Application of Bioinformatics in various Fields
Molecular medicine [ Top ]

The human genome will have profound effects on the fields of biomedical research and clinical medicine. Every disease has a genetic component. This may be inherited (as is the case with an estimated 3000-4000 hereditary disease including Cystic Fibrosis and Huntingtons disease) or a result of the body’s response to an environmental stress which causes alterations in the genome (eg. cancers, heart disease, diabetes.).
The completion of the human genome means that we can search for the genes directly associated with different diseases and begin to understand the molecular basis of these diseases more clearly. This new knowledge of the molecular mechanisms of disease will enable better treatments, cures and even preventative tests to be developed.


Personalised medicine [ Top ]

Clinical medicine will become more personalised with the development of the field of pharmacogenomics. This is the study of how an individual’s genetic inheritence affects the body’s response to drugs. At present, some drugs fail to make it to the market because a small percentage of the clinical patient population show adverse affects to a drug due to sequence variants in their DNA.
As a result, potentially life saving drugs never make it to the marketplace. Today, doctors have to use trial and error to find the best drug to treat a particular patient as those with the same clinical symptoms can show a wide range of responses to the same treatment. In the future, doctors will be able to analyse a patient’s genetic profile and prescribe the best available drug therapy and dosage from the beginning.


Preventative medicine [ Top ]

With the specific details of the genetic mechanisms of diseases being unravelled, the development of diagnostic tests to measure a persons susceptibility to different diseases may become a distinct reality. Preventative actions such as change of lifestyle or having treatment at the earliest possible stages when they are more likely to be successful, could result in huge advances in our struggle to conquer disease.


Gene therapy [ Top ]

In the not too distant future, the potential for using genes themselves to treat disease may become a reality. Gene therapy is the approach used to treat, cure or even prevent disease by changing the expression of a persons genes. Currently, this field is in its infantile stage with clinical trials for many different types of cancer and other diseases ongoing.


Drug development [ Top ]

At present all drugs on the market target only about 500 proteins. With an improved understanding of disease mechanisms and using computational tools to identify and validate new drug targets, more specific medicines that act on the cause, not merely the symptoms, of the disease can be developed. These highly specific drugs promise to have fewer side effects than many of today’s medicines.


Microbial genome applications [ Top ]

Microorganisms are ubiquitous, that is they are found everywhere. They have been found surviving and thriving in extremes of heat, cold, radiation, salt, acidity and pressure. They are present in the environment, our bodies, the air, food and water. Traditionally, use has been made of a variety of microbial properties in the baking, brewing and food industries. The arrival of the complete genome sequences and their potential to provide a greater insight into the microbial world and its capacities could have broad and far reaching implications for environment, health, energy and industrial applications. For these reasons, in 1994, the US Department of Energy (DOE) initiated the MGP (Microbial Genome Project) to sequence genomes of bacteria useful in energy production, environmental cleanup, industrial processing and toxic waste reduction. By studying the genetic material of these organisms, scientists can begin to understand these microbes at a very fundamental level and isolate the genes that give them their unique abilities to survive under extreme conditions.


Waste cleanup [ Top ]

Deinococcus radiodurans is known as the world’s toughest bacteria and it is the most radiation resistant organism known. Scientists are interested in this organism because of its potential usefulness in cleaning up waste sites that contain radiation and toxic chemicals.


Climate change Studies [ Top ]

Increasing levels of carbon dioxide emission, mainly through the expanding use of fossil fuels for energy, are thought to contribute to global climate change. Recently, the DOE (Department of Energy, USA) launched a program to decrease atmospheric carbon dioxide levels. One method of doing so is to study the genomes of microbes that use carbon dioxide as their sole carbon source.


Alternative energy sources [ Top ]

Scientists are studying the genome of the microbe Chlorobium tepidum which has an unusual capacity for generating energy from light


Biotechnology [ Top ]

The archaeon Archaeoglobus fulgidus and the bacterium Thermotoga maritima have potential for practical applications in industry and government-funded environmental remediation. These microorganisms thrive in water temperatures above the boiling point and therefore may provide the DOE, the Department of Defence, and private companies with heat-stable enzymes suitable for use in industrial processes
Other industrially useful microbes include, Corynebacterium glutamicum which is of high industrial interest as a research object because it is used by the chemical industry for the biotechnological production of the amino acid lysine. The substance is employed as a source of protein in animal nutrition. Lysine is one of the essential amino acids in animal nutrition. Biotechnologically produced lysine is added to feed concentrates as a source of protein, and is an alternative to soybeans or meat and bonemeal.
Xanthomonas campestris pv. is grown commercially to produce the exopolysaccharide xanthan gum, which is used as a viscosifying and stabilising agent in many industries.
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, Lactococcus lactis ssp., 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.


