Discrimination between Streptococcus pneumoniae and Streptococcus mitis based on sorting of their MALDI mass spectra

AbstractAccurate species-level identification of alpha-hemolytic (viridans) streptococci (VGS) is very important for understanding their pathogenicity and virulence. However, an extremely high level of similarity between VGS within the mitis group (S. pneumoniae, S. mitis, S. oralis and S. pseudopneumoniae) often results in misidentification of these organisms. Earlier, matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) has been suggested as a tool for the rapid identification of S. pneumoniae. However, by using Biotyper 3.0 (Bruker) or Vitek MS (bioMérieux) databases, Streptococcus mitis/oralis species can be erroneously identified as S. pneumoniae. ClinProTools 2.1 software was used for the discrimination of MALDI-TOF mass spectra of 25 S. pneumoniae isolates, 34 S. mitis and three S. oralis. Phenotypical tests and multilocus gene typing schemes for the S. pneumoniae (http://spneumoniae.mlst.net/) and viridans streptococci (http://viridans.emlsa.net/) were used for the identification of isolates included in the study. The classifying model was generated based on different algorithms (Genetic Algorithm, Supervised Neural Network and QuickClassifier). In all cases, values of sensitivity and specificity were found to be equal or close to 100%, allowing discrimination of mass spectra of different species. Three peaks (6949, 9876 and 9975 m/z) were determined conferring the maximal statistical weight onto each model built. We find this approach to be promising for viridans streptococci discrimination

Mediators and biomarkers of inflammation in meningitis: Cytokine and peptidome profiling of cerebrospinal fluid

© 2016, Pleiades Publishing, Ltd.Differential diagnosis of bacterial and viral meningitis is an urgent problem of the modern clinical medicine. Early and accurate detection of meningitis etiology largely determines the strategy of its treatment and significantly increases the likelihood of a favorable outcome for the patient. In the present work, we analyzed the peptidome and cytokine profiles of cerebrospinal fluid (CSF) of 17 patients with meningitis of bacterial and viral etiology and of 20 neurologically healthy controls. In addition to the identified peptides (potential biomarkers), we found significant differences in the cytokine status of the CSF of the patients. We found that cut-off of 100 pg/ml of IL-1β, TNF, and GM-CSF levels discriminates bacterial and viral meningitis with 100% specificity and selectivity. We demonstrated for the first time the reduction in the level of two cytokines, IL-13 and GM-CSF, in the CSF of patients with viral meningitis in comparison with the controls. The decrease in GM-CSF level in the CSF of patients with viral meningitis can be explained by a disproportionate increase in the levels of cytokines IL-10, IFN-γ, and IL-4, which inhibit the GM-CSF expression, whereas IL-1, IL-6, and TNF activate it. These observations suggest an additional approach for differential diagnosis of bacterial and viral meningitis based on the normalized ratio IL-10/IL-1β and IL-10/TNF > 1, as well as on the ratio IFN-γ/IL-1β and IFN-γ/ TNF < 0.1. Our findings extend the panel of promising clinical and diagnostic biomarkers of viral and bacterial meningitis and reveal opposite changes in the cytokine expression in meningitis due to compensatory action of proand antiinflammatory factors

RNA-Seq gene expression profiling of HepG2 cells: The influence of experimental factors and comparison with liver tissue

© Tyakht et al.; licensee BioMed Central. Background: Human hepatoma HepG2 cells are used as an in vitro model of the human liver. High-throughput transcriptomic sequencing is an advanced approach for assessing the functional state of a tissue or cell type. However, the influence of experimental factors, such as the sample preparation method and inter-laboratory variation, on the transcriptomic profile has not been evaluated. Results: The whole-transcriptome sequencing of HepG2 cells was performed using the SOLiD platform and validated using droplet digital PCR. The gene expression profile was compared to the results obtained with the same sequencing method in another laboratory and using another sample preparation method. We also compared the transcriptomic profile HepG2 cells with that of liver tissue. Comparison of the gene expression profiles between the HepG2 cell line and liver tissue revealed the highest variation, followed by HepG2 cells submitted to two different sample preparation protocols. The lowest variation was observed between HepG2 cells prepared by two different laboratories using the same protocol. The enrichment analysis of the genes that were differentially expressed between HepG2 cells and liver tissue mainly revealed the cancer-associated gene signature of HepG2 cells and the activation of the response to chemical stimuli in the liver tissue. The HepG2 transcriptome obtained with the SOLiD platform was highly correlated with the published transcriptome obtained with the Illumina and Helicos platforms, with moderate correspondence to microarrays. Conclusions: In the present study, we assessed the influence of experimental factors on the HepG2 transcriptome and identified differences in gene expression between the HepG2 cell line and liver cells. These findings will facilitate robust experimental design in the fields of pharmacology and toxicology. Our results were supported by a comparative analysis with previous HepG2 gene expression studies

Genome-Wide Mycobacterium tuberculosis Variation (GMTV) Database: A New Tool for Integrating Sequence Variations and Epidemiology

