Publications by authors named "Ksenia 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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Ovarian cancer often develops resistance to conventional therapies, hampering their effectiveness. Here, using ex vivo paired ovarian cancer ascites obtained before and after chemotherapy and in vitro therapy-induced secretomes, we show that molecules secreted by ovarian cancer cells upon therapy promote cisplatin resistance and enhance DNA damage repair in recipient cancer cells. Even a short-term incubation of chemonaive ovarian cancer cells with therapy-induced secretomes induces changes resembling those that are observed in chemoresistant patient-derived tumor cells after long-term therapy.

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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 study focuses on the diploid parthenogenetic lizard Darevskia unisexualis, which is a hybrid derived from two parental species, offering insights into sexual and asexual reproduction mechanisms.
  • - Researchers conducted a detailed analysis of the pericentromeric DNA sequences of the parental lizards, revealing unique species-specific sequences that helped create fluorescent probes to distinguish parental chromosomes in the hybrid.
  • - The team developed a computational method to find species-specific fluorescent probes for studying pericentromeres, laying the groundwork for future research on hybrids in both nature and labs.
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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 And Aim: Prolonged stress causes deleterious effects on both the organism and its microbiota. In this study, we examined the effects of exposure to variable frequency ultrasound (US) on the gut microbiota-liver-brain axis of mice.

Materials And Methods: This study was conducted on 20 mature clinically healthy sexually naive C57BL/6J male mice (42-45 days old).

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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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In light of the ever-increasing number of multidrug-resistant bacteria worldwide, bacteriophages are becoming a valid alternative to antibiotics; therefore, their interactions with host bacteria must be thoroughly investigated. Here, we report genome-wide transcriptional changes in a clinical SA515 strain for three time points after infection with the vB_SauM-515A1 kayvirus. Using an RNA sequencing approach, we identify 263 genes that were differentially expressed (DEGs) between phage-infected and uninfected host samples.

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  • G-quadruplexes (G4s) are unique DNA structures that may be targeted by antimicrobial compounds known as G4-stabilizing ligands, but their precise antibacterial mechanisms remain unclear.
  • A study utilized genome-wide RNA-sequencing to assess how bacterial genes respond to two G4 ligands, BRACO-19 and TMPyP4, revealing significant changes in gene expression profiles.
  • BRACO-19 affected genes related to replication, repair, and iron metabolism, while TMPyP4 influenced transcription factors and the arginine biosynthesis system, suggesting that different G4 ligands can impact various biological pathways.
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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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The SARS-CoV-2 pandemic is a big challenge for humanity. The COVID-19 severity differs significantly from patient to patient, and it is important to study the factors protecting from severe forms of the disease. Respiratory microbiota may influence the patient's susceptibility to infection and disease severity due to its ability to modulate the immune system response of the host organism.

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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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G-quadruplex (G4) sites in the human genome frequently colocalize with CCCTC-binding factor (CTCF)-bound sites in CpG islands (CGIs). We aimed to clarify the role of G4s in CTCF positioning. Molecular modeling data suggested direct interactions, so we performed in vitro binding assays with quadruplex-forming sequences from CGIs in the human genome.

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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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The Twort-like myoviruses ( genus) of are promising agents for bacteriophage therapy due to a broad host range and high killing activity against clinical isolates. This work improves the current understanding of the phage infection physiology by transcriptome analysis. The expression profiles of a typical member of the genus (vB_SauM-515A1) were obtained at three time-points post-infection using RNA sequencing.

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