"Real-time" monitoring of vibrissa contacts during rodent whisking

Rodent whisking behavior provides active touch as input into a widely studied model system of information processing and behavior. We previously developed a simple optoelectronic system to monitor whisker movements in "real time" in head held rats at rest or performing various tasks such as tactile discrimination. We now describe a simple piezioelectic film device for detecting initial whisker contacts during whisking also in real time. In some applications this is as effective as high-speed videos and can be configured to isolate the contacts from different whiskers. The construction of this simple device is detailed. In addition to providing information during recordings from awake animals, the device could be used, for example, as an operant "manipulandum" for contingent reinforcement of object detection with a whisker.     

Benefits of hierarchical generalization and storage of the representations of "object-place" associations in the hippocampal subfields (a hypothesis)

We analyzed the results of experimental research of features of processing sensory information in the hippocampus and neocortex available in literature and results of modelling the perception of information in the neocortex. It is noted that "place" fields of neurons become wider, and overlapping of receptive fields increases during upward moving in trisynaptic hippocampal pathway. These effects specify the generalization of the information processed. The results of our analysis allow us to put forward a hypothesis that a hierarchical complication of"object - place" associations occurs during upward propagation of signals through all hippocampal subfields. Complexity of neural representations of "object - place" associations that are formed and permanently stored in the hippocampal areas increases in process of propagation of signals from the entorhinal cortex to the hierarchically higher dentate gyrus, area CA3 and area CA1. Therefore, with the aim to extract information about "object - place" associations with certain details it is necessary to access that hippocampal area in which associations were processed and stored with the required degree of elaboration. By analogy with the neocortex, it is proposed that such processing of information in the hippocampus makes it possible to avoid the combinatorial explosion and provides storing (memory) the associations accumulated during the life. The proposed mechanism can serve as an addition to the known multiple trace theory, which states that the hippocampus is an integrating part of memory trace and is always involved in recall of long-delayed episodes.     

Variations on the topic of the "histone code"

Histones are the fundamental structural proteins intimately associated with eukaryotic DNA to form a highly ordered and condensed nucleoproteic complex termed chromatin. They are the targets of various posttranslational modifications including acetylation, methylation, phosphorylation and ubiquitination that modulate the structure/function of chromatin. The combinatorial nature of histone modifications is hypothesized to define a "histone code" that considerably extends the information potential of the genetic code, giving rise to epigenetic information. Moreover, most core histones consist of several nonallelic variants that can mark specific loci and could play an important role in establishment and maintenance of epigenetic memory. Here we will briefly present our current knowledge about histone posttranslational modifications and their implications in the regulation of epigenetic information. We will next describe core histone variants, insisting on their mode of incorporation into chromatin to discuss their epigenetic function and inheritance.     

Database on natural and transgenic luminous microorganisms: "BiolumBase"

The database "BiolumBase" is designed for the selection and systematization of available world information on microorganisms containing bioluminescent systems; it includes two sections: "natural" and "transgenic" luminous microorganisms. At present, logic schemes of divisions, classification of the objects, presentation of characteristics, and the inputs of relative information, as well as the necessary program modules including links to the database, are developed. The database is constructed on the basis of published data and our own experimental results; the subsequent linkage of the database to the Internet is envisaged. Users will be able to obtain not only the catalogues of strains but also information concerning the properties and functions of the known species of luminous bacteria, the structure, regulatory mechanisms, and application of bioluminescent systems and genetically engineered constructions with lux genes, as well as to find references and to search strains by using any set of attributes. The database will provide information that is of interest for the development of microbial ecology and biotechnology, in particular, for the prediction of biological hazard from the application of transgenic strains.     

Half a century of "the nuclear matrix"

A cell fraction that would today be termed "the nuclear matrix" was first described and patented in 1948 by Russian investigators. In 1974 this fraction was rediscovered and promoted as a fundamental organizing principle of eukaryotic gene expression. Yet, convincing evidence for this functional role of the nuclear matrix has been elusive and has recently been further challenged. What do we really know about the nonchromatin elements (if any) of internal nuclear structure? Are there objective reasons (as opposed to thinly veiled disdain) to question experiments that use harsh nuclear extraction steps and precipitation-prone conditions? Are the known biophysical properties of the nucleoplasm in vivo consistent with the existence of an extensive network of anastomosing filaments coursing dendritically throughout the interchromatin space? To what extent may the genome itself contribute information for its own quarternary structure in the interphase nucleus? These questions and recent work that bears on the mystique of the nuclear matrix are addressed in this essay. The degree to which gene expression literally depends on nonchromatin nuclear structure as a facilitating organizational format remains an intriguing but unsolved issue in eukaryotic cell biology, and considerable skepticism continues to surround the nuclear matrix fraction as an accurate representation of the in vivo situation.     