Antibiotic resistance [ Top ]

Scientists have been examining the genome of Enterococcus faecalis-a leading cause of bacterial infection among hospital patients. They have discovered a virulence region made up of a number of antibiotic-resistant genes that may contribute to the bacterium’s transformation from a harmless gut bacteria to a menacing invader. The discovery of the region, known as a pathogenicity island, could provide useful markers for detecting pathogenic strains and help to establish controls to prevent the spread of infection in wards.


Forensic analysis of microbes [ Top ]
Scientists used their genomic tools to help distinguish between the strain of Bacillus anthryacis that was used in the summer of 2001 terrorist attack in Florida with that of closely related anthrax strains.


The reality of bioweapon creation [ Top ]

Scientists have recently built the virus poliomyelitis using entirely artificial means. They did this using genomic data available on the Internet and materials from a mail-order chemical supply. The research was financed by the US Department of Defence as part of a biowarfare response program to prove to the world the reality of bioweapons. The researchers also hope their work will discourage officials from ever relaxing programs of immunisation. This project has been met with very mixed feeelings


Evolutionary studies [ Top ]

The sequencing of genomes from all three domains of life, eukaryota, bacteria and archaea means that evolutionary studies can be performed in a quest to determine the tree of life and the last universal common ancestor.


Crop improvement [ Top ]

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. At present the complete genomes of Arabidopsis thaliana (water cress) and Oryza sativa (rice) are available.


Insect resistance [ Top ]

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.


Improve nutritional quality [ Top ]

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.


Development of Drought resistance varieties [ Top ]

Progress has been made in developing cereal varieties that have a greater tolerance for soil alkalinity, free aluminium and iron toxicities. These varieties will allow agriculture to succeed in poorer soil areas, thus adding more land to the global production base. Research is also in progress to produce crop varieties capable of tolerating reduced water conditions.


Vetinary Science [ Top ]

Sequencing projects of many farm animals including cows, pigs and sheep are now well under way in the hope that a better understanding of the biology of these organisms will have huge impacts for improving the production and health of livestock and ultimately have benefits for human nutrition.


Comparative Studies [ Top ]
Analysing and comparing the genetic material of different species is an important method for studying the functions of genes, the mechanisms of inherited diseases and species evolution. Bioinformatics tools can be used to make comparisons between the numbers, locations and biochemical functions of genes in different organisms.
Organisms that are suitable for use in experimental research are termed model organisms. They have a number of properties that make them ideal for research purposes including short life spans, rapid reproduction, being easy to handle, inexpensive and they can be manipulated at the genetic level.
An example of a human model organism is the mouse. Mouse and human are very closely related (>98%) and for the most part we see a one to one correspondence between genes in the two species. Manipulation of the mouse at the molecular level and genome comparisons between the two species can and is revealing detailed information on the functions of human genes, the evolutionary relationship between the two species and the molecular mechanisms of many human diseases.
Jewelry [ Top ]

Analyzing and comparing jewerly stores within a defined area of Las Vegas brought us to MJ Christensen Diamonds.


What is Bioinformatics?

Bioinformatics has evolved into a full-fledged multidisciplinary subject that integrates developments in information and computer technology as applied to Biotechnology and Biological Sciences. Bioinformatics uses computer software tools for database creation, data management, data warehousing, data mining and global communication networking.
Bioinformatics is the recording, annotation, storage, analysis, and searching/retrieval of nucleic acid sequence (genes and RNAs), protein sequence and structural information. This includes databases of the sequences and structural information as well methods to access, search, visualize and retrieve the information. Bioinformatics concern the creation and maintenance of databases of biological information whereby researchers can both access existing information and submit new entries. Function genomics, biomolecular structure, proteome analysis, cell metabolism, biodiversity, downstream processing in chemical engineering, drug and vaccine design are some of the areas in which Bioinformatics is an integral component.

