When i sit on the chair...i dont feel like getting up and when i am standing...i dread to grab a seat, cause the transition between these two states...is what i dread the most of...! With the every bit of pain my neurons makes me feel...there are those connecting one's which bring the adventurous, fun filled and worth the pain moments of the trek...to "Rajmachi" back to life, chucking the pain away!!!
Yep, had been to a trek to "Rajmachi" a small village 20kms off lonavla...this weekend!
And this was one of a kind experience...cause there were many "first time" kinda events...!
The journey started from the bus-stop waitng for bus. no. 212/1 and after 5-10mins or so we were in the cab n heading towards Dadar TT...!
Buses came n buses went... none were ready to take us to Lonavla bus stand.(it rhymes)
Within a span of about 15-30 mins we actually managed to question the man at the inquiry counter...a hundred times.Also the conductors of the arriving buses were not spared from "Will this bus go to Lonavla?"The wait for the bus lasted for an hour or so...but then it was not boring at all...time was passing as were the buses..n we enjoyed as if we never cared...!
Grabed the last seats of an heading to Nanded ST...and begined with bus mein masti...!(this one rhymes too...whoa)
Inacting movies one after other...there was a splater of laughter ...in the other wise snoozing shant types gather!(its a threesome rhyme here)
The conductor was oversmart kinds...and cared more of we getting down off his bus at the destination.Memory game followed as the bus got packed ....Saxena-kutta-tempo-bus-chak-kobi-gas-acetabullum-czeckoslovakia...n on it went...
Finally at Lonavla we had a pick up "sumo" and at "Ram Krishna" we were "8+3=11" ka gang now!!!
Now as i said "Rajmachi" is about 20-22kms off Lonavla and the best part is we started at about 23-23.30 or so from Lonavla.
And this road...i must say was not even worth calling a kaccha road...was really bumpy...single vehicle pass...with no street lights...no sign boards...no human habitation...and pitch dark...wow! Frankly speaking it was adorned with pure darkness...and couldn't keep my eyes of the beauty of dark. we also managed to convince the driver to put off the headlights for that rare experience of absolute darkness!
I must tell the first sight of the tree adorned with fireflies was just mast...i mean how beautiful it looked in the dark! After that we spotted countless fireflies...wandering here an there...attracting their mates/prey.
Finally at around 1 o'clock we reached "Rajmachi"...this village with 20-22 houses...and no electricity...wow!!!
We headed to the house were we intended to spend that night...the floor was clad with cowdung and cold breeze made a feel good effect...! Spent the whole night in the verandha and the street just outside the house..doing nothing at all...listening to the golden silence!!!It almost felt like listening to the silence and observing the hide n seek game that the cloud and half moon played till eternity...!
It had hardly been an hour or so since my mind had shut off and i went to sleep, then the natural alarm of the hen began with advanced snooze set ups which was not supported with the snooze off algorithm...this created god save me kinda situation...!
At around 6.30-7 we began our climb on the "Manoranjan" fort...the climb wasn't difficult at all...still doing duniya bharka timepass and mazza masti we were heading with a snail's pace...enjoying the view, the caves. the on the way water bodies, sipping in cloud nine .(the trek superhit) After photoshots and relaxed moments up there on the fort we headed down to "Rajmachi" again....had lunch at one of the locals place were we stayed the previous night.
Then came the decision point...to go the way we came...to lonavla or to climb downhill to karjat, which according to the locals was "faster" and most recommended. We began heading to karjat at around 14hrs in the brightly shining sun...with the expectation of reaching Karjat early and without the trouble as it was to be in the Lonavla wala road...
But something totally bizare, unexpected and first time kinda thingy was in store for us...something which made this trek the most adventurous one...
We had no clue about the road to Karjat, we took few directions from the lady in whose house we stayed and in another 5 mins or so...one of us had to go back to her for directions again...! Finally we began on the right track...all 11 of us plus a black doggy called Raju or Raja (something like that) he himself volunteered to accompany us. In the scorching heat with our caps and scarfs and glares on...we walked. All was going good untill we came up to the first slope...wherein our actual journety downward began...frankly speaking i still remember the sight of that first slope and its steepness...and then continued the series of steep slopes. I have never seen such steep slopes, in my life.With frequent breaks of water and cloud nine we continued downwards. Other groups one by one overtaking us...but the loyal raja continued to stay with us...in return he enjoyed Parle G and few licks of water...from true dog lovers snehal and mihir.Along with this one there was another brown colored dog which accompanied us. The dog had a perfect overtaking timing, he would wish to overtake at the difficult patch of the route and scare me to the core...i hate dogs!
