Tuesday, April 24, 2012

roadmap for regenerative medicine

Stem cells, cloning and regenerative medicine are issues on which UK research is doing really well in global comparison, partially due to the fact that the pioneering development of IVF raised awareness here and led to a reasonably sensible regulatory framework.

I've published quite a few pieces on this field over the last ten years or so. The latest feature is pegged to the strategy plan for UK regenerative medicine that the Medical Research Council together with other funding agencies released at the end of March.

A roadmap for regenerative medicine

Current Biology, Volume 22, Issue 8, R251-R253, 24 April 2012
doi:10.1016/j.cub.2012.04.004

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(NB: my features remain on free access only until the next issue appears, i.e. normally 2 weeks, sometimes 3, and they return to free access a year after publication)

celldivision

Thursday, April 19, 2012

Haydn for cello and flute

Here's a score we prepared earlier (and played last year). It's from a string duet by Haydn, and we adapted it for the flute. It's quite easy to stick together as the rhythm is mostly identical in both parts, and the parts individually are grade 3-4 level I would guess.



Next up is an adaptation of Johann Nepomuk Hummel's trio for piano, cello and flute in A major, op.78, which is essentially a set of variations on a Russian folk song called "Beautiful Minka." As the piano is quite dominant in this work and we don't have a pianist in the house, this one involves quite a bit of rearranging. We did just the theme last year, and I have now added one of the variations. Work in progress here:

Russian theme & variations

Wednesday, April 18, 2012

how microtubules grow

I helped writing up this PR about research done at Birkbeck College, published in the current issue of Cell:


Research sheds light on magic of microtubule growth

Transport within the cell relies on a system of tracks, the microtubules, which continuously grow or decay at one end, while the other end remains tethered and static. Researchers at the ISMB have now elucidated how some of the proteins that coordinate the building work on a growing end recognise the sites where they are needed.

Research into dynamic cellular systems such as the ever-changing microtubule cytoskeleton is complicated by the fact that structural methods typically require static and stable molecular complexes. The group of Carolyn Moores at Birkbeck Crystallography / ISMB, working together with Thomas Surrey at Cancer Research UK, has created a static model of the dynamically growing microtubule end, allowing them to pin down the structural interactions that hold the building site together.

Protein building blocks (tubulin proteins) that are added to the growing end normally carry the energy-rich substance GTP, which is split up into GDP and phosphate within seconds of incorporation. By offering building blocks with a non-cleavable analogue of GTP, the researchers could create a microtubule arrested in its growth but retaining the characteristics of a growing (GTP-carrying) end. Moores’ group at the ISMB could then obtain detailed images of this structure using electron microscopy at very low temperatures (cryo-EM).

Specifically, their work published in the latest issue of the journal “Cell” shows how a crucial group of proteins needed for the extension of the tip and its interaction with cellular features, the End-Binding (EB) proteins, bind to the building blocks that carry the uncleaved (and uncleavable) GTP. The researchers found that each of the EB proteins bridges two strings of tubulin subunits running the length of the tube structure, the so-called protofilaments. Intriguingly, each microtubule has a “seam” where the protofilaments are connected in a different fashion, and the EB proteins appear to recognise that difference, as they don’t bridge the seam.

“The fascinating behaviour of growing microtubule ends has been tantalising biologists for some time,” says Moores. “The biophysical experiments performed in the Surrey lab were essential in optimising sample preparation for our cryo-electron microscopy structural experiments, but we never anticipated the secrets of microtubule biology we would uncover when we started our collaboration.”


With the help of this model system, further research will uncover more details of the wider context in the dynamic behaviour of the cytoskeleton made up of the microtubules.

“Of course, we now have many more questions about the coordination between EB activity and the ebb and flow of microtubule growth and shrinkage,” says Moores, “in particular,: What do microtubule ends look like in the wider context of the multi-protein complexes which the EBs help to assemble? But our futures studies promise to take us in exciting directions in understanding regulation of the microtubule cytoskeleton.”


