Megan Torres
Bioinformatics ‘09
Mentor: Dr. Brennan
Co-Mentor: Mrs. McMahon
Bronx Community College
George Washington Carver High School for the Sciences
This was my first year in Harlem Children’s society. I worked in Bronx
community college with Dr. Brennan as my mentor and Mrs. McMahon as my
co-mentor. I was in the bioinformatics group. I learned a lot this summer
about protein, bioinformatics, DNA, cancer and other diseases. The first
week there Dr. Brennan was the one teaching us but then after that week
Mrs. McMahon took over. I appreciate all their time and dedication to us.
There were more than 15 people in that classroom and as well as learning and
developing new skill I also made new friends and had a lot of fun.
The first day we did a packet that had 5 pages it was called “What do
genes do?” It spoke about chromosomes and DNA. It says that in the
chromosome there is DNA molecules which contain many genes. Each of
those genes is specific to a protein. It is written in a sequence of bases
containing base pairs (A-T and C-G). It also had a diagram of a small part of
one gene that carries coded instructions for one kind of protein. We each
got a sheet with base sequences of DNA. Then we compared them with our
partners. We had to see how the base sequences are similar, different and
if we think both DNA’s will have the same proteins. There was then another
paragraph that stated that genes aren’t able to leave the nucleus to carry
the instructions to the ribosome, also known as protein factories in the
cytoplasm. The packet then explains how a protein is made. A cell must make
copies of the coded information that it holds, so that it can move from the
nucleus to the ribosomes. The way this information is copied is an enzyme
transcribes the genes base sequence to make messenger RNA (mRNA)
molecules with opposite base sequences. There is no T is RNA so instead of
base pair A-T and T-A it is A-U and U-A, while the others remain the same.
Then we compared our mRNA sequences with our partners. We had to see
how they are similar, different and if we think both mRNA sequences will
have the same proteins. Then it continues on explaining the process of
mRNA. The mRNA leaves the nucleus in order to attach itself to a ribosome
in the cells cytoplasm. While in the ribosome, the mRNA base sequences are
translated to determine the order of amino acid building blocks that will
make up a specific protein. Then after we finished with everything with that
we had to research the protein affected by gene mutation and 2 symptoms
of five different diseases. The diseases were Sickle Cell Anemia, Cystic
Fibrosis, Tay-Sachs, PKU (phenylketonuria) and Muscular Dystrophy. That
was basically all we did for that first day I was present which was a
Wednesday.
The next activity we did on a different day was looking for a variation
in two different peoples DNA base sequences. Then we did an overview of
Sickle Cell Anemia. We were asked questions such as “What are the primary
symptoms of sickle cell disease? What happens in a persons body to cause
these symptoms?” I answered it by saying “some symptoms are coldness of
fingers and toes, chest pain, head aches, muscle/joint aches, dizziness,
organ/blood disorders, pale skin and this happens because the red blood
cells in the body are distorted. We also role played as if we were a doctor
and we tested a ladies two children and compared them to normal DNA
without this disease and to DNA with the disease. We had to read a gel
electrophoresis test to determine if the children had the disease, were
carriers or had no sign of it in their bodies. The tests concluded that the
ladies daughter was a carrier while her son did not express nor carry the
trait.
We also took an inventory of human traits. It asked us about noses,
ears, thumb, gender, dimples, hair, eye color, allergies, height, and wrist
circumference. After that we were asked to do a simple worksheet about
human variation. It asked us questions like “Describe some of the benefits
of human genetic variation. What are some of the potential problems that it
can cause?” On the 13th of July we had an AIM: how can we construct
contigs from DNA strips? She then told us that contigs were overlapping
genes. She explained to us we would be role playing as if we were working in
a company called Onconomics. An Oncogene allows cancer to develop in the
body. Then Mrs. McMahon shared a few facts with us. She told us that
breast cancer is most likely to happen after menopause but if women get it
before then they can be potentially carrying the BRACA gene. Estrogen is a
hormone that protects females from breast cancer to a certain extent. She
told us that a polymorphism is a variation in genetics that happen in a
population for example in eye color but generally this doesn’t cause disease.
If there is a change in DNA that causes a disease or disorder it is called a
mutation. She told us that a rational drug design uses DNA and amino acids
to find the disease and a specific way to treat it for that person. She gave
us DNA sequence to separate into codons which are 3 nucleotides of mRNA
which make an amino acid.