Actually we could quite frequently hear train ka engine...which later sometime...i designated as a "psuedosignal" cause it used to make us feel we are nearing to Karjat stn n it should be near by but it never was, it indeed was a psuedo signal!
Even we girls in the group managed to slip quite often...making the guys wonder...how someone can slip so frequently...! Waise toh at quite few points i had to sit down and push myself to the lower level...but at one point when i was in the process of doing so...the huge stone on which my hand took support went loose and was about to fall on my legs below...thankfully it was put on hold!
Steep slopes came and went by...but there was no "namo nishan" of any gaon "dur dur tak" forget Karjat. It looked like we were completely lost....It had been hours we were climbing down and heading nowhere it seemed...still we continued. The hopes of even finding a small village were diminshing now...we continued. Admist of all this situation we were doing all sorts of bakwas and laughing and giggling...and this was the prime reason due to which atleast i myself slipped quite a few times. Actually no one of us cared about the passing time and also about not seeing habitation "dur dur tak". We continued, finally at around 17hrs started the patch with no more slopes...and our expectations of expecting a village increased exponentially!
We got completely lost in the plane land, had to ask a group of co-downclimbers the way ahead...and were shocked to hear that there was this another village called "kondwae"(something like that) from where we can get a transport to Karjat which was 30-40 mins away from there(that village).We kept walking, villages came and villages went...at one point we saw a rick standing on the road and it seemed like an oasis in a desert! We were just walking walking and walking completely lost....till we spot a board "Karjat 9.5kms"...OMG!
We walked and walked and finally...actually finally reached this village "kondwae" and before even looking for a suitable transport gulped in a bottle of mango juice and quenched our thirst and recharged ourselves.We were lost and found! Took the 10 seater auto and threw ourselves into it and headed to Karjat stn...finally...finally came the Karjat stn and we were on the right track in the local!
I mean common never in our lives we had such an experience, such feeling of being unsure...of not even knowing whether the destination is going to even come or no, whether we were on the right track and still we were so tension free enjoying ourselves like insanes...!
It's amazing to be insane!!!
Tuesday, June 16, 2009
Monday, April 20, 2009
Behavior
Behavior is a tricky thing…one's behavior thoroughly depends on: the time, the place where you are, the people with whom you are, your previous interactions with them, your state of mind, your what not…basically; sometimes it depend on all of these and sometimes just on one of them.
One’s behavior is adorned with various shades…and even a very brief interaction with a person gives us an insight into his/her behavior, basically you are in a position to imply or be conclusive about the person’s behavior.
But then why is it that we find or at least I (do) find it difficult to comment on rather be sure of my own behavior or how I behave in general with people.
Basically why is self analysis, so difficult???
Generally what we seem to do is start building our own frame, based on the views that others put forward about us or start looking towards ourselves from others shoes!
This I think is really difficult task…what makes it difficult is precisely our unwillingness to accept our short comings rather we are unable to take care of our own biases about ourselves.
More than that even if you know, about certain shades of your own behavior, its practically impossible to be quantitative.
But it was just yesterday that I came to know that I was addicted to the internet by 35%(after answering to a questionnaire on facebook) Many such questionnaires are available on the world wide web and they are quantitative too and by answering those many like you and me are doing the complex task of self-analysis or rather getting an insight into our own behaviors. At this point we might think that we do it just for fun and nothing like “self analysis” is even closely related to this, is it really???
Before even worrying about the scores assigned to each questions and how exactly the quantitation is done, I think there is a great flaw right in the beginning of the process.
That is, for any human surveillance that you carry out, it is necessary that the subject is unaware of your motives behind the survey.
And this condition is no way met during the exercise, cause you choose to answer the questionnaire, in the first place, because you are interested in particular behavior or character of yours. And it’s always that you have some pre-assumptions about yourself on those grounds and you successfully introduce a bias…! Also one’s you know the purpose of the whole process, from the options available you can easily predict the options that will give you scores at the two extremes and at the mean. The whole process along with its purpose fails, and I think it fails miserably!
In spite of this we enjoy taking the weirdest and stupidest of the quizzes on the www and waste our time, even when there are assignments, submissions and sometimes even exams!!!
