Biological Objects Research Articles

Alpha, Delta, Omicron—Oh My! A SARS-CoV-2 Genome Alignment Activity to Understand Mutations and COVID Variants

COVID took over the world starting in 2020. Everyone quickly “knew” about the novel coronavirus, but how much do they actually know about the virus behind COVID-19? This classroom activity gives students real-world practice in evaluating actual genetic sequences from SARS-CoV-2 and working with genome alignments to identify mutations and cluster different emergence patterns. This activity works through alignments, mutations/variants, protein folding, structure and function, and medical/immunology implications of the different variants. There are seven parts to this activity, and each one can be incorporated alone into a lesson or collectively used for a lab, case study, or other supplemental activity to strengthen learning objectives in genetics, biology, immunology, and public health. This learning activity is scalable to different levels and has successfully been incorporated into K–12 education as well as college and graduate education.

Formation of subject competence students using competence-oriented tasks in biology

Introduction. Periodic updating of the content of education in accordance with the achievements in the study area and with the specifics of the discipline taught is one of the important conditions for improving the quality of education in secondary school. The integrated use of the competency-based approach is considered an important didactic condition for improving both the content and methods of teaching biology in secondary schools, which requires an analysis of the level of subject competencies and ways of their formation in the learning process. Materials and methods. The study involved 420 students of educational institutions of the Kyrgyz Republic (220 in the experimental group and 200 in the control group). Research methods: questioning, analysis of literary sources on the subject of the study. Methods of mathematical statistics: Pearson's chi-squared test. Research results. The levels of formation of subject competencies of students through the solution of competency-oriented biological tasks are revealed and experimentally tested. It has been established that students more effectively perform various options for laboratory and practical work in biology, can independently use conventional signs, diagrams and models of biological processes and objects, and are active in performing independent research work of varying degrees of complexity. On the basis of a comparative analysis of empirical data, statistical analysis, positive dynamics and a significant increase in the values of level indicators of subject competencies (χ2 = 15.825; p<0.01) were established. Conclusions. The introduction of competence-oriented tasks in the educational process in the subject of biology will help increase students' cognitive activity, interest in obtaining biological knowledge and applying the formed subject competencies in practical activities. Keywords: updating, content of biological education, activity approach, competence-based approach, subject standard in biology, subject activity, learning activity, learning task

Characteristics of Cold Atmospheric Plasma Jet when Excited by Sinusoidal and Positive Pulse Voltages for Medical Applications

Low-temperature plasma jets at atmospheric pressure generated by sinusoidal and positive pulsed voltages interact differently with the treated surface. In the experiment and in numerical simulations, we compare the operating modes of helium plasma jets for these types of operating voltages. The discharge current on the treated surface over time and the surface heating are studied for different discharge parameters acceptable for anticancer therapy. The intensity of the emission spectrum is analyzed to improve the effectiveness of the plasma jet. Surface heating is controlled in order to meet the safety conditions of plasma exposure to biological objects. For the case of pulsed voltage the effect of voltage pulse duration on the intensity of plasma-surface interaction is discussed. The results on cancer cells A549 and MCF-7 demonstrate the high efficiency of the cold plasma jet generated at found optimal modes.

NATURE-INSPIRED DESIGN IDEA GENERATION WITH GENERATIVE ADVERSARIAL NETWORKS

Generating new, creative, and innovative ideas in the early stages of the design process is crucial for developing better and original products. Human designers may become too attached to specific design ideas, preventing them from generating new concepts and achieving ideal designs. To come up with original design ideas, a designer needs to have a creative mind, as well as knowledge, experience, and talent. Verbal, written, and visual sources of inspiration can also be valuable for generating ideas and concepts. This study presents a visual integration model that uses a data-supported Artificial Intelligence (AI) method to generate creative design ideas. The proposed model is based on a generative adversarial network (GAN) that combines target object and biological object images to produce new creative product images inspired by nature. The model was successfully applied to an aircraft design problem and the resulting sketches inspired designers to generate new and creative design ideas and variants in a case study. It was seen that this approach improved the quality of the ideas produced and simplified the idea and concept generation process.

