Nanoscale soft x-ray tomography is a powerful new imaging technology for biomedical and translational research. This technique produces high spatial resolution, high-fidelity 3-Dimensional tomographic reconstructions of the specimen, and does so with unprecedented sample throughput. The work of this proposal will further enhance the applicability, usability and fidelity of soft x-ray tomography as a biomedical imaging technique, make it applicable to a greater range of specimen types, significantly increase spatial resolution, and extend the tools and options available for protein localization. We will continue development of our pioneering work on correlated cryogenic fluorescence microscopy. These efforts, and the planned instrumental and technological developments, will allow multi-modal imaging to be carried out on specimens containing endogenous or exogenous fluorescent labels. The end result will be a suite of imaging options that allow protein localization data to be optimally positioned within a 3-Dimensional reconstruction of the specimen. In soft x-ray tomography the image contrast is derived from the biochemical composition of the specimen. Apart from eliminating the need to fix and stain the specimen this results in each organelle having a signature linear x-ray absorption coefficient. This measurement can be used to identify and quantifiably characterize organelles within a specimen and between different specimens. This type of information, together with the location of specific molecules in the specimen is key to understanding the cellular effects of disease, identifying and validating drug targets, and determining modes of action of molecules with therapeutic potential.

Public Health Relevance

Technologies are being developed to visualize the effects of disease on cell structure and organization. This is important information in the identification and validation of targets for drug design, and for determining the mode of action of molecules with therapeutic potential. This technology can be applied to understanding the cellular effects of cancer, or infection, whether it be microbial, viral or parasitic in origin.

National Institute of Health (NIH)
National Institute of General Medical Sciences (NIGMS)
Biotechnology Resource Grants (P41)
Project #
Application #
Study Section
Special Emphasis Panel (ZRG1-BST-K (40))
Program Officer
Swain, Amy L
Project Start
Project End
Budget Start
Budget End
Support Year
Fiscal Year
Total Cost
Indirect Cost
University of California San Francisco
Anatomy/Cell Biology
Schools of Medicine
San Francisco
United States
Zip Code
Aho, Vesa; Myllys, Markko; Ruokolainen, Visa et al. (2017) Chromatin organization regulates viral egress dynamics. Sci Rep 7:3692
Ekman, Axel A; Chen, Jian-Hua; Guo, Jessica et al. (2017) Mesoscale imaging with cryo-light and X-rays: Larger than molecular machines, smaller than a cell. Biol Cell 109:24-38
Le Gros, Mark A; Clowney, E Josephine; Magklara, Angeliki et al. (2016) Soft X-Ray Tomography Reveals Gradual Chromatin Compaction and Reorganization during Neurogenesis In Vivo. Cell Rep 17:2125-2136
Myllys, Markko; Ruokolainen, Visa; Aho, Vesa et al. (2016) Herpes simplex virus 1 induces egress channels through marginalized host chromatin. Sci Rep 6:28844
Hammel, Michal; Amlanjyoti, Dhar; Reyes, Francis E et al. (2016) HU multimerization shift controls nucleoid compaction. Sci Adv 2:e1600650
Darrow, Michele C; Zhang, Yujin; Cinquin, Bertrand P et al. (2016) Visualizing red blood cell sickling and the effects of inhibition of sphingosine kinase 1 using soft X-ray tomography. J Cell Sci 129:3511-7
Tjong, Harianto; Li, Wenyuan; Kalhor, Reza et al. (2016) Population-based 3D genome structure analysis reveals driving forces in spatial genome organization. Proc Natl Acad Sci U S A 113:E1663-72
Ugarte, Fernando; Sousae, Rebekah; Cinquin, Bertrand et al. (2015) Progressive Chromatin Condensation and H3K9 Methylation Regulate the Differentiation of Embryonic and Hematopoietic Stem Cells. Stem Cell Reports 5:728-740
Elgass, Kirstin D; Smith, Elizabeth A; LeGros, Mark A et al. (2015) Analysis of ER-mitochondria contacts using correlative fluorescence microscopy and soft X-ray tomography of mammalian cells. J Cell Sci 128:2795-804
Do, Myan; Isaacson, Samuel A; McDermott, Gerry et al. (2015) Imaging and characterizing cells using tomography. Arch Biochem Biophys 581:111-21

Showing the most recent 10 out of 25 publications