perforin pore unveiled

The group of Helen Saibil at Birkbeck College determined the shape of the perforin pore, which killer cells of our immune system use to eliminate cancerous or virus-infected cells, which suggested how the protein subunits could be arranged. In collaboration with researchers at Monash University (Melbourne, Australia) who solved the crystal structure of the individual protein blocks that assemble to form this pore, the group has now come to a conclusive model, which is “the wrong way round” compared to what they were expecting based on similar bacterial pores.
Read my news item in Chemistry World here.




(image courtesy of Helen Saibil, Birkbeck College London)

Reference:
R.H.P. Law et al. Nature online DOI: 10.1038/nature09518

eyes like yours

warming up for the forthcoming European leg of Shakira's tour, here's a clip from the last one, Ojos asi live from Dubai:



PS watching that video again, it just occurred to me that Ojos asi was the first song I ever saw her playing live - see the ravings of my younger self here. No wonder it leaves me stirred and shaken.

Oxford Today relaunch

Oxford Today, the alumni magazine of Oxford University, has a new publisher and a new editor, so the first issue of the academic year was celebrated as a "relaunch" today with champagne, canapees, and speeches. Even the vice chancellor (organic chemist Andrew Hamilton) put in an appearance, and for me it was an opportunity to put faces to email addresses.

I've been writing science features for Oxford Today since 2004, and have now also taken over the science findings page which compiles very short news items on scientific results emerging from research conducted here (open the PDF version of the magazine and scroll down to page 11).

My latest feature, about data sharing in genetics, appears on pages 30 to 32 of the magazine and online here. As punishment for my recent rant on inverted helices I've been served with a wrong helix as well. Intriguingly, the same illustration also contains a correct (but much smaller) image of the double helix, on the 2-pound coin, so it can't be because someone flipped the image. Very pleased however that the spiral staircase appearing in the portrait of HELEX director Jane Kaye has the correct chirality.

We were told that not only the printed magazine has been spruced up, the website is also being relaunched in an improved format, with added content, including even music videos. I'll have to check those out.

PS I have been assured that links to earlier online content of Oxford Today will remain functional, so my previous pieces, such as this one on multiple sclerosis and epigenetics are still accessible via my website and blog.

the inverted helix

It is a fact widely ignored by people who design covers for science books and journals, but let me say it loud and clear, the normal version of the DNA double helix is RIGHT-HANDED, i.e. it is like an ordinary screw in that if you look down the axis and follow the ridge clockwise, the movement will lead away from you (see this example from the Ashmolean Museum's collection of glassware).

If, however, you take a picture of a DNA double helix and mirror it, you end up with something blatantly WRONG like the examples below:







PS in order to inject some scientific method into my rant, I've just done a Google image search for "DNA" and checked the first 30 double helix images shown. Giving those where the chirality isn't easy to see the benefit of the doubt, I have spotted three images with left-handed helices, so the error rate seems to be around 10%, even on websites that get high PageRank.


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Marina and the Diamonds at the Regal

Saw Marina and the Diamonds last night, and OMG she looked just like Shakira. Just kidding, this is a quote from her song "Hollywood", of course. But she does have some shakiesque features.



Great show, and I really liked the venue too. The Regal is a former Bingo hall that has been refurbished and converted to a music venue only recently, and this was the first time I saw it from the inside.

Room in Rome reviewed

I was a huge fan of Julio Medem’s small but exquisite oeuvre already, but Room in Rome easily made it into the top five of my all-time favourite films (where it competes with Medem’s Sex and Lucia). What, you may ask, makes it so special?

First the set-up – a one-night encounter in a hotel room, which the camera never leaves except to peep out onto the balcony or through the entrance of the room into the corridor. This would work brilliantly in a very small theatre as well. The basic idea is borrowed from a Chilean movie (En la cama) with a couple of very important tweaks. Medem turned the man of the first movie into a woman, and he moved the room to Rome, and embedded it in Italian art history. There are paintings on every wall and even on the ceilings, which play an important part in the movie.

