modelling the immune system

I heard an interesting seminar this week, on the efforts to better understand our immune system by modelling its function with computer programs. There is an EU-sponsored project underway, called Immunogrid (because it uses computer grids to model the immune system).

The web portal also provides access to educational resources where you (teachers, students, pupils, anybody, really) can have a play with the computer programs.

2007 reviewed

This time last year I did a review of research news of 2006, and as that turned out to be great fun, I did it again this year.

On page 26 of the current issue of Chemistry + Industry, you'll find my take on:

* genomes ranging from those of Watson and Venter through to the grapevine;

* chemistry in outer space;

* nanofluids;

* winding back the development clock;

* ... and immortality, of course.

Also, in the same issue, a book review of the tome: Nanoscopic Materials -- size-dependent phenomena. Enjoy!

Methane eaters from the gates of hell

Cows produce lots of methane, but our planet itself exhales large amounts of the greenhouse gas, too. Certain bacteria can use the geologically produced methane as a fuel and turn much of it into biomass – a very laudable contribution to our current concern of minimising greenhouse gas emissions. Soils in volcanic areas are often hot and acidic, so any bacteria gobbling up methane in those areas would have to be adapted to these extremes. Decades of research have failed to identify any species that can thrive on methane under such conditions, but now two independent research groups have simultaneously found two of them, and hints that there may be many more.

Researchers from Nijmegen in the Netherlands and Naples, found Acidomethylosilex fumarolicum in hot, acidic volcano mudpots in Italy. This bacterium can thrive in extremely acidic conditions, down to pH 0.8, and its preferred temperature is around 55 deg. C. Surprisingly, it is unrelated to any of the known methanotrophic bacteria, which are all found in one of two large phylogenetics groups, the alpha and the gamma proteobacteria. A. fumarolicum appears to belong to the phylum verrucomicrobia, only very distantly related to proteobacteria. The microbe hunters tracked it down by looking for a key enzyme of methane metabolism, methane mono-oxygenase. Eventually they found three copies of the corresponding gene in A. fumarolicum, but they were quite different from the ones in known methane eaters, explaining why the extreme bug hasn’t been found before.

Conversely, microbiologists from New Zealand, Hawaii, and China, using samples from a geothermal area known as Hell’s Gate in New Zealand, cultivated a microbial strain first, which they baptised Methylokorus infernorum, and which can metabolise methane at pH as low as 1.5. Being unable to identify the methane mono-oxygenase enzyme in this species, they went on to sequence its genome (as you do, these days) and found three copies, again. Like A. fumarolicum, this new methane eater is classified off the beaten track of methanotrophs, in the phylum of Verrucomicrobia.

Now that we know what acid-loving methane eaters look like (genetically speaking), there may be many more new species to follow. The Dutch group has already looked at unrelated samples from Yellowstone National Park (US) and found evidence that similar extremophiles live there, as well. Although they have failed to be discovered for decades, these bugs may in fact be widespread.

References:
A. Pol et al., Nature 2007, 450, 874.
P. F. Dunfield et al., Nature 2007, 450, 879.

Related books:
Life on the Edge: Amazing creatures thriving in extreme environments
Astrobiology: a brief introduction

NB: This story is a blog-exclusive one. From now on, I'll label such stories with the tag "sciencenews", while those published elsewhere have the tag "sciencejournalism".

embedding slide shows

I don't know much about slide, but I'm wondering, if I embed this code I found in Adri's slide page into my blog, will I really get a copy of her slide show?

Let's try it out:

PS woo-hoo, it works ! now I'll see whether I can do that in myspace too :)

a US general in the family ?

Way back in the early 80s, when Ronald Reagan kindly offered to station lots of Pershing II missiles in Germany, and we were involved in the movement trying to stop that from happening, we used to joke that the general John Joseph Pershing after whom the missiles were named, might be a relative of mine, as my great-grandmother was born Pfersching.

Now I've had a closer look at this, and while I can't quite prove it, the possibility appears to be quite real. The general, like most of the thousands of Pershings in America, is a descendant of Frederick Pershing (1724-1794), born Friedrich Pfersching in Alsace, who sailed from Amsterdam to Pennsylvania on the ship "Jacob" in 1749. While there is lots of information on the lives of Frederick and his descendants, I have found nothing whatsoever on his ancestors. Except that family traditions say they were French Huguenots (as the name Pfershing is definitely German, this tradition may refer to maternal lines?!)

My eponymous ancestor in that generation is Johann Leonhard Pfersching, who married Margaretha NN in Flehingen, Baden (just across the Rhine from Alsace!) in 1759. His father Johannes Pfersching was a cartwright, but I have no further information about him.

So beyond the name and geographic proximity, evidence for any link remains to be found ...

Update 2022: many years later I discovered in my possessions a French postage stamp showing General Pershing:

is heme a hormone ?

Well, the short answer is: probably not.

