Monthly Archives: January 2009

Reactions – Rachel O’Reilly

Posted on by
Reply

1. What made you want to be a chemist?

I was always interested in science even at primary school and developed a real passion for chemistry at about 14. It was also the only thing I was better than my older sister at! Then at university I did Natural Sciences and realised just how interesting and exciting chemistry was. I really enjoy the creative aspect of synthesis and this is really want started my love of chemistry.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

I would be a geologist as I have always had an interest in paleontology and earth tectonics. I think there is so much still to learn about the earth and its history so it would be an exciting and challenging career and also a great chance to see the world.

3. How can chemists best contribute to the world at large?

I hope we can contribute by helping solve some of the technological and environmental problems we currently face. Hopefully we can also engage with the public to encourage curiosity and the development of scientific knowledge.

4. Which historical figure would you most like to have dinner with – and why?

I would like to have dinner with Vincent van Gogh I love his work and would be fascinated to hear his views on modern art and how the world of art has changed since his lifetime.

5. When was the last time you did an experiment in the lab – and what was it?

It was just before Christmas I helped a student with the column chromatography of a radical initiator and it went wrong – they have not asked for my help again!

6. If exiled on a desert island, what one book and one CD would you take with you?

Difficult question as I love to read but I think I would have to take a book by one of my favourite authors John Fowles – probably The Magus. As for a CD I guess The Killers Hot Fuss would keep my spirits up – but I would prefer to take my iPod if possible

Rachel O’Reilly is in the Department of Chemistry at Cambridge University, and works on the design and synthesis of functional polymer micelles and nanoparticles for applications as delivery vehicles.

Science in trouble

Posted on by
Reply

I just discovered that it looks like a major Canadian funding institute has lost its place in the recent Canadian federal budget (see here and here for coverage). I’m wary of saying more than is supported by the limited information that I have, but it seems like a troubling turn for scientific research if this trend continues?! Anyone know more?

Catherine (associate editor, Nature Chemical Biology)

My little black book

Posted on by
1

My sister recently gave me ‘a mini guide to the periodic table’. The interesting fact for today is: Neodymium is magnetic, and in fact NIB (neodymium, iron, boron) magnets are so strong that you can put them on either side of your hand and they will stick. That’s kind of creepy.

Little things like this make me happy to be a chemist. The more I meet people who aren’t scientists (all 3 of them), the more I realize that it’s a privilege to be happy doing what you do.

[Addendum, or a quick note of clarification: I don’t mean at all to suggest that you need to be a scientist to be happy. Rather, I think it’s harder to accidentally become a scientist if you’re not fairly passionate about it. Or, just that I was talking to people who don’t like their jobs.]

Catherine (associate editor, Nature Chemical Biology)

NChem Research Highlights: π interactions, field-effect transistors and ion recognition

Posted on by
Reply

Tuesday already! How time flies… Wait no longer, here are this week’s Research Highlights.

The role of aromatic π-π interactions mustn’t be underestimated — they contribute to many biological functions, including pretty crucial ones like the stability of DNA, or drug binding. In previous studies benzene rings had received most of the attention, but you can now find out how heteroatoms affect these interactions.

How about a high-performance, photosensitive, nanoscale field-effect transistor? It is all possible thanks to the self-assembly of organic molecules into columns within the nanogaps of a carbon nanotube…

When it comes to ion recognition, selective binding to chloride (essential to human health) versus, say, cyanide (notably harmful) is essential. Steve tells us about a receptor that captures chloride and determines its concentration even in the presence of significant amounts of water, like in sports drinks.

And finally… although no metric can really quantify the value of scientific research, how can we estimate the importance of a particular paper? The number of citations? The Impact Factor of the journal? It looks like Google’s PageRank algorithm might be able to help…

Anne

Anne Pichon (Associate Editor, Nature Chemistry)

Reactions – Yun-Bao Jiang

Posted on by
4

1. What made you want to be a chemist?

I became interested in chemistry when I was in high school. I remember that I was quite good at identifying metal species in a solution based on solution colour change and/or precipitation when known chemicals were added, a subject I knew later as qualitative analysis. The most important event that made me want to be a chemist was that in the national examination for entering university I got a very good mark for chemistry, 97 out of 100, which qualified me to study chemistry in Xiamen University, an institution well-known for its chemistry.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

I would like to work as a garden designer. I think gardening needs a nice combination of science and art, and is full of challenges. The major reason for this is that I have been very much impressed by Chinese traditional gardens like those in Suzhou, and by Chinese calligraphy. Personally, I like and enjoy Chinese calligraphy very much.

