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Статья посвящена исследованию возможности переноса линий и элементарных геометрических фигур между пространствами, которое привело авторов к совершенно новому представлению об общей геометрии (метагеометрии). В результате, геометрическая теория Евклида и неевклидовы геометрии гармонично слились в единую систему. Попутно была решена проблема определения кривизны пространства. Авторы предлагают очевидное и простое соотношение в качестве критерия оценки кривизны.

The emergence of the new SARS-CoV-2 coronavirus has given rise to many enigmas, to which there are no answers yet. However, the degree of threat to humanity, due to the fact that by the beginning of February 2021, more than 100 million people were ill in the world, of which 2 million died, led to the fact that the efforts of many researchers were aimed at combating this disease, including massive sequencing of the complete genomes of SARS-CoV-2, as this is necessary for diagnostics and prediction of the epidemiological situation, including in the long term. Currently, a fairly high level of conservativeness of the SARS-CoV-2 genome is shown, but there is also a significant variability of intra-host viral RNA, confirming the concept of the existence of quasispecies for RNA-containing viruses. As of February 2021, the complete genomes of almost half a million coronavirus isolates have been sequenced worldwide, and a number of nomenclatures have been proposed to streamline their analysis, including the convenient dynamic nomenclature Pango lineage. Variations of SARS-CoV-2 genomes in the form of consensus SNPs (Single Nucleotide Polymorphism) and intra-host iSNVs (intra-host Single Nucleotide Variant) were demonstrated. Taking into account iSNV and minor mutations, about 85% of the 29.9 thousand nucleotides viral genome were changed at least once, but only a very few of them turned into major mutations due to certain features that ensure the predominant distribution of such strains. The example of the S-protein gene, taking into account iSNV, minor and major mutations, shows its significant variability, which is detected when sequencing hundreds of thousands of SARS-CoV-2 genomes. On the basis of the analysis of 400 complete SARS-CoV-2 genomes isolated on the territory of the Russian Federation during 2020, the dynamics of the circulation of individual strains with acquired major mutations, the representation of which is slightly different from the changes in the SARS-CoV-2 genome in the rest world, is estimated. The possibility of long-term persistence of the new coronavirus in the human body is note, while the reservoirs for the latent existence of SARS-CoV-2, in contrast, for example, to the herpes simple virus, remain unknown. There is no consensus on the possibility of reactivation of SARS-CoV-2 or reinfection. The latter is theoretically possible in cases where SARS-CoV-2 strains belonging to other genetic lineages and clades are found in the body of the "re-infected". This, however, does not exclude the possibility of mutating the virus within a single host. Despite significant progress in monitoring the spread of SARS-CoV-2, many questions remain, but as knowledge of the biology of the new coronavirus accumulates, they will also be answered.

In forensic medicine, it is necessary to establish the sexual identity of the owner of the analyzed biological material. To do this, it is necessary to use PCR to detect specific DNA sequences that are characteristic only of the Y chromosome. For these purposes, a number of loci are used, located on both the Y and X chromosomes but carrying certain differences in the nucleotide sequences (alpha satellites DYZ and DXZ; amelogenin loci AMELY and AMELX; STS steroid sulfatase genes; the genes of the neuroligin NLG4Y and NLG4X, etc.), and those located only on the Y-chromosome (sex-determining region SRY; gene of the specific testicular protein TSPY, etc.). At the same time, forensic experts often deal with damaged or old samples in which the DNA has been destroyed and extended fragments in it may simply not be, as a result of which false negative results will be formed. Thus, in DNA forensics, when detecting gender loci, the sizes of amplicons should tend to the minimum possible. Therefore, in this review article, a certain emphasis was placed on the size of amplicons, and as practice shows, for most loci, their minimization is in demand. Moreover, such a PCR analysis in a number of cases (in XX-men, XY-women, in persons with other sex chromosome abnormalities, in people who deliberately changed their gender identity) it can lead to a false definition of the phenotypic sex due to the genetic characteristics of such individuals. As a result, the ongoing investigation of a crime, focused on the search for a representative of a particular gender, can go down the wrong path. A cardinal solution to this problem in DNA criminology can be a universal DNA registration of the entire population, which will allow for the biological traces with high accuracy to establish a specific person to whom these traces belong and his real sex will no longer be important and it will not be relevant to determine it with the help of PCR. In addition to forensic medicine, the problem of establishing gender also exists in women's sports. For a whole decade, the PCR method and some of the loci listed above were used for this purpose, but since 2011 PCR has been abandoned and instead the level of the male hormone testosterone has became determined. However, with the gender of female athletes, there are much more ethical issues than genetic ones.