So, which is the quiz you are taking up next???
One’s behavior is adorned with various shades…and even a very brief interaction with a person gives us an insight into his/her behavior, basically you are in a position to imply or be conclusive about the person’s behavior.
But then why is it that we find or at least I (do) find it difficult to comment on rather be sure of my own behavior or how I behave in general with people.
Basically why is self analysis, so difficult???
Generally what we seem to do is start building our own frame, based on the views that others put forward about us or start looking towards ourselves from others shoes!
This I think is really difficult task…what makes it difficult is precisely our unwillingness to accept our short comings rather we are unable to take care of our own biases about ourselves.
More than that even if you know, about certain shades of your own behavior, its practically impossible to be quantitative.
But it was just yesterday that I came to know that I was addicted to the internet by 35%(after answering to a questionnaire on facebook) Many such questionnaires are available on the world wide web and they are quantitative too and by answering those many like you and me are doing the complex task of self-analysis or rather getting an insight into our own behaviors. At this point we might think that we do it just for fun and nothing like “self analysis” is even closely related to this, is it really???
Before even worrying about the scores assigned to each questions and how exactly the quantitation is done, I think there is a great flaw right in the beginning of the process.
That is, for any human surveillance that you carry out, it is necessary that the subject is unaware of your motives behind the survey.
And this condition is no way met during the exercise, cause you choose to answer the questionnaire, in the first place, because you are interested in particular behavior or character of yours. And it’s always that you have some pre-assumptions about yourself on those grounds and you successfully introduce a bias…! Also one’s you know the purpose of the whole process, from the options available you can easily predict the options that will give you scores at the two extremes and at the mean. The whole process along with its purpose fails, and I think it fails miserably!
In spite of this we enjoy taking the weirdest and stupidest of the quizzes on the www and waste our time, even when there are assignments, submissions and sometimes even exams!!!
So, which is the quiz you are taking up next???
Saturday, February 28, 2009
..... , ,,,,, ;: ::::: !
All the atoms and molecules around
Have been here for times unbound…
Something or the other kept them busy
Cause surviving here wasn’t easy…!
Every challenge faced was different from other
But there was no reason for them to bother…
Few of them always managed to find the key
To sail through the selection spree…
All of this was obviously at a high cost
Every time a majority of population was lost!
It was indeed a blessing in disguise
It assured the progeny the key choice…
It assured us a way to account the very selections
It assured us this through stable genetic mutations..!
Something so simple so reasonable so logical
Is unacceptable to some creationists classical…
Intelligent design is what they propagate
With ideas, data and views surrogate…!
Accept it or else forget but Evolution is the only explanation…
To the most complex and also to the simplest title of this poetic creation.,;:!
Have been here for times unbound…
Something or the other kept them busy
Cause surviving here wasn’t easy…!
Every challenge faced was different from other
But there was no reason for them to bother…
Few of them always managed to find the key
To sail through the selection spree…
All of this was obviously at a high cost
Every time a majority of population was lost!
It was indeed a blessing in disguise
It assured the progeny the key choice…
It assured us a way to account the very selections
It assured us this through stable genetic mutations..!
Something so simple so reasonable so logical
Is unacceptable to some creationists classical…
Intelligent design is what they propagate
With ideas, data and views surrogate…!
Accept it or else forget but Evolution is the only explanation…
To the most complex and also to the simplest title of this poetic creation.,;:!
Synthetic Biology: Engineer’s Approach to Biology
Abstract-
Contemporary biology recognizes the genes and proteins responsible for a particular cellular phenomenon, but today at this hour the focus is on deciphering the connectivity between those genes and proteins. Mathematical models best describes these circuits, which in reality resemble the electric circuits. In this scenario, biology is looked at through engineer’s perspective, providing the framework for the construction and analysis of the underlying sub modules that constitute the network. Thus synthetic biology creates a platform on which prediction and evaluation of dynamics of cellular processes is facilitated. In this review we will take a look at synthetic biology and the varied facets it offers.
Keywords: Synthetic biology, oscillator, reprissilator, cellular noise, biobricks.
“…the clock ticks life away…” teens hum on the tunes of Linkin park. (Popular band)
Though the lyrics refer to the passing time in context of digital clock or watch…the man created version. The same words hold true for the nature’s version of the clock…the biological clock as we may call it.
