What is bioinformatics?

1. What is bioinformatics? Daniel Svozil, Laboratoř informatiky a chemie svozild@vscht.cz http://ich.vscht.cz/~svozil

2. Studijní materiály • http://ich.vscht.cz/~svozil/teaching.html

3. Coursera • MOOC • Bioinformatic Methods I • https://class.coursera.org/bioinfomethods1-001 • Bioinformatics Algorithms (Part 1) • https://class.coursera.org/bioinformatics-001 • Computational Molecular Evolution • https://class.coursera.org/molevol-002

4. Definition • NCBI • Bioinformatics is the field of science in which biology, computer science, and information technology merge into a single discipline. The ultimate goal of the field is to enable the discovery of new biological insights and to create a global perspective from which unifying principles in biology can be discerned. • Wikipedia.org • The application of information technology and statistics to the field of molecular biology. • The creation and advancement of databases, algorithms, computational and statistical techniques, and theory to solve formal and practical problems arising from the management, analysis and interpretation of biological data. http://www.ncbi.nlm.nih.gov/About/primer/bioinformatics.html

5. Extraction of biological knowledge from data convert data to knowledge generate new hypotheses Experimental Data Knowledge From public databases design new experiments

6. Omes genome – DNA sequence in an organism transcriptome – mRNA of an entire organism proteome – all proteins in an organism metabolome – all metabolites in an organism interactome – all molecular interactions in an organism Organism Cell Tissue architectures Cell interactions Sigaling …… Genome Transcriptome Reactome Proteome Metabolome

7. Omes and Omics • Genomics • Primarily sequences (DNA and RNA) • Databanks and search algorithms • Supports studies of molecular evolution • Proteomics • Sequences (Protein) and structures • Mass spectrometry, X-ray crystallography • Databanks, knowledge bases, visualization • Functional Genomics (transcriptomics) • Microarray data • Databanks, analysis tools, controlled terminologies • Systems Biology (metabolomics) • Metabolites and interacting systems (interactomics) • Graphs, visualization, modeling, networks of entities

8. Genomics Transcriptomics Proteomics Metabolomics Interactomics …… Sequencing Microarrays LC/MS NMR Two hybrid …… includes measured by “Omics” High-throughput High-noise these data are Advanced pre-processing techniques To reduce noise Biological knowledge Medical knowledge Improved health Techniques to analyze high-dimensional data and knowledgebases Reliable high-throughput information source: Bios 560R Introduction to Bioinformatics, userwww.service.emory.edu/~tyu8/560R/560R_1.pptx

9. Key reasearch in bioinformatics • sequence bioinformatics • structural bioinformatics • systems biology • analysis of biological pathways to gain e.g. the understanding of disease processes

10. 21st century – complex systems • Designing (forward-engineering) • Understanding (reverse-engineering) • Fixing • Why is it so complex? • Can we make a sense of this complexity? • How is it robust? http://yilab.bio.uci.edu/ICSB2007_Tutorial_AM1.htm

11. Cell Biology Daniel Svozil

12. Molecular biology • Though all aspects of biology can be studied at the molecular level, molecular biology is usually restricted to the molecules of genes/gene products/heredity – molecular genetics • Experiments in molecular biology are done using model organisms • Two classes of organism • Prokaryotes • Eukaryotes

13. Prokaryotes vs. Eukaryotes • plasma membrane • nucleus • organelles • bacteria • 1 bacteria = 1 cell • lower organisms • Escherichia coli (E. coli)

14. Cells in eukaryotes • body (somatic) cells • differentiated into special cell types (brain cells, liver cells …) • produce by simple cell division – mitosis • sex cells (gametes) • egg, sperm • used for sexual reproduction (only eukaryotes) • meiosis – reduction of the amount of genetic material

15. Eukaryotic chromosomes • Threadlike DNA, carries genes • Each organism has specific number of chromosomes • Sex chromosomes (determine gender – XX (female), XY (male)), autosomal chromosomes • 46 in human, 2 sex, 44 autosomal • Come in pairs (two in a pair have the same shape and same set of genes (but different alleles)), homologs, diploid