The quantal theory of how the immune system discriminates between "self and non-self"

In the past 50 years, immunologists have accumulated an amazing amount of information as to how the immune system functions. However, one of the most fundamental aspects of immunity, how the immune system discriminates between self vs. non-self, still remains an enigma. Any attempt to explain this most intriguing and fundamental characteristic must account for this decision at the level of the whole immune system, but as well, at the level of the individual cells making up the immune system. Moreover, it must provide for a molecular explanation as to how and why the cells behave as they do. The "Quantal Theory", proposed herein, is based upon the "Clonal Selection Theory", first proposed by Sir McFarland Burnet in 1955, in which he explained the remarkable specificity as well as diversity of recognition of everything foreign in the environment. The "Quantal Theory" is built upon Burnet's premise that after antigen selection of cell clones, a proliferative expansion of the selected cells ensues. Furthermore, it is derived from experiments which indicate that the proliferation of antigen-selected cell clones is determined by a quantal, "all-or-none", decision promulgated by a critical number of cellular receptors triggered by the T Cell Growth Factor (TCGF), interleukin 2 (IL2). An extraordinary number of experiments reported especially in the past 20 years, and detailed herein, indicate that the T cell Antigen Receptor (TCR) behaves similarly, and also that there are several critical numbers of triggered TCRs that determine different fates of the T cells. Moreover, the fates of the cells appear ultimately to be determined by the TCR triggering of the IL2 and IL2 receptor (IL2R) genes, which are also expressed in a very quantal fashion. The "Quantal Theory" states that the fundamental decisions of the T cell immune system are dependent upon the cells receiving a critical number of triggered TCRs and IL2Rs and that the cells respond in an all-or-none fashion. The "Quantal Theory" accounts fully for the development of T cells in the thymus, and such fundamental cellular fates as both "positive" and "negative" selection, as well as the decision to differentiate into a "Regulatory T cell" (T-Reg). In the periphery, the "Quantal Theory" accounts for the decision to proliferate or not in response to the presence of an antigen, either non-self or self, or to differentiate into a T-Reg. Since the immune system discriminates between self and non-self antigens by the accumulated number of triggered TCRs and IL2Rs, therapeutic manipulation of the determinants of these quantal decisions should permit new approaches to either enhance or dampen antigen-specific immune responses.     

Regional medico-dosimetric register (RMDR) is a model for evaluation of long-term "low" dose ionizing radiation effects on Siberian group of chemical enterprises main production personnel

Medico-dosimetric register is an optimal model of epidemiological studies on evaluation of ionizing radiation effects. Regional medico-dosimetric register (RMDR) is a system of interrelating information blocks including data on Siberian Group of Chemical Enterprises (SGCE) personnel. At present SGCE personnel and Seversk residents RMDR database includes information on 138496 persons, 65538 of which are SGCE workers. SGCE personnel and Seversk residents RMDR is a scientific base for researches with the aim of evaluating long-term ionizing radiation effects in a "low" dose range. Information on mortality and morbidity rate as well as "thematic" registers of the main diseases potentiates in evaluating the spectrum of somatic stochastic effects and radiogenic risks in SGCE workers and Seversk residents as well as their offsprings. A practical significance of RMDR database is the formation of the main diseases "risk" groups depending on definite risk factors in certain groups that provides targeted diagnostic and preventive therapy both among high-dose establishments' workers and residents living near-by.     

"Vulnerable plaques"--ticking of the time bomb

Atherosclerosis and its sequelae are one of the leading causes of morbidity and mortality, especially in the developed nations. Over the years, treatment protocols have changed with the changing understanding of the disease process. Inflammatory mechanisms have emerged as key players in the formation of the atherosclerotic plaque. For the majority of its life span, the plaque develops silently and only some exhibit overt clinical manifestations. The purpose of this review is to examine the inherent properties of some of these "vulnerable" or symptomatic plaques. Rupture of the plaque is related to the thickness of the fibrous cap overlying the necrotic lipid core. A thin cap is more likely to lead to rupture. Multiple factors broadly grouped as the "determinants of vulnerability" are responsible for directly or indirectly influencing the plaque dynamics. Apoptosis is considered an important underlying mechanism that contributes to plaque instability. Inflammatory reactions within the plaque trigger apoptosis by cell-cell contact and intra cellular death signaling. Once started, the apoptotic process affects all of the components that make up the plaque, including vascular smooth muscle cells, endothelial cells, and macrophages. Extensive research has identified many of the key cellular and molecular regulators that play a part in apoptosis within the atherosclerotic lesion. This information will help us to gain a better understanding of the underlying mechanisms at the cellular and molecular level and enable us to formulate better therapeutic strategies to combat this disease.     

