RNA protects a nucleoprotein complex against radiation damage

Radiation damage during macromolecular X-ray crystallographic data collection is still the main impediment for many macromolecular structure determinations. Even when an eventual model results from the crystallographic pipeline, the manifestations of radiation-induced structural and conformation changes, the so-called specific damage, within crystalline macromolecules can lead to false interpretations of biological mechanisms. Although this has been well characterized within protein crystals, far less is known about specific damage effects within the larger class of nucleoprotein complexes. Here, a methodology has been developed whereby per-atom density changes could be quantified with increasing dose over a wide (1.3-25.0 MGy) range and at higher resolution (1.98 Å) than the previous systematic specific damage study on a protein-DNA complex. Specific damage manifestations were determined within the large trp RNA-binding attenuation protein (TRAP) bound to a single-stranded RNA that forms a belt around the protein. Over a large dose range, the RNA was found to be far less susceptible to radiation-induced chemical changes than the protein. The availability of two TRAP molecules in the asymmetric unit, of which only one contained bound RNA, allowed a controlled investigation into the exact role of RNA binding in protein specific damage susceptibility. The 11-fold symmetry within each TRAP ring permitted statistically significant analysis of the Glu and Asp damage patterns, with RNA binding unexpectedly being observed to protect these otherwise highly sensitive residues within the 11 RNA-binding pockets distributed around the outside of the protein molecule. Additionally, the method enabled a quantification of the reduction in radiation-induced Lys and Phe disordering upon RNA binding directly from the electron density

A Tailward Moving Current Sheet Normal Magnetic Field Front Followed by an Earthward Moving Dipolarization Front

A case study is presented using measurements from the Cluster spacecraft and ground-based magnetometers that show a substorm onset propagating from the inner to outer plasma sheet. On 3 October 2005, Cluster, traversing an ion-scale current sheet at the near-Earth plasma sheet, detected a sudden enhancement of Bz, which was immediately followed by a series of flux rope structures. Both the local Bz enhancement and flux ropes propagated tailward. Approximately 5 min later, another Bz enhancement, followed by a large density decrease, was observed to rapidly propagate earthward. Between the two Bz enhancements, a significant removal of magnetic flux occurred, possibly resulting from the tailward moving Bz enhancement and flux ropes. In our scenario, this flux removal caused the magnetotail to be globally stretched so that the thinnest sheet formed tailward of Cluster. The thinned current sheet facilitated magnetic reconnection that quickly evolved from plasma sheet to lobe and generated the later earthward moving dipolarization front (DF) followed by a reduction in density and entropy. Ground magnetograms located near the meridian of Cluster's magnetic foot points show two-step bay enhancements. The positive bay associated with the first Bz enhancement indicates that the substorm onset signatures propagated from the inner to the outer plasma sheet, consistent with the Cluster observation. The more intense bay features associated with the later DF are consistent with the earthward motion of the front. The event suggests that current disruption signatures that originated in the near-Earth current sheet propagated tailward, triggering or facilitating midtail reconnection, thereby preconditioning the magnetosphere for a later strong substorm enhancement

Structural basis for the nuclease activity of a bacteriophage large terminase

The DNA-packaging motor in tailed bacteriophages requires nuclease activity to ensure that the genome is packaged correctly. This nuclease activity is tightly regulated as the enzyme is inactive for the duration of DNA translocation. Here, we report the X-ray structure of the large terminase nuclease domain from bacteriophage SPP1. Similarity with the RNase H family endonucleases allowed interactions with the DNA to be predicted. A structure-based alignment with the distantly related T4 gp17 terminase shows the conservation of an extended β-sheet and an auxiliary β-hairpin that are not found in other RNase H family proteins. The model with DNA suggests that the β-hairpin partly blocks the active site, and in vivo activity assays show that the nuclease domain is not functional in the absence of the ATPase domain. Here, we propose that the nuclease activity is regulated by movement of the β-hairpin, altering active site access and the orientation of catalytically essential residues

Biological Properties and Molecular Genetic Characteristics of Bacillus Anthracis Strains Isolated During Anthrax Outbreaks in Kazakhstan in 2016

