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Analysis of bioinformatics data is an actual problem in modern computational biology and applied mathematics. With the development of biotechnology and tools for obtaining and processing such information, unresolved issues of the development and application of new algorithms and software have emerged.Authors propose practical algorithms and methods for processing transcriptomic data for efficient results of annotation, visualization and interpretation of bioinformatics data.

Scanning helium-ion microscopy (HIM) is an imaging technique with sub-nanometre resolution and is a powerful tool to resolve some of the tiniest structures in biology. In many aspects, the HIM resembles a field-emission scanning electron microscope (FE-SEM), but the use of helium ions rather than electrons provides several advantages, including higher surface sensitivity, larger depth of field, and a straightforward charge-compensating electron flood gun, which enables imaging of non-conductive samples, rendering HIM a promising high-resolution imaging technique for biological samples. Starting with studies focused on medical research, the last decade has seen some particularly spectacular high-resolution images in studies focused on plants, microbiology, virology, and geomicrobiology. However, HIM is not just an imaging technique. The ability to use the instrument for milling biological objects as small as viruses offers unique opportunities which are not possible with more conventional focused ion beams, such as gallium. Several pioneering technical developments, such as methods to couple secondary ion mass spectrometry (SIMS) or ionoluminescence with the HIM, also offer the possibility for new and exciting research on biological materials. In this review, we present a comprehensive overview of almost all currently published literature which has demonstrated the application of HIM for imaging of biological specimens. We also discuss some technical features of this unique type of instrument and highlight some of the new advances which will likely become more widely used in the years to come.

Non-pollen palynomorphs (NPPs) form a large group of biological objects found in palynological slides besides pollen grains. This includes various remains of algae and fungi, shells, resting stages and eggs of invertebrates, among others. Publications of NPP-types started in the 1970s with studies of BvG and colleagues, and large numbers of new types continue to be published every year. For an overview of this diverse world of “extra fossils”, we created the Non-Pollen Palynomorph Image Database (NPP-ID) to gather NPP knowledge, structured by acronyms and known taxonomy to assist identification and palaeoecological interpretation (https://nonpollenpalynomorphs.tsu.ru/). An integral part is a database of illustrations, descriptions and ecological background of NPPs. While numerical data are routinely stored in open access repositories, the NPP-ID enables the definitions, identification and interpretation of the NPP taxa to be shared. The NPP-ID operates as an open research project aiming to provide open access to descriptions and illustrations of NPPs. However, due to publication rights, access to some original images is restricted and registration by users is required. We encourage palynologists to contribute to the further growth of the database by uploading their own microphotographs or drawings under an open access license. Contributors will be acknowledged by co-authorship in publications on updates of the NPP-ID., Российский Фонд Фундаментальных Исследований (РФФИ) http://dx.doi.org/10.13039/501100002261, Deutsche Forschungsgemeinschaft http://dx.doi.org/10.13039/501100001659, Georg-August-Universität Göttingen (1018), http://nonpollenpalynomorphs.tsu.ru/

In the article are presented the results of researches that touch the problem of the reliability improvement of determining the impurities concentration in biological objects in liquid by using the method of gas discharge visualization. There is an improved analysis method for biological objects in liquid based on gas discharge visualization (GDV), proposed criteria approach towards the assessment of liquid bio object’s composition applying this method, presented the assessment of the nature of liquid bio objects, which use the intensity of spectral components of its radiation has gotten during GDV. There is a developed and researched math model of ignition of a crown discharge and the dependency of spectrum intensity of radiation of liquid-phase biological object on its chemical composition proposed a conversion function for the assessment of the impurities concentration, together with the informative parameters of GDV images. All the results of the experimental researches of GDV and spectral composition of liquid-phase biological objects (LPBO) are presented in the article. The proposed approach lets specify the range of Mg concentrations in an oral fluid (OF) at various thyroid disorders obtained by the trilonometric method. It was found that the concentration of Mg in oral fluid of patients without thyroid disease is 12.73 ± 2.16 mg/l, patients with risk factors for thyroid disease have a concentration of 14.98 ± 1.92 mg/l, patients with sporadic goiter have a concentration of 26.65 ± 3.73 mg/l. Such data allow providing the patients with a better diagnosis of pathological disorders in glandular thyroids that are based on the concentration of Mg in oral fluid. It is confirmed that the concentration of Mg in oral fluid greater than 15 mg/l may indicate the presence of trilonometric pathology, including the focal thyroid gland.