"Candidatus Cloacamonas acidaminovorans": genome sequence reconstruction provides a first glimpse of a new bacterial division

Many microorganisms live in anaerobic environments. Most of these microorganisms have not yet been cultivated. Here, we present, from a metagenomic analysis of an anaerobic digester of a municipal wastewater treatment plant, a reconstruction of the complete genome of a bacterium belonging to the WWE1 candidate division. In silico proteome analysis indicated that this bacterium might derive most of its carbon and energy from the fermentation of amino acids, and hence, it was provisionally classified as "Candidatus Cloacamonas acidaminovorans." "Candidatus Cloacamonas acidaminovorans" is probably a syntrophic bacterium that is present in many anaerobic digesters. This report highlights how environmental sequence data might provide genomic and functional information about a new bacterial clade whose members are involved in anaerobic digestion.     

Biographics art "I know me": image generation aiming at EEG control by biofeedback

"I know me" is an interactive artwork that produces images based on EEG measurements from human participants. Although artists have previously made some interactive image works, we considered using human physiological information as input because it reflects human feelings better. In this research we were interested in information about human's mental states, such as anger or sadness. Brain activity was observed with EEG, subjected to Fourier analysis and converted into an animation based on a Lissajous curve.We generated images corresponding to alpha or beta waves activity in real time and showed them to the observer. The observer understood his own mental condition from looking at the images, and could potentially control his own mental state with this interactive device.     

On the relative contribution of viscous flow vs. diffusional (frictional) flow to the stationary state flow of water through a "tight" membrane

The practice of calculating the diffusion contribution to the total pressure-driven flow of water through a tight membrane by using the self-diffusion coefficient for tritiated water is examined by a theoretical analysis. Equations of motion for water and membrane in pressure-driven water flow and water, membrane, and tritiated water in self-diffusion of tritiated water are adapted from Bearman and Kirkwood (1958). These equations of motion are used to develop an equation for the pressure-driven flow of water. Because of the lack of specific information about the detailed structure of most membranes, as well as considerations of the need to eliminate some of the mathematical difficulties, an "equivalent capillary" model is used to find a solution to the equation of motion. The use of the equivalent capillary model and possible ambiguities in distinctions between diffusion and hydrodynamic flow are discussed     

Whole-genome transcription profiling reveals genes up-regulated by growth on fucose in the human gut bacterium "Roseburia inulinivorans"

"Roseburia inulinivorans" is an anaerobic polysaccharide-utilizing firmicute bacterium from the human colon that was identified as a producer of butyric acid during growth on glucose, starch, or inulin. R. inulinivorans A2-194 is also able to grow on the host-derived sugar fucose, following a lag period, producing propionate and propanol as additional fermentation products. A shotgun genomic microarray was constructed and used to investigate the switch in gene expression that is involved in changing from glucose to fucose utilization. This revealed a set of genes coding for fucose utilization, propanediol utilization, and the formation of propionate and propanol that are up-regulated during growth on fucose. These include homologues of genes that are implicated in polyhedral body formation in Salmonella enterica. Dehydration of the intermediate 1,2-propanediol involves an enzyme belonging to the new B12-independent glycerol dehydratase family, in contrast to S. enterica, which relies on a B12-dependent enzyme. A typical gram-positive agr-type quorum-sensing system was also up-regulated in R. inulinivorans during growth on fucose. Despite the lack of genome sequence information for this commensal bacterium, microarray analysis has provided a powerful tool for obtaining new information on its metabolic capabilities.     

