Lung cancer is the leading cancer diagnosis worldwide and the number one cause of cancer deaths. Exposure to cigarette smoke, the primary risk factor in lung cancer, reduces epithelial barrier ...integrity and increases susceptibility to infections. Herein, we hypothesize that somatic mutations together with cigarette smoke generate a dysbiotic microbiota that is associated with lung carcinogenesis. Using lung tissue from 33 controls and 143 cancer cases, we conduct 16S ribosomal RNA (rRNA) bacterial gene sequencing, with RNA-sequencing data from lung cancer cases in The Cancer Genome Atlas serving as the validation cohort.
Overall, we demonstrate a lower alpha diversity in normal lung as compared to non-tumor adjacent or tumor tissue. In squamous cell carcinoma specifically, a separate group of taxa are identified, in which Acidovorax is enriched in smokers. Acidovorax temporans is identified within tumor sections by fluorescent in situ hybridization and confirmed by two separate 16S rRNA strategies. Further, these taxa, including Acidovorax, exhibit higher abundance among the subset of squamous cell carcinoma cases with TP53 mutations, an association not seen in adenocarcinomas.
The results of this comprehensive study show both microbiome-gene and microbiome-exposure interactions in squamous cell carcinoma lung cancer tissue. Specifically, tumors harboring TP53 mutations, which can impair epithelial function, have a unique bacterial consortium that is higher in relative abundance in smoking-associated tumors of this type. Given the significant need for clinical diagnostic tools in lung cancer, this study may provide novel biomarkers for early detection.
Gardnerella vaginalis is an important component of the human vaginal microflora. It is proposed to play a key role in the pathogenesis of bacterial vaginosis (BV), the most common vaginal condition. ...Here we describe the development, validation and comparative analysis of a novel molecular approach capable of G. vaginalis identification, quantification and subtyping in noncultured vaginal specimens. Using two quantitative PCR (qPCR) assays, we analysed G. vaginalis bacterial loads and clade distribution in 60 clinical vaginal-swab samples. A very high pathogen prevalence was revealed by species-specific qPCR not only among BV patients (100 %), but also in healthy women (97 %), although the G. vaginalis concentration was significantly lower in non-BV samples. G. vaginalis clades identified in vaginal specimens by subtyping multiplex qPCR, which targets four clade-specific genetic markers, had frequencies of 53 % for clade 1, 25 % for clade 2, 32 % for clade 3 and 83 % for clade 4. Multiple clades were found in 70 % of samples. Single G. vaginalis clades were represented by clade 1 and clade 4 in 28 % of specimens. A positive association with BV was shown for clade 1 and clade 3, while clade 2 was positively associated with intermediate vaginal microflora, but not with BV. Clade 4 demonstrated no correlation with the disorder. The presence of multiple clades had a high positive association with BV, whereas G. vaginalis identified as a single clade was negatively linked with the condition. Polyclonal G. vaginalis infection may be a risk factor for BV.
Abstract Lactobacilli play a key role in promoting vaginal health. Depletion of these bacteria is associated with bacterial vaginosis (BV), the most common vaginal disorder. Here we describe the ...development and laboratory validation of a novel single-tube multiplex TaqMan quantitative polymerase chain reaction (qPCR) assay for the identification and quantitative assessment of the four major vaginal Lactobacillus species: L. crispatus , L. jensenii , L. gasseri , and L. iners . The assay utility was evaluated by the analysis of lactobacilli in non-cultured clinical vaginal swab specimens collected from BV patients and healthy individuals. As confirmed by the assay, L. crispatus , L. jensenii , and to a lesser extent L. gasseri , are common in the vagina of healthy women, whereas L. iners dominance is associated with BV. The major assay limitation was preferential detection of dominant Lactobacillus species in samples with mixed lactobacilli resulting in lower sensitivity for minor species. The multiplex qPCR assay described here is an advance in the detection and quantitation of the major vaginal lactobacilli, potentially facilitating the molecular diagnosis of BV and post-therapy restoration of the vaginal microflora.
Following publication of the original paper 1, the authors submitted a new Additional file 5 to replace the one containing formatting issues. The updated Additional file 5 is published in this ...correction.
