AS E T 30 years A Perspective Talk on Biology Biology and its complexity

1. ASET 30 years A Perspective Talk on Biology Biology and its complexity Our own efforts here at Colaba campus: A brief introspection CONCLUDING THOUGHTS Where is Biology headed?

2. Biologists • Want to understand organisms and living systems • Discover underlying mechanisms that govern how organisms work • The knowledge is then used to develop or improve medical, industrial or agricultural processes. • Comfortable with uncertainty and intrinsic noise in their systems

3. Combinatorial explosion that can deal with complexity Assume each biological function depends on 2 genes (absurd, but still instructive) Total number of possible ‘functions’ would be (assuming ~40K functional genes/cell) 0.5 x 40,000 x 39,999 = 799,980,000 With more realistic assumptions about # of genes in each function, the figures are huge : at 100/function (~ 1.5 e302); for all combinations (~ 2 e166713) Feytmans, Noble & Peitsch, Transactions in Computational Systems Biology, 2004

4. NOBLE, D (2002) Nature Reviews Molecular Cell Biology3, 460-463. Unravelling complexity Need to work in an integrative way at all levels: organism organ tissue cellular sub-cellular pathways protein gene higher levels control celfunction & pathways higher levels control gene expression There are feed-downs as well as upward between all these levels

5. Unravelling complexity Top-Down or Bottom-Up? Middle-out!! Sidney Brenner 2001 Noble D (2002) The Rise of Computational Biology. Nature Reviews Molecular Cell Biology, 3, 460-463

6. Uncertainty Principle in Biology: The more we uncover the components, the less we seem to understand the ‘whole” of the system! Figure 1.The biocomplexity pyramid. A hierarchy of entities beginning with the gene and moving up to an entire organism is matched against a variety of corresponding technologies, thereby transforming biological information into knowledge.

7. ASET 30 years A Perspective Talk on Biology Biology and its complexity Our own efforts here at Colaba campus: A brief introspection CONCLUDING THOUGHTS Where is Biology headed?

8. BIOLOGY as seen through various model organisms MODEL ORGANISMS: Bakers yeast Chlamydomonas Dictyostelium Plasmodium Drosophila C. elegans Zebra Fish Mouse Rat Human (epidemiology) and cell lines SEVERAL FOCUS AREAS: Developmental biology Motor biology Parasitology Neurobiology Genome integrity and remodeling Genetics of phenotypes Biophysics – single molecule biology Metabolism and organismal physiology

9. Malarial Parasite Biology: Immunity, properties of novel protective proteins & Neuro-inflammatory responses

10. Genotype - Phenotype problem in “budding yeast” (QTL: Quantitative Trait Loci) Many genes cross-talk non-linearly

11. Chlamydomonas Life Cycle

13. Tissue specific functions Interaction with other nutrient sensing pathways Intracellular signaling Communication between organelles NAD-dependent deacetylase Sirtuins Trans-tissue effects Systemic changes cellular functions Organismal physiology Mediates molecular mechanisms linking nutrient sensing to development, growth, aging and disease

14. Chromosome territories are known to alter positions during differentiation, development, and disease (Foster, et al; 2005, Mehta, et al 2007, 2010). Bolzer, et al; 2005 Interphase chromosome territories • Each chromosome occupies a distinct three-dimensional space called the chromosome territory (CT) • These chromosome territories are organized in a non-random manner • These chromosome territories are known to intermingle (CT’s are not “hard-ball” entities) • The CT’s relocate (across several microns) during chromosomal repairs • Gene-rich CT’s seem to do this “feat” preferentially • Inhibition of Chromosomal repairs lead to loss of CT movements.