Sorghum (Sorghum bicolor (L.) Moench) is one of the world’s leading cereal crops in agricultural production, which has a special importance in the arid regions. However, unlike other cereals, sorghum grain has a lower nutritional value, which is caused, inter alia, by the resistance of its seed storage proteins (kafirins) to protease digestion. One of the effective approaches to improve the nutritional value of sorghum grain is to obtain mutants with partially or completely suppressed synthesis or altered amino acid composition of kafirins. The employment of genome editing may allow to solve this problem by introducing mutations into the nucleotide sequences of the α- and γ-kafirin genes. In this study, genomic target motifs (23 bp sequences) were selected for the introduction of mutations into the α- and γ-KAFIRIN genes of sorghum. The design of the gRNAs was conducted using the online tools CRISPROR and CHOPCHOP. Two most suitable targets were chosen for α-KAFIRIN (k1C5) and two for γ-KAFIRIN (gKAF1) genes. The insertion of respective sequences in the generic vector pSH121 was performed at the BsaI (Eco31I) sites. Validation of the cloning procedure was performed by DNA sequencing. Subcloning of the resulting constructs was performed using the SfiI restriction sites into the compatible binary vector B479p7oUZm-LH. The correct assembly of binary vectors was confirmed by restriction analysis using the MluI and SfiI cleavage sites. The four vectors created (1C - 4C) were transferred by electroporation into the Agrobacterium tumefaciens strain AGL0. Currently, this vector series is used for stable transformation of sorghum using immature embryo explants.

Background. An analysis of the spatial distribution of some taxonomically and ecologically related legumes in the Ural showed a nontrivial spatial distribution of related species of the genus Oxytropis DC of the Orobia Bunge section within the Uchalinsky uplands. Despite the similarities in ecology, these species practically do not grow together. Explicit spatial segregation of closely related plants over a relatively small area allows this phenomenon to be used as a convenient model for studying the effect of segregation of closely related legume species on the genetic composition of their nodule bacteria. Materials and methods. The genetic diversity of nodule bacteria entering into symbiosis with O. kungurensi s, O. baschkiriensis , O. approximata and O. gmelinii plants was studied. In addition, the polymorphism of their symbiotic genes has also been analyzed. Results. Phylogenetic characteristics of nodule bacteria endemic for the Southern Ural belonging to 4 species of leguminous plants of the genus Oxytropis of the section Orobia: O. kungurensis , O. baschkiriensis , O. approximata , O. gmelinii which are characterized by spatial separation of the growth sites, also called plant segregation, are given. It was shown that all of them belong to the genus Mesorhizobium despite certain phylogenetic differences of bacteria. Analysis of the symbiotic genes of the analyzed strains revealed a lack of congruence of their phylogeny with the core part of the genome. It was found that the microsymbionts of O. baschkiriensis plants differ in the phylogeny of nod-genes from nodule bacteria of other plants of the Oxytropis genus and are close to microsymbionts of plants of the Lupinaster genus growing in the Southern Urals. Conclusion. Acquisition of the property to enter into symbiosis with nodule bacteria of plants of the genus Lupinaster may turn out to be an adaptive mechanism that arose as a result of segregation of O. baschkiriensis from other species of Oxytropis .

In 2019, at the World Economic Forum, DNA data storage was indicated as one of the breakthroughs expected to radically impact the global socio-economic order. Indeed, dry DNA is a relatively stable substance and an extremely capacious information carrier. One gram of DNA can hold up to 455 exabytes, provided that one nucleotide encodes two bits of information. In this critical review, the main attention is paid to nucleinography, meaning the conversion of digital data into nucleotide sequences. The evolution and diversity of approaches intended for encoding data with nucleotides are demonstrated. The most noticeable examples of storing minor as well as considerable quantities of non-biological information in DNA are given. Some issues of DNA data storage are also reported.

