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Applications of Bioinformatics

BY: Madhu Bala Priyadarshi | Category: Bioinformatics | Submitted: 2014-09-18 06:47:18
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Article Summary: "Today, bioinformatics is used in large number of fields such as microbial genome applications, biotechnology, waste cleanup, Gene Therapy etc. In this article an effort is made to provide brief information of applications of bioinformatics in the field of Medicine, Microbial Genome Application and Agriculture..."


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Introduction

Bioinformatics was coined by Paulien Hogeweg and Ben Hesper in 1970. It was stated as "Study of Informatic processes in biotic systems"[1]. Basically bioinformatics deals with the information in the fields of Information Technology, Computer Science and Biology. Biologist performs research in laboratoty and collects DNA and protein sequences, gene expressions etc. Computer Scientists are involved in developing algorithms, tools, softwares to store and analyze data. Bioinformaticians study biological questions by analyzing molecular data with various programs and tools. Today, bioinformatics is used in large number of fields such as microbial genome applications, biotechnology, waste cleanup, Gene Therepy etc. In this article an effort is made to provide brief information of applications of bioinformatics in the field of Medicine, Microbial Genome Application and Agriculture.

Applications of Bioinformatics

In broad spectrum applications of bioinformatics is mainly used in the field of Medicine, Microbial Genome Applications and Agriculture.

1. Medicine

In the field of Medicine applications of bioinformatics is used for following areas:

a. Drug Discovery: The Idea of using X ray Crystallography in drug discovery emerged more than 30 years ago, when the first 3 dimensional structure of protein was determined. Within a decade, a radical change in drug design had begun, incarporating the knowledge of 3 dimensional structures of target protein into design process. Protein structure can influence drug discovery at every stage in design process. Classicaly, it is used in lead optimization, a process that uses structure to guide the chemical modification of a lead molecule to give an optimised fit in terms of shape, hydrogen bonds and other non -covalent interactions with the target[2].

b. Personal Medicine: Personalized medicine is a medical model that proposes the customization of healthcare, with all decisions and practices being tailored to the individual patient by use of genetic or other information. Practical application outside of long established considerations like a patient's family history, social circumstances, environment and behaviors are very limited so far and practically no progress has been made in the last decade. Personalized medicine research attempts to identify individual solutions based on the susceptibility profile of each individual. It is hoped that these fields will enable new approaches to diagnosis, drug development, and individualized therapy [3].

c. Preventive Medicine: Preventive medicine or preventive care consists of measures taken to prevent diseases, (or injuries) rather than curing them or treating their symptoms. This contrasts in method with curative and palliative medicine, and in scope with public health methods (which work at the level of population health rather than individual health)[4]. Simple examples of preventive medicine include hand washing, breastfeeding, and immunizations.

d. Gene Therapy: Gene therapy is a novel form of drug delivery that enlists the synthetic machinery of the patient's cell to produce a therapeutic agent. It involves the efficient introduction of functional gene into the appropriate cells of the patient in order to produce sufficient amount of protein encoded by transferred gene (transgene) so as to precisely and permanently correct the disorder. Strategies of Gene Therapy are following [5]:
- Gene addition
- Removal of harmful gene by antisense nucleotide or ribozymes
- Control of gene expression


2. Microbial Genome Applications

In the field of Microbial Genome Applications, applications of bioinformatics are used for following areas:

a. Waste Cleanup: In bioinformatics bacteria and microbes are identified which are helpful in cleaning waste. Deinococcus radiodurans Bacterium is listed in the Guinness Book of World Records as "the world's toughest bacterium." This bacterium has the ability to repair damaged DNA and small fragments from chromosomes by isolating damage segments in a concentrated area [6]. This is because it has additional copies of its genome. Genes from other bacteria have been inserted into D. radiodurans for environmental cleanup. It was used to break down organic chemicals, solvents and heavy metals in radioactive waste sites [7].

b. Climate Change: Climate change is caused by factors that include oceanic processes (such as oceanic circulation), variations in solar radiation received by Earth, plate tectonics and volcanic eruptions, and human-induced alterations of the natural world. By studying microorganisms genome scientists can begin to understand these microbes at a very fundamental level and isolated the genes that give them their unique abilities to survive under extreme conditions [8]. Rhodopseudomonas palustris is a purple non-sulfur phototrophic bacterium commonly found in soils and water. It converts sunlight to cellular energy by absorbing atmospheric carbon dioxide and converting it to biomass. This microbe can also degrade and recycle a variety of aromatic compounds that comprise lignin, the main constituent of wood and the second most abundant polymer on earth [9]. R. palustris is acknowledged by microbiologists to be one of the most metabolically versatile bacteria ever described. Not only can it convert carbon dioxide gas into cell material but nitrogen gas into ammonia, and it can produce hydrogen gas. It grows both in the absence and presence of oxygen. In the absence of oxygen, it prefers to generate all its energy from light by photosynthesis [10].

