"><br /><br />The data showed that a low dose of MDMA combined with sound caused decreased ECoG spectrum power significantly different from control, but no significant effect when MDMA was administered without sound. A high dose of MDMA combined with sound produced a dramatic effect that lasted for 5 days, while all other treatments had no long term effects. This powerful data shows a synergistic relationship between exposure to loud noise and the effect of MDMA on higher neural function, and suggests that higher doses only have long term effects when combined with loud noise. The authors do not suggest a possible mechanism for this effect, but they do warn that the drug may be more dangerous than commonly thought since most ecstasy users combine the drug with loud music.</span> <span style="font-family:georgia;"><br /><br /><br />* As a side note, some legislation around ecstasy was driven by the above mentioned discredited “findings”, which is disconcerting. An example is the RAVE act (3), introduced in 2002 by current Democratic VP candidate Joe Biden as part of the War On Drugs, which allows the law to shut down clubs and raves if ecstasy use is suspected to occur on their premises. The drug is still a dangerous one, but one would hope that laws would be revised after research they were based upon is discredited, which they were not.</span> <span style="font-weight: bold;font-family:georgia;" ><br /><br /><br />References</span><br /><span style="font-family:georgia;">1. Ronald Bailey: “</span><a style="font-family: georgia;" href="http://www.reason.com/news/show/34918.html">The Agony of Ecstasy Research</a><span style="font-family:georgia;">”. ReasonOnline.</span> <span style="font-family:georgia;"><br />2. </span><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=BMC+Neuroscience&rft_id=info%3Adoi%2F10.1186%2F1471-2202-7-13&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Electrocortical+effects+of+MDMA+are+potentiated+by+acoustic+stimulation+in+rats&rft.issn=14712202&rft.date=2006&rft.volume=7&rft.issue=1&rft.spage=13&rft.epage=0&rft.artnum=http%3A%2F%2Fwww.biomedcentral.com%2F1471-2202%2F7%2F13&rft.au=Michelangelo+Iannone&rft.au=Stefania+Bulotta&rft.au=Donatella+Paolino&rft.au=Maria+Zito&rft.au=Santo+Gratteri&rft.au=FrancescoS+Costanzo&rft.au=Domenicantonio+Rotiroti&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Michelangelo Iannone, Stefania Bulotta, Donatella Paolino, Maria Zito, Santo Gratteri, FrancescoS Costanzo, Domenicantonio Rotiroti (2006). Electrocortical effects of MDMA are potentiated by acoustic stimulation in rats <span style="font-style: italic;">BMC Neuroscience, 7</span> (1) DOI: <a rev="review" href="http://dx.doi.org/10.1186/1471-2202-7-13">10.1186/1471-2202-7-13</a></span> <span style="font-family:georgia;"><br />3. </span><a style="font-family: georgia;" href="http://en.wikipedia.org/wiki/RAVE_Act">http://en.wikipedia.org/wiki/RAVE_Act</a></span>Menelaos Symeonideshttp://www.blogger.com/profile/05361581879935604330noreply@blogger.com3tag:blogger.com,1999:blog-496263467300370264.post-45782276798015295962008-10-01T01:14:00.004+01:002009-01-31T00:39:17.547+00:00Environmental refugees?<div style="text-align: justify;">As we seem to be starting a new, shorter, form of post to guarantee that someone keeps writing in this blog, I decided to follow James' example. Here I just liked to mention a short article I read at Harvard's university website. The president of Kiribati, a south Pacific island nation has given recently a lecture at Harvard where he has presented his plan preparing his country for the eventuality (or should we call it certainty) of extinction. Apparently, with the sea-levels planned to raise by 1 meter in the next century due to climate change, the islands are starting to run out of space, and to eventually leave the islands for good seems to be the only option. However, the president seems to want to avoid creating what he describes as 'environmental refugees', a new word that we will perhaps become more and more familiar with in the future, as climate change starts having 'real' consequences that we cannot pretend to ignore anymore.<br /></div><br />Read the short article here: http://www.news.harvard.edu/gazette/2008/09.25/13-kiribati.htmlCathttp://www.blogger.com/profile/08645968914831610862noreply@blogger.com3tag:blogger.com,1999:blog-496263467300370264.post-44584875399488617562008-09-28T12:40:00.002+01:002009-01-31T00:38:50.022+00:00Facts about genesAs I am the saddest of the three musket-geneticists by far I have decided to post something. I bought a book called ‘a short guide to the Human Genome’. The booked is aimed at people with a background in genetics. Good for lecturers to liven up lectures with facts. The book is a series of questions on various parts of molecular biology and ‘omics’ with short, one page long, answers. These are interesting questions but difficult to find the answers to them without a lot and more importantly, knowing where to look. So here I will look at a few of the more interesting and simple questions.