Highly nonrandom features of synaptic connectivity in local cortical circuits

How different is local cortical circuitry from a random network? To answer this question, we probed synaptic connections with several hundred simultaneous quadruple whole-cell recordings from layer 5 pyramidal neurons in the rat visual cortex. Analysis of this dataset revealed several nonrandom features in synaptic connectivity. We confirmed previous reports that bidirectional connections are more common than expected in a random network. We found that several highly clustered three-neuron connectivity patterns are overrepresented, suggesting that connections tend to cluster together. We also analyzed synaptic connection strength as defined by the peak excitatory postsynaptic potential amplitude. We found that the distribution of synaptic connection strength differs significantly from the Poisson distribution and can be fitted by a lognormal distribution. Such a distribution has a heavier tail and implies that synaptic weight is concentrated among few synaptic connections. In addition, the strengths of synaptic connections sharing pre- or postsynaptic neurons are correlated, implying that strong connections are even more clustered than the weak ones. Therefore, the local cortical network structure can be viewed as a skeleton of stronger connections in a sea of weaker ones. Such a skeleton is likely to play an important role in network dynamics and should be investigated further.     

Simplified quantitative electron microscopy of biopolymers

Shape and molecular weight of DNA can be obtained with a new method involving spontaneous surface adsorption of DNA or of other macromolecules from a solution which contains formaldehyde and a critical amount of cytochrome c. Subsequent transfer to specimen grids and electron microscopy shows individual molecules suitable for quantitative evaluation. Adsorption of DNA and fd bacteriophages is proportional to (time)^0.75. Contour lengths of double-stranded DNA are not influenced by formaldehyde. A modification of this method requires only 2 × 10^?5 μg DNA.     

Stereology meets electron tomography: towards quantitative 3D electron microscopy

Stereological tools are the gold standard for accurate (i.e., unbiased) and precise quantification of any microscopic sample. The past decades have provided a broad spectrum of tools to estimate a variety of parameters such as volumes, surfaces, lengths, and numbers. Some of them require pairs of parallel sections that can be produced by either physical or optical sectioning, with optical sectioning being much more efficient when applicable. Unfortunately, transmission electron microscopy could not fully profit from these riches, mainly because of the large depth of field. Hence, optical sectioning was a long-time desire for electron microscopists. This desire was fulfilled with the development of electron tomography that yield stacks of slices from electron microscopic sections. Now, parallel optical slices of a previously unimagined small thickness (2-5 nm axial resolution) can be produced. These optical slices minimize problems related to overprojection effects, and allow for direct stereological analysis, e.g., volume estimation with the Cavalieri principle and number estimation with the optical disector method. Here, we demonstrate that the symbiosis of stereology and electron tomography is an easy and efficient way for quantitative analysis at the electron microscopic level. We call this approach quantitative 3D electron microscopy.     

Auger electron emitters: Insights gained from in vitro experiments

Summary This paper outlines the evolution of the current rationale for research into the biological effects of tissue-incorporated Auger electron emitters. The first section is a brief review of the research conducted by several groups in the last fifteen years. The second section describes the in vitro model used in our studies, dosimetric calculations, experimental techniques and recent findings. The third section focuses on the use of Auger electron emitters as in vitro microprobes for the investigation of the radiosensitivity of distinct subcellular components. Examination of the biological effects of the Auger electron emitter¹²⁵I located in different cellular compartments of a single cell line (V79 hamster lung fibroblast) verifies that DNA is the critical cell structure for radiation damage and that the sensitive sites are of nanometer dimensions. The data from incorporation of several Auger electron emitters at the same location within DNA suggest that there are no saturation effects from the decay of these isotopes (i.e. all the emitted energy is biologically effective) and provide some insight into which of the numerous physical mechanisms accompanying the Auger decay are most important in causing cell damage. Finally the implications of Auger electron emission for radiotherapy and radiation protection in diagnostic nuclear medicine are detailed and further research possibilities are suggested.     

Measurement of protein concentration by quantitative electron microscopy

The method of quantitative electron microscopy was applied to the measurement of protein concentration in thin sections. The human erythrocyte was selected as a model because of its apparently uniform protein concentration. Phosphotungstic acid (PTA) in aqueous solution was used as a reversible stain for protein, and PTA-stained Dowex resin spheres were embedded along with the red cells as standards for measurement of section thickness. The mass of stain removed from a given area of sectioned red cell by buffer (pH 7.4) was measured by quantitative electron microscopy. From the stoichiometry of the reaction between PTA and red cell protein established in this study, the amount of protein present in the measured area was calculated. From this amount of protein and the measured thickness, the concentration of protein was calculated and expressed as g/100 ml, for comparison with the clinical laboratory value for hemoglobin. Groups of red cells from the same sample were measured on 3 different days and their mean values (g/100 ml ± SD) were 29 ± 3.9, 30 ± 2.7, and 33 ± 4.6, compared to the clinical laboratory value of 32.1 g/100 ml packed cells, after correction for volume change and protein loss during fixation.     