Today, anthrax is recorded in many countries around the world, in Kazakhstan – in the form of sporadic cases or small outbreaks. Despite the endemicity of anthrax in Kazakhstan, the genetic diversity strains is not well described. At the moment, MLVA-25, which is sufficient for molecular and epidemiological monitoring, is recognized as one of the most discriminatory methods of genotyping.Objective: to determine the cultural and morphological properties, the genomic characteristics of the strains of the anthrax pathogen, their geographical distribution in the territory of Kazakhstan during the outbreaks in 2016, a comparative analysis with collection strains isolated since 1962.Methods: microbiological, genetic research methods were used in the work.Results. We investigated 11 strains of B. anthracis, which were isolated in 2016 in Kazakhstan. For comparison of genotypes, 26 strains were used from the collection of pathogenic microorganisms of the A.M. Aykimbaev’s Kazakh Scientific Center for Quarantine and Zoonotic Diseases. Phylogenetic analysis clustered 37 strains of B. anthracis into three clusters and 23 genotypes.The results of studying the phenotypic properties of anthrax strains by the main identification tests showed that all the strains studied in the experiment and isolated from 1961 to 2016 had biological properties characteristic of typical of B. anthracis strains.The anthrax strains isolated in 2016 are characterized as significant variability, as well as the circulation of the same genotypes and clusters in different areas of Kazakhstan. MLVA-profiles of analyzed Kazakhstan strains are unique and do not fully coincide with any studied strain from MLVAbank. On the MST-tree, Kazakhstan’s strains are located in three clusters, as on the phylogenetic tree.Conclusion: Molecular genetic analysis of B. anthracis strains enhances the ability of epidemiologists to track the sources and pathways of infection.It is necessary to improve the tracking system for strains of especially dangerous infections in  Kazakhstan using modern molecular genetic methods

Structural insights into thrombolytic activity of destabilase from medicinal leech

Destabilase from the medical leech Hirudo medicinalis belongs to the family of i-type lysozymes. It has two different enzymatic activities: microbial cell walls destruction (muramidase activity), and dissolution of the stabilized fibrin (isopeptidase activity). Both activities are known to be inhibited by sodium chloride at near physiological concentrations, but the structural basis remains unknown. Here we present two crystal structures of destabilase, including a 1.1 Å-resolution structure in complex with sodium ion. Our structures reveal the location of sodium ion between Glu34/Asp46 residues, which were previously recognized as a glycosidase active site. While sodium coordination with these amino acids may explain inhibition of the muramidase activity, its influence on previously suggested Ser49/Lys58 isopeptidase activity dyad is unclear. We revise the Ser49/Lys58 hypothesis and compare sequences of i-type lysozymes with confirmed destabilase activity. We suggest that the general base for the isopeptidase activity is His112 rather than Lys58. pKa calculations of these amino acids, assessed through the 1 μs molecular dynamics simulation, confirm the hypothesis. Our findings highlight the ambiguity of destabilase catalytic residues identification and build foundations for further research of structure–activity relationship of isopeptidase activity as well as structure-based protein design for potential anticoagulant drug development.</p

Characterization of tularemia foci in the Republic of Kazakhstan from 2000 to 2020

