Publications by authors named "Ksenia M Klimina"

Background: Multiple sclerosis (MS) is a neuroinflammatory disease triggered by a combination of genetic traits and external factors. Autoimmune nature of MS is proven by the identification of pathogenic T cells, but the role of autoantibody-producing B cells is less clear. A comprehensive understanding of the development of neuroinflammation and the identification of targeted autoantigens are crucial for timely diagnosis and appropriate treatment.

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Antimicrobial resistance poses a serious threat to global public health. The COVID-19 pandemic underscored the need to monitor the dissemination of antimicrobial resistance genes and understand the mechanisms driving this process. In this study, we analyzed changes to the oropharyngeal and fecal resistomes of patients with COVID-19 undergoing therapy in a hospital setting.

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  • The study focuses on how gut microbiota, particularly commensal bacteria like lactobacilli, interact with the host immune system's cytokines, which are critical in managing inflammation and gut health.
  • Using next-generation RNA sequencing, researchers examined the transcriptional responses of lactobacillus strains K32 and R19-3 to various cytokines, revealing significant changes in gene expression linked to metabolism and stress response, especially upon exposure to IL-8 and IL-10.
  • The findings highlight a complex adaptation mechanism where these bacteria adjust their gene expression in response to inflammatory signals, paving the way for potential probiotic therapies for conditions like inflammatory bowel disease (IBD).
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  • Expansion of CAG repeats in certain genes is linked to neurodegenerative diseases, but the mechanisms are not well understood; this study investigates how these repeats interact with RNA editing enzymes like ADAR.
  • Researchers used induced pluripotent stem cells (iPSCs) and brain organoids from Huntington's disease and ataxia type 17 patients to analyze RNA editing via next-generation sequencing.
  • Results showed that while some brain organoids with specific CAG repeats had decreased RNA editing, most cultures did not support the hypothesis that CAG repeats affect editing levels significantly.
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The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has significantly impacted global healthcare, underscoring the importance of exploring the virus's effects on infected individuals beyond treatments and vaccines. Notably, recent findings suggest that SARS-CoV-2 can infect the gut, thereby altering the gut microbiota. This study aimed to analyze the gut microbiota composition differences between COVID-19 patients experiencing mild and severe symptoms.

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Sweet-tasting proteins (SPs) are proteins of plant origin initially isolated from tropical fruits. They are thousands of times sweeter than sucrose and most artificial sweeteners. SPs are a class of proteins capable of causing a sweet taste sensation in humans when interacting with the T1R2/T1R3 receptor.

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Immunotherapy has proven to be a boon for patients battling metastatic melanoma, significantly improving their clinical condition and overall quality of life. A compelling link between the composition of the gut microbiome and the efficacy of immunotherapy has been established in both animal models and human patients. However, the precise biological mechanisms by which gut microbes influence treatment outcomes remain poorly understood.

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The World Health Organization (WHO) reports that tuberculosis (TB) is one of the top 10 leading causes of global mortality. The increasing incidence of multidrug-resistant TB highlights the urgent need for an intensified quest to discover innovative anti-TB medications In this study, we investigated four new derivatives from the quinoxaline-2-carboxylic acid 1,4-dioxide class. New 3-methylquinoxaline 1,4-dioxides with a variation in substituents at positions 2 and 6(7) were synthesized via nucleophilic aromatic substitution with amines and assessed against a spp.

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Background: RAPID ALKALINIZATION FACTOR (RALFs) are cysteine-rich peptides that regulate multiple physiological processes in plants. This peptide family has considerably expanded during land plant evolution, but the role of ancient RALFs in modulating stress responses is unknown.Results: Here, we used the moss Physcomitrium patens as a model to gain insight into the role of RALF peptides in the coordination of plant growth and stress response in non-vascular plants.

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  • Transcriptomics, specifically through RNA-Seq, was used to analyze gene expression in bifidobacteria during different growth phases, highlighting their importance in human gut health.
  • The study found that during the lag phase, there is increased expression of ABC transporters as bifidobacteria prepare for division, while the exponential phase is characterized by the activation of genes related to amino acid synthesis and energy metabolism to support rapid growth.
  • In the stationary phase, gene expression shifts to promote defense mechanisms, indicating a strategy for survival under nutrient scarcity as the rate of cell division decreases.
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is a bacterium belonging to the class . It causes acute and chronic infections of the urogenital tract. The main features of this bacterium are an absence of cell wall and a reduced genome size (517-622 protein-encoding genes).

