Gravitoviscous protoplanetary disks with a dust component: III. Evolution of gas, dust, and pebbles

Aims. We study the dynamics and growth of dust particles in circumstellar disks of different masses that are prone to gravitational instability during the critical first Myr of their evolution. Methods. We solved the hydrodynamics equations for a self-gravitating and viscous circumstellar disk in a thin-disk limit using the FEOSAD numerical hydrodynamics code. The dust component is made up of two different components: micron-sized dust and grown dust of evolving size. For the dust component, we considered the dust coagulation, fragmentation, momentum exchange with the gas, and dust self-gravity. Results. We found that the micron-sized dust particles grow rapidly in the circumstellar disk, reaching a few cm in size in the inner 100 au of the disk during less than 100 kyr after the disk formation, provided that fragmentation velocity is 30 ms-1. Due to the accretion of micron dust particles from the surrounding envelope, which serves as a micron dust reservoir, the approximately cm-sized dust particles continue to be present in the disk for more than 900 kyr after the disk formation and maintain a dust-to-gas ratio close to 0.01. We show that a strong correlation exists between the gas and pebble fluxes in the disk. We find that radial surface density distribution of pebbles in the disk shows power-law distribution with an index similar to that of the Minimum-mass solar nebula regardless the disk mass. We also show that the gas surface density in our models agrees well with measurements of dust in protoplanetary disks of AS 209, HD 163296, and DoAr 25 systems. Conclusions. Pebbles are formed during the very early stages of protoplanetary disk evolution. They play a crucial role in the planet formation process. Our disc simulations reveal the early onset (<105 yr) of an inwards-drifting flux of pebble-sized particles that makes up approximately between one hundredth and one tenth of the gas mass flux, which appears consistent with mm-observations of discs. Such a pebble flux would allow for the formation of planetesimals by streaming instability and the early growth of embryos by pebble accretion. We conclude that unlike the more common studies of isolated steady-state protoplanetary disks, more sophisticated global numerical simulations of circumstellar disk formation and evolution, including the pebble formation from the micron dust particles, are needed for performing realistic planet formation studies. © ESO 2020.We thank the anonymous referee for a insightful report, which helped to improve this paper. Research was financially supported by the Ministry of Science and Higher Education of the Russian Federation (State assignment in the field of scientific activity, Southern Federal University, 2020). V.G.E. acknowledges the Swedish Institute for a visitor grant allowing to conduct research at Lund University. A.J. was supported by the Swedish Research Council (grant 2018-04867), the Knut and Alice Wallenberg Foundation (grant 2012.0150) and the European Research Council (ERC Consolidator Grant 724687-PLANETESYS). M.L. was supported by the Knut and Alice Wallenberg Foundation (grant 2012.0150). V.A. was supported by RFBR grant 18-52-52006

Bastroviruses (<i>Astroviridae</i>): genetic diversity and potential impact on human and animal health

Introduction. Bastroviruses were discovered in the Netherlands in 2016 in human stool samples and show partial genetic similarities to astroviruses and hepatitis E viruses. Their association with disease onset has not yet been established. Materials and methods. Metagenomic sequencing of fecal samples of Nyctalus noctula bats collected in the Russian Federation in 2023 was performed. Two almost complete genomes of bastroviruses were assembled. The zoonotic potential of these viruses was assessed using machine learning methods, their recombination was studied, and phylogenetic trees were constructed. Results. A nearly complete bastrovirus genome was de novo assembled in one of the samples, and it was used to assemble another genome in another sample. The zoonotic potential of the virus from one of these samples was estimated as high. The existence of recombination between structural and non-structural polyproteins was demonstrated. Conclusion. Two bastrovirus genomes were assembled, phylogenetic and recombination analyses were performed, and the zoonotic potential was evaluated

