3-D Ultrastructure of O. tauri: Electron Cryotomography of an Entire Eukaryotic Cell

The hallmark of eukaryotic cells is their segregation of key biological functions into discrete, membrane-bound organelles. Creating accurate models of their ultrastructural complexity has been difficult in part because of the limited resolution of light microscopy and the artifact-prone nature of conventional electron microscopy. Here we explored the potential of the emerging technology electron cryotomography to produce three-dimensional images of an entire eukaryotic cell in a near-native state. Ostreococcus tauri was chosen as the specimen because as a unicellular picoplankton with just one copy of each organelle, it is the smallest known eukaryote and was therefore likely to yield the highest resolution images. Whole cells were imaged at various stages of the cell cycle, yielding 3-D reconstructions of complete chloroplasts, mitochondria, endoplasmic reticula, Golgi bodies, peroxisomes, microtubules, and putative ribosome distributions in-situ. Surprisingly, the nucleus was seen to open long before mitosis, and while one microtubule (or two in some predivisional cells) was consistently present, no mitotic spindle was ever observed, prompting speculation that a single microtubule might be sufficient to segregate multiple chromosomes

Marker-free image registration of electron tomography tilt-series

<p>Abstract</p> <p>Background</p> <p>Tilt series are commonly used in electron tomography as a means of collecting three-dimensional information from two-dimensional projections. A common problem encountered is the projection alignment prior to 3D reconstruction. Current alignment techniques usually employ gold particles or image derived markers to correctly align the images. When these markers are not present, correlation between adjacent views is used to align them. However, sequential pairwise correlation is prone to bias and the resulting alignment is not always optimal.</p> <p>Results</p> <p>In this paper we introduce an algorithm to find regions of the tilt series which can be tracked within a subseries of the tilt series. These regions act as landmarks allowing the determination of the alignment parameters. We show our results with synthetic data as well as experimental cryo electron tomography.</p> <p>Conclusion</p> <p>Our algorithm is able to correctly align a single-tilt tomographic series without the help of fiducial markers thanks to the detection of thousands of small image patches that can be tracked over a short number of images in the series.</p

Evolutionary tradeoffs in cellular composition across diverse bacteria

One of the most important classic and contemporary interests in biology is the connection between cellular composition and physiological function. Decades of research have allowed us to understand the detailed relationship between various cellular components and processes for individual species, and have uncovered common functionality across diverse species. However, there still remains the need for frameworks that can mechanistically predict the tradeoffs between cellular functions and elucidate and interpret average trends across species. Here we provide a comprehensive analysis of how cellular composition changes across the diversity of bacteria as connected with physiological function and metabolism, spanning five orders of magnitude in body size. We present an analysis of the trends with cell volume that covers shifts in genomic, protein, cellular envelope, RNA and ribosomal content. We show that trends in protein content are more complex than a simple proportionality with the overall genome size, and that the number of ribosomes is simply explained by cross-species shifts in biosynthesis requirements. Furthermore, we show that the largest and smallest bacteria are limited by physical space requirements. At the lower end of size, cell volume is dominated by DNA and protein content—the requirement for which predicts a lower limit on cell size that is in good agreement with the smallest observed bacteria. At the upper end of bacterial size, we have identified a point at which the number of ribosomes required for biosynthesis exceeds available cell volume. Between these limits we are able to discuss systematic and dramatic shifts in cellular composition. Much of our analysis is connected with the basic energetics of cells where we show that the scaling of metabolic rate is surprisingly superlinear with all cellular components

A Reflection on Economic Uncertainty and Fertility in Europe: The Narrative Framework

none5openVignoli, Daniele; Guetto, Raffaele; Bazzani, Giacomo; Pirani, Elena; Minello, AlessandraVignoli, Daniele; Guetto, Raffaele; Bazzani, Giacomo; Pirani, Elena; Minello, Alessandr

Noise Contributions in an Inducible Genetic Switch: A Whole-Cell Simulation Study

Stochastic expression of genes produces heterogeneity in clonal populations of bacteria under identical conditions. We analyze and compare the behavior of the inducible lac genetic switch using well-stirred and spatially resolved simulations for Escherichia coli cells modeled under fast and slow-growth conditions. Our new kinetic model describing the switching of the lac operon from one phenotype to the other incorporates parameters obtained from recently published in vivo single-molecule fluorescence experiments along with in vitro rate constants. For the well-stirred system, investigation of the intrinsic noise in the circuit as a function of the inducer concentration and in the presence/absence of the feedback mechanism reveals that the noise peaks near the switching threshold. Applying maximum likelihood estimation, we show that the analytic two-state model of gene expression can be used to extract stochastic rates from the simulation data. The simulations also provide mRNA–protein probability landscapes, which demonstrate that switching is the result of crossing both mRNA and protein thresholds. Using cryoelectron tomography of an E. coli cell and data from proteomics studies, we construct spatial in vivo models of cells and quantify the noise contributions and effects on repressor rebinding due to cell structure and crowding in the cytoplasm. Compared to systems without spatial heterogeneity, the model for the fast-growth cells predicts a slight decrease in the overall noise and an increase in the repressors rebinding rate due to anomalous subdiffusion. The tomograms for E. coli grown under slow-growth conditions identify the positions of the ribosomes and the condensed nucleoid. The smaller slow-growth cells have increased mRNA localization and a larger internal inducer concentration, leading to a significant decrease in the lifetime of the repressor–operator complex and an increase in the frequency of transcriptional bursts

