Spatial Structure of <i>Yersinia pestis</i> Population Belonging to Altai Biovar, Subspecies central asiatica Acording to Genome-Wide Sequencing Data

The aim of the work was to conduct phylogenetic analysis of Y. pestis strains, biovar altaica ssp. central asiatica, isolated in Gorno-Altai high-mountain and Sailyugem natural plague foci on the territory of Russia and Mongolia in 1965–2020, by full-genome sequencing data.Materials and methods. To determine the population structure of the biovar altaica ssp. central asiatica, 34 whole genome sequences were used (including 20 Y. pestis strains of the biovar altaica, 18 of which were sequenced by us). To isolate DNA from the Y. pestis strains, a PureLink Genomic DNA Mini Kit (Invitrogen, USA) was applied. Sequencing of the nucleotide sequences of Y. pestis strains was carried out in Ion PGM system Lifetechnologies. The analysis and processing of the obtained data were performed with the help of Newblergs Assembler 2.6 and IonTorrent Suite software package, 3.4.2. The search for SNPs was performed using the Wombac 2.0 program. The Maximum Likelihood dendrogram was built in the PhyML 3.1. The dendrogram was visualized using the FigTree 1.4.3 software.Results and discussion. Based on the data of whole genome analysis, taking into account the 1871 revealed polymorphic nucleotides, the spatial structure of the biovar altaica ssp. central asiatica has been determined. It includes several phylogeographic branches: the Kurai-Tarkhatinskaya (cluster 0.PE4a-1) and the Ulandryk-Mongolian (0.PE4a-2), which is in agreement with the geographical regions of the isolation of strains forming these branches in the Altai Mountains. The Kurai-Tarkhatinskaya branch is further divided into the Kurai (sub-cluster 0.PE4a-1-1, formed by the strains of 2009–2018) and Tarkhatinskaya (subcluster 0.PE4a-1-2, formed by the strains of 2012–2020) sub-branches, while the Ulandryk-Mongolian branch of evolution is split into sub-branches represented by strains from the Ulandryk meso focus (sub-cluster 0.PE4a-2-2, strains 1965–2010) and the Sailyugem focus of Mongolia (sub-cluster 0.PE4a-2-1, strains 1964–1990)

The First Case of <I>Yersinia Pestis</I> Subsp. <I>Pestis</I> Isolation in the Territory of Altai Mountain Natural Plague Focus. Communication 1. Microbiological Characteristics, Molecular-Genetic and Mass-Spectrometric Identification of the Isolate

Performed is a complex microbiological, molecular-genetic and mass-spectrometric identification of Yersinia pestis main ssp. strain, which was isolated for the first time in the history of surveillance over the Altai mountain natural plague focus in June, 2012. Determined is its high universal virulence. Plasmid screening, multi-locus VNTR- and mass-spectrometric analyses have revealed the strain to be more closely related to the plague agent variant, circulating in the territory of the natural focus Khuukh-Serkh-Munkh-Khairkhan, Bayan-Ul’giisk aimak, Mongolia

Mongolian Part of the Transboundary Sailugem Natural Plague Focus in 2017. Communication 1. Epizootic condition

Objective – estimation of current epizootic condition of Mongolian part of transboundary Sailugem natural plague focus. Materials and methods. Epizootiological survey was performed for the area of 2335 km2, 277 mammals and 516 ectoparasites were investigated for plague. Results and conclusions. Eight Yersinia pestis subsp. pestis strains were isolated, including 7 strains – from grey marmots (6 – from the remains of meals of predatory birds, 1 from a corpse) and 1 – from long-tailed souslik (corpse). Y. pestis DNA was detected in 52 objects. Serological samples showed 40 positive results. Epizootic manifestations, confirmed by isolation of Y. pestis cultures, detection of plague microbe DNA, and positive serological results, were observed across the area of 1611 km2 covering 69 % of the inspected territory. Epizootic results indicated high infection rate of mass mammal species and first of all grey marmots. The data demonstrated that the extended plague epizooty caused by Y. pestis of the main subspecies occurred in the inspected territory in the carrier settlements. For the first time the circulation of Y. pestis subsp. pestis was registered in the Mongolian part of the transboundary Sailugem focus

Investigations of Structural-Functional Aspects of Epizootic Process in Natural Plague Foci in Siberia

Comprehensively studied have been structural elements of ecosystems of Siberian natural plague foci, as well as levels of integration among epizootic process components, and ways of their functional interaction. Application of the complex approach to the surveillance over structural-functional elements of the parasitic system along with investigations of epizootic process dynamics has provided for identification of peculiarities as regards epizootics development, transformation and evolution of population and carrier/vector coenosis structure in time and space. Revealed is the genetic diversity of plague microbe circulating within the bounds of separate foci and zones of focality. Determined is a long-lasting anti-epidemic effect (more than 20 years) of the field desinsection in the Saglinsk meso-focus of the Tuva natural plague focus

A Case of Human Infection with Plague in the Kosh-Agach Region of the Republic of Altai in 2015. Communication 1. Clinical-Epidemiological and Epizootiological Aspects