ALMA and VLA Observations of EX Lupi in Its Quiescent State

Extreme outbursts in young stars may be a common stage of pre-main-sequence stellar evolution. These outbursts, caused by enhanced accretion and accompanied by increased luminosity, can also strongly impact the evolution of the circumstellar environment. We present Atacama Large Millimeter Array (ALMA) and Very Large Array observations of EX Lupi, a prototypical outburst system, at 100, 45, and 15 GHz. We use these data, along with archival ALMA 232 GHz data, to fit radiative transfer models to EX Lupi's circumstellar disk in its quiescent state following the extreme outburst in 2008. The best-fit models show a compact disk with a characteristic dust radius of 45 au and a total mass of 0.01 M☉. Our modeling suggests grain growth to sizes of at least 3 mm in the disk, possibly spurred by the recent outburst, and an ice line that has migrated inward to 0.2-0.3 au post-outburst. At 15 GHz, we detected significant emission over the expected thermal disk emission which we attribute primarily to stellar (gyro)synchrotron and free-free disk emission. Altogether, these results highlight what may be a common impact of outbursts on the circumstellar dust

The Russian database of HIV antiretroviral drug resistance

The development of sequencing technologies and bioinformatic analysis made it possible to conduct molecular and epidemiological studies, in which nucleotide sequences of the human immunodeficiency virus (HIV) are used as information added to the patient profile. From a practical perspective, studies of prevalence of HIV drug resistance (HIVDR) are of the highest significance. To promote such studies, different countries use databases that serve as repositories of genetic and epidemiological information. The Russian HIVDR database (https://hivresist.ru/) was created in 2009. Nevertheless, it was characterized by limited applicability for a long time. Since 2021, after the regulatory documents had been revised and updated, the entry of HIVDR research results into the Russian HIVDR database has been mandatory. Therefore, the priority attention has been given to upgrading the database and improving its functional capabilities. Different methods have been developed to enter clinical, epidemiological and genetic data. At the time of this study, the Russian database HIVDR contained 10,626 unique records about patients and 13,126 nucleotide sequences deposited by 10 institutions. The following functions have been provided for data analysis: quality control of the epidemiological and clinical information about a patient, quality control of nucleotide sequences, contamination check, subtyping, detection of DR mutations, identification of viral tropism and generation of standardized reports. The efforts toward further development of the Russian HIVDR database will be focused on designing tools for detection and analysis of molecular clusters, adaptation to routine application for epidemiological surveillance of HIV infection

Results of screening for antibodies to varicella-zoster virus in healthcare workers of a multidisciplinary hospital in Moscow

Introduction. Given the unfavorable epidemic situation with chickenpox and shingles in Russia, there is a high risk of virus introduction and spread in healthcare settings, including among medical staff who are not immune to varicella zoster virus (VZV). The objective of this study is to assess the immunity of employees of a multidisciplinary hospital in Moscow to VZV. Materials and methods. A selective screening study was carried out. Venous blood serum samples were taken from 1546 hospital employees as material for detection of IgG antibodies to VZV antigens using a commercial solid-phase enzyme immunoassay (ELISA) test system "Vecto VZV-IgG". All employees were questioned to obtain information about their infectious and vaccine history in relation to VZV. Results and discussion. Screening for antibodies to VZV in the hospital workers revealed that 6.3% of those workers are not immune to VZV. The proportion of seronegative individuals was the highest (12.6 ± 2.4%) in the age group of 29 years and younger. VZV seronegative healthcare workers were found in various departments, but the presence of non-immune individuals among the staff of the obstetrics and gynecology departments (6.5%) is of epidemiologic concern. The results of the survey showed that documented data on infection and vaccination history cannot be used to assess the protection of healthcare workers against VZV infection. Conclusion. The results of serologic screening for antibodies to VZV made it possible to identify a significant number of susceptible employees of the multidisciplinary hospital. In order to prevent the formation of multiple epidemic foci of varicella in medical organizations, it is advisable to include anti-VZV testing of medical staff in the state prevention programs with subsequent vaccination of non-immune individuals

Production of Bst polymerase for diagnosis of different infections using loop-mediated isothermal amplification