c. Biotechnology: The wide concept of "biotech" or "biotechnology" encompasses a wide range of procedures for modifying living organisms according to human purposes, going back to domestication of animals, cultivation of plants, and "improvements" to these through breeding programs that employ artificial selection and hybridization. Modern usage also includes genetic engineering as well as cell and tissue culture technologies [11]. In the field of bioinformatics, biotechnology has identified organisms and microorganisms which can be very useful in dairy industry and food manufacturers. Lactococcus Lactis is one of the most important micro-organisms involved in the dairy industry, it is a non-pathogenic rod-shaped bacterium that is critical for manufacturing dairy products like buttermilk, yogurt and cheese. This bacterium, is also used to prepare pickled vegetables, beer, wine, some breads and sausages and other fermented foods. Researchers anticipate that understanding the physiology and genetic make-up of this bacterium will prove invaluable for food manufacturers as well as the pharmaceutical industry, which is exploring the capacity of L. lactis to serve as a vehicle for delivering drugs [12].

d. Alternative Energy: Scientists are studying the genome of the microbe Chlorobium tepidumwhich has an unusual capacity for generating energy from light. Chlorobium tepidumis a thermophilic Gram-negative green sulfur bacterium isolated from a hot spring in New Zealand in which it forms a dense mat. The bacterium carries out photosynthesis in ways that are different from plants and other bacteria. Unlike plants, the green bacteria do not produce oxygen from photosynthesis. According to some researchers, photosynthesis may have its evolutionary origins in organisms like C. tepidum. Such species would have been able to harvest energy from light at a time when the Earth's atmosphere had little oxygen. In addition, the organisms' ability to grow in low-light environments may have helped them limit their exposure to UV irradiation, which was likely at higher levels in the early days of Earth [13].

3. Agriculture

In the field of Agriculture, applications of bioinformatics are in following areas:

a. Crop Improvement: Comparative genetics of the plant genomes has shown that the organisation of their genes has remained more conserved over evolutionary time than was previously believed. These findings suggest that information obtained from the model crop systems can be used to suggest improvements to other food crops. Arabidopsis thaliana (water cress) and Oryza sativa (rice) are examples of available complete plant genomes [14]. Arabidopsis thaliana was the first plant to be sequenced and is considered the model species for investigating plant genetics and biology. There are many genes which are similar in all plants and the study of genes in a model organism like A. thaliana facillitates our understanding of gene expression and function in all plants. Furthermore, since animals and plants are both eukaryotes, many of the genes found in A. thaliana have homologs in animals. Arabidopsis has the smallest genome of any flowering plant, which is the main reason it was selected as a model organism for genome sequencing The DNA of Arabidopsis is made up of about 140 million bases, which are parcelled into five chromosomes [15]. Oryza sativa (rice) is the most important crop for human consumption, providing staple food for more than half of the world population. Oryza sativa was the cereal selected to be sequenced as a priority and has gained the status "model organism". It has the smallest genome of all the cereals: 430 million nucleotides and it can serve as a model genome for one of the two main groups of flowering plants, the monocotyledons. Because it has been the subject of studies on yield, hybrid vigor, genetic resistance to disease and adaptive responses, scientists have taken advantage of the existence of a multitude of varieties that have adapted to a very wide range of environmental conditions, from dry soil in temperate regions to flooded cultures in tropical regions[16].


b. Insect Resistance: Genes from Bacillus thuringiensis that can control a number of serious pests have been successfully transferred to cotton, maize and potatoes. This new ability of the plants to resist insect attack means that the amount of insecticides being used can be reduced and hence the nutritional quality of the crops is increased [17]. Bacillus thuringiensis is a pathogenic bacteria used for insect control. It is Gram-positive spore-forming, rod-shaped aerobic bacteria in the genus Bacillus. B. thuringiensisis an insecticidal bacterium, marketed worldwide for control of many important plant pests - mainly caterpillars of the Lepidoptera (butterflies and moths) but also mosquito larvae, and simuliid blackflies that vector river blindness in Africa. B. thuringiensis products represent about 1% of the total 'agrochemical' market (fungicides, herbicides and insecticides) across the world. The commercial B. thuringiensis products are powders containing a mixture of dried spores and toxin crystals. They are applied to leaves or other environments where the insect larvae feed. The toxin genes have also been genetically engineered into several crop plants [18].