<br /><br />How many genes are there?<br />22,740 predicted and known genes. All genes minus predicted transcripts gives us only 18,357.<br />What is the typical size of a gene?<br />The median sixe is 16,995 nucleotides.<br />Which are the largest genes?<br />CNTNAP2 is 2.3 Mb (remember the genome of E. coli is only 4.63 Mb) and it generates a mRNA of 9.9 Kb. DMD which makes dystrophin is the second largest gene at 2.22 Mb making an mRNA of 14.1 Kb.<br />Largest proteins?<br />TTN gene which makes titin, which is 33,423 amino acid residues long. Mucin 16 is the second largest at 14,507 amino acid residues.<br />How much of the genome is made up of transposable elements?<br />45%: SINEs 13%, LINEs 21%, LTRs 8% and DDNA transposons 3%.<br />How many pseudogenes are there?<br />There are ~5000 pseudogenes with a median size of 1200 nucleotides.<br />The books seems good but I would suggest you borrow it off me rather than buy a copy.James Lloydhttp://www.blogger.com/profile/08219295648051788360noreply@blogger.com2tag:blogger.com,1999:blog-496263467300370264.post-14209734807932334592008-08-10T21:29:00.004+01:002009-01-31T15:50:49.772+00:00Cross presentation: presenting unexpected antigens to the cell-mediated immune response.Please cast your minds back to basic immunology. I am sure you remember there is the innate immune response (boring) and the acquired/adaptive immune response (very interesting). Perhaps the most interesting part of it is the gene re-arrangement to generate antibodies and T cell receptors (TCRs). But this re-arrangement is random; how can they tell self from non-self? The very basic explanation is seems to be that antigen (Ag) presenting cells (APCs) shows lymphocytes these Ag in the local draining lymph nodes when the body knows it is ill (ie the innate immune system is acting up). (Sorry for this long introduction to the topic but I need to remind myself of this while I type on the train myself.)<br /><br />A problem comes when we remember a bit of basic immunology. Peptide Ag presented on MHC class II molecules to CD4+ T cells (T helper cells) are taken up by APCs and are exogenous Ag. However, peptides shown on MHC class I to CD8+ T cells are generated from endogenous proteins. So how can a virus that infects only the liver like hepatitis or the respiratory system (like rhinovirus or flu) show their peptide Ag to naive CD8+ T cells (cytotoxic T cells or CTLs for short) which live in the lymph organs. Unless all viruses also affect the APCs as well then it seems impossible! Let’s forget how ridicules that idea is first and remember CTLs also attack tumour cells expressing mutant proteins. Cross presentation appears to be the answer. Somehow, APCs such as dendritic cells (DC) take up proteins from other cells and process these in a manner that means they are treated like endogenous proteins and therefore processed to be peptide Ag loaded onto MHC class I. This is called cross presentation, when CTLs are activated this way they are cross primed. The fine details of this appear to be missing but a lot of evidence is mounting that shows this must be the case. Other than this I can see no other way apart from the naive CTLs circulating the body and activating their; but no evidence has been found for this that I can see (I am pretty sure this also flies in the face of most accepted ideas in immunology). There are four ways for DC to capture extracellular proteins; (i) endocytosis (ii) pinocytosis (cell drinking) (iii) phagocytosis and (iv) macropinocytosis. For example, phagocytosis can be the uptake of a bacterium or cellular debris such as an apoptotic body. When cells are signalled to undergo apoptosis the dying cell starts to bleb and releases intact fragments of the cell called apoptotic bodies that express ‘eat-me’ signals. It is not a huge leap of the imagination to think this could be a major way tumour proteins are presented to naive CTLs.