Bioinformatics is the branch of science which through the use of high electronic beam screen computer technology summates all the biological data mainly the genetic aspects that has been produced over the years by the research scientists. It mainly involves the construction, updating and maintenance of the database containing a wealth of biological information and at the same time enable the users to analyze and explore the data. The term medical informatics deals with the application of fast growing computer technology to the field of medicine; it could be either medical education or for the purpose of medical research which ultimately enhances our understanding in the treatment of disease. Health informatics
With the advancement of science and technology, bioinformatics now emerges as a new facet of science which combines the fields of Molecular Biology and Genetics, Biotechnology and Microbiology making them interpreted and explored by means of computer technology. The establishment of NCBI (national centre for biotechnology information) in 1988 as a public database, has helped in disseminating information across the world thereby facilitates in tracking out the molecular processes of the disease (Fig 2a). In the later phase many other databases were created such as Ensembl aiding in tracking the genetic mechanism responsible for the pathogenesis of the disease.
Fig 2a: Figure showing the NCBI database page. The page shows the establishment of database in the year 1988 and the various parameters that can be explored using this database.
Bioinformatics, genomics and Disease
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Cracking the human genome code and the publication of 3.2 billion sequences making up the human chromosomes on the internet by the US department of energy (DOE) and National Institute of Health has revolutionized the field of pharmacogenomics. It helps the other scientist and doctors to understand the molecular DNA code (the blueprint of an individual) in detail. The findings of the genome project are: 1) There are approximately 30,000 genes in human 2) The DNA sequence between two individuals are 99.9 % same and the differences lies only in the 0.1 % which contribute to our individuality. Single nucleotide polymorphism (SNP) contributes to the 0.1 % differences make up. Till now 3.2 million polymorphic SNPs have been mapped and these SNPs aids in finding the human predisposition to any particular diseases. They are serving as a genetic markers in correlating the drug efficacy and toxicity potential of any individual (Fig 3a). Bioinformatics softwares are in current use to track these hidden SNPs in human genome. Copy number variations (CNVs) are also the other factor adding up another contribution in 0.1 % differences and causes diseases in humans. The microarray technologies along with the array algorithm are in current use to track out these variations.
Fig 3a: Figure showing the human chromosomes 1, 2, 3 and 4 with the gene loci mapped responsible for the diseases. VHL gene on chromosome 3 mapped for example is a factor that participates sometimes in the pathogenesis of cancer.
Bio-informatics and Proteomics:
The expression level of any particular gene is not correlated with the level of mRNA present in the cell. Hence studying mRNA and DNA sequences alone are not able to give the correct expression status of the genes dominating in a particular disease. Also the human genes undergo alternative splicing and RNA editing mechanism which enhances a gene potential in coding different proteins. Now the fields of bioinformatics have also collaborated with the science of proteins to analyze and explore every protein in the human body (Fig 4a). With the advent of X-ray crystallography and NMR (Natural Magnetic Resonance), it is possible to capture and study proteins on the screen in their 3D structure. Today scientists are on the verge of creating human proteome map and if they will be successful in their proteome map there will be a better quality of life serving to minute details.
Figure 4a: Figure showing the diagnosis of renal carcinoma using the 2D-Gel electrophoresis technique. Normal: indicates normal without carcinoma, RCC: Renal cell carcinoma.
Bioinformatics and Pharmacology
The 1994 noble prize winner for decoding cellular signaling mechanism, Alfred Gilman, a pharmacologist is now working on a project to trace the cellular signaling mechanism map and transcribed that knowledge on the computer screen. Now all the drug companies are using the technology of bioinformatics to develop more algorithms that can be used to predict the function of proteins encoded by newly discovered genes. These have been possible by the use of various multiple alignment software that is in current use to establish the phylogenetic relationships of the proteins under study. Drug docking is the most powerful technology, possible through the bioinformatics knowledge are in most common use to find the docking site of the drug in the active cleft of the proteins. The proteins participating in the pathogenesis of diseases can be easily mapped out and docked on the computer screen which has revolutionized the filed of pharmacology. Scientists nowadays are able to map the mutations in proteins giving drug-resistant property to the cells. For e.g., scientists have even mapped out mutations in HIV protease and HIV reverse transcriptase isolated from heavily drug treated HIV I infected patients (Fig 5a, 6a). This will definitely enhance the knowledge of better understanding the drug resistant mechanism which are the common scenario observed in AIDS, Cancer and Tuberculosis. For tuberculosis, the genome of Mycobacterium tuberculosis has been sequenced and mapped to explore the ABC transporters proteins present in the bacteria giving drug resistant property.
Figure 5a: Figure showing the X-ray crystallography structure of HIV I protease enzyme. Red colour indicates the mutations in the active site of the enzyme while purple colour indicates accessory changes.
Figure 6a: Figure showing the drug resistant potential of HIV I resistant drugs. The upper half showing the drug resistant against HIV I protease and the second half indicates drug resistant profiling against HIV I reverse transcriptase. AZT:, DDI:, DDC:, D4T:, ABC;, 3TC
APV:, IDV;, NFV;, RTV;, SQV;.
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From the event in the history leading to the discovery of exchange of DNA strands by homologous chromosomes (Joshua Lederberg in 1958) resulting in genetic variation till the present day discovery by the Mario Capecchi and Oliver Smithies in 2007 who have applied the homologous recombination in mammalian cells, homologous recombination can occur between introduced DNA and the cell chromosomes also repair with the help of induced genes. They have prominently focused to target the genes which are involved in mammalian organ development. Several inborn errors that arise in the event of malformation can also be corrected. If the experiments successful on the mouse model as a gene therapy source, the art of medicine will be enriched with biology as a source of future developments in medicine.
Current Technologies in complete merging of informatics with medicine:
The function of many genes encoded by the human genomes is yet to be determined. Bioinformatics failed to decode the functions of some novel genes which does not exhibit homology sequence pattern with the other genes published in the database. For this in vitro research (wet lab) is required to perform the necessary manipulations. The human genomes submitted by both public and private sectors have gaps in them.
95 % of human DNA is junk. Bio-informatics failed to signify the importance of these non-coding sequences and their existence.
We still do have complete expression libraries that are a expression signature of the genes present in a tissue or organ. Proteins, their location and modification are not characterized.
Not all diseased genes have been characterized so far and the genetic differences between normal and disease state are not known.
NMR and X-ray crystallography techniques are labour intensive and required a month or two.
Bioinformatics failed to predict the functions of novel proteins whose structure are not similar to that of the other proteins present in the databases. The procedure of molecular docking is very much time consuming.
Gene patenting should be banned because it halt the outshining future of the patented gene.
Bio-informatics programmer should be encouraged among students from MSc and PhD field.