O'Really?

May 4, 2010

Ian Wilmut on the World after Dolly the Sheep

Filed under: biotech — Duncan Hull @ 7:39 am
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Bicolor sheep by Tambako the Jaguar, on FlickrAs part of the Gates Distinguished Lecture Series, Ian Wilmut will be giving a public lecture today in Cambridge titled Cloning, Stem Cells and Regenerative Medicine: The World After Dolly. More details below from talks.cam.ac.uk:

“Ian Wilmut soared to international prominence when Dolly, a baby lamb created from the cells of an adult sheep [1,2], was revealed to the world. Dolly was the first genetic replica of a living creature created from cells from an adult animal. The accomplishment sparked amazement and controversy as scientists, philosophers, ethicists and religious leaders perceived the potential to extend such work to humans.”

All are encouraged to attend, lecture starts at 6pm today the Cambridge Union Society see press release from the University. [Update: Note last minute change from previously advertised venue at Emmanuel College, Cambridge. See also the accompanying podcast page].
Audio of talk available

References

  1. Campbell, K., McWhir, J., Ritchie, W., & Wilmut, I. (1996). Sheep cloned by nuclear transfer from a cultured cell line Nature, 380 (6569), 64-66 DOI: 10.1038/380064a0
  2. Wilmut, I., Schnieke, A., McWhir, J., Kind, A., & Campbell, K. (1997). Viable offspring derived from fetal and adult mammalian cells Nature, 385 (6619), 810-813 DOI: 10.1038/385810a0

April 30, 2010

Daniel Cohen on The Social Life of Digital Libraries

Filed under: biocuration,data mining,publishing — Duncan Hull @ 7:12 am
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Day 106 - I am a librarian by cindiann, on FlickrDaniel Cohen is giving a talk in Cambridge today on The Social Life of Digital Libraries, abstract below:

The digitization of libraries had a clear initial goal: to permit anyone to read the contents of collections anywhere and anytime. But universal access is only the beginning of what may happen to libraries and researchers in the digital age. Because machines as well as humans have access to the same online collections, a complex web of interactions is emerging. Digital libraries are now engaging in online relationships with other libraries, with scholars, and with software, often without the knowledge of those who maintain the libraries, and in unexpected ways. These digital relationships open new avenues for discovery, analysis, and collaboration.

Daniel J. Cohen is an Associate Professor at George Mason University and has been involved in the development of the Zotero extension for the Firefox browser that enables users to manage bibliographic data while doing online research. Zotero [1] is one of many new tools [2] that are attempting to add a social dimension to scholarly information on the Web, so this should be an interesting talk.

If you’d like to come, the talk starts at 6pm in Clare College, Cambridge and you need to RSVP by email via the talks.cam.ac.uk page

References

  1. Cohen, D.J. (2008). Creating scholarly tools and resources for the digital ecosystem: Building connections in the Zotero project. First Monday 13 (8)
  2. Hull, D., Pettifer, S., & Kell, D. (2008). Defrosting the Digital Library: Bibliographic Tools for the Next Generation Web PLoS Computational Biology, 4 (10) DOI: 10.1371/journal.pcbi.1000204

April 28, 2010

Philip Campbell on Science Facts and Frictions

Filed under: publishing — Duncan Hull @ 6:28 am
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Philip Campbell: Will you pay for good online stuff, Dammit? (Libraries do, thankfully)As part of the Gates Distinguished Lecture Series editor Philip Campbell is giving a public lecture at 6.30pm tonight titled Science – facts and frictions at Emmanuel College, Cambridge. The abstract and text below is reproduced from talks.cam.ac.uk:

‘Climategate’, MMR vaccine, GM crops, stem cells – these are examples of public debates in which science and scientists have come under attack. And yet the processes of science were no different in kind from those in calmer territories, such as cancer research, where the public not only trusts researchers but directly donates half a billion pounds every year in their support. Why are there such contrasts? And what can scientists and others do in response to such attacks? The talk will offer some suggestions.

As Editor-in-Chief of Nature, Philip Campbell heads a team of about 90 editorial staff around the world. Dr. Campbell takes direct editorial responsibility for the content of Nature editorials, writing some of them. He is the seventh [1] Editor-in-Chief since the journal was launched in 1869.

Dr. Campbell’s role as Editor-in-Chief of Nature publications (of which there are many editorially independent journals and several websites) is to ensure that the quality and integrity appropriate to the Nature name are maintained, and that appropriate individuals are appointed as chief editors. He sits on the executive board of Nature’s parent company, Nature Publishing Group.