Polymerase chain reaction (PCR) is the most widely used method for nucleic acids amplification. To date, a huge number of versatile PCR techniques have been developed. One of the relevant goals is to shorten PCR duration, which can be achieved in several ways. Here, we report on the results regarding nucleic acids amplification by convective PCR (cPCR) in standard 0.2 ml polypropylene microtubes. The following conditions were found to be optimal for such amplification: 1) 70 μl reaction volume, 2) the supply of external temperature 145°С for the denaturation zone and 0°С for the annealing zone, 3) ∼30° inclination of the microtube main axis, 4) the use of nearby primers, and 5) duration of the reaction 15-20 min. At these conditions, the amplification products are accumulated in an amount sufficient to be registered by gel electrophoresis, and high sensitivity of the reaction comparable to that of conventional PCR is achieved. cPCR provided the reliable detection of SARS-CoV-2 coronavirus RNA isolated from nasopharyngeal swabs of COVID-19 patients.

CRISPR/Cas technology of genome editing is a powerful tool for making targeted changes in the DNA of various organisms, including plants. The choice of the precise nucleotide sequence (protospacer) in the gene to be edited is important in the design of guide RNA, which can be carried out by specialized software. We review and compare all the known on-line and off-line resources for guide RNA design, with special attention paid to tools capable of searching for off-target edits sites in plant genomes. The use of Cas12a may be preferable to Cas9. Techniques allowing C→T and G→A base editing without DNA cleavage are discussed along with the basic requirements for the design of effective and highly specific guide RNAs. Ways for improving guide RNA design software are presented. We also discuss the lesser risks of off-target editing in plant genomes as opposed to animal genomes. Examples of edited plant genomes including those that do not lead to the creation of transgenic plants are reviewed.

For the first time, summarized data on the production of nine species and ten hybrids of pondweed (Potamogeton, Stuckenia, Potamogetonaceae) are given for ecosystems of small and medium rivers in the north of European Russia. The pondweed is shown to be an important producer of primary organic matter. A significant contribution to primary production in rivers in the region is due to large-size pondweeds and their hybrids, which form dense monodominant stands: P. lucens, P. natans, P. perfoliatus, P. × angustifolius, P. × nitens, P. × salicifolius, P. × sparganiifolius. The production characteristics for the widespread species (P. lucens, P. natans, P. perfoliatus) in the rivers of the region are more than 1.5 times greater than those in reservoirs. Most pondweed species and hybrids show medium productivity and produce

В 2020 году исполнилось 100 лет термину «геном», предложенному немецким ботаником Г.Винклером при описании партеногенеза в растительном и животном царствах. Этимология данного слова неясна, но нам представляется, что Винклер использовал игру слов, соединив морфемы «ген», «сома» и получив “genosom” (нем.), после чего решил удалить один слог, что и привело к краткому и емкому слову «геном», объединяющему гены и составляющем для них нечто целое, что также совпало с окончаниями «–ом» отдельных биологических терминов, обозначающих некое множество (в данном случае для генома – генов). Первоначально под геномом подразумевался гаплоидный набор хромосом, и таким образом хромосомы служили элементарной единицей генома. Сейчас же с появлением возможности секвенировать полный геном его элементарной единицей стала пара нуклеотидов, но и хромосомы оказались задействованными, поскольку нуклеотидные последовательности распределяются в базах данных по хромосомам, когда такое по результатам полногеномного секвенирования становится возможным. На протяжении столетия менялись взгляды ученых, что считать геномом, подразумевая под этим его гаплоидную или диплоидную природу. Сейчас принято считать, что геном - это нуклеотидные последовательности всей совокупности генов и прочих участков ДНК гаплоидного набора хромосом конкретного вида организмов, однако и габитус и функциональное состояние каждого организма определяется его полным диплоидным геномом, тогда как при сборке гаплоидного генома a priori происходит игнорирование тех или иных азотистых оснований в отличающихся аллелях, поскольку выбирается лишь один какой-то нуклеотид, что сразу снижает ценность такого генома, которая все равно очень высока, поскольку секвенирование полных гаплоидных геномов уже очень большого числа видов организмов различного уровня генетической сложности дало весьма важную информацию о Живом. Тем не менее, для персонифицированной медицины будущего нужны знания об исключительно диплоидных геномах людей, получение которых пока представляет серьезную проблему, в отличие от нынешних квази-гаплоидных геномов, которые секвенируются почти массово. Диплоидные геномы растений также представляют интерес, в том числе для CRISPR/Cas геномного редактирования, когда необходимо произвести изменения в обоих аллелях парных хромосом, и для этого знать их возможно отличающиеся нуклеотидные последовательности крайне необходимо. Равно как и по завершении такого редактирования следует с помощью полногеномного диплоидного секвенирования выявить произведенные целевые и нецелевые мутации. Разрабатываемые подходы полногеномного секвенирования, в том числе протяженных участков ДНК вкупе с компьютерными программами, рассчитанными на фазировку данных, недавно вызвали к жизни новый термин «гаплотиг», представляющий собой гаплотип-специфичный контиг. Вне всякого сомнения, все это позволит со временем перейти к уверенному установлению полных диплоидных геномов, что придаст термину «геном» новый смысл, считая его для эукариотических организмов диплоидным, что будет к тому же отражать и саму сущность организации генома, имеющего в норме двуродительскую природу.

