Sunday, 27 July 2008

Gija Jumulu

Kings Park in Western Australia was gifted a 750 year old Boab tree from the Gija Aboriginals of Australia last week. The Jumulu (meaning ‘Boab’) was transported from the Kimberley region in an overt operation on the back of a large open truck. Settled in its new home at Two Rivers lookout in Kings Park, the tree stands at approximately 14 m in height and just over 2 m in width. Since its arrival, visitors have flocked to view the tree as it protrudes from its enclosure, surrounded by Eucalypts.


Saturday, 26 July 2008

R.I.P Randy Pausch

Randy Pausch, a well-known computer scientist from Carnegie Mellon University (CMU) in Pennsylvania, sadly passed away on July 25th 2008 after a long battle with pancreatic cancer. Regarded as a prominent scientist in the field of computer science, he was thrust into the public spotlight after delivering an inspirational presentation titled ‘The Last Lecture: Really achieving your childhood dreams’, which was delivered to a full house at CMU in September 2007. In his speech he described his childhood ambitions (one which included ‘being Captain Kirk’), the ways in which he achieved them and advised the audience on how to reach their dreams. This humourous yet profound speech, which touched many people around the world, conveyed his positive outlook on life and strong, brave spirit despite his circumstances. His ‘Last Lecture’ speech was released as a book in early 2008.

Below are a couple of quotes delivered in his "Last Lecture" speech:

"The brick walls are there for a reason. The brick walls are not there to keep us out; the brick walls are there to give us a chance to show how badly we want something. The brick walls are there to stop the people who don't want it badly enough. They are there to stop the other people!"

“Experience is what you get when you didn't get what you wanted."

- Randy Pausch

Thursday, 24 July 2008

The Acacia and the Ant

There are many symbiotic relationships in nature. Some relationships are visible: For example, cleaner fish remove parasites/dead skin from other fish and in doing so, provide a meal for themselves and clean the surface of the other fish. Other relationships are not so visible. One such invisible relationship occurs between the Bullhorn acacia and the ant. The Bullhorn acacia gets its name from the thorn-like structures on its branches, which resemble horns of a male bull. Unlike most acacias, the Bullhorn acacia lacks the bitter alkaloid which would normally protect the tree from attack by insects or grazing livestock. To compensate for the lack of this defence mechanism, the Bullhorn acacia produces protein-lipid nodules (Beltian bodies) which are used as a food source by ants living on the tree. These ants, which are harboured in the thorns of the Acacia, use the protein-lipid nodules to produce and secrete pheromones which are picked up as a deterrent by other insects and grazing animals. Furthermore, the ants are capable of a nasty sting which acts as an additional deterrent.

(2) Image: Dan L. Perlman ( /Ant,Bullhorn_Acacia,thorn,Pseudomyrmex,EL_DP162.jpg)

Saturday, 19 July 2008

Look ma, I’m a freelance science journalist!

Well, I don’t know at which point I can call myself this but late last week I scored a job writing articles as a freelance science journalist for an on-line science newsletter. My first article was published on Friday after a hectic but exciting week. My week involved pitching a story, tracking down a voice recorder, attending a seminar to capture the main point of my story, liaising with media officers, conducting an interview, writing the article and then nervously waiting to hear the editor's opinion after submission of the article. I would describe this new experience as an exciting adventure that spiced up what would normally be a relatively mundane week for a laboratory scientist.

Saturday, 12 July 2008

Dance like nobody's watching (Warning: Tear-jerking video clip)

Here’s another New York Times (NYT)-inspired blog post. No extra words are needed to describe this article and video (below) which featured in the NYT on July 10th 2008. Please watch the video clip, read the article and then the numerous comments that follow :-)

Where the Hell is Matt? (2008) from Matthew Harding on Vimeo.