Alternatively, to relate it to a better known movie, one could call it an all-female “Before sunrise” set indoors and in a different city. In one rollercoaster night the protagonists get to know each other and learn to trust and love each other.

So in that room, we have two women, not too many clothes, lots of art, and modern IT equipment enabling them to show each other their outside lives via Google Earth. Oh, and a splendid view from the balcony over the roofs of Rome. (One could have called it Room with a view, had the title not been taken by some other movie.)


(still from official site)

Let’s get the clothes issue out of the way first, as it seems to have scared UK distributors to an extent that they didn’t give the film a chance in the cinemas. Yes, both women are undressed for most of the length of the movie, but after about two minutes that appears completely normal and one stops noticing it. In a sense, considering their respective vulnerabilities and difficult path towards mutual trust and truthfulness, one could argue that most of their nakedness is psychological rather than physical. Seen this way, the cosy white bath robes they put on for breakfast in the end seem to represent the comfort and protection of a trusting (if time-limited) relationship.

More interestingly, the art, chosen by Medem’s wife and art director Montse Sanz, tells us something not only about the story and its possible interpretations, it also offers insights into Medem’s philosophy when Natasha cites the Renaissance artist Leon Battista Alberti, seen in one of the paintings, as saying: “The artist must know at all times what he is representing.”

I would argue that the film contains more classical art than we see on the walls. Many of the poses of the women remind me of paintings – most of them reclining nudes, obviously. Towards the end, Medem acknowledges artworks as a source of inspiration explicitly when he makes Natasha copy the pose of the Venus de Milo, which is present in the room as a small scale model. Come to think of it, with all the gorgeous lighting and colours, many of the frames would make nice paintings.

Ironically, the state of the art IT equipment including a smartphone and a laptop running Google Earth (or the Microsoft equivalent) almost seamlessly becomes as important as the Renaissance paintings, as it’s the only connection to the previous and outside life of the protagonists. Talking of technology, I also love the fact that Alba turns out to be an engineer who came to Rome to plug an invention she made. While she failed to score a contract on this occasion, her business seems to be going ok, judging by the quality of the hotel room she booked. And as Natasha is an art historian, the story could be read as a “two cultures” dialogue as well.

The five languages – some of the most touching moments involve each character speaking their native language (Spanish / Russian), assuming the other won’t understand. But the English dialogue, with just enough of an accent to identify the origin of each character worked surprisingly well for me (I do like my Spanish films and am not necessarily happy if people switch to English). It’s sad and ironic, however, that Medem’s first film to feature dialogue mostly in English wasn’t actually shown in UK or US cinemas. We also get some Italian (via the singing room service waiter) and some Basque via a video, reminding us of Medem’s cultural background (I understand that, genetically, he is as much German as Basque, namely 1/4 each).

The music of Spanish (but English singing) singer-songwriter Lourdes Hernandes, aka Russian Red (a pseudonym she borrowed from her favourite lipstick, apparently) is perfect for the movie, not only because her accent matches Alba’s.

So in summary, buy the DVD, you can’t borrow mine, as I need to watch the movie another five times.






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C'est la lutte finale

I had a crazy week, but finding this made my day:

The illustrations by Gerhard Seyfried with the German lyrics of the Internationale were originally a poster typically found on the toilet walls of shared student flats in the late 70s. Hitching his cartoons up to a recording is a brilliant idea. And of course there is plenty of stuff in there that fits this week's events in the UK amazingly well.

loca loca loca

Have received my copy of Sale el Sol yesterday and played it on closed loop for last 24 hours (OK, I did sleep a bit, too). With the volume up and the bass boost on, I'm expecting the neighbours to come knocking on the door any minute ...



Am really puzzled now - is it me or is this album a million miles better than the English language She Wolf album? It may be that her recent attempts to adapt to the English speaking US market just don't work for me, or it might be that the songs she writes in Spanish are really better (and I mean musically more than linguistically). And to me the gap is much bigger than between the two Oral fixation albums (OF 2 had some really interesting tracks that should have been singles, such as How do you do, and Timor).

Any opinions from fans or others ?

PS really looking forward to the concerts now !