Objective of the study is to characterize the case of human plague in the territory of Gorno-Altaisk high-mountain natural focus in 2015 and to analyze the initiated measures, associated with localization and elimination of epidemic focus. Materials and methods. Utilized are the data contained in reporting and source (primary) documentation of the FGHI “Altai Plague Control Station”, records of the Rospotrebnadzor Administration in the Republic of Altai, and information collected by the FGHI “Irkutsk Research Anti-Plague Institute”. Results and conclusions. Human infection occurred as a result of gray marmot dressing, which was caught in the Elangash River-Valley, against the background of unfavorable epizootic situation, caused by proliferation of the plague agent of main subspecie in the territory of the focus. Clinical material investigations, performed by means of bacteriological and molecular-genetic methods, showed negative findings. Applying serological method within the system of indirect hemagglutination test (IHAT)/antigen neutralization test (ANT), in blood sera, obtained at the time of hospitalization, low-titred specific antibodies to plague microbe (recognized as post-vaccinal ones) were detected. In blood serum sample, obtained 7 days later, identified were high-titer antibodies, which allowed for confirmation of clinical diagnosis - “bubonic plague”. Due to efficient cooperation between Rospotrebnadzor institutions and medical facilities, as well as municipal authorities it was possible to avoid further development of anthropogenic transmission of plague; to localize and eliminate epidemic outbreak of this dangerous infectious disease in Kosh-Agach Region of the Republic of Altai in the shortest possible time

Non-Specific Prophylaxis of Plague in the Gorno-Altai High-Mountain Natural Focus in 2016

Objective of the study is to substantiate performance, assess the conditions, and analyze the results of activities on non-specific plague prophylaxis in the epizootic territory. Materials and methods. Utilized were archival data and operational reports of Altai Plague Control Station, Irkutsk RAPI, RusRAPI “Microbe”, Center of Hygiene and Epidemiology in the Republic of Altai, and Rospotrebnadzor Administration in the Republic of Altai, as well as literature sources. Spatial analysis was carried out using GIS-technologies. Results and conclusions. Concerted and coordinated activities of the Rospotrebnadzor institutions, medical and veterinary institutions, local executive authorities have allowed for complex prophylactic and anti-epidemic measures on prevention of plague dissemination and transmission in the territory of the Republic of Altai in 2016. Demonstrated has been the necessity to expand the scope and scale of operations and scientific research in the focus, deploying advanced toolkit of methods and means

Capturing wheat phenotypes at the genome level

Recent technological advances in next-generation sequencing (NGS) technologies have dramatically reduced the cost of DNA sequencing, allowing species with large and complex genomes to be sequenced. Although bread wheat (Triticum aestivum L.) is one of the world’s most important food crops, efficient exploitation of molecular marker-assisted breeding approaches has lagged behind that achieved in other crop species, due to its large polyploid genome. However, an international public–private effort spanning 9 years reported over 65% draft genome of bread wheat in 2014, and finally, after more than a decade culminated in the release of a gold-standard, fully annotated reference wheat-genome assembly in 2018. Shortly thereafter, in 2020, the genome of assemblies of additional 15 global wheat accessions was released. As a result, wheat has now entered into the pan-genomic era, where basic resources can be efficiently exploited. Wheat genotyping with a few hundred markers has been replaced by genotyping arrays, capable of characterizing hundreds of wheat lines, using thousands of markers, providing fast, relatively inexpensive, and reliable data for exploitation in wheat breeding. These advances have opened up new opportunities for marker-assisted selection (MAS) and genomic selection (GS) in wheat. Herein, we review the advances and perspectives in wheat genetics and genomics, with a focus on key traits, including grain yield, yield-related traits, end-use quality, and resistance to biotic and abiotic stresses. We also focus on reported candidate genes cloned and linked to traits of interest. Furthermore, we report on the improvement in the aforementioned quantitative traits, through the use of (i) clustered regularly interspaced short-palindromic repeats/CRISPR-associated protein 9 (CRISPR/Cas9)-mediated gene-editing and (ii) positional cloning methods, and of genomic selection. Finally, we examine the utilization of genomics for the next-generation wheat breeding, providing a practical example of using in silico bioinformatics tools that are based on the wheat reference-genome sequence

Coordination of Measures of Plague Control Institutions, Aimed at Rehabilitation and Sanitation of Gorno-Altai High-Mountain Natural Plague Focus in 2016

Objective of the study is to sum-up the results of prophylactic (anti-epidemic) measures associated with elimination of epidemic focus in Kosh-Agach Region of the Republic of Altai in 2016. Materials and methods. Utilized were the data of reporting and source documentation from Altai Plague Control Station, Rospotrebnadzor Administration in the Republic of Altai, RusRAPI “Microbe”, and Irkutsk RAPI. Results and conclusions. It is pointed out that carried out in 2016 complex of organizational, anti-epidemic, and sanitary-prophylactic activities against plague is the importnant stage of rehabilitation of Gorno-Altai high-mountain natural plague focus, the final goal of which is maximally possible decrement of risks of primary human infection with plague, and in case of occurrence of such – performing of prompt response measures on localization and elimination of epidemic focus. It has been substantiated that for epidemic risk minimization in 2017 it is necessary to continue prophylactic vaccination, desinsection and deratization in the areas of predictive epizootic situation aggravation, which is contained in “Complex Action Plan of the Rospotrebnadzor Institutions for Sanitation and Rehabilitation of Gorno-Altai high-mountain natural plague focus in Kosh-Agach Region of the Altai Republic in 2017”. It is also necessary to provide for implementation of the Program on lowering risks of importation from cross-border Sailyugemsky natural focus and spread of plague in the territory of the Russian Federation, within the frames of RF Government Order No 1864-p, dated 05.09.2016