In order to understand how exactly the clock ticks or works…one may have to break open a clock and look at its components…best way to get a better insight into its working, is to try creating one’s own clock out of similar parts!
The previous is what contemporary biology deals with, using genetic and biochemical techniques to isolate genes and proteins involved in feedback loops of gene expression, that are necessary for clock functioning of biological clocks e.g. circadian rhythms.( Cyran, S. A. et al., 2003)
But the later, is the one which helps us answer insightful questions pertaining to the clock like-
1. What sets the period of the oscillation?
2. How does the clock operate reliably in diverse cellular conditions? and
3. What features of its design are responsible for its reliable operation?
The above mentioned i.e. creating a new clock; is the way Synthetic Biology approaches the biological dead ends! Several synthetic genetic clocks have now been constructed in bacteria and mammalian cell lines too.( Fung, E. et al, 2005; Tigges Marcel et al, 2009) These circuits are simpler versions of the actual naturally found biological clocks.
What exactly is synthetic biology?
Marc W. Kirschner (Department of Systems Biology Harvard Medical School) sheds light on it…
“Synthetic biology is the study of the behaviour of complex biological organization and processes in terms of the molecular constituents. It is built on molecular biology in its special concern for information transfer, on physiology for its special concern with adaptive states of the cell and organism, on developmental biology for the importance of defining a succession of physiological states in that process, and on evolutionary biology and ecology for the appreciation that all aspects of the organism are products of selection, a selection we rarely understand on a molecular level. Systems biology attempts all of this through quantitative measurement, modeling, reconstruction, and theory. Systems biology is not a branch of physics but differs from physics in that the primary task is to understand how biology generates variation. No such imperative to create variation exists in the physical world. It is a new principle that Darwin understood and upon which all of life hinges. That sounds different enough for me to justify a new field and a new name”
Synthetic biology deals with ‘programming’ of the cell. Reprogramming a cell involves the creation of synthetic biological components by adding, removing, or changing genes and proteins. Design, fabrication, integration, and testing of new
Cellular hardware lies at the core of this field. But the tools and methods necessary for same are derived from experimental biology. The process begins with the abstract design of devices, modules, or organisms, and is often guided by mathematical models. The synthetic biologist then tests the newly constructed systems experimentally. However, such initial attempts rarely yield fully functional implementations because of incomplete biological information. Rational redesign
Based on mathematical models comes for rescue in such situations.
Newer approaches to address and deal with synthetic constructs are also being developed-
1. One can just apply directed evolution to genes comprising a simple genetic circuit and what you get is evolution of improperly matched non-functional components to functional ones.( Yokobayashi Yohei et al, 2002)
2. In silico evolutionary procedure is also being used to create gene networks performing basic tasks. Main highlights of this procedure are that small functional modules with diverse functions can be created.( Franc¸ois Paul et al, 2004)
3. Yet another approach could be just to couple simple models into complex networks with behaviour that can be predicted from individual components. Thus properties of regulatory sub-systems can be used to predict behaviour of larger more complex regulatory networks.( Guido Nicholas et al, 2006)
Designing constructs…
Modeling and construction of many and varied gene regulatory circuits are reported till date. Oscillators being the most popular, are constructed by coupling positive and negative feedback loops, such that the whole system oscillates or moves back and forth between the two steady states. Also lots of variations are also possible here, in terms of the components that make the whole system oscillate.
In case of E.coli itself it is possible to construct oscillatory circuit using IPTG, lacI protein and arabinose regulatory sites, together.( Stricker Jesse et al, 2008; M Rachael et al, 2002) Similar is the deal with reprissilator in which three transcriptional repressor systems build an oscillator, but the twist is that the period of oscillation is shorter than cell-division cycle, so the state of oscillator needs to be transmitted to the next generations. Thus such reprissilator make possible, design and construction of artificial genetic networks with new functional properties from generic components that naturally occur in other contexts.( Elowitz et al, 2000)
In the same E.coli one can also create oscillations by exploiting glycolytic flux i.e. construction of a metabolator! In this acetyl phosphate acts as a signalling metabolite and under its control the two metabolite pools interconvert.( Fung, E. et al, 2005)
Toggle switches are another kind of circuits tried and tested in E.coli which require only transient induction and hence can function as a cellular memory unit. This can very well be exploited in industries, since it permits high induction of recombinant proteins without the high cost of large quantities of inducer. (Gardner Timothy et al, 2000)
Establishment of communication between bacteria by constructing an artificial quorum sensor has not only enabled intraspecies but also intrespecies communication possible, leading to various behaviours and phenotypes. It facilitates achievement of co-operative transcriptional response.(Garcia-Ojalvo Jordi et al, 2004; Bulter Thomas et al, 2004)
Mammalian cells are also being used for construction of oscillators which give self-sustained, tunable autonomous and robust oscillations, thus opening new vistas for future gene and cell therapies.( Tigges Marcel et al, 2009)
The untold story…
Synthetic biology is not just messing around with the genome (as it may seem to be from the above text) to make useful constructs, basically its not tinkerer’s approach but engineers approach to a problem.
