This presentation provides the basic understanding of varous genomics and proteomics techniques.Systems biology studies life as a system .It includes the study of living system using various omic technologies .
All-domain Anomaly Resolution Office U.S. Department of Defense (U) Case: “Eg...
Systems biology & Approaches of genomics and proteomics
1. Systems biology
(integrative biology)
Systems biology is the study of an
organism, viewed as an integrated and
interacting network of genes, proteins and
biochemical reactions which give rise to
life.o (Institute of Systems Biology).
Ultimate goal:to predict de novo biological
outcomes given the list of components
involved. (Genome Institute of Singapore).
2. Systemic perturbation of biological system
Monitoring the pathway responses
Integration of the data
Formulation of mathematical models that
describe the structure of the system &
its response to pertubations.
6. 09/04/15
Concepts in systems biology
• System
• Systems thinking
• Complexity theory
• Nonlinear dynamics
• Feedback control
• Robustness
• Emergent properties
• Network
8. A FRAMEWORK FOR SYSTEMS
BIOLOGY
Define all of the components of the system.
Systematically perturb and monitor the components.
Reconcile the experimentally observed responses with those
predicted by the model.
Design and perform new perturbation experiments to distinguish
between multiple or competing model hypotheses.
After choosing the set of new perturbations, repeat steps 2
through 4 and iterate.
9. Structure of systems :
Networks
APPROACHES:
1.Bottom up approach
•tries to construct a gene regulatory network
based on the compilation of independent
experimental data
2.Top down approach
•tries to make use of high throughput data
11. GENOMICS
• The branch of molecular biology concerned with the
structure, function, evolution, and mapping of
genomes i.e.study of genome.
• GENOME : the collection of genes contained within
a complete (haploid) set of chromosomes. The
genome is a static information resource with a
defined gene content.
15. In this process ,four reactin mixtures are set up; each one including:
1.DNA to be sequenced 2.DNA polymerase
3.A supply of nucleotides(A,G,C,T)
4.A small amount of labelled chain
terminating nucleotide :one in each of reaction mixture.
.
16. DNA polymerase synthesise the DNA but incorporation
of terminating nucleotide cause polymerization
to stop.
17.
18. Ending chain at every possible nucleotide position creates a no.
of DNA terminated at same nucleotide but different
positions(shown for 1 reaction mixture)
26. Proteomics
The term proteomics describes the study and
characterization of complete set of proteins
present in a cell, organ, or organism at a given
time .
28. Mass spectrometry (MS)
• Mass spectrometry (MS) is used to determine
the accurate masses of molecules.
• Mass spectrometry (MS) is an extremely
valuable analytical technique in which the
molecules in a test sample are converted to
gaseous ions that are subsequently separated
in a mass spectrometer according to their
mass-to-charge (m/z) ratio and detected.
40. Systems Biology vs. traditional
cell and molecular biology
• Experimental techniques in systems biology are high
throughput;but Intensive computation is involved from
the start in systems biology, in order to organize the data
into usable computable databases.
• Exploration in traditional biology proceeds by
successive cycles of hypothesis formation and testing;
data accumulates during these cycles;while Systems
biology initially gathers data without prior hypothesis
formation; hypothesis formation and testing comes
during post-experiment data analysis and modeling.
42. Understanding environment
•Understanding microbes interaction with
ecosystems
• Explain and predict consequences of complex
phenomena such as climate changes
•Recombine various mechanisms within these
diverse organisms to deal with some
extraordinary human problems
43. APPLICATIONS IN FIELD OF
MEDICINE
• In DRUG DISCOVERY
• Understanding complex situations such
as cancer
• Understanding developmental
neurotoxicology
44. CHALLENGES
1.MODELLING CHALLENGES
• Providing the means for checking the constraints and devising
modeling schemes with sound compositional mechanisms;
and
• managing models that may not be consistent with each other,
either across schemes or across scales
45. 2.CHALLENGES IN PROTEOMICS
• Membrane Proteome
• Serum Proteomics and Biomarker
Discovery
3.CHALLENGES IN HANDLING LARGE AMOUNT
OF DATA GENERATED AND COMBINING
THEM TO CREATE NETWORKS
4.SOME TIMES HYPOTHETICAL NETWORKS
GET CREATED