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  • All living organisms possess biological clocks that regulate circadian rhythms, influencing various bodily functions like metabolism and hormone levels, and the gut microbiota plays a crucial role in health and stress response.
  • A study involving male rats revealed that the intake of Lactobacillus brevis 47f improved cellular health and redox balance after exposure to different light cycles, demonstrating its potential to restore depleted cellular components.
  • The administration of L. brevis 47f positively impacted the gut microbiota by increasing beneficial bacteria (Faecalibacterium and Roseburia) and decreasing potentially harmful ones (Prevotella and Bacteroides), highlighting its role in maintaining gut health.
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  • Tuberculosis (TB) poses a significant health threat, with finding new drugs and treatments being crucial for its control.
  • Imidazo[1,2-][1,2,4,5]tetrazines have shown effectiveness against TB strains, but resistance arises from mutations that enhance operon expression, complicating treatment.
  • Research indicates that these compounds may disrupt mycobacterial iron metabolism by upregulating genes related to siderophore synthesis in response to different drug concentrations.
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Since periodontitis and type 2 diabetes mellitus are complex diseases, a thorough understanding of their pathogenesis requires knowing the relationship of these pathologies with other disorders and environmental factors. In this study, the representability of the subgingival periodontal microbiome of 46 subjects was studied by 16S rRNA gene sequencing and shotgun sequencing of pooled samples. We examined 15 patients with chronic periodontitis (CP), 15 patients with chronic periodontitis associated with type 2 diabetes mellitus (CPT2DM), and 16 healthy subjects (Control).

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Tuberculosis (TB), caused by , is a global burden, responsible for over 1 million deaths annually. The emergence and spread of drug-resistant strains (MDR-, XDR- and TDR-TB) is the main challenge in global TB-control, requiring the development of novel drugs acting on new biotargets, thus able to overcome the drug-resistance. Tryptanthrin is a natural alkaloid, with great therapeutic potential due to its simple way of synthesis and wide spectrum of biological activities including high bactericidal activity on both drug-susceptible and MDR strains.

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  • Bifidobacteria, important members of the gut microbiota, adapt to the host's immune response, but their survival mechanisms during inflammation are not well understood.
  • The study proposes a new method using high-throughput sequencing and transcriptome analysis to identify genes affected by pro-inflammatory cytokines IL-6 and TNFα in bifidobacteria.
  • Findings revealed that these cytokines influence gene expression without significantly affecting growth, leading to the identification of potential regulatory pathways that help bifidobacteria resist inflammatory responses, highlighting their anti-inflammatory role in the gut.
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Deciphering the mechanism of action of novel anti-tuberculosis compounds is a key step in the drug development process. We have previously described a number of imidazo[1,2-][1,2,4,5]tetrazines with a promising activity on [1]. These compounds had predicted activity as serine‑threonine protein kinase inhibitors, however spontaneous drug resistant (formerly ) revealed only the mycobacterial mechanism of resistance to imidazo[1,2-][1,2,4,5]tetrazines: mutations in gene lead to overexpression of the operon in , thus providing resistance to imidazo[1,2-][1,2,4,5]tetrazines via enhanced efflux [2].

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  • The human gastrointestinal microbiota (HGM) is highly diverse, but most studies only analyze it at the family level due to limitations in current profiling methods.
  • The study introduces type II toxin-antitoxin systems (TAS) as a new way to characterize strain diversity in the HGM, using updated software called TAGMA to detect specific TAS systems in various bacterial strains.
  • Although the analysis revealed some strain-level differences, it did not show significant variations in bacterial species when compared to traditional analysis methods, demonstrating the potential usefulness of the updated TAS gene catalog for detailed HGM characterization.
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Background: Fecal microbiota transplantation (FMT) has been recently approved by FDA for the treatment of refractory recurrent clostridial colitis (rCDI). Success of FTM in treatment of rCDI led to a number of studies investigating the effectiveness of its application in the other gastrointestinal diseases. However, in the majority of studies the effects of FMT were evaluated on the patients with initially altered microbiota.

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  • - The study investigated how different lighting conditions (normal cycles, darkness, and constant light) affect the physiological health and gut microbiota of rats, revealing that changes in light can disrupt the body's internal clock and overall balance.
  • - After monitoring various physiological markers over three months, results showed that constant light conditions led to significant hormonal and metabolic changes in the rats, indicating a breakdown in their internal synchronization.
  • - The findings suggest that while the gut microbiota's composition changed in response to lighting conditions, its overall functional activity remained relatively stable, indicating that these changes may be the organism's way of compensating for new environmental conditions.
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Recent research has indicated that in addition to the unique genotype each individual may also have a unique microbiota composition. Difference in microbiota composition may emerge from both its species and strain constituents. It is important to know the precise composition especially for the gut microbiota (GM), since it can contribute to the health assessment, personalized treatment, and disease prevention for individuals and groups (cohorts).

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The draft genome sequences of Bifidobacterium angulatum GT102 and Bifidobacterium adolescentis 150 strains isolated from the human intestinal microbiota are reported. Both strains are able to produce gamma-aminobutyric acid (GABA). Detailed genomes analysis will help to understand the role of GABA in the functioning of gut-brain axis.

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In this study, we report the first completely annotated genome sequence of the Russia origin Bifidobacterium longum subsp. longum strain GT15. Comparative genomic analysis of this genome with other available completely annotated genome sequences of B.

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