The May 17th Notebook

Day One at NCBS


 * People at NCBS-study

-Molecules -MacroMolecules -Cells -Tissues -Organs(very few people in NCBS study organs) Organs on their own might themselves not be Intersting -Body -Populations(Families, Groups of Individuals- Populations in really large Scales) -Ancient DNA.(Samples from fossils)

Process

Powders cutting DNA, Sequencing DNA Machines: Microscopes, Influencing movement of molecules Electrophysiology- Studying Neurons

DNA sequencing is very slow, so nothing much seems to be happening. To truely understand this, you need to go through an entire excercise.

Microscope

-4 people

DNA experiment

-5 people

How do we divide work?

Everybody wants to do both and then we can switch.

Tomorrow at about 10 in the morning;we go through microscopy and half a round of DNA and on Wednesday ,we finish the DNA experiment.

For the last 10 years the image is acquired on film or CCD chips once the image is done we look at the digital image and we can look at the file and then extract the images.

Use MATLAB for image processing.

What are/were the big questions in Biology?

-Evolution -Cell structure? (became important after the microscope). -Before darwin it was about classifications and taxonomy. -traits of offspring-how this information was transmitted. -Homunculus-babies grow into bigger babies.

-Where are these instructions stored? studying diseases-they saw aberrations in chromosomes studying chromosomes during meiosis In the 40s the big question was -How does DNA store and transmit information -DNA contains information ATCG: -Allows you to replicate the information.

Hargobind Khurana figured out - -How to read the information -the series of letters help you make a protien-insulin

Since the 40,50's the questions haven't changed that much:

Notes:

-If you give someone the full genome of the organism- They will have no idea what that means-I can guess what proteins it produces. How does an animal form from the genome? No idea. How signals in cells work? No Idea. Can you make life from scratch? No idea.

Today in factories, we can synthesize every molecule in a cell but we cannot synthesize a cell.

We can synthezise a virus(not a living thing)

We cannot make a cell (?)

How does the brain work?

Cells have a property of self-organisation.

Cells don't need to make themselves from scratch-It happened once in history

Mukund works with E-Coli. Ecoli has been studied for about 100 years, we know almost everything about it( genes, proteins, shape and structure)


 * E coli has 4000 genes and can make 4000 different proteins
 * The length of its genes is 4 million base pairs
 * One needs atleast 3 letters to make an amino acid
 * It however only makes a 1000 protiens

There's something called Junk DNA, which is primarily misunderstood.

--Switch--->Controller>genes-->

We take genes and the switches that regulate them and make these circuit


 * Make a DNA(switch) Gene(switch) DNA(switch)


 * Then inject this into a cell


 * The cell runs the program.

Why not just have a bunch of Genes? Why have a network?

Cell needs to process information. Can we make a switch from scratch that responds only when the sugar is high AND temperature is high?

What else can switches do that genes cannot do:


 * There are emergent properties
 * the collection of oscillator
 * memory
 * positive feedback

Also understanding real cells:

Building instrumentation

Making cells from scratch.