State-of-the-art FISHing: automated analysis of cytogenetic aberrations in interphase nuclei

Interphase fluorescence in situ hybridization (i-FISH) is a powerful tool for visualizing various molecular targets in non-dividing cells. Manual scoring of i-FISH signals is a labor intensive, time-consuming, and error-prone process liable to subjective interpretation. Automated evaluation of signal patterns provides the opportunity to overcome these difficulties. The first report on automated i-FISH analysis has been published 20 years ago and since then several applications have been introduced in the fields of oncology, and prenatal and fertility screening. In this article, we provide an insight into the automated i-FISH analysis including its course, brief history, clinical applications, and advantages and challenges. The lack of guidelines for describing new automated i-FISH methods hampers the precise comparison of performance of various applications published, thus, we make a proposal for a panel of parameters essential to introduce and standardize new applications and reproduce previously described technologies.     

Characteristics of heterochromatin of heterophase nuclei from interphase neurons of various brain structures selected for the nervous system excitability

Quantitative characteristics (the area and number of chromocenters) of the interphase C-heterochromatin in the nuclei of pyramidal neurons of the midbrain reticular formation, sensorimotor cortex, and hippocampus (CA3) of rat strains with different genetically determined excitability were studied in the normal state of the animals and after exposure to a short-term emotional pain stress. The results indicate a relationship between the excitability of the nervous system and structural-functional state of the neuronal interphase heterochromatin. The role of cytogenetic features of different brain structures in the CNS functioning and behavior and their relation with genetically determined excitability of the nervous system are discussed.     

Open-field behavior of rats with different levels of nervous system excitability

The dependence was studied of characteristics of organization of orienting-investigating behaviour in the open field test on the level of nervous system excitability in rats selected by the threshold of excitability of the peripheral nervous system. It is established that the studied rats lines can be divided into groups according to entropy level of their behaviour. Rats of highly excitable line build their behaviour in highly probable stereotypes as compared with the animals of low-excitable line, which organize their behaviour with more plasticity, diversity. Differences in the nervous system excitability influence first of all the organization of animals behaviour.     

Smart 3D-FISH: automation of distance analysis in nuclei of interphase cells by image processing.

BACKGROUND: Detection of fluorescent probes by fluorescence in situ hybridization in cells with preserved three-dimensional nuclear structures (3D-FISH) is useful for studying the organization of chromatin and localization of genes in interphase nuclei. Fast and reliable measurements of the relative positioning of fluorescent spots specific to subchromosomal regions and genes would improve understanding of cell structure and function. METHODS: 3D-FISH protocol, confocal microscopy, and digital image analysis were used. RESULTS: New software (Smart 3D-FISH) has been developed to automate the process of spot segmentation and distance measurements in images from 3D-FISH experiments. It can handle any number of fluorescent spots and incorporate images of 4',6-diamino-2-phenylindole counterstained nuclei to measure the relative positioning of spot loci in the nucleus and inter-spot distance. Results from a pilot experiment using Smart 3D-FISH on ENL, MLL, and AF4 genes in two lymphoblastic cell lines were satisfactory and consistent with data published in the literature. CONCLUSION: Smart 3D-FISH should greatly facilitate image processing and analysis of 3D-FISH images by providing a useful tool to overcome the laborious task of image segmentation based on user-defined parameters and decrease subjectivity in data analysis. It is available as a set of plugins for ImageJ software.     

Membrane properties of identified embryonic nerve and glial cells of the leech central nervous system

Summary The membrane potential of identified nerve (Retzius) cells and neuropil glial cells from 11 (±1) day-old embryos of the leechHirudo medicinalis was recorded using conventional intracellular microelectrodes. At this stage all ganglia of the segmental nervous system are formed. The membrane potential of Retzius cells was –68±4 mV (±SD,n=8), and showed a slope of 42 mV between 10 mM and 100 mM external K concentration. Retzius cells were able to fire action potentials which had a fast Na-dependent component, and, under appropriate conditions, also generated slow Ca (Ba) action potentials. The mean membrane potential of the neuropil glial cell at physiological K concentration (4 mM) was –83±5 mV (±SD,n=10), and showed a dependence of 56 mV for a tenfold change in the external K concentration (> 4mM). Neuropil glial cells showed no signs of voltage-activated excitability, but they repeatedly depolarized in the presence of 0.1 mM 5-HT.     

Effect of prenatal emotional-pain stress on the status of interphase chromatin in neurons of the rat developing brain with various excitation of the nervous system

A short-term emotional-painful stress, experienced by pregnant rat females differing in threshold of excitability of their nervous system, was used to assess the state of interphase condensed chromatin and C-heterochromatin of neuron nuclei in developing brains of 16-17 day old embryos. To reveal relationships between the genetically determined excitability of rats and the state of interphase chromatin in their neuron nuclei a computer information system has been used that enabled us to classify the neuronal nuclei according to their specific DNA image cytometry features. The results indicate an obvious relationship between excitability of the nervous system and structural-functional state of the neuronal interphase chromatin.     

Proliferative activity and structure-functional organization of chromosomes in cells from the developing brain in respect to genetically determined excitability of the rat nervous system]

Neuroblasts of developing hippocampus of 16-17-day old rat embryo of the line with high threshold excitability are characterised by a high level of proliferative activity and chromosome aberration, as well as high degree of brain chromatin concentration as compared with embryos of a line with low threshold excitability.     

