CRISPR is used as a genome-editing
tool by scientist to change a genome by altering, adding or completely removing
portions of the DNA sequence. To do this Cas9, an enzyme and guide RNA (gRNA)
must work together. The gRNA will bind the segment of DNA that is complementary
to its own transcribed bases. Because it will only bind to a section of DNA that
is complementary to its own bases, scientists are able to introduce their
pre-designed gRNA into the body that are transcribed to target certain
sequences of the DNA. Cas9 simply follows whatever gRNA attaches to it so
scientists are able to fully harness its unique DNA cutting abilities. Cas9 is
able to cut through the two strands DNA which causes the DNA to try to repair
itself. Without a proper template the gene will “turn off” allowing researchers
to study its function. By modifying Cas9, scientists can make it instead turn
on that gene or edit the genome so that the gene can be removed or new DNA can
be added. In short, CRISPR can be programmed to edit specific sections of DNA,
allowing the addition, subtraction and alteration of an organism’s genome.

The CRISPR-Cas system was first
discovered in bacterium. It is the defense system of bacteria against phages
and viruses by protecting bacteria against repeat phage infection. CRISPR is
short for clustered regularly interspaced short palindromic repeats. As
its name suggests, CRISPR is made up of repeating DNA sequences with spaces in between.
When a phage infects a bacterium, its DNA is inserted into the bacteria’s
genome, between two of its repeating sequences, creating these spaces. In
bacteria these spaces contain the DNA of phages who have previously attacked
it. These spaces act as reminders of the previous attack so that if the same
invaders return, the CRISPR-Cas system will be able to recognize and destroy
them. Cas, which stands for CRISPR-associated, are the proteins that are able
to cut out the DNA that the phages are trying to insert into the cell’s genome.
In order to do this, guide RNA (gRNA) are transcribed with the DNA information
the phage left behind in the spacer slot. Then they attach to Cas-9 proteins
and locate the phages by matching their transcribed DNA sequences with the
invaders. Once they have located the phage, which is trying to infect the
prokaryote by inserting its DNA into the bacterium’s genome, the Cas9 enzyme
cuts out the DNA, destroying it and avoiding infection.

Because of the way the CRISPR
system is able to be so easily personalized it has great potential in treating
many genetic disorders in humans. In diabetes mellitus type 1 the autoimmune
system mistakes the cells that make insulin as a foreign invader and destroys
them, so that the body can’t make its own insulin anymore. Several genes
variants from the human leukocyte antigen family of genes have been found to
increase the risk of developing type 1 diabetes and others have been found to
be protective against it. The CRIPSR technology may be able to find the DNA
sequence that includes these harmful genes that cause the immune system to
attack its pancreatic beta cells and turn them off or even insert some of the
protective genes in their place. Another possible solution would be to insert a
segment of DNA that would change which cells were the ones to create insulin,
since the immune system is only attacking those specific beta cells. Scientists
are very excited and hopeful for all the possible uses for the CRISPR system,
but as of now testing on humans is not allowed.

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Topic 2: Bioinformatics 


Bioinformatics is the science of
storing and analyzing sequenced genomes and their behaviors; all the data
curated from genomics. The need for bioinformatics came about in the 90’s when
the Human Genome Project was under way and the need for organization and
storage came to light. Now that all the databases are available online, mass
dissemination has occurred which has progressed DNA sequence analysis far
faster than would have been possible without bioinformatics. There are small
databases online from facilities that focus around a specific topic as well as
massive databases from around the world that collect as many sequences as
possible. One of the smaller more focused databases, called the Protein Data
Bank, is the combined effort of Rutgers University and the University of
California, San Diego. Their database is a collection of all three-dimensional
protein structures that have ever been determined. The large scale online
databases are NCBI in the United States, the BGI in China, The European
Molecular Biology Laboratory, and the DNA Bank of Japan who are all able to
share their data. There are many programs on NCBI’s website that help
researchers to identify any new sequence they have happened upon. There are
programs to compare a specific DNA sequence with every other recorded DNA
sequence in their database, as well as compare predicted protein sequences, and
search any protein sequence for matching amino acids, to help determine what
their function may be.


By enabling the ability to analyze
genome sequences online, it has become easier to identify new protein-coding
sequences. To determine a genes function, we are now able to compare a new gene
with a known gene and find shared pieces in the same or other species which may
lead to the new genes function. We are now also able to inactivate a gene to
determine what its phenotypic effects are. By being able to compare genomes and
study sequences of genes and proteins as a whole system, scientists have been
able to discover more in a shorter amount of time than ever before. The NCBI
database for instance is estimated to double in size every 18 months.
Bioinformatics is crucial for furthering scientific discover in genomics,
systems biology and many other fields.












Topic 3: Describe the work of Barbara
McClintock that led to her receiving a Nobel Prize in Physiology or Medicine

Barbara McClintock was a
cytogeneticist at Cornell University. She dedicated her entire life to the
development and research of maize cytogenetics, the study of chromosomes and
their genetic content and expressions. From the late 1920s throughout the rest
of her life she studied the genetics of maize from genetic recombination to the
enthnobotany of maize races in South America. Unfortunately, for decades her research
was discounted and scoffed at, so much so that she quit publishing her research
in 1953.


 McClintock continually studied how maize
inherited characteristics, such as corn kernel color, throughout generations. She
studied maize chromosomes using microscopic analysis with her research she was
able to create the first genetic map for maize. This map connected certain
areas of the maize’s chromosomes with phenotypic traits. Looking further she
noticed that during reproduction the maize’s chromosomes would become altered
and the corn’s kernels would present a different color than expected. By
tracking the patterns in corn kernels throughout many generations of corn and recording
the changes in colors she saw in the kernels and the maize’s chromosomes, she
came to the conclusion that some of the maize’s genes were able to move from
their original location in a genome to the location where kernel color gene was
located, changing that gene sequence and causing nearby genes to turn “on” or “off”
so that the color of the kernels were altered.


 These “jumping genes” are actually known as transposable
elements. Transposable elements go through a process called transposition in
which they are able to move from one location in a cell’s genome to a target
area through a recombination process. Transposable elements do not actually
detach from their cell’s DNA but rather the genes original site and its target
location are brought quite close together by the help of enzymes and proteins that
bend the DNA so that they are much closer to each other than they would normally
be. At this point the gene moves into the target location and alters that
sequence. Transposable elements and their related sequences make up 75% of
repetitive DNA, which in turn makes up 44% of the entire human genome, clearly
McClintock’s findings were of extreme importance.


 Unfortunately, at the time the prevailing
theory was that genes were not able to move and only occurred in their specific
area on a chromosome. Therefore, all her research was discounted for decades
until decades later the same jumping genes were also found in bacteria. Since
her research was now indisputably correct, almost 40 years after her discovery
she was finally granted the Nobel Prize she deserved. She is the only woman to get
an unshared Nobel prize in the Physiology or Medicine category. This discovery
was what paved the way for modern molecular genetics. Thanks to McClintock’s
work we now know that prokaryotic and eukaryotic organisms have transposable
elements, or jumping genes.


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