Express control of toxic substances and pathogenic microorganisms. Immune analysis and immune sensors

In the review the overall characteristics of biological warfare components, which represent danger to people in the case of their application by military or terrorist groups are discussed. The main part of the review is devoted to modern approaches of antibody obtaining and, in particular, preparation of specific recombinant immunoglobulins as well as to different immune chemical methods of determination of individual toxins and pathogenic microorganisms. A special attention is paid to existing data about the development of rapid, selective, high sensitive, simple and fully automated instrumental methods on the basis of biosensor technology which is designed for the control of components of biological warfare in environmental objects. Additionally industrially manufactured biosensors and their characteristics are given and analyzed.     

Immunological monitoring of the tumor immunoenvironment for clinical trials

Monitoring of immunotherapeutic clinical trials has undergone a considerable change in the last decade resulting in a general agreement that immune monitoring should guide the development of cancer vaccines. The emphasis on immune cell functions and quantitation of antigen-specific T cells have been playing a major role in the attempts to establish meaningful correlations between therapy-induced alterations in immune responses and clinical endpoints. However, one significant unresolved issue in modern immunotherapy is that when a tumor-specific cellular immune response is observed following the course of immunotherapy, it does not always lead to clinically proven cancer regression. This disappointing lack of a correlation between the tumor-specific cytotoxic immune responses and the clinical efficacy of immunotherapy may be explained, among other reasons, by the notion that the analysis of any single immunological parameter is not sufficient to provide clinically feasible information about the complex interactions between different cell subsets in the peripheral blood and immune, tumor, and stromal cells in the tumor milieu. By contrast, a systemic approach is required for improving the quality of a serial monitoring to ensure that it adequately and reliably measures potential changes induced in patients by administered vaccines or immunomodulators. Comprehensive evaluation of the balance between the immunostimulatory and immunosuppressive compartments of the immune system could be critical for a better understanding of how a given immunotherapy works or does not work in a particular clinical trial. New approaches to characterize tumor-infiltrating leukocytes, their phenotypic, biochemical, and genetic characteristics within the tumor microenvironment need to be developed and validated and should complement current monitoring techniques. These immune-monitoring assays for the local tumor immunoenvironment should be developed, validated, and standardized for reliability and consistency in order to establish the overall performance standards.     

Islet cell transplantation and other new technologies for treating type 1 diabetes: a paediatric view

Recent advances in diabetes care have facilitated the achievement and maintenance of excellent metabolic control. New insulin pumps and continuous glucose monitoring systems provide cause for optimism that an artificial pancreas may soon be developed. In addition, transplantation biology has advanced to the point where pancreas and islet transplants are being performed with increasing frequency. Recent reports suggest that improved techniques for isolation of islets and immune suppression may allow these procedures to become more commonplace. However, serious questions regarding long-term safety and efficacy need to be answered in older individuals before consideration is given to their more routine use in children and adolescents with diabetes.     

The development and applications of thermal biosensors for bioprocess monitoring

Enzyme thermistors are biosensors that use thermal resistors to measure the heat change caused by an enzymatic reaction. They combine the selectivity of enzymes with the sensitivity of biosensors and allow continuous analysis in a flow-injection mode. They can be used to monitor fermentation systems, biocatalysis, enzyme-catalysed synthesis and clinical and food technology. This article gives an overview of the general principles of enzyme thermistors, the sampling process and the ongoing developments in the field of bioprocess monitoring.     