<br /><br />So how do these exogenous proteins within sub-cellular compartments such as the endosome or phagosome get loaded onto the MHC class I molecules? It is a good question and various routes have been suggested and evidence for some of these have been found. In DC exogenous proteins have been shown to be exported into the cytosol before they are degraded in the lysosome. This means they can be substrate for the proteasome and broken down to short peptides to be exported across the ER membrane by TAP. When here they can bind to the peptide binding cleft of MHC class I molecules and move to the cell surface like normal endogenous proteins in the classical presentation pathway. Another pathway acts in the endosome. This TAP/proteasome independent pathway uses cathepsin S to generate some peptide Ag. It is unclear whether other peptides here also act but currently appears unlikely. What I find amazing is how this protease produces peptides of the correct size of 8 or 9 amino acids residues long to load onto MHC class I molecules. This pathway even produces the same peptide Ag as the much more complex proteasome based pathway. When both pathways are knocked out most of the cross-presentation in vivo is lost.<br />Interestingly, tolerance to an Ag can be generated using these mechanisms when no stimulator of the immune system is present, and this has been called cross tolerance. It is now clear cross presentation is not some strange phenomenon like originally thought when discovered but is a key part of the immune system. When you knockout these pathways for cross-presentation none occurs. The next step is to manipulate this with vaccines to stimulate the cell-mediated immune response. Often only antibodies are produced because the antigens are not cross-presented.<br /><br />A short and sweet review:<br />Brode and Macary (2004) Cross-presentation: dendritic cells and macrophages bite off more than they can chew!<br /><br />A full and great review:<br />Rock and Shen (2005) Cross-presentation: underlying mechanisms and role in immune surveillance.James Lloydhttp://www.blogger.com/profile/08219295648051788360noreply@blogger.com2tag:blogger.com,1999:blog-496263467300370264.post-31721961214659181152008-07-24T17:13:00.010+01:002009-04-11T17:15:25.995+01:00Uncommon ways of looking at common problems- gene therapy for mitochondrial DNA diseases<div align="justify"><span style="padding: 5px; float: left;"><a href="http://www.researchblogging.org/"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border: 0pt none ;" /></a></span>I’m always very interested in less conventional approaches to conventional problems and a recent review found while looking for a paper for a journal club provided a good example.
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<br />As you know, gene therapy aims at correcting a genetic deficiency by the introduction and/or substitution of the mutated gene by a functional copy into relevant cells. The classic examples for gene therapy are normally diseases such as Cystic Fibrosis- monogenic, recessive, autosomal diseases, as these are, for obvious reasons, those that theoretically offer higher chances of success. There are, however, other types of genetic diseases that offer more space for original, unconventional gene therapy approaches.
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<br />Mitochondrial DNA diseases are a good example. The human mitochondrial genome is small (16kb) and is housed in the mitochondrial matrix. As most of its genes encode proteins involved in oxidative phosphorylation necessary for cellular respiration and ATP production, is not too surprising that mutations in such genes can cause a variety of diseases, many of which with symptoms associated with progressive defects in muscle and nerve systems.
<br /></div><p align="justify"><img id="BLOGGER_PHOTO_ID_5226615013632375122" style="margin: 0px auto 10px; display: block; text-align: center;" alt="" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiWSgLS6k2JkYt_1jm22GnmCxOc1L-uNxJGn8xsPGJcbcJpJcsz-nitwVsHO4o_hrUosCXs20i0ZrH0Jk6h8OLx8Lh8kpiFoyweIARZd-C3e4-QCSs_0L2kMHUNlDjcTdkeYwEYCmYnMlU/s320/mtDNA+genome.bmp" border="0" />
<br />There are two obvious strategies to tackle this problem using gene therapy. One is to introduce the functional copy of the mutated gene into the nucleus. The protein, with an appropriate mitochondrial targeting sequence, can then be transported to the mitochondria. This is the so-called allotropic expression of the gene, and has been shown to produce promising results in culture. Other option is to target the plasmid containing the functional gene into the mitochondria itself, as these organelles contain all the ribosomal RNA and tRNAs necessary for intra-mitochondrial protein synthesis (assuming that these are not the mutated genes). These strategies have been tried out with some success both using a wild type sequence of the mutated gene, or a gene from another species, known to perform its function in the pathway more efficiently (xenotopic expression).
