It’s in the
Genes!
- A person’s genome contains information showing possible
advance of a disease, or a propensity for the individual to develop a
particular disorder. However, you need a fast, reliable and economical way of
sequencing each patient's genes to take full advantage of them. This is not a
one-time deal and there is the need to continually sequence an individual's DNA
over his or her lifetime, because the genetic code can be modified by many
factors.
DNA Primer
- Deoxyribonucleic acid is a nucleic acid,
in a ladder-like, double helix structure (discovered in 1953 by James Watson
and Francis Crick), containing the genetic
instructions used in the development and functioning of all known living organisms
(with the exception of RNA viruses). The rungs of the ladder-like
helix DNA consists of the consistent pairing of A==T and G==C base pairs. This
complementary relationship is critical in gene function. Within cells, DNA is
organized into long structures called chromosomes
The DNA segments carrying this genetic information
are called genes.
During cell division these chromosomes are duplicated
in the process of DNA replication, providing each cell its own
complete set of chromosomes. Along with RNA and proteins,
DNA is one of the three major macromolecules
that are essential for all known forms of life.
- DNA consists of two long polymers
of simple units called nucleotides, with backbones
made of sugars and phosphate
groups joined by ester
bonds. Genomic DNA is tightly and orderly packed in the process called DNA
condensation to fit the small available volumes of the cell. In
eukaryotes (animals,
plants,
fungi,
and protists),
DNA is located in the cell nucleus, as well as small amounts in mitochondria
and chloroplasts.
Eukaryotic
organisms store most of their DNA inside the cell nucleus
and some of their DNA in organelles, such as mitochondria
or chloroplasts.[1] Eukaryotic cells, in general, are bigger and
more elaborate than bacteria and archaea. In many species,
only a small fraction of the total sequence of the genome
encodes protein. Only about 1.5% of the human genome consists of protein-coding
exons, with
over 50% of human DNA consisting of non-coding repetitive sequences.[2]
- Bioinformatics (one of the thrusts of this
website) involves the manipulation, searching, and data mining
of biological data, and this includes DNA sequence data. Computer science,
utilizing string searching string algorithms, machine learning, and database
theory have led to big advances in genomics. Many of these processes deal with
pattern recognition. The technology involved in DNA sequencing is quite
expensive, running into the thousands. There is therefore a demand for a more
cost-effective method for this job.
New Approach to Old Data…
- Researchers from the
National Institute of Standards and Technology (NIST) and Columbia University's
School of Engineering and Applied Science are collaborating[3] to
devise a new rapid and less-expensive procedure that can be commercialized
effectively. If this pushes through that means that doctors and other health
personnel will be able to order these tests from their clinic or offices with
greater ease.
- The new method, which is
some kind of molecular ticker-tape, can perform DNA sequences by attaching
distinct molecular "tags" to each of the four chemical building
blocks, or "bases," that comprise the genetic information in a strand
of DNA —abbreviated as G, A, C and T. That’s G=Guanine, A=Adenine, C=Cytosine,
and T=Thymine. Each of these polymer tags can then be cut from the strand and
passed, one by one, through a nanometer-size hole in a membrane. A steady
stream of fluid and ions flows through this "nanopore,"[4] which is large enough to contain only
one tag at a time. As the polymer tags are different sizes, the change in
electrical current caused by altered fluid flow shows which of the four bases
sits at each point on the DNA strand. Columbia University has applied for
patents for the commercialization of the technology.
DNA Works
- Transcription factors are the DNA binding proteins that
carry out the organic process whereby the DNA sequence in a gene is copied into
mRNA.[5] Gene expression, then, is the process by which a gene’s
coded information is converted into the structures present and operating in the
cell. Expressed genes include those that are transcribed into mRNA and then
translated into protein, and, those that are transcribed into RNA but not
translated into protein (e.g., transfer and ribosomal RNAs).
- DNA can be damaged, wherein there is a DNA
alteration that has an abnormal structure, which cannot itself be replicated
when the DNA is replicated, but which may be repaired. Mutation can occur too,
wherein there is a change in the sequence of DNA base pairs, but which may be
replicated and thus inherited. DNA is subject to a wide variety of chemical
reactions that might be expected of any such molecule in a warm aqueous medium.