Phosphorescent O2-Probes Based on Ir(III) Complexes for Bioimaging Applications

The design, synthesis, and investigation of new molecular oxygen probes for bioimaging, based on phosphorescent transition metal complexes are among the topical problems of modern chemistry and advanced bioimaging. Three new iridium [Ir(N^C)2(N^N)]+ complexes with cyclometallating 4-(pyridin-2-yl)-benzoic acid derivatives and different di-imine chelate ligands have been synthesized and characterized by mass spectrometry and NMR spectroscopy. The periphery of these complexes is decorated with three relatively small “double-tail” oligo(ethylene glycol) fragments. All these complexes exhibit phosphorescence; their photophysical properties have been thoroughly studied, and quantum chemical calculations of their photophysical properties were also performed. It turned out that the changes in the nature of the di-imine ligand greatly affected the character of the electronic transitions responsible for their emission. Two complexes in this series show the desired photophysical characteristics; they demonstrate appreciable quantum yield (14–15% in degassed aqueous solutions) and a strong response to the changes in oxygen concentration, ca. three-fold increase in emission intensity, and an excited state lifetime upon deaeration of the aqueous solution. The study of their photophysical properties in model biological systems (buffer solutions containing fetal bovine serum—FBS) and cytotoxicity assays (MTT) showed that these complexes satisfy the requirements for application in bioimaging experiments. It was found that these molecular probes are internalized into cultured cancer cells and localized mainly in mitochondria and lysosomes. Phosphorescent lifetime imaging (PLIM) experiments showed that under hypoxic conditions in cells, a 1.5-fold increase in the excitation state lifetime was observed compared to aerated cells, suggesting the applicability of these complexes for the analysis of hypoxia in biological objects.

UWB-Modulated Microwave Imaging for Human Brain Functional Monitoring.

Morphological microwave imaging has shown interesting results on reconstructing biological objects inside the human body, and these parameters represent their actual biological condition, but not their biological activity. In this paper, we propose a novel microwave technique to locate the low-frequency (f≃1 kHz) -modulated signals produced by a microtag mimicking an action potential and proved it in a cylindrical phantom of the brain region. A set of two combined UWB microwave applicators, operating in the 0.5 to 2.5 GHz frequency band and producing a nsec interrogation pulse, is able to focus its radiated field into a small region of the brain containing the microtag with a modulated photodiode. The illuminating UWB microwave field was first modulated by the low-frequency (f≃1 kHz) electrical signal produced by the photodiode, inducing modulated microwave currents into the microtag that reradiating back towards the focusing applicators. At the receiving end, the low-frequency (f≃1 kHz) -modulated signal was first extracted from the full set of the backscattered signals, then focused into the region of interest and spatially represented in the corresponding region of the brain, resulting in a spatial resolution of the images in the order of 10 mm.

Photo-Crosslinkable Polymeric Coatings Providing Chemically Versatile Reactive Surfaces on Various Substrates

We demonstrate a chemical route to attain simple, clean, scalable, photopatternable, chemically adjustable, and versatile systems to fabricate reactive organic thin films. Their surfaces exhibit effective biocompatibility, controlled reactivity, and processability on various surface types, i.e., photo-crosslinkable polymeric thin films with various functionalities, further applicable for the definition of surface activity for interfacing biological objects. The copolymers were synthesized with three monomers: a poly(ethylene glycol)-containing monomer, a monomer releasing a primary amine upon exposure to UV light, and a monomer bearing cyclic dithiocarbonate or glycidyl groups that are highly reactive with the amine. The resulting copolymers were processed with polar solvents such as water or alcohol for coating and were readily crosslinked under UV light illumination to form a highly stable molecular network, beneficial for defining selective reactive surfaces in a desired region on a variety of organic and inorganic substrates. The designed system was chemically versatile in immobilizing biologically relevant molecules on the surfaces by (i) post-crosslinking modification through the reaction of bovine serum albumin on the remaining surface reactive group with a primary amine in the protein and (ii) pre-crosslinking formulation with reactive gelatin that has the functionality to crosslink in the composite thin film. We further showed that the resulting coating on a glass or polystyrene substrate provided excellent biocompatibility and growth of C2C12 murine myocytes.