15. Molecular Motors in Intracellular Transport Generate cargo in cell body Recruit motors Direct motor-cargo complex to start-point Move processively Release cargo at the correct destination Take care of the free motors

16. Single molecule studies of Molecular motors and Motor complexes

17. Cell Volume 152, Issues 1?2 2013 172 - 182 Molecular Adaptations Allow Dynein to Generate Large Collective Forces inside Cells http://dx.doi.org/10.1016/j.cell.2012.11.044 Arpan?K. Rai , Ashim Rai , Avin?J. Ramaiya , Rupam Jha , Roop Mallik

18. Regulation of pre-synaptic vesicle transport by neuronal activity • Generate cargo in the cell body • Recruit motors • Direct motor-cargo complex to axon • Move processively along axon • Release cargo at the correct destination • Take care of the free motors

19. Epidermis: A stratified epithelium

20. Questions ? ? ?

21. Cytoskeletal organisation Geometry Cell dynamics Mechanical stresses Chemistry Mechanical stresses and geometry directed cytoskeletal dynamics actomyosin

22. SPACIAL PATTERNING OF MAMMALIAN BRAIN : Regional Functionalization Problem In wild type brains, the hem (green) and the antihem (red) flank the expanse of cortical neuroepithelium. Medial neuroepithelium is the hippocampalprimordium (dark blue) and lateral neuroepithelium is the neocortical primordium (grey). In Lhx2 -/- embryos, both medial and lateral cortical primordium is lost and the hem and antihem expand.

24. 2. Role of early environment in shaping adult responses to stress and antidepressants: Molecular and cellular mechanisms Neurobiology of Depression in mammals Hippocampus Medial Prefrontal Cortex • Animal models • of depression (2) Targets of rapid action Antidepressant Treatments

25. Cytochrome C – LEE / Photon Interaction Soft electrons or photons interact with biomolecules leading to Biologically relevant changes such as DNA strand breaks! e- hν + + Heme with Iron To the best of our knowledge this is the first attempt to study LEE interaction with whole Proteins

26. ASET 30 years A Perspective Talk on Biology Biology and its complexity Our own efforts here at Colaba campus: A brief introspection CONCLUDING THOUGHTS Where is Biology headed?

27. Rewiring signalling pathways. The pheromone and osmolarity response pathways in yeast use protein scaffolds (Ste5 and Pbs2) to avoid crosstalk through the shared component Ste11. By constructing a modified fusion protein of Pbs2 and Ste5, the authors constructed a rewired pathway in which cells produce osmolarity stress responses after pheromone induction

28. 1. Complexity in Biology 2. Can this complexity be split into modules/units 3. If so, are engineering approaches implementable for (A) Tuning existing Biology (B) Generate new “Biology” (C) etc.etc..

29. The Yeast system • Scaffold proteins • Mediating recruitment • Improve efficiency of signal transfer. • Facilitate interactions among different signal pathways • Control localization of signal proteins within a cell.

30. MODULAR APPROACH DOES WORK:The Diverter story

31. Digital Cells MeetSynthetic Biology • Model the circuit of its modules • Validate the circuit • Tinker with the circuit at module or inter-module levels • Then… • Alter the gene to build a new protein • SNPs will give you a ‘first approach’ • See if the new protein is ‘well tolerated’

32. Reprogramming the Cell • The cell is a molecular system where all parts also participate in an information system. • We model that system, and then attempt to alter the ‘internal influences’ to create different functional outputs.

33. Strong applications are expected (just one example): Cell and Tissue Engineering • Cell and Tissue Engineering allows us to repair or replace the function of natural tissue with bioengineered substitutes. • Principles of engineering, chemistry, and biology are combined to create tissue substitutes from living cells and synthetic materials. Tissue Engineered Skin New Companies: Advanced Tissue Sciences, Inc. Organogenesis

34. Uncertainty Principle in Biology: The more we learn about the components, the less we seem to understand the ‘whole” of the system! However the exciting journey continues, forever!! Figure 1.The biocomplexity pyramid. A hierarchy of entities beginning with the gene and moving up to an entire organism is matched against a variety of corresponding technologies, thereby transforming biological information into knowledge.