According to the accompanying press release from the University, Campbell:

“is particularly interested in groups of scientists who regularly produce blogs in order to help the public and journalists gain access to their perspectives on scientific developments and controversies.”

So, if you’re in or near Cambridge tonight, this talk is open the public and looks like it will be enlightening.

[Update, some interesting things mentioned in this talk in no particular order:

Refererences

  1. Philip Campbell (1995). Postscript from a new hand Nature, 378 (6558), 649-649 DOI: 10.1038/378649b0
  2. Daniel Sarewitz (2004). How science makes environmental controversies worse Environmental Science & Policy, 7 (5), 385-403 DOI: 10.1016/j.envsci.2004.06.001

April 8, 2010

Embracing Open Science

Filed under: Open Notebook Science,web of science — Duncan Hull @ 10:37 pm
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Open Push (Oklahoma, Manchester)There’s an interesting article [1] by Chelsea Wald in Science magazine published today, about Open Science including Open Source Code, Open Notebook Science, Open Data and Open Access Publishing.

It interviews some of the advocates and sceptics of a more open approach to doing Science, including:

It’s well worth a read, despite being a bit US-centric, and looks like it’s freely available via Open Access Publishing [2] too.

[Update: There is some follow-up commentary on the original article here and here]

References

  1. Chelsea Wald (2010). Scientists Embrace Openness Science (2010-04-09) DOI: 10.1126/science.caredit.a1000036
  2. Declan Butler (2010). US seeks to make science free for all Nature, 464 (7290), 822-823 DOI: 10.1038/464822a

8-OHdG: Entity of the Month

Filed under: ChEBI — Duncan Hull @ 11:04 am
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DNA Origami by Alex BatemanChemical Entities of Biological Interest (ChEBI) release 67 is now available, containing 548,850 total entities, of which 20,565 are annotated entities and 720 were submitted via the ChEBI submission tool. New in this release, the ChEBI ontology is now available in the Web Ontology Language (OWL), which is part of an ongoing research project to automate the classification of small molecules in ChEBI. If you’re using this data, we’d like to hear from you! This month’s entity of the month is 8-OHdG. Text below reproduced from ChEBI website:

8-Hydroxy-2′-deoxyguanosine (8-OHdG, ChEBI:40304) is an important molecule in oxidative stress used as a biomarker of many processes involving reactive oxygen species. Also known as 8-oxo-dG (this abbreviation derived from its tautomeric name 8-oxo-7,8-dihydro-2′-deoxyguanosine) and as HMDB03333 in the Human Metabolome Database [1], it has been used especially as a sensitive marker of the DNA damage caused by hydroxyl radical attack at C-8 of guanine. This damage, if left unrepaired, has been proposed to contribute to mutagenicity and cancer promotion [2]. This use of 8-OHdG as a biomarker for DNA damage extends over a wide range of scenarios [3,4,5,6], because it is one of the major products of DNA oxidation.

More recent work by Junko Fujihara and his colleagues at Shimane University in Japan has demonstrated how 8-OHdG can be used as a possible marker for arsenic poisoning, since antiquity a method of dispatch frequent in homicide and suicide cases [7]. Fujihara’s study however focuses principally on the use of arsenic in medicine, and specifically in demonstrating a relationship between concentrations of 8-OHdG and various arsenic compounds in the urine of a patient with acute promyelocytic leukaemia being treated with arsenic trioxide. Their conclusions that 8-OHdG in urine can be used therapeutically as a key biomarker for arsenic compounds may also find application in the diagnosis of arsenic poisoning when arising from the consumption of seafood such as fish, shrimp, oysters and seaweeds, organisms known to contain appreciable amounts of arsenic compounds.

[Picture of Alex Bateman‘s DNA origami in action from The Wellcome Trust Sanger Institute.]