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<br />However, as you might have already noticed, a mitochondrial DNA disease is characterised by the fact that not all the mitochondrial genome copies in a cell are necessarily mutated (the presence of different genome types within the same cell is known as heteroplasmy). This has two main implications: firstly, mtDNA diseases are threshold diseases: only when around 60-95% of copies in a cell are mutated will symptoms appear. This threshold will obviously vary depending on the disease. Secondly, rather than trying to introduce a functional copy into the mutated mitochondria, a much more interesting approach can be to just manipulate the relative amounts of the mutated and the wild type populations of mitochondria.
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<br />One approach is to promote specific types of exercise training to promote mitochondrial biogenesis. However, as the geneticist that I am, the alternative strategy- to manipulate the mutated mt genome- is much more interesting. A brilliant idea, in my point of view, is to take advantage of the fact that some mutation types introduce restriction sites. That way, rather than trying to express a functional copy of the mutated gene, it may be more successful to express a specific restriction enzyme that will degrade the mutated genome altogether. This is limited, obviously, to those diseases in which a unique new site is introduced, or in those where the number of restriction sites is higher enough in the mutated population to have a significant effect.
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<br />Another clever idea is to methylate the mutated mt genome so that it is not expressed, allowing the wild type population to proliferate and overcome the mutated one with time. The use of mitochondrial targeted PNAs (peptide nucleic acids) were a potential method, but were shown not to cross the inner membrane of the mitochondria. However, the use of zinc-finger peptides with DNA sequence specific binding capacities have been used to successfully methylate differently the mutated mitochondrial genome. If these domains are linked to a nuclease, it may be possible to degrade the mutated genome as well.
<br />
<br />These are all new strategies, only attempted in cell culture and their usefulness in in vivo models and ultimately in patients is yet to be determined. Nevertheless, I think these novel approaches just show that even standard problems can be approached in innovative ways.
<br /></p><p align="justify">References:</p><p align="justify"><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Gene+Therapy&rft_id=info%3Adoi%2F10.1038%2Fgt.2008.91&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Progress+and+prospects%3A+gene+therapy+for+mitochondrial+DNA+disease&rft.issn=0969-7128&rft.date=2008&rft.volume=15&rft.issue=14&rft.spage=1017&rft.epage=1023&rft.artnum=http%3A%2F%2Fwww.nature.com%2Fdoifinder%2F10.1038%2Fgt.2008.91&rft.au=Kyriakouli%2C+D.&rft.au=Boesch%2C+P.&rft.au=Taylor%2C+R.&rft.au=Lightowlers%2C+R.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Kyriakouli, D., Boesch, P., Taylor, R., & Lightowlers, R. (2008). Progress and prospects: gene therapy for mitochondrial DNA disease <span style="font-style: italic;">Gene Therapy, 15</span> (14), 1017-1023 DOI: <a rev="review" href="http://dx.doi.org/10.1038/gt.2008.91">10.1038/gt.2008.91</a></span></p><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Gene+Therapy&rft_id=info%3Adoi%2F10.1038%2Fgt.2008.11&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Selective+elimination+of+mutant+mitochondrial+genomes+as+therapeutic+strategy+for+the+treatment+of+NARP+and+MILS+syndromes&rft.issn=0969-7128&rft.date=2008&rft.volume=15&rft.issue=7&rft.spage=516&rft.epage=523&rft.artnum=http%3A%2F%2Fwww.nature.com%2Fdoifinder%2F10.1038%2Fgt.2008.11&rft.au=Alexeyev%2C+M.&rft.au=Venediktova%2C+N.&rft.au=Pastukh%2C+V.&rft.au=Shokolenko%2C+I.&rft.au=Bonilla%2C+G.&rft.au=Wilson%2C+G.&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Alexeyev, M., Venediktova, N., Pastukh, V., Shokolenko, I., Bonilla, G., & Wilson, G. (2008). Selective elimination of mutant mitochondrial genomes as therapeutic strategy for the treatment of NARP and MILS syndromes <span style="font-style: italic;">Gene Therapy, 15</span> (7), 516-523 DOI: <a rev="review" href="http://dx.doi.org/10.1038/gt.2008.11">10.1038/gt.2008.11</a>
