An improved and extended dual-index multiplexed 16S rRNA sequencing for the Illumina HiSeq and MiSeq platform.

BACKGROUND: Recent advancements in next-generation sequencing (NGS) technology have ushered in significant improvements in sequencing speed and data throughput, thereby enabling the simultaneous analysis of a greater number of samples within a single sequencing run. This technology has proven particularly valuable in the context of microbial community profiling, offering a powerful tool for characterizing the microbial composition at the species level within a given sample. This profiling process typically involves the sequencing of 16S ribosomal RNA (rRNA) gene fragments. By scaling up the analysis to accommodate a substantial number of samples, sometimes as many as 2,000, it becomes possible to achieve cost-efficiency and minimize the introduction of potential batch effects. Our study was designed with the primary objective of devising an approach capable of facilitating the comprehensive analysis of 1,711 samples sourced from diverse origins, including oropharyngeal swabs, mouth cavity swabs, dental swabs, and human fecal samples. This analysis was based on data obtained from 16S rRNA metagenomic sequencing conducted on the Illumina MiSeq and HiSeq sequencing platforms. RESULTS: We have designed a custom set of 10-base pair indices specifically tailored for the preparation of libraries from amplicons derived from the V3-V4 region of the 16S rRNA gene. These indices are instrumental in the analysis of the microbial composition in clinical samples through sequencing on the Illumina MiSeq and HiSeq platforms. The utilization of our custom index set enables the consolidation of a significant number of libraries, enabling the efficient sequencing of these libraries in a single run. CONCLUSIONS: The unique array of 10-base pair indices that we have developed, in conjunction with our sequencing methodology, will prove highly valuable to laboratories engaged in sequencing on Illumina platforms or utilizing Illumina-compatible kits.

The Effect of Drugs with α-Glutamyl-Tryptophan for Cytokine Secretion and Level of Surface Molecule ICAM-1 In Vitro.

The study of the molecular mechanisms underlying the action of immunomodulatory drugs is important for substantiating their therapeutic effect. In the present work, spontaneous and TNFα-induced secretion of IL-1α and IL-8 pro-inflammatory cytokines, as well as the level of the ICAM-1 adhesion molecule in EA.hy 926 endothelial cell culture and peripheral blood mononuclear cells of healthy donors, is studied using an in vitro model of inflammation in the presence of α-glutamyl-tryptophan (α-Glu-Trp) and Cytovir-3. The aim was to evaluate cellular mechanisms mediating the immunomodulatory effect of α-Glu-Trp and Cytovir-3 drugs. It was shown that α-Glu-Trp reduced TNFα-induced IL-1α production and increased TNFα-stimulated level of the ICAM-1 surface molecule of endothelial cells. At the same time, the drug reduced secretion of the IL-8 cytokine induced by TNFα and increased the spontaneous level of ICAM-1 in mononuclear cells. Cytovir-3 had an activating effect on EA.hy 926 endothelial cells and human peripheral blood mononuclear leukocytes. In its presence, there was an increase in the spontaneous secretion of IL-8 by endothelial and mononuclear cells. In addition, Cytovir-3 increased the level of TNFα-induced ICAM-1 on endothelial cells and increased the spontaneous level of this surface molecule on mononuclear cells. Suppression of stimulated production of pro-inflammatory cytokines under the action of α-Glu-Trp both separately and as a part of Cytovir-3 may determine its anti-inflammatory properties. However, an increased level of the surface ICAM-1 molecule indicates mechanisms that enhance the functional activity of these cells, which is equally important for the implementation of an effective immune response to infection and repair of damaged tissues during inflammatory response.

[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.

[Composition of oropharyngeal microbiota in patients with COVID-19 of different pneumonia severity].

AIM: To identify features of the taxonomic composition of the oropharyngeal microbiota of COVID-19 patients with different disease severity. MATERIALS AND METHODS: The study group included 156 patients hospitalized with confirmed diagnosis of COVID-19 in the clinical medical center of Yevdokimov Moscow State University of Medicine and Dentistry between April and June 2021. There were 77 patients with mild pneumonia according to CT (CT1) and 79 patients with moderate to severe pneumonia (CT2 and CT3). Oropharyngeal swabs were taken when the patient was admitted to the hospital. Total DNA was isolated from the samples, then V3V4 regions of the 16s rRNA gene were amplified, followed by sequencing using Illumina HiSeq 2500 platform. DADA2 algorithm was used to obtain amplicon sequence variants (ASV). RESULTS: When comparing the microbial composition of the oropharynx of the patients with different forms of pneumonia, we have identified ASVs associated with the development of both mild and severe pneumonia outside hospital treatment. Based on the results obtained, ASVs associated with a lower degree of lung damage belong predominantly to the class of Gram-negative Firmicutes (Negativicutes), to various classes of Proteobacteria, as well as to the order Fusobacteria. In turn, ASVs associated with a greater degree of lung damage belong predominantly to Gram-positive classes of Firmicutes Bacilli and Clostridia. While being hospitalized, patients with severe pneumonia demonstrated negative disease dynamics during treatment significantly more often. CONCLUSION: We have observed differences in the taxonomic composition of the oropharyngeal microbiota in patients with different forms of pneumonia developed outside hospital treatment against COVID-19. Such differences might be due to the presumed barrier function of the oropharyngeal microbiota, which reduces the risk of virus titer increase.

