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The Role of Bioinformatics in Infectious Diseases

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A Few Basic Concepts of Molecular Biology: Genetic material - DNA & RNA. ... urgently needed to prevent infection by severe acute respiratory syndrome (SARS) ... – PowerPoint PPT presentation

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Title: The Role of Bioinformatics in Infectious Diseases


1
The Role of Bioinformatics in Infectious Diseases
  • Prof Jamuna Vadivelu
  • Dept of Medical Microbiology
  • Faculty of Medicine
  • University Of Malaya

2
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3
A Few Basic Concepts of Molecular Biology
  • Genetic material - DNA RNA.
  • DNA as a sequence of bases (A,C,T,G).
  • Watson-Crick complementation.
  • Proteins.
  • The central dogma of molecular biology.

4
Central Dogma
Cells express different subset of the genes in
different tissues and under different conditions
5
Centarl Paradigm of Molecular Biology
DNA RNA Protein
Symptomes (Phenotype)
6
Central Paradigm of Bioinformatics
Genetic information
7
Central Paradigm of Bioinformatics
Molecular Structure
Genetic Information
8
Central Paradigm of Bioinformatics
Molecular Structure
Biochemical Function
Genetic Information
9
Central Paradigm of Bioinformatics
Molecular Structure
Genetic Information
Biochemical Function
Symptoms
10
What is BIOINFORMATICS ?
A field of science in which Biology, Computer
Science and Information Technology merge into a
single discipline. Goal To enable the
discovery of new biological insights and create
a global perspective for biologists.
11
  • Disciplines
  • Development of new algorithms and statistics
    to
  • assess relationships among members of large
    data
  • sets.
  • Analysis and interpretation of various types
    of
  • data.
  • Development and implementation of tools to
  • efficiently access and manage different types
    of
  • information.

12
Why use BIOINFORMATICS ?
  • An explosive growth in the amount of
    biological information necessitates the use of
    computers for cataloging and retrieval.
  • A more global perspective in experimental
    design
  • (from one scientist one gene/protein/disease
    paradigm to whole organism consideration).
  • Data mining - functional/structural
    information is
  • important for studying the molecular basis of
    diseases (and evolutionary patterns).

13
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14
Genome Sequencing
  • On June 26, 2000, "working draft" of the human
    genome.
  • Project goals were to
  • identify all the approximately 20,000-25,000
    genes in human DNA,
  • determine the sequences of the 3 billion chemical
    base pairs that make up human DNA,
  • store this information in databases,
  • improve tools for data analysis,
  • transfer related technologies to the private
    sector, and
  • address the ethical, legal, and social issues
    (ELSI) that may arise from the project.

15
Scientists Spell Out Recipe for Human Beings 
  • With new techniques and powerful computers,
    scientists have finally pieced together the
    entire human genome.
  • all three billion biochemical rungs of our spiral
    ladder-shaped DNA molecule have been strung
    together in the correct order.
  • What we now have is the entire book of life for
    making a human being.

16
Why microbes?
  • microbes make up most of the earths biomass,
  • evolved for some 3.8 billion years.
  • found in virtually every environment, surviving
    and thriving in extremes of heat, cold,
    radiation, pressure, salt, acidity, and darkness
  • microbes are in the air we breathe, the ground we
    walk on, the food we eatthey're even inside us!

17
What are microbes?
  • Microbe is a term for tiny creatures that
    individually are too small to be seen with the
    unaided eye.
  • Microbes include
  • bacteria
  • fungi
  • viruses

18
Bacterium
19
Virus
20
Fungus
21
Why Microbes?
  • broad and far-reaching implications for
    environmental, energy, health, and industrial
    applications.
  • cleanup of toxic-waste
  • production of novel therapeutic agents
  • energy generation (e.g., methane and hydrogen).
  • production of chemical catalysts, reagents, and
    enzymes for industrial processes.

22
Why Microbes?
  • management of environmental carbon dioxide, which
    is related to climate change.
  • detection of disease-causing organisms and
    monitoring of the safety of food and water
    supplies.
  • use of genetically altered bacteria as living
    sensors (biosensors)
  • understanding of specialized systems used by
    microbial cells to live in natural environments
    with other cells.

23
Teen's Research Points to Possible Danger in
Water Supplies
  • could a kid do scientific research that even real
    scientists would take note of?
  • 17-year-old Ashley Mulroy did.
  • she set out to test drinking water for traces of
    antibiotic drugs.
  • two issues
  • water safety, and
  • the growing threat of antibiotic resistance.

24
Challenges in Tropical Diseases
  • avian influenza emerged in east Asia and
    continues today.
  • the probability that this virulent virus will
    acquire genetic traits for increased
    person-to-person transmissibility,
  • potential to set the stage for the next global
    influenza pandemic

25
Challenges in Tropical Diseases
  • antimicrobial resistance is common, has developed
    against every class of antimicrobial drug,
  • developing effective and safe vaccines is
    urgently needed to prevent infection by severe
    acute respiratory syndrome (SARS)
  • dengue fever continues to plague South East Asia

26
Microbial Genome Project
  • In 1995, the first microbe sequencing project,
    Haemophilus influenzae (a bacterium causing upper
    respiratory infection) was completed
  • continue to sequence other medically important
    organisms
  • bacteria that cause tuberculosis, gonorrhea,
    chlamydia and cholera, and
  • organisms that are considered agents of
    bioterrorism.
  • protozoan pathogens such as the organism causing
    malaria

27
Benefits of Genome Sequencing
  • the availability of microbial and human DNA
    sequence and advances in
  • molecular biology,
  • immunology,
  • human and pathogen genetics,
  • plus the computational sciences (bioinformatics)
  • suggest rapid progress in the search for new
    chemotherapeutic agents and new vaccines to treat
    and prevent infection

28
How can bioinformatics help?
  • Current research in bioinformatics can be
    classified into
  • genomics sequencing and comparative study of
    genomes to identify gene and genome
    functionality,
  • proteomics identification and characterization of
    protein related properties and reconstruction of
    metabolic and regulatory pathways,
  • cell visualization and simulation to study and
    model cell behavior, and
  • application to the development of drugs and
    anti-microbial agents.

29
How can Bioinformatics Help?
  • Bioinformatics research can be classified under
    three major approaches
  • analysis based upon the available experimental
    wet-lab data,
  • the use of mathematical modeling to derive new
    information, and
  • an integrated approach that integrates search
    techniques with mathematical modeling

30
How can Bioinformatics Help?
  • The major impact of bioinformatics research is to
  • automate the genome sequencing, and development
    of integrated genomics and proteomics databases,
  • automate genome comparisons to identify the
    genome function,
  • automate derivation of metabolic pathways, and
  • gene expression analysis to derive regulatory
    pathways,
  • develop statistical techniques, clustering
    techniques and data mining techniques to derive
    protein-protein and protein-DNA interactions

31
How can Bioinformatics Help?
  • model 3D structure of proteins and 3D docking
    between proteins and biochemicals for rational
    drug design,
  • differential analysis between pathogenic and
    non-pathogenic strains to identify candidate
    genes for vaccines and anti-microbial agents, and
  • the whole genome comparison to understand the
    microbial evolution

32
Limitations and Future Challenges for
Bioinformaticians
  • current analysis is limited by
  • the lack of available gene-functionality from the
    wet-lab data,
  • the lack of computer algorithms to explore vast
    amount of data with unknown functionality,
  • limited availability of protein-protein and
    protein-DNA interactions, and
  • the lack of knowledge of temporal and transient
    behavior of genes and pathways.

33
THANK YOU
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