Interaction of Solanum tuberosum L. translation initiation factors eIF4E with potato virus Y VPg: Apprehend and avoid.

Potato virus Y (PVY) is one of the most dangerous agricultural pathogens that causes substantial harm to vegetative propagated crops, such as potatoes (Solanum tuberosum L.). A necessary condition for PVY infection is an interaction between the plant cap-binding translation initiation factors eIF4E and a viral protein VPg, which mimics the cap-structure. In this study, we identified the point mutations in potato eIF4E1 and eIF4E2 that disrupt VPg binding while preserving the functional activity. For the structural interpretation of the obtained results, molecular models of all the studied forms of eIF4E1 and eIF4E2 were constructed and analyzed via molecular dynamics. The results of molecular dynamics simulations corresponds to the biochemical results and suggests that the ß1ß2 loop plays a key role in the stabilization of both eIF4E-cap and eIF4E-VPg complexes.

Acute Kidney Injury in Hospitalized Patients with COVID-19: Risk Factors and Serum Biomarkers.

BACKGROUND: AKI is one of the COVID-19 complications with high prognostic significance. In our research, we studied the prognostic role of several biomarkers that could help us understand AKI pathogenesis in patients with COVID-19. METHODS: We evaluated the medical data of 500 patients hospitalized with COVID-19 in Tareev Clinic from 5 October 2020 to 1 March 2022. The diagnosis of COVID-19 was confirmed with positive RNA PCR in nasopharyngeal swabs and/or typical radiological findings on CT scans. Kidney function was assessed in accordance with KDIGO criteria. In the selected 89 patients, we evaluated serum levels of angiopoetin-1, KIM-1, MAC, and neutrophil elastase 2 and their prognostic significance. RESULTS: The incidence of AKI in our study was 38%. The main risk factors for kidney injury were male sex, cardiovascular diseases, and chronic kidney disease. High serum angiopoetin-1 levels and a decrease in blood lymphocyte count and fibrinogen level also increased the risk of AKI. CONCLUSIONS: AKI is an independent risk factor for death in patients with COVID-19. We propose the prognostic model of AKI development, which includes the combination of serum levels of angiopoetin-1 and KIM-1 on admission. Our model can help to prevent AKI development in patients with coronavirus disease.

How temperature-dependent silicate weathering acts as Earth's geological thermostat.

Earth's climate may be stabilized over millennia by solubilization of atmospheric carbon dioxide (CO2) as minerals weather, but the temperature sensitivity of this thermostat is poorly understood. We discovered that the temperature dependence of weathering expressed as an activation energy increases from laboratory to watershed as transport, clay precipitation, disaggregation, and fracturing increasingly couple to dissolution. A simple upscaling to the global system indicates that the temperature dependence decreases to ~22 kilojoules per mole because (i) the lack of runoff limits weathering and retains base metal cations on half the land surface and (ii) other landscapes are regolith-shielded and show little weathering response to temperature. By comparing weathering from laboratory to globe, we reconcile some aspects of kinetic and thermodynamic controls on CO2 drawdown by natural or enhanced weathering.

Assessment of academic achievements in m-learning.

The paper analyzes the teaching experiment regarding the use of mobile apps in the assessment of student learning. The study involved survey and self-description methods offered to students and instructors to assess the effectiveness of using mobile apps in learning. The study was conducted among 320 s-year students of the I.M. Sechenov First Moscow State Medical University and 8 instructors between September 1 and December 28, 2021, during the academic semester. Socrative and Plickers apps have been found to contribute to: better learning (φ* = 8.94, p ≤ 0.01); developing cognitive motivation among students resulting from diverse learning resources used with apps (φ* = 7.6, p ≤ 0.01); convenience of learning activities because students can work with the app both in the classroom and at home (φ* = 13.66, p ≤ 0.01); improved digital competence (φ* = 2.4, p ≤ 0.05). The research findings can be used by instructors in universities and secondary schools. Since didactic opportunities offered by mobile apps are quite significant, and considering other positive results of their use, this technology may be considered as an important tool for training young people and strengthening their cognitive motivation.

