Holliday junction resolution resolved to solve cancer problem

Sometimes I wonder where the breakdown in communication between scientists and journalists lies. In this article about a recent study on a DNA damage checkpoint enzyme, the Beeb describes the study as such:

Research into how the human body repairs damaged DNA has been described as a "major breakthrough".
The way that cells protect themselves from diseases like cancer has been the focus of a study by scientists at Dundee and Leeds Universities.

The enzyme studied¹ indeed has a crucial role in DNA damage repair, a mechanism that prevents the DNA in cells from getting more and more mangled with every replication cycle. But to conflate a study on structural analysis of a bacteriophage² enzyme with cancer in humans annoys me a little. It's sexing up the topic beyond its current reach³.

Some of the responsibility for conflation of basic science with translational/clinical applications lies with scientists. We have to justify what we do: to the funding agencies, to our peers, to the editors of journals, and to the public that ultimately funds our research by taxation. So everything we do has to somehow, however tenuously, be tied in to some disease or some way to make human life better⁴. So every time we publish our findings, we make that link, however thin, to some major health concern: cancer, heart disease, obesity, cancer, diabetes, cancer, auto-immune diseases, cancer, blah blah blah. And the journalists, with their need to write an interesting article, take a lot of our fatuous crap on faith. Don't ask for solutions. I have none. I am guilty of the same damn crime.

¹ Sorry, it's not open access. You're unlikely to be able to read the full thing outside of a first world university/college. It's a bugger isn't it? Incidentally, does anyone else get annoyed that they don't link to the studies in PubMed or even list the first author? Then again, if they had, I wouldn't have seen via PubMed that one of the authors, David Lilley, has published in both Nature AND Science in the space of a week. That's rare.
² Bacteriophages are a type of virus that "infect" bacteria. Yep. Even bacteria get viral infections. Isn't nature amazing?
³ Don't get me wrong. I think this structural analysis of the protein is a great step forward in understanding how DNA damage repair works. The next step may happen yet. I just don't think the next immediate step is preventing cancer.
⁴ Caveat: I refer here to research funded by the Medical Research Council in the UK or the various National Institutes of Health etc in the US. My world is very narrow.

Gene targeting ruined my life

While we're blathering about science, the recent award of a Nobel prize to Mario Capecchi, Martin Evans and Oliver Smithies made me remember how much I used to curse their blasted brains during the PhD years. You guys deserve a Nobel prize for making 3 years of my nascent scientific life hell. Then again, without your pioneering work, there'd be no work for the skill-less people in the world like me.

Intelligent female scientist seeks solution

I've been thinking about the future¹, my place in it, and my place in scientific research. Having bored myself silly with self-centeredness, I looked further afield. Back in July², Professor Greenfield was deploring the lack of female scientists in the higher echelons of her profession. She makes a few fair points, but, as can only be expected with such a complex problem, has no solutions. I'd only add that many male scientists face the same problems as female scientists³: publish or perish, wave farewell to a life outside the lab, bid your aging reproductive organs good day and goodbye⁴, watch all peers ascend on the property ladder while you slum it out, suffer from intense self-doubt⁵, blah, blah, moan, whinge, whine. Oh, we're back to self-centeredness again. Regardless of the problems and lack of solutions, I got a darn good laugh out of this comment to Prof. Greenfield's article:

"Maybe women scientists are that much more intelligent so they realise that as a career, scientific research is a joke?" --WinstonTheChair

So true.

¹ And no, it's not orange.
² When my head was so far down a microscope there was no light input save that of the very expensive laser. And no, it wasn't orange either.
³ I should know; I live with one.
⁴ Granted, this is more a problem for XX than XY. But without XX, XY in a partnership with a scientist XX can't do much about it.
⁵ Believe me, even the most arrogant of scientists has moments of self-doubt. There is perhaps, though, a reciprocal relationship between success in science and self-doubt.

Step right up; predict a promoter and win...