Comparative genetic analysis of the excitability of the nervous system and of certain types of motor activity in rats

The significant correspondence between neural excitability and investigatory activity in novel environments was demonstrated when studying in four selected rat strains. In order to explain this kind of correlated response, one should assume that the interstrain differences between other peripheral and central parts of neural system also exist.     

An automated continuous-flow system for the extraction and fluorometric analysis of histamine

The automated continuous-flow system for the extraction and fluorometric analysis of histamine is accurate, specific, precise, rapid, and very sensitive. The method was made possible by the use of a simple connector for separating the organic-aqueous phases at two steps in the procedure. Samples with and without protein can be analyzed successfully. The method can quantitate as little as 0.5 ng of histamine base.     

An automated system for detection and analysis of locomotor behavior in crustaceans

An efficient and simple system is presented for the analysis of crustacean locomotor behavior. The system is composed by six dual-compartment actographic chambers with photocoupling circuits for movement detection, and a device for acquisition and analysis of data. Such device is made by a digital interface which feeds into a microcomputer with disc unit and printer. Information is processed in real time during the experiment, with a simultaneous printout and storage in a floppy disc.     

Evaluation of automated threshold selection methods for accurately sizing microscopic fluorescent cells by image analysis

The accurate measurement of bacterial and protistan cell biomass is necessary for understanding their population and trophic dynamics in nature. Direct measurement of fluorescently stained cells is often the method of choice. The tedium of making such measurements visually on the large numbers of cells required has prompted the use of automatic image analysis for this purpose. Accurate measurements by image analysis require an accurate, reliable method of segmenting the image, that is, distinguishing the brightly fluorescing cells from a dark background. This is commonly done by visually choosing a threshold intensity value which most closely coincides with the outline of the cells as perceived by the operator. Ideally, an automated method based on the cell image characteristics should be used. Since the optical nature of edges in images of light-emitting, microscopic fluorescent objects is different from that of images generated by transmitted or reflected light, it seemed that automatic segmentation of such images may require special considerations. We tested nine automated threshold selection methods using standard fluorescent microspheres ranging in size and fluorescence intensity and fluorochrome-stained samples of cells from cultures of cyanobacteria, flagellates, and ciliates. The methods included several variations based on the maximum intensity gradient of the sphere profile (first derivative), the minimum in the second derivative of the sphere profile, the minimum of the image histogram, and the midpoint intensity. Our results indicated that thresholds determined visually and by first-derivative methods tended to overestimate the threshold, causing an underestimation of microsphere size. The method based on the minimum of the second derivative of the profile yielded the most accurate area estimates for spheres of different sizes and brightnesses and for four of the five cell types tested. A simple model of the optical properties of fluorescing objects and the video acquisition system is described which explains how the second derivative best approximates the position of the edge.     

Isolation of mononuclear cells from the central nervous system of rats with EAE

Whether studying an autoimmune disease directed to the central nervous system (CNS), such as experimental autoimmune encephalomyelitis (EAE, 1), or the immune response to an infection of the CNS, such as poliomyelitis, Lyme neuroborreliosis, or neurosyphilis, it is often necessary to isolate the CNS-infiltrating immune cells.In this video-protocol we demonstrate how to isolate mononuclear cells (MNCs) from the CNS of a rat with EAE. The first step of this procedure requires a cardiac perfusion of the rodent with a saline solution to ensure that no blood remains in the blood vessels irrigating the CNS. Any blood contamination will artificially increase the number of apparent CNS-infiltrating MNCs and may alter the apparent composition of the immune infiltrate. We then demonstrate how to remove the brain and spinal cord of the rat for subsequent dilaceration to prepare a single-cell suspension. This suspension is separated on a two-layer Percoll gradient to isolate the MNCs. After washing, these cells are then ready to undergo any required procedure. Mononuclear cells isolated using this procedure are viable and can be used for electrophysiology, flow cytometry (FACS), or biochemistry. If the technique is performed under sterile conditions (using sterile instruments in a tissue culture hood) the cells can also be grown in tissue culture medium. A given cell population can be further purified using either magnetic separation procedures or a FACS.     

Evolution of structure and information processing in the nervous system: Part IV of a general theory

Starting from fundamental principles, evolution of the nervous system is modelled as a random walk process in a multidimensional representation space (the F-space). This space is not flat, it is highly structured in terms of step probability. Fundamental considerations of evolutionary speed, efficiency of information processing, and priorities lead to specific theoretical predictions of the most probable pathways of evolution of the nervous system and its mechanisms of information processing. These processes are represented as vector paths (F-paths) in the F-space. Cognition becomes a process of correlations of the input signal to information stored in memories. Higher level brain processes involve extrapolation and interpolation along F-paths, input data reduction by clearly specifiable abstraction methods, and a unique process using abstracted analogs. These processes define and limit what the brain does and how it can do it. These considerations lead to certain inevitable conclusions (consequences of the fundamental principles) for the basis of our logical reasoning, decision-making, the process of dreaming (conscious and sleep), and explicit definitions of consciousness, unconsciousness, and personality. Detailed applications of this theory for analyzing empirical findings are suggested in the final paragraphs.