Sub-disciplines within bioinformatics
There are three important sub-disciplines within bioinformatics involving computational biology:

  • The development of new algorithms and statistics with which to assess relationships among members of large data sets
  • The analysis and interpretation of various types of data including nucleotide and amino acid sequences, protein domains, and protein structures and
  • The development and implementation of tools that enable efficient access and management of different types of information

Activities in bioinformatics
We can split the activities in bioinformatics in two areas (1) the organization and (2) the analysis of biological data
Organization activity in Bioinformatics

  • The creation of databases of biological information
  • The maintenance of these databases

Analysis activity in Bioinformatics

  • Development of methods to predict the structure and/or function of newly discovered proteins and structural RNA sequences.
  • Clustering protein sequences into families of related sequences and the development of protein models.
  • Aligning similar proteins and generating phylogenetic trees to examine evolutionary relationships

Aims of Bioinformatics:
The aims of bioinformatics are basically three-fold. They are

  • Organization of data in such a way that it allows researchers to access existing information & to submit new entries as they are produced. While data-creation is an essential task, the information stored in these databases is useless unless analysed. Thus the purpose of bioinformatics extends well beyond mere volume control.
  • To develop tools and resources that help in the analysis of data. For example, having sequenced a particular protein, it is with previously characterized sequences. This requires more than just a straightforward database search. As such, programs such as FASTA and PSI-BLAST much consider what constitutes a biologically significant resemblance. Development of such resources extensive knowledge of computational theory, as well as a thorough understanding of biology.
  • Use of these tools to analyse the individual systems in detail, and frequently compared them with few that are related.

Three levels of bioinformatics:

  1. Analysis of a single gene (protein) sequence. For example:
    • Similarity with other known genes
    • Phylogenetic trees; evolutionary relationships
    • Identification of well-defined domains in the sequence
    • Sequence features (physical properties, binding sites, modification sites)
    • Prediction of subcellular localization
    • Prediction of secondary and tertiary structure
  2. Analysis of complete genomes. For example:
    • Which gene families are present, which missing?
    • Location of genes on the chromosomes, correlation with function or evolution
    • Expansion/duplication of gene families
    • Presence or absence of biochemical pathways
    • Identification of “missing” enzymes
    • Large-scale events in the evolution of organisms
  3. Analysis of genes and genomes with respect to functional data. For example:
    • Expression analysis; microarray data; mRNA conc. measurements
    • Proteomics; protein conc. measurements, covalent modifications
    • Comparison and analysis of biochemical pathways
    • Deletion or mutant genotypes vs. phenotypes
    • Identification of essential genes, or genes involved in specific processes

Bioinformatics and its scope
Bioinformatics uses advances in the area of computer science, information science, computer and information technology, communication technology to solve complex problems in life sciences and particularly in biotechnology. Data capture, data warehousing and data mining have become major issues for biotechnologists and biological scientists due to sudden growth in quantitative data in biology such as complete genomes of biological species including human genome, protein sequences, protein 3-D structures, metabolic pathways databases, cell line & hybridoma information, biodiversity related information. Advancements in information technology, particularly the Internet, are being used to gather and access ever-increasing information in biology and biotechnology. Functional genomics, proteomics, discovery of new drugs and vaccines, molecular diagnostic kits and pharmacogenomics are some of the areas in which bioinformatics has become an integral part of Research & Development. The knowledge of multimedia databases, tools to carry out data analysis and modeling of molecules and biological systems on computer workstations as well as in a network environment has become essential for any student of Bioinformatics. Bioinformatics, the multidisciplinary area, has grown so much that one divides it into molecular bioinformatics, organal bioinformatics and species bioinformatics. Issues related to biodiversity and environment, cloning of higher animals such as Dolly and Polly, tissue culture and cloning of plants have brought out that Bioinformatics is not only a support branch of science but is also a subject that directs future course of research in biotechnology and life sciences. The importance and usefulness of Bioinformatics is realized in last few years by many industries. Therefore, large Bioinformatics R & D divisions are being established in many pharmaceutical companies, biotechnology companies and even in other conventional industry dealing with biological. Bioinformatics is thus rated as number one career in the field of biosciences.