Win what? Well, nothing more than a few months of hard work, hopefully followed by a nice wee paper...

We're in the mood for science on akatsuki talks rot. Perhaps this has come about since I've acknowledged that I will always be a mediocre blogger, but I could become a better science communicator if I practice writing about things I work on more. And all that stuff about the bloody Viagra-jet lag story (and the media coverage of it) made me realise there is a middle-ground for scientists in the know to discuss hot topics without resorting to the extremes of technobabble (which we're used to applying in our daily work) nor the overly condensed data-free reportage by the media.¹

I've toyed with the thought of using this blog to practice writing mini-reviews of interesting published scientific studies, but have been to lazy to date. This may continue, or it may not. But given that nobody actually reads this crap, it doesn't matter. (Hi P! You still reading this surreptitiously? I have a site counter, you know...)

At any rate, since my laptops have a tendency to die after a few years, and I'm not very good at backing up non-essential data, here follows an email I spent a good 15-20 minutes on this evening to a colleague. I think I was being Ms Good Postdoc, but I often fear that I don't give good advice. Time will tell.

The premise: a friend of a colleague needed a starting point for a promoter assay s/he is planning.

My reply to the request, slightly edited:

Hi [colleague],
There are several approaches to finding the promoter of a gene. The first would be to do a quick literature search to see if anyone has already determined the components of that gene's promoter.
If not, the second approach would be to retrieve the gene information from a genomic database (like Ensembl or the UCSC genome browser). These two sites are particularly useful because they allow very quick and easy comparisons across species (e.g. human/mouse/rat/fish). Such comparisons often show what sequence is most conserved: usually the exons and any regulatory elements that are essential (like promoter elements). This only works some of the time and will only highlight very conserved regions. There will be species-specific differences in promoter sequence.
The third, slightly more laborious approach, is to take several kilobases of sequence upstream of the first known exon and perform a promoter prediction. This has become relatively easy on the internet. A quick Google search found these possibilities.
Of course, the difficulty is in choosing one. I cannot recommend one over the other because I haven't tested them myself. There is one particular site I know of that is quite easy to use: Promoter 2 prediction. It looks for known promoter motifs based on already studied PolII promoters.
After that, your friend will have to make the decision of how much of the promoter to clone, and how many different construct lengths he/she wants to try. I guess it will also depend on the restriction sites available in the sequence and how big the sequence is.
As for getting the DNA, it can either be cloned by PCR if it's very small (around 10kb), or it can be "cut" out of a BAC (bacterial artificial chromosome) or PAC or cosmid (large-capacity plasmid) that already contains the genomic region (can be bought from places like the BAC/PAC resource or Invitrogen or Roswell depending on species). The restriction digest method is preferred because it will have no additional errors, and it is also easier to change the length of the promoter region by choosing different restriction enzymes. Some people even use the entire BAC and make small deletions to eliminate predicted regulatory elements.
I hope this is will be helpful in getting your friend started. The real difficulty will be making the construct and testing it; I wish your friend the very best of luck with this!

After sending it, I read what I wrote² and thought: goddamit, it's all too simplistic. They probably already know all this crap and were probably looking for something concrete. Like a real protocol. Unfortunately, for this and quite a lot of the other molecular biology I do, I do it on the hoof. At some point in the last 10 years, I followed somebody else's protocol (usually the postgrad/postdoc/technician I was asking advice from at the time). Then found alternatives, some of which I now use routinely, some of which I was too lazy to follow-up. Then I switched specialities. Twice. Now, I am used as a mol bio repository by my (ex-)lab. They sometimes even think of me as an expert. But a real expert wouldn't feel so fraudulent in giving advice, would she? Self-doubt creeps in... Oh what if I've screwed up somebody's project giving bad advice?

¹ I'm in no way implying real media gets it wrong (although some, like the gawd-awful Daily Mail, get it wrong and deliberately so!); just that they make the assumption that folk just want the headlines. Which may be true. But not this particular folk or her ilk.

