Bacteria constitute the majority of the world's biomass and are responsible for most bioconversion on the planet. Bacterial pathogens, on the other hand, present major threats to human health, causing numerous infectious diseases in humans. Moreover, bacteria also serve as model organisms for us to understand fundamental biological processes, especially at the molecular and cellular levels. It is thus of paramount importance to understand how molecules coordinate and interact inside bacterial cells to support life processes. In bacteria, life processes take place in a small volume of <1

Public Health Relevance

In this project, we propose to determine a quantitative, high-resolution map of cellular architecture of E. coli with single-molecule sensitivity, nanometer-scale spatial resolution and molecular specificity of each individual gene, and to profile changes of this architecture in response to environmental conditions with a set of bioimaging and systems biology tools. This system-wide view of bacterial architecture with ultimate sensitivity and resolution will not only advance fundamental microbiology and cell biology, but may also suggest new therapeutic targets for bacteria-based infectious diseases. The new high-sensitivity, high-resolution imaging techniques and proteomic analysis tools developed here will also have broad applications to other areas of biomedical research.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Research Project (R01)
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Special Emphasis Panel (ZRG1-BCMB-A (51))
Program Officer
Lewis, Catherine D
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Harvard University
Schools of Arts and Sciences
United States
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Wang, Siyuan; Su, Jun-Han; Beliveau, Brian J et al. (2016) Spatial organization of chromatin domains and compartments in single chromosomes. Science 353:598-602
Wang, Chong; Han, Boran; Zhou, Ruobo et al. (2016) Real-Time Imaging of Translation on Single mRNA Transcripts in Live Cells. Cell 165:990-1001
Moffitt, Jeffrey R; Pandey, Shristi; Boettiger, Alistair N et al. (2016) Spatial organization shapes the turnover of a bacterial transcriptome. Elife 5:
Chen, Huiyi; Shiroguchi, Katsuyuki; Ge, Hao et al. (2015) Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli. Mol Syst Biol 11:808
Sigal, Yaron M; Speer, Colenso M; Babcock, Hazen P et al. (2015) Mapping Synaptic Input Fields of Neurons with Super-Resolution Imaging. Cell 163:493-505
Chen, Kok Hao; Boettiger, Alistair N; Moffitt, Jeffrey R et al. (2015) RNA imaging. Spatially resolved, highly multiplexed RNA profiling in single cells. Science 348:aaa6090
Chen, Huiyi; Shiroguchi, Katsuyuki; Ge, Hao et al. (2015) Genome-wide study of mRNA degradation and transcript elongation in Escherichia coli. Mol Syst Biol 11:781
Zhao, Ziqing W; Roy, Rahul; Gebhardt, J Christof M et al. (2014) Spatial organization of RNA polymerase II inside a mammalian cell nucleus revealed by reflected light-sheet superresolution microscopy. Proc Natl Acad Sci U S A 111:681-6
Chong, Shasha; Chen, Chongyi; Ge, Hao et al. (2014) Mechanism of transcriptional bursting in bacteria. Cell 158:314-326
Jia, Shu; Vaughan, Joshua C; Zhuang, Xiaowei (2014) Isotropic 3D Super-resolution Imaging with a Self-bending Point Spread Function. Nat Photonics 8:302-306

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