References

  1. Wishart, D., Knox, C., Guo, A., Eisner, R., Young, N., Gautam, B., Hau, D., Psychogios, N., Dong, E., Bouatra, S., Mandal, R., Sinelnikov, I., Xia, J., Jia, L., Cruz, J., Lim, E., Sobsey, C., Shrivastava, S., Huang, P., Liu, P., Fang, L., Peng, J., Fradette, R., Cheng, D., Tzur, D., Clements, M., Lewis, A., De Souza, A., Zuniga, A., Dawe, M., Xiong, Y., Clive, D., Greiner, R., Nazyrova, A., Shaykhutdinov, R., Li, L., Vogel, H., & Forsythe, I. (2009). HMDB: a knowledgebase for the human metabolome Nucleic Acids Research, 37 (Database) DOI: 10.1093/nar/gkn810
  2. Kuchino, Y., Mori, F., Kasai, H., Inoue, H., Iwai, S., Miura, K., Ohtsuka, E., & Nishimura, S. (1987). Misreading of DNA templates containing 8-hydroxydeoxyguanosine at the modified base and at adjacent residues Nature, 327 (6117), 77-79 DOI: 10.1038/327077a0
  3. Wu LL, Chiou CC, Chang PY, & Wu JT (2004). Urinary 8-OHdG: a marker of oxidative stress to DNA and a risk factor for cancer, atherosclerosis and diabetics. Clinica chimica acta; international journal of clinical chemistry, 339 (1-2), 1-9 PMID: 14687888
  4. Schriner, S. (2005). Extension of Murine Life Span by Overexpression of Catalase Targeted to Mitochondria Science, 308 (5730), 1909-1911 DOI: 10.1126/science.1106653
  5. Sumida S, Doi T, Sakurai M, Yoshioka Y, & Okamura K (1997). Effect of a single bout of exercise and beta-carotene supplementation on the urinary excretion of 8-hydroxy-deoxyguanosine in humans. Free radical research, 27 (6), 607-18 PMID: 9455696
  6. Tarng DC, Huang TP, Wei YH, Liu TY, Chen HW, Wen Chen T, & Yang WC (2000). 8-hydroxy-2′-deoxyguanosine of leukocyte DNA as a marker of oxidative stress in chronic hemodialysis patients. American journal of kidney diseases : the official journal of the National Kidney Foundation, 36 (5), 934-44 PMID: 11054349
  7. Fujihara, J., Agusa, T., Tanaka, J., Fujii, Y., Moritani, T., Hasegawa, M., Iwata, H., Tanabe, S., & Takeshita, H. (2009). 8-Hydroxy-2′-deoxyguanosine (8-OHdG) as a possible marker of arsenic poisoning: a clinical case study on the relationship between concentrations of 8-OHdG and each arsenic compound in urine of an acute promyelocytic leukemia patient being treated with a Forensic Toxicology, 27 (1), 41-44 DOI: 10.1007/s11419-008-0062-x

April 1, 2010

Καλό Πάσχα: Happy Easter: Frohe Ostern

Filed under: book review — Duncan Hull @ 11:24 am
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Easter Bunny 1 "My arse hurts"... Easter Bunny 2 "What?"Whatever your inclination, it’s difficult to ignore that sandwiched between the Vernal equinox and Beltane, it’s Easter time already. So Happy Easter, Frohe Ostern or Καλό Πάσχα, as they say down south, to all readers of this O’Really? blog.

If you’re gorging yourself on chocolate (see picture right), you might like to consider the food science behind it all thanks to a book [1] by Stephen Beckett published by the Royal Society of Chemistry. Ever wondered why melted chocolate that is put back in the fridge doesn’t quite taste the same? This book will tell you, and a whole lot more besides.

As for the chocolate bunnies, my language skills (german and greek) are a load of old arsch, but the cartoon over on the right roughly translates as follows.

  • Chocolate Bunny #1, with missing posterior: “Mein arsch tut weh!!” (“My arse hurts!!”)
  • Chocolate Bunny #2, with missing ears: “Was?” (“What?”)

Happy Chocolatey Holidays wherever you are…

References

  1. Stephen T. Beckett (2000). The Science Of Chocolate Royal Society of Chemistry Publihshing DOI: 10.1039/9781847552143
  2. Anon (2010). Book Review of The Science of Chocolate The Science of Chocolate. By Stephen T. Beckett (Nestle Product Technology Centre). Royal Society of Chemistry , Cambridge . 2008. xii + 240 pp. 6 × 9 in. £24.95. ISBN 78-0-85404-970-7. Journal of Natural Products DOI: 10.1021/np100172s

March 17, 2010

Hunkin’s Hypothesis: Technology Is What Makes Us Human

Filed under: biotech,education — Duncan Hull @ 11:27 am
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Tim Hunkin: Technology is What Makes Us HumanCartoonist and engineer Tim Hunkin is probably best known for his exhibits at the Science Museum in London and his Under The Pier Show “a mad arcade of home-made slot machines & simulator rides on Southwold Pier, Suffolk”.  His website is a treasure trove of weird and wonderful things.

Tim has an interesting proposition, let’s call it Hunkin’s Hypothesis [1], that technology is what makes us human:

“Technology isn’t just something outside ourselves, it’s an innate part of human nature, like sex, sleeping or eating, and that its been a major driving force in evolution. Tool using, along with language and bipedalism, is essentially what makes us human. The complicated theories used to explain why we first stood up are largely unnecessary. Our hands simply became too useful for holding tools to waste them on walking.”

