Combination of Endobronchial Ultrasound and Modern Cytological Diagnosis in Patients With Intrathoracic Lesions

Objective: To evaluate the effectiveness of endobronchial (EBUS) and endoscopic ultrasound (EUS) in cytomorphological verification of a malignant process using the transbronchial needle aspiration (TBNA) of the lymph nodes and mediastinal organs.Materials and methods: In 2017–2019 we analyzed the cytological samples (standard and cell block) of 172 patients (115 males and 57 females) with an average age of 61 years (25–82 years) in the clinical diagnostic laboratory of Scientific Research Institute – Ochapovsky Regional Clinical Hospital No. 1 (Krasnodar, Russian Federation). Of them 111 were used for immunocytochemical analysis. The majority of the studies (77) were performed in patients with lung cancer in order to identify the stage of the disease. We used combined bronchoscopy under general anesthesia in the operating room with high-frequency ventilation and a rapid on-site evaluation (ROSE).Results: We found the lymph node and mediastinal invasion in 140 (81%) patients who underwent EBUS-EUS TBNA. The non-diagnostic results were obtained in 32 (19%) patients. The combination of EUS and EBUS with TBNA showed the highest effectiveness in the mentioned clinical cases. The sensitivity, specificity, and accuracy of the cytologic analysis during EBUS and EUS with TBNA and no ROSE were 89%, 100%, and 90%, respectively. ROSE reduced the rate of non-diagnostic results and increased the sensitivity (96%), specificity (100%), and accuracy (97%) of the cytologic evaluation.Conclusions: According to the obtained results, we recommend using EBUS-EUS TBNA modalities for morphological verification of the mediastinal lymph nodes as a routine invasive diagnosis component of the preoperative evaluation in patients with lung cancer

Biology of archaea from a novel family Cuniculiplasmataceae (Thermoplasmata) ubiquitous in hyperacidic environments

The order Thermoplasmatales (Euryarchaeota) is represented by the most acidophilic organisms known so far that are poorly amenable to cultivation. Earlier culture-independent studies in Iron Mountain (California) pointed at an abundant archaeal group, dubbed 'G-plasma'. We examined the genomes and physiology of two cultured representatives of a Family Cuniculiplasmataceae, recently isolated from acidic (pH 1-1.5) sites in Spain and UK that are 16S rRNA gene sequence-identical with 'G-plasma'. Organisms had largest genomes among Thermoplasmatales (1.87-1.94 Mbp), that shared 98.7-98.8% average nucleotide identities between themselves and 'G-plasma' and exhibited a high genome conservation even within their genomic islands, despite their remote geographical localisations. Facultatively anaerobic heterotrophs, they possess an ancestral form of A-type terminal oxygen reductase from a distinct parental clade. The lack of complete pathways for biosynthesis of histidine, valine, leucine, isoleucine, lysine and proline pre-determines the reliance on external sources of amino acids and hence the lifestyle of these organisms as scavengers of proteinaceous compounds from surrounding microbial community members. In contrast to earlier metagenomics-based assumptions, isolates were S-layer-deficient, non-motile, non-methylotrophic and devoid of iron-oxidation despite the abundance of methylotrophy substrates and ferrous iron in situ, which underlines the essentiality of experimental validation of bioinformatic predictions

A Temperate <i>Sinorhizobium</i> Phage, AP-16-3, Closely Related to Phage 16-3: Mosaic Genome and Prophage Analysis

Soil Sinorhizobium phage AP-16-3, a strain phylogenetically close to Rhizobium phage 16-3, was isolated in a mountainous region of Dagestan, belonging to the origin of cultivated plants in the Caucasus, according to Vavilov N.I. The genome of phage AP-16-3 is 61 kbp in size and contains 62 ORFs, of which 42 ORFs have homologues in the genome of Rhizobium phage 16-3, which was studied in the 1960s–1980s. A search for Rhizobium phage 16-3-related sequences was performed in the genomes of modern strains of root nodule bacteria belonging to different species, genera, and families. A total of 43 prophages of interest were identified out of 437 prophages found in the genomes of 42 strains, of which 31 belonged to Sinorhizobium meliloti species. However, almost all of the mentioned prophages contained single ORFs, and only two prophages contained 51 and 39 ORFs homologous to phages related to 16-3. These prophages were detected in S. meliloti NV1.1.1 and Rh. leguminosarum OyaliB strains belonging to different genera; however, the similarity level of these two prophages did not exceed 14.7%. Analysis of the orphan genes in these prophages showed that they encoded predominantly virion structural elements, but also enzymes and an extensive group of hypothetical proteins belonging to the L, S, and E regions of viral genes of phage 16-3. The data obtained indicate that temperate phages related to 16-3 had high infectivity against nodule bacteria and participated in intragenomic recombination events involving other phages, and in horizontal gene transfer between rhizobia of different genera. According to the data obtained, it is assumed that the repetitive lysogenic cycle of temperate bacteriophages promotes the dissolution of the phage genetic material in the host bacterial genome, and radical updating of phage and host bacterial genomes takes place

<i>Ensifer meliloti</i> L6-AK89, an Effective Inoculant of <i>Medicago lupulina</i> Varieties: Phenotypic and Deep-Genome Screening

This paper presents a deep analysis of the accessory genome of an economically promising strain of Ensifer (Sinorhizobium) meliloti, L6-AK89, obtained as a result of next-generation high-throughput sequencing (MiSeq, MinIon). Strain L6-AK89 is a StrR mutant of the native strain CIAM1775, a symbiont of Medicago lupulina that adapted to a saline and arid habitat in NW Kazakhstan. CIAM1775 is an effective inoculant of M. lupulina cv. Mira (fodder type standard), cultivated on moderately acid soils in the NW agricultural region of Russia. Strain L6-AK89 makes it possible to obtain the expected high (>150%) increases in dry mass of the same plant variety in plant tests. The L6-AK89 genome has an increased proportion of sequences related to the accessory elements relative to reference strain Rm1021, 7.4% versus 4.8%. A set of 53 nod/noe/nol/nif/fdx/fix genes and 32 genes involved in stress tolerance together with 16S rRNA and recA–atpD–glnII–gyrB–dnaJ were evaluated. The high symbiotic efficiency of L6-АК89 with hop clover is most likely due to unique features of its genome, in combination with structural differences in its nod and stress-related genes, as well as unique clusters of quorum-sensing genes and osmoprotector synthesis