One can say that success of synthetic biology is essential to understand life…this is because in this whole process of modelling, construction and testing the understanding of the system itself is achieved in a better way. This holds true not only for the insight into working of the cell cycle (a mitotic oscillator is at work there) (Goldbeter Albert, 1991) but also in understanding of the sleep-wake cycle or the circadian rhythms.
It is only while working with the synthetic constructs a phenomenon of “noise” comes into light. Noise is the one which can actually collapse your circuit or rather may give your circuit an insignificant and non-functional look! Trying to reduce the noise level in one’s own construct(Orrell David et al, 2004) leads to design enhancement and also appreciation of the noise resistant constructs found in the nature built circuits!( Vilar, J. M et al, 2002)
Fascinating shades…
A giant leap of synthetic biology is to “write the genome” as Craig Venter puts it! As a step in this direction not only have they constructed synthetic whole genomes(Smith Hamilton et al, 2003) but also expanded the genetic code with a functional quadruplet codon.(Which can incorporate unnatural amino acids into proteins.)(Anderson Christopher et al, 2004)
In order to bring all these constructs and related research in laboratories around the world under a common umbrella standard protocols and registry of the constructed parts has been developed on the World Wide Web http://partsregistry.org/Main_Page. It actually involves efforts to develop “tool box” of standardized genetic parts with known performance characteristics—analogous to the transistors, capacitors, and resistors used in electronic circuits—from which bioengineers can build functional Devices and, someday, synthetic micro organisms. The registry is made up of components called “BioBricks,” short pieces of DNA that constitute or encode functional genetic elements. Examples of BioBricks are a “promoter” sequence that initiates the transcription of DNA into messenger RNA, a “terminator” sequence that halts RNA transcription, a “repressor” gene that encodes a protein that blocks the transcription of another gene, a ribosome-binding site that initiates protein synthesis, and a “reporter” gene that encodes a fluorescent protein. A BioBrick must have a genetic structure that enables it to send and receive standard biochemical signals and to be cut and pasted into a linear sequence of other BioBricks. Further, work on the lines of improvising the repository of biobricks and methods for their easier handling is being done, actively.( Peccoud Jean et al, 2008; Shetty Reshma et al, 2008) Also work on the lines of developing an organism with minimum essential genes(Glass John et al, 2005), so that the organism can be exploited efficiently for integrating the constructs, is in progress.
Excellent examples of intelligent use of the toolbox involves -
1. Engineering a metabolic pathway for the synthesis of artemisinic acid in yeast, which is the immediate precursor of the drug artemisinin( a natural product) that is highly effective in treating malaria, thus reducing the cost of the drug.( Ro Dae-Kyun et al, 2006)
2. Construction of a sensory synthetic kinase that allows a lawn of bacteria to function as a biological film, such that the projection of a pattern of light on to the bacteria produces a high-definition (about 100 megapixels per square inch), two-dimensional chemical image. Thus using spatial control of bacterial gene expression to 'print' complex biological materials, for example, to investigate signalling pathways through precise spatial and temporal control of their phosphorylation steps.( Levskaya Anselm et al, 2005)
It is crystal clear that the field of synthetic biology has the potential to bring about epochal changes in science and a few decades from now it may have a profound influence on the definition of life, itself!
Perhaps the most intriguing problem right now is to observe how the designed circuit operates in the context of a complete organism. There are no dotted lines inside the cell isolating circuits from one another. The ultimate test for this synthetic approach is to delete natural circuits and replace them with synthetic counterparts within organisms. This will lead to interference of the synthetic circuits with the rest of the cell. Obviously these circuits would be less functional than their natural counterparts. But at this stage one can learn more by putting together a simple, though inaccurate, pendulum Clock, than one can by disassembling the finest Swiss timepiece.