Reference:
P. Maurer, Franck J. Fourniol, Gergő Bohner, Carolyn A. Moores, Thomas Surrey:
EBs Recognize a Nucleotide-Dependent Structural Cap at Growing Microtubule Ends
Cell 2012, 149, 371-382, 13 April 2012




Image source: Cell

Tuesday, April 17, 2012

The strange case of ... Halestorm

I’ve only discovered Halestorm very recently, coming across the video for Love Bites on Kerrang and loving the frantic energy of it. My closest reference point is Within Temptation, whose complete works I love and cherish. Viewed from that direction, Halestorm is a different kind of offering. Where Sharon’s soprano floats etherically above the metal grumble, Lzzy mostly sticks to the lower registers that are mixing right within the instrumental sounds and doesn’t stand out so much. What makes the metal tracks irresistible for me is the mix of crazy energy and bad girl swagger in the lyrics (as witnessed even in the titles, such as: you call me a bitch like it’s a bad thing). The ballads are perfectly nice as rock ballads, though some of them (eg here’s to us) sound like melodies I have heard before.



In other music news, I also ordered “Best intentions” by We are the in crowd at the same time and have played that CD a few times, but find it less addictive. Nothing wrong with it really, I don’t mind playing it, it’s just it doesn’t blow me away.

Tuesday, April 10, 2012

astrobiology feature

As public interest in all things astrobiology is flying high right now, I have written another feature on the area, focusing on the search for life on Earth and in the rest of the Universe. Featuring exoplanets, Curiosity, Chile's Atacama desert, Lake Vostok, Carl Sagan, Galileo (spacecraft) ...

The feature is out in today's issue of Current Biology, you can freely access the

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or download the

PDF file.

(NB: my features remain on free access only until the next issue appears, i.e. normally 2 weeks, sometimes 3, and they return to free access a year after publication)

If that leaves you hungry for more, you could always try to get hold of a copy of this book:



which came out in its second, fully revised and updated edition last year - full details here

Monday, April 09, 2012

Dvorak for cello and flute

the young cellist in my family has arranged Dvorak's famous humoreske (originally a piano piece, but also found in the Suzuki string methods) for cello and flute, so I can play it with her (the limiting factor being, as she likes to put it, that I should first learn to count to four). The score is in noteflight and registered users can view it there, but for everybody else I am now trying to embed it here:



Wow, it actually works (requires Flash, though). If you press the button on the left above the score you can hear an approximation to the music (the cello sound doesn't sound much like a cello, and it's too metronomical for a romantic piece!) Check here for the kind of style we're aiming at :D

Seeing there seems to be very little repertoire available for cello and flute, I may put our other pieces online as well, by and by. They'll be around grade 5 level and are aiming to have a good balance between the two instruments.

Friday, April 06, 2012

halestorm

I'm loving the frantic video for "Love Bites" by Halestorm so much, I've ordered their CD ... watch this space.



Oh, and their cover of Lady Gaga's Bad Romance is also brilliant.

Friday, March 30, 2012

planet spotting

Now that Venus, Jupiter, and our Moon are going separate ways again, here's a group photo in memory of the amazing sights we had in the evenings of the last few weeks. This was a day or two after new moon, when the Moon approached the Venus-Jupiter pairing we've had for a while.



Actually, I didn't know that I could take photos of planets with my cheap little compact camera, until I tried it on the height of this month's encounters. And I wouldn't have known when and where to look for planets until I joined twitter a couple of years ago and started following lots of astro people.

Here's an earlier one I took before the Moon got involved:

venus and jupiter

Friday, March 23, 2012

chaperone movies

Back in the 90s I did some research on the molecular chaperone GroEL, which at the time didn't even have a crystal structure to its name. It is a great pleasure to see that the accumulation of structural and functional knowledge on this protein has now reached the stage where researchers can assemble snapshots to a movie showing plausible twists and turns that the seen subunits of each ring may carry out during their functional cycle.

The paper from Helen Saibil and colleagues at Birkbeck College, London, appeared in Cell (online) yesterday (D K Clare et al, Cell, 2012, DOI: 10.1016/j.cell.2012.02.047) and I wrote a news item for Chemistry World which has gone live today:

Molecular chaperones caught on film.


