Week 8 - Placement 1

This week Derek brought me straight to the lab to work with Carol again. Derek informed me that himself and Carol had looked at the results yesterday and saw that the results didn't turn out as well as planned. So for today I would do the same as what I did last week, however on a much smaller scale and only analyse 28 samples of DNA at a time.


Carol had taken out the DNA from the freezer already so I didn't need to wait for them to defrost. This week I preformed all of my work on ice to prevent any of the DNA and mix from evaporating from the dish. The very same as last week, I made sure that all of the samples were mixed properly by flicking them and spinning them on a centrifuge machine.  I then pipetted 2 micro-liters of DNA into 28 wells on the dish. Once I completed this I made up the master mix and then pipetted 2 micro-liters of it into each hole. After, I set up the geno-typing machine that would be used to analyse the DNA. While I waited for the machine to finish analysing the DNA I read some more tutorials about different discoveries made in the genetic field.


After lunch I looked at the results produced by the geno-typing machine. Afterwards, I took the next 28 samples and prepared them for geno-typing just as I did earlier. I then set up the machine again to analyse the DNA and Carol would show me the results next week.

Person peparing the DNA for geno-typing

Derek then explained to me how I would be working with Sinéad next week in the neuropsychology department. I would use the results that I came up with today and Sinéad would show me the next step after geno-typing the DNA. However, if it turned out that my results aren't as good as we had hoped, we will use an old sample template instead. I look forward to next week and discovering the next part of the process.

Week 7 - Placement 1

This week Derek explained the project I would be working on over the course of the next 4 weeks. He took into consideration the areas which I found most interesting which were genotyping the DNA and look at neuropsychology. Derek then took me to the lab where I would be working with carol for the day.

In the Lab Carol explained how I would take 96 different samples and label them on an excel document and on a sheet. Then I would take a small sample of each individual sample and transfer them into a smaller container, using a pipette, which would be  used to analyse the DNA later in the day.

Different types of pipettes

Once I had finished labelling and moving the samples by myself, Carol showed me how to make up the master mix which is mixed with the DNA samples so that they can be read by the genotyping machine. Once I made this up, Carol taught me how to pipette 8 samples at a time. I first had to practise on water just to make sure I have the hang of it.

Pipetting 8 samples at one time

Once I had finished with this I sealed the dish and carol and I set up the genotyping machine up and made sure that everything matched the name of the sample that I labelled earlier. Just before I left Carol explained how she would hove to go and fine a mixing machine somewhere in the building in order to make sure that the mater mix was mixed in with the DNA samples. She would later activate the machine and would let it run for the 2 hours and then she would save the results and show them to me next week on work experience. 

Week 6 - Placement 1

This week Derek brought me to a completely different side of the centre. He introduced me to Sinead who actually works with the patients of schizophrenia who donate samples of their DNA to the lab to be used in research. 

Firstly I went with Sinead to a room in the library upstairs where she would show me some of the tests she gives on the patients. Sinead explained to me some of the sin tomes of schizophrenia patients. These include; pronunciation, short term memory, problem solving, remembering faces and emotional recognition of the face and eyes.

For the pronunciation test the patient is given a list of words to read and if it matches the correct pronunciation they are correct. For the short term memory test 2, 3, and 4 digit numbers flash up on  a computer screen really fast in a sequence. The patient then has to click the mouse when he/she see the same number repeated one after another. The emotional recognition test involved looking at just a picture of some-one’s eyes and saying what type of emotion they were feeling at that moment. For the problem solving test the patient is given nine blocks of plastic half white and half read. The patient then must make the shape or picture which is drawn on the card in front of them. 

After Sinead finished showing me all of the tested I went back to her office where she showed me some images from previous projects she had worked on to do with neuropsychology. She was able to highlight different parts of the brain and show me the connections between certain areas of the brain. This looked really interesting and I was really intercepted by it. 

An example of what the connections look like

Later I met with Omar another person who works in neuropsychology. However he works with patients who preform different tests while in an MRI scanner. While the patient is solving different problems in the scanner the machine is taking digital images of the person’s brain every few seconds. Omar showed me some of the test performed by some of the patients while in the MRI scanner. 

