Bioinformatics and Biotechnology

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Table of Contents

Define Bioinformatics
The Evolution of Bioinformatics
Applications of Bioinformatics
Conclusion
References

Biotechnology is an important field in science. Biotechnology enables mankind to develop cutting-edge technologies when it comes to drug design. Biotechnology enables the capability to develop pest-resistant and drought-resistant varieties of high-value crops such as corn and rice. One of the most important components of biotechnology is the creation and maintenance of a mechanism that will allow for the storage and retrieval of biological data.

An example of biological data is nucleotide and amino acid sequences (National Centre for Biotechnological Information, 2004, p.1). Due to the staggering amount of data that has to be processed based on a single organism alone, it became compulsory to use Information Technology.

The use of IT in the creation of an efficient mechanism to store, retrieve and analyse data is called bioinformatics. The purpose of this study is to provide an overview of bioinformatics and to illustrate how bioinformatics can be utilised in the design of drugs and the enhancement of agricultural products.

It has to be pointed out that biotechnology is the “use of living organisms by humans” (Biotechnology Institute, 2010, p.1). Biotechnology utilises complicated processes. Biotechnology combines the sciences of “biology, chemistry, physics, engineering, computers and information technology in order to harness the best traits nature could offer in order to develop safe and beneficial crops, medical treatments, biofuels and household products” (Biotechnology Institute, 2010, p.1).

The best way to study and harness biological traits of living organisms is to go through the molecular level, specifically, through genetic material and protein sequence. The amount of information that can be generated from genome mapping and protein sequencing can easily overwhelm an ordinary database.

Define Bioinformatics

Before going any further it is important to point out that “Bioinformatics is an emerging interdisciplinary area of Science & Technology encompassing a systematic development and application of IT solutions to handle biological information by addressing biological data collection and warehousing, data mining, database searches, analysis and interpretation, modelling and product design” (Latha, 2012, p.1).

Bioinformatics can be seen as an interface between biology and modern information systems. Therefore, bioinformatics can be used not only to store and retrieve information but also in the discovery of new knowledge.

The significance of bioinformatics can be fully appreciated if one will compare it to other forms of data storage and retrieval system used in the past. It can be argued that a library is an example of a data storage and data retrieval system. A library is known all over the world as a repository of knowledge.

But at the same time people construct libraries not only as a safe place to store information but also as a way to efficiently retrieve information when needed. In order for this to happen, there must be a way to organise and track down the books. The user will come in and retrieve the books from the library but if the librarian has no system in place to locate the books, then, it will take a long time before someone can access the information contained in those books.

In the modern age, the library system proved to be an effective way to gather important information in one place and then dispense it to those who needed knowledge that will be used to solve social and scientific problems. As a result bigger libraries were built to house hundreds of thousands of books. The library classification system made it possible to sort books and retrieve them with ease.

The system was proven reliable even when it comes to libraries that contain hundreds of thousands of materials that range from books to audio tapes. It has been made clear that the present library system can deal with the storage and retrieval of information through its collection of books and other methods of data storage and delivery such as maps, microfilms, and others. But when it comes to biotechnology there are requirements that even a giant-sized library cannot fulfil.

When it comes to biotechnology the amount of information that can be generated from genome mapping and protein sequencing can be staggering. This assertion is based on the fact that the genetic material contained in the DNA of a human being is not only comprised of large amounts of data but each data set is unique to the individual.

It took years before scientists were able to establish the correct protocols to map the genome of a bacterium. There is no need to elaborate the implications of a bacterium when compared to the gene map of a human being. The data collected from gene mapping and protein sequencing can easily multiply if one begins to factor in the genome mapping of plants and other organisms.

Imagine the kind of structure that needed to built in order to house all the information that can be generated as a result of biotechnology research especially when it comes to the hereditary material found in living organisms. The storage problem is one facet of the overall challenge.

The next problem that has to be tackled is the retrieval of information and it has to be made available 24 hours a day, seven days a week. Finally, researchers needed to have access to the biological database even if they are not in the same building. Researchers collaborate on certain projects, while others use the research findings of other scientists to create their own solutions to pressing problems in the field of biotechnology.

It is clear that the library system can no longer support the technological requirement needed for quick and efficient storage and retrieval of immense volumes of data. But the most problematic feature of a traditional library system is that it is unable to share information in the most expedient and most cost-effective manner.

