The production of fats and oils represents a task that is in demand in a variety of industries, including the food industry. Presently, the predominant method of acquiring them is through the processing of plant and animal products, a process that substantially increases the cost of production at all stages. Oleaginous yeasts can serve as an alternative source for obtaining edible oils, as demonstrated by yeast strains employed in the development of palm oil analogues. In this study, we created and characterized a collection of oil-producing yeast species obtained from various natural sources. These species were identified using MALDI-TOF and Sanger sequencing. The isolates were qualitatively and quantitatively tested for their ability to grow on various culture media compositions. The oil-producing strains were characterized by their fatty acid profile and lipidome composition. In addition, we evaluated the biotechnological potential of these organisms as producers of fatty acid- and fat-related products. As a result, the collection contains 100 strains, 31 of which are oleaginous yeasts, and three strains show potential as promising producers of edible oil analogues. Our research demonstrates the benefits of searching for and studying natural yeast strains, both from a fundamental science perspective and for the creation of future innovative biotechnological solutions in the food industry.

The white poplar (Populus alba L.) is an economically significant tree species with a natural distribution spanning an extensive region of Eurasia. Nevertheless, there is currently no hypothesis regarding the historical shaping of this range. In this study, we collected and sequenced 36 individuals of white poplar from disparate regions of Russia and Kazakhstan. Additionally, we employed available genomic data of white poplars from Italy, Hungary, and China. A genomic approach was employed to collate data on the location of glaciers in different periods, along with information on the natural and artificial distribution of white poplar. This enabled the formulation of the first hypothesis regarding the formation of the modern range of this plant. It is hypothesized that during the period of maximum glaciation, three refugia existed: the South European, Transcaucasian, and Altai–Middle Asian refugia. Postglacial migration from these refugia led to the formation of modern populations of P. alba in Eastern Europe (including the European part of Russia), the Caucasus, and Siberia, respectively.

The black garden ant (Lasius niger) is a widely distributed species across Europe, North America, and North Africa, playing a pivotal role in ecological processes within its diverse habitats. However, the microbiome associated with L. niger remains poorly investigated. In the present study, we isolated a novel species, Paenarthrobacter lasiusi, from the soil of the L. niger anthill. The genome of P. lasiusi S21 was sequenced, annotated, and searched for groups of genes of physiological, medical, and biotechnological importance. Subsequently, a series of microbiological, physiological, and biochemical experiments were conducted to characterize P. lasiusi S21 with respect to its sugar metabolism, antibiotic resistance profile, lipidome, and capacity for atmospheric nitrogen fixation, among others. A notable feature of the P. lasiusi S21 genome is the presence of two prophages, which may have horizontally transferred host genes involved in stress responses. P. lasiusi S21 synthesizes a number of lipids, including mono- and digalactosyldiacylglycerol, as well as steroid compounds that are typically found in eukaryotic organisms rather than prokaryotes. P. lasiusi S21 exhibits resistance to penicillins, lincosamides, fusidins, and oxazolidinones, despite the absence of specific genes conferring resistance to these antibiotics. Genomic data and physiological tests indicate that P. lasiusi S21 is nonpathogenic to humans. The genome of P. lasiusi S21 contains multiple operons involved in heavy metal metabolism and organic compound inactivation. Consequently, P. lasiusi represents a novel species with an intriguing evolutionary history, manifesting in distinctive genomic, metabolomic, and physiological characteristics. This species may have potential applications in the bioaugmentation of contaminated soils.

Non-pathogenic natural and recombinant strains of human Enteroviruses are the subject of ongoing study with some strains having been approved for use as anticancer agents. The efficacy of oncolytic virotherapy depends upon identifying the receptor utilized by a specific strain for cell entry, and the presence of this receptor on the surface of cancer cells. Accordingly, a rapid and straightforward approach to determining the enteroviral receptors is necessary for developing an effective patient-specific, virus-based cancer therapy. To this end, we created a panel of seven lines with double knockouts on the background of the HEK293T cell line, which lacks the IFNAR1 gene. In these lines, the main viral receptor genes, including PVR, CXADR, CD55, ITGA2, SCARB2, ICAM1, and FCGRT, were knocked out using the CRISPR/Cas9 system. The panel of lines was validated on twelve different Enteroviruses types, providing a basis for studying the molecular mechanisms of enterovirus entry into cells, and for developing new therapeutic strains.