² And after writing this post, I read it and thought: WTH? Why can't you stay on topic? I give up. It's time for dinner.

No sex to have babies? We all want some of that!1

While I'm in a mini talk-about-science mode, have a look at the female hammerhead who didn't need a male (Is anyone else bothered by the way these news articles never provide a link to the scientific article being quoted? I've had a cursory look at Biology Letters and can't find it. This bugs me because I can't accept it on the word of a journalist; I need to see the data. And I'll forget by tomorrow to have a look for the published article again.)

Parthenogenesis, the somewhat sci-fi process of asexual reproduction, even in vertebrates doesn't particularly surprise me². What does surprise me is that they didn't ask DTB for a quote³...

¹ Or is it the other way round?

² But it makes me think again of why we (as in the generic we) evolved to require sexual reproduction, why parthogenesis doesn't happen more often, and what have those "Red Queen" proponents been up?

³ For P's benefit...

Viagra enhances... jet-lag recovery

BBC picks up on the hot jet-lag study of the day: Sildenafil accelerates reentrainment of circadian rhythms after advancing light schedules, PNAS U S A, 2007.

Some initial thoughts:

• It's not so much that Viagra, saviour of many a marriage, is the new wonder-drug that will eradicate jet-lag a la melatonin, but that it works via a pathway already known to have an effect on jet-lag.
• Viagra works through the NO/cGMP/PKG signalling pathway (explanations may follow if I can be bothered)
• At least one component of this pathway, protein kinase G (PKG), has previously been shown to modulate the "speed" of reentrainment¹ (aka switch to new timezone). Update: The same group has shown the involvement of the pathway in phase shifts before too, but I was being lazy earlier.
• Work has probably already been done on this, but this is a nice example of the difference between phase advance (flying east) and phase delay (flying west) mechanisms. (Sildenafil appears to shorten the time it takes to adapt to flying east)
• Does the media have someone sit by PubMed and trawl through it for interesting stories²?
• Why can't I think of cool experiments like this?³

Maybe more on this later. While the world gets excited by yet another use of the blue pill, I still have to ask people for money to fund my somewhat less titillating work. Hmm... Maybe I can incorporate this into my grant application. But somehow, I think jumping on the bandwagon will not go down so well. If only I could think of a clever selling ploy to convince reviewers of the importance of my work⁴.

¹ This is just one of many examples; I'm too lazy to dig them all up right now.

² For interesting, read: involving sex, drugs and rock and roll. Titillation galore!

³ Well, the thought struck me when I read a colleague's paper on our common model and he mentioned how Viagra worked via the same pathway as the molecule we work on. But I didn't act on it because... I am not as inspired as these clever folk down South.

⁴ It's perhaps not commonly known (or rather, I didn't know this when I was a lot younger and a lot more naive) that scientists also have to be good salespersons. It's obvious once you get to the post-graduate level (or before if you're somewhat less cossetted), but the more I get into this, the more I wonder about whether the amount of bullshitting that is done is actually detrimental to the science (even though it is currently the default; no bullshit, no funding). But this mini-rant deserves a full post at some point. Not now. Not until I've finished prostituting my work.

No enzymes here unless you want enzyme-linked immunosorbent assays

Can anyone tell me what the hell an akatsuki enzyme is and why it keeps popping up in my keyword search¹? Is this predicting the day that I discover a new enzyme and egotistically name it after myself? Or is it some crappy New Age bullshit treatment²? You will be sorely disappointed if you're here for that. If anything, I should be joining Ben Goldacre in rubbishing these pseudo-science pieces of crap that purport to make people's lives better when all they do is make them poorer.

¹ Statwhore admission: once in a while, I look to see if anyone from an interesting country has stumbled onto my insignificant spot on the www. And I was slightly surprised to find a Kiribati ISP in the collection this week. Hello. I hope I wasn't overly offensive with that silly off-the-cuff remark about coconut oil. And how are the Atollettes?