Background Tuberculosis (TB) poses a worldwide threat due to advancing multidrug-resistant strains and deadly co-infections with Human immunodeficiency virus. Today large amounts of Mycobacterium tuberculosis whole genome sequencing data are being assessed broadly and yet there exists no comprehensive online resource that connects M. tuberculosis genome variants with geographic origin, with drug resistance or with clinical outcome. Description Here we describe a broadly inclusive unifying Genome-wide Mycobacterium tuberculosis Variation (GMTV) database, (http://mtb.dobzhanskycenter.org) that catalogues genome variations of M. tuberculosis strains collected across Russia. GMTV contains a broad spectrum of data derived from different sources and related to M. tuberculosis molecular biology, epidemiology, TB clinical outcome, year and place of isolation, drug resistance profiles and displays the variants across the genome using a dedicated genome browser. GMTV database, which includes 1084 genomes and over 69,000 SNP or Indel variants, can be queried about M. tuberculosis genome variation and putative associations with drug resistance, geographical origin, and clinical stages and outcomes. Conclusions Implementation of GMTV tracks the pattern of changes of M. tuberculosis strains in different geographical areas, facilitates disease gene discoveries associated with drug resistance or different clinical sequelae, and automates comparative genomic analyses among M. tuberculosis strains

Data on gut metagenomes of the patients with Helicobacter pylori infection before and after the antibiotic therapy

© 2017Antibiotic therapy can lead to the disruption of gut microbiota community with possible negative outcomes for human health. One of the diseases for which the treatment scheme commonly included antibiotic intake is Helicobacter pylori infection. The changes in taxonomic and functional composition of microbiota in patients can be assessed using “shotgun” metagenomic sequencing. Ten stool samples were collected from 4 patients with Helicobacter pylori infection before and directly after the H. pylori eradication course. Additionally, for two of the subjects, the samples were collected 1 month after the end of the treatment. The samples were subject to “shotgun” (whole-genome) metagenomic sequencing using Illumina HiSeq platform. The reads are deposited in the ENA (project ID: PRJEB18265)

Методы сохранения оптических свойств поверхности зеркал космического телескопа Т-170М проекта «Спектр-УФ» на этапе предполётной подготовки

Astrophysical observations in the ultraviolet band have many advantages. At present, the «Spektr-UF» project is under implementation to create a large space observatory for operation in the ultraviolet spectrum.Requirements for the ultraviolet telescope optics quality are extremely high. Therefore, both to manufacture such a large space telescope as the T-170M and to transport it to the launch complex are rather difficult challenges in terms of technology.When manufacturing optical elements of the telescope T-170M, a combination of Al+MgF2 coatings has been preferred. At the same time, atmospheric oxygen penetrates through the pores in the magnesium fluoride, thereby forming a Al2O3 oxide layer on the sputtered aluminum, which significantly degrades the UV reflectivity of the mirror surface. It is also necessary to fulfill the requirements for surface cleanliness of optical system elements of the telescope during the finished product transportation and its storage and to provide for the autonomous operation of the system that maintains atmosphere control.To solve the set tasks:1)    a dust-proof-and-moisture-proof sheath (DPAMPS) was designed to prevent the optical system mirror surfaces of the telescope from coming in contact with atmosphere;2)    to provide a controlled atmosphere inside the DPAMPS the need is justified to blow gaseous nitrogen of special purity (grade 1) in accordance with GOST 9293-74 with a dew point temperature of -50°С, at most, inside the telescope; calculations have proved that charging with the super-atmospheric pressure of 10 kPa provides the optimal conditions for maintaining the optical properties of the space telescope mirrors surface, and also minimizes the loads on the easily damaging elements of the telescope;3)    to ensure the required cleanliness of the optical system elements surfaces of the telescope inside the DPAMPS, a class of purity Class 7 ISO, at worst, is established in accordance with GOST ISO 14644-1-2002; contamination tolerance of optical system components being, at most, 0.03% of the total surface area (300 p.p.m.) is provided by the rational choice of the blow-down scheme of the telescope with feeding nitrogen through the equipment bay;4)    a rational design of the supercharger using a gas analyzer and boost valves with external feedback provides driving pressure and operation autonomy of the system that maintains atmosphere control.Астрофизические наблюдения в УФ-диапазоне обладают многими преимуществами. В настоящее время идёт выполнение проекта «Спектр-УФ», направленного на создание крупной космической обсерватории для работы в ультрафиолетовом участке спектра.Требования к качеству оптики ультрафиолетового телескопа предельно высоки, поэтому изготовление такого крупного космического телескопа, как Т-170М, а также его транспортировка на стартовый комплекс – весьма сложные технологические задачи.При изготовлении оптических элементов телескопа Т-170М сделан выбор в пользу сочетания покрытий Al+MgF2. При этом через поры во фториде магния проникает атмосферный кислород, приводя к образованию на напылённом алюминии слоя оксида (Al2O3), который значительно ухудшает УФ-отражательную способность поверхности зеркала. Также необходимо выполнить требования к чистоте поверхностей элементов оптической системы телескопа при транспортировке готового изделия и его хранении и предусмотреть автономность работы системы поддержания контролируемой атмосферы.Для решения поставленных задач:1) был разработан пылевлагозащитный чехол (ПВЗЧ), предотвращающий контакт поверхностей зеркал оптической системы телескопа с атмосферой;2) для создания внутри ПВЗЧ контролируемой атмосферы обоснована необходимость выполнения поддува внутрь телескопа газообразного азота особой чистоты (сорт 1) в соответствии с ГОСТ 9293-74 с температурой точки росы не выше -50°С; расчётами подтверждено, что наддув избыточным давлением 10 кПа обеспечивает оптимальные условия сохранения оптических свойств поверхности зеркал космического телескопа, а также минимизирует нагрузки на легкоповреждаемые элементы телескопа;3) для обеспечения требуемой чистоты поверхностей элементов оптической системы телескопа внутри ПВЗЧ установлен класс чистоты не хуже класса 7 ИСО в соответствии с ГОСТ ИСО 14644-1-2002; допустимое загрязнение деталей оптической системы не более 0,03% от общей площади поверхности (300 p.p.m.) обеспечено рациональным выбором схемы продува телескопа подачей азота через инструментальный отсек;4) рабочее давление и автономность работы системы поддержания контролируемой атмосферы обеспечены рациональной конструкцией агрегата наддува с использованием газоанализатора и клапанов наддува с внешней обратной связью

