Virtual nanoscopy: Generation of ultra-large high resolution electron microscopy maps

A key obstacle in uncovering the orchestration between molecular and cellular events is the vastly different length scales on which they occur. We describe here a methodology for ultrastructurally mapping regions of cells and tissue as large as 1 mm(2) at nanometer resolution. Our approach employs standard transmission electron microscopy, rapid automated data collection, and stitching to create large virtual slides. It greatly facilitates correlative light-electron microscopy studies to relate structure and function and provides a genuine representation of ultrastructural events. The method is scalable as illustrated by slides up to 281 gigapixels in size. Here, we applied virtual nanoscopy in a correlative light-electron microscopy study to address the role of the endothelial glycocalyx in protein leakage over the glomerular filtration barrier, in an immunogold labeling study of internalization of oncolytic reovirus in human dendritic cells, in a cryo-electron microscopy study of intact vitrified mouse embryonic cells, and in an ultrastructural mapping of a complete zebrafish embryo slice.     

Characterizing the spatio-temporal behavior of cell populations through image auto- and cross-correlation microscopy

We propose two methods for characterizing the spatio-temporal behavior of cell populations in culture. The first method, image auto-correlation microscopy (IACM), allows us to characterize the variation in the number of objects as a function of time, thus enabling the quantification of the clustering properties of cell populations to be performed. The second method, image cross-correlation microscopy (ICCM), allows us to characterize the migration properties of cell populations. The latter method does not require estimation or measurement of the trajectories of individual cells, which is very demanding when populations of >100 cells are examined. The capabilities of the two methods are demonstrated with simulated cell populations, and their usefulness is illustrated with experiments involving invasive and noninvasive tumor cell populations.     

Cell volume changes during apoptosis monitored in real time using digital holographic microscopy

Cellular volume changes play important roles in many processes associated with the normal cell activity, as well as various diseases. Consequently, there is a considerable need to accurately measure volumes of both individual cells and cell populations as a function of time. In this study, we have monitored cell volume changes in real time during apoptosis using digital holographic microscopy. Cell volume changes were deduced from the measured phase change of light transmitted through cells. Our digital holographic experiments showed that after exposure to 1 μM staurosporine for 4 h, the volumes of KB cells were reduced by ~50-60%, which is consistent with previous results obtained using electronic cell sizing and atomic force microscopy. In comparison with other techniques, digital holographic microscopy is advantageous because it employs noninvasive detection, has high time resolution, real time measurement capability, and the ability to simultaneously investigate time-dependent volume changes of both individual cells and cell populations.     

Plant molecular diversity and applications to genomics

Surveys of nucleotide diversity are beginning to show how genomes have been shaped by evolution. Nucleotide diversity is also being used to discover the function of genes through the mapping of quantitative trait loci (QTL) in structured populations, the positional cloning of strong QTL, and association mapping.     

Expression of both I-A and I-E/C subregion antigens on accessory cells required for in vitro generation of cytotoxic T lymphocytes against alloantigens or TNBS-modified syngeneic cells

We have previously reported that radioresistant, Thy 1-negative accessory cells (SAC) are required for the in vitro generation of cytotoxic T-effector cells to allogeneic or trinitrophenyl-modified syngeneic cells. These SAC were found to provide accessory functions irrespective of whether they were syngeneic, semi-syngeneic, or allogeneic to the responding cells. To further characterize the accessory cells active in CML, the expression of Ia antigens on this functional population was assessed by pretreated SAC with anti-Ia reagents and complement and by testing the accessory cell function of these treated populations. The results of these studies demonstrated that the relevant accessory cells for allogeneic and TNP-self CTL express Ia determinants encoded by genes mapping in the I-A and I-E/C subregions. For the TNP-self CTL the accessory function of both SAC syngeneic or allogeneic to the responding and stimulating cells was specifically abrogated by treatment with anti-Ia reagents and complement.     