3. How can chemists best contribute to the world at large?

The best way is to help understand what happens in many processes involving chemistry in order to guide a suitable handling of those chemicals, and to produce environmentally friendly chemicals.

4. Which historical figure would you most like to have dinner with – and why?

I would like to have a dinner with Mr. Lan-Fang Mei, the most famous contemporary Peking Opera master. He was known at playing the role of and singing as a woman and later promoting the international reputation of Peking Opera. What really impressed me were his perfect performances and amazing voice on the stage, which, in my opinion, shaped Peking Opera very much.

5. When was the last time you did an experiment in the lab – and what was it?

I still conducted experiments when I was just promoted to full professor in 1996, when we started to develop chemical sensing based on intramolecular charge transfer dual fluorescence in micelles, for which I did syntheses of the fluorophores and fluorescence titrations. Even up to now I still like to show to young students skills, such as recrystallizations, and do organic syntheses in my non-organic laboratory.

6. If exiled on a desert island, what one book and one CD would you take with you?

I would bring a book on cooking as I like to cook, it’s a kind of chemistry-related art, and it would be good to help someone in a desert island to survive. A CD of Chinese folk music would be my favourite in that situation.

Yun-Bao Jiang is in the Department of Chemistry at Xiamen University, and works on electron/proton transfer photophysics and supramolecular photochemistry for molecular recognition.

Learning to learn again

Posted on by
1

A while ago I posted some ideas about ‘people who know things’ and ‘people who look things up’, with a minor reference to ‘people who don’t know anything but pretend that they do’. I thought it was time to talk about those people.

Upon further reflection, I think a better name for this category of people is ‘people who seem to know things, but don’t’. The question then is whether the person knows they don’t know the thing (and are exaggerating what they actually know for their own reasons) or doesn’t (and thus is genuinely trying to be helpful). This also makes me think there should be a category called ‘people who don’t seem to know things’ (which would then be broken down into people who do know things but aren’t convincing and people who really don’t know things… however, that’s a topic for another day).

It’s hard to quibble with people who are trying to be helpful, although I have run my share of wild goose chases inspired by some well-intentioned coworker. It’s easier to quibble with people who are aware that they might not have all the information, and yet pretend to be knowledgeable. My sympathetic interpretation is that they are scared to admit they don’t know things. This reminds me of the age-old complaint from undergraduates, that when they ask a question in class, they frequently feel like the professor will offer stipulations or qualifications or possible answers when the ‘real’ answer is, in fact, ‘I don’t know’.

It’s funny… though I think this hypothesis is probably applicable to most scientists, it seems counterintuitive: in the broadest sense, our mission in life is to find out things that no one knows yet. So why is it scary? In this job, I have to admit that I have rediscovered my joy of admitting that I do not know things. Since it’s impossible that I could ever begin to know (in great detail) the various topics that I read about every day, I ask lots of questions. People are always excited to explain things to me.

So, what to do about these pretenders? In my opinion, it is great to offer ideas and suggestions, but not at the expense of making someone believe information that’s not correct. So, stop pretending. Feel free to admit you aren’t an expert on everything. Or set a new year’s resolution of being an inquisitive and engaging person and go out and learn what the real answer is.

As a bit of journal promotion, one way that we’re hoping to help people learn things is via a new content type called Primers (see here for the first one, published in our Feb issue which is now online [Hooray, as always], and here for our January editorial, which talks about why we’re doing this). These are perhaps most akin to mini-mini-reviews – short and sweet summaries of basic topics in chemical biology. I particularly wanted to draw your attention to it here because it’s going to be a bit tricky to strike the right balance between topics that are obvious to everyone (not good), topics that are obvious to only some people (good) and topics that aren’t obvious to anyone (great). So if you have a topic in mind – perhaps you went to a talk recently and were lost after the first 5 minutes because some concept wasn’t explained, or perhaps you’ve never grasped the distinction between some related ideas, or similar – let me know!