Development of potato (Solanum tuberosum L.) plants with StLEAFY knockout.

MAIN CONCLUSION: StLFY-knockout potato plants were developed using CRISPR/Cas9 system. Inflorescences of edited plants transited to flowering, but inflorescence structures lacked flowers and were indeterminate, producing multiple shoot meristems. The tetraploid potato (Solanum tuberosum L.) is an important agricultural crop worldwide. In this study, we used CRISPR/Cas9 to inactivate the potato homolog (StLFY) of the LEAFY gene-a key regulator of the transition to flowering and floral meristem identity-in a tetraploid potato cultivar. We achieved high rates of all-allelic knockouts. Frameshift indels led to phenotypic alterations, including indeterminate inflorescence development and the replacement of flowers with the leafy-like structures.

Potential Urine Proteomic Biomarkers for Focal Segmental Glomerulosclerosis and Minimal Change Disease.

Primary focal segmental glomerulosclerosis (FSGS), along with minimal change disease (MCD), are diseases with primary podocyte damage that are clinically manifested by the nephrotic syndrome. The pathogenesis of these podocytopathies is still unknown, and therefore, the search for biomarkers of these diseases is ongoing. Our aim was to determine of the proteomic profile of urine from patients with FSGS and MCD. Patients with a confirmed diagnosis of FSGS (n = 30) and MCD (n = 9) were recruited for the study. For a comprehensive assessment of the severity of FSGS a special index was introduced, which was calculated as follows: the first score was assigned depending on the level of eGFR, the second score-depending on the proteinuria level, the third score-resistance to steroid therapy. Patients with the sum of these scores of less than 3 were included in group 1, with 3 or more-in group 2. The urinary proteome was analyzed using liquid chromatography/mass spectrometry. The proteome profiles of patients with severe progressive FSGS from group 2, mild FSGS from group 1 and MCD were compared. Results of the label free analysis were validated using targeted LC-MS based on multiple reaction monitoring (MRM) with stable isotope labelled peptide standards (SIS) available for 47 of the 76 proteins identified as differentiating between at least one pair of groups. Quantitative MRM SIS validation measurements for these 47 proteins revealed 22 proteins with significant differences between at least one of the two group pairs and 14 proteins were validated for both comparisons. In addition, all of the 22 proteins validated by MRM SIS analysis showed the same direction of change as at the discovery stage with label-free LC-MS analysis, i.e., up or down regulation in MCD and FSGS1 against FSGS2. Patients from the FSGS group 2 showed a significantly different profile from both FSGS group 1 and MCD. Among the 47 significantly differentiating proteins, the most significant were apolipoprotein A-IV, hemopexin, vitronectin, gelsolin, components of the complement system (C4b, factors B and I), retinol- and vitamin D-binding proteins. Patients with mild form of FSGS and MCD showed lower levels of Cystatin C, gelsolin and complement factor I.

Features of Psychomotor Coordination in Adolescents with Neuropsychiatric Pathology Enrolled in a Standard Educational Program.

The imbalance between the speed and accuracy of cognitive-motor operations can lead to the formation of abnormal behavioral programs fraught with serious negative consequences for the individual. For successful correction and prevention of social disadaptation in adolescents with nervous and mental diseases and functional disorders in mental sphere in general education schools, the peculiarities of their psychomotor activity should be taken into account. We measured some parameters of visual-motor coordination and sensorimotor reaction in adolescents with mental disorders with (n = 36) or without (n = 27) organic brain damage. Adolescents from both groups showed higher speed, but poorer accuracy and smoothness, of movements than typically developing students (n = 70). The visual and acoustic reaction times were longer in adolescents with mental disorders without organic brain damage than in reference groups.

Effects of Vertically Heterogeneous Soil Salinity on Genetic Polymorphism and Productivity of the Widespread Halophyte Bassia prostrata.

