20.6.13

Date: 20.6.13
Time: 13:35
Location: St. Edmund Hall, Oxford, England

Chart of Eukaryote supergroups

This morning one of the members of the lab from Japan explained his work to me.  There are two different types of cells, prokaryotes and eukaryotes.  Prokaryotes are simple cells such as bacteria while eukaryotes are complex, like humans and yeasts. 

Chromosome splitting
Orange is kinetochore

When cells divide, the chromosomes must divide as well.  In order for this to happen, the chromosome pair (which looks like two graphs of a trigonal bi-pyramidal atom with two lone pairs), is recognized by two microtubules which attach to the kinetochore (a series of proteins on the chromosome), and pull the two chromosomes in opposite directions, separating them.  While the contents of the kinetochore of other eukaryotes is known, that of the Trypanosome is not.  With 90,000 genes in the Trypanosome, that's a large gap in knowledge.  It also just so happens that this member of the lab finds the kinetochore of the Trypanosome incredibly interesting and decided to study it.  For other eukaryotes, such as humans, there is a relatively large number of proteins in the kinetochore (100 in humans and 30 in yeast).  Where there was once no information on this area, there are now 19 identified proteins.  This is incredibly important information for the study of Trypanosomes and HAT because it allows us to understand how the cell splits and recreates DNA.  Understanding this process is also very important because, when both microtubules attach to one side, the entire pair is pulled to the side with the microtubules, killing the cell, or, in older cells, causing cancer.  Also, chromosome 21 splitting into three pairs instead of the usual two, causes Down Syndrome.  Being able to understand the nature of the chromosome splitting in a Trypanosome through microtubule attachment and kinetochore contents can allow for the production of a drug that would target these proteins or microtubules, preventing chromosome splitting and cell growth, causing the parasite to die.

DNA sequence
Can be identified as a protein because of the leading ATG tag
The capital letters below indicate the enzyme that breaks that strand

Rebinding of DNA thanks to Ligase!

Next, Jack and I worked to identify and code some DNA.  First, the DNA which had been chopped up into smaller pieces using enzymes, is filtered out using special vials.  These vials have a filter that will trap only the DNA and allow the enzymes to pass through and be disposed of after a quick ride on the centrifuge.  After the chopping enzymes have been discarded, a new enzyme called ligase is introduced.  This enzyme binds the proteins together again, repairing the strand of DNA.  Once the ligase has bound the strands of DNA back together they are brought to bacteria, which essentially act as a xerox for DNA. As the bacteria grow, they reproduce the DNA which can then be used later.  

DNA sequence with coded DNA underneath

Vladimir followed with a quick overview of DNA sequencing.  The Green Fluorescent Protein (GFP), which earned Martin Chalfie, Osamu Shimomura, and Roger Y. Tsien the Nobel Prize in 2008, can be used to tag and identify certain proteins. This system replaced the time consuming and expensive method of tagging the antibodies which then attached themselves to the proteins.  DNA is made up of 4 bases, which combine in sets of three called triplets to form amino acids which bind together to create proteins.  The four bases are guadine, denoted by a G, thymine, denoted by a T, adenine, denoted by an A, and cystosine, denoted by a C.  When you want to look at DNA, you take a sample of a plasmid, which is a circular structure as well as a primer, which is a small strand that is complementary to that plasmid and can provide 1000 spaces of DNA downstream, and send them to a company that processes the DNA and sends it back in the form of a word document.  This word document contains the letters of the four bases organized into triplets that can then be sorted into amino acids with a chart.

Chart used to code DNA sequence

Each amino acid has its own letter assigned to it and these letters are put together in an order that is called the genetic code.   You can sort of think of coding as either one of those secret-message wheels 

Secret-message wheel

or as factoring a polynomial by substitution.  The genetic sequence is the giant strand of factors where like values have not been combined and the polynomial has not been placed in standard form.

Really long, complicated
polynomial

  The code is like when the polynomial is being solved and you use substituent which is basically like creating a definition for a variable, so if x=45y+17, you only have to write x because they are synonymous  making the equation look much cleaner and smaller. Trypanosomes are special in that they take DNA put into them and incorporate it into their own genome.  Therefore, they are great subjects for the affects of mutating a portion of a strand of DNA because the parasite will absorb the changed DNA and act accordingly.  

Process of adding foreign DNA to a pre-existing strand of DNA
The diagram upper-centre shows the DNA and plasmid combining
The lower-left-hand corner shows the bacteria creating more
samples of the DNA which can be seen at the macroscopic level
on the lower-right-hand corner where the bacteria with the modified
DNA is grown before the new larger sample of the modified DNA is extracted