Immunosensors: sources of origin, achievements and perspectives

The analysis of the recent data in the literature and results of investigations in the field of the development and study of function efficiency of different types of immune sensors, that are performed at the Department of Biochemistry Sensory and Regulatory Systems of the A. V. Palladin Institute of Biochemistry of Ukrainian National Academy of Sciences are presented. Sources of origination and perspectives of the devlopment of biosensors are discussed as well. The paper also gives an overview of main research projects at the Department, mainly in the filed of biosensors. They include development of the scientific bases for the creation of a new generation of chemo- and biosensors for their application in medicine and ecology. Multi-immune, multi-enzyme and combined multi-parametrical sensors can provide express analyses in laboratory and field conditions with the purpose to perform immune chemical diagnostics of diabet, kidney diseases, immune defficiencies, autoimmune, allergic, pre-infarction and pre-tumor states as well as to control total toxicity of the environment and identification of main types of toxic elements in it. The investigations are based on the latest achivements in the field of physics, chemistry, information technology and electronics with the use of different types of planar electrodes, ion sensitive field effect transistors (ISFETs), semiconductor capacitive structures, termistors, optrodes, piezocrystalls and application of such methods and effects as laser correlation spectroscopy, chemiluminescence, fluorescence, surface plasmon resonance, photoluminescence of porous silicon, interferometry, evanescent wave technique, nonemmiting energy transfer and holography.     

The aerobic degradation of dichloromethane: Structural-functional aspects (a review)

This review summarizes current notions on the mechanisms of transport and degradation of dichloromethane (DCM) by aerobic methylotrophic bacteria as well as enzymological and genetic aspects of DCM dehalogenation, including probable pathways used by cells to overcome accompanying stresses (acid, osmotic, and oxidative). The topicality of the problem of the degradation of this genotoxic solvent is associated with the search for and creation of new DCM-destroying strains, which would provide for more efficient bioremediation of industrial sewage and ecosystems with extreme pH and salinity and could be used for the development of modern techniques for DCM degradation on the basis of existing strains. Special attention is given to the consideration of methodological approaches to the interpretation of physiological—biochemical and molecular bases of adaptation of bacteria to the utilization of DCM and other halogenated pollutants.     

野生动物监测技术和方法应用进展与展望

野生动物是生态系统研究和保护管理的重要生物类群, 对调控生态系统结构和功能, 维持生态系统健康平衡具有显著作用。科学监测数据是野生动物研究、保护、管理决策的前提基础, 但由于传统监测技术的限制, 野生动物的多样性特征及其与环境、生态系统的平衡机制未得到充分关注和研究。随着自动化、智能化、信息化技术的发展及应用, 野生动物监测技术和方法出现较大突破和变革。该文论述了近年来野生动物监测研究领域的重要新技术, 包括红外相机技术、全球定位系统(GPS)追踪技术、DNA条形码技术和高通量测序技术等。通过综合介绍相关的基础概念、基本原理, 该文总结了新技术的应用优势和重大应用进展, 同时探讨了新技术应用中存在的问题, 并对未来野生动物监测技术的发展趋势进行了展望。     

Maternal communication with gametes and embryos

Mechanisms for gametes and embryos to interact with their maternal environment are crucial in achieving reproductive success, both in livestock and the human. Long-range (hormones) and short-range signalling molecules play important roles in mediating cell-cell maternal interactions/communications with gametes and embryos. Slight malfunctions or disturbances of the environment that host this interaction can retard embryonic development. This may lead to creation of a memory for the embryo leading to offspring prone to degenerative diseases in adulthood. Despite an overwhelming amount of research and the literature, not all signalling molecules involved and their relationship with each other are known. Progress in the application of high-throughput genomic and proteomic analytical tools, such as microarrays and quantitative proteomic technologies has had a positive impact on our understanding of various aspects of maternal communication with gametes and embryos. Recent advances point to the presence of a local mechanism in the female reproductive tract capable of recognising the arrival of gametes and embryos and modulating the tract's environment accordingly for the next stage. Further investigations are underway to characterise the details of this system. It is important to consider spatial or temporal components of maternal communication with gametes and embryos that may confer consequences for developmental potential. Finally, it seems that the application of a systems biology approach for creation of an interactome map of maternal communication with gametes and embryos is essential and provides an excellent opportunity for an inter-disciplinary collaboration with engineers and mathematical modellers.     