PS (23.4.2012): a related paper that just came out in Biophys J. and is freely accessible: Prying Open Single GroES Ring Complexes by Force Reveals Cooperativity across Domains Akiko Ikeda-Kobayashi, Yukinori Taniguchi, David J. Brockwell, Emanuele Paci and Masaru Kawakami Biophysical Journal, Volume 102, Issue 8, 1961-1968, 18 April 2012 doi:10.1016/j.bpj.2012.03.046

Tuesday, March 20, 2012

symmetry and complexity

My latest feature in Current Biology deals with complexes built from several identical or different protein subunits. There are good reasons why nature likes to build highly symmetrical assemblies from identical protein units, but on the other hand there are also good reasons why such structures may diversify and evolve highly complex arrangements of different subunits, with the proteasome, shown below, being a case in point.


Symmetry and complexity in protein oligomers
Current Biology, Volume 22, Issue 6, R175-R177, 20 March 2012
doi:10.1016/j.cub.2012.03.001

summary page

PDF file

(NB: my features remain on free access only until the next issue appears, i.e. normally 2 weeks, sometimes 3, and they return to free access a year after publication)

(image: © Prof. Michael Groll/Technische Universitaet München.)

Friday, March 16, 2012

writing, sharing, privacy ...

As this is the 1000th entry in my blog on blogspot, I think I can get away with a bit of navel-gazing re. what I’m trying to achieve, what I’m sharing and why, privacy issues, and all that.

First some history

Back in the early noughties, I was very happily addicted to manually updating my rather large website, and I didn’t get the point of these new-fangled blogs at all. Only in 2006, on joining MySpace, where you had a blog by default, whether you wanted or not, did I start to try this timeline format and began to enjoy it. As a control freak, however, one wants to have more order in one’s thoughts than simply a chronological one, so I looked for some platform where I could maintain at least some sort of logical connectedness of the kind I had on my website. I tried Yahoo360 (as my website was on Yahoo’s Geocities and that blended in seamlessly), but after running various formats in parallel, I ended up using blogspot as the primary blog (though I did post copies of entries in MySpace for a while, until that site turned into a ghost town).

I do like the way Blogspot allows finding blogposts easily by date, by keyword, and by search, and with the additional “link-within” app I think the connectivity between things is practically perfect for me.


What to share and when

My main justification for blogging is of course to find additional audiences for my writing published in books and magazines. I like to think of it as a funnel, where, with luck, the media that have wider audiences with shorter attention times guide some of these audiences on to the media that require a bit more concentration, so for instance: twitter – blog – magazine article – book. I don’t have much evidence that this funnel is actually working and pulling the crowds in, but hey, there’s no harm in trying.

In addition, I do like to share random bits that I happen to be interested in with the wider world (if only because sometimes there are so few people interested in the same thing that the next person may be quite far away, so there would be no use shouting in the street or going to the pub to talk about these interests). A lot of this random sharing, when it is just a link or a picture has now migrated to Twitter, and for my own photos I mainly use flickr, so the blog is left with the somewhat more text-heavy stuff, such as short excerpts of science journalism pieces (funnelling towards the full-length piece), rants on politics, economy, life, and raves about music and movies. I also try to review every book I read, though in recent months I didn’t find time to read anything beyond the books I was commissioned to review anyway.

With these things, there is still enough material to do 3-4 blog entries a week (have done fewer in the last few months, as I had two book projects to finish at the same time, which swallowed a lot of my spare time). Ideally, it would be great to do daily posts on a variety of subjects, maybe visiting each area no more often than once a week. People writing about how to monetise blogs say you have to find a niche and stick to it, but that approach would hold no interest for me. I can do niche business with the existing niche magazines any time I want, but the beauty of blogging for me is that I can write on the whole spectrum of my interests, without having a chemistry editor complaining that there isn’t enough chemistry in my story.