<br /></span><link rel="File-List" href="file:///C:%5CUsers%5CCCVICE%7E1%5CAppData%5CLocal%5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml"><!--[if gte mso 9]><xml> <w:worddocument> <w:view>Normal</w:View> <w:zoom>0</w:Zoom> <w:punctuationkerning/> <w:validateagainstschemas/> <w:saveifxmlinvalid>false</w:SaveIfXMLInvalid> <w:ignoremixedcontent>false</w:IgnoreMixedContent> <w:alwaysshowplaceholdertext>false</w:AlwaysShowPlaceholderText> <w:compatibility> <w:breakwrappedtables/> <w:snaptogridincell/> <w:wraptextwithpunct/> <w:useasianbreakrules/> <w:dontgrowautofit/> </w:Compatibility> <w:browserlevel>MicrosoftInternetExplorer4</w:BrowserLevel> </w:WordDocument> </xml><![endif]--><!--[if gte mso 9]><xml> <w:latentstyles deflockedstate="false" latentstylecount="156"> </w:LatentStyles> </xml><![endif]--><style> <!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";} @page Section1 {size:612.0pt 792.0pt; margin:72.0pt 90.0pt 72.0pt 90.0pt; mso-header-margin:36.0pt; mso-footer-margin:36.0pt; mso-paper-source:0;} div.Section1 {page:Section1;} --> </style><!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabela normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;} </style> <![endif]--><span style=";font-family:";font-size:12;" ></span><meta equiv="Content-Type" content="text/html; charset=utf-8"><meta name="ProgId" content="Word.Document"><meta name="Generator" content="Microsoft Word 11"><meta name="Originator" content="Microsoft Word 11"><link rel="File-List" href="file:///C:%5CUsers%5CCCVICE%7E1%5CAppData%5CLocal%5CTemp%5Cmsohtml1%5C01%5Cclip_filelist.xml"><!--[if gte mso 9]><xml> <w:worddocument> <w:view>Normal</w:View> <w:zoom>0</w:Zoom> <w:punctuationkerning/> <w:validateagainstschemas/> <w:saveifxmlinvalid>false</w:SaveIfXMLInvalid> <w:ignoremixedcontent>false</w:IgnoreMixedContent> <w:alwaysshowplaceholdertext>false</w:AlwaysShowPlaceholderText> <w:compatibility> <w:breakwrappedtables/> <w:snaptogridincell/> <w:wraptextwithpunct/> <w:useasianbreakrules/> <w:dontgrowautofit/> </w:Compatibility> <w:browserlevel>MicrosoftInternetExplorer4</w:BrowserLevel> </w:WordDocument> </xml><![endif]--><!--[if gte mso 9]><xml> <w:latentstyles deflockedstate="false" latentstylecount="156"> </w:LatentStyles> </xml><![endif]--><style> <!-- /* Style Definitions */ p.MsoNormal, li.MsoNormal, div.MsoNormal {mso-style-parent:""; margin:0cm; margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:12.0pt; font-family:"Times New Roman"; mso-fareast-font-family:"Times New Roman";} @page Section1 {size:595.3pt 841.9pt; margin:72.0pt 90.0pt 72.0pt 90.0pt; mso-header-margin:35.4pt; mso-footer-margin:35.4pt; mso-paper-source:0;} div.Section1 {page:Section1;} --> </style><!--[if gte mso 10]> <style> /* Style Definitions */ table.MsoNormalTable {mso-style-name:"Tabela normal"; mso-tstyle-rowband-size:0; mso-tstyle-colband-size:0; mso-style-noshow:yes; mso-style-parent:""; mso-padding-alt:0cm 5.4pt 0cm 5.4pt; mso-para-margin:0cm; mso-para-margin-bottom:.0001pt; mso-pagination:widow-orphan; font-size:10.0pt; font-family:"Times New Roman"; mso-ansi-language:#0400; mso-fareast-language:#0400; mso-bidi-language:#0400;} </style> <![endif]--> <p class="MsoNormal">(the most recent paper I could find in this field, using the restriction enzyme approach in