For another day we continued to work on the Onconomics corporation
project. We received a letter from the research director speaking about the
OncoX drug which will be entering clinical trials soon. They told us that we
must carefully design the most trials to provide the maximum amount of
data regarding which types of cancer OncoX is effective treatment. They
told us that there sequencing department will send us raw sequence data for
assembly and analysis. The DNA sequences they will send us will come from
cancer patients and members of their immediate families who have agreed to
help them in their efforts. Also they will be sending us a control sequence
from a healthy individual who does into have cancer in his or her family. The
received samples can be linked with identifiable information. Our lab team
assignments were to assemble the complete DNA sequence then to compare
the sequences with other lab teams then to consider whether the sequence
difference are genetic polymorphisms or a result from errors in sequencing.
The last thing we had to do was consider whether the informed consent
form signed by the donors provides adequate protection to the individual and
to Onconomics. We also had to fill out a sheet called OncoX multiple DNA
sequence alignment. We had to go on a website and go through a few things,
we then had to use a specific DNA sequence we were assigned and check for
mutations. We then had to fill out a worksheet called OncoX
electropherogram analysis. We had to go on a website called
www.bscs.org/onco then click on the sequencing department, and then click
on the sequencing protocols. We had to examine 3 sample
electropherograms. We had to fill out a few questions as well.
Another day we had to translate reading frames from a DNA strand.
It was pretty easy for me and it was kind of fun. She gave us a genetic code
amino acid translation chart. It has what amino acid the three codons stand
for, for example UUU = Phenylalanine and GAG = Glutamate etc. With that
we also had to do an OncoX multiple amino acid sequence alignment
worksheet. We had to look at every sequence in each reading from we
translated and check for amino acids that were mutated and carried
diseases. We also did something called BLAST which stand for Basic Local
Alignment Search Tool. There’s two types of Blast’s, there’s BLASTN and
BLASTP the And N in BLASTN stands for nucleotide while the P in BLASTP
stands for protein. “Which means that the nucleotide or amino acid
sequences can be compared depending on which search tool is used”.
On another day we played a life game where we had to roll the dice
and use the number to see what choices you will make in life. It was pretty
fun and I was very healthy at the end and lived for a long time. After we
played the game we had a worksheet about the game and what it was for.
After we played that game we spoke about small scale mutations. There are
base substitutions, deletions and insertions. A base substitution is when
there is one nucleotide in error which can cause the whole amino acid to be
wrong. There are three types of base substitutions. One of them is called a
silent mutation which causes no change and no difference in the amino acid.
The second one is a nonsense mutation which is the worst kind because it
changes the amino acid to a STOP codon. The last kind of base substitution
is called a missense mutation which leads to a new amino acid which can be
conservative meaning that it contains the same characteristics or non
conservative where it does not contain the same characteristics. Then there
is a mutation called deletion which basically some nucleotides are deleted
and are missing. Last but no least of the mutation is the insertion which is
basically some nucleotides are added to the strand. Then we took a report
form from Onconomics. It asked us a few questions about differences in
polymorphisms and mutations etc.
On another day in this program we searched on line at bscs and pulled
up reading frames. We searched through 11 reading frames to look for
founder mutation, if affected or a carrier by A-T. We also extracted DNA
from a strawberry, it was a GREAT experience. Ho we carried this out was
we took a half of a strawberry and placed it into a small baggie and we
mashed it. Then we squeezed that into test tube. Then we added soap water
and ethanol. The ethanol created a barrier between the two level and we
were able to kind of fish out the DNA.
On another day we read an article about a gene newly discovered for
intelligence. We were asked a few questions such as “what is intelligence and
how can it be measured?” I answered that question by saying there is a
traditional IQ test but I believe you can measure intelligence by the lack of
ignorance. We also watched a few video clips about a lady who might have
breast cancer and had to answer questions. One video was about considering
if she should take the gene test or not. Another was about talking to her
family about this etc.
On another day we learned about gene expression. It was said that
our genes and our environments mold who we are and our behavior. There
was another day that we did a packet about a noel trait. We had to read this
packet answer question, record data, transfer data and make graphs. We
also tried to see our novelty seeking trait by taking a survey that asked yes
or no questions like Would you: drive a car 100 mph, travel alone in a new
city, hit a stranger in an argument etc. There were 65 questions like that
and I answered 51 of them with a yes which was the highest in our group.
That means im more willing to take risks than other people.
This was a great learning experience for me and I also learned a lot
about myself. Mrs. McMahon is a great person and a great teacher. She
always cheered me up because she is just an enriching person. Dr. Brennan is
also very intelligent and good at what he does. This program taught me so
much, it is hard to try and sum it all up in an essay. I developed skills and had
experiences I would have had in a million years. All the HCS staff was very
helpful, willing and supportive. Dr. Sat is a great man for starting this
program and I thank all of you from the bottom of my heart for letting me
experience something so great. THANK YOU ALL SO VERY MUCH =]