WHAT IS BIOINFORMATICS? Daniel Svozil, Laboratoř informatiky a chemie svozild@vscht.cz svozil
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- WHAT IS BIOINFORMATICS? Daniel Svozil, Laborato informatiky a
chemie svozild@vscht.cz http://ich.vscht.cz/~svozil
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- Canceled lecture Wed, 4. 3. 2015, lecture is canceled
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- Studijn materily http://ich.vscht.cz/~svozil/teaching.html
http://ich.vscht.cz/~svozil/teaching.html
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- Coursera MOOC www.coursera.org Bioinformatic Methods I, II
Bioinformatics: Life Sciences on Your Computer Bioinformatics
Algorithms 1, 2 Algorithms, Biology, and Programming for Beginners
Computational Molecular Evolution
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- edX www.edx.org Data Analysis for Genomics
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- studuj.bioinformatiku.cz
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- 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
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- Extraction of biological knowledge from data DataKnowledge
convert data to knowledge generate new hypotheses design new
experiments Experimental From public databases
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- Omes Genome Transcriptome Proteome Reactome Tissue
architectures Cell interactions Sigaling Metabolome Cell Organism
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
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- 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
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- Omics Biological knowledge Medical knowledge Improved health
Genomics Transcriptomics Proteomics Metabolomics Interactomics
includes Sequencing Microarrays LC/MS NMR Two hybrid measured by
these data are High-throughput High-noise To reduce noise Advanced
pre-processing techniques Reliable high- throughput information
Techniques to analyze high-dimensional data and knowledge bases
source: Bios 560R Introduction to Bioinformatics,
userwww.service.emory.edu/~tyu8/560R/560R_1.pptx
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- Key reasearch in bioinformatics sequence bioinformatics
structural bioinformatics systems biology analysis of biological
pathways to gain e.g. the understanding of disease processes
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- 21 st 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
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- CELL BIOLOGY Daniel Svozil
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- 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
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- Prokaryotes vs. Eukaryotes bacteria 1 bacteria = 1 cell lower
organisms Escherichia coli (E. coli) plasma membrane nucleus
organelles
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- 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
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- 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
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- Cell cycle Division of the cell in two exact copies.
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- Genetics for Dummies, Tara Robinson homologous chromosomes
homologous chromosomes copied
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-
http://www.bothbrainsandbeauty.com/wp-content/uploads/2009/11/chromosomes.jpg
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- Karyotype Genetics for Dummies, Tara Robinson
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- Mitosis 2n2n 4n4n 2n2n2n2n diploid (2n) mother cell identical
diploid (2n) daughter cells division DNA synthesis
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- 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)
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- 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
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- DNA The Basis of Life
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- DNA Biomacromolecule Consists of repeating units DNA in
organism does not usually exist in one piece chromosomes
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- Deconstructing DNA http://www.umass.edu/molvis/tutorials/dna/
bases, deoxyribose sugar, phosphate nucleotide Bases are flat
stacking pYrimidines C, T puRines A, G
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- O3 O5 C3 C5 base sugar Nucleoside
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- Nucleotide nucleosides are interconnected by phospohodiester
bond nucleotide monophosphate nucleoside
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- Bases complement each other. Chargaffs rules amount of G = C
amount of A = T
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- DNA conformations B-DNA A-DNA Z-DNA B A Z
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- Biological role of different DNAs B-DNA canonical DNA
predominant A-DNA Conditions of lower humidity, common in
crystallographic experiments. However, theyre 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.
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- Different sets of DNA nuclear DNA cells 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
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- Structure of DNA in the eukaryotic cell DNA in human
chromosomes: 3.2 10 9 bp. As were diploid: 6.4 10 9 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
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- Chromatin nucleosome
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- Nucleosome
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- Central dogma of molecular biology Wikipedia
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- Molecular Cell Biology, Harvey Lodish