Monthly Archives: December 2011

Large scale synchronisation of biosensors using synergistic coupling

One of the major hurdles in synthetic biology has been the construction of bio-sensors that are accurate over a large scale and that can be monitored without the aid of sophisticated microscopes. Getting a bacteria to signal in one way or another when it encounters an environmental toxin (or something else) is one thing but getting a colony of bacterial cells to signal together in synchrony is a whole lot more difficult. Orchestrating thousands of colonies of bacterial cell is an entirely different ball-game. Yet this is exactly what a group of scientists from the University of California, San Diego have achieved. They report their findings in an article published in the Advanced Online Publications section of Nature. And this is the article that I want to briefly review over here.

To synchronise the bacterial cells within a colony they tapped into a natural mechanism used by bacteria to communicate among themselves, quorum sensing. However, quorum sensing is only effective over a  range of a few micrometers. So they used a different communication molecule, one that is in the gaseous phase and hence can diffuse quickly to longer distances. But gaseous  molecules are weak and short-lived, being in the vapour phase, they disperse a lot quicker. However when these two communicating mechanisms were synergistically coupled, the results were quite surprising.

To achieve the intracellular coupling they used quorum sensing involving acyl-homoserine lactone (AHL). The principle here is quite simple, each bacterial cell synthesises a certain amount of AHL which acts as an inducer. When this inducer binds with a receptor it causes the expression of certain genes which among other products also include the genes for synthesizing the inducer itself. Thus the inducer is technically inducing its own production, rendering it an autoinducer. However the amount of this inducer molecule, AHL in this case, produced by any bacterial cell is not enough to initiate this positive feedback loop. It is only when that the colony reaches a certain size and when a certain critical concentration of the autoinducer has been achieved, that the expression of the downstream proteins occur. As a result, if you insert fluorescent proteins among them, you get a colony of bacterial cells fluorescing in unison. But mind you, this only gets you a coordinated bacterial colony over a very small range. You need something else to scale this up.

So they put a copy of a gene coding for NADH dehydrogenase ll (ndh) under the control of another lux promoter. Now NADH dehydrogenase II is a respiratory enzyme that produces low levels of H2O2   and superoxide. Now H2O being a in the vapour state is able to pass between the 25 micron thick PDMS walls that is used to separate the colonies. This H2O, being a reactive oxygen species, initiates a defence mechanism in bacterial cells once it enters them. Among the different global regulatory systems that mediate this defence mechanism is one called the ArcAB system, which (lo and behold!) has a binding site in the lux promoter region. Under normal conditions, ArcAB is partially active, rendering the lux promoter partially repressed. But once H2O enters the cell, ArcAB swings into action, thus activating the lux promoter and hence initiating the same quorum sensing mediated communication system and hence synchronising this new colony. Now the researchers did a lot of tests to confirm that it was the external H2O, and not endogenously produced molecules, which brought about the desired effects. Describing them is out of scope here but the results confirmed their hypothesis.

So what it is that they finally achieved? Synchronisation of approximately 2.5 million cells over a distance of about 5 mm, exhibiting consistent oscillation with a temporal accuracy of 2 minute compared to the 5-10 minute accuracy of a single oscillator!

The paper includes a bit more about the construction of an arsenic detecting biosensor using this technique but I don’t think that’s entirely relevant here. For a brief description of the experiment and the potential applications of it, watch the video:

 

 

Merry Mythmas and Happy New Year to all our readers!

– Debayan

 

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A little tribute to Hitchens.

Hiya there, Ankur here.

Sometimes, people turn a blind eye to dogmatism, cruelty and oppression. Hitchens wasn’t one of them. I shall remember his for the passionate and indomitable demeanour with which he stood up for the oppressed, and for his clarion calls against the evils of dogmatism and all the misery it wrought.

I shall remember him for his sharp and acerbic wit, his dulcet tones he brought forth as he spoke, his lucid analysis of situations and events, and for his immense courage, for he countered first hand, fascists in Lebanon and ended up being assaulted for standing up to them, and underwent waterboarding personally and revised his stance on the technique, acknowledging that it is torture and nothing less and because he exposed the sinister facade of the appalling, inhuman attitudes that were espoused by “Mother” Teresa and her contemptible Missionaries of “Charity”. I know that no words that I express shall be able to express the magnitude of the influence he’s had on me, or to express how much I admire him and his work, but I shall try nonetheless, for words must flow and resisting is futile; as should tears, plentiful that they are. I shall remember him for the way he promptly, with wit and the wielding of facts as they comprised a razor, ripped apart the Catholic Church’s pretensions to being a force for good in that famous debate.

