Biophysics Reports

2017 Vol. 3, No. 1-3

Cover Story

Correlative cryo-fluorescence and cryo-electron microscopy (cryo-CLEM) system has been fast becoming a powerful technique with the advantage to allow the fluorescent labeling and direct visu-alization of the close-tophysiologic ultrastructure in cells at the same time,offering unique insights into the ultrastructure with specific cellular function.There have been various engineered ways to achieve cryo-CLEM including the commercial FEI iCorr system that integrates fluorescence microscope into the column of transmission electron microscope.In this study,the authors applied the approach of the cryo-CLEM-based iCorr to image the syntaphilinimmobilized neuronal mitochondria in situ to test the performance of the FEI iCorr system and determine its correlation accuracy.This study revealed the various mor-phologies of syntaphilin-immobilized neuronal mitochondria that interact with microtubules and suggested that the cryo- CLEM procedure by the FEI iCorr system is suitable with a half micronmeter correlation accuracy to study the cellular organelles that have a discrete distribution and large size,e.g.mitochondrion,Golgi complex, lysosome,etc.

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Opinion:hazards faced by macromolecules when confined to thin aqueous films

Robert M. Glaeser, Bong-Gyoon Han

2017, 3(1-3): 1-7. doi: 10.1007/s41048-016-0026-3

Abstract(1672)

PDF(216)

Abstract:
Samples prepared for single-particle electron cryo-microscopy (cryo-EM) necessarily have a very high surface-to-volume ratio during the short period of time between thinning and vitrification. During this time, there is an obvious risk that macromolecules of interest may adsorb to the air-water interface with a preferred orientation, or that they may even become partially or fully unfolded at the interface. In addition, adsorption of macromolecules to an air-water interface may occur even before thinning. This paper addresses the question whether currently used methods of sample preparation might be improved if one could avoid such interfacial interactions. One possible way to do so might be to preemptively form a surfactant monolayer over the air-water interfaces, to serve as a structure-friendly slide and coverslip. An alternative is to immobilize particles of interest by binding them to some type of support film, which-to continue using the analogy-thus serves as a slide. In this case, the goal is not only to prevent the particles of interest from diffusing into contact with the air-water interface but also to increase the number of particles seen in each image. In this direction, it is natural to think of developing various types of affinity grids as structure-friendly alternatives to thin carbon films. Perhaps ironically, if precautions are not taken against adsorption of particles to air-water interfaces, sacrificial monolayers of denatured protein may take the roles of slide, coverslip, or even both.

Using integrated correlative cryo-light and electron microscopy to directly observe syntaphilin-immobilized neuronal mitochondria in situ

Shengliu Wang, Shuoguo Li, Gang Ji, Xiaojun Huang, Fei Sun

2017, 3(1-3): 8-16. doi: 10.1007/s41048-017-0035-x

Abstract(825)

PDF(259)

Abstract:
Correlative cryo-fluorescence and cryo-electron microscopy (cryo-CLEM) system has been fast becoming a powerful technique with the advantage to allow the fluorescent labeling and direct visualization of the close-to-physiologic ultrastructure in cells at the same time, offering unique insights into the ultrastructure with specific cellular function. There have been various engineered ways to achieve cryo-CLEM including the commercial FEI iCorr system that integrates fluorescence microscope into the column of transmission electron microscope. In this study, we applied the approach of the cryo-CLEMbased iCorr to image the syntaphilin-immobilized neuronal mitochondria in situ to test the performance of the FEI iCorr system and determine its correlation accuracy. Our study revealed the various morphologies of syntaphilin-immobilized neuronal mitochondria that interact with microtubules and suggested that the cryo-CLEM procedure by the FEI iCorr system is suitable with a half micron-meter correlation accuracy to study the cellular organelles that have a discrete distribution and large size, e.g. mitochondrion, Golgi complex, lysosome, etc.

The advent of structural biology in situ by single particle cryoelectron tomography

Jesús G. Galaz-Montoya, Steven J. Ludtke

2017, 3(1-3): 17-35. doi: 10.1007/s41048-017-0040-0

Abstract(520)

PDF(341)

Abstract:
Single particle tomography (SPT), also known as subtomogram averaging, is a powerful technique uniquely poised to address questions in structural biology that are not amenable to more traditional approaches like X-ray crystallography, nuclear magnetic resonance, and conventional cryoEM single particle analysis. Owing to its potential for in situ structural biology at subnanometer resolution, SPT has been gaining enormous momentum in the last five years and is becoming a prominent, widely used technique. This method can be applied to unambiguously determine the structures of macromolecular complexes that exhibit compositional and conformational heterogeneity, both in vitro and in situ. Here we review the development of SPT, highlighting its applications and identifying areas of ongoing development.

Accelerating electron tomography reconstruction algorithm ICON with GPU

Yu Chen, Zihao Wang, Jingrong Zhang, Lun Li, Xiaohua Wan, Fei Sun, Fa Zhang

2017, 3(1-3): 36-42. doi: 10.1007/s41048-017-0041-z

Abstract(794)

PDF(298)

Abstract:
Electron tomography (ET) plays an important role in studying in situ cell ultrastructure in threedimensional space. Due to limited tilt angles, ET reconstruction always suffers from the "missing wedge" problem. With a validation procedure, iterative compressed-sensing optimized NUFFT reconstruction (ICON) demonstrates its power in the restoration of validated missing information for low SNR biological ET dataset. However, the huge computational demand has become a major problem for the application of ICON. In this work, we analyzed the framework of ICON and classified the operations of major steps of ICON reconstruction into three types. Accordingly, we designed parallel strategies and implemented them on graphics processing units (GPU) to generate a parallel program ICON-GPU. With high accuracy, ICON-GPU has a great acceleration compared to its CPU version, up to 83.7×, greatly relieving ICON's dependence on computing resource.

Particle segmentation algorithm for flexible single particle reconstruction

Qiang Zhou, Niyun Zhou, Hong-Wei Wang

2017, 3(1-3): 43-55. doi: 10.1007/s41048-017-0038-7

Abstract(119)

PDF(146)

Abstract:
As single particle cryo-electron microscopy has evolved to a new era of atomic resolution, sample heterogeneity still imposes a major limit to the resolution of many macromolecular complexes, especially those with continuous conformational flexibility. Here, we describe a particle segmentation algorithm towards solving structures of molecules composed of several parts that are relatively flexible with each other. In this algorithm, the different parts of a target molecule are segmented from raw images according to their alignment information obtained from a preliminary 3D reconstruction and are subjected to single particle processing in an iterative manner. This algorithm was tested on both simulated and experimental data and showed improvement of 3D reconstruction resolution of each segmented part of the molecule than that of the entire molecule.