Imagine the constraints brought about by the removal of thousands of books from a library in London and then, ship it to a researcher located in Boston, USA. When the scientist in America completed his research work he had to ship the books back to the United Kingdom. One can just imagine the hassles and the expenses that will be incurred by both parties.

Bioinformatics solves the problem when it comes to the storage, retrieval and sharing of voluminous amounts of data. Bioinformatics can be seen as an interface between biology and informatics that will result in the “discovery, development and implementation of computational algorithms and software tools that facilitate an understanding of the biological processes with the goal to serve primarily agriculture and healthcare sectors with several spin-offs” (Latha, 2012, p.2).

It has be made clear that bioinformatics is not possible without the invention of computers, the Internet and World-Wide-Web.

The Evolution of Bioinformatics

As late as the 20^th century, scientists were constrained to use ink on paper when they need to record data and to write down their analysis of a particular experiment. They use ink on paper when they record their insights and various observations when it comes to the study of scientific phenomenon. But the invention of computers changed everything.

The evolution of bioinformatics began with the invention of modern computers. In the past, the computing machines resembled those of ancient bead counting devices that were used as crude calculators. In the 20^th century, the perfection of electrical technology paved the way for the creation of electronic technology. It did not take long before scientists and engineers developed the first computer, the predecessor to the personal computer that will change the course of history.

The modern version of computers proved to be more powerful than ancient computing devices made of wood and steel. The electronic circuits of a modern computer enabled the user to perform complex computations. The only downside to the first generation computer design was the inability of engineers to shrink the size of computers and make them portable.

It required the visionary genius of Steve Jobs of Apple Computer and Bill Gates of Microsoft to set a chain-reaction of event that resulted in the construction of portable computers that are powerful enough and effective enough to be use in offices and homes. The end result was like having the capability to type words using a typewriter and yet the output of the action is recorded in an electronic device simply referred to us the computer.

The revolution came in the form of computer software the enable the user not only to perform complex computations but other activities that replaced traditional accounting, secretarial, and design functions. In tracing the development of the PC and the Operating System one commentator said that, “In the first wave came software contractors.

They established the software industry in the 1950s selling large-scale software projects to the United States government and large corporations. In the 1960s the industry slowly shifted towards software products… After IBM… unbundled software from hardware in 1969, the software product market took off” (Valimaki, 2005, p. 14).

The word “unbundling” simply means that computer devices were sold separate from the software that runs it. This business strategy revolutionized computer software design because companies like Microsoft can focus on the creation of cutting-edge software without the need to deal with the computer hardware requirements of the business.

The revolutionary design of the personal computer forms only a part of the IT story that changed the world. The revolution was completed with the creation of the World-Wide-Web and the Internet. This new technology radically transformed the way people communicate to each other. It is not just about the capability to solve mathematical problems in a personal computer but the impact of the networks that were created via the Internet.

There is a need to clarify the difference between the Internet and the World-Wide-Web. The Internet can be defined as a computer network of networks that allow computers to link together using standardized protocols (Cerf, 2010). It was Tim Berners-Lee who made this possible. It was Berners-Lee who paved the way so that computers can locate and access files (Wilde, 2008). There was no longer any need for a librarian. This method allowed for an efficient way to share data. It can also be argued that computers can communicate to another computer.

There was already a network of computers present in many office buildings, government agencies and universities. But there was no way to make these computers function as an interlinked system until the Internet came along. Scientists and engineers discovered a way to view data and other forms of information online without the need to travel from one place to the next.

Tim Berners-Lee created a client program called the World-Wide-Web and became popular all over the world as the Web. The invention became the precursor to the websites that can be efficiently used to send, retrieve and view information through texts, images, and audio or vide files.

Without the said World-Wide-Web it will be impossible for ordinary individuals to communicate using programming language (Cerf, 2010). Finally, computer scientists created a more effective way to enhance communication and data sharing through a graphical user interface. Scientific collaboration and other types of project can be completed with less time and resources because of the Internet and World-Wide-Web.

Applications of Bioinformatics

According to one report “An important step in providing sequence database access was the development of Web pages that allow queries to be made of the major sequence of database. An early example of this technology at the National Centre for Biotechnology Information was a menu-driven program called GENINFO” (Mount, 2004, p.9).