Engineering and Two-Stage Evolution of a Lignocellulosic Hydrolysate-Tolerant Saccharomyces cerevisiae Strain for Anaerobic Fermentation of Xylose from AFEX Pretreated Corn Stover

The inability of the yeast Saccharomyces cerevisiae to ferment xylose effectively under anaerobic conditions is a major barrier to economical production of lignocellulosic biofuels. Although genetic approaches have enabled engineering of S. cerevisiae to convert xylose efficiently into ethanol in defined lab medium, few strains are able to ferment xylose from lignocellulosic hydrolysates in the absence of oxygen. This limited xylose conversion is believed to result from small molecules generated during biomass pretreatment and hydrolysis, which induce cellular stress and impair metabolism. Here, we describe the development of a xylose-fermenting S. cerevisiae strain with tolerance to a range of pretreated and hydrolyzed lignocellulose, including Ammonia Fiber Expansion (AFEX)-pretreated corn stover hydrolysate (ACSH). We genetically engineered a hydrolysate-resistant yeast strain with bacterial xylose isomerase and then applied two separate stages of aerobic and anaerobic directed evolution. The emergent S. cerevisiae strain rapidly converted xylose from lab medium and ACSH to ethanol under strict anaerobic conditions. Metabolomic, genetic and biochemical analyses suggested that a missense mutation in GRE3, which was acquired during the anaerobic evolution, contributed toward improved xylose conversion by reducing intracellular production of xylitol, an inhibitor of xylose isomerase. These results validate our combinatorial approach, which utilized phenotypic strain selection, rational engineering and directed evolution for the generation of a robust S. cerevisiae strain with the ability to ferment xylose anaerobically from ACSH.     

The enigma of deep-body thermosensory specificity

Information provided by the analysis of peripheral cold and warm receptors may be considered a useful guide for assessing the specificity of thermal information originating in deep-body tissues. A wealth of data concerning the location of deep-body thermosensors and their neuronal correlates and modes of transduction permits the following theses to be proposed. 1. Unlike the peripheral warm and cold receptors, deep-body thermosensors are only in part represented by afferent fibers, mostly warm sensitive ones that are not character- ized in detail, as the source of thermal information outside the central nervous system (CNS). The more important thermal information generated in the CNS originates mainly from warm-sensitive neurons but contributions of cold-sensitive neurons are not definitely excluded. 2. Unlike the peripheral thermoreceptors, monomodality with respect to natural physical stimuli does not seem to be an essential property of deep-body thermosensors. By contrast, multimodality may underlie at least some of the multitude of interactions between thermoregulatory and other homeostatic control systems. 3. Temperature transduction seems to utilize molecular mechanisms that are also found in neurons that lack any thermosensory functions, and so the transduction mechanisms identified in warm-sensitive CNS neurons do not seem to be specific per se. 4. The observation of a multitude of temperature/response characteristics for thermosensitive CNS neurons has been helpful for categorizing these neurons, but there is no clear information that any one might be particularly relevant. 5. Originating from the peripheral cold and warm receptors two separate but interacting cold- and warm-signal pathways ascend multisynaptically to the hypothalamus as the highest level of thermoregulatory control, and to some extent go further to the sensory cortex. The signal contributed by a deep-body thermosensitive neuron, irrespective of its location, attains specificity by being fed properly into one of the two ascending thermosensory pathways. Received: 25 January 2000 / Accepted: 10 April 2000     

The methodological problems of the correlation of biochemistry and physiology in current research

An attempt to treat critically the key methodological positions of modern biochemistry, primarily, the medical biochemistry with reference to the physiologic, pathophysiologic and clinical tasks is made. The author puts forward questions: 1) if it is possible to apply traditional approaches (principles) of biochemical investigation developed on purified systems to the whole organism systems in situ and etc.; 2) if it coincides the methodical approaches of biochemistry on the one hand and physiology (pathophysiology)--on the other one, considering the mechanisms of disease development and correspondingly the assessment and choice of therapeutic methods; 3) if there exists a necessity to create a unite methodology of biochemical and physiologic knowledge as a basis of modern medical science as a whole. Some examples showing the possible ways of new methodic consideration of traditional conceptions of in vitro biochemistry are given.     