This paper presents new data on the species of genus Vaucheria in Russia from analysis of original and museum collections. In total, 20 species were identified in 152 locations of 22 administrative regions of the European Russia, Western Siberia, and the Russian Far East. Vaucheria lii, a rare multiregional species new to Russia, has been found in 6 locations of the Vologda, Moscow, Nizhny Novgorod, Yaroslavl regions and North Ossetia. V. cruciata, V. schleicheri, V. taylorii, V. uncinata were recorded for the European Russia for the first time. V. birostris and V. pseudogeminata are new records for Western Siberia. Rank of V. terrestris var. nuoljae was raised up to separate species with V. terrestris var. major as a new synonym. The distributions of the frequently reported species, V. dichotoma and V. geminata, are critically analyzed.

Specific amplification of nucleic acids is a convenient and quick alternative to the culture-based method of detecting bacterial cells. However, conventional PCR and other amplification reactions can not differentiate between live bacteria and dead or dormant ones, and are also capable of amplifying DNA that persists for a long time and in a cell-free state. Several methods have been developed in order to establish the viability of microorganisms by amplification of specific sequences of nucleic acids, both those controlled by changing temperatures and isothermal ones. For some of them, DNA modified by phenanthridine dyes serves as a target, and simultaneous use of monoazides of ethidium and propidium was shown to be preferable for the purpose. For other methods, the targets are directly RNA molecules or their cDNA copies. Pre-rRNA detection seems to be the most preferable approach, due to the presence of these types of RNA exclusively in living cells.

The paper considers the problematic aspects of detecting a new coronavirus infection using RT-PCR, which often lead to false negative diagnostic results, which occur both at the preanalytic stage and during nucleic acid amplification, including the interpretation of the obtained data. The viral load in humans was evaluated and assumptions were made about the expected number of viral particles in the studied oropharyngeal and nasopharyngeal samples. The list of diagnostic test systems approved for use in the Russian Federation for detecting SARS-CoV-2 with their brief characteristics is given. The necessity of simultaneous use of several targets in the coronavirus genome in one test system detected by probes with the same fluorochrome is noted, which on the one hand increases the probability of detection by increasing the signal, and on the other hand eliminates the false negative results that could occur in the case of mutations in the virus genome at the sites of annealing primers and hybridization probes.

The study considers the history of establishment, current condition and perspective of the legislative regulation in establishing and functioning of national DNA database systems in some European and Asian countries. The authors study the peculiarities in establishing systems of DNA registration regarding a case study of Great Britain, China and the USA as the countries having a considerable experience in this field and the biggest national DNA databases. Thus, the main developmental characteristics in the forensic registration of these countries are identified. The aim of the study is to examine the theoretical aspects of the legislative regulation in establishing and functioning of national DNA database systems including the purposes to create the best model of the legislative regulation to meet the requirements of a modern society. The gaps in the state regulation of genomic registration are noted. It is determined that the existing laws and regulations in Russia do not completely satisfy the demands of the times for they considerably limit the sphere of application of DNA registration systems. As a result, the real potential of the DNA registration system in Russia is identified. Consequently, it will assist in establishment of a more effective model of DNA registration system taking into account the world’s experience. Regulatory developments in legal activities as ways to improve legislative regulation of the genomic registration in Russia are set.