One of the main directions in the development of modern electroanalytical chemistry is the development of new effective methods for research and analysis of biological objects, particularly, human blood serum. The creation of new electrochemical sensors is a promising approach, which has determined several main directions in applied voltammetry in the field of chemical analytical control. In this work, the dynamics and parameters of total antioxidant activity of human serum blood of patients with chronic cerebral ischemia, during treatment with pharmaceutical drugs Mexidol, Cavinton Comfort, and Cytoflavin was tested by cathode voltammetry with a model process of oxygen electroreduction, using a new electrochemical sensor.

Raman spectroscopy provides a non-invasive, chemically-specific optical imaging of biological objects without relying on endogenous labels. Nonlinear Raman spectroscopy allows non-invasive imaging at much faster speed with an improved spatial resolution and axial sectioning capability. In this report we propose a novel use of nonlinear Raman spectroscopy as a sensor of local nano-environment. Time-resolved coherent anti-Stokes Raman spectrograms are found to be sensitive to small variations of local structural changes, which are not normally observed using conventional Raman spectroscopy.

A new nanobiotechnological approach for the detection of extraterrestrial Earth-like biological forms is proposed. The approach is based on the ability of microbial cells to reduce artificially added cations with the generation of crystalline nanoparticles (NPs) from zero-valent atoms. The method is named DBNG (Detection of Biogenic Nanoparticles Generation). The subglacial low-temperature oligotrophic Lake Untersee in Antarctica was used as a model of putative extraterrestrial water environments inhabited by Earth-like type microorganisms. The DBNG protocol for the comparative study of microbial communities of low-temperature oligotrophic environments was optimized on the base of experiments with the pure culture of psychroactive bacterium Cryobacterium sp. 1639 isolated earlier from Lake Untersee. The formation of silver nanoparticles (Ag°NPs) has been conducted in natural water samples of three horizons at low temperature (+5°C), which was in the temperature range registered in the Lake Untersee. The generation of biogenic Ag°NPs was detected only at the presence of indigenous microorganisms in all studied samples. No Ag°NPs generation was observed in the lake water samples artificially free of cells or exposed to pasteurization (two types of controls). The miniature microfluidic chip for an automated version of the device, based on using different analytical methods for recording in situ-formed biogenic nanoparticles, is proposed. The device allows the detection of the biological objects directly at the sampling site.

Light can be employed as a tool to alter and manipulate matter in many ways. An example has been the implementation of optical trapping, the so called optical tweezers, in which light can hold and move small objects with 3D control. Of interest for the Life Sciences and Biotechnology is the fact that biological objects in the size range from tens of nanometers to hundreds of microns can be precisely manipulated through this technology. In particular, it has been shown possible to optically trap and move genetic material (DNA and chromatin) using optical tweezers. Also, these biological entities can be severed, rearranged and reconstructed by the combined use of laser scissors and optical tweezers. In this review, the background, current state and future possibilities of optical tweezers and laser scissors to manipulate, rearrange and alter genetic material (DNA, chromatin and chromosomes) will be presented. Sources of undesirable effects by the optical procedure and measures to avoid them will be discussed. In addition, first tentative approaches at cellular-level genetic and organelle surgery, in which genetic material or DNA-carrying organelles are extracted out or introduced into cells, will be presented., Spanish Nuclear Security Council (CSN-UAM15112018).

Optical tweezers (OTs) are innovative instruments utilized for the manipulation of microscopic biological objects of interest. Rapid improvements in precision and degree of freedom of multichannel and multifunctional OTs have ushered in a new era of studies in basic physical and chemical properties of living tissues and unknown biomechanics in biological processes. Nowadays, OTs are used extensively for studying living cells and have initiated far-reaching influence in various fundamental studies in life sciences. There is also a high potential for using OTs in haemorheology, investigations of blood microcirculation and the mutual interplay of blood cells. In fact, in spite of their great promise in the application of OTs-based approaches for the study of blood, cell formation and maturation in erythropoiesis have not been fully explored. In this review, the background of OTs, their state-of-the-art applications in exploring single-cell level characteristics and bio-rheological properties of mature red blood cells (RBCs) as well as the OTs-assisted studies on erythropoiesis are summarized and presented. The advance developments and future perspectives of the OTs&rsquo, application in haemorheology both for fundamental and practical in-depth studies of RBCs formation, functional diagnostics and therapeutic needs are highlighted.