16. Cell cycle • Division of the cell in two exact copies.

17. homologous chromosomes homologous chromosomes copied Genetics for Dummies, Tara Robinson

18. http://www.bothbrainsandbeauty.com/wp-content/uploads/2009/11/chromosomes.jpghttp://www.bothbrainsandbeauty.com/wp-content/uploads/2009/11/chromosomes.jpg

19. Karyotype Genetics for Dummies, Tara Robinson

20. Mitosis 2n diploid (2n) mother cell DNA synthesis 4n division 2n 2n identical diploid (2n) daughter cells

21. Sexual reproduction • Egg gets fertilized by sperm. Zygote is cretaed. • Zygote is diploid (divides by mitosis), thus the gametes must be haploid! • In organism with diploid cells, how do you get haploid? • Meiosis (another type of cell division)

22. Meiosis • The result of meiosis is a haploid cell. • From one parent diploid cell you get four haploid cells. In addition, homologous chromosomes go through recombination. http://www.britannica.com

23. DNA – The Basis of Life

24. DNA • Biomacromolecule • Consists of repeating units • DNA in organism does not usually exist in one piece • chromosomes

25. Deconstructing DNA • http://www.umass.edu/molvis/tutorials/dna/ • bases, deoxyribose sugar, phosphate – nucleotide • Bases are flat → stacking • pYrimidines – C, T • puRines – A, G

26. Nucleoside base O5‘ C5‘ sugar C3‘ O3‘

27. Nucleotide • nucleosides are interconnected by phospohodiester bond • nucleotide monophosphate nucleoside

28. Bases complement each other. • Chargaffs’ rules • amount of G = C • amount of A = T

29. DNA conformations A B Z A-DNA Z-DNA B-DNA

30. Biological role of different DNAs • B-DNA • canonical DNA • predominant • A-DNA • Conditions of lower humidity, common in crystallographic experiments. However, they’re artificial. • In vivo – local conformations induced e.g. by interaction with proteins. • Z-DNA • No definite biological significance found up to now. • It is commonly believed to provide torsional strain relief (supercoiling) while DNA transcription occurs. • The potential to form a Z-DNA structure also correlates with regions of active transcription.

31. Different sets of DNA • nuclear DNA • cell’s nucleus • majority of functions cell carries out • sequencing the genome – scientists mean nuclear DNA • mitochondrial DNA • mtDNA • circular, in human very short (17 kbp) with 37 genes (controling cellular metabolism) • all mtDNA comes from mom, no recombination- Mitochondrial Eve • chloroplast DNA • cpDNA • circular and fairly large (120 – 160 kbp), with only 120 genes • inheritance is either maternal, or paternal

32. Structure of DNA in the eukaryotic cell • DNA in human chromosomes: 3.2  109 bp. As we’re diploid: 6.4  109 bp. • 0.33 nm per bp  2.1 m in each nucleus, size of the nucleus: 5-10 m across • DNA is highly compacted. Combination DNA + proteins. • During interphase, when cells are not dividing, the genetic material exists as a nucleoprotein complex called chromatin, which is dispersed through much of the nucleus. • Further folding and compaction of chromatin during mitosis produces the visible metaphase chromosomes. • euchromatin – extended • heterochromatin – condensed

33. Chromatin nucleosome

34. Nucleosome

36. Central dogma of molecular biology Wikipedia

37. Molecular Cell Biology, Harvey Lodish

38. studying genomes

39. Studying DNA

40. Enzymes for DNA manipulation • Before 1970s, the only way in which individual genes could be studied was by classical genetics. • Biochemical research provided (in the early 70s) molecular biologists with enzymes that could be used to manipulate DNA molecules in the test tube. • Molecular biologists adopted these enzymes as tools for manipulating DNA molecules in pre-determined ways, using them to make copies of DNA molecules, to cut DNA molecules into shorter fragments, and to join them together again in combinations that do not exist in nature. • These manipulations form the basis of recombinant DNA technology.