Introduction. The large fragment of DNA polymerase I from Geobacillus stearothermophilus GIM1.543 (Bst DNA polymerase) possesses 5'-3' DNA polymerase activity, 5'-3' displacement activity and high processivity. These properties make it possible to use Bst DNA polymerase in loop-mediated isothermal amplification (LAMP), which provides highly specific amplification of the target sequence and is used for rapid detection of agents causing human infectious diseases. The purpose of the study was to produce a recombinant Bst polymerase enzyme in the bacterial expression system and to assess its properties for LAMP-based diagnostics of infectious diseases. Materials and methods. Expression constructs carrying the Bst polymerase gene were obtained using genetic engineering techniques. Different Escherichia coli strains were used for protein expression. Metal-chelate and gel filtration chromatography techniques were used for protein purification. Catalytic characteristics of the enzyme were assessed in loop-mediated isothermal amplification reactions using AmpliSens SARS-CoV-2-IT, AmpliSens IAV-IT and AmpliSens IBV-IT diagnostic systems designed for high-quality detection of SARS-CoV-2, influenza A virus (IAV) and influenza B virus (IBV) RNA, respectively. Results. The offered protocol for production, extraction and purification of recombinant Bst polymerase makes it possible to produce the enzyme in the bacterial expression system using E. coli cells in a soluble form and reaching the yield up to 20% of the total cell mass. In LAMP reactions, the obtained enzyme demonstrates activity comparable with that of the commercial enzyme Bst 2.0 (NEB). Conclusion. Considering the fast purification and production of the enzyme, the obtained recombinant Bst polymerase can be used in LAMP-based diagnostic kits

Studying the genetic diversity of the varicella-zoster virus in selected regions of the Russian Federation using high-throughput sequencing

Introduction. Varicella-zoster virus (VZV), the causative agent of the disease of the same name and herpes zoster, is phylogenetically divided into 8 clades, the distribution of which is characterized by geographic reference to certain regions of the world. For most countries, VZV clades circulating in their territories have been identified, however, such information is almost unavailable for Russia. The purpose of the study is to develop an effective method for VZV typing using high-throughput sequencing technologies to identify the prevalence of various VZV clades in Moscow, Moscow Region, and Stavropol Territory. Materials and methods. To genotype VZV, it is enough to refer to 7 nucleotide positions. Their unique combinations can be used to assign the virus to one of the clades. Short sections of nucleotide sequences of open reading frames were obtained using a developed set of primers. Results. A VZV genotyping technique has been developed and optimized. Using this technique, primary data on the distribution of VZV clades in the studied regions have been obtained. Thus, it has been established that in Moscow and a number of other regions, the 1st, 3rd, and 5th clades of VZV are predominantly distributed. Conclusion. The developed technique, including a primer panel and a genotyping algorithm, allows VZV typing in a short time while reducing specimen preparation costs and simultaneously increasing the number of specimens in one sequencing cycle. The results obtained using this assay allow us to assume that in Moscow, Moscow Region, Stavropol Territory, VZV, clades 1, 3, and 5 are the most represented ones. To confirm this hypothesis, it is necessary to include a larger number of clinical specimens in subsequent studies, including from other regions of the country

ALMA and VLA Observations of EX Lupi in its Quiescent State

Extreme outbursts in young stars may be a common stage of pre-main-sequence stellar evolution. These outbursts, caused by enhanced accretion and accompanied by increased luminosity, can also strongly impact the evolution of the circumstellar environment. We present ALMA and VLA observations of EX Lupi, a prototypical outburst system, at 100 GHz, 45 GHz, and 15 GHz. We use these data, along with archival ALMA 232 GHz data, to fit radiative transfer models to EX Lupi's circumstellar disk in its quiescent state following the extreme outburst in 2008. The best fit models show a compact disk with a characteristic dust radius of 45 au and a total mass of 0.01 M$_{\odot}$. Our modeling suggests grain growth to sizes of at least 3 mm in the disk, possibly spurred by the recent outburst, and an ice line that has migrated inward to $0.2-0.3$ au post-outburst. At 15 GHz, we detected significant emission over the expected thermal disk emission which we attribute primarily to stellar (gyro)synchrotron and free-free disk emission. Altogether, these results highlight what may be a common impact of outbursts on the circumstellar dust.Comment: Accepted to ApJ, 15 pages, 8 figure