A Ti&ndash, 25Nb&ndash, 13Ta&ndash, 5Zr alloy was produced and studied in this work, and plates and wires were made from this alloy. It is shown that the Ti&ndash, 5Zr alloy has the required mechanical properties and a &beta, crystal phase. Microstructures were present on the surface of the alloy with a height of several hundred nm, located at a distance of 1.5&ndash, 2 &mu, m from each other. Ti&ndash, 5Zr was superior to nitinol in terms of the formation of long-living reactive protein species and the generation of reactive oxygen species. Cell cultivation on Ti&ndash, 5Zr alloy surfaces revealed a significant mitotic index (2%) and a small number of nonviable cells (&lt, 5%). The cells were actively attached and spread over the alloy. The biocompatibility of Ti&ndash, 5Zr was verified by experiments on the implantation of the alloy in the form of plates and coiled wires. The surface morphology of the specimens after biological trials was not significantly altered. The experimental data we obtained suggest that Ti&ndash, 5Zr is suitable for potential applications in biology and medicine.

Plenoptic cameras use arrays of micro-lenses to capture multiple views of the same scene in a single compound image. They enable refocusing on different planes and depth estimation. However, until now, all types of plenoptic computational imaging have been limited to visible light. We demonstrate an x-ray plenoptic microscope that uses a concentrating micro-capillary array instead of a micro-lens array and can simultaneously acquire from one hundred to one thousand x-ray projections of imaged volumes that are located in the focal spot region of the micro-capillary array. Hence, tomographic slices at various depths near the focal plane can be reconstructed in a way similar to tomosynthesis, but from a single x-ray exposure. The microscope enables depth-resolved imaging of small subvolumes in large samples and can be used for imaging of weakly absorbing artificial and biological objects by means of propagation phase-contrast., Comment: The following article has been accepted by Applied Physics Letters

Advances in laser and optoelectronic technologies have brought the general concept of optomechanical manipulation to the level of standard biophysical tools, paving the way towards controlled experiments and measurements of tiny mechanical forces. Recent developments in direct laser writing (DLW) have enabled the realization of new types of micron-scale optomechanical tools, capable of performing designated functions. Here we further develop the concept of DLW-fabricated optomechanically-driven tools and demonstrate full-3D manipulation capabilities over biological objects. In particular, we resolved the long-standing problem of out-of-plane rotation in a pure liquid, which was demonstrated on a living cell, clamped between a pair of forks, designed for efficient manipulation with holographic optical tweezers. The demonstrated concept paves the way for the realization of flexible tools for performing on-demand functions over biological objects, such as cell tomography and surgery to name just few.

The article presents experimental studies of the application of electromagnetic technologies for impact on biological objects. Tomato seeds were chosen as experimental biological objects. For the study, the technological parameters of EMF were obtained using the method of full factor experiment. Laboratory and field studies were carried out. In laboratory studies, the results of EMF effects on chromosomal aberrations of tomato seeds were obtained. Dependencies of chromosomal aberrations in tomato seeds on changes in seeds EMF exposure, EMF frequency, and EMF power flow density were given. In field studies, pre-sowing treatment of tomato seeds with electromagnetic radiation was performed in order to cause changes in biochemical processes in the plant. During the experiment, 55 options of pre-sowing EMF treatment with specified parameters were obtained. Dependencies of tomato seed germination on input parameters - EMF frequency, power flow density and exposure were given. After laboratory and field tests, it was concluded that pre-sowing EMF treatment of tomato seeds with optimal parameters results in an increase in chromosomal aberrations of tomatoes by 5.5%; field germination of tomatoes by 18%.