Ab initio predictions and laboratory validation for consistent ozone intensities in the MW, 10 and 5 µm ranges.

Reliable ozone spectral data consistent over several spectral ranges are a challenge for both experiment and theory. We present ab initio calculations for strong lines that lead to consistent results from the microwave to mid-infrared regions. The results agree well with established microwave line lists and our new measurements in the fundamental and first overtone regions of ozone at 5 and 10 µm. The calculations and their agreement to within 1% with measurements provide an important step toward consistent and accurate spectroscopic ozone data. The results imply that actual databases need to be corrected by about 3% in the corresponding mid-infrared spectral intervals. Appropriate recommendations for the consistency of strong line intensities of the ozone molecule in microwave, 10 and 5 µm ranges, in HITRAN (HIgh-resolution TRANsmittance and molecular apbsorption) and GEISA (Gestion et Etude des Informations Spectroscopiques Atmosphériques) databases are suggested.

[Bioinformatics analysis of antimicrobial resistance genes and prophages colocalized in human gut metagenomes]. / Bioinformaticheskii analiz kolokalizatsii genov rezistentnosti i profagov v metagenomakh kishechnika cheloveka.

The constant increase of antibiotic-resistant strains of bacteria is caused by extensive uses of antibiotics in medicine and animal breeding. It was suggested that the gut microbiota serves as a reservoir for antibiotics resistance genes that can be carried from symbiotic bacteria to pathogenic ones, in particular, as a result of transduction. In the current study, we have searched for antibiotics resistance genes that are located inside prophages in human gut microbiota using PHASTER prophage predicting tool and CARD antibiotics resistance database. After analysing metagenomic assemblies of eight samples of antibiotic treated patients, lsaE, mdfA and cpxR/cpxA genes were identified inside prophages. The abovementioned genes confer resistance to antimicrobial peptides, pleuromutilin, lincomycins, streptogramins and multidrug resistance. Three (0.46%) of 659 putative prophages predicted in metagenomic assemblies contained antibiotics resistance genes in their sequences.

[Monocytes of human blood as a target of Streptococcus pyogenes components].

AIM: Study the effect of components of destroyed streptococci on human blood monocyte functions related to processes of trans-endothelial migration in vitro. MATERIALS AND METHODS: Mononuclear leukocytes, isolated from blood of healthy donors, endothelial cells of EA.hy 926 line and supernatant of ultrasound disintegrated Streptococcus pyogenes (DSS) were the objects of the study. Evaluation of adhesion and monocyte migration, level of expression of adhesion molecules and phosphokinases on monocytes was carried out by flow cytometry using monoclonal antibodies. Cytokine concentration was determined by using standard commercial test systems in enzyme immunoassay. RESULTS: Under the effect of DSS, expression of adhesion molecules CD162 and CD11b, as well as phospho-p38 MAPK changed, IL-6 and IL-8 secretion induction took place. DSS caused enhancement of migration and adhesive activity of monocytes, however, inhibited intensity of trans-endothelial migration. CONCLUSION: Products of destroyed streptococci have a multi-directional effect on human blood monocytes, that could be explained by the presence of components with varying biological activity in DSS.

Does the "reef structure" at the ozone transition state towards the dissociation exist? New insight from calculations and ultrasensitive spectroscopy experiments.

Since the discovery of anomalies in ozone isotope enrichment, several fundamental issues in the dynamics linked to the shape of the potential energy surface in the transition state region have been raised. The role of the reeflike structure on the minimum energy path is an intricate question previously discussed in the context of chemical experiments. In this Letter, we bring strong arguments in favor of the absence of a submerged barrier from ultrasensitive laser spectroscopy experiments combined with accurate predictions of highly excited vibrations up to nearly 95% of the dissociation threshold.

Effect of galectin-1 on apoptosis of CD4(+) lymphocytes differentiated in vitro towards regulatory T cells.

We studied the effect of galectin-1 on apoptosis of CD4(+) lymphocytes intact and in vitro differentiated towards regulatory T cells. An increase in the content of apoptotic CD4(+) lymphocytes was observed after exposure of intact cells with 15 ng/ml galectin-1 and after exposure of regulatory T cells with 10 and 15 ng/ml galectin-1. Apoptosis of regulatory T cells induced by galectin-1 was accompanied by an increase in the content of proapoptotic protein Bad.

