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what is synthetic biology?
WARNING: an "essay" much longer than those i've ever submitted to ang lai kuin. DO NOT READ UNLESS BORED.
to those that are curious about where/what i've been doing for the past few months, i've basically been slaving in the lab for an average of 8 hrs per day for the past 12 wks haha. i've decided to write this post cos when i was chatting with some pple, those with biological backgrounds will end up asking me what i've been doing in the lab. normally, i couldn't progress beyond "oh, doing stuff on synthetic biology", cos it'll take ages for me to explain what it actually is haha. since i'm now back home and feeling abit bored, i'll try to excite those pple interested in doing some research in the future with the concept of synthetic biology. it's gonna be a force to be reckoned in the future! =)
so what does the phrase mean? wikipedia's first few lines read "Synthetic biology has long been used to describe an approach to biology that attempts to integrate different areas of research in order to create a more holistic understanding of life. More recently the term has been used in a different way, signaling a new area of research that combines science and engineering in order to design and build novel biological functions and systems." the synthetic biology that i've been dealing with is that of the second definition - using engineering principles to make a biologist's life much easier =P this field is quite new, and most of the progress in this field is at most 10 years old.
let me start off with an anecdote. when an engineer builds a house, he'd buy bricks, cement, roof tiles etc and then assemble it into a house; a biologist, however, would have to create their own bricks, their own brand of cement and roof tiles before making a house. (ok la, i skipped the part where that engineer will hire workers to finish his job for him; the biologist would hire phd students to do the sai kang instead =P) engineers take for granted that the parts that they buy would perform in an expected way - standard batteries would provide power of a certain amount, screws can be tightened by spanners of the correct size. biologists, however, are usually wary of using other pple's work cos they are convinced that biological systems are so complex that it can never be broken into standard interchangeable parts. a certain gene expressed in e. coli, say, would get silenced in humans, while overexpressed in c. elegans.
however, there is a bunch of biologists that think otherwise. they are convinced that biological "parts" can be characterized individually, and when assembled into "devices", it would produce predictable outcomes in the cell. imagine a "device" that could report on the strength of a promoter sequence - it would be really convenient to be able to stick your promoter in front of the device, and the resulting output would tell you how strong the promoter is, wouldn't it? actually, imagine is a bad word to use. this "device" has been made and used widely, and the physical piece of DNA looks something like this:
..EcoRI..XbaI............................SpeI..PstI..
----|------|---(RBS)--[ GFP gene ]--(T)----|-----|---
where RBS stands for "ribosome binding site" and T for "terminator". EcoRI, XbaI, SpeI and PstI stand for some very commonly used restriction sites, of which importance will be made known later =) (ignore the dots, i had to add it in cos blogger automatically removes any extra spaces in between words).
this stretch of DNA is present in a plasmid sequence, btw, cos it's much easier to toy with DNA sequences in plasmids than when it's in the bacterial chromosome.
the inclusion of a promoter sequence in front of the RBS would result in a complete gene - hence, it is not hard to imagine that if the promoter is strong, the cell would glow a brighter green than if the promoter is weak. the beauty of this device is that it can be extended to test for whether certain promoters are induced by certain molecules - for example, we've been using a promoter involved in the metabolism of arabinose, a type of sugar. when this promoter is placed in front of the RBS, graded increases of arabinose led to a somewhat proportional increase in fluorescence. i found it to be pretty coooooool =)
so how can the promoter be introduced in front of the reporter device? i'll let the next picture explain it - ASCII art is tedious to draw haha.
just to clarify, cutting with XbaI produces sticky ends that can anneal to those produced by SpeI, as the ends are complementary. the annealing of these ends would destroy both cutting ends, producing a "scar". this entire process is termed "standard assembly". just to confuse u guys abit, when we say we want to insert a promoter in front of the device, we carry it out by instead inserting the device AFTER the promoter. it's bcos after a double digest is carried out, small bits of DNA is harder to purify (by gel extraction) than bigger pieces. the promoter is present in a plasmid with similar cutting sites, hence standard assembly can still be carried out. inserting stuff at the back requires different enzymes from those in the picture above, but the concept is largely similar.
the possibilities for potential devices are INFINITE. student groups participating in the iGEM (international Genetically Engineered Machines) have dreamt up stuff like counting devices (Zurich 2005), photography devices (U of Austin, 2004), amplifiers (several schools), and communicating devices (several groups also). our group this year is trying to create a way for e. coli cells, which are gram-negative, to be able to talk to b. subtilis cells, which are gram-positive. it's very much still WIP haha. one thing interesting of iGEM teams are that they consist of biologists and engineers. engineers do the dreaming, while biologists do the sai kang at the start... and then force the engineers to do it as well =P
for ultra bored people, extra reading material:
wiki article on synthetic biology
the iGEM 2007 competition
the Cambridge iGEM 2007 wiki website (yeah, we document our progress as we go in a wiki. the layout of the main page was designed by.. yours truly =D)
the MIT Registry of Parts (documents the parts and devices designed by iGEM teams)
i hope this "essay" is readable and understandable, as well as able to excite the biological urges (let's not think dirty here..) of the budding synthetic biologists in 78 =P if u're interested and wanna know more, msn me or email me la haha.
Yi Jin lived on 4:25 PM
- 03S78 forever -
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