c. Improve Nutritional Quality: Scientists have recently succeeded in transferring genes into rice to increase levels of Vitamin A, iron and other micronutrients. This work could have a profound impact in reducing occurrences of blindness and anaemia caused by deficiencies in Vitamin A and iron respectively. Scientists have inserted a gene from yeast into the tomato, and the result is a plant whose fruit stays longer on the vine and has an extended shelf life [19]. One little gene may be all that stands between a fresh, juicy, homegrown tomato and its bland, store-bought counterpart. Biologists announced that they've identified the gene that controls the ripening process in the humble fruit. If this "rin" gene can be manipulated effectively, scientists will be able to create breeds of tomatoes that will be more flavorful even after the long journey from the vine to the produce department. Today, tomatoes are plucked from the vine early, when still green and firm, to ensure that they survive shipping without bruising and rotting. Picking tomatoes early means they have less chance to develop flavor, color, and nutrients naturally. By manipulating the "rin" gene, scientists will be able to slow the ripening process, letting the tomato develop on the vine for longer - but still keeping it firm enough to ship safely. The scientists responsible for the "rin" gene findings are from the U.S. Department of Agriculture and the Boyce Thompson Institute for Plant Research, on the campus of Cornell University. They hope that their technique may also be applied to other fruits - such as strawberries, bananas, bell peppers, and melons - which suffer from the same shipping and storage complications[20][21].

Summary and Conclusions

In a developing country like India, bioinformatics has a key role to play in areas like agriculture where it can be used for increasing the nutritional content, increasing the volume of the agricultural produce and implanting disease resistance etc [16]. There are large number of applications of bioinformatics in the fields of medicine, microbial genome applications and agriculture. Using them will allow researchers to reach a new height in their experiments. Major discoveries can be made faster and more efficiently. Today, every large molecular or systems biology project has a bioinformatics component. Bioinformatics applications will allow biologists to extend expertise far more efficiently and effectively for data analysis and planning of experiments.

References:

1. Alla L. Lapidus "Bionformatics and its Applications". http://bioinformaticsinstitute.ru/sites/default/files/lapidus_1_0.pdf
2. Tom L. Blundell, Bancinyane L. Sibanda, Rinaldo Wander Montalvao, Suzanne Brewerton, Vijayalakshmi Chelliah, Catherine L. Worth, Nicholas J. Harmer, Owen Davies and David Burke. Structural biology and bioinformatics in drug design: Opportunities and challenges for target identification and lead discovery. Phil.Trans. R. Soc. B (2006) 361, 413-423.
3. Personalised Medicine, Postnote, Parliament Office of Science and Technology. http://www.parliament.uk/documents/post/postpn329.pdf.
4. http://www.efim.org/fields-of-interest/preventive-medicine
5. Rashmi Sharma, Ruchi Khajuria, C.L. Sharma, B.Kapoor, K.C. Goswami and K,Kohli. Gene Therapy: Current Concepts. JK Science. http://www.jkscience.org/archieve/volume62/gene.pdf
6. http://en.wikipedia.org/wiki/Deinococcus_radiodurans
7. http://sohs-amyjames.pbworks.com/f/Deinococcus+Radiodurans.ppt
8. http://mscbioinformatics.uab.cat/base/base3.asp?sitio=msbioinformaticsen&anar=core&item=areasbioinfo
9. http://genome.jgi-psf.org/rhopa/rhopa.home.html
10. http://www.ebi.ac.uk/2can/genomes/bacteria/Rhodopseudomonas_palustris.html
11. http://en.wikipedia.org/wiki/Biotechnology
12. http://bioinfo.bact.wisc.edu/themicrobialworld/Lactococcus.html
13. http://www.genomenewsnetwork.org/articles/07_02/tepidum.shtml
14. http://bioinformaticsweb.net/applications.html
15. http://abc.cbi.pku.edu.cn/2can/genomes/eukaryotes/Arabidopsis_thaliana.html.
16. http://abc.cbi.pku.edu.cn/2can/genomes/eukaryotes/Oryza_sativa.html
17. http://www.ebi.ac.uk/2can/genomes/bacteria/Bacillus_thuringiensis.html
18. http://archive.bio.ed.ac.uk/jdeacon/microbes/bt.htm
19. http://www.academia.edu/6808947/ROLE_OF_BIOINFORMATICS_IN_AGRICULTURE_AND_SUSTAINABLE_DEVELOPMENT
20. http://www.ebi.ac.uk/2can/bioinformatics/bioinf_realworld_1.html#2.5
21. http://www.riverdeep.net/current/2002/04/042902t_gmfoods.jhtml
22. Jayaram B., Bhushan K. "Bioinformatics for Better Tomorrow". www.scfbio-iitd.res.in

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