In any cell, however, some DNA damage may remain unrepaired despite repair
processes.
Animation of a rotating DNA structure.
Created
in the free program RasMol 2.7.2.1.1
using the bdna.pdb dataset and the following commands:
GUI options were: Options->Specular,
Display->Sticks
Then, in the command line
where script.txt was a separate text file
in the same
directory, consisting of the
same two repeating lines:
rotate
x 3
write
frame-07.gif
rotate
x 03
write
frame-05.gif
rotate
x 3
write
frame-03.gif
...
from 001 up to 119
(for a total of 120 images when
combined with frame-000.gif).This was then loaded
in Adobe ImageReady, and saved as an
animated GIF.
Father of Genetics
- In 1866, Gregor Mendel, an Augustinian monk, put forth
the postulates of inheritance based on a decade long work in pea plants. Today,
we can have a DNA test in an hour or so. Mendel did his work before the
structure and role of chromosomes were known. About 20 years after his work,
advances in microscopy allowed researches to identify chromosomes and to
establish that in eukaryotic organisms (meaning those with a nucleus and cell
membranes), each species has a identifiable characteristic number of
chromosomes called the diploid number. You and I have a diploid number of 46.
Chromosomes in diploid cells exist in pairs called homologous chromosomes, and
members of a pair are identical in size and location of the centromere where
the spindle fibers attach to during division.
From Genotype to Phenotype
- In living organisms DNA does not usually exist as a
single molecule, but instead as a pair of molecules that are held tightly
together. These two long strands entwine like vines, in the shape of the now
known double helix.
DNA is a long polymer
made from repeating units called nucleotides.
Polymers comprising multiple linked nucleotides are called a polynucleotide.
The backbone of the DNA strand is made from alternating phosphate
and sugar
residues. The D in DNA stands for 2-deoxyribose, which is a pentose
(five-carbon)
sugar. In turn, the sugars are joined together by phosphate groups that form phosphodiester bonds between the third and
fifth carbon atoms
of adjacent sugar rings.
- Proteins are the end products of gene expression. Once a
protein is made, its action or location plays a role in producing a phenotype.
When mutation alters a gene, it may abolish or alter that protein’s function
and cause an altered phenotype. Genomics grew out of recombinant DNA technology
which began in the early 1970s, when researchers discovered that bacteria could
protect themselves by making enzymes that restrict or block infection by
cutting viral DNA at specific sites. When cut, the viral DNA could not
orchestrate the synthesis of more phage particles which when released kill the
infected bacterial cell.
Genome Libraries
- A cell’s genome, that
is, the entire library of genetic information in its DNA, provides a genetic
program that instructs the cell how to function, and, for plant and animal
cells, how to grow into an organism with hundreds of different cell types. The
DNA contains the information that not only determines form, but also the
function of the cell and organism. Once genomic “libraries” became available,
researchers started working on ways and means to sequence all the clones in a
genomic library in an organized way, so as to obtain the neucleotide sequence
of an organism’s genome.
- In 2001, the Human Genome Project reported the first
template of the human genome. Then in 2003, the remaining portion of the genome
sequence was published. Work is focused now on the non-coding portions of the
genome. Genomics arose as a new field of Medicine as more complete genomes were
discovered and published. Now, we have gene sequences of a variety of
organisms, ranging from bacteria and fungi, to insects, all the way to large mammals.
Hemophilus influenza, which causes respiratory illness and meningitis, was the
first free-living organism to have its genome sequenced. The third generation
of model organisms include the roundworm (C. elegans), the plant Arabidopsis,
and , the Zebrafish. We also have gene sequences of plants, which is a boon to
the agricultural industry. It is estimated that more than 60% of the processed
food in the United States contains ingredients made from genetically modified
crop plants.[6] These
modifications are done to provide crops with different enhancements, ranging
from herbicide resistance, drought- or flood-resistance, all the way to delayed
ripening.