Salinity is one of the environmental factors that affects both productivity and genetic diversity in plant species. Within the soil profile, salinity is a dynamic indicator and significantly changes with depth. The present study examined the effects of the vertical heterogeneity of soil salinity chemistry on the plant height, fresh and dry biomass accumulation, water content, level of genetic polymorphism, and observed and expected heterozygosity in seven populations of halophyte Bassia prostrata in natural habitats. Soil salinity ranged from slight (Ssalts = 0.11-0.25%) to extreme (Ssalts = 1.35-2.57%). The main contributors to salinity were Na+, Ca2+, and Mg2+. Multivariate analysis revealed that biomass accumulation is positively affected by moderate/high salinity in 20-60 cm soil layers, which may be associated with the salt required for the optimal growth of the halophyte B. prostrata. The formation of seed genetic diversity is negatively affected by slight/moderate salinity in the 0-40 cm layers. An increase in divalent ion content can reduce genetic diversity and increase the local adaptation of B. prostrata to magnesium-calcium sulfate salinity. The effect of the in-depth distribution of soil salinity on productivity and genetic diversity may be related to seasonal variables during biomass accumulation (summer) and seed formation (autumn).

Imaging-Guided Delivery of a Hydrophilic Drug to Eukaryotic Cells Based on Its Hydrophobic Ion Pairing with Poly(hexamethylene guanidine) in a Maleated Chitosan Carrier.

Imaging-guided delivery is developed for hydrophobic drugs, and to a much lesser extent, hydrophilic ones. In this work we have designed a novel strategy for real-time monitoring of hydrophilic drug delivery. Traditionally, the drug and the dye are covalently attached to a nanocarrier or are electrostatically adsorbed. Recently, we found an efficient way to bind the drug by ion-paring with an appropriate counter-ion to form the aggregate that embeds a hydrophobic dye with a considerable fluorescence enhancement. We synthesized a series of carbocyanine dyes of hydrophobicity sufficient for solubilization in hydrophobic ion pairs, which restores their emission in the near-infrared (NIR) region upon the formation of the ternary aggregates. To avoid using toxic surfactants, we applied an amphiphilic polymer-oligomer poly(hexamethylene guanidine) (PHMG) as a counter-ion. Сeftriaxone was used as a model hydrophilic drug ensuring the highest fluorescent signal. The so-formed drug-counter-ion-dye aggregates were encapsulated into a cross-linked maleated chitosan carrier. Confocal laser scanning microscopy (CLSM) studies have demonstrated internalization of the encapsulated model drug by breast adenocarcinoma cells at 40 min after treatment. These results suggest the potential application of hydrophobic ion pairs containing an NIR dye in imaging-guided delivery of hydrophilic compounds.

VPg of Potato Virus Y and Potato Cap-Binding eIF4E Factors: Selective Interaction and Its Supposed Mechanism.

Potato virus Y (PVY) is one of the most common and harmful plant viruses. Translation of viral RNA starts with the interaction between the plant cap-binding translation initiation factors eIF4E and viral genome-linked protein (VPg) covalently attached to the viral RNA. Disruption of this interaction is one of the natural mechanisms of plant resistance to PVY. The multigene eIF4E family in the potato (Solanum tuberosum L.) genome contains genes for the translation initiation factors eIF4E1, eIF4E2, and eIF(iso)4E. However, which of these factors can be recruited by the PVY, as well as the mechanism of this interaction, remain obscure. Here, we showed that the most common VPg variant from the PVY strain NTN interacts with eIF4E1 and eIF4E2, but not with eIF(iso)4E. Based on the VPg, eIF4E1, and eIF4E2 models and data on the natural polymorphism of VPg amino acid sequence, we suggested that the key role in the recognition of potato cap-binding factors belongs to the R104 residue of VPg. To verify this hypothesis, we created VPg mutants with substitutions at position 104 and examined their ability to interact with potato eIF4E factors. The obtained data were used to build the theoretical model of the VPg-eIF4E2 complex that differs significantly from the earlier models of VPg complexes with eIF4E proteins, but is in a good agreement with the current biochemical data.

