Image formation modeling in cryo-electron microscopy.

Accurate modeling of image formation in cryo-electron microscopy is an important requirement for quantitative image interpretation and optimization of the data acquisition strategy. Here we present a forward model that accounts for the specimen's scattering properties, microscope optics, and detector response. The specimen interaction potential is calculated with the isolated atom superposition approximation (IASA) and extended with the influences of solvent's dielectric and ionic properties as well as the molecular electrostatic distribution. We account for an effective charge redistribution via the Poisson-Boltzmann approach and find that the IASA-based potential forms the dominant part of the interaction potential, as the contribution of the redistribution is less than 10%. The electron wave is propagated through the specimen by a multislice approach and the influence of the optics is included via the contrast transfer function. We incorporate the detective quantum efficiency of the camera due to the difference between signal and noise transfer characteristics, instead of using only the modulation transfer function. The full model was validated against experimental images of 20S proteasome, hemoglobin, and GroEL. The simulations adequately predict the effects of phase contrast, changes due to the integrated electron flux, thickness, inelastic scattering, detective quantum efficiency and acceleration voltage. We suggest that beam-induced specimen movements are relevant in the experiments whereas the influence of the solvent amorphousness can be neglected. All simulation parameters are based on physical principles and, when necessary, experimentally determined.

Gigantism in unique biogenic magnetite at the Paleocene-Eocene Thermal Maximum.

We report the discovery of exceptionally large biogenic magnetite crystals in clay-rich sediments spanning the Paleocene-Eocene Thermal Maximum (PETM) in a borehole at Ancora, NJ. Aside from previously described abundant bacterial magnetofossils, electron microscopy reveals novel spearhead-like and spindle-like magnetite up to 4 microm long and hexaoctahedral prisms up to 1.4 microm long. Similar to magnetite produced by magnetotactic bacteria, these single-crystal particles exhibit chemical composition, lattice perfection, and oxygen isotopes consistent with an aquatic origin. Electron holography indicates single-domain magnetization despite their large crystal size. We suggest that the development of a thick suboxic zone with high iron bioavailability--a product of dramatic changes in weathering and sedimentation patterns driven by severe global warming--drove diversification of magnetite-forming organisms, likely including eukaryotes.

Calcification and inorganic carbon acquisition in coccolithophores.

A number of species of coccolithophorid phytoplankton precipitate calcite inside intracellular vesicles (coccolith vesicles). They can form vast blooms under certain conditions, and account for major fluxes of inorganic carbon (Ci) to the ocean floor. The functions of calcification have been debated for many years, and a role in carbon acquisition has been proposed by several workers. The precipitation of calcite from HCO3- involves the production of protons that can potentially be used to facilitate the use of external HCO3- as a photosynthetic substrate. For this function to be feasible, certain criteria must be met. HCO3- (rather than CO32-) should be the external substrate for calcification, photosynthesis should be facilitated by HCO3- in calcifying cells when CO2 availability is limiting, and the transport of Ci and Ca2+ to the site of calcification should be energetically and kinetically feasible. Considerable evidence exists for HCO3- as the substrate for calcification in coccolithophores. However, evidence for a direct role for calcification in supply of Ci for photosynthesis is less clear. The environmental factors that regulate calcification are still uncertain but appear to be related as much to the availability of nutrients as CO2. Transport of Ci to the intracellular site of calcification and removal of H+ from the coccolith vesicle appear to present few energetic or kinetic constraints. However, the large sustained transcellular fluxes of Ca2+ required for calcification probably occur via a pathway that does not involve diffusion across the cytoplasm.