PPS Sony UK is being completely hopeless again. While the CD was available in Germany at the end of last week and in the rest of the world at the beginning of this week, the UK release date is end of November. I ordered mine from Germany, but amazon uk now also has some used copies.

recycling without separating

From today, Oxford City Council introduces a new collection system for recyclables, where all dry recyclable materials go into a blue bin:



i.e. all plastics, glass, cardboard, paper, tins, etc. together. The little green thing takes food waste, while the big green bin is for the residual non-recyclable waste, of which there is very little. The council says it hopes to improve its recycling rate from around 40 % to over 50% with this scheme.

While the new system includes more types of material than the previous one and saves me the trouble to take some stuff to bring banks, I am having trouble to imagine how they plan to separate the stuff out. And after 30 years of separating recyclables, it goes against all my instincts to throw them all in the same bin. Guess our blue bin will be unusual in that it will always contain a layer of plastic, then a layer of paper, then glass ...

bumblebees for Britain

Had a great evening at the Earthwatch debate yesterday, where 5 groups of species competed for the title of environmental mascot for britain, and the bumblebees won:



Left to right: Tony Juniper (song thrush), Stephen Hopper (oak), Samantha Burgess (coldwater corals), George McGavin (bumblebee), Johannes Vogel (bluebell), and host Andrea Catherwood (a former Earthwatch volunteer).

George McGavin championed the bumblebee pointing out that it is a keystone in the ecological network, upon which many other species depend, and that the 25 bumblebee species found in the UK today represent 10% of the global bumblebee fauna.

Twitter hashtag for the event is#SpeciesForBritain

quince season

Quince season has begun! My little tree has produced a nice crop this year, though not as many as this one at St. Hilda's College, overhanging the river Cherwell (but sadly out of reach):

turning the world upside down

After the Science is Vital demo on Saturday, I revisited Anish Kapoor's mirrors in Kensington Gardens, this time all polished and without fencing. Love the way they inspire people to interact, eg by turning themselves upside down to look at the upside down reflection:




or by lifting things high up to see them in this one:




The clear sky mirror, with its frameless, very sharp border reminds me of Philip Pullman's subtle knife, which cuts windows into the fabric of our universe to give access to parallel universes. In this case, the universe behind the mirror seems to be sunnier than ours:




Couldn't think of much to say about the red-tinged sky mirror, so I hired a duck to swim across its reflection:



The exhibition website isn't finished yet apparently, but you can pick up a leaflet containing a map with the location of the works from the Serpentine Gallery or the Red Pavilion next door.

wine, games, and geometry

Articles out in German this month include circled squares, quiz chemistry, the science of wine, and the computer game that folds proteins:

Die Quadratur des Kohlenstoffs, Chemie in unserer Zeit 44, 317, DOI: 10.1002/ciuz.201090063
abstract and access to pdf
(my blog entry on this story in English)

Ausgeforscht: Quizfragen für Computer, Nachrichten aus der Chemie 58, 1002.

Biowissenschaften: In vino Wissenschaft, Nachrichten aus der Chemie 58, 1028.

Proteinfaltung als Computerspiel, Spektrum der Wissenschaft Nr 10, 16.
full text
(my blog entry on this story in English)

Oh, and talking about protein folding, here's a swan folding back its flexible domain onto the compact core domain:

the song of the potter

Many years ago, I heard an April's fool story on the radio that went a bit like this:

Archaeologists have investigated the banded decorations on ancient Egyptian vases and found out that the potter had been singing during his work, and the vibrations transmitted through his arm were engraved in the vase, much like the early gramophones and the vinyl records. Building a special gramophone for Egyptian vases, the scientists managed to play back the song recorded thousands of years earlier. I think they actually played a soundclip they claimed to be a remastered version of that ancient recording. It was April 1st, though.