Primary human CD4+ T cells have diverse levels of membrane lipid order that correlate with their function

Membrane lipid microdomains (lipid rafts) play an important role in T cell function by forming areas of high lipid order that facilitate activation. However, their role in regulating T cell differentiation and function remains controversial. In this study, by applying a new approach involving microscopy and flow cytometry, we characterize membrane lipid order in ex vivo primary human CD4(+) T cells. We reveal that differential membrane lipid order dictates the response to TCR stimulation. T cells with high membrane order formed stable immune synapses and proliferated robustly, intermediate order cells had reduced proliferative ability accompanied by unstable immune synapse formation, whereas low order T cells were profoundly unresponsive to TCR activation. We also observed that T cells from patients with autoimmune rheumatic disease had expanded intermediate order populations compared with healthy volunteers. This may be important in dictating the nature of the immune response since most IFN-γ(+)CD4(+) T cells were confined within intermediate membrane order populations, whereas IL-4(+)CD4(+) T cells were contained within the high order populations. Importantly, we were able to alter T cell function by pharmacologically manipulating membrane order. Thus, the results presented from this study identify that ex vivo CD4(+) T cells sustain a gradient of plasma membrane lipid order that influences their function in terms of proliferation and cytokine production. This could represent a new mechanism to control T cell functional plasticity, raising the possibility that therapeutic targeting of membrane lipid order could direct altered immune cell activation in pathology.     

Most chloroplast DNA of maize seedlings in linear molecules with defined ends and branched forms

We used pulsed-field gel electrophoresis, restriction fragment mapping, and fluorescence microscopy of individual DNA molecules to analyze the structure of chloroplast DNA (cpDNA) from shoots of ten to 14 day old maize seedlings. We find that most of the cpDNA is in linear and complex branched forms, with only 3-4% as circles. We find the ends of linear genomic monomers and head-to-tail (h-t) concatemers within inverted repeat sequences (IRs) near probable origins of replication, not at random sites as expected from broken circles. Our results predict two major and three minor populations of linear molecules, each with different ends and putative origins of replication. Our mapping data predict equimolar populations of h-t linear concatemeric molecules differing only in the relative orientation (inversion) of the single copy regions. We show how recombination during replication can produce h-t linear concatemers containing an inversion of single copy sequences that has for 20 years been attributed to recombinational flipping between IRs in a circular chromosome. We propose that replication is initiated predominantly on linear, not circular, DNA, producing multi-genomic branched chromosomes and that most replication involves strand invasion of internal regions by the ends of linear molecules, rather than the generally accepted D-loop-to-theta mechanism. We speculate that if the minor amount of cpDNA in circular form is useful to the plant, its contribution to chloroplast function does not depend on the circularity of these cpDNA molecules.     

Prospects for admixture mapping of complex traits

Admixture mapping extends to human populations the principles that underlie linkage analysis of an experimental cross. For detecting genes that contribute to ethnic variation in disease risk, admixture mapping has greater statistical power than family-linkage studies. In comparison with association studies, admixture mapping requires far fewer markers to search the genome and is less affected by allelic heterogeneity. Statistical-analysis programs for admixture mapping are now available, and a genomewide panel of markers for admixture mapping in populations formed by West African-European admixture has been assembled. Some of the remaining technical challenges include the ability to ensure that the statistical methods are robust and to develop marker panels for other admixed populations. Where admixed populations and panels of markers informative for ancestry are available, admixture mapping can be applied to localize genes that contribute to ethnic variation in any measurable trait.     

Real‐time interactive two‐photon photoconversion of recirculating lymphocytes for discontinuous cell tracking in live adult mice

The potential usefulness of intravital two‐photon microscopy for fate mapping is limited by its inability to track cells beyond the confines of the imaging volume. Therefore, we have developed and validated a novel method for in vivo photolabelling of spatially‐restricted cells expressing the Kaede optical highlighter by two‐photon excitation. This has allowed us to optically mark a cohort of follicular B cells and track their dissemination from the original imaging volume in the lymph node to the spleen and contralateral lymph node. We also present the first demonstration, to our knowledge, of in vivo photoconversion of a freely moving single cell in a live adult animal. This method of `discontinuous' cell tracking therefore significantly extends the fate mapping capabilities of two‐photon microscopy to delineate the spatiotemporal dynamics of cellular processes that span multiple anatomical sites at the single cell level. (© 2014 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)     