Monday, 7 July 2008

JAMA poetry

I have to give credit (and a plug) to the New York Times (NYT) for initiating this blog post. A few days ago I read an article in the NYT (which may I add is one of my favourite publications right now) which brought my attention to the Journal of the American Medical Association’s poetry publications written by patients, researchers and doctors. While perusing the JAMA, the name it is commonly referred to in medical research circles, I realised that the journal does not limit itself to just scientific publications and poetry, it also publishes book and media reviews (of medical relevance) and short literary pieces describing experiences of doctors (in “a piece of my mind”), among other things. In addition, the cover of the journal (journals have covers?....just kidding) features beautiful artworks of prominent and less prominent artists. I guess this is one of pitfalls of having literature that is easily accessible on-line - we never get in touch with the real thing. Anyway, although JAMA is not related to my field of research, i know that I will appreciate this medical journal for being a bit different to most journals I read.
Below I have posted two profound poems from the “poetry and medicine” section of JAMA.

The Suit
When the time comes to donate your clothes
i will leave the gray check suit in your closet for the foreseeable future.
I'm not so foolish to think that you're coming back and will need it again
rather, i want some tangible item other than pictures documents and death certificates glossy flat and thin.
With your suit i am able to
put my hand into its sleeve
roll my arm in the pant leg
puff out the jacket and feel your silken space.
There's something so substantial in its emptiness
that i need now after five months
when the memories are still strong
but your reality is slowly eroding.

- Frank DeCicco MD

Everything is nervous here, vibrating
to the hum of air conditioning.
Outside, the palms are never still.
Inside, palms sweat in high anxiety.
Even the indifferent chameleon
sunning on the hot veranda
blows his red sac as a warning.
On the Gulf a tropical depression
brews a hurricane. Depression
in this place is deeper still,
this space where hopes die,
wishes fail, silent waiting ends
as the next white-coated person
speaks of trying everything.
And the coldness that comes then
makes the heat of anger welcome,
like the coming storm.

- Robert L Jones

(1) The NYT:
(2) DeCicco F (2008) The Suit. The Journal of the American Medical Association 229(12): 1404
(3) Jones RL (2008) Thermostat. The Journal of the American Medical Association 299(16): 1878
(4) Cover image (2006) The Journal of the American Medical Association 295(9): cover. This cover features a painting by Henri Matisse (1869–1954), La méditation: après le bain (the Meditation: After the Bath), 1920, French. Oil on canvas.

Saturday, 5 July 2008


No, this is not a form of medieval torture nor is it a social/political movement; it is in fact a common medical condition afflicting many people. Bruxism (pronounced brucks-ism) is a physical condition where a person grinds their teeth and clenches their jaw during sleep.

Sufferers of bruxism can often feel the effects of a night of good teeth grinding the following day by presenting with symptoms including headaches, jaw pain, tooth chipping and fractures, and even tooth loss! If symptoms of the condition are not immediate, then overtime-bruxism-sufferers will notice tooth wear. Alternatively some people will not present with any symptoms at all unless the wear and tear is picked up by a dentist. Bruxism sufferers can often be made aware of their suffering by partners and family members as teeth grinding can be forceful and consequently audible.

The cause of bruxism is questionable but it is diagnosed to be a result of a number of ailments including, but not limited to, stress and anxiety, disturbed sleep, sleep disorders, an abnormal bite, large consumption of stimulants (eg. coffee), digestive problems and consumption of drugs/stimulants.

Bruxism is most commonly controlled with the aid of a custom-made splint or mouth guard. This uncomfortable-to-wear guard is made of durable plastic moulded from a sufferer’s teeth/gum impression and stops wear and tear of teeth. Various forms of relaxation (eg. meditation) before bedtime are recommended for sufferers if stress/anxiety is thought to be the cause. Sore mouth/jaw muscles often manifests as a result of teeth grinding so Botox has been proven as a successful form of treatment as it relaxes the muscles in the area and prevents further muscle contraction.


Wednesday, 2 July 2008

Conversations with proteins

Olga Kuchment is a researcher in the Kuriyan laboratory in the Department of Molecular and Cell Biology & Department of Chemistry at the University of California, Berkeley. The Kuriyan laboratory study the mechanism of Src activation at the molecular level. To find out more about the Src proteins, Olga decided to interview the v-Src protein. With Olga’s permission I have posted the transcript of this entertaining and ingenious interview (which i highly recommend reading) as it appears in “The Scientist” (Proteins gone wild, 26th June 2008).

