While I Wait…

Guess who is stuck in lab on a Saturday with the cheering prospect of being back on Sunday?

For the past few days, i’ve been super distressed because the cloning I was doing didn’t work. No reason. Just didn’t work. For the life of me, i couldn’t figure out what i did wrong. So i said “Screw it. Imma gonna redo the goddamn thing.” Hence the weekend dash to the lab. Thankfully, i still had prepped-DNA lying about, all digested, purified, and ready to be glued together. Saves me a lot of time.

Step 1 was to glue together the gene I want with some other DNA in a tightly coiled ring. I got the DNA-gluing step going last night. Then I went out and got drunk. I came back to lab in the morning to finish Step 2. This step involves coercing bacteria into accepting my gift of knitted together DNA. My gift makes them resistant to ampicillin. A gift that keeps on giving I tell you! and yet, I must heat shock them into accepting!  Step 3 is to take these cells carrying the extra DNA i added and spread them out on plated of agar so i can get nice individual colonies of cells. The agar plates contain ampicillin. This way, only the cells that have my DNA in them will grow (because they are resistant) and everything else won’t. :D  That, in short, is the process. If it works, i’ll be VERY happy. If it doesn’t, i’ll be less happy. I’ll have to repeat everything! Not just these three steps, but all the steps leading to these three steps… That’s almost a week’s worth of work.

Anyway, while my media plates were being prepped, i decided to read random blogposts to while away the time. And the very first post i landed on was this one. This blogger’s colleague had the same problem as me. Transformation didn’t work. And she DID find a solution to why not. Her solution won’t work for me though, because I’m positive i’m using ampicillin plates for ampicillin resistant bugs. I checked. Thrice. But it comforts me, sitting alone in lab on a saturday night, to know that there exist other researchers in the world who have technical problems similar to mine.  Much like this xkcd comic.

Here’s hoping my experiment works this time. If it doesn’t, i’ll cry.

Not really.

OK, maybe a little.

Also, you really should consider heading over to my #Scifund project page and helping out. Much obliged.

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So i have a guest-post up at the #SciFund blog. You should read it if you like:
a) Rowan Atkinson

b) Monty Python

c) LOLcats

d) Dexter’s laboratory

e) SCIENCE!!

Here’s the link – http://scifund.wordpress.com/2011/11/16/on-the-complementarity-of-crowdfunding-and-traditional-grants/

Check it out!! Oh and please fund me. Thanks much!

 

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My Science II (The project in Simple Words)

As you already know I work with Chlamydomonas to study how things assemble and function within the cilia (Cilia being short hair like structures on cells). And this is important because all cells (nearly all) have cilia and they are VERY important for the proper functioning of cells. Which means that if you don’thave properly functioning cilia, you could have serious symptoms like retardation, lung disorders, urinary problems etc etc.

Now… This post is not about the general background of the work… This post is about what I am doing right now… And i am doing really cool stuff.

I take genes from humans or mice that i know are important for cilia (I know this from previous studies) and i put them in bacteria. Why? Because bacteria are easy to grow, easy to kill, AND given the proper nourishment will keep my gene of interest in very good condition. This act of putting a gene into the bacteria is called cloning (bacterial cloning in this case). Once i’ve cloned the gene in, the bacteria start making many copies of it. This happenes because when they replicate, they replicate all the DNA present in them, including the gene i put in!

Now, provided i did everything right and there wasn’t any contamination, i have a culture of bacteria all of which have the gene i want. And ALL of them are activating the gene… The gene then produces a Protein. Proteins, as you’ll recall, are the building blocks of cells. They are the stuff that most things, including cilia, are made of within the cell.  And through a very clever trick (called overexpressing) i’m forcing the bacteria to make unusually large amounts of this one protein that i’m interested in.

Since there’s a large amount of this protein, i can purify large amounts of it from the culture. And once i have these large amounts… I can do biochemical tests (more on those later) on it to see how it works. I can figure out what it looks like, What chemical properties it has, what physical properties it has and what other proteins it interacts with. From this i can make guesses about what its over all role in cilia might be… Is it a structural element? Meaning, is it a part of thestructure itself, like a brick? Or is it a regulatory element, meaning it facilitates the production of the bricks? Or maybe it transports the bricks? Or maybe it tells the cell when it has enough bricks… All of these are possibilities… And very exciting possibilities at that!

All this i can do with just one protein made in large quantities! What about if i made TWO proteins in large volumes?

I could then mix them together… and see if they work with each other… I could ask questions like “is the activity of one protein hindered, or enhanced, by the other?”  I can get answers to these questions by doing a set of very innovative experiments!

In the coming weeks, I’ll go through these experiments in greater detail… And also explain the techniques i use in greater detail. Stick around! And also ask me any questions you might have! I’d be more than happy to answer them and help you understand my science better!

And don’t forget to check out my #Scifund project at Rockethub!

Until next time, Happy Sciencing and Happy Scifunding! (Yes, they are both verbs!)

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Launch!

Hey all!!

The #Scifund project is LIVE!!!

Yours truly can be found at this link – http://www.rockethub.com/projects/3792-c-cilia-in-motion

I really appreciate the your support!!

Thanks in advance for helping out with this brilliant project!!

Cheers!

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My Science

The System I study:

 The organism I chose to study is Chlamydomonas. It’s a tiny little single-celled creature with, and this is important, TWO flagella. The flagella are whip-like projections which it uses to move about, to sense its environment, to find a mate and to mate.

Now, like any other such organelle in the cell, flagella are also made up of proteins. A very precise architecture governs the way these proteins are built and assembled. Think of them as very tiny parts in a Lego complex. The thing with Lego is that you can assemble a few blocks into a component, and then you can bring together many such components to make a bigger structure. That’s what happens here. Each individual block comes together with some other blocks and makes small complexes. This happens in the main body of the cell (the cytoplasm). These complexes are then carried by an intricate transport system to the flagella where they become integrated into the main machinery of the flagellum.