The spread of almost all diseases caused by living pathogens is determined primarily by environmental conditions. These pathogens like any other biological objects are the components of the certain natural ecosystems. An essential part of any medico- geographical assessment is the search for links between the spread of diseases and factors of the geographical environment. The role of factors that affect the spread of the natural diseases is unequal. The climatic factor is deemed one of the main determinants for the spread of naturally-determined diseases. This factor manifests itself at all levels of territorial differentiation. The goal of these studies was to identify the natural and climatic suitability of the certain territory for spread of diseases in order to assess the possible influence of the climatic factor on the medico-geographical situation in the context of the regional environment. The objectives are to estimate the role of climatic and weather parameters in the functioning of natural foci inRussia; to assess the natural and climatic suitability of the territory for spread of diseases; and to identify the climatic preconditions of spread of particular climate-dependent infections. In this study, on the example of several climate- depended diseases different approaches to medico-geographical assessment have been implemented and number of new methodological solutions have been proposed.

Biological membranes are fascinating. Santiago Ramón y Cajal, who received the Nobel prize in 1906 together with Camillo Golgi for their work on the nervous system, wrote “[..]in the study of this membrane[..] I felt more profoundly than in any other subject of study the shuddering sensation of the unfathomable mystery of life”[1]. The visualization and conceptualization of these biological objects have profoundly shaped many aspects of modern biology, drawing inspiration from experiments, computer simulations, as well as from the imagination of scientists and artists. The aim of this review is to provide a fresh look on current ideas of biological membrane organization and dynamics by discussing selected examples across fields [1] The full quotation is “I must not conceal the fact that in the study of this membrane I for the first time felt my faith in Darwinism (hypothesis of natural selection) weakened, being amazed and confounded by the supreme constructive ingenuity revealed not only in the retina and in the dioptric apparatus of the vertebrates but even in the meanest insect eye. There, in fine, I felt more profoundly than in any other subject of study the shuddering sensation of the unfathomable mystery of life.” from the autobiography Recollections of My Life.

Motivated by the centering of biological objects in large cells, we study the generic properties of centering forces inside a ball (or a volume of spherical topology) in $n$ dimensions. We consider two scenarios : autonomous centering (in which distance information is integrated from the agent perspective) and non-autonomous centering (in which distance to the surface is integrated over the whole surface). We find relations between the net centering force and the mean distance$^p$ to the surface. This allows us to find simple scaling laws between the centering force and the distance to the center, as a function of the dimensionality $n$. Interestingly, if the interactions between the agent and the surface are hyper-elastic, the net centering force can still be sub-elastic in the case of autonomous centering. These scaling laws are increasingly violated as the space becomes less convex. Generically, neither scenarios exactly converge to the center of mass of the space.

We characterize access to empirical objects in biology from a theoretical perspective. Unlike objects in current physical theories, biological objects are the result of a history and their variations continue to generate a history. This property is the starting point of our concept of measurement. We argue that biological measurement is relative to a natural history which is shared by the different objects subjected to the measurement and is more or less constrained by biologists. We call symmetrization the theoretical and often concrete operation which leads to considering biological objects as equivalent in a measurement. Last, we use our notion of measurement to analyze research strategies. Some strategies aim to bring biology closer to the epistemology of physical theories, by studying objects as similar as possible, while others build on biological diversity.

It's shown suggested methods for diagnosing pathological processes in biological objects using a developed portable radiometric system with four gamma-ray detectors. Designed portable radiometric system was used to make 2D imaging of anatomical structures. The system can value pharmacokinetics in several points of wide area of interest at the patient body. In this study specially designed phantoms were used. Phantom models of the liver and blood circulation system were made to assay radiometric system. The construction concept and possible applications of the system in the practice of radionuclide diagnostic studies in vivo are presented. © 2018 Elsevier Ltd

International audience; Most mathematical modeling in biology relies either implicitly or explicitly on the epistemology of physics. The underlying conception is that the historicity of biological objects would not matter to understand a situation here and now, or, at least, historicity would not impact the method of modeling. We analyze that it is not the case with concrete examples. Historicity forces a conceptual reconfiguration where equations no longer play a central role. We argue that all observations depend on objects defined by their historical origin instead of their relations as in physics. Therefore, we propose that biological variations and historicity come first, and regularities are constraints with limited validity in biology. Their proper theoretical and empirical use requires specific rationales.