Impact of network topology on inference of synaptic connectivity from multi-neuronal spike data simulated by a large-scale cortical network model

Many mechanisms of neural processing rely critically upon the synaptic connectivity between neurons. As our ability to simultaneously record from large populations of neurons expands, the ability to infer network connectivity from this data has become a major goal of computational neuroscience. To address this issue, we employed several different methods to infer synaptic connections from simulated spike data from a realistic local cortical network model. This approach allowed us to directly compare the accuracy of different methods in predicting synaptic connectivity. We compared the performance of model-free (coherence measure and transfer entropy) and model-based (coupled escape rate model) methods of connectivity inference, applying those methods to the simulated spike data from the model networks with different network topologies. Our results indicate that the accuracy of the inferred connectivity was higher for highly clustered, near regular, or small-world networks, while accuracy was lower for random networks, irrespective of which analysis method was employed. Among the employed methods, the model-based method performed best. This model performed with higher accuracy, was less sensitive to threshold changes, and required less data to make an accurate assessment of connectivity. Given that cortical connectivity tends to be highly clustered, our results outline a powerful analytical tool for inferring local synaptic connectivity from observations of spontaneous activity.     

Viruses and the development of quantitative biological electron microscopy

The electron microscope has become an important tool for determining the structure of biological materials of all kinds. Many technical advances in specimen preparation and in sophisticated methods of image analysis, initially based on optical systems but latterly on computer processing, have contributed to the development of the subject. Viruses of various kinds have often provided a convenient and appropriate test specimen. This paper describes the major technical advances and shows how viruses have had an important role in most of the developments.     

Analysis of human chromosomal variants by quantitative electron microscopy

Two human ring chromosomes 18 were isolated intact in a Langmuir trough, critical-point dried, and studied by quantitative electron microscopy. The portion of deleted genetic material is calculated from dry-mass determinations and is found to be comparable to the total genetic material present in the bacterium Salmonella typhimurium.Preliminary presentation of this study was made (Golomb and Bahr, 1971a).This study has been supported by American Cancer Society Grant No. P259-j.The opinions or assertions contained herein are the private views of authors and are not to be construed as official or as reflecting the views of the department of the Army or the Department of Defense.     

激光共聚焦扫描显微镜和透射电镜观察大鼠纹状体内谷氨酸能突触连接的对比观察

目的 探讨使用激光共聚焦扫描显微镜 (Laser scanning confocal microscope,LSCM)观察大鼠纹状体内谷氨酸能突触连接的方法的可行性.方法 12只正常大鼠分为两组,6只大鼠进行纹状体中等棘刺神经元的CM-DiI 单细胞标记,然后Ⅰ型囊泡膜谷氨酸转运体(vesicular glutamate transporter 1,VGluT1 )免疫荧光标记,LSCM层扫后三维重建,观察VGluT1阳性位点在中等棘刺神经元树突上的分布.另外6只大鼠用TEM观察不对称性突触在纹状体神经元树突上的分布.对两种方法的结果进行比较.结果 用LSCM 和TEM方法观察到的纹状体神经元上谷氨酸能突触连接分布情况一致,没有统计学差异.但LSCM更具优越性的是,可以对图像进行三维重构,从而有利于对神经元之间突触连接的空间分布观察和定量分析.结论 神经细胞荧光标记技术结合LSCM观察是考察纹状体神经元上谷氨酸能突触连接的有效方法.     

Determination of the mass of viruses by quantitative electron microscopy.

The photometric method of quantitative determination of dry mass by electron microscopy has been applied to the study of various types of viruses: animal, plant, insect, and bacterial. The method is applicable to all viruses having a mass of 1 x 10-18g or greater. The molecular weight of viruses can be calculated from the mass value by multiplying it by Avogadro's number. In comparison to other methods of determining the molecular weight of viruses, sedimentation and diffusion, sedimentation equilibrium, light scattering, and electron microscopy counting, the method of quantitative electron microscopy is competitive. In some ways quantitative electron microscopy is superior to other methods for the determination of molecular weight: There is no limitation to the size of the virus, no experimental time involved and no concentration and purity of virus preparations required, and finally it is independent of the geometry of the virion. In one important aspect it is unique when compared to other methods; namely, it affords one the capacity to analyse individual virus particles.     

Automated detection and segmentation of synaptic contacts in nearly isotropic serial electron microscopy images

We describe a protocol for fully automated detection and segmentation of asymmetric, presumed excitatory, synapses in serial electron microscopy images of the adult mammalian cerebral cortex, taken with the focused ion beam, scanning electron microscope (FIB/SEM). The procedure is based on interactive machine learning and only requires a few labeled synapses for training. The statistical learning is performed on geometrical features of 3D neighborhoods of each voxel and can fully exploit the high z-resolution of the data. On a quantitative validation dataset of 111 synapses in 409 images of 1948×1342 pixels with manual annotations by three independent experts the error rate of the algorithm was found to be comparable to that of the experts (0.92 recall at 0.89 precision). Our software offers a convenient interface for labeling the training data and the possibility to visualize and proofread the results in 3D. The source code, the test dataset and the ground truth annotation are freely available on the website http://www.ilastik.org/synapse-detection.     