On the concepts of biochemical ecology and hydrobiology: Ecological chemomediators

Earlier, the author published two books and some papers, in which he described conceptual foundations of new scientific disciplines — biochemical ecology and biochemical hydrobiology. These trends in research include studies of the role of chemical substances in interorganismal interactions, in communication and regulation of supraorganismal systems. Another part of biochemical ecology concerns studies of the destiny and transformation of external chemical substances when they interact with the organisms. Both natural and man-made compounds are interesting for biochemical ecology. The basic concepts of biochemical ecology include ecological chemomediators and ecological chemoregulators that have already been included in the body of modern conceptions and are used in modern ecological literature. Application of biochemical ecology to aquatic ecosystems creates the basis for development of biochemical hydrobiology.     

Anaerobic Fusiform-shaped Bacteria Isolated from the Caecum of Conventional Mice

Twenty-four strains of anaerobic fusiform-shaped bacteria were isolated from the caecum of conventional mice. Ten of the isolates belonged to the genus Clostridium , nine to Fusobacterium and five to Bacteroides. The clostridia were put into eight biotypes on the basis of their ability to: hydrolyze mucin and esculin; produce indole and hydrogen; utilize pyruvate, and ferment arabinose, cellobiose, fructose, glucose, galactose, maltose, mannose and N-acetylglucosamine and on the acid end-products of such fermentations. The fusobacteria were assigned to six biotypes based on their ability to hydrolyze casein, mucin and starch, and to ferment arabinose, lactose, maltose and N-acetylglucosamine. Each of the bacteroides was deemed to be a separate biotype because of the differences in their ability to hydrolyze casein and starch, grow in bile medium, utilize pyruvate, and to ferment arabinose, maltose, xylan and N-acetylglucosamine. Five of the Fusobacterium isolates resembled F. russii. The remaining 19 isolates did not resemble previously described species of anaerobic bacteria.     

代谢组及其在真菌研究中的应用

代谢组学是利用现代分析化学手段对一定条件下生物体内小分子代谢产物（初级和次级代谢产物）定性及定量,从而揭示生命现象及其内在规律的学科。相对于基因组、转录组和蛋白质组,代谢组是一定条件下生物学过程完成后的最终代谢产物的集合,因而是各种组学研究中最接近表型的一种组学,可以直接动态地反映出细胞的生理生化过程,从而有效地检测和发现特定的生化途径,准确地解释生理或者病理现象。代谢组学作为系统生物学中基因组学、转录组学以及蛋白质组学三大组学的延伸和补充,是目前的研究热点之一。目前代谢组学在真菌领域的研究得到日益重视和发展。本文首先从历史发展和技术路线简述了代谢组学的发展历程和常见的代谢组学研究方法。接着从真菌的分类鉴定、生物膜研究、代谢途径、代谢工程、天然产物发现与植物互作这6个方面介绍了代谢组学在真菌研究领域的应用。     

Sequence information and preparation of resolved by; two-dimensional gel electrophoresis: no longer just spots on gels

In 1975 O'Farrell described, in detail, a procedure to separate proteins by polyacrylamide gel electrophoresis in two dimensions. This powerful new technique relied on two characteristics of proteins: charge and molecular mass. In the first dimension, proteins were separated on the basis of net charge in a pH gradient by isoelectric focusing, and in the second dimension the proteins were further fractionated exclusively on the basis of their molecular mass by SDS gel electrophoresis. Since two-dimensional gel electrophoresis (2DGE) has a resolving power of at least 20 fold greater than one-dimensional electrophoresis, it has found wide spread application in modern biological research. However, beyond the detection of a given protein, 2DGE provides little additional information about a specific protein other than molecular mass, isoelectric point, and approximate relative abundance. In recent years, the development of new technologies have made it possible to directly obtain sequence information, and produce specific antisera for proteins resolved by 2DGE. These new technological developments serve to further increase the power and utility of 2DGE in the analysis of proteins of importance to plant physiology.     