² For the record, I enjoy the occasional reflexology massage. I don't buy into any of the claims of direct linkage of my big toe to my brain, ok? It's just a damn foot massage. It feels nice when you've spent the whole day standing while doing experiments to go home and massage your foot. Or hire someone to do it for you. There are no other significant health benefits.

So, the kryptonite story is old hat now. But the article made me wonder why the makers of Superman Returns used "sodium lithium boron silicate hydroxide" as the chemical formula for kryptonite when we already have an element named krypton (Kr), which they could easily have faked a compound name with. They missed a trick there. (Unless there's some kosher DC Comic reason for it.)

fundamentalism

is a dangerous thing indeed. we live in dark times, my friends

eggcellent scare story

From the Scotsman: EU warns of bird flu danger in chicken and eggs.

Ah ha ha ha. I laugh in the face of danger and will have a soft-boiled egg for my supper tonight. Take that, Mr/Ms Scaremonger Media. (The key question is: how will this affect spiceone's and cooksister's EoMEoTE?)

Useless piece of science trivia for the day: the annual vaccine for "regular" flu is harvested from vast quantities of deliberately infected fertilised poultry eggs, the supply of which is now under threat from the new strain of avian flu. Oh the irony!

P. M. S.

The acronym that many men fear...

A sudden slew of papers in the last week on the subject of the female hormonal cycle, which all try to explain why some women behave differently prior to their menstrual periods. This is a phenomenon with which hetero men use to explain away what they think of as irrational behaviour in women. And how many have witnessed foolhardy men asking a woman: "You on your period, or what?"?

Silly human behaviour aside, some people take the issue of PMS and its associated behaviour quite seriously:

• Hormonal Cycle Modulates Arousal Circuitry in Women Using Functional Magnetic Resonance Imaging, by Goldstein et al. in the Journal of Neuroscience this week. Their findings? That MRI scans showed an increase in acvitity in the parts of the brain involved in the stress response in the early follicular phase (i.e. start of the menstrual period) when the women were shown unpleasant images. (This was, honestly, quite a yucky paper to read, stuffed to the gills with jargon and completely free of clear statements of facts... In fact, it reminded me of those crappy business-speak articles, and of the Dilbert comic strip. Someone really needs to send up scientists the way Scott Adams has with the cubicle-world...)
• PMS brain, an article about the work of I. Mody at UCLA (I know... add an "o"... You'd be surprised how many scientists have very fitting names for their subject matter... Mine is one too...). This isn't a paper, which makes it SO much easier to read, and more understandable too. OK, I'm a little biased because they do some REAL science here, looking at the different ways neurons fire electrical signals at different parts of the ovarian cycle, and not that hand-waving guesstimation of brain imaging (I'll eat my words soon, no doubt). They found that a receptor in the brain actually changes its subunits (the components of the receptor), which causes changes in intensity of electrical firing in the neurons. While it's not very accurate to compare a rodent's oestrus cycle to a human, this could provide a mechanism for the above finding. The paper's here if anyone's interested.

So, essentially, the cycling hormones can cause changes in brain activity, and as such, lead to behavioural changes. The mechanism proposed by the second paper suggests a reason why different women have different responses to their fluctuating hormones, with some suffering from depression while others become more aggressive. All still pie-in-the-sky though...

Changing drug resistance of the AIDS virus

From BBC news: Aids virus 'could be weakening'

I'm not familiar with the HIV field of research, nor have I read this particular paper, but I strongly suspect that this refers to a small cohort, probably in Belgium (facts need to be checked when I have access to the paper). The way the AIDS virus is spread probably means that in different populations, the strains are vastly different. While it sounds like the recent viral samples they've extracted from their (untreated?) patients are more sensitive to drug treatment in cultured cells than virus samples collected 15-20 years ago, there's no guarantee that the viruses in other populations are undergoing the same "attenutation" (or weakening). While I'm happy for those who have the weaker, more treatable, virus, I've seen reports that the exact opposite is happening in other studies, where an increase in drug-resistance is seen.