Herpes simplex virus type 1 (HSV-1), newly named as Simplexvirus humanalpha1 is one of the most common pathogens in the human population, which can cause severe disease, often with fatal outcomes. Diagnostic methods currently in use are specific and sensitive, but time-consuming, require expensive laboratory equipment and highly qualified personnel. Existing therapeutic agents have a number of significant drawbacks. To successfully treat and prevent the spread of the infection, new rapid, easy-to-use, and highly sensitive diagnostic tools and effective therapeutic agents are required. One approach to achieve this goal is CRISPR-based technology. This review analyzes information obtained from a literature search in the Scopus, Web of Science and MedLine databases on the topics «HSV-1, structure, distribution, life cycle», «new methods for molecular diagnosis of HSV-1-infection», «classification of CRISPR-Cas systems», «nucleic acid amplification methods», «CRISPR-Cas effector proteins», «application of CRISPR-Cas systems in molecular diagnostics of HSV-1-infection», «application of CRISPR-Cas systems in therapy of HSV-1-infection». New approaches of CRISPR using effector proteins Cas12 and Cas13 in the diagnosis of HSV-1 infections are reviewed. The article discusses the progress in the development of CRISPR-Cas-based therapies against HSV-1-infection in vitro and in vivo. CRISPR gene therapy in vivo has a great clinical potential, but its safety and efficacy require further investigation. An analysis of the available data suggests that CRISPR-based technologies offer promising prospects for expanding the arsenal of diagnostic tools and antiviral drugs in the context of current and future outbreaks of viral diseases.

Schizophrenia is a severe mental disorder whose etiology and pathogenesis are significantly influenced by hereditary factors. Genome-wide association studies have shown that most genetic variants associated with high risk of schizophrenia are located in the regulatory regions of genes. This brief review presents data on the general structure of the major regulatory regions of genes, focusing on enhancers, i.e., regions of the genome which enhance gene activity. The involvement of transcription factors interacting with the regulatory regions of genes in various molecular and cellular processes whose disruption is associated with the pathogenesis of schizophrenia is considered in detail.

The Al-1Fe-1Zr alloy exploits the non-equilibrium solidification dynamics inherent to laser powder bed fusion, characterized by high thermal gradients and rapid solidification front velocities. Here, we investigate the alloy's 3D microstructure using state-of-the-art synchrotron-based nano-tomography techniques. High-resolution holographic and near-field ptychographic X-ray computed tomography were employed, achieving spatial resolutions as small as 57 nm. Our comparative analysis shows that near-field ptychographic tomography offers superior signal-to-noise ratio and spatial resolution, while holographic tomography allows for faster data acquisition with minimal loss in quality. These methods reveal the 3D distribution, morphology, and interconnectivity of Fe-rich and Zr-rich intermetallic phases. Complementary X-ray fluorescence computed tomography further provides quantitative local information on elemental wt%, revealing Fe and Zr distribution with a resolution of 0.1 wt%. The findings highlight key microstructural features that contribute to the alloy's enhanced strength and thermal conductivity, offering critical insights for optimizing its performance in LPBF applications.