culture)</p> Cathttp://www.blogger.com/profile/08645968914831610862noreply@blogger.com5tag:blogger.com,1999:blog-496263467300370264.post-53578743916367015202008-07-16T22:28:00.009+01:002009-03-03T21:32:47.734+00:00Yet another twist in the world of gene expression - transcription factories<span style="padding: 5px; float: left;"><a href="http://www.researchblogging.org/"><img alt="ResearchBlogging.org" src="http://www.researchblogging.org/public/citation_icons/rb2_large_gray.png" style="border: 0pt none ;" /></a></span>When I went to a conference on post translational modification and chromatin, one talk really grabbed me, ironically it was the one that didn’t relate to the topic of the conference. I was going to facebook people about it and then remembered this existed.<br /><br />First of all I will ask you, did you know that transcription only happened at a few sites within the nucleus? In mouse cells from the animal there are between 100-300 of these but in cultured cells such as HeLa cells there are many more. Transcription factories also known as RNAPII foci are where most, if not all mRNA is produced. This amazed me and raises the obvious questions of why and how. The why may be obvious. It is a good idea to keep the nucleus as I see it ‘tidy’ but in more technical terms it is a way of keeps gene expression organised and regulating it (see below). The how this work I don’t think has been addressed! All I can say is watch this space.<br /><br />Another interesting feature of mammalian gene expression that has come out of these studies is that most ‘active genes’ are not on all the time like classically thought. Most genes appear to show a pulse fashion of expression. Travelling to transcription factories and being expressed then returning to a dormant stage until they travel back to transcription foci for another round of expression and so on. However, some genes show the classical continuous expression pattern and are seen at these sites all the time. One example is Beta-globin. Genes like these are relatively rare compared to those showing the pulse type expression but both are continuously on in there cell type. If elements of the beta-globin promoter is deleted then not only is overall expreesion decreased but it shows the pulse type expression.<br /><br />One of the most interesting things is that some genes will co-localize to the same transcription factory more often than you expect by pure chance. What is more interesting is these genes can be separated by several megabases! or even be on different chromosome. Using the 3C and 4C assay you can join different pieces of DNA together from different parts of the genome that have transcribed within the same transcription foci. These have shown along with RNA FISH the physical movement of genes to the same place to be transcribed. One of the two Beta-globin alleles within a cell was found to enter the same factory with some other genes at a rate of ~25% with a background rate expected to be less than 2%. These gene’s promoters were searched and a simple motif was found: CCACC. This is actually a binding site for a regulator of Haem biosynthesis and haemoglobhin production called Eklf. When Eklf is knocked out the association between these genes stops! This transcription factor must recruit to these genes to the transcription factories it is located at. I can see two mutually exclusive models here (tell me what you think or extra ones to consider). Either 1) something, perhaps Eklf recruits genes to these sites and physically moves them there or 2) genes with this motif move to all transcription foci and only stay to be transcribed at ones that have Eklf present. I would guess the second is more likely but I see no evidence for either model at this time. Another question I would like answered is whether other or maybe all transcription factors work in this way. I think it is unlikely but perhaps that is the case!