Studies on three microsomal electron transfer enzyme systems: Specificity of electron flow pathways

The routes of microsomal electron flow to the three terminal oxidative enzymes, the mixed function oxidase, the fatty acyl CoA desaturase, and the lipid peroxidase have been examined by the use of specific antibodies, by alteration of electron transfer enzyme levels, and with the inhibitor NADP⁺. From these studies a number of conclusions are drawn: (1) NADH-supported lipid peroxidation utilizes NADH-cytochrome b₅ reductase, but electron flow does not go via cytochrome b₅. (2) The positive modifier effect of type I substrates on NADPH-driven cytochrome P-450 reduction is seen also with NADH-supported cytochrome P-450 reductase activity. The latter reaction proceeds via cytochrome b₅ while the former does not. (3) Cross-reactivity can occur between NADH-cytochrome b₅ reductase and NADPH-cytochrome c reductase, but at a rate too slow to support most reactions. (4) Cytochrome b₅ appears to exist in two pools; one pool is readily inhibited by antibody and the other pool is either inaccessible to or incompletely inhibited by antibody. The various cytochrome b₅-dependent reactions show different abilities to use the noninhibited hemoprotein. NADH-cytochrome c reductase activity and NADH-synergism appear to utilize only the former pool and are completely inhibitable by antibody. Other NADH-supported reactions (Δ⁹-desaturation and mixedfunction oxidation) utilize the total cytochrome b₅ population. Fortification studies show that the extra bound cytochrome b₅ is distributed in the same manner as the endogenous cytochrome b₅.     

Absolute DNA values from Feulgen microspectrophotometric measurements and quantitative electron microscopy. A comparison of two species

Quantitative electron microscopy (QEM) and microspectrophotometry were used to correlate the Feulgen stain absorption values to the calculated picograms of DNA. Measurements were made in human lymphocytes, rainbow trout lymphocytes and nuclei of trout erythrocytes. The median dry weight of the nucleus, as determined by QEM, was 35.9 pg for a human lymphocyte and 30.5 pg for a trout lymphocyte. Using Salzman's value of 20% DNA per chromosome (i.e., chromatin), a human lymphocyte nucleus thus contains 7.18 pg of DNA and a trout lymphocyte nucleus 6.1 pg of DNA. The mean Feulgen absorption value of the nucleus, given in arbitrary units (AU), was 14.5 for a human lymphocyte, 12.7 for a trout lymphocyte and 12.0 for a trout erythrocyte. From these values, it was derived that each picogram of DNA of a human lymphocyte nucleus is represented by 2.02 arbitrary Feulgen units while the values for trout nuclei were 2.08 AU and 1.97 AU. On the average, we find that each picogram of DNA is represented by two arbitrary Feulgen units in our microspectrophotometric measurements.     

Neurotrophic regulation of retinal ganglion cell synaptic connectivity: from axons and dendrites to synapses

This review highlights important events during the morphological development of retinal ganglion cells (RGCs), focusing on mechanisms that control axon and dendritic arborization as a means to understand synaptic connectivity with special emphasis on the role of neurotrophins during structural and functional development of RGCs. Neurotrophins and their receptors participate in the development of visual connectivity at multiple levels. In the visual system, neurotrophins have been shown to exert various developmental influences, from guiding the morphological differentiation of neurons to controlling the functional plasticity of visual circuits. This review article examines the role of neurotrophins, and in particular of BDNF, during the morphological development of RGCs, and discusses potential interactions between activity and neurotrophins during development of neuronal connectivity.     

Procoagulant platelet balloons: evidence from cryopreparation and electron microscopy

Visualisation of the procoagulant transformation of human platelets has recently become possible through use of an in vitro approach combined with fluorescence and phase contrast microscopy. Here, we extended these studies to the ultrastructural level by employing both rapid freezing/freeze-substitution and conventional ambient-temperature chemical fixation for transmission and scanning electron microscopy. Procoagulant transformation was only inducible by adhering platelets to collagen fibrils or to the collagen-related peptide and exposing them to physiological extracellular Ca2+ levels. Under these conditions prominent, 2- to 4-micron-wide balloon-like structures were regularly observed, regardless of the specimen fixation protocol. In strong contrast to normal platelets in their vicinity, the balloons' subcellular architecture proved remarkably poor: dilute cytoplasm, no cytoskeleton, only a few, randomly distributed organelles and/or their remnants. Cryofixed balloons displayed intact and smooth surfaces whereas conventional specimen processing caused plasma membrane perforations and shrinkage of the balloons. Our results clearly show that neither the balloons themselves, nor their simple ultrastructure reflect fixation artefacts caused by inadequate membrane stabilisation. The balloons are interpreted as to be transformed and/or fragmented procoagulant platelets. Thus, the generation of balloons represents a genuine, final stage of platelet ontogenesis, presumably occurring alternatively to aggregate formation.