Retroelement-guided protein diversification abounds in vast lineages of Bacteria and Archaea

Major radiations of enigmatic Bacteria and Archaea with large inventories of uncharacterized proteins are a striking feature of the Tree of Life1-5. The processes that led to functional diversity in these lineages, which may contribute to a host-dependent lifestyle, are poorly understood. Here, we show that diversity-generating retroelements (DGRs), which guide site-specific protein hypervariability6-8, are prominent features of genomically reduced organisms from the bacterial candidate phyla radiation (CPR) and as yet uncultivated phyla belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota and Nanohaloarchaea) archaeal superphylum. From reconstructed genomes we have defined monophyletic bacterial and archaeal DGR lineages that expand the known DGR range by 120% and reveal a history of horizontal retroelement transfer. Retroelement-guided diversification is further shown to be active in current CPR and DPANN populations, with an assortment of protein targets potentially involved in attachment, defence and regulation. Based on observations of DGR abundance, function and evolutionary history, we find that targeted protein diversification is a pronounced trait of CPR and DPANN phyla compared to other bacterial and archaeal phyla. This diversification mechanism may provide CPR and DPANN organisms with a versatile tool that could be used for adaptation to a dynamic, host-dependent existence

Layer size polydispersity in hydrated montmorillonite creates multiscale porosity networks

The aluminosilicate layers of the swelling clay mineral montmorillonite, and the saturated pores they delineate, control the mechanical properties and the transport of solutes in many natural and engineered environments. However, the structural basis of montmorillonite porosity remains poorly characterized due to the difficulty in visualizing hydrated samples in their native state. Here, we used cryogenic transmission electron microscopy (cryo-TEM) and cryo electron tomography (cryo-ET) to show that stacking defects within minimally altered, fully hydrated montmorillonite particles define multiscale porosity networks. Variations in layer lateral dimensions over tens to thousands of nanometers cause a range of topological and dynamic defects that generate pervasive curvature and introduce previously uncharacterized solute transport pathways. Observations of long-range rotational order between neighboring layers indicate that the layer-layer interactions that govern clay swelling involve three dimensional orienting forces that operate across nanoscale pores. These direct observations of the hierarchical structure of hydrated montmorillonite pore networks with nanoscale resolution reveal potentially general aspects of colloidal interactions in fluid-saturated clay minerals

Formation and restacking of disordered smectite osmotic hydrates

Clay swelling, an important phenomenon in natural systems, can dramatically affect the properties of soils and sediments. Of particular interest in low-salinity, saturated systems are osmotic hydrates, forms of smectite in which the layer separation greatly exceeds the thickness of a single smectite layer due to the intercalation of water. In situ X-ray diffraction (XRD) studies have shown a strong link between ionic strength and average interlayer spacing in osmotic hydrates but also indicate the presence of structural disorder that has not been fully described. In the present study the structural state of expanded smectite in sodium chloride solutions was investigated by combining very low electron dose, highresolution cryogenic-transmission electron microscopy observations with XRD experiments. Wyoming smectite (SWy-2) was embedded in vitreous ice to evaluate clay structure in aqua. Lattice-fringe images showed that smectite equilibrated in aqueous, low-ionic-strength solutions, exists as individual smectite layers, osmotic hydrates composed of parallel layers, as well as disordered layer conformations. No evidence was found here for edge-to-sheet attractions, but significant variability in interlayer spacing was observed. Whether this variation could be explained by a dependence of the magnitude of long-range cohesive (van der Waals) forces on the number of layers in a smectite particle was investigated here. Calculations of the Hamaker constant for layer-layer interactions showed that van der Waals forces may span at least five layers plus the intervening water and confirmed that forces vary with layer number. Drying of the disordered osmotic hydrates induced re-aggregation of the smectite to form particles that exhibited coherent scattering domains. Clay disaggregation and restacking may be considered as an example of oriented attachment, with the unusual distinction that it may be cycled repeatedly by changing solution conditions