Let's just hope those who pretend that AIDS is an epidemic that will just go away of its own accord fail to latch on to this particular finding.

Update: The BBC page has an audio link to an interview with Dr. Eric Artz. In summary, he refers to the way viruses lose pathogenicity (i.e. are less lethal) over time as the mechanism for survival of the virus. And suggests this may be happening with HIV-1, and could mean the virus will cause fewer fatalities in several decade.

My understanding: With viruses that are dependent on their hosts to survive and replicate, the adage "survival of the fittest" is not always true. A super-strong virus that ends up killing its host soon runs out of warm bodies to infect (in an idealised world, where local populations stay local and don't move about too much...). Case in point: the ebola virus. My guess is that these viruses die out with their local population of hosts, and the weaker mutants, which don't cause immediate death, will survive another day to infect another host.

Update 2: Having skimmed through the paper, it looks like they looked at two different scenarios: one where they allowed pairs viruses to infect cells in culture and compared the historical and recent viruses' abilities to replicate in competition with each other (indicator of their pathogenicity, don't know how it works), and another where they treated uninfected cells in culture with entry inhibitors, then infected them (measure of drug-resistance).

Their findings? Recent viruses are less "fit", and lose out in direct competition with the historical ones. And recent viruses are a little less able to infect cells treated with entry inhibitors.

[Disclaimer: This is super-simplified and over-generalised. I really don't know anything about viruses, let alone the ins-and-outs of HIV-1. Other factors to take into account include period, method and range of infection, immune response, disease progress and bloodymindedness of humans and drug companies...]

And as is pretty obvious, I'm work-avoiding... Pseudo-science on a blog being easier to write my own stuff.

Technorati tags: AIDS, HIV-1.

As Darwin turns in his grave

Just catching up on life science news. This article from Nature caught my eye: Intelligent design. The most startling statistics are that:

• 43% of American teenagers believe that "human beings have developed over millions of years from less advanced forms of life, but God guided this process";
• 38% believe that "God created human beings pretty much in their present form at one time within the last 10,000 years or so"; and only
• 18% think that humans have developed from less advanced forms of life, and God had nothing to do with it. (don't ask me where the other 1% went)

As for the theory of evolution as first set out by Darwin (note scientist's use of theory vs hypothesis), I can understand why 33% "don't know enough about it to say", 30% think it "isn't backed up by evidence", with only 37% assured that it is a well-supported theory (this is to do with education, or lack of it). Assuming the 18% who don't hold truck with creationism nor intelligent design are part of the 30% who agree that the theory of evolution holds true, what's happened to the other 12%? (The other assumption is, of course, that the same population was asked both questions... Polls being less reliable that laboratory-based experiments...)

It appears that some teens think Darwin and friends got it right, but still believe that to be compatible with supernatural intervention. OK, that's over simplifying things a bit. The intelligent design argument is that you need not involve theology, and this is how creationism is sneaking it's way back into the classroom. It worries me that there is little common ground between Darwinists and creationists. How can scientists and school teachers explain to their students and the lay public that acknowledging that a deity had nothing to do with our evolution is not being unfaithful to their religious beliefs? Is it PC to say to people with religious convictions that perhaps the tomes they put their faith in should not be taken literally? For me, it seems to come down to a question of faith. I have faith in my own ability to understand and draw logical conclusions from published evidence, and they have faith in their teachings. For me, evolution is a fact, whatever the current hypothesis on the workings of evolution are (i.e. How it comes about. The fact that it happens at all is just that. A fact.). Hey, maybe I should find out if Darwinism is a recognised religion; then we could argue that schools that refuse to teach evolution are discriminating against our religion!

If you want a layman's explanation of how humans came to be who we are today, have a look at a BBC site on prehistoric life: Human Evolution. Then look at BBC's History of Evolution pages for the story of how scientists evolved their ideas on evolution.

Technorati tag: evolution.