I’m off to learn what the rest of the day holds…

Catherine (associate editor, Nature Chemical Biology)

Chemiotics: The death of the synonymous codon

Posted on by
3

Posted on behalf of Retread

For years, stretches of DNA not coding for protein were called noncoding DNA. As we came to know more about DNA, sites coding for just where the transcription of DNA to messenger RNA (mRNA) should begin, along with the DNA coding for the RNA in ribosomes were grandfathered in. Then about 30 years ago, we found that most genes coding for proteins contained large stretches of DNA not coding for amino acids at all.

Dystrophin, the defective gene causing Duchenne muscular dystrophy contains 3685 amino acids, but the gene stretches over 2.2 million contiguous positions in DNA. It only takes 11,055 positions to code 3685 amino acids. However the 11,055 occur in 79 stretches (called exons), separated by 78 much larger stretches of DNA (called introns). The whole 2.2 megaBases is transcribed into mRNA and then the introns are lopped (spliced) out by a gigantic protein and RNA machine called the spliceosome, a molecular machine even larger and more complicated than the ribosome (300 proteins, 5 RNAs [see: Science vol. 307 pp. 863-864, 2005]).

Ever since the human genome project ended, people have wondered why we have so few protein coding genes (around 20,000 at last count). The humble E. Coli contains 4300 [see: Nature vol. 385 p. 472, 1997]. Not to worry, we make lots of different proteins from the same gene, by using different combinations of exons – some exons are skipped by the spliceosome when it removes introns. Different tissues (or different states of the same tissue) skip different exons depending on (as yet obscure) conditions, so lots of different variants of the same protein are made. The process is called alternative splicing and is quite common – it happens in 92-94% of human protein genes according to a recent paper [see: Nature vol. 456 pp. 470-476, 2008 and here].

What determines which exons are left in the final product and which are skipped? This is where it gets really interesting. There exist stretches of DNA called exonic splicing enhancers (ESEs) and other stretches inhibiting the splicing in of a particular exon – the exonic splicing inhibitors (ESIs). Where are the ESEs and ESIs found? In the exons themselves.

So what? And what does this have to do with synonymous codons? The commonest genetic disease of Caucasians is cystic fibrosis (CF). Using the 12th exon of CFTR (the gene mutated in CF), when one synonymous codon was switched to another, 25% of the time it resulted in skipping of exon 12 and a defective protein [see: Proc. Natl Acad. Sci. USA vol. 102 pp. 6368-6372, 2005]. So synonymous codons aren’t synonymous at all. A completely different cellular use of synonymous codons will follow in the next post, but why should chemists be interested in any of this?

Because DNA isn’t sitting there passively waiting to be read in just one way. All sorts of new chemistry is involved. There is not enough space in this post for the next two examples, but their chemistry does not involve protein-DNA interaction.

So even if we had 15 amino acids and a stop codon to begin with (as per the last post) we could never give up that extra position and all that redundancy now. We need the coding overkill because it is being used for other things. This work also has profound implications for our understanding of protein evolution. That’s also for next time.

NChem Research Highlights: Straight iron, protein binding and H-graphene

Posted on by
1

Like a cricket pitch with autumnal goal-posts, here’s a small sign of time passing: Research Highlights are now going to be more like 200 words than 250. Why? Because the print version of Nature Chemistry will require shorter stories, so we need to get in the habit now! I hope you’ve enjoyed the bonus 50 or so words per article – you’ll never have it so good again!

So anyway, onto the science. Of the few two-coordinate iron complexes known, most aren’t straight because the sneaky iron atom tries to increase its coordination by latching onto the other bits of the ligands. The tertiary-butyl amide complex recently made, however, IS linear. This gives rise to some slightly odd magnetic properties.

How proteins fold up into their beta-sheets is pretty important, especially because misfolding is implicated in some diseases/disorders. Some aminopyrazole derivatives could prevent misfolding, and now how they interact with peptides has been investigated in the gas phase. This led to all sorts of information about the conformation and H-bonding.