Подходы к таксономическому определению изображений животных (по материалам сибирских петроглифов)

The article discusses the possibilities of taxonomic determinations of zoomorphic rock representations and the significance of these data for further interpretations, indirect dating and other scientific tasks. In addition to the applied method of zoomorphological description on the depicted animal’s exterior features, two approaches to the analysis of proportions have been proposed. The first basic-zoological approach is focused on the animal as a biological object and describes the ratio of animal body measurements according to the zoological standard of body measurements of large mammals. The second comparative-zoological approach requires the selection of proportions that are significant for each particular species, based on the morphological features of the animal exterior features. Both approaches have been tested on a sample of 30 petroglyphs from the rock art sites Kalbak-Tash I and Shalabolino, representing images of wild boars and bears. The obtained data on the proportions were analyzed using the principal component analysis (PCA), which allowed to verify the degree of differentiation between the images of the two selected species. As a result, we conclude that the comparative-zoological approach as a tool aimed at distinguishing the most significant features for taxonomic definitions of rock images is expedient.

Possibilities of Studying Biological Objects on a Pulsed Reactor

Small-angle scattering makes it possible to solve structural biology problems without specific sample preparation, which is typical for methods such as X-ray diffraction of protein crystals or cryo-electron microscopy of proteins. In our review, it is shown how to use small-angle scattering to address biological problems. The use of small-angle scattering is suggested for applications as a tool to control the quality of the assembly of proteins and protein complexes and to test the identity of the structural organization of biological objects in the native state and in prepared samples before measurements by X-ray diffraction or cryo-electron microscopy. This work demonstrates the possibilities of the small-angle neutron scattering spectrometer YuMO based on the IBR-2 pulsed reactor (Laboratory of neutron physics, Joint Institute for Nuclear Research, Dubna, Russia) to solve a whole array of problems, with an eye toward applying these in biophysics, structural biology, and biotechnology. This review presents and discusses the main findings of the studies of various biological systems obtained by using the setup small-angle scattering of neutrons YuMO. The possibilities of development of structural biology methods with the help of small-angle scattering, including protein crystallization, are shown.

A Method Based on Temporal Embedding for the Pairwise Alignment of Dynamic Networks

In network analysis, real-world systems may be represented via graph models, where nodes and edges represent the set of biological objects (e.g., genes, proteins, molecules) and their interactions, respectively. This representative knowledge-graph model may also consider the dynamics involved in the evolution of the network (i.e., dynamic networks), in addition to a classic static representation (i.e., static networks). Bioinformatics solutions for network analysis allow knowledge extraction from the features related to a single network of interest or by comparing networks of different species. For instance, we may align a network related to a well known species to a more complex one in order to find a match able to support new hypotheses or studies. Therefore, the network alignment is crucial for transferring the knowledge between species, usually from simplest (e.g., rat) to more complex (e.g., human). Methods: In this paper, we present Dynamic Network Alignment based on Temporal Embedding (DANTE), a novel method for pairwise alignment of dynamic networks that applies the temporal embedding to investigate the topological similarities between the two input dynamic networks. The main idea of DANTE is to consider the evolution of interactions and the changes in network topology. Briefly, the proposed solution builds a similarity matrix by integrating the tensors computed via the embedding process and, subsequently, it aligns the pairs of nodes by performing its own iterative maximization function. Results: The performed experiments have reported promising results in terms of precision and accuracy, as well as good robustness as the number of nodes and time points increases. The proposed solution showed an optimal trade-off between sensitivity and specificity on the alignments produced on several noisy versions of the dynamic yeast network, by improving by ∼18.8% (with a maximum of 20.6%) the Area Under the Receiver Operating Characteristic (ROC) Curve (i.e., AUC or AUROC), compared to two well known methods: DYNAMAGNA++ and DYNAWAVE. From the point of view of quality, DANTE outperformed these by ∼91% as nodes increase and by ∼75% as the number of time points increases. Furthermore, a ∼23.73% improvement in terms of node correctness was reported with our solution on real dynamic networks.

