Beam-induced motion of vitrified specimen on holey carbon film

The contrast observed in images of frozen-hydrated biological specimens prepared for electron cryo-microscopy falls significantly short of theoretical predictions. In addition to limits imposed by the current instrumentation, it is widely acknowledged that motion of the specimen during its exposure to the electron beam leads to significant blurring in the recorded images. We have studied the amount and direction of motion of virus particles suspended in thin vitrified ice layers across holes in perforated carbon films using exposure series. Our data show that the particle motion is correlated within patches of 0.3-0.5 μm, indicating that the whole ice layer is moving in a drum-like motion, with accompanying particle rotations of up to a few degrees. Support films with smaller holes, as well as lower electron dose rates tend to reduce beam-induced specimen motion, consistent with a mechanical effect. Finally, analysis of movies showing changes in the specimen during beam exposure show that the specimen moves significantly more at the start of an exposure than towards its end. We show how alignment and averaging of movie frames can be used to restore high-resolution detail in images affected by beam-induced motion.     

Outcome of the first electron microscopy validation task force meeting

This Meeting Review describes the proceedings and conclusions from the inaugural meeting of the Electron Microscopy Validation Task Force organized by the Unified Data Resource for 3DEM (http://www.emdatabank.org) and held at Rutgers University in New Brunswick, NJ on September 28 and 29, 2010. At the workshop, a group of scientists involved in collecting electron microscopy data, using the data to determine three-dimensional electron microscopy (3DEM) density maps, and building molecular models into the maps explored how to assess maps, models, and other data that are deposited into the Electron Microscopy Data Bank and Protein Data Bank public data archives. The specific recommendations resulting from the workshop aim to increase the impact of 3DEM in biology and medicine.     

Maturation in Action: CryoEM Study of a Viral Capsid Caught during Expansion

Bacteriophage HK97 maturation involves discrete intermediate particle forms, comparable to transitional states in protein folding, before reaching its mature form. The process starts by formation of a metastable prohead, poised for exothermic expansion triggered by DNA packaging. During maturation, the capsid subunit transitions from a strained to a canonical tertiary conformation and this has been postulated to be the driving mechanism for initiating expansion via switching hexameric capsomer architecture from skewed to 6-fold symmetric. We report the subnanometer electron-cryomicroscopy reconstruction of the HK97 first expansion intermediate before any crosslink formation. This form displays 6-fold symmetric hexamers, but capsid subunit tertiary structures exhibit distortions comparable to the prohead forms. We propose that coat subunit strain release acts in synergy with the first crosslinks to drive forward maturation. Finally, we speculate that the energetic features of this transition may result from increased stability of intermediates during maturation via enhanced inter-subunit interactions.     

A novel role for non-neutralizing antibodies against nucleoprotein in facilitating resistance to influenza virus

Current influenza vaccines elicit Abs to the hemagglutinin and neuraminidase envelope proteins. Due to antigenic drift, these vaccines must be reformulated annually to include the envelope proteins predicted to dominate in the following season. By contrast, vaccination with the conserved nucleoprotein (NP) elicits immunity against multiple serotypes (heterosubtypic immunity). NP vaccination is generally thought to convey protection primarily via CD8 effector mechanisms. However, significant titers of anti-NP Abs are also induced, yet the involvement of Abs in protection has largely been disregarded. To investigate how Ab responses might contribute to heterosubtypic immunity, we vaccinated C57BL/6 mice with soluble rNP. This approach induced high titers of NP-specific serum Ab, but only poorly detectable NP-specific T cell responses. Nevertheless, rNP immunization significantly reduced morbidity and viral titers after influenza challenge. Importantly, Ab-deficient mice were not protected by this vaccination strategy. Furthermore, rNP-immune serum could transfer protection to naive hosts in an Ab-dependent manner. Therefore, Ab to conserved, internal viral proteins, such as NP, provides an unexpected, yet important mechanism of protection against influenza. These results suggest that vaccines designed to elicit optimal heterosubtypic immunity to influenza should promote both Ab and T cell responses to conserved internal proteins.     