The Src protein helped teach the world about the molecular basis of cancer. The animal Src protein, c-Src, was first discovered because its mutant, v-Src, was spread among chickens by the tumor-causing Rous Sarcoma Virus. Both proteins are tyrosine kinases, cell signaling enzymes that activate other enzymes by moving a phosphate from ATP to a tyrosine amino acid. Animals require c-Src activity for proper bone development and T-cell development and activation, among other things. c-Src is only active when it receives specific cellular signals, but v-Src is less inhibited and much more active.

The two faces of Src (adapted from Young et. al., 2001.)

My lab mates and I here at the University of California, Berkeley, study the mechanism of Src activation at the molecular level. Unable to reach c-Src for this interview, I invited v-Src, a very dynamic molecule, for a drink at our local pub. The protein got a little tipsy, and it was waving its phosphorylated activation loop like mad.

v-Src: You know, I'm the most important molecule in a Rous Sarcoma Virus infected cell. I help cells ignore signals to die, or help them divide uncontrollably and invade healthy tissue.

Kuchment: That is impressive! One type of rogue molecule can cause incredible damage. I know the DNA that codes for you has some mutations, which is why you always misbehave. But what causes the overall genetic instability in the infected cells, making them accumulate more and more mutations in various cell signaling proteins?

v-Src: That's not very interesting. Let's talk about me.

At this point, we were unexpectedly joined by c-Src. Not noticing that v-Src was there, it came directly toward me. c-Src takes extreme care in its appearance; not a single loop was out of place. Its SH2 and SH3 domains were docked neatly behind its kinase domain.

c-Src: Kuchment, I've been looking for you. I am outraged. People have no appreciation for the good work my family and I do. We work toward cell proliferation, differentiation, survival, and when necessary, cell death. All I ever hear is that I'm a target for cancer drug design!

Kuchment: I apprec...

c-Src: The name "Src" is just a throwback to "sarcoma." I have nothing to do with it. For every one of us that gets out of control due to a couple of mutations, there are millions that do their jobs carefully. Just because v-Src was the first to be studied doesn't mean it's representative of all of us!

Kuchment: I agree, and I'm a big fan of your work. I've been studying your regulation for several years, as you know.

A pregnant pause.

c-Src: Thank you, that means a lot. But I can't stress it enough: I am not affiliated with v-Src. At first we were the same, but when the Rous Sarcoma Virus stole a copy of the src gene from a chicken cell, it cut off the tail and made several other mutations. As a result, v-Src is completely unregulated. It phosphorylates its substrates always, without paying attention to signals from proteins like Csk. Oh, v-Src! I didn't see you there.

v-Src: Are you jealous of the way I live? I'm free, and you're just a tool. You live your life in the service of the cell. And you spend most of it sitting around with your tail in your SH2 domain.

c-Src: Leisure is underrated.

v-Src: Your regulatory domains hold you back! Your SH2 is bound to the phospho-tyrosine in your tail, your SH3 is bound to the SH2-kinase domain linker, your kinase domain is inactive, and stuck that way!

c-Src: That's simply because I'm waiting for a signal from someone like a growth factor receptor tyrosine kinase. Once the regulatory domains are bound by the right ligand, they release, then my activation loop is more likely to get phosphorylated so that my kinase domain can become more active. You wouldn't understand.

v-Src: Give me your activation loop! I'll phosphorylate it, and...

c-Src: Sorry, maybe some other time. My activation loop is tied up right now.

v-Src: Then I'm leaving. But I'll get you later!

Kuchment: c-Src, as you know, I've been studying how you move from the inactive state to the active. Could I see it?

c-Src: Ah... No, I really can't stay. I have to catch a vesicle to the cell membrane.

Kuchment: Wait! Let me see! What happens to the SH2 and SH3 domains, how do you move the alphaC-helix in, and what do you do with the activation loop? Oh, darn.

So it went. Maybe the pub wasn't the best place to get serious answers from tyrosine kinases. I decided to finish my drink and go back to the bench.

Source: The Scientist, Proteins gone wild, 26th June 2008