The wide distribution of tularemia in the territory of Kazakhstan is associated with landscape and geographical characteristics. This is explained by a combination of natural factors: the presence of certain types of rodents—reservoirs and sources, ectoparasites—carriers of the causative agent of tularemia. The study of the current spatial and temporal characterization of tularemia in Kazakhstan from 2000 to 2020 will determine the epidemiological status of tularemia and improve the monitoring system in Kazakhstan. In this work we demonstrated the results of a retrospective survey of natural foci of tularemia: analysis of vector, small mammal and human data. The spatial and temporal characteristics of tularemia from 2000 to 2020 in the territory of Kazakhstan were studied in comparison with historical data, including the description of tularemia outbreaks, the clinical picture, and the source of infection, transmission factors, and geographical coordinates of outbreak registration. Sampling was carried out by trapping rodents on snap traps and collecting ticks by rodent combing and by "flagging" methods. For the last 20 years, 85 human cases of tularemia have been reported. During the period from 2000 to 2020, more than 600 strains of F. tularensis were isolated from field rodents and ticks in the natural foci of tularemia. MLVA typing of F. tularensis strains isolated from natural foci of tularemia in Kazakhstan over the past 20 years. The results of retrospective monitoring indicate that currently active foci of tularemia include the Aktobe, West Kazakhstan, Almaty, East Kazakhstan, and Pavlodar regions. Low-activity natural foci are located in the territory of the Akmola, Karaganda, North Kazakhstan, Kostanay, Atyrau, Zhambyl, and Kyzylorda regions. There are no active natural foci of tularemia in the Mangystau and Turkestan regions. The widespread occurrence of tularemia in the country is associated with landscape and geographical features that contribute to the circulation of the pathogen in the natural focus. An analysis of natural foci of tularemia showed that it is necessary to continue monitoring studies of carriers and vectors for the presence of the causative agent of the F. tularensis, in order to prevent mass cases of human disease

Morphological, Physiological and Genetic Characteristics of Populations of the Main Plague Host Rhombomys opimus Licht., 1823 in the Central Asian Desert Natural Focus of Plague

Revealed by morphological characters, physiological status, and genetic diversity of populations of the main plague host Rhombomys opimus Licht., 1823 in Central Asia desert natural focus is described.Differences in the skull parameters of R. opimus from different populations were revealed. It’s shown that gerbils from Moyunkum are separate autonomous populations group. Samples from Moyunkum and Mangyshlak differed from other samples. In Balkhash-Alakol depression found two regional complexes: Pre-Balkhash and Dzungarian.Study results of free amino acids level in R. opimus blood serum obtained by gas-liquid chromatography of blood sera from animals captured in different zones of Central Asian focus gave statistically significant differences. To determine genetic variability in ecological and geographical isolation of R. opimus populations the DNA was genotyped.DNA samples analysis combined the studied gerbil from the desert focus into four clusters with eighteen haplotypes. R. opimus sequence analysis taking into account data from territories of Iran, Kazakhstan and China, clustered into three large clusters. First cluster combined the sequences of Kazakhstan and China samples, while great gerbil captured in Kazakhstan is located in a separate treasure. Second and third clusters include sequences of a great gerbil captured in Iran

Anthrax in the East Kazakhstan Region

Almost every year in Kazakhstan, cases of diseases of animals and people with anthrax are recorded. The incidence rate of people with anthrax in the period from 2000 to 2018 ranged from 0.01 to 0.24 per 100 thousand people. In the territory of the East Kazakhstan region, the incidence rate is higher than in the republic.Objective: a retrospective analysis of anthrax outbreaks in the East Kazakhstan region from 2000 to 2018.Methods: a retrospective analysis using statistical, cadastral data, archival funds, the results of participation in the investigation of outbreaks of infection.Results. Since 1938, cases of animal and human disease of anthrax have been recorded in East Kazakhstan. Infection of humans occurs during the slaughter of animals. In Zharma, Urjar, and Ayagozskiy areas most of all are anthrax foci of soil. In 67 % of cases, outbreaks of anthrax were recorded in these areas.Conclusion. The relative incidence rate of anthrax in people in East Kazakhstan is from 0.07 to 0.27, since 2001 it is higher than the republican indicator.In the East Kazakhstan region from 1997 to 2018, 37 people fell ill with anthrax. The form of the disease is skin, in 8.1 % secondary sepsis. In the remaining patients, the diseases were mild (70.3 %), ended in recovery. The source of human infection is mainly cattle. The isolated strains of B. anthracis have typical properties, they are included in cluster A1a, A3b (MLVA-8). The strains isolated in 2016 are similar to the strains isolated in the Almaty region (MLVA-25). Grouped with a number of European, Asian and African strains from France, Germany, Italy, Tajikistan, Pakistan, Korea and Namibia. The presence of a significant number of soil foci of anthrax in the territory of the East Kazakhstan region, not fully the implementation of veterinary and sanitary preventive measures leads to an exacerbation of the situation for anthrax