The said program enabled researchers to search rapidly through previously indexed sequence database” (Mount, 2004, p.9). In other words there is no need to replicate the experiment and there is no need to construct the data sequence so that other scientists can view it and use it as foundations for new studies.

One of the best examples when it comes to the power of bioinformatics is the use of this type of technology to develop a more effective drug design to combat diseases. For example, the Acquired Immunodeficiency Syndrome (“AIDS”) is a lethal medical condition caused by the Human Immunodeficiency Virus (“HIV”).

It is a known fact that since HIV is a type of virus, then, it is comprised of organic building blocks that can be studies in order to develop a drug that can weaken or eradicate it from the system of the human being. The application bioinformatics revealed that this particular virus has an aspartyl protease. It is a type of enzyme unique to HIV.

Based on conventional drug design processes it is important to understand the pertinent details with regards to the molecular structure of the said enzyme. Since an enzyme is an initiator of a specific action, then, if scientists can limit the availability of the enzyme, then, it is possible to stop the replication of the virus.

But the first thing that has to be done is to determine the crystal structure of the said enzyme. With the use of bioinformatics, numerous teams all over the world collaborated to determine the mechanism of the enzyme and the layout of the active site was carefully mapped (Harisha, 2007, p.177).

It was a promising start in a continuing struggle to find a cure for AIDS. Scientists working in the pharmaceutical industry were convinced that the use of bioinformatics can shorten the amount of time needed to develop new drugs that can help solve the AIDS epidemic. They will use sophisticated software to develop simulations in the computer and therefore eliminate their mistakes through a mathematical process. It is more efficient compared to laboratory experiments that require a great deal of resources to complete (Cerf V 2012).

Those who continue to question the practical applications of bioinformatics need to be informed with the successful design of drugs to combat debilitating diseases. Consider the following examples “Dorzolamid (trade name Trusopt) marketed since 1995 which is used for the treatment of glaucoma is a carbonic anhydrase inhibitor that originated as the first drug form a program involving structure-based rational design” (Selzer, Marhofer & Rohwer, 2008, p.133). Another example is Captopril. It is a drug that lowers blood pressure.

An example of a bioinformatics tool is sequence alignment. The use of this particular tool enables researchers to: “query databases for sequences similar to an input sequence, find previously characterized sequences, detect relationships amongst sequences, as well as identify possible functions based on similarity to known sequences” (Jain & Brar, 2010, p.104).

An example of biological information database for crops is the Arabidopsis Genome Initiative of 2000 and the model monocot rice as well as the ongoing sequencing projects of crop plant species (Kang & Priyadarshan, 2007, p.95). The end result is bioengineered plant species resistant to drought, pestilence, and yet provide higher yield for farmers.

Conclusion

The most important thing to remember is that bioinformatics is the interface between biology and Information Technology. Data sets that resulted from genome mapping and protein sequencing can be stored and retrieved in the most cost-efficient manner. But at the same time it can be shared to other researchers.

Thus, there is access to voluminous amounts of data and at the same time there is no need to replicate the sequencing activities completed in the past. It frees up time and other resources so that scientists can use their talents to solve problems and not worry about the data needed to support their claims. As a result it is relatively easier to design drugs that can help solve the AIDS epidemic. At the same time it is relatively easier to bioengineer high value crops that can help solve food shortages all over the world.

References

Biotechnology Institute. What is biotechnology? Web.

Internet pioneers. Web.

Harisha, S. Fundamentals of bioinformatics. New Delhi: I.K. International Publishing; 2007.

Jain M, Jain, B. Molecular techniques in crop improvement. New York: Springer; 2010.

Kang M, Priyadarshan P. Breeding major food staples. Oxford: Blackwell Publishing; 2007.

Latha J. Bioinformatics for a better tomorrow. Web.

Mount D. Bioinformatics: sequence and genome analysis. New York: Cold Springs Harbour Laboratory Press; 2004.

National Centre for Biotechnology Information. Bioinformatics. Web.

Selzer P, Marhofer R, Rohwer A. Applied bioinformatics: an introduction. New York: Springer; 2008.

Valimaki M. The Rise of Open Source Licensing. Finland: Helsinki University Printing House; 2005.

Wilde E. Architecture of the world wide web. Web.

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