利用原子力显微镜识别成像

细胞膜和细胞内特异蛋白的有效定位与定性,对于了解细胞运动、移植和分化等机制及细胞之间的相互作用非常关键。原子力显微镜灵敏的力学性质在研究生物分子的相互作用和特定分子的免疫识别中得到了广泛的应用,在细胞表面的特异性分子的定位过程中,不像免疫荧光成像一样需要复杂的样品准备,更重要的是能有效地进行特异性和非特异性的识别,并对识别位点可视化。本文从分子识别、功能化探针、基于力-体积成像及与动态力学显微镜结合成像等模式方面,综述了原子力显微镜在生物应用中的识别成像。     

Quantitative trait locus mapping in natural populations: progress, caveats and future directions

Over the last 15 years quantitative trait locus (QTL) mapping has become a popular method for understanding the genetic basis of continuous variation in a variety of systems. For example, the technique is now an integral tool in medical genetics, livestock production, plant breeding and population genetics of model organisms. Ten years ago, it was suggested that the method could be used to understand continuous variation in natural populations. In this review I: (i) clarify what is meant by natural population in the QTL context, (ii) discuss whether evolutionary biologists have successfully mapped QTL in natural populations, (iii) highlight some of the questions that have been addressed by QTL mapping in natural populations, (iv) describe how QTL mapping can be conducted in unmanipulated natural populations, (v) highlight some of the limitations of QTL mapping and (vi) try to predict some future directions for QTL mapping in natural populations.     

Visualizing mechanical tension across membrane receptors with a fluorescent sensor

We report a fluorescence-based turn-on sensor for mapping the mechanical strain exerted by specific cell-surface proteins in living cells. The sensor generates force maps with high spatial and temporal resolution using conventional fluorescence microscopy. We demonstrate the approach by mapping mechanical forces during the early stages of regulatory endocytosis of the ligand-activated epidermal growth factor receptor (EGFR).     

Preparation of spermatogenic cell populations at specific stages of differentiation in the human.

Studying biochemical events in human spermatogenesis requires separated populations of spermatogenic cells. Dissociation of these cells was performed by a Trypsin-DNAse method adapted from the technique used for rodents. Cell separation was performed by centrifugal elutriation. Seven populations were collected, one further purified by Percoll gradient centrifugation, giving nine different cell populations. The efficiency of the cell separation was evaluated by phase contrast microscopy, flow cytometric DNA analysis, and electron microscopy. Five populations were enriched in spermatids: two in round spermatids (87% and 73%), another in round (52%) and elongating (44%) spermatids, another constituted by 80% elongating spermatids, and the last by 90% elongated spermatids. Two of the four remaining populations were enriched in primary spermatocytes (74% and 54%); another population was the upper part of the Percoll gradient and constituted cytoplasmic lobes and residual bodies (89%); the last population was made up of various cells, with no specific enrichment. Electron microscopic observations revealed good preservation of the separated cells; only the flagella from elongated spermatids were lost. Furthermore, an unusual pattern of nucleoplasm distribution during stages 2-4 of spermatid differentiation was observed and its signification is discussed with regard to the shape of the human spermatozoon.     

Information processing with population codes

Information is encoded in the brain by populations or clusters of cells, rather than by single cells. This encoding strategy is known as population coding. Here we review the standard use of population codes for encoding and decoding information, and consider how population codes can be used to support neural computations such as noise removal and nonlinear mapping. More radical ideas about how population codes may directly represent information about stimulus uncertainty are also discussed.     

IDENTIFICATION OF MAST CELLS IN THE SCANNING ELECTRON MICROSCOPE BY MEANS OF X-RAY SPECTROMETRY

In mixed populations of rat peritoneal fluid cells, the mast cells can be differentiated from other cell types in the scanning electron microscope by virtue of the X-ray emission referable to their sulfur content. Both stationary probe and X-ray mapping are feasible; the amount of sulfur eliciting a signal is estimated to be about 8 x 10^-18 g.     