To give an impression of what I blog about, these are the 20 most-used tags in the first 999 blog entries:

1-10
sciencejournalism 202 (label for science stuff published elsewhere)
sciencenews 182 (for science stuff not published elsewhere)
oxford 147
photo 114 (for every entry that contains one of my photos)
bookreview 86
currentbiology 85
biochemistry 84
environment 77
germany 72
medicine 63
11-20
pop 63
shakira 56
rants 55
nanoworld 54
literature 52
astrobiology 48
travel 48
history_of_science 47
genome 45
miscellaneous 44

So adding the first two labels together gives us a science content of 38%. Sounds about right.


What not to share

Given the recent developments around Google, Facebook et al, one has to consider privacy issues as well. Personally, I’d like to believe that I’m too weird for any algorithms to figure out what ads I might click on. As evidence I can point to amazon.com who have tried to figure me out pretty much since the company started in the US and haven’t succeeded to this day. What their bots can’t get their heads round is that I buy books and other things in different countries (have used US, UK, DE, FR and ES versions of amazon), and for different people (not always ticking the gift options), and that I also use their site as an author, as a marketplace vendor, not to mention as a reviewer – in which case I look up the details of the book, but get it sent via a magazine I write for. After 15 years or so, suggestions I get from amazon are still mostly useless – if it is something I’m interested in, I normally own it already. So good luck to google if they want to work out who I am, I’ll keep you posted on their progress.

Having said that, it is of course only sensible to withhold information when I can gain no benefit by revealing it. If only because nasty people from some “intelligence” agencies I could think of will probably be working on ways of tapping into Google’s information on people already. I don’t reveal my address, don’t say where my tweets are from, and seeing the recent cross-platform information sharing that google is starting now, I may want to do something to protect my searches.

In Facebook, I don’t fill in most of the details that the site asks for, and I happily accept friendships from random people who I don’t really know (as my profile is public, it doesn’t make any difference anyway). Just to confuse Facebook a bit more, I occasionally switch the language I use the site in. I don’t use the like button outside of facebook, and generally only create cross-links to divert traffic out of facebook, not to pull it in. I see facebook as a human zoo where people are caged for the benefit of the visitors / advertisers, so I still prefer the wild open spaces of the web to the zoos.


Who reads what

I haven’t done any serious visitors statistics on my blog, but the occasional look at the tracker that runs at the bottom of the right hand side column suggests that there is only modest traffic, some 20-30 visits per day, and that most of it comes from searches. There was a time when tweeting blog entries helped, but that has stopped working, not sure why. Tweeting links to a specific photo on flickr still gives me 15 extra clicks within a minute, but tweeting a blog entry gives one or two at best.

Google searches are especially successful in attracting visitors to topics that aren’t adequately covered by the English language media, e.g. Spanish language pop music or cinema. So if somebody using a search engine set to English as the preferred language looks for information on movies like Julio Medem’s Caotica Ana or Shakira’s impact on society, they are likely to end up on my blog. (Amazingly I get Medem and Shakira related visits practically on a daily basis, while areas where I can actually claim some level of expertise, like nanotechnology or extremophiles, pull in much less traffic, presumably because they are adequately covered by higher-ranking sites.) Other popular search terms include the philosophy of Lady Gaga and that of capitalism as well, the Headington shark and the architecture of Santiago Calatrava. For further popular search terms see this analysis I did in 2010.

All in all, I’m still happy with what this blog enables me to do and communicate, so I guess I’ll just keep going.

Wednesday, March 14, 2012

7 days in Havana

I'm hoping to catch Julio Medem's latest work, which is a seventh of the 7-episodes film 7 days in Havana, at some time this year. Medem's contribution is the Wednesday, and it's called La tentación de Cecilia. Am a bit nervous as his last two feature films didn't get cinematic releases in the UK, but let's wait and see.

UPDATE 21.7.2012): in theory, the film was released in the UK at the beginning of July, but a check at our local indpendent cinema revealed they are planning to show it "off-release" i.e. later ...

In the meantime we can enjoy the rather lovely official website of the film co-sponsored by my favourite rum, Havana Club. What's not to like?

Just keeping all limbs crossed and hoping that I actually get to see the movie.



official poster of the movie