Single-shot isotropic differential interference contrast microscopy

Differential interference contrast (DIC) microscopy allows high-contrast, low-phototoxicity, and label-free imaging of transparent biological objects, and has been applied in the field of cellular morphology, cell segmentation, particle tracking, optical measurement and others. Commercial DIC microscopy based on Nomarski or Wollaston prism resorts to the interference of two polarized waves with a lateral differential offset (shear) and axial phase shift (bias). However, the shear generated by these prisms is limited to the rectilinear direction, unfortunately resulting in anisotropic contrast imaging. Here we propose an ultracompact metasurface-assisted isotropic DIC (i-DIC) microscopy based on a grand original pattern of radial shear interferometry, that converts the rectilinear shear into rotationally symmetric along radial direction, enabling single-shot isotropic imaging capabilities. The i-DIC presents a complementary fusion of typical meta-optics, traditional microscopes and integrated optical system, and showcases the promising and synergetic advancements in edge detection, particle motion tracking, and label-free cellular imaging.

BioGraph: Data Model for Linking and Querying Diverse Biological Metadata.

Studying the association of gene function, diseases, and regulatory gene network reconstruction demands data compatibility. Data from different databases follow distinct schemas and are accessible in heterogenic ways. Although the experiments differ, data may still be related to the same biological entities. Some entities may not be strictly biological, such as geolocations of habitats or paper references, but they provide a broader context for other entities. The same entities from different datasets can share similar properties, which may or may not be found within other datasets. Joint, simultaneous data fetching from multiple data sources is complicated for the end-user or, in many cases, unsupported and inefficient due to differences in data structures and ways of accessing the data. We propose BioGraph-a new model that enables connecting and retrieving information from the linked biological data that originated from diverse datasets. We have tested the model on metadata collected from five diverse public datasets and successfully constructed a knowledge graph containing more than 17 million model objects, of which 2.5 million are individual biological entity objects. The model enables the selection of complex patterns and retrieval of matched results that can be discovered only by joining the data from multiple sources.

Autophagy and LC3-associated phagocytosis: similarities and differences

Previously, autophagy was termed as a mechanism used by the cells with a lack of essential nutrients supporting homeostasis. Over the decade of studies, autophagy proved to be a more complex, ambiguous mechanism. Its activation depends on the nature of stimulus, type of immune cells and the final result. Both canonical and non-canonical autophagy, being similar in molecular events, but showing their own distinctive features, are key processes in protecting the body from penetration of intracellular pathogens, maintaining the required level of nutrients in the cell, and removing damaged organelles and cells. Canonical autophagy probably evolved as a homeostatic response to cellular stress and nutritional deficiencies, whereas non-canonical autophagy emerged as a response to suppression of inflammation. Non-canonical autophagy, hereinafter referred to as LC3-associated phagocytosis (LAP), combines the molecular mechanism of phagocytosis with an autophagy mechanism characterized by ingestion of exogenous pathogens, formation of phagosomes (laposomes) and enhanced fusion with lysosomes, followed by degradation of their contents.Significant differences were found between the processes of LAP- and canonical autophagy, which are similar in its mechanism of action. The presence of PI3K complexes in both processes, utilization and intracellular degradation of the “cargo” which is not required for the cells and organism proceeding in the lysosomes, and involvement of almost the same proteins provide similarity of their mechanisms. However, there are differences in the initiation of the processes, e.g., different types of PI3K complexes (in autophagy, PI3K III class 1 and 2 types; in LAP PI3K III, class 3 type), usage of reactive oxygen species in LAP, different types of regulatory proteins involved (ULK1, FIP200, ATG13 , Ambra1, WIPI2, ATG14 in autophagy; and Rubicon and NOX2 in LC3-associated phagocytosis), different number of layers in the membrane structure in which lysis occurs (double-membrane autophagolysosome and single-layer membrane in laposomes) clearly depict the variety of canonical and non-canonical autophagy. The two pathways are directed for different types of biological objects, i.e., intracellular pathogens, dysfunctional proteins and organelles in autophagy, and extracellular pathogens, apoptotic bodies, bacteria, utilized in LAP, thus making these mechanisms completely different in their significance.Collectively, the new data indicate that autophagy performed via both canonical and non-canonical pathways, has evolved into a host defense mechanism capable of resisting immunological and pathogenic stress and mediating immunological tolerance to both intra- and extracellular threats. The present review discusses fundamental molecular differences between these mechanisms, as well as their role in immunity, based on the latest literature data.