A lysine instead of the usual carboxyl group is in place of the internal proton donor to the retinal Schiff base in the light-driven proton pump of Exiguobacterium sibiricum (ESR). The involvement of ...this lysine in proton transfer is indicated by the finding that its substitution with alanine or other residues slows reprotonation of the Schiff base (decay of the M intermediate) by more than 2 orders of magnitude. In these mutants, the rate constant of the M decay linearly decreases with a decrease in proton concentration, as expected if reprotonation is limited by the uptake of a proton from the bulk. In wild type ESR, M decay is biphasic, and the rate constants are nearly pH-independent between pH 6 and 9. Proton uptake occurs after M formation but before M decay, which is especially evident in D2O and at high pH. Proton uptake is biphasic; the amplitude of the fast phase decreases with a pKa of 8.5 ± 0.3, which reflects the pKa of the donor during proton uptake. Similarly, the fraction of the faster component of M decay decreases and the slower one increases, with a pKa of 8.1 ± 0.2. The data therefore suggest that the reprotonation of the Schiff base in ESR is preceded by transient protonation of an initially unprotonated donor, which is probably the ε-amino group of Lys-96 or a water molecule in its vicinity, and it facilitates proton delivery from the bulk to the reaction center of the protein.
Aspergillus fumigatus is an important cause of life-threatening invasive fungal disease in patients with compromised immune systems. Resistance to itraconazole in A. fumigatus is closely linked to ...amino acid substitutions in Cyp51A that replace Gly54. In an effort to develop a new class of molecular diagnostic assay that can rapidly assess drug resistance, a multiplexed assay was established. This assay uses molecular beacons corresponding to the wild-type cyp51A gene and seven mutant alleles encoding either Arg54, Lys54, Val54, Trp54, or Glu54. Molecular beacon structure design and real-time PCR conditions were optimized to increase the assay specificity. The multiplex assay was applied to the analysis of chromosomal DNA samples from a collection of 48 A. fumigatus clinical and laboratory-derived isolates, most with reduced susceptibility to itraconazole. The cyp51A allelic identities for codon 54 were established for all of the strains tested, and mutations altering Gly54 in 23 strains were revealed. These mutations included G₅₄W (n = 1), G₅₄E (n = 12), G₅₄K (n = 3), G₅₄R (n = 3), and G₅₄V (n = 4). Molecular beacon assay results were confirmed by DNA sequencing. Multiplex real-time PCR with molecular beacons is a powerful technique for allele differentiation and analysis of resistance mutations that is dynamic and suitable for rapid high-throughput assessment of drug resistance.
The aim of the present study was to compare different methods of health status assessment in organized cohort of penitentiary employees in Saratov Region, Russian Federation.
1,014 penitentiary ...employees (81.8% male) aged 33.4±6.8 years were included in the cohort study. All participants underwent an annual preventive health examination in the Center of Medical and Social Rehabilitation of Russian Federal Penitentiary Service in Saratov Region. The prevalence of common cardiovascular risk factors was assessed. Risk Score and the number of fulfilled health metrics proposed by American Heart Association (AHA) were calculated for each participant.
It is shown that penitentiary staff in Saratov Region is characterized by low current risk score (1.2±0.8%), but high prevalence of such risk factors as increased body weight and obesity (51%), tobacco use or passive smoking (81%), and unhealthy diet (55%). 98.4% of participants had the Score level of ≤5%, but only 4.5% of penitentiary staff met the ideal cardiovascular health (they met all seven AHA health metrics). One fifth of the participants met three or less AHA health metrics. A statistically significant correlation between the risk Score and the number of fulfilled AHA health metrics is revealed (Chi-square = 5.1, p=0.024). The probability of fulfilment of less than 5 AHA health metrics in subjects with medium risk score is shown to be almost twofold greater than in subjects with low risk Score. However, there are a lot of differences in the assessment of cardiovascular health by risk Score and AHA health metrics.
AHA health metrics are more preferable than the risk Score or assessment of separate cardiovascular risk factors for preventive management in organized cohorts with low current cardiovascular risk such as penitentiary staff in Saratov Region.
In this study, we prepared soldered joints of 2G HTS wires from three different manufacturers: SuNAM, SuperPower, and SuperOx. We used Pb 39 Sn 61 solder and varied the pressure applied on the joint ...during soldering in the 3.9-10.5 MPa range. We found that for all samples, joint resistivity decreased with increasing applied pressure. Practically important, very low joint resistivity values in the 10-15 nΩ·cm 2 range were reproducibly achieved in joints made with SuperPower and SuperOx wire. Resistivity of joints made with SuNAM wire was rather high, in the 40-90 nΩ·cm 2 range. No degradation in I c across joints occurred in joints made at up to 8 MPa applied pressure. In joints made with SuperOx wire at applied pressure above 8 MPa, there was I c degradation comparing to the initial I c of individual wires before joining. We speculate on the possible reasons for the different resistivity and I c degradation behavior of joints made with wires from different manufacturers.
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