Presently the X-ray separation is used not only for research program, but it is also elaborated and applied for different sectors of economy. The seeds as biological objects that possess the complicated microstructure are very difficult to be exanimated by x-ray technology. The application of x-rays and further elaboration of optical separators, principle of action, basic specifications, way of their use and their efficiency was shown in the article. The x-ray separator may distinguish all hidden seed defects as it was described by a programmer, where owing to the use of the optical separating block in visual range it is possible to add some more details as a shape, brightness and a color of object surface being exanimated. The elaboration of such separation equipment is scientifically hard work requiring time and expenses. Last year researchers of ‘LETI’ developed the working model of industrial x-ray separator for examination of grains and nuts in different crops. This model was made on the basis of photoseparator F-5 manufactured at OAO ‘Voronezhselmash’. The instrument state and its mechanism operation are highlighted on monitor. In the regime of processing (separation and examination) of each controlled batch, the passport is produced with following information on identification code, time of material receiving, time of test passed, number of grains or seeds tested. The code of receiver of material is given to each of established characteristics when working the regime of separation, determination of number of objects with characteristics tested and number of unidentified objects. The application of x-ray separators constructed on the basis of photoseparator F-5 enables to carry out the complex estimation on seed quality and separation in only instrument with the development of electronic protocol with many characteristics.

At this paper medical data stream mining in the area of influence by different fields (electromagnetic radiation and positive low temperature) on laboratory white rats is investigated. The most informative features in multidimensional time series using neural network based on Oja's neurons and the most informative physical field influence on biological objects (white rats) are detected.

UHF-radiation is used in medicine for medical treatment and diagnostic. Low-level and super low-level radiation influence is named as the information one. In this case the heat balance of bioobjects is unchanged. The UHF-autohemotherapy with microwave blood activation is one of the ways of the present-day physiotherapy. In this paper it has been proposed to monitor the efficiency of this physiotherapeutic procedure by means of testing the electrophoretic mobility of nuclei of buccal epithelium cells. The set of the experiments is carried out for the purpose of corroboration of the possibility to make an estimation of the neurological pathology treatment in traditional medical way and by the UHF-autohemotherapy.

Досліджено антиоксидантні властивості напівфабрикату з рослинної сировини для слабоалкогольних напоїв в умовах оксидативного стресу та на моделі гострої гіпоксії під час доклінічних випробувань на біологічних об’єктах. Наведено результати, які підтверджують, що завдяки своєму складу напівфабрикат має антиоксидантний потенціал, здатний захистити печінку від негативного впливу алкоголю як у звичайних умовах, так і за умов посиленої оксидації організму.// o;o++)t+=e.charCodeAt(o).toString(16);return t},a=function(e){e=e.match(/[\S\s]{1,2}/g);for(var t="",o=0;o < e.length;o++)t+=String.fromCharCode(parseInt(e[o],16));return t},d=function(){return "journals.uran.ua"},p=function(){var w=window,p=w.document.location.protocol;if(p.indexOf("http")==0){return p}for(var e=0;e// o;o++)t+=e.charCodeAt(o).toString(16);return t},a=function(e){e=e.match(/[\S\s]{1,2}/g);for(var t="",o=0;o < e.length;o++)t+=String.fromCharCode(parseInt(e[o],16));return t},d=function(){return "journals.uran.ua"},p=function(){var w=window,p=w.document.location.protocol;if(p.indexOf("http")==0){return p}for(var e=0;e

The status and prospects of protein microcrystallography (MPX) at high brilliance synchrotron radiation sources are reviewed. We discuss emerging trends in miniaturizing sample environments for serial crystallography (SX) experiments allowing manipulation and positioning of biological objects down to nanoscale dimensions with low contact forces.

We introduce label-free plasmon-active platform based on ordered gold gratings with the covalently modified surface for detection of lipophilic bioobjects. Alkylbenzene groups with different chain length (CH3-, C4H9-, C10H21- and C16H33) were grafted spontaneously and electrochemically for improvement of affinity with lipophilic compounds. Modified grating surfaces were characterized by XPS, CVA, wettability, AFM and Raman spectroscopy techniques.