- The screening of an individual’s genome to determine a
person’s risk for developing a disease uses DNA microarrays or DNA chips. Each
chip contains thousands of fields, each carrying a different gene. Chips
containing the human genome are widely available, making it feasible to scan
one’s entire genome to check for a propensity for a disease. Pharmagenomics
checks out which chemical compound best treats a certain illness. In addition,
we have gene therapy, which involves transferring normal genes into an abnormal
cell or tissue. The molecular basis for hundreds of genetic disorders is now known. We must remember that genetic studies rely on
known model organisms. Gene sequencing involves the comparison of gene
sequences of one organism to a reference sequence.
We are all connected
- So now, one can visit
the BLAST portal online, for access to gene sequences from many organisms with
known sequences. Model organisms used to
study human disease include, for example, yeast, for: cell cycle, cancer, and
Werner Syndrome; Drosophila (fruit fly) for: cell signaling, cancer, and human
neurodegenerative disease[7]; Zebrafish, for developmental pathways,
and cardiovascular disease. These model organisms have a rich history in
genetic studies. One should remember that whatever controls a certain process
in yeast will also be the same for the human. The development and use of model
organisms is only one of the ways genetics and biotechnology are rapidly
changing every aspect of our lives. I hope that the reader will look into the
wealth of material on genetics, epigenetics, as well as the other omics (e.g.
proteomes, exomes).
Some Tools of the Trade
- There are an ever-growing number of bioinformatics resources that are available to the interested
worker. Depending on what area of specialty you’re in, you will find work
opportunities as well. To get one started, do read further on in all the published
documents available now on the Web. Check out the BLAST portal here. Equipment
can range from a light microscope all the way to the transmission- and scanning
electron microscope. On the software side, there are several sequencing programs
available. Some are free and open-sourced, while others come at a big price. A
brief listing of software is on this site. As new developments are pursued, the
armamentarium of the bioinformatics worker will grow exponentially. All it
takes is a good helping of resourcefulness and you’re on your way to making the
next big discovery.
Think Big. Think Forward
- Fernando Yaakov Lalana, M.D.
References:
1) Russell, Peter (2001). iGenetics.
New York: Benjamin Cummings. ISBN 0-8053-4553-1.
2)
Wolfsberg T, McEntyre J, Schuler G (2001). "Guide to the
draft human genome". Nature 409 (6822): 824–6. doi:10.1038/35057000. PMID 11236998.
3) Engineers collaborate on inexpensive DNA sequencing method. R & D
Magazine http://www.rdmag.com/News/2012/10/Life-Science-Genetics-Analytical-Instrumentation-Engineers-collaborate-on-inexpensive-DNA-sequencing-method/?et_cid=2880813&et_rid=424458894&linkid=http%3a%2f%2fwww.rdmag.com%2fNews%2f2012%2f10%2fLife-Science-Genetics-Analytical-Instrumentation-Engineers-collaborate-on-inexpensive-DNA-sequencing-method%2f
4) PEG-Labeled
Nucleotides and Nanopore Detection for Single Molecule DNASequencing by
Synthesis, Shiv Kumar, Chuanjuan, Tao, Minchen, Chien, Hellner, Brittney,
Balijepalli, Arvind Robertson,
Joseph W. F. , Li, Zengmin, Russo, James J., Reiner, Joseph E., Kasianowicz, John
J.,& Ju,, Jingyue.; Nature.com,
Scientific Reports.
5) Leff ,Todd and Granneman, James G., in Encyclopedia of Molecular
Cell Biology and Molecular
Medicine, 2nd Edition. Edited by Robert A. Meyers., Copyright
2004 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim. ISBN: 3-527-30543-2
6) Klug, William S., Cummings, Michael R., Spencer Charlotte A.,
Concepts Of Genetics 8th Ed.,©2006,2003,2000,1997 by William S. Klug and
Michael R. Cummings. Published by Pearson Education, Inc. Pearson Prentice Hall.
ISBN: 0131918338
7) Fortini, M. and
Bonini,N.M.;2000 Modeling human neurodegenerative disease in Drosophila. Trends
Genet.16:161-167
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