MRI Scanner

He also showed me which parts of the brain are active when answering and solving different problems. Once Omar has tested out at least 100 patients with schizophrenia and 100 patients without, he complies the images together to create one general image. He can then easily compare the images of the brain with the person of schizophrenia and the person without schizophrenia. 

This is what some of the scans can look like

I found today one of the most interesting days of my work experience so far. Although I wasn't completing a lot of practical work, I felt I defiantly learnt a great deal. 

Week 5 - Placement 1

This week I was working with Paul once again on bioinformatics. Paul explained how he sequence the 2 reads in every lane as far as lane 16 over the course of the week while I was at school. 

Firstly we had to download all of the information form the servers in order to align the DNA. This was a very slow proses as the file was very large. While waiting for the file to load I looked at some more tutorials online about the history of genetics and DNA. The website that I was using went through all of the individual discoveries by different scientists over the years in relation to genetics. It also showed me some of the Nobel prizes won by scientist working in the field of genetics and what they discovered. A lot of what they discovered we kind of take for granted now but it was very interesting to see the experiments they had to perform in order to come to that conclusion.

 Once all of the Results from the DNA sequencing was downloaded we allied all of the files onto one program so that we could compare the lanes and reads equally. some parts of it were very interesting as not all of the lanes matched up. This indicated that there was either a mutation on that read if it may just be a fault. However for some of the mutations we went online to check and clarify. Unfortunately we found no new mutations, so we didn't get a paper published out of that ;) 

After our DNA was allied Paul showed me how to create a dot line graph to represent our results. 

Graph

Today I learnt that in science you need a lot of evidence in order to come to some sort of conclusion. i.e needing 16 lanes in order to compare the reads. You also cannot take anything for granted, you but check to see if you are correct first. Today has shown me that you must be very precise when researching and carrying out tests. 

Week 4 - Placement 1

It was very quite today as most of the staff were at a genetics conference in Germany, therefore I worked with Paul, who works with bioinformatics and sequencing DNA.

Over the coarse of the morning Paul introduced me to using the different commands on a different type of computer software called linux. He also taught me how to download and install new computer programmes on the computer. 

Command	Action
pwd	"Print working directory" - show what dir you're in.
ls	List the contents of a dir.
ls -l	List the contents of a dir and show additional info of the files.
ls -a	List all files, including hidden files.
cd	Change directory.
cd ..	Go to the parent directory.

A list of some of the commands used in linux.

He explained how the servers and the computer systems work at St.James's and how they are connected to Trinity aswell. Later on I looked at some youtube videos on the way in which the DNA is sequenced to make sure I fully understood how it worked. I also had to reseach different sites in order to explain the computer software behind it. 

Paul showed me a sample result of what the sequencing should look like at the end. We then began sequencing the first read of Lane 4 of the DNA. Once this was finished we sequenced the second read of DNA of lane 4. It is a quite slow process as it takes the server some time to process all of the information and pick out the correct information needed. While the computer/server sequenced all of the DNA smaple, I look at different programmes which anylsis the DNA sequencing result. You basically have to look for mutations in the DNA and compair it with a control. Some of the mutations can have an effect on the person and some cannot. The more reads you have to work with the surer you can be with your judgement. Paul discribed how he would continue running different reads over the coarse of the next week and then have them for me to work on next Wednesday.

http://www.genome.ucsc.edu/cgi-bin/hgTracks?hgsid=304466077

 Here is a link to the website used to analysis the DNA that is sequenced.

I really enjoyed today as it was a completely different experience for me working with different forms of software. I thuraly enjoyed working with Paul today as he not only taught me a great deal about computer science, he also explained to me about collage choices and job opportunities in the subject of science. 

Week 3 - Placement 1

Today I looked at the results from the genotyping experiment that I performed last week. Carol explained how the different types of DNA are sorted into three groups, AA, AG or AT. We then looked up the results on the internet also to see if they matched our results.