CRISPR/Cas genome editing of plants is realized in three basic variants, including knockout mutations as indels, insertion of alien DNA fragments, and base editing via deamination of nitrogenous bases. The most important stages of the CRISPR/Cas-based genome editing are the choice of a target site, design of guide RNAs, creation of genetically engineered constructions, and delivery of CRISPR/Cas components into a plant cell. Rapid developments in the field of plant genome editing with the use of CRISPR/Cas systems requires more detailed consideration of the last stage, so this review is dedicated to the description of the main ways to deliver CRISPR/Cas components into cells of higher plants. In the first studies on the genome editing of different plant species, these components were delivered to the target site mainly by Agrobacterium tumefaciens. This approach supposes integration of T-DNA into a genome and a stable expression of CRISPR/Cas components or their transient expression in the case of agroinfiltration. Another widespread approach included the use of plant viruses as delivery platforms; in this case, viruses were used mainly for production of an increased amount of guide RNAs that significantly improved the efficiency of genome editing. Another approach provides for the use of another bacterium, A. rhizogenes, as a platform for delivery of CRISPR/Cas components. This bacterium induces hairy root formation that may be an indirect confirmation of successful genome editing and assist in the selection of genetically modified forms. Other common ways to obtain genetically edited plants are the biolistic delivery of genetically engineered constructions into explants and various protoplast transformation technologies. The review also considers some issues transgenic and GM status of CRISPR/Cas-edited plants to transgenic and GM plants. There are a number of cases in which new organisms created by a CRISPR/Cas genome editing without any introduction of alien DNA were not considered as transgenic ones; it is quite possible that such plants will not fall under Russian legislation prohibiting GMO cultivation.

Aim and Objective:Antibiotic resistance is a serious constraint to the development of new effective antibacterials. Therefore, the discovery of the new antibacterials remains one of the main challenges in modern medicinal chemistry. This study was undertaken to identify novel molecules with antibacterial activity.Materials and Methods:Using our unique double-reporter system, in-house large-scale HTS campaign was conducted for the identification of antibacterial potency of small-molecule compounds. The construction allows us to visually assess the underlying mechanism of action. After the initial HTS and rescreen procedure, luciferase assay, C14-test, determination of MIC value and PrestoBlue test were carried out.Results:HTS rounds and rescreen campaign have revealed the antibacterial activity of a series of Nsubstituted triazolo-azetidines and their isosteric derivatives that has not been reported previously. Primary hit-molecule demonstrated a MIC value of 12.5 µg/mL against E. coli Δ tolC with signs of translation blockage and no SOS-response. Translation inhibition (26%, luciferase assay) was achieved at high concentrations up to 160 µg/mL, while no activity was found using C14-test. The compound did not demonstrate cytotoxicity in the PrestoBlue assay against a panel of eukaryotic cells. Within a series of direct structural analogues bearing the same or bioisosteric scaffold, compound 2 was found to have an improved antibacterial potency (MIC=6.25 µg/mL) close to Erythromycin (MIC=2.5-5 µg/mL) against the same strain. In contrast to the parent hit, this compound was more active and selective, and provided a robust IP position.Conclusion:N-substituted triazolo-azetidine scaffold may be used as a versatile starting point for the development of novel active and selective antibacterial compounds.

We present current information on the conservation of aquatic vascular plants in West and East Siberia and the Russian Far East. This includes the region from the Ural Mountains in the west to the eastern seaboard of Russia from Kamchatka and Chukotka in the north to Vladivostok in the south, including Sakhalin, the Kuril and Commander Islands. A list of aquatic vascular plant species protected in the region is presented with an indication of their conservation status derived from regional Red Data Books, combined with population trend data from the literature, as well as field observations made by the authors. The region as a whole supports a total of 246 aquatic plant species, of which 96 are listed as threatened in regional Red Lists. The main threats to these species are habitat degradation, eutrophication and pollution of water bodies as a consequence of human activity and climate change. Many species which are specialized, relict or endemic, and others occurring here on the edge of their range, are vulnerable because of these factors. The main conservation action needed includes protection of natural habitats, establishment of monitoring protocols for the most severely threatened species and research into the autecology of threatened species. There is also a need to resolve taxonomic questions obstructing conservation.