Fluctuating asymmetry in bank vole populations (Rodentia, Arvicolinae) reflects stress caused by landscape fragmentation in the Mont-Saint-Michel Bay

In intensively farmed, reclaimed areas (polders) of Mont-St-Michel Bay, France, bank voles ( Clethrionomys glareolus ) live in fragmented hedgerows, where populations are small and dispersal rates and genetic diversity are low. These small populations are likely to have been exposed to potential environmental and/or genetic stress. The sensitivity of development to stress can be measured by fluctuating asymmetry (FA). FA was calculated for three samples from a disturbed area and one sample from an adjacent, more connected and undisturbed landscape. Size FA was estimated from 16 measurements of the skull and teeth whilst shape asymmetry was estimated from the skull alone. Bank voles in fragmented hedgerows of the disturbed area had a higher degree of FA than bank voles from the more extensive and more connected hedges of the undisturbed area. These results were confirmed by the study of shape asymmetry, body mass and centroid size of the skull. There were no differences in FA between the three disturbed area samples. We conclude that FA does not reveal differences in the development of bank voles living in isolation under different local conditions in the various parts of the disturbed area. However, FA may allow differentiation between populations from greatly contrasting landscapes.  © 2003 The Linnean Society of London, Biological Journal of the Linnean Society , 2003, 80, 37–44.     

Automated Identification of Filaments in Cryoelectron Microscopy Images

Since the foundation for the three-dimensional image reconstruction of helical objects from electron micrographs was laid more than 30 years ago, there have been sustained developments in specimen preparation, data acquisition, image analysis, and interpretation of results. However, the boxing of filaments in large numbers of images--one of the critical steps toward the reconstruction at high resolution--is still constrained by manual processing even though interactive interfaces have been built to aid the tedious and sometimes inaccurate boxing process. This article describes an accurate approach for automated detection of filamentous structures in low-contrast images acquired in defocus pairs using cryoelectron microscopy. The performance of the approach has been evaluated across various magnifications and at a series of defocus values using tobacco mosaic virus (TMV) preserved in vitreous ice as a test specimen. By integrating the proposed approach into our automated data acquisition and reconstruction system, we are now able to generate a three-dimensional map of TMV to approximately 10-A resolution within 24 h of inserting the specimen grid into the microscope.     

Plant palatability and disturbance level in aquatic habitats: an experimental approach using the snail Lymnaea stagnalis (L.)

1. The palatability of aquatic macrophytes to the snail Lymnaea stagnalis was investigated in the laboratory. Eight species of macrophyte were selected from habitats that differed in either flood disturbance regime or nutrient status.
2. In a non-choice test, single macrophyte species were offered to individual snails. The average amount of plant dry mass consumed per Lymnaea dry mass ranged from 3.6 ± 1.4 (±SE) to 63.6 ± 13.9 mg g^–1 day^–1 across plant species. In a choice test, all eight plant species were presented simultaneously to sets of five snails. The average total consumption was 66.1 ± 3.8 mg g^–1 day^–1 and the maximum average consumption for a single plant was 26.2 ± 3.6 mg g^–1 day^–1.
3. In both tests, the amount consumed by snails differed significantly between the plant species. The species growing in undisturbed habitats were the least consumed. Habitat nutrient status was unrelated to plant palatability.
4. These results suggest that macrophyte species growing in habitats that are rarely disturbed by floods allocate a greater proportion of their resources to resisting herbivory.     

Climatic effects on the breeding phenology and reproductive success of an arctic-nesting goose species

Climate warming is pronounced in the Arctic and migratory birds are expected to be among the most affected species. We examined the effects of local and regional climatic variations on the breeding phenology and reproductive success of greater snow geese ( Chen caerulescens atlantica ), a migratory species nesting in the Canadian Arctic. We used a long-term dataset based on the monitoring of 5447 nests and the measurements of 19 234 goslings over 16 years (1989–2004) on Bylot Island. About 50% of variation in the reproductive phenology of individuals was explained by spring climatic factors. High mean temperatures and, to a lesser extent, low snow cover in spring were associated with an increase in nest density and early egg-laying and hatching dates. High temperature in spring and high early summer rainfall were positively related to nesting success. These effects may result from a reduction in egg predation rate when the density of nesting geese is high and when increased water availability allows females to stay close to their nest during incubation recesses. Summer brood loss and production of young at the end of the summer increased when values of the summer Arctic Oscillation (AO) index were either very positive (low temperatures) or very negative (high temperatures), indicating that these components of the breeding success were most influenced by the regional summer climate. Gosling mass and size near fledging were reduced in years with high spring temperatures. This effect is likely due to a reduced availability of high quality food in years with early spring, either due to food depletion resulting from high brood density or a mismatch between hatching date of goslings and the timing of the peak of plant quality. Our analysis suggests that climate warming should advance the reproductive phenology of geese, but that high spring temperatures and extreme values of the summer AO index may decrease their reproductive success up to fledging.