Study of the K- -> pi0 e- nu decay

The decay K- -> pi0 e- nu has been studied using in-flight decays detected with "ISTRA+" setup operating at the 25 GeV negative secondary beam of the U-70 PS. About 130K events were used for the analysis. The lambda_+ parameter of the vector formfactor has been measured: lambda_+ = 0.0293 +- 0.0015(stat) +- 0.002(syst). The limits on the possible tensor and scalar couplings have been derived: f_T/f_+(0)=-0.044 +0.059 -0.057 (stat) f_S/f_+(0)=-0.020 +0.025 -0.016 (stat)Comment: 11 pages, Latex, 9 picture

Human gut microbiota community structures in urban and rural populations in Russia

The microbial community of the human gut has a crucial role in sustaining host homeostasis. High-throughput DNA sequencing has delineated the structural and functional configurations of gut metagenomes in world populations. The microbiota of the Russian population is of particular interest to researchers, because Russia encompasses a uniquely wide range of environmental conditions and ethnogeographical cohorts. Here we conduct a shotgun metagenomic analysis of gut microbiota samples from 96 healthy Russian adult subjects, which reveals novel microbial community structures. The communities from several rural regions display similarities within each region and are dominated by the bacterial taxa associated with the healthy gut. Functional analysis shows that the metabolic pathways exhibiting differential abundance in the novel types are primarily associated with the trade-off between the Bacteroidetes and Firmicutes phyla. The specific signatures of the Russian gut microbiota are likely linked to the host diet, cultural habits and socioeconomic status. © 2013 Macmillan Publishers Limited. All rights reserved

Study of the resistome of human microbial communities using a targeted panel of antibiotic resistance genes in COVID-19 patients

Aim. To study overall drug resistance genes (resistome) in the human gut microbiome and the changes in these genes during COVID-19 in-hospital therapy. Materials and methods. A single-center retrospective cohort study was conducted. Only cases with laboratory-confirmed SARS-CoV-2 RNA using polymerase chain reaction in oro-/nasopharyngeal swab samples were subject to analysis. The patients with a documented history of or current comorbidities of the hepatobiliary system, malignant neoplasms of any localization, systemic and autoimmune diseases, as well as pregnant women were excluded. Feces were collected from all study subjects for subsequent metagenomic sequencing. The final cohort was divided into two groups depending on the disease severity: mild (group 1) and severe (group 2). Within group 2, five subgroups were formed, depending on the use of antibacterial drugs (ABD): group 2A (receiving ABD), group 2AC (receiving ABD before hospitalization), group 2AD (receiving ABD during hospitalization), group 2AE (receiving ABD during and before hospitalization), group 2B (not receiving ABD). Results. The median number of antibiotic resistance (ABR) genes (cumulative at all time points) was significantly higher in the group of patients treated with ABD: 81.0 (95% CI 73.8–84.5) vs. 51.0 (95% CI 31.1–68.4). In the group of patients treated with ABD (2A), the average number of multidrug resistance genes (efflux systems) was significantly higher than in controls (group 2B): 47.0 (95% CI 46.0–51.2) vs. 21.5 (95% CI 7.0–43.9). Patients with severe coronavirus infection tended to have a higher median number of ABR genes but without statistical significance. Patients in the severe COVID-19 group who did not receive ABD before and during hospitalization also had more resistance genes than the patients in the comparison group. Conclusion. This study demonstrated that fewer ABR genes were identified in the group with a milder disease than in the group with a more severe disease associated with more ABR genes, with the following five being the most common: SULI, MSRC, ACRE, EFMA, SAT