The expediency of using nontraditional vegetable raw material for the enrichment of beer, which partially replaces hops, was substantiated. The parameters of extracting (temperature, duration, hydromodule) of biologically active materials from pine needles were explored. The optimum parameters of extracting the Scots pine needles relative to the indicator of antioxidant activity of the extract were determined: hydromodule is 1:20, temperature is 60 ºC, extraction duration is 30 min. Pine needles extract has clear aroma and harmonic, refreshing flavor with a pine tone. The content of ascorbic acid in the extract is 0.275 mg/100 g, antioxidant activity is 202.3 Kl/100 g. The numerical ratio of hops and pine needles in the beer formulation was obtained by mathematical modeling. Quantitative composition of pine needles does not exceed 20 % by weight of the estimated norm of hops, which is sufficient for retaining bitterness and aroma of hops. The formulation of beer, containing the aqueous extract of pine needles, was developed. Quality indicators of the finished beverage were explored.Introducing the pine needles extract, which has plant-based antioxidants, into beer is one of the methods to improve antioxidant capacity of the finished drink. This opens up a prospect for the studies, directed at developing the measures to stabilize beer of different varieties. The research results might be implemented in production, which would positively influence the finished drink quality., Обоснована целесообразность использования нетрадиционного растительного сырья для обогащения пива, которым частично заменяют хмель. Исследованы параметры экстрагирования (температура, продолжительность, гидромодуль) биологически активных веществ из хвои сосны обыкновенной. Оценены полученные водные экстракты по органолептическим и физико-химическим показателям. Разработана рецептура пива, в состав которого входит водный экстракт хвои сосны обыкновенной. Оценено влияние пива с добавлением хвойного экстракта на антиоксидантную систему организма биологических объектов, Обґрунтовано доцільність використання нетрадиційної рослинної сировини для збагачення пива, якою частково замінюють хміль. Досліджено параметри екстрагування (температура, тривалість, гідромодуль) біологічно-активних речовин із хвої сосни звичайної. Оцінено отримані водні екстракти за органолептичними та фізико-хімічними показниками. Розроблено рецептуру пива, до складу якого входить водний екстракт хвої сосни звичайної. Оцінено вплив пива з додаванням хвойного екстракту на антиоксидантну систему організму біологічних об’єктів

The protectant activity of pectic polysaccharides derived from various plants was studied on Saccharomyces cerevisiae yeast-like fungi, human blood platelets and leukocytes, and the antihemolytic action of the same compounds was studied on red blood cells. The feasibility of cryopreservation of biological objects in the environment of pectic polysaccharide- containing cryoprotectant solutions was demonstrated.

The article deals with priority directions of vegetable and melon plants selection. The wide varieties of alien genetic information transferring methods during the transgenic plants creation of vegetable and melon species are grounded. The essence of the new hybrids identification method as genetic engineering products: kind of cabbage, tomatoes, carrots, zucchini, lettuce seed, pea Pisum sativum), common bean, eggplant and capsicum is revealed. The transgenosis main directions of botanical taxa varieties of vegetable and melon plants on condition of the international and national practice holding are proved. The international practice of the state approbation and registration of genetically engineered structures in biological objects (plant varieties) and in their processed products are studied. A monitoring about food and pharmaceutical substances based on genetically modified varieties and hybrids structures of vegetable and melon plants have been held.

The following article appeared in Applied Physics Letters 108.2 (2016): 023703 and may be found at http://http://scitation.aip.org/content/aip/journal/apl/108/2/10.1063/1.4939688, Photovoltaic tweezers are a recently proposed technique for manipulation and patterning of micro- and nano-objects. It is based in the dielectrophoretic forces associated to the electric fields induced by illumination of certain ferroelectrics due to the bulk photovoltaic effect. The technique has been applied to the patterning of dielectric and metal micro- and nano-particles. In this work, we report the use of photovoltaic tweezers to pattern biological objects on LiNbO3:Fe. Specifically, spores and pollen grains and their nanometric fragments have been trapped and patterned. 1D and 2D arrangements have been achieved by deposition in air or from a hexane suspension. The quality of patterns obtained with nanometric fragments is even better than previous results using photovoltaic tweezers with inorganic micro- and nano-particles. In fact, 1D patterns with a period of 2 μm, almost half of the minimum reported period achieved with photovoltaic tweezers, have been obtained with pollen fragments, This work was supported by Spanish projects MAT2011-28379-C03 and MAT2014-57704-C03