House-dust mites and mold fungi as a source of indoor allergens

In this work information on the biology and ecology of synanthropic mites and mold fungi, proved to be the sources of indoor allergens in different premises, is presented. The authors propose the algorithm of the ecological monitoring of dwellings, developed on the basis their investigations. The types of dwellings, the time and situations when ecological monitoring should be carried out are analyzed. Grounds for the necessity of controlling the number of mites and the concentration of Micromyces spores, as well as their elimination from the environment, are given.     

A fungal perspective on human inborn errors of metabolism: alkaptonuria and beyond

Crucial for the establishment and development of biochemical genetics as a self-standing discipline was Beadle and Tatum's choice of Neurospora crassa as experimental organism some 60 years ago. Although Garrod's insights on biochemical genetics and his astonishingly modern concepts of biochemical individuality and susceptibility to disease had been ignored by their contemporaries, Beadle acknowledged on several occasions how close Garrod had come to the "one-gene-one-enzyme" hypothesis. In an unexpected turn of events, several genes involved in human inborn errors of metabolism, including the gene for Garrod's favorite disease, alkaptonuria, have been characterized by exploitation of the experimental advantages of another mold, Aspergillus nidulans, which shares with N. crassa the experimental advantages that prompted pioneers of biochemical genetics to use them: rapid growth, facile genetic manipulation, and an environment (the composition of the growth medium) that can be manipulated à la carte.     

Two thermosensors in Drosophila have different behavioral functions

Insects inhabit extreme temperature environments and have evolved mechanisms to survive there. Small insects are especially susceptible to rapid changes in body temperature. Therefore, the rapid detection of environment and body temperature is important for their survival. Little, however, is known about the thermosensors that detect those temperatures. Using rapid thermosensitivity assays with temperature step gradients and a spatial learning paradigm (the heat-box) in which elevated temperature serves as the negative reinforcer, two thermosensors were identified and their behavioral functions assessed. A low-temperature thermosensor is located on the antenna, detects relatively low temperatures, and can detect spatial temperature gradients directly. Thus, the antennae can be used by Drosophila to quickly orient with respect to temperature cues. A high-temperature thermosensor of unknown location appears to have a roughly similar sensitivity to temperature differences as the low-temperature thermosensor (< or = 3 degrees C) and is both necessary and sufficient for memory formation in the heat-box spatial learning paradigm. Therefore, the high-temperature thermosensor is important for remembering spatial positions in which dangerously high temperatures were encountered.     

Development of research into the physiology and pathophysiology of the fibrinolysis system

A modern data review on the importance of fibrinolysis system is given. A considerable success has been scored during the study of molecular parameters of fibrinolysis system: the plasminogen, plasmin, its inhibitors, plasminogen activators and the mechanism of activation system have been characterized. The entrance of A, K, C, P and PP vitamins has been established to be necessary for the normal functioning of the fibrinolysis system; the dependence of the blood fibrinolytic activity upon the initial plasminogen content and concentration of its activators in blood has been revealed. The plasminogen activator depletion in tissues has been shown to be one of the reasons of some pathological states development, especially at cardiovascular diseases. The increase of fibrinolysis level by the active fibrinolytic ferment injection in blood has a medical effect at thrombosis. The ferment fibrinolysin received in the laboratory is successfully used in clinical practice. Some other activators of fibrinolytic system: tricholysine and longolytin from the culture of saprophyte fungi, plasminogen activator from the pig heart and the cells culture of the calf kidney have been received and are being studied.