[Regulation of the genes expression of CD4+ T-lymphocytes differentiation transcription factors by galectin-3 in vitro].

Now a number of CD4+ T-lymphocytes, known as Th1, Th2, Treg and Th17, is currently identified and well- studied. The methods basing on the targeted regulation of differentiation process of the Th-lymphocytes that carry out the immune response polarization attract an attention of scientists dealing with a correction of immune-mediated. In the present study, endogenous beta-galactoside-binding protein of the lectin family, galectin-3, was investigated as a regulator of T-cell homeostasis. A galectin-3 is known to be actively produced by tumor cells in malignant transformation and able to influence the processes of signal transduction, cell-cell cooperation and the implementation of programmed death. As cell differentiation processes are directly connected with the regulation of gene expression, we investigated the effect of recombinant galectin-3 on expression of mRNA of transcription.factors, which guide the differentiation of CD4+ lymphocytes. The study was performed on peripheral blood mononuclear cells of healthy individuals. The gene expression levels were evaluated by a real-time PCR. In the experiments in vitro, it has been first found the recombinant galectin-3 (0.5 mg/mL) up-regulating the expression of transcription factors Gata-3 and Rorc mRNAs and down-regulating the mRNA expression of transcription factors T-bet and FoxP3. Up to a concentration of 1 mg/mL recombinant galectin-3 stimulates Th-cells by dose-dependent manner, whereas at higher concentrations stimulating effect weakens, and inhibiting action starts prevailing. Thus, one can suppose that galectin-3 through regulation of lymphocytes differentiation promote development of allergic, autoimmune and neoplastic diseases that allows us to consider the galectin-3 as a.potential target for therapy of these diseases.

[Intracellular targets of proapoptotic influence of gaseous transmitters].

Main molecular targets of nitric oxide, hydrogen sulfide and carbon monoxide proapoptotic action in Jurkat cells were determined in this study. Decrease of mitochondrial transmembrane potential was shown during all three gases action. Reason of this event is the Bcl-2 family members disbalance. Proapoptotic proteins release after mitochondrion membranes permeabilisation could be abolished by protein xIAP inhibition of caspase -9 and -3 activity during NO and CO application.

[Intracellular gaseous messengers, nitric oxide, carbon monoxide and hydrogen sulfide participate in apoptosis regulation].

In this paper, participation of gases, nitric oxide, carbon monoxide and hydrogen sulfide, in cell apoptosis regulation has been analyzed according to the literature data and our own findings. Different mechanisms of nitric oxide influence on apoptotic reaction including modulation of transcription factors activity and increase in mitochondrion membrane permeabilisation are described. Brief description of the generation and signal transduction pathways of carbon monoxide is presented. Pro- and antiapoptotic mechanisms of hydrogen sulfide influence on cell fate are analyzed.

[Regulation of endothelial cells functions by ultrasonic supernatant of Streptococcus pyogenes].

Angiogenesis and vascular remodeling are vital components of inflammation. As an inflammation evolves, vessels expand to supply nutrients and inflammatory mediators, sustaining the accumulation of activated immune cells in the affected tissues. This study demonstrates that ultrasonic supernatant of Streptoccocus pyogenes has anti-angiogenic properties: inhibit EA.hy 926 human endothelial cells metabolism, adhesion, migration, proliferation. At the same time Streptococcal components inhibit signaling pathways that involve FAK and ERK1/2. These effects are not associated with necrosis or apoptosis in cell culture. Taking together, our results suggest that impairing angiogenic function of endothelial cells might contribute to the reduced tissue perfusion, hypoxia, and subsequent regional tissue necrosis caused by Streptococci group A.

In vitro studies of changes in human endothelial cell functions under the effect of imiquimod.

Imiquimod (1-(2-methylpropyl)-1H-imidazo[4,5-c]quinolin-4-amine) is an active immunomodulator with antiviral effects. In addition to its stimulatory effect on cell-mediated immunity, in vivo studies have detected its antiviral and antiangiogenic effects. Possible direct effect of imiquimod on endothelial cells remains not studied. We have shown that imiquimod inhibited proliferation and migration of human endothelial cells (EA.hy 926 strain) in vitro and induced apoptosis (but not necrosis) of endothelial cells and production of IL-6 cytokine. These results suggest that imiquimod inhibits angiogenesis via direct modulation of endothelial cell function.

Role of hydrogen sulfide in the regulation of cell apoptosis.

