The journal club at MIT has ended.
We now meet Wednesdays at HMS at 12:30 in the Warren Alpert cafeteria on the left side as you face the food.
Email Sabrina if you'd like to be added to the weekly email list (spencers[at]mit[dot]edu).
Lehar J., Zimmermann G.R., et al. (2007). "Chemical combination effects predict connectivity in biological systems." Mol Syst Biol. 3:80.
Efforts to construct therapeutically useful models of biological systems require large and diverse sets of data on functional connections between their components. Here we show that cellular responses to combinations of chemicals reveal how their biological targets are connected. Simulations of pathways with pairs of inhibitors at varying doses predict distinct response surface shapes that are reproduced in a yeast experiment, with further support from a larger screen using human tumour cells. The response morphology yields detailed connectivity constraints between nearby targets, and synergy profiles across many combinations show relatedness between targets in the whole network. Constraints from chemical combinations complement genetic studies, because they probe different cellular components and can be applied to disease models that are not amenable to mutagenesis. Chemical probes also offer increased flexibility, as they can be continuously dosed, temporally controlled, and readily combined. After extending this initial study to cover a wider range of combination effects and pathway topologies, chemical combinations may be used to refine network models or to identify novel targets. This response surface methodology may even apply to non-biological systems where responses to targeted perturbations can be measured.
In the queue:
Mar, J.C., Rubio, R., et al. (2006). "Inferring steady state single-cell gene expression distributions from analysis of mesoscopic samples." Genome Biology 7:R119.
Background: A great deal of interest has been generated by systems biology approaches that attempt to develop quantitative, predictive models of cellular processes. However, the starting point for all cellular gene expression, the transcription of RNA, has not been described and measured in a population of living cells. Results: Here we present a simple model for transcript levels based on Poisson statistics and provide supporting experimental evidence for genes known to be expressed at high, moderate, and low levels. Conclusion: Although what we describe as a microscopic process, occurring at the level of an individual cell, the data we provide uses a small number of cells where the echoes of the underlying stochastic processes can be seen. Not only do these data confirm our model, but this general strategy opens up a potential new approach, Mesoscopic Biology, that can be used to assess the natural variability of processes occurring at the cellular level in biological systems.
Nelson, D. E., A. E. Ihekwaba, et al. (2004). "Oscillations in NF-kappaB signaling control the dynamics of gene expression." Science 306(5696): 704-8.
Signaling by the transcription factor nuclear factor kappa B (NF-kappaB) involves its release from inhibitor kappa B (IkappaB) in the cytosol, followed by translocation into the nucleus. NF-kappaB regulation of IkappaBalpha transcription represents a delayed negative feedback loop that drives oscillations in NF-kappaB translocation. Single-cell time-lapse imaging and computational modeling of NF-kappaB (RelA) localization showed asynchronous oscillations following cell stimulation that decreased in frequency with increased IkappaBalpha transcription. Transcription of target genes depended on oscillation persistence, involving cycles of RelA phosphorylation and dephosphorylation. The functional consequences of NF-kappaB signaling may thus depend on number, period, and amplitude of oscillations.
Becskei, A., B. B. Kaufmann, et al. (2005). "Contributions of low molecule number and chromosomal positioning to stochastic gene expression." Nat Genet 37(9): 937-44.
The presence of low-copy-number regulators and switch-like signal propagation in regulatory networks are expected to increase noise in cellular processes. We developed a noise amplifier that detects fluctuations in the level of low-abundance mRNAs in yeast. The observed fluctuations are not due to the low number of molecules expressed from a gene per se but originate in the random, rare events of gene activation. The frequency of these events and the correlation between stochastic expressions of genes in a single cell depend on the positioning of the genes along the chromosomes. Transcriptional regulators produced by such random expression propagate noise to their target genes.
Papers read at HMS journal club (in chronological order):
Gordon, A., Colman-Lerner, A., et al. (2007). "Single-cell quantification of molecules and rates using open-source microscope-based cytometry." Nature Methods (4): 175 - 181.
Amir, A., Kobiler, O., et al. (2007). "Noise in timing and precision of gene activities in a genetic cascade." Mol Syst Biol 3:71.
Bean, J.M., Siggia E.D., et al. (2007). "Coherence and timing of cell cycle start examined at single-cell resolution." Mol Cell (21): 3-14.
McClean, M.N., Mody, A., et al. (2007). "Cross-talk and decision making in MAP kinase pathways." Nat Genet (39): 409-414.
Huang, B., Wu, H., et al. (2007). "Counting Low-Copy Number Proteins in a Single Cell." Science 315 (5808): 81 - 84.
Lim, H.N. and van Oudenaarden, A. (2007). "A multistep epigenetic switch enables the stable inheritance of DNA methylation states." Nat Genet (39): 269-275.
Anderson, A.R.A., Weaver, A.M., et al. (2006). "Tumor morphology and phenotypic evolution driven by selective pressure from the microenvironment." Cell 127: 905-15.
Suel, G.M., Kulkarni, R. P., et al. (2007). "Tunability and Noise Dependence in Differentiation Dynamics." Science 315(5819) 1716:9.
Amit, I., Citri, A., et al (2007). "A module of negative feedback regulators defines growth factor signaling." Nat Genet (39): 503-12
Chait, R. Craney, A., and Kishony, R. (2007). "Antibiotic interactions that select against resistance." Nature (446): 668-71
Rothbauer, U., Zolghadr, K., et al. (2006). "Targeting and tracing antigens in live cells with fluorescent nanobodies." Nat Meth (3): 887 - 889.
Papers read at MIT journal club (in alphabetical order):
Acar, M., A. Becskei, et al. (2005). "Enhancement of cellular memory by reducing stochastic transitions." Nature 435(7039): 228-32.
