Automatic particle picking of biological molecules imaged by electron microscopy

One of the next great challenges of cell biology is the determination of the enormous number of protein structures encoded in genomes. In recent years, advances in electron cryo-microscopy and high-resolution single particle analysis have developed to the point where they now provide a methodology for high resolution structure determination. Using this approach, images of randomly oriented single particles are aligned computationally to reconstruct 3-D structures of proteins and even whole viruses. One of the limiting factors in obtaining high-resolution reconstructions is obtaining a large enough representative dataset ($>100,000$ particles). Traditionally particles have been manually picked which is an extremely labour intensive process. The problem is made especially difficult by the low signal-to-noise ratio of the images. This paper describes the development of automatic particle picking software, which has been tested with both negatively stained and cryo-electron micrographs. This algorithm has been shown to be capable of selecting most of the particles, with few false positives. Further work will involve extending the software to detect differently shaped and oriented particles.

Infrared spectra of Mg-SiO smokes : comparison with analytical electron microscopy studies

An important component of current models for interstellar and circumstellar evolution is the infrared (IR)spectral data collected from stellar outflows around oxygen-rich stars and from the general interstellar medium [1]. IR spectra from these celestial bodies are usually interpreted as showing the general properties of sub-micron sized silicate grains [2]. Two major features at 10 and 20 microns are reasonably attributed to amorphous olivine or pyroxene (e.g. Mg2Si04 or MgSi03) on the basis of comparisons with natural standards and vapor condensed silicates [3-6]. In an attempt to define crystallisation rates for spectrally amorphous condensates, Nuth and Donn [5] annealed experimentally produced amorphous magnesium silicate smokes at 1000K. On analysing these smokes at various annealing times, Nuth and Donn [5] showed that changes in crystallinity measured by bulk X-ray diffraction occured at longer annealing times (days) than changes measured by IR spectra (a few hours). To better define the onset of crystallinity in these magnesium silicates, we have examined each annealed product using a JEOL 1OOCX analytical electron microscope (AEM). In addition, the development of chemical diversity with annealing has been monitored using energy dispersive spectroscopy of individual grains from areas <20nm in diameter. Furthermore, the crystallisation kinetics of these smokes under ambient, room temperature conditions have been examined using bulk and fourier transform infrared (FTIR)spectra.

Analytical electron microscopy of Mg-SiO smokes; a comparison with infrared and XRD studies

Experimentally obtained Mg.SiO smokes were studied by analytical electron microscopy using the same samples that had been previously characterized by repeated infrared spectroscopy. Analytical electron microscopy shows that unannealed smokes contain some degree of microcrystallinity which increases with increased annealing for up to 30 hr. An SiO2 polymorph (tridymite) and MgO may form contemporaneously as a result of growth of forsterite (Mg2SiO4) microcrystallites in the initially nonstoichiometric smokes. After 4 hr annealing, forsterite and tridymite react to enstatite (MgSiO3). We suggest that infrared spectroscopy and X-ray diffraction analysis should be complemented by detailed analytical electron microscopy to detect budding crystallinity in vapor phase condensates.

Analytical electron microscopy of fine-grained phases in primitive interplanetary dust particles and carbonaceous chondrites

In order to describe the total mineralogical diversity within primitive extraterrestrial materials, individual interplanetary dust particles (IDPs) collected from the stratosphere as part of the JSC Cosmic Dust Curatorial Program were analyzed using a var ...