Transcript Biotechnology and Bioinformatics

Biotechnology and
Bioinformatics:
Bioinformatics
Essential Idea: Bioinformatics is the use of
computers to analyze sequence data in
biological research.
TOK
Knowledge claims justified by reference to databases
raise unique knowledge questions. How reliable are
knowledge claims justified by reference to data
sources developed for different purposes by different
researchers using different methods?
Databases
A database is a set of related data that has been
organized and made available for access by many
users.
This data can be easily accessed by users anywhere
in the world.
http://www.werc.usgs.gov/ProjectSubWebPage.aspx?SubWebPageID=6&ProjectID=258
Databases
Due to the rapid increase in data acquisition and the
ease of input of this data into such databases, the
amount of information being stored is increasing
exponentially--essentially doubling every 18 months.
Databases
In the biological sciences, DNA sequence and protein
sequence data is the most often accessed.
These databases can be searched to compare newly
identified sequences with sequences of known
function in other organisms.
Databases
This allows
researchers to use
multiple sequence
alignment to look at
the evolutionary
relationship of the
organisms being
studied--such as
with phylogenetics.
http://bcrc.bio.umass.edu/intro/content/phylogenetics-dna-protocol
Multiple Sequence
Alignment
When studying
evolutionary
relationships,
scientists often
look at the
sequences of
multiple
organisms.
http://www.nature.com/ncomms/2014/140902/ncomms5734/fig_tab/ncomms5734_F7.html
Multiple Sequence
Alignment
The gene function and
the gene sequence can
be studied in model
organisms with similar
sequences to learn more
about them.
This allows researchers
to make inferences,
develop hypotheses, and
to design and test
treatment protocols for
people with genetic
disorders.
http://www.nature.com/ncomms/2014/140902/ncomms5734/fig_tab/ncomms5734_F7.html
Sequence Alignment
Sequence alignment software is what allows people
to make a comparison of sequences from different
organisms.
This software can be accessed online.
For instance, the SDSC Biology Workbench we’ve used.
Searching databases for comparative purposes
allows newly identified sequences to be compared
with sequences of known function in other organisms.
BLAST
BLAST stands for Basic Local Alignment Search Tool.
It is an algorithm for comparing biological sequence
information.
Users input and access data from anywhere.
There are many different ways in which this can be
used.
BLASTn is a nucleotide sequence alignment tool.
BLASTp is a protein alignment tool.
BLASTn
Using this program, a DNA sequence can be input
and the software will return the most similar DNA
sequences from the DNA database specified by the
user.
BLASTp
As with the BLASTn, BLASTp allows the user to
query a protein sequence and get the most similar
protein sequence from the specified database.
EST
EST stands for Expressed Sequence Tag.
Living organisms produce mRNAs from splicing
together exons.
http://www.mun.ca/biology/scarr/Expressed_Sequence_Tags.html
EST
In vitro studies of tissue
samples of organisms
about which little is
known allows for the
reverse transcription of
these mRNA transcripts
to yield cDNA that
corresponds to the
genes expressed in that
tissue.
http://www.mun.ca/biology/scarr/MGA2-08-04.html
EST
Thus, an EST is a short “sub-sequence” of cDNA. It
is often used to identify gene transcripts, and plays an
important role in gene discovery and sequence
determination.
Simply put, the cDNA is complementary to mRNA and
represents portions of expressed genes.
This technique allows for a comparison ESTs from
lesser-known species with those from a species
whose genome has been well-characterized enabling
researchers to identify the function of gene loci in the
new organism.
EST
The development of a complete EST library is an
important step in the mapping of a new genome.
ESTs can be mapped to specific chromosome
locations using a variety of methods (radiation hybrid
mapping, Happy mapping, FISH).
EST Uses
ESTs give information that allows for the design of
DNA microarrays and subsequent determination of
gene expression.
EST Uses
The use of EST information
gives researchers
knowledge about the
function of a gene.
This information can be
used in the diagnosis and
treatment of disease.
Researchers are currently
designing methods to mine
databases for EST
information and gene
discovery.
http://www.nature.com/ng/journal/v47/n2/fig_tab/ng.3205_F1.html
Gene Knockout Technology
Gene knockout technology is also used to determine
the function of a gene.
This technique is commonly used on mice and other
model organisms.
In this process, a gene that has been sequenced, but
for which little to no function is known is “knocked out”
of the organism.
Gene Knockout Technology
Organisms in which the gene has been knocked out
are compared to normal organisms enabling
researchers to draw conclusions about the function of
the gene.
How it Works:
The genetic information of individual cells is altered in
some way creating a transgenic animal with an
altered gene.
Once this has been accomplished, the goal is to get
embryonic stem cells transformed and inserted into
early embryos.
This results in animals with a genetic change in their
germ-line cells that can pass the genetic alteration on
to their offspring.
How it Works:
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