He bases this idea, on a paper published by Frances Evans [2] about the creative engineering mind. This idea has at least two important implications:

  1. Engineering is a creative and intellectual process that humans do instinctively, not an obsolete and dying skill practiced by dinosaurs
  2. Engineering is an essential part of education, that needs to be taught more in schools and universities. Tim encourages his grand-children to use spot-welders, glue-guns and soldering irons at every opportunity! In UK schools health and safety regulations, plus the fear of being sued often make this tricky.

I’m not sure what to make of Hunkin’s Hypothesis yet, but it’s an intriguing idea that deserves investigation.

References

  1. Tim Hunkin (2006). Technology is what makes us human. timhunkin.com
  2. Frances Evans (1998). Two legs, thing using and talking: The origins of the creative engineering mind AI & Society, 12 (3), 185-213 DOI: 10.1007/BF01206195
  3. Tim Hunkin – The Seaside Inventor, Southwold Pier, Suffolk

[Picture of Tim Hunkin taken from his talk at Cambridge Science Festival, 2010.]

March 16, 2010

DNA, Diversity and You at Cambridge Science Festival

Filed under: communication,data mining — Duncan Hull @ 8:40 am
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Sequence BraceletsAs part of Cambridge Science festival last weekend, I joined a group of about 40 volunteers from The Sanger and EBI at an event “DNA, diversity and you”. This was a series of education and outreach events designed to explore how differences in your genetic code make you different from other individuals, and what makes the humans different from other living things –  with a bit of computational biology thrown in for good measure.  Here are some notes on a selection of the activities, in case you ever find yourself trying to explain biology, computer science or bioinformatics to anyone aged 4-18 and beyond. These resources are all tried, tested and fun to work with, for students and teachers alike:

  1. DNA origami create your own origami DNA molecule, and hands on way of learning abou tthe double helix structure of DNA
  2. DNA sequence bracelets (see picture right). Thread coloured beads according to sequence sections from a range of organisms including trout, chimpanzee, butterfly, a flesh-eating microbe and rotting corpse flower.
  3. Yummy gummy DNA (under 5’s) build your own DNA helix out of sweets and cocktail sticks. Then scoff it all afterwards.
  4. What’s my name in DNA? find out what your name is in DNA, and what the corresponding (hypothetical) protein is using software from deCODE.
  5. Function Finders translate DNA into a sequence of amino acids using wooden translator blocks, then find out which organism the amino acid sequence is from.
  6. Genome sizes (with seatbelts) Rank organisms (inc. human, zebrafish, mosquito, sugar cane and yeast) and find out if they are in the right order. Results are often not what you would expect.
  7. Play your genes right. A card-based guessing game which compares the number of genes in the human genome with the number of genes from a range of different organisms include the flu virus, E. coli bacteria, armadillo, rice plant and others.
  8. Genome Jigsaws for illustrating the process of finishing supposedly “finished” genomes, by putting together a square sequence jigsaw following base pairing rules to end up with a complete finished square.
  9. DNA Time Team examines of aspects ancestry and evolution. The activity encourages people to work out the sequence of a common ancestor by filling in the gaps on a simple evolutionary tree.
  10. Spot the difference with proteins. Comparing Heat Shock Protein (HSP) in human and other organisms to illustrate how different regions of the protein vary between different organisms and how this affects function.
  11. Ready, steady sort: a sorting network that demonstrates one technique that computers use to sort through large amounts of information like sequence data. This comes straight from Computer Science Unplugged by Tim Bell, Mike Fellows and Ian Witten. This activity can be done either as a smaller board game, or as a larger floor game. Either way, it’s a lot of fun, especially if you time people for an added competitive element (see video below)

There were a whole bunch of new activities at the festival this year, maybe these will appear on the your genome website in the future. Anyway, it was great fun to get involved, there is nothing quite like the challenge of explaining parallel computing to young kids, teenagers and their parents – actually much easier than you’d think if you’ve got access to great teaching materials.

Thanks to Francesca Gale and Louisa Wright for all the hard work that went into organising this fun and successful event.