Metrological Support of Nucleic Acid Sequence Analysis

Metrological support for the process of molecular genetic identification is proposed. An establishment of a nucleotide sequence is the main objective of the DNA/RNA analysis. Such nucleotide sequence provides key information about the role and function of nucleic acids in living systems, as well as the origin of biological objects during molecular genetic identification. The molecular genetic identification is based on the modern methods of studying DNA sequences, which are inherited by the living organisms from generation to generation. In some cases, comparison of DNA sequences is required to establish the authenticity of biological objects, as well as determine biological affiliation or kinship with other biological objects. The problems of metrological support of molecular genetic identification by Sanger DNA sequencing using fluorescent-labeled reaction terminators and capillary electrophoresis are considered. Methods and means of metrological support of the DNA/RNA analysis were developed, which include the determination of a nucleotide as a nucleic acid monomer, the use of a nucleotide sequence of nucleic acids used in certified methods and procedures, the use of a genetic analyzer as a measurement tool along with related auxiliary equipment, as well as the use of a standard sample of a fragment of human mitochondrial DNA has been developed and approved. A Nanofor 05 domestic genome analyzer was tested. The following two procedures were developed and certified: for measuring the nucleotide sequence of the section of the control region of mitochondrial DNA of fish (sturgeon and paddlefish families) by Sanger sequencing, and for measuring the nucleotide sequence of the 5' region of the COI gene of the mitochondrial DNA of aquatic biological resources by Sanger sequencing. Both measurement procedures are based on the use of fluorescent-labeled reaction terminators and capillary electrophoresis. The results are important for use in the DNA studies in the field of biological sciences, food industry, biotechnology, and DNA forensics.

Modern approaches to the application of mathematical modeling methods in biomedical research

This paper presents a brief overview of the main approaches to mathematical modeling of the interaction of optical radiation with biological tissues. In the case of light propagation in tissue, the Monte Carlo method is an approximation of the solution of the radiation transfer equation. This is done by sampling the set of all possible trajectories of light quanta (photon packets) as they pass through the tissue. Such a stochastic model makes it possible to simulate the propagation of light in a turbid (scattering) medium. The main types of interaction between photons and tissue are considered: scattering, absorption, and reflection/refraction at the boundary of the medium. The algorithm of the method is based on the statistical approximation of the estimated parameters instead of using non-linear functional transformations. Efficient methods for modeling the problem of Raman spectroscopy in turbid media are shown, taking into account the parameters of the detector and the sample size. Two fundamental approaches to the numerical simulation of Raman scattering are considered. Based on data from open literary sources, a variant of modeling Raman scattering in normal multilayer human skin in the near infrared wavelength range is shown. The Raman spectra of ex vivo normal skin tissue sections are presented to quantify various intrinsic micro spectral properties of different skin layers. The reconstructed Raman spectrum of the skin is compared with clinically measured skin spectra in vivo. The overall good agreement between the simulated process and experimental data is shown. The possibility of using the sequential Monte Carlo method for data processing in correlation wide-field optical coherence tomography for the study of biological objects is shown.

The Possibilities of Studying Biological Objects on a Pulsed Reactor

The Possibilities of Studying Biological Objects on a Pulsed Reactor

Analysis of the phase images obtained during the collection of a holographic registration system based on the geometric phase effect and a polarization camera

The results of measuring the surface depth of the test object using digital holography are presented. The resulting image was compared to a model based on the calibration slide documentation. In the presented holographic microscope, instead of an eyepiece, a lens with a geometric phase effect is used, which converts a beam with linear polarization into a pair of beams with circular polarizations (diverging and converging). The parallel phase shift method was used to obtain phase distribution. Using a polarization camera, four interferograms corresponding to four different linear projections of interfering waves with right and left circular polarizations were recorded in one exposure. Holograms of a phase object-micrometer were obtained, according to which, by the method of parallel phase shift, the distribution of phase lag introduced by the object was restored. To correct the aberration, subtraction of the recorded phase raid of the illuminating wave — the experimentally obtained phase of the wavefront without an object is used. The developed digital holographic phase microscope based on a geometric phase lens and a polarization camera makes it possible to correctly visualize the surface relief profile. The microscope can be used as a tool for monitoring the state of biological objects exposed to external effects.

The Long Road to a Synthetic Self-Replicating Central Dogma.

