Robert B. Cary

Digitally collected cryo‐electron micrographs for single particle reconstruction

Several advantages and disadvantages have been cited for image collection with a slow‐scan CCD camera. Here we explore its use for cryo‐EM single particle reconstruction and present two practical examples. The icosahedral adenovirus (Ad) type 2 (∼150 MDa) was reconstructed from 396 particle images. The Fourier shell correlation (FSC) 0.5 threshold and the Fourier shell phase residual (FSPR) 45°criterion yielded 17 ÅA resolution for the ordered viral capsid. Visual comparison with the filtered Ad2 crystallographic hexon confirmed a resolution range of 15–17 Å. The asymmetric DNA‐PKcs protein (470 kDa) was reconstructed from 9,473 particle images, using a previously published reconstruction based on class‐sum images as an orientational search model [Chiu et al. (1998) J. Mol. Biol. 284:1075–1081]. FSC and FSPR methods yielded 17 Å resolution for the new DNA‐PKcs reconstruction, indicating a small but noticeable improvement over that of the class‐sum based reconstruction. Despite the lack of symmetry for DNA‐PKcs and its lower image contrast compared to Ad2 (0.8% vs. 2.5%), the same resolution was obtained for both particles by averaging significantly more DNA‐PKcs images. Use of the CCD camera enables the microscopist to adjust the electron beam strength interactively and thereby maximize the image contrast for beam sensitive samples. On‐line Fourier transformation also allows routine monitoring of drift and astigmatism during image collection, resulting in a high percentage of micrographs suitable for image processing. In conclusion, our results show that digital image collection with the YAG‐scintillator slow‐scan CCD camera is a viable approach for 3D reconstruction of both symmetric and asymmetric particles. Microsc. Res. Tech. 49:224–232, 2000.

Microarray analysis of the DNA-dependent protein kinase catalytic subunit knock-out mouse: global effects on gene regulation and the cellular response to ionizing radiation

Microarray analysis of the DNA-dependent protein kinase catalytic subunit knock-out mouse: global effects on gene regulation and the cellular response to ionizing radiation