Residents of the International Space Station (ISS) are various types of bacteria that can act as potential biodegraders of structural materials, which entails disruptions in the operation of various equipment and, indirectly, provoke medical risks and affect the health of crew members with reduced immunity. Since the beginning of ISS exploitation sanitary and microbiological monitoring of the habitat has been carried out for the purpose of timely detection and inactivation of potentially dangerous strains. The study was conducted to investigate the dynamics of the composition and number of bacterial strain species detected on the internal surfaces of the ISS interior and equipment for the period covering from Expedition 46 to Expedition 67 (2016–2022). Samples collected from ISS interior surfaces were grown on nutrient media. Strains were identified by 16S RNA sequencing and MALDI-TOF analysis. The results obtained showed that the number of bacterial community species increases with the increase of the ISS RS operation period. However, this growth was not linear, but was a wave-like repetitive process of changing phases of activation and stagnation of the microbiome. During the period of work of Expeditions 46-67, species of the genera Bacillus and Staphylococcus dominated in the microbiome. Among representatives of the genus Bacillus, the species B. licheniformis dominated. The predominance of bacteria of this genus, apparently, is due to their high resistance to physical and chemical parameters of the ISS habitat, including DNA-damaging factors, such as increased radiation background, which, in turn, can be explained by their ability to spore formation. The results obtained once again indicate the high evolutionary plasticity of B. licheniformis strains, which we discovered earlier in other studies.

It is estimated that nearly all individuals have been infected with herpesviruses, with herpes simplex virus type 1 (HSV-1) representing the most prevalent virus. In most cases, HSV-1 causes non-life-threatening skin damage in adults. However, in patients with compromised immune systems, it can cause serious diseases, including death. The situation is further complicated by the emergence of strains that are resistant to both traditional and novel antiviral drugs. It is, therefore, imperative that new methods of combating HSV-1 and other herpesviruses be developed without delay. CRISPR/Cas systems may prove an effective means of controlling herpesvirus infections. This review presents the current understanding of the underlying molecular mechanisms of HSV-1 infection and discusses four potential applications of CRISPR/Cas systems in the fight against HSV-1 infections. These include the search for viral and cellular genes that may serve as effective targets, the optimization of anti-HSV-1 activity of CRISPR/Cas systems in vivo, the development of CRISPR/Cas-based HSV-1 diagnostics, and the validation of HSV-1 drug resistance mutations.

Harnessing of CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR-associated genes) systems for detection, chemical modification, and sequence editing of nucleic acids dramatically changed many fields of fundamental science, biotechnology, and biomedicine [...]

The piezoelectric response is a measure of the sensitivity of a material's polarization to stress or its strain to an applied field. Using in-operando x-ray Bragg coherent diffraction imaging, we observe that topological vortices are the source of a five-fold enhancement of the piezoelectric response near the vortex core. The vortices form where several low symmetry ferroelectric phases and phase boundaries coalesce. Unlike bulk ferroelectric solid solutions in which a large piezoelectric response is associated with coexisting phases in the proximity of the triple point, the largest responses for pure BaTiO3 at the nanoscale are in spatial regions of extremely small spontaneous polarization at vortex cores. The response decays inversely with polarization away from the vortex, analogous to the behavior in bulk ceramics as the cation compositions are varied away from the triple point. We use first-principles-based molecular dynamics to augment our observations, and our results suggest that nanoscale piezoelectric materials with large piezoelectric response can be designed within a parameter space governed by vortex cores. Our findings have implications for the development of next-generation nanoscale piezoelectric materials.

The Cas9 endonuclease of the CRISPR/Cas type IIA system from Streptococcus pyogenes is the heart of genome editing technology that can be used to treat human genetic and viral diseases. Despite its large size and other drawbacks, S. pyogenes Cas9 remains the most widely used genome editor. A vast amount of research is aimed at improving Cas9 as a promising genetic therapy. Strategies include directed evolution of the Cas9 protein, rational design, and domain swapping. The first generation of Cas9 editors comes directly from the wild-type protein. The next generation is obtained by combining mutations from the first-generation variants, adding new mutations to them, or refining mutations. This review summarizes and discusses recent advances and ways in the creation of next-generation genomic editors derived from S. pyogenes Cas9. Key points • The next-generation Cas9-based editors are more active than in the first one. • PAM-relaxed variants of Cas9 are improved by increased specificity and activity. • Less mutagenic and immunogenic variants of Cas9 are created.

Using lab-based operando X-ray and post-mortem techniques, researchers visualize the origins of electrochemical capacity fade under high-voltage conditions in pilot line single-crystalline LiNi${}_{0.8}$Mn${}_{0.1}$Co${}_{0.1}$O${}_{2}$-graphite cells.