(these days i am going gaga... over synthetic biology...so after my paper ppt my review follows...again on synthetic biology! nothing like it if get to work in relation to the field...hopefully!)
Contemporary biology recognizes the genes and proteins responsible for a particular cellular phenomenon, but today at this hour the focus is on deciphering the connectivity between those genes and proteins. Mathematical models best describes these circuits, which in reality resemble the electric circuits. In this scenario, biology is looked at through engineer’s perspective, providing the framework for the construction and analysis of the underlying sub modules that constitute the network. Thus synthetic biology creates a platform on which prediction and evaluation of dynamics of cellular processes is facilitated. In this review we will take a look at synthetic biology and the varied facets it offers.
Keywords: Synthetic biology, oscillator, reprissilator, cellular noise, biobricks.
“…the clock ticks life away…” teens hum on the tunes of Linkin park. (Popular band)
Though the lyrics refer to the passing time in context of digital clock or watch…the man created version. The same words hold true for the nature’s version of the clock…the biological clock as we may call it.
In order to understand how exactly the clock ticks or works…one may have to break open a clock and look at its components…best way to get a better insight into its working, is to try creating one’s own clock out of similar parts!
The previous is what contemporary biology deals with, using genetic and biochemical techniques to isolate genes and proteins involved in feedback loops of gene expression, that are necessary for clock functioning of biological clocks e.g. circadian rhythms.( Cyran, S. A. et al., 2003)
But the later, is the one which helps us answer insightful questions pertaining to the clock like-
1. What sets the period of the oscillation?
2. How does the clock operate reliably in diverse cellular conditions? and
3. What features of its design are responsible for its reliable operation?
The above mentioned i.e. creating a new clock; is the way Synthetic Biology approaches the biological dead ends! Several synthetic genetic clocks have now been constructed in bacteria and mammalian cell lines too.( Fung, E. et al, 2005; Tigges Marcel et al, 2009) These circuits are simpler versions of the actual naturally found biological clocks.
What exactly is synthetic biology?
Marc W. Kirschner (Department of Systems Biology Harvard Medical School) sheds light on it…
“Synthetic biology is the study of the behaviour of complex biological organization and processes in terms of the molecular constituents. It is built on molecular biology in its special concern for information transfer, on physiology for its special concern with adaptive states of the cell and organism, on developmental biology for the importance of defining a succession of physiological states in that process, and on evolutionary biology and ecology for the appreciation that all aspects of the organism are products of selection, a selection we rarely understand on a molecular level. Systems biology attempts all of this through quantitative measurement, modeling, reconstruction, and theory. Systems biology is not a branch of physics but differs from physics in that the primary task is to understand how biology generates variation. No such imperative to create variation exists in the physical world. It is a new principle that Darwin understood and upon which all of life hinges. That sounds different enough for me to justify a new field and a new name”
Synthetic biology deals with ‘programming’ of the cell. Reprogramming a cell involves the creation of synthetic biological components by adding, removing, or changing genes and proteins. Design, fabrication, integration, and testing of new
Cellular hardware lies at the core of this field. But the tools and methods necessary for same are derived from experimental biology. The process begins with the abstract design of devices, modules, or organisms, and is often guided by mathematical models. The synthetic biologist then tests the newly constructed systems experimentally. However, such initial attempts rarely yield fully functional implementations because of incomplete biological information. Rational redesign
Based on mathematical models comes for rescue in such situations.
Newer approaches to address and deal with synthetic constructs are also being developed-
1. One can just apply directed evolution to genes comprising a simple genetic circuit and what you get is evolution of improperly matched non-functional components to functional ones.( Yokobayashi Yohei et al, 2002)
2. In silico evolutionary procedure is also being used to create gene networks performing basic tasks. Main highlights of this procedure are that small functional modules with diverse functions can be created.( Franc¸ois Paul et al, 2004)
3. Yet another approach could be just to couple simple models into complex networks with behaviour that can be predicted from individual components. Thus properties of regulatory sub-systems can be used to predict behaviour of larger more complex regulatory networks.( Guido Nicholas et al, 2006)
Designing constructs…
Modeling and construction of many and varied gene regulatory circuits are reported till date. Oscillators being the most popular, are constructed by coupling positive and negative feedback loops, such that the whole system oscillates or moves back and forth between the two steady states. Also lots of variations are also possible here, in terms of the components that make the whole system oscillate.