The construction of a biochemical system capable of self-replication is a key objective in bottom-up synthetic biology. Throughout the past two decades, a rapid progression in the design of in vitro cell-free systems has provided valuable insight into the requirements for the development of a minimal system capable of self-replication. The main limitations of current systems can be attributed to their macromolecular composition and how the individual macromolecules use the small molecules necessary to drive RNA and protein synthesis. In this Perspective, we discuss the recent steps that have been taken to generate a minimal cell-free system capable of regenerating its own macromolecular components and maintaining the homeostatic balance between macromolecular biogenesis and consumption of primary building blocks. By following the flow of biological information through the central dogma, we compare the current versions of these systems to date and propose potential alterations aimed at designing a model system for self-replicative synthetic cells.

Metrological support of sequence analysis of nucleic acids

Metrological support for the process of molecular genetic identification is provided. An establishment of a nucleotide sequence is the general aim in nucleic acids analysis. A nucleotide sequence of DNA/RNA is the key information which gives an idea of the role and functioning of nucleic acids in living systems, as well as it allows establishing the origin of biological objects during molecular genetic identification. The molecular genetic identification is based on modern methods of research in the sequencing of DNA, which is inherited from generation to next generation of living organisms. DNA sequence comparison in some cases is mandatory to establish the authenticity of biological objects and to determine biological affiliation or kinship with other biological objects. The problems of metrological support of molecular genetic identification by Sanger DNA sequencing using fluorescently labeled reaction terminators and the use of capillary electrophoresis on the example of fish identification are considered. Metrological support of the process includes the use of such definitions as a nucleotide (the nucleic acid monomer), a sequence of nucleotides of nucleic acids. Also, it involves the procedures used in certified methods, a standard sample of a known DNA sequence of an approved type, and a genetic analyzer.Standard Reference Materials of a fragment of human mitochondrial DNA was developed, approved, entered into the Federal registry. The tests of the domestic genetic analyzer Nanophore 05 were carried out. Two measurement procedures “The measurement methodology the partial nucleotide sequence of the control region of mitochondrial DNA of fish (families Acipenseridae and Polyodontidae) by Sanger sequencing with fluorescently-labeled terminators and using capillary electrophoresis” and “The measurement methodology the nucleotide sequence of the 5’ region of the mitochondrial COI gene of water biological resources by Sanger sequencing with fluorescently-labeled terminators and using capillary electrophoresis” were tested and certified. The results are relevant to research in biological sciences, the food industry, biotechnology, and DNA forensics.

The problem of open and tension pneumothorax at the prehospital stage of emergency care and prospects for its solution

The purpose of the study is experimental testing of Russian medical devices for the elimination of tension and open pneumothorax.Objectives of the research. Perform an analysis of the volume of therapeutic measures in the wounded and injured with open and tension pneumothorax. Conduct experimental testing of Russian samples to eliminate tension and open pneumothorax.Materials and methods. A retrospective analysis of the medical histories of 232 patients with polytrauma admitted for treatment at the war surgery department of the Kirov Military Medical Academy in the period from 2015 to 2019. An experimental study was carried out on large biological objects (pigs) to evaluate the effectiveness of eliminating open and tension pneumothorax using products from the UD-02f (paramedic) kit.Results. A retrospective analysis of the medical histories of 232 patients with polytrauma admitted for treatment at the clinic in the period from 2015 to 2019 was carried out. The incidence of tension pneumothorax was 11.6%. In 44.4% of cases, it was eliminated; in 55.6% of the ambulance teams, tension pneumothorax was not eliminated. Open pneumothorax was diagnosed in 21.1% of those admitted at the prehospital stage. In all cases, the elimination of open pneumothorax was carried out by applying an improvised sealing bandage to the chest. An experimental study of the effectiveness of the UD-02f set showed that the use of products included in this set allows to effectively eliminate the life-threatening consequences of wounds and chest injuries.Conclusion. Open and tension pneumothorax are severe life-threatening consequences of chest injuries with a development rate of up to 12.1% and 11.6%, respectively. The inclusion of a set for eliminating tension and open pneumothorax disposable, sterile (paramedical) UD-02f, in the complete equipment and training of medical personnel in the procedure for its use, will allow timely and effective elimination of tension or open pneumothorax at the prehospital stage of emergency medical care.