Analysis of the Microbiome of Human Lungs and Respiratory System in Lung Disorders: a Review

Микробиота легочной системы способна оказывать значимое влияние на стабильность структуры и функциональную активность легких. Инициация и прогрессирование некоторых заболеваний легких зависит от патогенных факторов, экспрессируемых легочной микробиотой, и состояния дисбиоза в целом. Метагеномные исследования, основанные на секвенировании генов 16S рРНК, позволили получить актуальные данные о составе легочной микробиоты. Гены 16S рРНК состоят из 9 вариабельных участков (V1- V9). Определение более консервативных в эволюционном плане участков последовательностей 16S рРНК гена позволяет относить исследуемые геномы бактерий к таксонам более высокого порядка, в то время как получение информации о менее консервативных участках позволяет определять принадлежность бактерий к роду или виду. В настоящее время также активно развивается метатранскриптомика, основанная на оценке числа копий транскриптов легочной микробиоты. Существование разнообразия и избыточности генов, а также вариабельность их активности в разных условиях предполагает использование таких высокопроизводительных технологий, как секвенирование РНК и методы параллельного секвенирования. Полученные данные по метатранскриптомному анализу в значительной степени дополняют результаты метагеномных исследований, в то же время предполагается, что метатранскриптомный подход более информативен, что касается исследований функциональных взаимодействий между микробиотой и организмом-хозяином. Эти подходы предполагают оценку биологической активности различных компонентов микробиома в норме и патологии. В обзоре рассмотрены методические особенности применения метагеномного анализа, а также метатранскриптомных исследований при некоторых тяжелых заболеваниях легочной системы (рак легкого, хроническая обструктивная болезнь легких, астма и муковисцидоз)The structural stability of the respiratory system and the functional activity of the lungs are influenced by the local microflora. The initiation and the progression of some lung diseases are determined by pathogenic factors produced by the lung microbiota and the dysbiotic conditions in general. Metagenomic studies based on sequencing of the genes for 16S ribosomal RNA have been used to collect direct data on the composition of the lung microbiota. 16S rRNA genes consist of 9 variable regions (V1-V9). By determining highly conservative 16S rRNA regions, bacterial genomes can be assigned to higher-level taxa, while based on information about less conservative regions of these genes, the genera or species of bacteria can be identified. Metatranscriptomics, which is based on estimating the number of copies of transcripts from the pulmonary microbiota, is also rapidly developing. The diversity and redundancy of genes and their variable activity in different conditions are prerequisites for using high-performance technologies such as RNA‑seq and parallel sequencing methods. The metatranscriptomic analysis data significantly complement metagenomics; at the same time, metatranscriptomics is assumed to be more informative in examination of functional interactions between microbiome and host organism. These approaches offer an estimation of the biological activity of different components in the microbiome under normal and pathological conditions. This review summarizes the results of recent metagenomic and metatranscriptomic studies regarding a number of serious diseases of the respiratory system (lung cancer, chronic obstructive lung disease, asthma, and cystic fibrosis

Search for rare or forbidden decays of the D0 meson

We present a search for nine lepton-number-violating and three lepton-flavor-violating neutral charm decays of the type D0→h'−h−ℓ'+ℓ+ and D0→h'−h+ℓ'±ℓ∓, where h and h′ represent a K or π meson and ℓ and ℓ′ an electron or muon. The analysis is based on 468 fb−1 of e+e− annihilation data collected at or close to the Υ(4S) resonance with the BABAR detector at the SLAC National Accelerator Laboratory. No significant signal is observed for any of the twelve modes, and we establish 90% confidence level upper limits on the branching fractions in the range (1.0–30.6)×10−7. The limits are between 1 and 3 orders of magnitude more stringent than previous measurements.publishedVersio

Measurements of the absolute branching fractions of B± →k±Xc c

A study of the two-body decays B±→Xc¯cK±, where Xc¯c refers to one charmonium state, is reported by the BABAR Collaboration using a data sample of 424 fb−1. The absolute determination of branching fractions for these decays are significantly improved compared to previous BABAR measurements. Evidence is found for the decay B+→X(3872)K+ at the 3σ level. The absolute branching fraction B[B+→X(3872)K+]=[2.1±0.6(stat)±0.3(syst)]×10−4 is measured for the first time. It follows that B[X(3872)→J/ψπ+π−]=(4.1±1.3)%, supporting the hypothesis of a molecular component for this resonance.publishedVersio