In case of E.coli itself it is possible to construct oscillatory circuit using IPTG, lacI protein and arabinose regulatory sites, together.( Stricker Jesse et al, 2008; M Rachael et al, 2002) Similar is the deal with reprissilator in which three transcriptional repressor systems build an oscillator, but the twist is that the period of oscillation is shorter than cell-division cycle, so the state of oscillator needs to be transmitted to the next generations. Thus such reprissilator make possible, design and construction of artificial genetic networks with new functional properties from generic components that naturally occur in other contexts.( Elowitz et al, 2000)
In the same E.coli one can also create oscillations by exploiting glycolytic flux i.e. construction of a metabolator! In this acetyl phosphate acts as a signalling metabolite and under its control the two metabolite pools interconvert.( Fung, E. et al, 2005)
Toggle switches are another kind of circuits tried and tested in E.coli which require only transient induction and hence can function as a cellular memory unit. This can very well be exploited in industries, since it permits high induction of recombinant proteins without the high cost of large quantities of inducer. (Gardner Timothy et al, 2000)
Establishment of communication between bacteria by constructing an artificial quorum sensor has not only enabled intraspecies but also intrespecies communication possible, leading to various behaviours and phenotypes. It facilitates achievement of co-operative transcriptional response.(Garcia-Ojalvo Jordi et al, 2004; Bulter Thomas et al, 2004)
Mammalian cells are also being used for construction of oscillators which give self-sustained, tunable autonomous and robust oscillations, thus opening new vistas for future gene and cell therapies.( Tigges Marcel et al, 2009)
The untold story…
Synthetic biology is not just messing around with the genome (as it may seem to be from the above text) to make useful constructs, basically its not tinkerer’s approach but engineers approach to a problem.
One can say that success of synthetic biology is essential to understand life…this is because in this whole process of modelling, construction and testing the understanding of the system itself is achieved in a better way. This holds true not only for the insight into working of the cell cycle (a mitotic oscillator is at work there) (Goldbeter Albert, 1991) but also in understanding of the sleep-wake cycle or the circadian rhythms.
It is only while working with the synthetic constructs a phenomenon of “noise” comes into light. Noise is the one which can actually collapse your circuit or rather may give your circuit an insignificant and non-functional look! Trying to reduce the noise level in one’s own construct(Orrell David et al, 2004) leads to design enhancement and also appreciation of the noise resistant constructs found in the nature built circuits!( Vilar, J. M et al, 2002)
Fascinating shades…
A giant leap of synthetic biology is to “write the genome” as Craig Venter puts it! As a step in this direction not only have they constructed synthetic whole genomes(Smith Hamilton et al, 2003) but also expanded the genetic code with a functional quadruplet codon.(Which can incorporate unnatural amino acids into proteins.)(Anderson Christopher et al, 2004)
In order to bring all these constructs and related research in laboratories around the world under a common umbrella standard protocols and registry of the constructed parts has been developed on the World Wide Web http://partsregistry.org/Main_Page. It actually involves efforts to develop “tool box” of standardized genetic parts with known performance characteristics—analogous to the transistors, capacitors, and resistors used in electronic circuits—from which bioengineers can build functional Devices and, someday, synthetic micro organisms. The registry is made up of components called “BioBricks,” short pieces of DNA that constitute or encode functional genetic elements. Examples of BioBricks are a “promoter” sequence that initiates the transcription of DNA into messenger RNA, a “terminator” sequence that halts RNA transcription, a “repressor” gene that encodes a protein that blocks the transcription of another gene, a ribosome-binding site that initiates protein synthesis, and a “reporter” gene that encodes a fluorescent protein. A BioBrick must have a genetic structure that enables it to send and receive standard biochemical signals and to be cut and pasted into a linear sequence of other BioBricks. Further, work on the lines of improvising the repository of biobricks and methods for their easier handling is being done, actively.( Peccoud Jean et al, 2008; Shetty Reshma et al, 2008) Also work on the lines of developing an organism with minimum essential genes(Glass John et al, 2005), so that the organism can be exploited efficiently for integrating the constructs, is in progress.