Spasticity in patients with cerebral palsy (CP) is the main impediment to normal locomotion. The function of the Central Pattern Generator (CPG), i.e. a group of neural chains in the spinal cord, stands at the core of any rhythmical movement. CPG can generate locomotion patterns without supraspinal control, which can have both positive and negative impact on the ability to move. Performing the motor tasks such as walking, running and swimming, creates the consistent rhythmical movement of legs and arms through interaction between CPGs of upper and lower extremities. This interaction can cause the activation of pathological movement patterns in lower extremities in response to upper limb spasticity. Thus, neural chains in the spinal cord become the generator of pathologically increased excitation which has developed as a result of a focal lesion in the CNS. All the statements described above show the importance of introducing the upper limb injections of bFotulinum toxin A in the protocol in order to develop normal locomotion. The PUL study approved the optimal level of efficacy and favourable safety profile of botulinum toxin A in children with CP and upper limb muscle spasticity.Спастичность при детском церебральном параличе — основное препятствие для полноценной локомоции. В основе любого ритмичного движения, в том числе ходьбы, лежит работа генератора центральных паттернов (CPG) — нейронных цепей в спинном мозге. CPG в отсутствие надспинального контроля способен генерировать локомоторные паттерны самостоятельно, что может влиять на способность к перемещению как положительно, так и отрицательно. Выполнение двигательных задач, таких как ходьба, бег и плавание, приводит к ритмичному движению рук вместе с ногами посредством связи между CPG верхних и нижних конечностей. Эта связь может быть причиной активации патологических двигательных паттернов нижней конечности в ответ на спастику в верхней конечности. Таким образом, нейронные цепи спинного мозга становятся генератором патологически усиленного возбуждения, сформированного в результате очагового органического поражения ЦНС. Вышеперечисленные положения указывают на необходимость включать в протокол инъекций ботулинического токсина типа А (БТА) верхнюю конечность с целью формирования правильной локомоции. На основании исследования PUL подтверждены оптимальный уровень эффективности и благоприятный профиль безопасности применения препарата БТА (абоботулотоксина) у детей с детским церебральным параличом со спастичностью мышцы верхней конечности.

— Detection and quantification of biotargets are important analytical tasks, which are solved using a wide range of various methods. In recent years, methods based on the isothermal amplification of nucleic acids (NAs) have been extensively developed. Among them, a special place is occupied by rolling circle amplification (RCA), which is used not only for the detection of a specific NA but also for the analysis of other biomolecules, and is also a versatile platform for the development of highly sensitive methods and convenient diagnostic devices. The present review reveals a number of methodical aspects of RCA-mediated analysis; in particular, the data on its key molecular participants are presented, the methods for increasing the efficiency and productivity of RCA are described, and different variants of reporter systems are briefly characterized. Differences in the techniques of RCA-mediated analysis of biotargets of various types are shown. Some examples of using different RCA variants for the solution of specific diagnostic problems are given.

Mutagenesis of Triticum sinskajae was performed using sodium azide. The optimal concentration was 0.1 mM. Changes were observed in the length of the spike and stem in the experimental plants as compared with the control ones.

Tobacco hairy roots with constitutive expression of the NtEXPA5 expansin gene were obtained and analyzed, which were characterized by higher growth rates and increased productivity under normal conditions, as well as the action of stress factors.

Experiments on CRISPR/Cas9 mediated knock-in approaches in the PDS gene of various genes of interest were planned. Biolistic bombardment mediated delivery of target vectors to plant explants was suggested.

The genetic diversity and phylogeny of root nodule bacteria, microsymbionts of plants of the genus Lupinaster Adans. (L. albus Link and L. pentaphyllus Moench), were studied, and also their symbiotic genes were analyzed. The bacterial strains studied were shown to be phylogenetically different; however, all of them are related to the Mezorhizobium genus with the exception of the single strain which is related to the Rhizobium genus. Analysis of the symbiotic genes nifH and nodC revealed their high homology among all strains independently of strain phylogeny, as well as the phylogenetic relation of these genes to those of Mezorhizobium. Mezorhizobium bacteria are likely specific microsymbionts of these plants, while the Rhizobium strain acquired its symbiotic genes and became capable of nodule formation in Lupinaster plants through horizontal gene transfer. Thus, the genetic composition of nodule bacteria inhabiting Lupinaster plants represents additional support for the idea that they do not belong to the Trifolium genus.