Because of stochasticity in the gene expression process, protein and mRNA copy numbers in a single cell vary among a population of cells and fluctuate by time. However, quantification of heterogeneity and fluctuation of gene expression products, especially in low copy genes, was difficult because of lack of sensitivity. To approach this problem, we utilized single molecule fluorescence microscopy to quantify heterogeneity and dynamics of gene expressions in single cells with single molecule sensitivity. Measurements on 1,018 genes in model organism Escherichia coli show that distributions of protein copy numbers among a cell population are generally described with gamma distributions, whose parameters are controlled by transcription and translation rates. Furthermore, simultaneous measurements of protein and mRNA expression indicate that both copy numbers in a single cell are uncorrelated.
Clonal heterogeneity of phenotypic traits is often associated with the fitness differences of single cells. Fitness-phenotype correlation causes the population statistics for the phenotypes of interest deviated from the single-cell statistics, imposing fundamental uncertainty in estimating the cellular properties from the population measurements. Recently, microfluidics-based single-cell measurement has become available, which potentially allows us to understand how the population properties are shaped by the heterogeneous and fluctuating single-cell phenotypes. To introduce this issue, we first review the studies on bacterial persistence, in which phenotypic heterogeneity has an apparent relevance to cellular fitness and population survival in stress environments. Next, we discuss how the population-level statistics is biased by the phenotype-fitness correlation using a simple cell proliferation model. Lastly, we show that the experimental examples of single-cell statistics and phenotype-fitness correlation are accumulating by the aid of the novel microfluidics techniques.
Recently, author and colleagues demonstrated that TEM images of Mycobacterium tuberculosis (MTB) processed through rapid freeze-substitution provided exquisite preservation of the ultrastructure distinct from samples prepared through conventional chemical fixation. Here, we show data obtained from structome (quantitative three-dimensional structural information of whole cells at the electron microscopic level) analysis of MTB cells with examination of serial ultrathin sections, including the basic morphological properties and the ribosome density. This is the first structome data of prokaryote. Comparison of ribosome density between MTB and yeast cells was performed and relationship between ribosome density and resistance mechanism of ribosome-targeted anti-tuberculosis drug was discussed.
The cell structures have been studied only qualitatively and two-dimensionally since 1932 when the electron microscope was invented. “Structome” was defined as “quantitative three-dimensional structural information of whole cells at the electron microscopic level”. This is a fundamental concept equal to genome and proteome. In this paper, first structome analysis of Saccharomyces cerevisiae using rapid freeze-freeze substitution method and serial ultrathin sectioning technique is described and discussed about its features. Also, example is shown that leads to the discovery of an unknown microorganism by performing the structome analysis. Finally, difference between the serial slice SEM methods and our method will be discussed.
Recent popularization of 2-photon fluorescence microscopy has enabled us to image cellular structures such as synapses located in deep tissue at the high spatial resolution. However, signal transduction mechanisms in synapse has been still elusive because of the lack of techniques to visualize protein activities or protein-protein interactions. Recently, the improvement of 2-photon fluorescence lifetime imaging microscopy (2pFLIM) to visualize the Förster resonance energy transfer (FRET) has overcame such a difficulty and has enabled us to visualize biochemical reactions. Using this technique, we have recently succeeded in imaging the activity of small GTPases. Here I introduce the principle of the 2pFLIM for monitoring intracellular protein activities and protein-protein interactions with an example: detecting small GTPase (Cdc42 and RhoA) activity in dendrites and synapses of hippocampal neurons in brain slices.
Local atomic configurations of amorphous materials are one of the long-standing problems in materials science. The local atomic configurations have been determined experimentally using average structural information from large volumes using conventional diffraction and spectroscopic methods. Three-dimensional atomic positions have been achieved only by using simulation methods such as reverse Monte Carlo and molecular dynamics simulations. Therefore direct experimental evidence of local structural order in amorphous alloys is much needed. For this purpose we have developed sub-nanometer scale electron diffraction technique using a scanning transmission electron microscope. The obtained results were interpreted through structural models calculated using an ab-initio molecular dynamics simulation. We further extend this technique to the observation of medium-range order where a similar diffraction vector is hold beyond 1 nm.
Magnetic structures of magnetic materials are not easy objects for visualizing by electron microscope because strong magnetic field caused by electron lens modulates their structure. Therefore, a specially customized electron microscope, named Lorentz microscope, has been used for the observation. Recently, however, the observation technology of the magnetic structures is improved in Lorentz microscopy and small angle electron diffraction, for example, the development of Foucault imaging method by using a non-dedicated transmission microscope. This paper introduces the principle of Lorentz microscopy and the latest methods.
Insect compound eye comprises a unit called ommatidium, which houses 7-8 photoreceptors. Visual signals perceived by photoreceptors are processed in the underlying optic lobe, which consists of three discrete neuropils (from the distal, the lamina, the medulla and the lobula complex). The first visual neuropil, the lamina is located beneath the retina, and composed of an array of units termed cartridges. After the lamina, visual information is conveyed to the central brain through the medulla and the lobula complex. In the optic lobe, several tens of thousands of neurons exist, and they form neural connections (synapses) each other to build neural circuits, where several feature of objects such as motion, color, shape and contrast is extracted. The lamina of the fruit fly, Drosophila melanogaster is one of insect neuropils, whose cellular components and synaptic partnerships in which are most well characterized. Here, we overview its ultrastructure.
Electron microscopy elucidated on an atomic scale the transformation mechanism of synchronized long-period stacking ordered (LPSO) structure of Mg97Zn1Y2 alloys. The irregular stacking sequence of a fragment of 24R-type LPSO acts as a catalyst for the transformation from 18R-type to 14H-type LPSO. The elementary step of transformation from 18R-type to 24R-type LPSO takes place by ledge-pair movement on different (0001)Mg planes with Shockley partial dislocations. Each ledge has a transition region in front of it. Because the transition regions have HCP-type stacking sequences, the solute elements migrate easily in the region. Therefore, structural modulation occurs by a mechanism resembling diffusional–displacive transformation. Local strain analysis using high-angle annular dark-field scanning transmission electron microscopy (HAADF-STEM) images has elucidated that lattice spacing of (0001)Mg in the FCC-type enrichment layer is shorter than that in the HCP-type transition region. These structural and compositional irregularities are an elementary step in the transformation of LPSO in Mg97Zn1Y2 alloys. This elementary step is valid for the transformation between polytypes 18R-type and 14H-type LPSOs. A pair of mutually neighboring transition regions should move on different basal planes in a cooperative manner. The important point is that they should have single shift and double shift of the basal planes.
Most recent electron microscopes are commonly equipped with high-resolution digital camera which provides us remote image-sharing with laboratory colleagues and research collaborators by means of internet-video conference system.The provided images are available on a personal computer with secured account permission by the provider. It is highly anticipated that this application will promote not only the experimental research but also the development of young investigators by exchanging mutual opinions with electron microscopic findings in real time. Here, we introduce the equipment and practical use in fine structural research for future.
We developed a phase-controlled coherent Raman microscope to image the concentration distribution of small molecules in vivo (inhalation anesthetic molecules, steroid molecules, amino acids, vitamins). Using this instrument, we were successful in imaging the anesthetic molecules, detecting drug molecules in squid nerve cells, and measuring permeation process of taurine molecules through the mouse cornea.