We studied the effect of a gas transmitter hydrogen sulfide (H(2)S) on the realization of apoptosis in Jurkat cells and mononuclear leukocytes from healthy donors. Treatment with H(2)S donor NaHS was accompanied by a dose-dependent intensification of cell death via apoptosis and necrosis. T-cell leukemia cells were more sensitive to H2S than mononuclear leukocytes from healthy donors. H(2)S-induced cell apoptosis was accompanied by activation of caspase-3 and caspase-9.

[CD14++CD16- and CD14+CD16+ human monocytes adhesion to endothelial cells].

Two subsets of monocytes were identified in humans and other mammals blood based on different levels of CD14 and CD16 expression. These subsets have different patterns of adhesion molecules and chemokine receptors, which suggest different modes of interaction with endothelium and tissue traffic. Here, we investigated the ability of CD14+CD16+ and CD14++CD16- monocytes to adhesion to endothelial cells monolayer in presence and in the absence of pro- and anti-inflammatory cytokines. We demonstrated that CD14+CD16+ monocytes had higher level of adhesion to intact endothelial cells monolayer than CD14++CD16- monocytes. Significant increase in adhesion of CD14++CD16- and CD14+CD16+ monocytes subpopulations was observed in the presence of both TNF alpha and TNF alpha combinations with other cytokines. IFN gamma and IL-4 showed no independent effects on adhesion of monocytes. These results have demonstrated that both CD14++CD16- and CD14+CD16+ monocytes can be recruited to inflamed endothelium, but, in the absence of inflammation, CD14+CD16+ monocytes adhere to endothelial cells two times stronger than CD14++CD16- monocytes.

[Effect of sutent and celecoxib on the properties of endothelial cells in vitro].

We studied the anti-angiogenic properties of sutent (SU11248) and celecoxib in human endothelial cell line EA. hy 926 in vitro. Sutent 0.05-0.5 microg/ml suppressed their proliferation and migration depending on dose while celecoxib did the same at 5.0 microg/ml. We were the first to demonstrate that endothelial cell incubation was followed by increase in 5'-nucleotidase activity in the presence of sutent while celecoxib did not produce such effect. It may be suggested that elevated 5'-nucleotidase concentration at the membranes of endothelial cells might in turn contribute to the pool of extracellular adenosine to stimulate antiinflammatory effect. Our data also contribute to the knowledge about the anti-angiogenic properties of sutent and celecoxib.

[The role of p53 and NF-kappaB transcription factors in redox-dependent dysregulation of mononuclear leukocyte apoptosis].

The aim of this work was to study programmed death of blood mononuclear leukocytes taken from healthy donors and patients with acute inflammatory diseases (acute appendicitis, community-acquired pneumonia). Cellular p53 and NF-kappaB transcription factors were detected by western blotting. Active form of NF-kappaB was shown to appear in mononuclear leukocytes undergoing oxidative stress in experiment and during acute inflammation, p53 was found only under oxidative stress conditions in vitro. Despite enhanced expression of target gene mRNA of these transcription factors in oxidative stress (proapoptotic protein Bax and antiapoptotic protein Bcl-XL), the resulting vector of p53 and NF-kappaB activation is stimulation of cell's apoptotic reaction.

[Mitogenactivated protein kinases JNK and p38 as redox-dependent molecular targets correction of programmed cell death disturbances in oxidative stress condition].

The article summarizes information from recent literature and results of the author's own investigations concerning role of mitogenactivated protein kinases JNK and p38 in disturbances of programmed cell death regulation in oxidative stress condition.

[The role of redox-dependent signal systems in the regulation of apoptosis under oxidative stress condition].

Programmed death of peripheral blood mononuclear cells from donors with acute inflammatory diseases (an acute appendicitis, a community-acquired pneumonia) was investigated under condition of oxidative stress in vitro and under effect of selective inhibitors of MAP-kinases JNK and p38. Levels of active and inactive forms of MAP-kinases, and factors of transcription were determined by immunoblotting (western blot analysis). The increase in the activity of apoptosis under condition of oxidative stress in vivo and during the acute inflammatory diseases is associated with the increase in the level of reactive oxygen species (ROS) in the cells. The action of inhibitors of MAP-kinases JNK (SP600125) and p38 (ML3403) in vitro under condition of oxidative stress prevents increase in the quantity of annexin-positive mononuclear leucocytes that testifies to involving JNK and p38 MAP-kinases in apoptosis deregulation oxidative mechanisms. The appearance of NF-kappaB in the mononuclear leucocytes under condition of oxidative stress during the acute inflammatory diseases and at the experiment was shown; p53 was registered only under condition of oxidative stress in vitro. The effect of p53 and NF-kappaB results in the increase in the quantity of apoptosis annexin-positive mononuclear leucocytes that testify to inoperativeness of antiapoptotic regulation NF-kappaB.