Excellent examples of intelligent use of the toolbox involves -
1. Engineering a metabolic pathway for the synthesis of artemisinic acid in yeast, which is the immediate precursor of the drug artemisinin( a natural product) that is highly effective in treating malaria, thus reducing the cost of the drug.( Ro Dae-Kyun et al, 2006)
2. Construction of a sensory synthetic kinase that allows a lawn of bacteria to function as a biological film, such that the projection of a pattern of light on to the bacteria produces a high-definition (about 100 megapixels per square inch), two-dimensional chemical image. Thus using spatial control of bacterial gene expression to 'print' complex biological materials, for example, to investigate signalling pathways through precise spatial and temporal control of their phosphorylation steps.( Levskaya Anselm et al, 2005)
It is crystal clear that the field of synthetic biology has the potential to bring about epochal changes in science and a few decades from now it may have a profound influence on the definition of life, itself!
Perhaps the most intriguing problem right now is to observe how the designed circuit operates in the context of a complete organism. There are no dotted lines inside the cell isolating circuits from one another. The ultimate test for this synthetic approach is to delete natural circuits and replace them with synthetic counterparts within organisms. This will lead to interference of the synthetic circuits with the rest of the cell. Obviously these circuits would be less functional than their natural counterparts. But at this stage one can learn more by putting together a simple, though inaccurate, pendulum Clock, than one can by disassembling the finest Swiss timepiece.
(these days i am going gaga... over synthetic biology...so after my paper ppt my review follows...again on synthetic biology! nothing like it if get to work in relation to the field...hopefully!)
Wednesday, February 18, 2009
Abstract to paper ppt...scheduled 21st feb
yet another sem and yet another paper ppt....though my preparations ...hardly any preps...i m in love with synthetic bio these days...so here it is...abstract to my paper...no sorry abstract to the paper i selected...
A Tunable Synthetic Mammalian Oscillator
Marcel Tigges, Tatiana T. Marquez-Lago, Jo¨rg Stelling & Martin Fussenegger
Nature, Vol. 457,309-312 (15 January 2009)
Abstract
Oscillator circuits mediating the periodic induction of specific target genes are time-keeping devices found in circadian clocks. Here, is described the first controllable mammalian oscillator, constructed based on an auto-regulated sense–antisense transcription control circuit. The circuit encodes a positive and a time delayed negative feedback loop, enabling autonomous, self sustained and tunable oscillatory gene expression. The designed system was monitored using oscillating concentrations of green fluorescent protein with tunable frequency and amplitude, by time-lapse microscopy in real time in individual Chinese hamster ovary cells. This synthetic mammalian clock may provide insight into dynamics of natural periodic processes and also enable complex gene therapy treatments by automating physiological processes in future gene and cell therapies.
References-
1. Jesse Stricker, Scott Cookson (2008) A fast, robust and tunable synthetic gene oscillator. Nature, Vol. 456, 516-520
2. Crosthwaite, S. K. (2004) Circadian clocks and natural antisense RNA. FEBS Lett. 567, 49–54
3. Gossen, M. & Bujard, H. (1992) Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl Acad. Sci. USA 89, 5547–5551
A Tunable Synthetic Mammalian Oscillator
Marcel Tigges, Tatiana T. Marquez-Lago, Jo¨rg Stelling & Martin Fussenegger
Nature, Vol. 457,309-312 (15 January 2009)
Abstract
Oscillator circuits mediating the periodic induction of specific target genes are time-keeping devices found in circadian clocks. Here, is described the first controllable mammalian oscillator, constructed based on an auto-regulated sense–antisense transcription control circuit. The circuit encodes a positive and a time delayed negative feedback loop, enabling autonomous, self sustained and tunable oscillatory gene expression. The designed system was monitored using oscillating concentrations of green fluorescent protein with tunable frequency and amplitude, by time-lapse microscopy in real time in individual Chinese hamster ovary cells. This synthetic mammalian clock may provide insight into dynamics of natural periodic processes and also enable complex gene therapy treatments by automating physiological processes in future gene and cell therapies.
References-
1. Jesse Stricker, Scott Cookson (2008) A fast, robust and tunable synthetic gene oscillator. Nature, Vol. 456, 516-520
2. Crosthwaite, S. K. (2004) Circadian clocks and natural antisense RNA. FEBS Lett. 567, 49–54
3. Gossen, M. & Bujard, H. (1992) Tight control of gene expression in mammalian cells by tetracycline-responsive promoters. Proc. Natl Acad. Sci. USA 89, 5547–5551
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