In short, Bioinformatics deals with database creation, data analysis and modeling. Data capturing is done not only from printed material but also from network resources. Databases in biology are generally in the multimedia form organized in relational database model. Modeling is done not only on single biological molecule but also on multiple systems thus requiring a use of high performance computing systems.

The Potential of Bioinformatics
The potential of Bioinformatics in the identification of useful genes leading to the development of new gene products, drug discovery and drug development has led to a paradigm shift in biology and biotechnology-these fields are becoming more & more computationally intensive. The new paradigm, now emerging, is that all the genes will be known “in the sense of being resident in database available electronically”, and the starting point of biological investigation will be theoretical and a scientist will begin with a theoretical conjecture and only then turning to experiment to follow or test the hypothesis. With a much deep understanding of the biological processes at the molecular level, the Bioinformatics scientist have developed new techniques to analyse genes on an industrial scale resulting in a new area of science known as ‘Genomics’.

The shift from gene biology has resulted in the development of strategies-from lab techniques to computer programmes to analyse whole batch of genes at once. Genomics is revolutionizing drug development, gene therapy, and our entire approach to health care and human medicine.

The genomic discoveries are getting translated in to practical biomedical results through Bioinformatics applications. Work on proteomics and genomics will continue using highly sophisticated software tools and data networks that can carry multimedia databases. Thus, the research will be in the development of multimedia databases in various areas of life sciences and biotechnology. There will be an urgent need for development of software tools for datamining, analysis and modelling, and downstream processing. Security of data, data transfer and data compression, auto checks on data accuracy and correctness will also be major research area of bioinformatics. The use of virtual Reality in drug design, metabolic pathway design, and unicellular organism design, paving the way to design and modification of muticellular organisms, will be the challenges challenges which Bioinformatics scientist and specialist have to tackle. It has now been universally recognized that Bioinformatics is the key to the new grand data-intensive molecular biology that will take us into 21 century.

Bioinformatics – Industry Overview
The Bioinformatics industry has grown to keep up with the information explosion, growing at 25-50% a year. In 2000, the US market Research company Oscar Gruss estimated that the value of the Bioinformatics industry would touch $2 billion. Now it s demand for individuals capable of doing bioinformatics is soaring. Industry’s demand for scientists with skills in Bioinformatics far exceeds the supply of qualified specialists in the field, Seems likely that this figure will be reached within the coming year. Therefore, companies are developing methods of spotting potential Bioinformatics experts and then training them on the job.

Bioinformatics and computational biology
Bioinformatics and computational biology each maintain close interactions with life sciences to realize their full potential. Bioinformatics applies principles of information sciences and technologies to make the vast, diverse, and complex life sciences data more understandable and useful. Computational biology uses mathematical and computational approaches to address theoretical and experimental questions in biology. Although bioinformatics and computational biology are distinct, there is also significant overlap and activity at their interface.

Biocomputing is often used as a catch-all term covering all this area at the intersection of Biology and Computation , although many other terms are used to name the same area. We can distinguish in to (non-disjoint) sub-fields:

  • Bioinformatics – this includes management of biological databases, data mining and data modeling, as well as IT-tools for data visualization
  • Computational Biology – this includes efforts to solve biological problems with computational tools (such as modeling, algorithms, heuristics)
  • DNA computing and nano-engineering – this includes models and experiments to use DNA (and other) molecules to perform computations
  • Computations in living organisms – this is concerned with constructing computational components in living cells, as well as with studying computational processes taking place daily in living organisms

Computational Biology
Computational Biology is application of core technology of computer science (eg. algorithms, artificial intelligence, databases etc) to problems arising from biology. Computational biology is particularly exciting today because the problems are large enough to motivate the efficient algorithms and moreover the demand of biology on computational science is increasing.

The most pressing tasks in bioinformatics involve the analysis of sequence information. Computational Biology is the name given to this process, and it involves the following:

  • Finding the genes in the DNA sequences of various organisms
  • Developing methods to predict the structure and/or function of newly discovered proteins and structural RNA sequences.
  • Clustering protein sequences into families of related sequences and the development of protein models.
  • Aligning similar proteins and generating phylogenetic trees to examine evolutionary relationships. Thanks to for their work in web development and SEO.