March 8, 2010

Cambridge Science Festival, 8th-21st March 2010

Filed under: communication — Duncan Hull @ 8:25 am
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Cambridge Science Festival, 8-21 March 2010Madder than the Mad March Hare, more entertaining and surreal than Alice down-a-rabbit-hole in Wonderland: today marks the start of this years Cambridge Science festival:

“Delve into the diversity of science at the Cambridge Science Festival 2010! All aspects of science, technology, engineering and mathematics will be available to visitors of all ages at more than 150 mostly free events over two weeks. This year is the International Year of Biodiversity and the Festival is celebrating this by inviting you to learn more about the colourful creatures on the land and beneath the waves at the many events on offer in University departments and museums.

This year, a Schools Zone has been added into the programme of events, where pupils from local schools will be showcasing their work with interactive exhibits at the University Centre on the 20th March.

Also look out for scientists from the BBSRC in the Grafton Centre during the Festival, who will be on hand to answer your tricky science questions. Watch out for video and audio coverage before and during the Festival on the Guardian website.”

A team of scientists and engineers from the Wellcome Trust Sanger Institute and The EBI will be participating, on Saturday 13th March with a session on DNA, diversity and you and also tackling the thorny issue of Who Owns Science? on Friday 19th March. So if you’re in or near Cambridge over the next couple of weeks, come and say hello, and check out the  details in the full programme.

March 4, 2010

Sildenafil citrate: Entity of the Month

Filed under: ChEBI — Duncan Hull @ 12:29 pm
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30 St Mary Axe or the Gherkin - London by Patrick MayonRelease 66 of Chemical Entities of Biological Interest (ChEBI) is now available, containing 534,521 total entities, of which 20,151 are annotated entities and 698 were submitted via the ChEBI submission tool. This months entity of the month is Viagra, also known as Sildenafil citrate: (Text below reproduced from ChEBI website)

Few chemical compounds are better known to the general public than sildenafil citrate (CHEBI:58987), traded under the name of “Viagra”.The compound was first synthesised by chemists working at Pfizer, with a view to using it for the treatment of hypertension and angina pectoris. Whilst having been found to be ineffective against angina in clinical trials, it has been observed to induce penile erections and was therefore marketed by Pfizer as a drug for the treatment of erectile dysfunction.

A number of synthetic routes for the preparation of the parent sildenafil have been reported [1]. A common industrial synthetic route is through reaction of 4-amino-1-methyl-3-N-propylpyrazole-5-carboxamide and 2-ethoxy-5-(4-methylpiperazin-1-yl)sulfonylbenzoic acid followed by subsequent cyclisation to sildenafil through heating under acidic conditions.

Sildenafil has been shown to be an inhibitor of cyclic guanosine monophosphate specific phosphodiesterase type 5, an enzyme which is responsible for the degradation of 3′,5′-cyclic GMP (cyclic guanosine monophosphate, cGMP) in the corpus cavernosum. This leads to the presence of increased levels of cGMP, which, in turn causes vasodilation of the helicine arteries and thus increased blood flow into the spongy tissue of the penis [2].

Apart from the treatment of sexual dysfunction, sildenafil is also used in the treatment of pulmonary arterial hypertension and works again through relaxation of the arterial wall, which leads to a decrease in arterial resistance [3]. Furthermore – and arguably most interestingly – sildenafil has been found to decrease the time necessary for the re-entrainment of circadian rhythms after phase advances in the light–dark cycle (such as occur on transmeridian eastbound flights) in members of the Cricetidae family [4]*. The discovery was rewarded with the award of an Ig Nobel Prize in Aviation in 2007.

* or as wikipedia puts it…”Viagra aids jet lag recovery in hamsters” …that’s an interesting side effect.

References

  1. Dunn, P. (2005). Synthesis of Commercial Phosphodiesterase(V) Inhibitors Organic Process Research & Development, 9 (1), 88-97 DOI: 10.1021/op040019c
  2. Webb DJ, Freestone S, Allen MJ, & Muirhead GJ (1999). Sildenafil citrate and blood-pressure-lowering drugs: results of drug interaction studies with an organic nitrate and a calcium antagonist. The American journal of cardiology, 83 (5A) PMID: 10078539
  3. Richalet, J. (2004). Sildenafil Inhibits Altitude-induced Hypoxemia and Pulmonary Hypertension American Journal of Respiratory and Critical Care Medicine, 171 (3), 275-281 DOI: 10.1164/rccm.200406-804OC
  4. Agostino, P., Plano, S., & Golombek, D. (2007). Sildenafil accelerates reentrainment of circadian rhythms after advancing light schedules Proceedings of the National Academy of Sciences, 104 (23), 9834-9839 DOI: 10.1073/pnas.0703388104

[Creative Commons licensed picture of 30 St Mary Axe or the Gherkin – London by Patrick Mayon, see comments on this post at friendfeed]

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