—The study of molecular and genetic mechanisms of sex determination in the poplar is of interest not only in the fundamental science, but also in the applied research. In landscaping of large settlements, it is advisable to use male individuals of the Populus genus due to their hypoallergenicity and increased resistance to environmental pollution, stress conditions, and pathogens. However, sex determination in poplars is complicated by the complex genetic structure of the sex-determining region of the genome (SDR). In this review, the emergence, evolution, structure, and function of the SDR in the genus Populus are discussed. Current insights into the structure and function of the key regulator of sex selection in poplars, orthologue of the ARR16 / ARR17 gene and the possible roles of other genes that are differentially expressed between male and female plants, including microRNAs, in this process are discussed in detail. The great diversity of species and the high complexity of SDR organization justify the need for further study of the molecular mechanisms of sex determination in poplars.

The white poplar (Populus alba) is a dioecious woody plant with significant potential for the phytoremediation of soils. To realize this potential, it is necessary to utilize growth-promoting microorganisms. One potential source of such beneficial microorganisms is the rhizosphere community of wild-growing trees. However, the structure, dynamics, and metabolism of the rhizosphere community of wild-growing white poplar remain poorly understood. To ascertain seasonal dynamics, species diversity, and metabolic potential, we sequenced 16S rRNA genes in metagenomes derived from 165 soil samples collected in spring and autumn from the root surfaces of 102 trees situated in disparate geographical locations. The three most prevalent phyla across all samples are Proteobacteria, Actinobacteriota, and Acidobacteriota. At the order level, the most prevalent orders are Sphingomonadales and Rhizobiales. Accordingly, the families Sphingomonadaceae and Rhizobiaceae were identified as dominant. The rhizospheric microbiome exhibited substantial inter-seasonal variation. Six families, including Caulobacteraceae, Xanthomonadaceae, Chitinophagaceae, Chthoniobacteraceae, Sphingomonadaceae, and Rhizobiaceae, exhibited alterations (spring-to-autumn) across all geographical locations under study. Members of the Rhizobiaceae family, which includes nitrogen-fixing bacteria, can provide poplar with plant-available forms of nitrogen such as nitrate and ammonium. The rhizosphere microbiome may facilitate the conversion of inorganic sulfur into sulfur-containing amino acids, cysteine and methionine, that are bioavailable to plants. Furthermore, the rhizosphere microbiome is capable of synthesizing amino acids, organic acids (including Krebs cycle acids), and some lipids and sugars. Consequently, the rhizosphere community can stimulate poplar growth by providing it with readily available forms of nitrogen and sulfur, as well as building blocks for the synthesis of proteins, nucleic acids, and other macromolecules. Many of these pathways, including nitrogen fixation, were subjected to seasonal changes.

Bacillus cereus sensu lato comprises genetically, morphologically, and physiologically similar gram-positive spore-forming bacterial species with high pathogenic potential, such as B. anthracis, B. cereus, and B. thuringiensis. Toxin-producing strains of B. cereus s.I. pose a major threat to human health. The high degree of similarity between these species makes it very difficult to identify them and to take adequate measures to treat the diseases they cause. Previously, we characterized the clinical isolate CCGC 19/16 belonging to B. cereus s.l. that exhibited features of both B. cereus and B. cytotoxicus. In the present work, CCGC 19/16 was identified as B. cytotoxicus using multilocus sequence typing (MLST) and mass spectrometric analysis. It was also shown that, unlike other representatives of the B. cytotoxicus species, strain CCGC 19/16 is not thermotolerant. Unlike B. cereus, strain CCGC 19/16 is sensitive to most antibiotics and shows increased motility. Like B. cereus strain CCGC 19/16 forms β-hemolysis zones in blood agar. In addition, it has been shown that prolonged storage of samples prior to analysis can lead to misidentification of the isolate. Our results indicate that "rapid methods" of analysis using single genes have insufficient resolving power in the identification of B. cereus s.l. species. The combination of MLST analysis with MALDI-TOF MS provides sufficient resolution.