How the protein is produced from the DNA

Later I met with Game who explained the latest project that he is working on which is, growing cells from the very beginning and then taking the protein produced by the DNA in the cells and analgising the protein. However it is a very long and time consuming process. We mostly talked about X factor or One Direction to fill the the time! ;D We had to stylized everything and all of the work had to be conducted in a hood to prevent any enzymes coming in contact with the cells.  I was given my own flask to work with, is if i mucked up it wouldn't matter! ha :) 

After lunch I attended a seminar for a half an hour, however I missed the introduction so I didn't really have a clue what was being presented. After, Derek introduced me to Paul who works at sequencing the DNA on a computer, also know as bioinformatics. He showed me how the software he uses work. He also explained how to sequence the DNA properly. He then explained what I would working on with him over the next 2-3 weeks. All of the work I do with him I will have to present at the end of the work experience, wish me luck with that ;)

This week I really enjoyed working with new people and seeing different aspects of the lab.I think today I learnt the most by far.

Week 2 - Placement 1

First of all I met with Derek who told me what I would be doing today. He brought me up to where Ciara and Carol and other Ph.D. students work. I was given a computer for the day. Derek showed me a website called DNA from the Beginning which basically told you about the discovery of DNA and genes from the very beginning. I found the website extremely helpful and interesting as it linked into a lot of the Biology course that I studied for my Junior Cert.

http://www.dnaftb.org/ 

( Just in case you want to have a look) 

Just before lunch I went with Ciara to the lab to help me prepare my DNA and 5 others samples for a genotyping test I would be preforming after lunch with Carol.

Once I returned from lunch I went straight to the lab with Carol to set up the DNA to put in a machine which looks for mutations on the DNA which is also known as genotype. Once again Carol allowed me to pipette which was really fun and interesting. After completing the protocol for the preparation on the DNA we put the DNA samples in the machine for reading. 

This week I was trained how to pipette properly and how to use various machines with in the lab. 

Next week Derek said that I will be working with others form different labs. I look forward to see other aspects of the Institute. I can't wait for next week! 

This is basically what the genotyping machine looks like. Most of the machines in the lab are given nick names, the genotyping machine is called Patrick from Spongebob Squarepants :)

Week 1 - Placement 1

This Wednesday was my first day of work experience at the Institute of Molecular Medicine at St. James's hospital. I was quite nervous, but also very excited and eager to know what I would get up to over the course of the day. My employer Derek was very welcoming and I began to relax once I started talking to him.

Firstly Derek brought me to his office and showed me the basics of genetics and how they work. I know it may seem boring but it was actually so interesting as it linked into a lot of my junior cert science course.After, Derek introduced me to Ciara who works in the research lab. Ciara showed me around the rest of the building and different machines used. She also showed me actually results from different experiments and explained what they show the scientists. I really enjoyed working with Ciara as she explained everything in simple form and was very friendly and chatty and was also very easy to talk to and get along with.

Just before lunch I gave a saliva sample in order to do a DNA extraction test (I know it sounds horrible!) . We added a chemical to help separate the saliva and the DNA from each other and left it in an oven at 50 degrees for an hour. We then prepared the gel which would be used later in the experiment. I was given my own lab coat and gloves, I felt so professional! :)

After lunch I met with carol, who also works in Derek's research lab. She completed the DNA extraction test with me. It was very exciting as I got to pipette and use a "spinning machine". Although I was very very nervous using the "spinning machine" (can't remember the fancy name for it) as it is very expensive. 

Once there was only pure DNA left we added a colour and but it on a gel. Electricity then flows through the gel from negative to positive electrodes in order to drag the DNA out. After about a half an hour we used the "Ray" machine (named after Ray Darcy). That was the most interesting part of the day for me as it showed me how long my DNA is. It also showed me how incredibly small DNA is as well.  I didn't understand it at all at first but once carol showed me the results it suddenly clicked with me!
The best part of the day was the practical side of things and working with the different machines. The only bad part of the day was properly lunch as I didn't have a clue where to sit and there were loads of collage students around, but I will know for next week! ;) 

 

This is what you basically saw then you looked though the "Ray" machine. The Ladder at the edge is used measure the length of the DNA. the other 4 holes are 4 different samples of DNA.