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Single Cell Variability

Single Cell Variability. The contribution of noise to biological systems. Outline . Background Why single cells? Noise in biological systems Cool studies Conclusions. Background – Microscale Life Sciences Center. Funded by NIH CEGS To develop technologies for single cell research

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Single Cell Variability

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  1. Single Cell Variability The contribution of noise to biological systems

  2. Outline • Background • Why single cells? • Noise in biological systems • Cool studies • Conclusions

  3. Background – Microscale Life Sciences Center • Funded by NIH • CEGS • To develop technologies for single cell research • Lab-on-a-chip modality • Collaborative approach

  4. Why Single Cells? • Variable of interest • Bulk data represents averages • Averages may not represent behavior of subpopulations

  5. Why Single Cells? – One Example =? =?

  6. Why Single Cells? – One Example Gaussian Bimodal

  7. Why Single Cells? – One Example Gaussian = Bimodal

  8. Variability in populations – What we know so far • Population response is governed by: • Variability at the single cell level • Subpopulations • Noise inherent to any complex system

  9. Noise in biological systems • “Chemical analysis are affected by two types of noise: chemical noise and instrumental noise”* • What is chemical noise? • What is instrument noise? • In general: Noise = σ/mean *Principals of Instrumental Analysis. 1998. Skoog, Holler, and Nieman.

  10. Noise in biological systems • “Chemical analysis are affected by two types of noise: chemical noise and instrumental noise”* • What is chemical noise? • Fluctuations in Temp, concentration, vibrations, light, gradients, etc • What is instrument noise? • Composite of noise from individual components of a system *Principals of Instrumental Analysis. 1998. Skoog, Holler, and Nieman.

  11. Noise in biological systems • Noise in a nutshell • Chemical noise = intrinsic (inherent) variability • Instrument noise = extrinsic (global) variability • Will show examples from literature and my research

  12. Noise in biological systems • Intrinsic noise: • Inherent • Order of events • Entropy • Binding of substrate to enzyme

  13. Noise in biological systems • Extrinsic noise: • Concentrations of system components • Regulatory proteins, polymerase • Chemical flux through components • Enzyme activities • Substrate to product conversion • Global effects of all components

  14. Extrinsic Noise – cell growth • Global variability that is a composite of intrinsic noise from each component of a system. • First observed by Kelly and Rahn in 1932* • Measured 2-3 fold variation in the division times of single E. coli cells • No correlation between division time of mother cell and division time of either of the two daughter cells *Kelly & Rahn, J. Bacteriol., 1932

  15. Extrinsic Noise – cell growth Cells imbedded in soft agar *Kelly & Rahn, J. Bacteriol., 1932

  16. Extrinsic Noise – cell growth Light Source Air tank vent hv Pump Environmental Chamber Reservoir Lung (50ft tubing) Objective Waste

  17. Extrinsic Noise LSM Data

  18. Extrinsic Noise Single Cell Growth over Time Strovas et al. In preparation.

  19. Extrinsic Noise Single Cell Growth over Time 0.73 mm/hr 0.55mm/hr Strovas et al. In preparation.

  20. Extrinsic Noise Methanol Succinate 3.73 +/- 0.63 hrs (N = 195) 3.12 +/- 0.55 hrs (N = 115) • Over 2 fold range in division rates • Extrinsic noise differs based on carbon source Strovas et al. In preparation.

  21. Intrinsic Noise - Transcription • The noise inherent to a system component • What are components of a biological system? • Focus on noise in transcription • How does one measure transcription rates?

  22. Intrinsic Noise - Transcription Promoter Activities via Transcriptional Fusions light Plac

  23. Intrinsic Noise - Transcription http://meds.queensu.ca/~mbio318/EXTRA_MATERIAL.html

  24. Intrinsic Noise - Transcription http://meds.queensu.ca/~mbio318/EXTRA_MATERIAL.html

  25. Intrinsic Noise • Elowitz et al, 2002 • Elegant experiment to show intrinsic noise • Made two transcriptional fusions in E. coli: • Plac-YFP • Plac-CFP • Observed YFP and CFP fluorescence w/ and w/out IPTG present

  26. Intrinsic Noise Elowitz et al, Science, 297, 1183-1186, 2002

  27. Intrinsic Noise Fluorescence vs. Growth rate Methanol Succinate R2 = 0.0257 R2 = 0.0049 Strovas et al. In preparation.

  28. Intrinsic Noise Succinate -> Methanol Carbon Shift Succinate: 1993.15 +/- 468.14 RFU/mm^2 (N = ~1000) Methanol: 3075.30 +/- 243.35 RFU/mm^2 (N = ~1000) Strovas et al. In preparation.

  29. Noise in biological systems - Summary • Variability in biological systems at the population and single cell level is governed by intrinsic and extrinsic noise. • Extrinsic noise dominates variability as a whole • Intrinsic noise dominates the variability observed from individual components of a system • Intrinsic noise can be independent of extrinsic noise

  30. Now what? • Since noise in biological systems can govern biological variability, can’t we cure cancer and move on? • No! Like all complex systems we must characterize them! • What we know is just the tip of the iceberg!

  31. Nifty stuff – Balaban et al. • Bacterial persistence as a phenotypic switch • Balaban et al. 2004. Science. 305: 1622-1625 • Demonstrated the ability of single cells from an E. coli clonal population to survive treatment with antibiotics.

  32. Nifty stuff – Balaban et al.

  33. Nifty stuff – Balaban et al.

  34. Nifty stuff – Balaban et al. • Persister cells were susceptible to subsequent antibiotic treatment • Heterogeneity (variance) within the population attributed to presence of persisters • Why can persisters survive and how is it useful? • What type of noise governs this response?

  35. Nifty stuff – Raser and Shea • Control of stochasticity in eukaryotic gene expression • Raser and Shea. 2004. Science. 304: 1811-1814 • Used similar methods to Elowitz et al. only using yeast. • Suggests that noise is an evolvable trait that can help balance fidelity and diversity

  36. Nifty stuff – Raser and Shea Time course during phosphate starvation

  37. Nifty stuff – Raser and Shea • Showed extrinsic noise dominates total noise in yeast • Intrinsic noise only contributed 2-20% • Transcription in eukaryotes has been described as pulsative • Results in variable mRNA levels from cell to cell • Causes phenotypic diversity in clonal yeast populations

  38. Conclusions • Population averages skew the underlying contributions of subpopulations • Subpopulations are the result of variable cellular response within a clonal population • Cellular variability arises from intrinsic noise, but governed by extrinsic noise • Cellular variability allows for adaptation to environmental perturbations

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