Graphene is the two-dimensional nanocarbon poster-child that lots of people are getting excited about – it’s even on the BBC website. But what if you could add hydrogen atoms to the sheets, and create ‘graphane’? Well…Andre ‘Mr Graphene’ Geim and Kostya Novoselov have hydrogenated graphene and found that it not only buckles up, but also changes into an insulator. Graphene for hydrogen storage, anyone??

And finally…while some things change (JACS has got cover “artwork” [mmm, nice spectra]), other things don’t (the RSC has got a press release with no discernable science)!

Neil

Neil Withers (Associate Editor, Nature Chemistry)

Reactions – Paul Plieger

Posted on by
Reply

1. What made you want to be a chemist?

Three things, really. Firstly I have a love of symmetry and structural – some structures of chemical molecules are really visually stunning. Secondly people kept giving me money and jobs related to chemistry. OK, so thats only two things and that’s probably another reason why I am a chemist and not a mathematician.

2. If you weren’t a chemist and could do any other job, what would it be – and why?

If I don’t think about this too hard I think I would have been an archaeologist. Maybe working on a dig discovering a new tomb in Egypt or a new civilisation in the Amazon jungle. Possibly in the 1950’s, maybe I would need a whip to get out of trouble…

3. How can chemists best contribute to the world at large?

I think we as chemists are already doing a fantastic job at contributing science to the world. From materials science through to environmental monitoring a chemist is in the mix somewhere!

4. Which historical figure would you most like to have dinner with – and why?

I first thought of Jesus Christ because I would want to ask him straight out if he was really the son of God. However, the way that guy talked in riddles I am not sure I would get a straight answer out of him. So I think a less intense evening with Sir Arthur Conan Doyle might be in order. Some fine dining then perhaps a story or two by a large fire in a Scottish castle with some good wine.

5. When was the last time you did an experiment in the lab – and what was it?

About mid-way through last year. I was having trouble getting a strong diffraction pattern on one of our helicate systems, so I thought I would add a heavier anion to it as I thought it might improve the scattering. What I got for my troubles was a structurally characterised encapsulated bromide triple helicate which I liked so much that I promptly made a movie of the molecule twirling around – it’s probably not going to be a motion picture anytime soon though…

6. If exiled on a desert island, what one book and one CD would you take with you?

I think I would take the Bible. It is the sort of book that you can read time and time again and find new meanings and encouragement and there are some great stories in there too. I am sure I would have the time on a desert island to fully digest it! As for a CD I think I would go for some of my favourite trance tracks, something like Dave Pearce Trance Anthems 2008 – a bit of a cheat as its actually a three cd set. Nothing like a good trance track blaring out when you have to build a shelter!

Paul Plieger is in the Institute of Fundamental Science at Massey University and works on projects utilising supramolecular and coordination chemistry.

NChem Research Highlights: Cheap fuel cells, biopolymer threading and biosensors

Posted on by
Reply

Happy New Year! Here are the first batch of Research Highlights of 2009. (Although I should confess that we wrote them last year…)

So, we all know fuel cells are going to rule the energy world soon…but not if they’re stuffed full with platinum and similarly expensive metals. Which is why replacing such precious metals with cheaper ones, like silver, at the cathode is so important. [FYI: I checked out the market and silver is about 100 times cheaper than platinum]

The biological world is full of long chain molecules, like DNA or proteins. How exactly these chains manage to thread through pores – either in enzymes or membranes – is pretty challenging. We’re getting closer to understanding thanks to some clever chemistry: threading a fluorescent polymer through a macrocycle until it reaches a certain point, at which it stops fluorescing. The kinetics of threading can therefore by studied by the fluorescence quenching.

Hyperpolarised xenon has been investigated as an alternative to using gadolinium compounds as contrast agents in MRI – it can be probed directly instead of protons. And now Ivan Dmochowski and colleagues have used 129-Xe as a biosensor that can determine the difference between two isozymes of carbonic anhydrase.

So, apart from the honour of being featured on In the Pipeline, what else have we been checking out in the new year? Steve’s been looking at some pretty pictures, thanks to his former home Lab on a Chip and their Art in Science feature. I’ve been learning how to make your home-brew nice and cloud-free – it’s all down to Stokes Law and a galactose polymer (carrageenan)…

Neil

Neil Withers (Associate Editor, Nature Chemistry)