Emergence of Hybrid Resistance and Virulence Plasmids Harboring New Delhi Metallo-ß-Lactamase in Klebsiella pneumoniae in Russia.

The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) is a new threat to healthcare. In this study, we analyzed nine CR-hvKp isolates of different sequence-types (ST) recovered from patients with nosocomial infections in two hospitals in Saint Petersburg. Whole-genome sequencing showed that eight of them harbored large mosaic plasmids carrying resistance to carbapenems and hypervirulence simultaneously, and four different types of hybrid plasmids were identified. BLAST analysis showed a high identity with two hybrid plasmids originating in the UK and Czech Republic. We demonstrated that hybrid plasmids emerged due to the acquisition of resistance genes by virulent plasmids. Moreover, one of the hybrid plasmids carried a novel New Delhi metallo-beta-lactamase (NDM) variant, differing from NDM-1 by one amino acid substitution (D130N), which did not provide significant evolutionary advantages compared to NDM-1. The discovery of structurally similar plasmids in geographically distant regions suggests that the actual distribution of hybrid plasmids carrying virulence and resistance genes is much wider than expected.

Acute kidney injury and mortality in coronavirus disease 2019: results from a cohort study of 1,280 patients.

BACKGROUND: The development of acute kidney injury (AKI) in patients with coronavirus disease 2019 (COVID-19) is associated with a high risk of death. Published data demonstrate the possibility of severe kidney injury in patients suffering from COVID-19. However, these data are still controversial. METHODS: A total of 1,280 patients with a proven diagnosis of COVID-19 were included in our study. COVID-19 was confirmed in all patients using reverse transcriptase polymerase chain reaction test of a nasopharyngeal swab, and based on the typical computed tomography findings. Demographic data, underlying comorbidities, and laboratory blood tests were assessed. We assessed the incidence of AKI and its associated mortality defined by survival status at discharge. RESULTS: Proteinuria was identified with 648 patients (50.6%) with COVID-19. AKI was identified in 371 patients (29.0%). Ten of these patients (2.7%) required dialysis. The risk factors for AKI included age of > 65 years, augmentation of C-reactive protein, ferritin and an increase in values of activated partial thromboplastin time. Overall, 162 of the 1,280 hospitalized patients (12.7%) and 111 of the 371 patients (29.9%) with AKI did not survive. The hazard ratio (HR) for mortality was 3.96 (95% confidence interval, 2.83-5.54) for patients with AKI vs. no AKI. CONCLUSION: AKI was a relatively common finding among patients with COVID-19. The risk factors for AKI in COVID-19 included old age, the inflammatory response, the severity of lung involvement, and disseminated intravascular coagulation. These same factors, in addition to arterial hypertension, were found to increase the risk of mortality.

An ERF121 transcription factor from Brassica oleracea is a target for the conserved TAL-effectors from different Xanthomonas campestris pv. campestris strains.

Transcription activator-like effectors (TALEs), which induce the expression of specific plant genes to promote infection, are the main pathogenic determinants of various Xanthomonas bacteria. However, investigation of TALEs from Xanthomonas campestris pv. campestris, which causes black rot disease of crucifers, received little attention. In this study, we used PCR-based amplification followed by SMRT amplicon sequencing to identify TALE genes in several X. campestris pv. campestris strains. Computational prediction in conjunction with quantitative reverse transcription PCR analysis was used to find their targets in the Brassica oleracea genome. Transcription factor ERF121, from the AP2/ERF family, was identified as target gene for the conserved TALEs from multiple X. campestris pv. campestris strains. Several members of this family from diverse plants were previously identified as targets of TALEs from different Xanthomonas species. We propose that TALE-dependent activation of AP2/ERF transcription factors promotes susceptibility to Xanthomonas through the misregulation of plant defence pathways.