Динамика частоты встречамости уропатогенов и антимикробных детерминант резистентности при детской значимой бактериурии в 2017 и 2019 годах: моноцентровое исследование

Urinary tract infections are the second most common infections in children with spreading of antimicrobial resistance among uropathogens currently poses a high epidemiological threat.Purpose. Analysis of species prevalence and the presence of genetic determinants of antibiotic resistance.Materials and methods. In the study 215 midstream urine samples were retrospectively analyzed. Samples were obtained during 2017 and 2019 from patients aged 4 weeks to 17 years at the National Medical Research Center for Children's Health Federal State Autonomous Institution of the Ministry of Health of the Russian Federation.Results. Species of pathogen were identified in 93 samples, while the bacterial composition of other samples was classified as «intestinal flora» (n = 17), «coccus flora» (n = 16) or «mixed flora» (n = 89). The most common types of uropathogens in monopathogenic infections in 2017 and 2019 were Escherichia coli (37.5% and 29.2%, respectively). Among infections caused by multiple pathogens, the most common etiological agents were Pseudomonas aeruginosa and Staphylococcus spp. Among all studied samples, 31.9% contained CTX-M-like genes, 5% VIM genes, 1.8% NDM genes, and 3.0% — OXA-48-like genes, and 5.6% of samples contained two and more genetic determinants associated with resistance, with the most prevalent gene combination being the combination of CTX-M- and OXA-48-like genes. In 69 samples with identified species of uropathogens, resistance profile to antimicrobial, determined by microbiological methods, correlated with detected resistance genetic determinants.Conclusion. Authors suggest that introduction of testing for the presence of genes associated with antibacterial resistance to general clinical practice would not only provide an opportunity to conduct epidemiological monitoring of the genetic determinants of antibiotic resistance, but also provide an opportunity to select the correct timely treatment of childhood bacteriuria caused by antibiotic-resistant infectious agents.Инфекции мочевыводящих путей (ИМП) являются вторыми по частоте встречаемости инфекциями у детей, в то время как распространение среди уропатогенов антимикробной резистентности представляет в настоящее время высокую эпидемиологическую угрозу.Цель. Провести анализ видового состава и наличия генетических детерминант антибиотикорезистентности.Материалы и методы. В ходе исследования был проведен ретроспективный анализ 215 образец средней порций мочи. Образцы были получены в течение 2017 и 2019 годов от пациентов в возрасте от 4 недель до 17 лет в ФГАУ «Национальный медицинский исследовательский Центр Здоровья Детей» Министерства здравоохранения Российской Федерации.Результаты. Видовая принадлежность патогенов была установлена в 93 образцах, в то время как бактериальный состав других образцов был классифицирован как «кишечная флора» (n = 17), «кокковая флора» (n = 16) или «смешанная флора» (n = 89). Наиболее распространенными видам уропатогенов при монопатогенных инфекциях в 2017 и 2019 являлась Escherichia coli (37,5% и 29,2%, соответственно). Среди инфекций, вызванных множественными патогенами, наиболее часто встречающимися этиологическими агентами являлись Pseudomonas aeruginosa и Staphylococcus spp. Среди всех исследованных образцов 31,9% содержали CTX-M-подобные гены, 5% гены VIM, 1,8% гены NDM, а также 3,0 % — OXA-48-подобные гены, а также 5,6% образцов содержали две и более генетические детерминанты, ассоциированные с резистентностью, при этом наиболее превалирующей комбинацией генов было сочетание CTX-M- и OXA-48-подобных генов. В 69 образцах с идентифицированными видами уропатогенов профиль устойчивости к противомикробным препаратам, определенный микробиологическими методами, соответствовал обнаруженным генам устойчивости.Выводы. Авторы полагают, что введение в общую клиническую практику тестирования на наличие генов, ассоциированных с антибактериальной резистентностью, предоставит не только возможность проведения эпидемиологического мониторинга за генетическими детерминантнами антибиотикоустойчивости, но также предоставит возможность подбирать корректное своевременное лечение детских бактериурий, вызванных антибиотикорезистентными инфекционными агентами