Light meson spectroscopy from Dalitz plot analyses of ηc decays to η0 K+K− , η0 π + π − , and ηπ + π − produced in two-photon interactions

We study the processes γγ→ηc→η′K+K−, η′π+π−, and ηπ+π− using a data sample of 519  fb−1 recorded with the BABAR detector operating at the SLAC PEP-II asymmetric-energy e+e− collider at center-of-mass energies at and near the Υ(nS) (n=2, 3, 4) resonances. This is the first observation of the decay ηc→η′K+K− and we measure the branching fraction Γ(ηc→η′K+K−)/(Γ(ηc→η′π+π−)=0.644±0.039stat±0.032sys. Significant interference is observed between γγ→ηc→ηπ+π− and the nonresonant two-photon process γγ→ηπ+π−. A Dalitz plot analysis is performed of ηc decays to η′K+K−, η′π+π−, and ηπ+π−. Combined with our previous analysis of ηc→K¯Kπ, we measure the K∗0(1430) parameters and the ratio between its η′K and πK couplings. The decay ηc→η′π+π− is dominated by the f0(2100) resonance, also observed in J/ψ radiative decays. A new a0(1700)→ηπ resonance is observed in the ηc→ηπ+π− channel. We also compare ηc decays to η and η′ final states in association with scalar mesons as they relate to the identification of the scalar glueball.publishedVersio

Assessment of radioactivity of environmental components in the Kostomuksha State Nature Reserve

The radiological state of the land and water areas constantly attracts public interest. Specially protected natural reservations deserve special attention when it comes to studying radiological conditions. This study presents findings of radioecological investigations conducted in the Kostomuksha State Nature Reserve in 2012 – 2015. The Kostomuksha Mining Company, which is developing the Kostomuksha iron ore deposit was identified as a potentially hazardous facility that might affect the radioecological situation in the naturel reserve, since production of iron ores at the deposit involves extraction to the ground surface of acid rocks characterised by a naturally high content of radioactive elements (granitic gneiss). Furthermore, several sources of radioactive radon gas have been identified within the reserve boundaries. The study included investigation of natural and anthropogenic radioactivity in the environmental components of the nature reserve and adjacent territories, including soil, plants, bottom sediments, ambient air and natural waters. It was found that development of the Kostomuksha iron ore deposit and operations of the mining and processing plant do not exert any considerable impact on the radiological situation in the nature reserve. Data obtained during the study indicate that the overall radiological situation in the reserve is acceptable and meets the relevant radiation safety standards. High levels of radiocesium were found in the moss and bottom sediments of the nature reserve, which requires additional research to determine a wider pattern of distribution of anthropogenic radioactivity across the adjacent territories and to study the processes of buildup and migration of radionuclides in aquatic organisms of Kamennoye Lake

Sputum Microbiota in Coal Workers Diagnosed with Pneumoconiosis as Revealed by 16S rRNA Gene Sequencing

Coal worker’s pneumoconiosis (CWP) is an occupationally induced progressive fibrotic lung disease. This irreversible but preventable disease currently affects millions across the world, mainly in countries with developed coal mining industries. Here, we report a pilot study that explores the sputum microbiome as a potential non-invasive bacterial biomarker of CWP status. Sputum samples were collected from 35 former and active coal miners diagnosed with CWP and 35 healthy controls. Sequencing of bacterial 16S rRNA genes was used to study the taxonomic composition of the respiratory microbiome. There was no difference in alpha diversity between CWP and controls. The structure of bacterial communities in sputum samples (β diversity) differed significantly between cases and controls (pseudo-F = 3.61; p = 0.004). A significant increase in the abundance of Streptococcus (25.12 ± 11.37 vs. 16.85 ± 11.35%; p = 0.0003) was detected in samples from CWP subjects as compared to controls. The increased representation of Streptococcus in sputum from CWP patients was associated only with the presence of occupational pulmonary fibrosis, but did not depend on age, and did not differ between former and current miners. The study shows, for the first time, that the sputum microbiota of CWP subjects differs from that of controls. The results of our present exploratory study warrant further investigations on a larger cohort