Separation by velocity sedimentation of the gill epithelial cells and their ATPases activities in the seawater adapted eel Anguilla anguilla L

The separation of cell populations by sedimentation was carried out on heterogeneous suspensions of branchial cells of the seawater adapted eel Anguilla anguilla. The cell sedimentation rates vary mainly in relation to size and permit the separation of enriched fractions of chloride cells and respiratory cells. The method is described and discussed. The homogeneity of the separated populations was checked by microscopy and particle counting. An enrichment of 95% by volume concentration of the two main cell types was obtained. The separated cells had good viability (85-95% viable). This was controlled by Trypan blue exclusion tests. The adenosine triphosphatase activities of the different cell populations were measured and compared.     

Genetically encoded neural activity indicators

Recording activity from identified populations of neurons is a central goal of neuroscience. Changes in membrane depolarization, particularly action potentials, are the most important features of neural physiology to extract, although ions, neurotransmitters, neuromodulators, second messengers, and the activation state of specific proteins are also crucial. Modern fluorescence microscopy provides the basis for such activity mapping, through multi-photon imaging and other optical schemes. Probes remain the rate-limiting step for progress in this field: they should be bright and photostable, and ideally come in multiple colors. Only protein-based reagents permit chronic imaging from genetically specified cells. Here we review recent progress in the design, optimization and deployment of genetically encoded indicators for calcium ions (a proxy for action potentials), membrane potential, and neurotransmitters. We highlight seminal experiments, and present an outlook for future progress.     

Dual secretory and myoepithelial differentiation in the transplantable R3230AC rat mammary carcinoma

The hormone-responsive R3230AC mammary carcinoma, serially transplantable in Fisher rats, shows striking functional and morphological similarities to the normal mammary gland. We have studied its cellular composition by both light and electron microscopy, employing markers of myoepithelial and epithelial cells. We identified two cell types: the major cellular component corresponded to epithelial milk-protein secreting cells, while a second component showed immunocytochemical and ultrastructural characteristics of the myoepithelial cells. These cells were positive with a monoclonal antibody detecting alpha smooth muscle actin. The dual differentiation which normally occurs in breast ducts is therefore reproduced in a malignant experimental tumor. The coexistence of neoplastic cell populations, divergent in morphology and function, that persist in a tumor despite many transplant generations, leads to reconsideration of the relationship between cellular differentiation and malignant transformation.     

Visualizing circuits and systems using transgenic reporters of neural activity

Genetically encoded sensors of neural activity enable visualization of circuit-level function in the central nervous system. Although our understanding of the molecular events that regulate neuronal firing, synaptic function, and plasticity has expanded rapidly over the past 15 years, an appreciation for how cellular changes are functionally integrated at the circuit level has lagged. A new generation of tools that employ fluorescent sensors of neural activity promises unique opportunities to bridge the gap between cellular level and system level analysis. This review will focus on genetically encoded sensors. A primary advantage of these indicators is that they can be nonselectively introduced to large populations of cells using either transgenic-mediated or viral-mediated approaches. This ability removes the nontrivial obstacles of how to get chemical indicators into cells of interest, a problem that has dogged investigators who have been interested in mapping neural function in the intact CNS. Five different types of approaches and their relative utility will be reviewed here: first, reporters of immediate-early gene (IEG) activation using promoters such as c-fos and arc; second, voltage-based sensors, such as GFP-coupled Na+ and K+ channels; third, Cl*-based sensors; fourth, Ca2+-based sensors, such as Camgaroo and the troponin-based TN-L15; and fifth, pH-based sensors, which have been particularly useful for examining synaptic activity of highly convergent afferents in sensory systems in vivo. Particular attention will be paid to reporters of IEG expression, because these tools employ the built-in threshold function that occurs with activation of gene expression, provoking new experimental questions by expanding the timescale of analysis for circuit-level and system-level functional mapping.