The "French Paradox" and beyond: neuroprotective effects of polyphenols

Chronic ethanol ingestion is known to cause oxidative damage to a number of organs including the brain. This is partly due to the ability of ethanol to enhance oxygen free radical production and lipid peroxidation. Increase in oxidative stress has been regarded as an important underlying factor for a number of human health problems including cardiovascular diseases, aging, as well as many age-related neurodegenerative diseases. The strikingly low incidences of coronary heart diseases (CHD) in France, despite intake of a high-fat diet, have been attributed to the consumption of red wine containing high levels of polyphenolic compounds. In recent years, understanding the "French Paradox" has stimulated new research interest to investigate whether polyphenolic antioxidants may offer protective effects beyond the cardiovascular system, and whether polyphenols from other botanical sources may similarly offer beneficial effects to human health. Our studies with animal models have provided information clearly indicating the ability of grape polyphenols to ameliorate neuronal damages due to chronic ethanol consumption. Studies with resveratrol, an important component of grape polyphenols, also show protective effects on neuron cell death induced by ethanol and other oxidative agents. These studies demonstrate an urgent need to extend research beyond the "French Paradox" towards better understanding molecular mechanisms of action of polyphenolic compounds and their application to human health.     

The use of multifolded pericranial flaps as "plugs" and "pads"

Pericranial flaps are thin and, hence, their volumes are small. Therefore, their use for soft-tissue augmentation has not been popular. In this article, the author introduces a new concept: the use of a multifolded pericranial flap as a "plug" or a "pad" for localized contour defects. Eight patients were included in the study. In all cases, an anteriorly based pericranial flap was used, and the flap was folded on itself several times to increase its bulk. The results were satisfactory in all patients. The literature on the topic is reviewed, and the blood supply of pericranial flaps is discussed.     

Audiovisual integration: an investigation of the "streaming-bouncing" phenomenon

Temporal aspects of the perceptual integration of audiovisual information were investigated by utilizing the visual "streaming-bouncing" phenomenon. When two identical visual objects move towards each other, coincide, and then move away from each other, the objects can either be seen as streaming past one another or bouncing off each other. Although the streaming percept is dominant, the bouncing percept can be induced by presenting an auditory stimulus during the visual coincidence of the moving objects. Here we show that the bounce-inducing effect of the auditory stimulus is paramount when its onset and offset occur in temporal proximity of the onset and offset of the period of visual coincidence of the moving objects. When the duration of the auditory stimulus exceeded this period, visual bouncing disappears. Implications for a temporal window of audiovisual integration and the design of effective audiovisual warning signals are discussed.     

The computer program package "SAMSON" for analysis of primary structure of biopolymers

A program package "SAMSON" for the computer analysis of biopolymer primary structures is described. All possible modes of sequence investigation are considered. The programs for sequence comparison are described in some details. The general principles of a program package organisation and of its user interface are also mentioned. For more complete information see Vernoslov S.E. et al. "Program package "SAMSON" for the analysis of the polymer primary structures", parts 1 and 2, Poustchino, ONTI NCBI, 1989.     

Body mass and foraging ecology predict evolutionary patterns of skeletal pneumaticity in the diverse "waterbird" clade

Extensive skeletal pneumaticity (air-filled bone) is a distinguishing feature of birds. The proportion of the skeleton that is pneumatized varies considerably among the >10,000 living species, with notable patterns including increases in larger bodied forms, and reductions in birds employing underwater pursuit diving as a foraging strategy. I assess the relationship between skeletal pneumaticity and body mass and foraging ecology, using a dataset of the diverse "waterbird" clade that encompasses a broad range of trait variation. Inferred changes in pneumaticity and body mass are congruent across different estimates of phylogeny, whereas pursuit diving has evolved independently between two and five times. Phylogenetic regressions detected positive relationships between body mass and pneumaticity, and negative relationships between pursuit diving and pneumaticity, whether independent variables are considered in isolation or jointly. Results are generally consistent across different estimates of topology and branch lengths. "Predictive" analyses reveal that several pursuit divers (loons, penguins, cormorants, darters) are significantly apneumatic compared to their relatives, and provide an example of how phylogenetic information can increase the statistical power to detect taxa that depart from established trait correlations. These findings provide the strongest quantitative comparative support yet for classical hypotheses regarding the evolution of avian skeletal pneumaticity.     

Ill-conditioning associated with the "end-point" method for the determination of kinetic parameters describing irreversible enzyme inactivation by an unstable inhibitor

Study of the complete time-course of irreversible enzyme inhibition by an unstable inhibitor yields more information than can be obtained by recording data only at the end point of reaction. Time-course analysis of co-operative irreversible enzyme inhibition by an unstable inhibitor has been shown to be considerably less susceptible to ill-conditioning than the "end-point" method for the determination of kinetic parameters describing inactivation. As a result, mechanisms that cannot be distinguished by the "end-point" method are readily differentiated by time-course analysis without the need to isolate intermediate species.