Coking is a common catalyst deactivation route in industrial processes involving carbonaceous species. While coking is easy to diagnose, this is often performed by bulk analysis. Understanding specific symptoms such as pore blockage and obstruction of active sites is especially challenging for technical catalysts and requires a spatially-resolved approach. Here a combination of ptychographic X-ray computed tomography (PXCT) and X-ray fluorescence nanotomography (XRF-CT) could identify and allocate regions of coke deposition within a technical zeolite-based propane dehydrogenation catalyst. PXCT is sensitive to the quantitative electron density of the sample, therefore indirectly visualising coke deposition in meso- and macropores with 56-61 nm 3D spatial resolution. For more direct visualisation the catalysts were treated with Cu solution as fluorescent marker, whereby complementary XRF-CT analysis could distinguish accessible and blocked pores based on the presence or absence of adsorbed Cu. This strategy was used to assess coking as a function of time on stream, to evaluate coke removal by oxidative regeneration, and to distinguish the presence of coke deposits separately within the zeolite and binder components. This strategy is applicable to virtually any porous solid catalyst and can deliver previously unknown insights into the common phenomenon of coke deposition particularly in technical catalysts. X-ray nanotomography visualises and distinguishes coke deposition sites within individual components of a technical catalyst composite. An accurate nanoscale view of catalyst deactivation and regeneration is achieved. image

Objective: Multidrug-resistant, highly pathogenic Escherichia coli strains are the primary causative agents of intestinal and extraintestinal human diseases. The extensive utilization of antibiotics for farm animals has been identified as a contributing factor to the emergence and dissemination of E. coli strains that exhibit multidrug resistance and possess high pathogenic potential. Consequently, a significant research objective is to examine the genetic diversity of pathogenic E. coli strains and to identify those that may pose a threat to human health. Methods: In this study, we present the results of genome sequencing and analysis, as well as the physiological characterization of E. coli strain APEC 36, which was isolated from the liver of a broiler chicken with generalized colibacillosis. Results: We found that APEC 36 possess a number of mechanisms of antibiotic resistance, including antibiotic efflux, antibiotic inactivation, and antibiotic target alteration/replacement/protection. The most widely represented group among these mechanisms was that of antibiotic efflux. This finding is consistent with the strain’s documented resistance to multiple antibiotics. APEC 36 has an extremely rare variant of the beta-lactamase CTX-M-169. Notwithstanding the multitude of systems for interfering with foreign DNA present in the strain, seven plasmids have been identified, three of which may possess novel replication origins. Additionally, qnrS1, which confers resistance to fluoroquinolones, was found to be encoded in the genome rather than in the plasmid. This suggests that the determinants of antibiotic resistance may be captured in the genome and stably transmitted from generation to generation. Conclusions: The APEC 36 strain has genes for toxins, adhesins, protectins, and an iron uptake system. The obtained set of genetic and physiological characteristics allowed us to assume that this strain has a high pathogenic potential for humans.

Proteasome inhibitors are used in the therapy of several cancers, and clinical trials are underway for their use in the treatment of glioblastoma (GBM). However, GBM becomes resistant to chemotherapy relatively rapidly. Recently, the overexpression of ribonucleotide reductase (RNR) genes was found to mediate therapy resistance in GBM. The use of combinations of chemotherapeutic agents is considered a promising direction in cancer therapy. The present work aimed to evaluate the efficacy of the combination of proteasome and RNR inhibitors in yeast and GBM cell models. We have shown that impaired proteasome function results in increased levels of RNR subunits and increased enzyme activity in yeast. Co-administration of the proteasome inhibitor bortezomib and the RNR inhibitor hydroxyurea was found to significantly reduce the growth rate of S. cerevisiae yeast. Accordingly, the combination of bortezomib and another RNR inhibitor gemcitabine reduced the survival of DBTRG-05MG compared to the HEK293 cell line. Thus, yeast can be used as a simple model to evaluate the efficacy of combinations of proteasome and RNR inhibitors.