Aguilaniu, H., L. Gustafsson, et al. (2003). "Asymmetric inheritance of oxidatively damaged proteins during cytokinesis." Science 299(5613): 1751-3.
Austin, D. W., M. S. Allen, et al. (2006). "Gene network shaping of inherent noise spectra." Nature 439(7076): 608-11.
Bar-Even, A., J. Paulsson, et al. (2006). "Noise in protein expression scales with natural protein abundance." Nat Genet 38(6): 636-43.
Betzig, E., et al. (2006). "Imaging Intracellular Fluorescent Proteins at Nanometer Resolution." Science 313(5793): p. 1642-1645.
Cai, L., N. Friedman, et al. (2006). "Stochastic protein expression in individual cells at the single molecule level." Nature 440(7082): 358-62.
Colman-Lerner, A., A. Gordon, et al. (2005). "Regulated cell-to-cell variation in a cell-fate decision system." Nature 437(7059): 699-706.
Cookson, S., N. Ostroff, et al. (2005). "Monitoring dynamics of single-cell gene expression over multiple cell cycles." Mol Syst Biol 1: 2005 0024.
Elowitz, M. B., A. J. Levine, et al. (2002). "Stochastic gene expression in a single cell." Science 297(5584): 1183-6.
Fennell, D. A., A. Pallaska, et al. (2005). "Stochastic modelling of apoptosis kinetics." Apoptosis 10(2): 447-52.
Geva-Zatorsky, N., N. Rosenfeld, et al. (2006). "Oscillations and variability in the p53 system." Mol Syst Biol 2: 2006 0033.
Gibson, M. C., A. B. Patel, et al. (2006). "The emergence of geometric order in proliferating metazoan epithelia." Nature 442(7106): 1038-41.
Golding, I., J. Paulsson, et al. (2005). "Real-time kinetics of gene activity in individual bacteria." Cell 123(6): 1025-36.
Henderson, C. J., E. Aleo, et al. (2005). "Caspase activation and apoptosis in response to proteasome inhibitors." Cell Death Differ 12(9): 1240-54.
Janes, K. A., S. Gaudet, et al. (2006). "The response of human epithelial cells to TNF involves an inducible autocrine cascade." Cell 124(6): 1225-39.
Kollmann, M., Løvdok, L., et al. (2005). "Design principles of a bacterial signalling network." Nature 438: 504-507.
Legewie, S., N. Bluthgen, et al. (2006). "Mathematical Modeling Identifies Inhibitors of Apoptosis as Mediators of Positive Feedback and Bistability." PLoS Comput Biol 2(9).
Meraldi, P., V. M. Draviam, et al. (2004). "Timing and checkpoints in the regulation of mitotic progression." Dev Cell 7(1): 45-60.
Mettetal, J. T., D. Muzzey, et al. (2006). "Predicting stochastic gene expression dynamics in single cells." Proc Natl Acad Sci U S A 103(19): 7304-9.
Natarajan, M., K. Lin, et al. (2006). "A global analysis of cross-talk in a mammalian cellular signaling network." Nat Cell Biol 8(6): 571-80.
Newman, J. R., S. Ghaemmaghami, et al. (2006). "Single-cell proteomic analysis of S. cerevisiae reveals the architecture of biological noise." Nature 441(7095): 840-6.
Ozbudak, E. M., M. Thattai, et al. (2002). "Regulation of noise in the expression of a single gene." Nat Genet 31(1): 69-73.
Pedraza, J. M. and A. van Oudenaarden (2005). "Noise propagation in gene networks." Science 307(5717): 1965-9.
Queitsch, C., T. A. Sangster, et al. (2002). "Hsp90 as a capacitor of phenotypic variation." Nature 417(6889): 618-24.
Raj, A., C. S. Peskin, et al. (2006). "Stochastic mRNA Synthesis in Mammalian Cells." PLoS Biol 4(10): e309.
Rehm, M., H. J. Huber, et al. (2006). "Systems analysis of effector caspase activation and its control by X-linked inhibitor of apoptosis protein." Embo J 25(18): 4338-49.
Rosenfeld, N., J. W. Young, et al. (2005). "Gene regulation at the single-cell level." Science 307(5717): 1962-5.
Rossi, F. M., A. M. Kringstein, et al. (2000). "Transcriptional control: rheostat converted to on/off switch." Mol Cell 6(3): 723-8.
Rust, M. J., M. Bates, et al. (2006). "Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM)." Nat Meth 3(10): 793-796.
Sasagawa, S., Y. Ozaki, et al. (2005). "Prediction and validation of the distinct dynamics of transient and sustained ERK activation." Nat Cell Biol 7(4): 365-73.
Sigal, A., R. Milo, et al. (2006). "Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins." Nat Methods 3(7): 525-31.
Suel, G. M., J. Garcia-Ojalvo, et al. (2006). "An excitable gene regulatory circuit induces transient cellular differentiation." Nature 440(7083): 545-50.
Taff, B. M., Voldman, J. (2005). "A Scalable Addressable Positive-Dielectrophoretic Cell-Sorting Array." Anal. Chem. 77(24): 7976-7983.
Volfson, D., J. Marciniak, et al. (2006). "Origins of extrinsic variability in eukaryotic gene expression." Nature 439(7078): 861-4.
Weinberger, L. S., J. C. Burnett, et al. (2005). "Stochastic gene expression in a lentiviral positive-feedback loop: HIV-1 Tat fluctuations drive phenotypic diversity." Cell 122(2): 169-82.
Willig, K.I., Kellner, R.R., et al. (2006). "Nanoscale resolution in GFP-based microscopy." Nat Meth 3(9): 721-723.