41. Recombinant DNA technology • The enzymes available to the molecular biologist fall into four broad categories: • DNA polymerase – synthesis of new polynucleotides complementary to an existing DNA or RNA template • Nucleases – degrade DNA molecules by breaking the phosphodiester bonds • restriction endonucleases (restriction enzyme) – cleave DNA molecules only when specific DNA sequences is encountered • Ligases – join DNA molecules together • End modification enzymes – make changes to the ends of DNA molecules

42. source: Brown T. A. , Genomes. 2nd ed. http://www.ncbi.nlm.nih.gov/books/NBK21129/

43. DNA cloning • DNA cloning (i.e. copying) – logical extension of the ability to manipulate DNA molecules with restriction endonucleases and ligases • vector • DNA sequence that naturally replicates inside bacteria. • It consists of an insert (transgene) and larger sequence serving as the backbone of the vector. • Used to introduce a specific gene into a target cell. Once the expression vector is inside the cell, the protein that is encoded by the gene is produced by the cellular-transcription and translation machinery ribosomal complexes. • plasmid (length of insert: 1-10 kbp), cosmid (40-45 kbp), BAC (100-350 kbp), YAC (1.5-3.0 Mbp)

44. Vectors • plasmid • DNA molecule that is separated from, and can replicate independently of, the chromosomal DNA. • Double stranded, usually circular, occurs naturally in bacteria. • Serves as an important tool in genetics and biotechnology labs, where it is commonly used to multiply (clone) or express particular genes. • BAC (bacterial artificial chromosome) • It is a particular plasmid found in E. coli. A typical BAC can carry about 250 kbp. source: wikipedia

45. restriction endonuclease ligase DNA cloning source: Brown T. A. , Genomes. 2nd ed. http://www.ncbi.nlm.nih.gov/books/NBK21129/

46. PCR – Polymerase chain reaction • DNA cloning results in the purification of a single fragment of DNA from a complex mixture of DNA molecules. • Major disadvantage: it is time-consuming (several days to produce recombinants) and, in parts, difficult procedure. • The next major technical breakthrough (1983) after gene cloning was PCR. • It achieves the amplifying of a short fragment of a DNA molecule in a much shorter time, just a few hours. • PCR is complementary to, not a replacement for, cloning because it has its own limitations: the need to know the sequence of at least part of the fragment.

47. Mapping genomes

48. What is it about? • Assigning/locating of a specific gene to particular region of a chromosome and determining the location of and relative distances between genes on the chromosome. • There are two types of maps: • genetic linkage map – shows the arrangement of genes (or other markers) along the chromosomes as calculated by the frequency with which they are inherited together • physical map – representation of the chromosomes, providing the physical distance between landmarks on the chromosome, ideally measured in nucleotide bases • The ultimate physical map is the complete sequence itself.

49. Genetic linkage map • Constructed by observing how frequently two markers (e.g. genes, but wait till next slides) are inherited together. • Two markers located on the same chromosome can be separated only through the process of recombination. • If they are separated, childs will have just one marker from the pair. • However, the closer the markers are each to other, the more tightly linked they are, and the less likely recombination will separate them. They will tend to be passed together from parent to child. • Recombination frequency provides an estimate of the distance between two markers.

50. Genetic linkage map • On the genetic maps distances between markers are measured in terms of centimorgans (cM). • 1cM apart – they are separated by recombination 1% of the time • 1 cM is ROUGHLY equal to physical distance of 1 Mbp in human Value of genetic map – marker analysis • Inherited disease can be located on the map by following the inheritance of a DNA marker present in affected individuals (but absent in unaffected individuals), even though the molecular basis of the disease may not yet be understood nor the responsible gene identified. • This represent a cornerstone of testing for genetic diseases.