In an obituary of the physicist and Nobel laureate Georges Charpak published in El Pais (5.10.10) I now came across this story again, and it was no joke this time. Apparently, Charpak performed experiments to verify whether sound (in his case shouting, not singing) produced by potters could be recorded in the pottery. The paper reports that his colleagues at the institute thought he had gone potty, but sadly it doesn't relate the outcome of the experiment.

intrinsically disordered proteins

Intrinsically disordered proteins in biomedicine, IRB Barcelona, 4.-6.10.2010

Some 13 years ago, Kevin Plaxco told me about an intriguing piece of research done by geneticist friends of his, involving a signalling protein that is exported through the hollow core of the bacterial flagella under construction, until the finished flagellum is closed off with a cap. Writing a News and Views commentary for Nature, we discussed this system as a prime example of a protein that has to be unfolded in order to carry out its biological function (The importance of being unfolded, Nature 386, 657-659, 1997, PDF).

We weren’t aware of any other literature specifically discussing this issue at the time (we missed one paper that had used the horrid terminology “natively unfolded” which we hadn’t thought of), but there were already a few examples of other proteins to discuss in this context. Incidentally, the geneticist authors of the paper we pegged our piece to weren’t very interested in the protein folding implications of their work, so we were free to take the issue and run with it.

The new field whose birth we assisted as midwives has grown quite remarkably in the years since, witness the recent research conference organised by the IRB Barcelona, “Intrinsically Disordered Proteins in Biomedicine”, attended by some 120 researchers and held in this rather wonderful building (The Institut d'Estudis Catalans in the centre of Barcelona, 100 metres away from Las Ramblas):



The conundrums that we already discussed in 1997, namely how can you tell that the disorder isn’t an artefact of your experimental conditions in vitro, and how can disordered proteins survive in the cell, are still being kicked around, although on a much higher level. And with more examples: there are now more than 1200 intrinsically disordered proteins (IDPs) listed in the database disprot.org.

The in vivo vs. in vitro question is now being addressed with a range of sophisticated methods that also allow in vivo studies of protein structure (and lack thereof).
To the stability question, an answer is emerging in the shape of the realisation that disordered proteins involved in signalling are often meant to be present only in small concentrations and for a short time.

Technical advances reported at the meeting included he “live” (though debated in discussion) observation of movements of a disordered chain by high-speed AFM, single molecule dynamics measurements by fluorescence, as well as variations on NMR, SAXS, and combinations between these two complementary techniques.

The biomedical applications promised in the title of the conference aren’t quite ready yet, though the fact that many IDPs work in transcription regulation suggests that their understanding will be useful for cancer research. Thus, the much-studied tumour repressor gene product p53 featured in several talks and posters. Amyloid-forming proteins such as alpha-synuclein also feature in the IDP roll call. Also, linear peptide motifs, recognition sites often found within intrinsically disordered regions, appear to serve as prime targets for viruses to mimic.

All in all, definitely a research field to keep an eye on, even though I have to admit sentimental bias when I’m saying this.

PS Other impressions from Barcelona (and Paris) to appear on flickr soon.

london art and architecture

Busy day at London yesterday - saw the Gauguin exhibition at Tate Modern on its first day:



I'm afraid I have to agree with the review in the Evening Standard - a biographical approach would have been more enlightening. Gauguin only discovered art in his 20s and became a professional painter in his 30s, then turned his back on the Parisian art scene to live in the South Pacific. Just how this unusual biography came to happen doesn't become clear in the exhibition.

I caught the tail end of the exhibition "Exposed" as well - Tate Modern offers a very affordable combined ticket for the two events while they overlap. More on that exhibition some other time.

I also visited the allegedly ugliest new building in the UK:




and still find it beautiful. What most puzzles me about the "ugly award" is that if you look round Elephant & Castle everything else (shopping centre, 60s tower blocks) is truly hideous, so the one way in which the "owl" doesn't fit in is that it is more beautiful than everything within a mile radius. (It isn't in fact substantially higher than the surrounding tower blocks.) Pleased to see that the Latin American restaurant "La Bodeguita" is still there in the Elephant & Castle shopping centre, it has in fact a perfect view onto the front side of the owl.

And I saw Anish Kapoor's mirrors in Hyde Park:



and the red pavillion at the Serpentine Gallery of which I posted a few (all-red) images on my flickr photostream.

Oh and I had a coffee that was just the right size:



Perfect day.