The emergence of hypervirulent blaNDM-1-positive Klebsiella pneumoniae sequence type 395 in an oncology hospital.

Fifteen hypermucoviscous isolates (13 blaNDM-1-positive) obtained from 11 oncology patients were analyzed by whole genome sequencing, and selected isolates were assessed in a murine model of sepsis. ST395/K2 isolates harboring rmpA, rmpA2, peg-344, aerobactin, enterobactin, yersiniabactin, type I fimbriae, etc. displayed maximal virulence in the mouse lethality assay (LD50 = 102 CFU). ST147/K20 isolates lacking yersiniabactins were relatively less virulent (LD50 = 104 CFU), ST395/K2 isolates lacking rmpA, rmpA2, peg-344, and aerobactin, but harboring yersiniabactin demonstrated minimal virulence (LD50 = 105 CFU). Isolates represent various paths and stages of evolution directed towards convergence of multidrugresistant classical Klebsiella pneumoniae and hypervirulent K. pneumoniae.

Streptozotocin (STZ)-Induced Diabetes Affects Tissue Trace Element Content in Rats in a Dose-Dependent Manner.

The objective of the present study was investigation of tissue trace element distribution in a streptozotocin model of DM1 in rats. DM1 was modeled in 2-month-old male Wistar rats (n = 30) using intraperitoneal injection of 45 mg/kg b.w. (STZ1) and 55 mg/kg b.w. streptozotocin (STZ2), whereas control animals were injected with physiological saline. The rats were subjected to oral glucose tolerance test (OGTT) and HbA1c level assessment at day 14. At day 30, blood serum, liver, kidney, and heart samples were collected for tissue trace element assessment using inductively coupled plasma mass spectrometry (ICP-MS). STZ-treated rats were characterized by lack of significant weight gain and elevated HbA1c and blood glucose levels. ICP-MS analysis demonstrated a dose-dependent accumulation of Cu, Mn, Mo, and Se levels in the liver. Correspondingly, the dose-dependent increase in renal Cu, Mn, V, and Zn levels was significant, whereas the observed trend for kidney V and Mo accumulation was nearly significant. The patterns of trace element content in the myocardium of STZ-exposed rats were quite different from those observed for liver and kidney. Only cardiac Zn content was characterized by a significant decrease. Serum Co, Cr, Cu, Se, V, and Mo levels were characterized by a significant decrease in response to STZ-induced diabetes. Generally, the obtained data demonstrate that diabetes is associated with altered copper, manganese, molybdenum, chromium, and vanadium handling. In turn, only altered Zn status may provide a link to diabetic cardiotoxicity. However, the particular mechanisms of both impaired metal handling in STZ diabetes and their potential anti-diabetic activity require further investigation.

On the integrated assessment of the technogenic risk of accidents on the territory of a city.

A new approach is proposed for assessing the integrated indicator of the technogenic risk of accidents on the city territory. The indicator is determined by the values of the individual indicators: potential danger, security, and vulner-ability of the territory. This approach allows us to assess the technogenic risk qualitatively and quantitatively and to take into account the complex of important factors affecting the safety of the city territory.

CRISPR/Cas9 genome editing through in planta transformation.

In this review, the application of CRISPR/Cas9 plant genome editing using alternative transformation methods is discussed. Genome editing by the CRISPR/Cas9 system is usually implemented via the generation of transgenic plants carrying Cas9 and sgRNA genes in the genome. Transgenic plants are usually developed by in vitro regeneration from single transformed cells, which requires using different in vitro culture-based methods. Despite their common application, these methods have some disadvantages and limitations. Thus, some methods of plant transformation that do not depend on in vitro regeneration have been developed. These methods are known as "in planta" transformation. The main focus of this review is the so-called floral dip in planta transformation method, although other approaches are also described. The main features of in planta transformation in the context of CRISPR/Cas9 genome editing are discussed. Furthermore, multiple ways to increase the effectiveness of this approach and to broaden its use in different plant species are considered.