<br /><br />One more interesting thing related to this is the story in B cells of mice. It has been shown that the proto-oncogene Myc is expressed in the same foci as immunoglobulin heavy chain (IgH) a very high proportion of the time. The interesting part is that these two genes have been show in many blood cancers to be translocated to be on the same chromosome so perhaps there is a link between transcription factories and cancer. Well that is what the people doing the research on it want to think. After all related to cancer equal more funding as I told a friend of mine earlier. A new lab has been set up by the post-doc who led most of the described research to explore the cancer link.<br /><br /><br /><br /><a href="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXM3_ygJ_uFjbyIK_n57vjb_mHs63bFvnH8J_fmY16KawF61VB9kUBJcBl0vZu6oFu-4KUCctfyfEkYmtTwXFeQj5LNLqsQIi70pnyNh1pt8n49v-lCrMl2YPaAvmbnpunHLLmQgzzSo0/s1600-h/Factories.bmp"><img style="margin: 0pt 10px 10px 0pt; float: left; cursor: pointer;" src="https://blogger.googleusercontent.com/img/b/R29vZ2xl/AVvXsEiXM3_ygJ_uFjbyIK_n57vjb_mHs63bFvnH8J_fmY16KawF61VB9kUBJcBl0vZu6oFu-4KUCctfyfEkYmtTwXFeQj5LNLqsQIi70pnyNh1pt8n49v-lCrMl2YPaAvmbnpunHLLmQgzzSo0/s320/Factories.bmp" alt="" id="BLOGGER_PHOTO_ID_5223951195836929346" border="0" /></a>And I now realise one very important thing, I should have been writing my result section now I have a deadline as well as lab work, S#£!!%$! Hell!<br /><br /><br /><br /><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=PLoS+Biology&rft_id=info%3Adoi%2F10.1371%2Fjournal.pbio.0050192&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Myc+Dynamically+and+Preferentially+Relocates+to+a+Transcription+Factory+Occupied+by+Igh&rft.issn=1544-9173&rft.date=2007&rft.volume=5&rft.issue=8&rft.spage=0&rft.epage=0&rft.artnum=http%3A%2F%2Fbiology.plosjournals.org%2Fperlserv%2F%3Frequest%3Dget-document%26doi%3D10.1371%252Fjournal.pbio.0050192&rft.au=Cameron+S.+Osborne&rft.au=Lyubomira+Chakalova&rft.au=Jennifer+A.+Mitchell&rft.au=Alice+Horton&rft.au=Andrew+L.+Wood&rft.au=Daniel+J.+Bolland&rft.au=Anne+E.+Corcoran&rft.au=Peter+Fraser&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Cameron S. Osborne, Lyubomira Chakalova, Jennifer A. Mitchell, Alice Horton, Andrew L. Wood, Daniel J. Bolland, Anne E. Corcoran, Peter Fraser (2007). Myc Dynamically and Preferentially Relocates to a Transcription Factory Occupied by Igh <span style="font-style: italic;">PLoS Biology, 5</span> (8) DOI: <a rev="review" href="http://dx.doi.org/10.1371/journal.pbio.0050192">10.1371/journal.pbio.0050192</a></span><br /><br /><span class="Z3988" title="ctx_ver=Z39.88-2004&rft_val_fmt=info%3Aofi%2Ffmt%3Akev%3Amtx%3Ajournal&rft.jtitle=Nature+Genetics&rft_id=info%3Adoi%2F10.1038%2Fng1423&rfr_id=info%3Asid%2Fresearchblogging.org&rft.atitle=Active+genes+dynamically+colocalize+to+shared+sites+of+ongoing+transcription&rft.issn=1061-4036&rft.date=2004&rft.volume=36&rft.issue=10&rft.spage=1065&rft.epage=1071&rft.artnum=http%3A%2F%2Fwww.nature.com%2Fdoifinder%2F10.1038%2Fng1423&rft.au=Cameron+S+Osborne&rft.au=Lyubomira+Chakalova&rft.au=Karen+E+Brown&rft.au=David+Carter&rft.au=Alice+Horton&rft.au=Emmanuel+Debrand&rft.au=Beatriz+Goyenechea&rft.au=Jennifer+A+Mitchell&rft.au=Susana+Lopes&rft.au=Wolf+Reik&rft.au=Peter+Fraser&rfe_dat=bpr3.included=1;bpr3.tags=Biology%2CGenetics%2C+Molecular+Biology%2C+Cell+Biology">Cameron S Osborne, Lyubomira Chakalova, Karen E Brown, David Carter, Alice Horton, Emmanuel Debrand, Beatriz Goyenechea, Jennifer A Mitchell, Susana Lopes, Wolf Reik, Peter Fraser (2004). Active genes dynamically colocalize to shared sites of ongoing transcription <span style="font-style: italic;">Nature Genetics, 36</span> (10), 1065-1071 DOI: <a rev="review" href="http://dx.doi.org/10.1038/ng1423">10.1038/ng1423</a></span>James Lloydhttp://www.blogger.com/profile/08219295648051788360noreply@blogger.com3