As in any production process, there are many checks and balances on when a block is produced, how many are produced, which blocks come together to form a complex, which complexes come together and when, how many such complexes are needed, what other supporting things like nuts and bolts etc., are needed,  and so on and so forth.

So, this, in very simple terms is the system I study.

Why do I study it?

It isn’t considered easy to explain the motivation for many kinds of science even to other scientists, much less to non-scientists. However, I’m of the opinion that the broad relevance of any scientific endeavor becomes easy to understand if explained in the right context. I’ll attempt now to do just that by trying to take you through things which most of you would agree are important to study, and then showing you the connection between my work and the things for which you take the motivation to be obvious.

Most of you, I hope, will agree that human diseases are a worthy subject of study.

And if I were to tell you that there is a disease which causes the formation of many cysts in kidneys and that approximately 600000 Americans are affected by it and many more worldwide, you’d start to say “something should be done about this!”

This disease is called Polycystic Kidney disease. It’s pretty bad. And it is only one of many things (and perhaps the least) that can go wrong with humans who don’t have properly functioning cilia/flagella.

This is “all very well” you say, “but what has it to do with a tiny little green cell you grow in your lab?”

The answer lies in many factors:

1)       It is hard to study humans due to a lot of practical and ethical questions. So we need to study something simpler.

2)      Eventhough this is a very different organism from mammals, it shares a fair amount of commonality (or homology) in certain proteins with mammals. These are the highly ‘conserved’ proteins.

3)      It is the only standardized study system that we know of in which one can isolate the flagella/cilia and study them on their own without having to deal with background interference.

4)      It provides a fast way to screen a LOT of different genes for potential relevance before studying those genes in mammals like mice or humans.

To recap, diseases are nasty. A lot of nasty diseases come about through the faulty functioning of cilia. It is hard to study cilia in human cells (or any mammalian cells). There’s an alga which makes it easy for us to isolate and study cilia in the lab. The findings from these studies are of critical importance in understanding the mechanisms through which cilia work and therefore critical in understanding how to prevent diseases.

That, in short, is the gist of the question of what system I use and why. I hope I’ve been successful in convincing you of the viability of such an approach. There are constraints unique to addressing a broad audience and also of time and space which limit me from expounding more on the subject. I’d be happy, however, to address any specific questions you might have about my work. 

In my next post, I’ll address the specific project that I hope to work on through your help. Until then, take care!

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My Experiments with Crowdfunding

Hullo and welcome! My name is Aditya and i’m a graduate student currently working in the lab of Dr. David Mitchell. I study, through many biochemical and biophysical techniques, the swimming mechanism of a tiny little critter called Chlamydomonas rheinhardtii. Chlamydomonas is a single-celled organism and has two whip-like organelles called ‘flagella’ or ‘cilia’ (interchangeable terms for the most part) which help it swim. These flagella are in themselves, marvels of engineering. The reason i say this is because it isn’t a trivial thing to produce the hundreds of proteins that make up the flagella and then assemble and  transport these proteins out into the flagella and then make them move at exact intervals of time in response to very specific signals with microsecond accuracies. That is the inherent allure of the system. The complexity and the fun one can have in figuring out the various bits and pieces of this complex structure. Why is of interest to humanity at large? Because EVERY cell has at least one flagellum or cilium. Even if the cell is not motile, i.e. does not swim, it needs a cilium to help it interact with the world around it. Defects in cilia lead to various conditions such as abnormal formation of the heart, loss of assymetry in the body, polycystic kidney disease etc. Which is why it is important for us to study the specific roles that various proteins play in the formation and regulation of ciliary motility. Chlamydomonas is the ideal system for us to study because it is easy to grow in the lab, it has TWO flagella per cell (so twice the yeild!), AND these cilia are easy to pull off the cell and isolate. This makes a myriad of experiments possible which would just not be possible with other test subjects.

With the help of the good scientists Jai and Jarrett, and the people at Rockethub, I plan on embarking on a journey to fund some of my research through the power of Crowdfunding. The realtime/realworld/real people approach of this method is an exceptionally powerful and inherently interesting phenomenon. I’ve long been a fan of the webcomic Saturday Morning Breakfast Cereal and when Zach demonstrated the use of crowdfunding platforms to raise money for projects i thought “WOW! I wonder if it’ll work for science!??!?”

The answer, hopefully, is a resounding “YES!”

This is where you come in, dear reader. Patron extraordinaire. A lover of the sciences. Nourisher (if that’s a word) of the intellect. Benefactor of the downtrodden masses of grad students and impoverished Professors. You are all that is good with the world, all that is noble and pure and simple. You are the last bastion of that elusive attribute – Kindness. Also, you want the wonderful rewards promised in return for your patronage (More on that in later posts). Rewards you couldn’t get from a supermarket. Or even from a specialty store online. Rewards that are intimate and personal. An inside conversation shared only between you and the scientist you adopted. The satisfaction that comes with having known you’ve done a good deed. The deep personal peace that is a hallmark of having been part of something bigger and more beautiful than oneself. Of having had an impact on humanity at large and having been thanked for it.

With that piece of hyperbole (which is sincere but won’t be in any grant application), let me take this opportunity to welcome you all to this page and hopefully to many others like this at the #SciFund Challenge.

Over the next few weeks, i will be putting up details of my project and outlining your role in helping me achieve its goals.

Here’s hoping that you, wonderful reader, will find my work just as interesting as I do and would be willing to show your support for it by way of generous monetary contributions.

WELCOME! and THANK YOU!

Aditya

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