His demise is sadder than anything else, but it is also a moment to reflect upon what he brought to the table, his writings, his oratory, and pursuit of freedom were, and are, a joy to behold still, and it is a slight consolation, perhaps, that he will live on through his works and that he will live on through the thoughts and spirits of the people he influenced through his work, which was always marked by finesse, elegance and utter class.

I am slightly glad that I had the opportunity to write to him thanking him for his work with fellow comrades-in-free-thought, and I shall let an excerpt from that letter do my bidding here insofar the significance of his life to me is concerned. “We thank you by avowing our own commitments to critical thought and analysis combined with fearless free speech, which represent humanity at its very best and which have led to some of our biggest leaps as a species in terms of genuine progress. We will carry on defending those values which each of us shares with you and which you have so effectively expounded throughout your inspiring career.”

Here’s to a celebration of his life and to pensive mourning of his passing. It was a life well lived, courageous, influential, and one that has left behind a strong legacy. I can only fervently hope that it will live on, as we seek to earn for the oppressed the freedoms we enjoy but they do not, and to free people from the irrational shackles of society that constrain their freedoms so that they may live full, happy lives free of oppression and suffering.

Christopher, my good fellow, here’s a toast to you, you will be remembered.

Hitchens.

Dear Hitch

Hi all, it’s been a while.

Death is a funny thing. When faced with mortality, people seem obliged to speak up, to take note and pay tribute to the recently deceased’s short time as a person on this planet. I’m guilty of this as well and today has been a perfect example. Last night the world lost a great man. I loved, admired, and revered Christopher Hitchens, but have never really expressed it in words, until now, which is of course a few fleeting moments too late for him to appreciate. Of course he knew he was appreciated by many people like me, and I highly doubt that he would ever have stumbled upon this little article had I written it when he was alive, but it seems a shame that it is only after we have lost someone that we truly appreciate their contribution to our lives.

He was beloved by atheists for his extraordinary and highly entertaining ability to leave his religious debate opponents floundering within minutes, (even if some were ever so slightly too deluded to pick up on it (*cough* Tony Blair *cough*)), but let us not forget the other causes he held dear. An outspoken political campaigner, his relentless fight for a better world was motivating and courageous, and words were his ultimate weapon. It is rare nowadays to encounter such daring eloquence which forces people, blinking, into the harsh light of reality, and pushes them to take action. His unforgiving character dissections of various respected public figures were a much needed second opinion, and often showed that the prevailing view if subject to a bit of scrutiny, is not always accurate.

With the power of his writing, I was convinced that Mother Teresa was a fraud. Please do not think I am easily led. Alas, I had  a lifetime of hearing nothing but praise for her saintliness; certainly for a long time I believed that anyone devoting their life to helping the poor was a good person. In an instant, Hitch changed my mind. After all, he explained so succinctly; she cared not for the suffering of the poor, or for trying to stop the vicious cycle of poverty. He made me comprehend that the religiously motivated charity work was a mere plaster on a wound; hiding a problem away when what it really needs is some fresh air, a fresh approach: ‘the empowerment of women and the emancipation of them from a livestock version of compulsory reproduction’.

‘The Topic of Cancer’ was by far one of the most moving and raw essays I’ve ever read. Even when first diagnosed with cancer, his words did not fail him as they would (understandably) fail so many others. In fact with their rawness, they became stronger and more compelling than ever, as he ever-so-elegantly and valiantly described the process of coming to terms with his newly-stricken state.

More recently, and bravely as ever, Hitch gave a his acceptance speech for the Richard Dawkins award at The Texas Freethought Convention. Whilst clearly weaker in body, with his voice quieter than before but never silenced, his mind was as sharp as ever, and his words still rung true.

At the very foundation of it all, he made me love words and realise their might. He made me want to take action and speak out; he was one of the people who encouraged me to write in the first place. What an exciting life he must have lived. I hope to narrate my own life even half as well.

Juliet
xx