But this is a long story, and an intriguing one (at least for people interested in protein biochemistry). I spent much of this week researching, writing, rewriting etc. the news item which is based on a paper in Nature Structural Biology, this press release, and communications with five different experts in the relevant fields. Essentially, the researchers found that heme (or haem), the cofactor in haemoglobin and other important proteins, binds to the receptors REV-ERBalpha and REV-ERBbeta, which were known to influence circadian rhythm, but were "orphan" receptors, meaning that nobody knows which hormone controls them.

In the paper, the researchers just report that heme binds the receptors, suggesting it may have a signalling role linking metabolism and the biological clock. No objections so far. In the significantly sexed-up press release, however, heme is referred to as a "hormone" and all kinds of wonderful medical applications are promised. The trouble is, hormones normally travel around and convey information from one cell type to another, and there is no evidence of heme doing that. This aspect is discussed in detail in my news piece.

After the piece was finished I hit on another fly in the ointment. I found out that there are two crystal structures of the REV-ERBbeta ligand binding domain in the Protein Data Bank, which the authors of the NSB paper hadn't mentioned to me. According to the crystallographers, these structures include the hormone binding site. Now the authors of the heme paper say that the crystal structures don't include the heme binding site which they confirmed by mutagenesis.

So if heme binds in a place that is distant from the hormone binding site, to me that says loud and clear that heme is not the hormone that regulates REV-ERBbeta. If anything, it is a co-regulator, and the receptors are still semi-orphaned.

Oh, and the claim for medical applications isn't much better. I wouldn't want to take a drug that competes for heme binding sites. I guess the take-home lesson is never to trust a press release ...


PS, the whole heme story reminded me of a classic Irving Geis illustration, where heme is shown as the light source illuminating the protein cytochrome c from within. The picture is shown here as Fig. 2.

found in translation

Not many books, it appears, get translated into Arabic, or out of Arabic, for that matter. Now, the Kalima project aims to get 100 books each year translated from Western languages into Arabic by providing grants to pay for translation work and rights. I think a quarter of those books will be about science, but I don't think they'll bother with mine. In the long term, the project will also improve the success of works written in Arabic by getting them translated to other world languages.

local authors

Writers in Oxford, our local writers' club, has about 200 members I think. Until recently, there were three of us living in my street. Mary, who interviews authors for the local newspaper, Tilly who writes erotic fiction, and myself. Here is Mary interviewing Tilly in full swing.

The most prominent member of our club right now is Philip Pullman, of course. The new movie "The Golden Compass" is based on his book "Northern Lights", and interviews with him are currently practically everywhere.

all things german

here's the monthly roundup of publications in German. This time I made fun of the people inventing pointless new names for companies (they are practically asking for it!) and covered the Nobel prize for knockout mice:

Groß M:
Nachrichten aus der Chemie 55, Nr 12, 1185
Kreativität und Selbsterneuerung

Groß M:
Spektrum der Wissenschaft Nr 12, 20-22
K.o.-sieg für Mäuse und Menschen

Also, a reminder that my German blog on the WissensLogs site is here:

http://www.wissenslogs.de/wblogs/blog/gro-klein

flash memory stacked higher

To me, the introduction of the USB stick (flash drive) was the point where the boundaries between technology and magic started to blur. How on Earth do you squeeze a 2 Gbyte memory into that ?

Now, scientists in Korea have developed a way of multiplying the capacity of flash memory devices, using stacked layers of nanoparticles. Read my story

here.

The story also gave me a chance to catch up with the fast-moving technology/magic boundary and to understand (for a fleeting moment) what a flash memory is and how it works. Don't ask me now, though, the moment has passed and I have a new story to write up.

drugs and mental illness

deutsche Version

I can get quite furious about certain parts of the media that want us to believe that drugs (e.g. cannabis) cause mental illness (e.g.schizophrenia), when there is absolutely no evidence at all that the observed statistical link is causal in this direction. There are at least two other interpretations of the same data, namely

1) that an as yet undiagnosed, early stage mental illness makes people more likely to try and enjoy mind-altering drugs, and

2) that both the mental illness and the drug addiction are consequences of the same or similar neural disorders.

A paper in Behavioral Neuroscience, published by the American
Psychological Association (APA), now presents evidence that -- at least in rats -- damage to the amygdala has effects that support explanation no. 2.

Wouldn't it be nice if this could put an end to the headlines screaming that drug X "causes" mental disease Y ? Sadly, I guess that this will be largely ignored by the press. (I proposed a news item on this but was turned down!)

earthwatch

One of the perks of living in Oxford is the fact that the headquarters of Earthwatch Europe are here. Over the last few years I did a few nice stories about Earthwatch in general and about specific research projects.

Yesterday I popped round to the office to talk to Mark Huxham about his mangrove studies in Kenya and in Sri Lanka. See whether I can get a story out of that, too.

PS I forgot to mention that mangroves are a nice example of life under extreme conditions (high salt concentrations in tidal swamps) that I was unaware of when I wrote Life on the Edge. One day I'll need to write a sequel to that, to incorporate all the things I've learned since it appeared. "Life on the Edge and Beyond" would be a catchy title for that ....