1 / 24

Bioinformatics The big picture

Bioinformatics The big picture. Knowledge discovery and Problem solving Molecular data Drug discovery Research on cancer and other diseases Clinical data Improvements in medical care. Molecular Biology in the context of Bioinformatics . Within The Central Dogma Gene discovery

keitha
Download Presentation

Bioinformatics The big picture

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. Bioinformatics The big picture Knowledge discovery andProblem solving Molecular data Drug discovery Research on cancer and other diseases Clinical data Improvements in medical care

  2. Molecular Biology in the context of Bioinformatics • Within The Central Dogma • Gene discovery • Protein function • Protein structure prediction • Beyond The Central Dogma • Ribozyme and DNAzyme structure prediction • microRNA prediction

  3. The Omics fields Genomics – The study of gene sequences in living organisms Transcriptomics – The mRNA complement of an entire organism, tissue type, or cell Proteomics – The study of proteins Metabolomics – Metabolites in an organism Lipidomics – Lipids Glycomics – glycans, carbohydrate structures of an organism

  4. Genomics The study of an organism's entire genome http://en.wikipedia.org/wiki/List_of_sequenced_eukaryotic_genomes

  5. Types of genomes ChromosomeI 15080555 bytes ChromosomeII 15279385 Chromosome III 13783354 ChromosomeIV 17493875 ChromosomeV 20922323 ChromosomeX 17705097 100264589 total B 100264.589 total KB ~100 total MB

  6. Types of genomes Sources Virus Single stranded DNA Double stranded DNA Single stranded RNA Double stranded RNA Prokaryotic (Bacteria) Archaebacteria Eubacteria Eukaryotic Plants Animals Humans

  7. Types of genomes • Single-stranded RNA viruses and RNA Sense • negative-sense, positive-sense and ambisense • Positive-sense viral RNA is identical to viral mRNA • Negative-sense viral RNA is complementary to mRNA • Ambisense RNA viruses transcribe genes from both • the positive or negative strand

  8. Types of genomes • Chromosome morphology • Circular – most bacteria • in eukaryotic cells in the form of mitochondrial DNA. • Linear – some bacteria, mostly found in Eukaryotes mitochondria bacteria

  9. Types of genomes

  10. Proteomics – The large-scale study of proteins Instrumentation: Mass Spectrometry – MALDI and SELDI 2D PAGE gel Conceptual: Protein-protein interaction Protein-DNA interaction Isoelectric point – PI 25,000 identified genes but an estimated ~500,000 proteins because of alternative splicing, protein modification

  11. SELDI Mass Spectrometry Instrumentation

  12. Proteomics – Mass Spectrometry What does the data look like?

  13. Proteomics – 2D gel electrophoresis Instrumentation Coomassie stained 2D gels

  14. Protein-DNA interaction Binding of Proteins to DNA are important for gene expression.

  15. Transcriptomics The set of all messenger RNA (mRNA) molecules, or "transcripts", produced in one or a population of cells Relevant Instrumentation: Reverse transcription PCR (RT-PCR) Real-time PCR (QRT-PCR) Microarrays http://en.wikipedia.org/wiki/Transcriptomics

  16. Example of an approximately 40,000 probe spotted oligo microarray with enlarged inset to show detail. Instrumentation

  17. Metabolomics The study of an organism's low-molecular weight molecules or metabolites (eg, amino acids, peptides, lipids, carbohydrates) Systematic study of the unique chemical fingerprints that specific cellular processes leave behind Instrumentation: Mass Spectrometry http://en.wikipedia.org/wiki/Metabolite

  18. Lipidomics The large-scale study of non-water-soluble metabolites (lipids or Lipidome) Key technologies used include electrospray ionization, mass spectrometry and liquid chromatography-mass spectrometry. http://en.wikipedia.org/wiki/Lipidomics

  19. Where does the data-DNA come from? Gene sequencing: Squishy-DNA goes into the wet-lab and data-DNA is written to the hard-drive cDNA: some gene expression may be induced by an experiment done in the wet-lab. mRNA is extracted that corresponds to the induced expression. The mRNA is converted to cDNA for analysis.

  20. Molecular Biology in the context of Bioinformatics • Given a sequence of DNA what can we learn • about its function? • Find the six reading frames • Pull the best amino acid sequence • Test the sequence for protein function prediction • Test the sequence for protein trans-membrane • prediction • Blast search

  21. Link to NPR Story Mycoplasma is the smallest living cell, which is why scientists chose it as the first bacterium to build from scratch. Here, an artist's conception of Mycoplasma. Time Life Pictures/Getty Images

  22. FBI's New Technology Revolutionizes DNA Analysis

More Related