Biology subjects

Demin, K. A.

Publications and source records attributed to Demin, K. A..

6 recordsLinked to original sources

bioRxiv2026

Bidirectional modulation of pain by neurofeedback: Preliminary findings with fMRI at 7T

Previous brain decoding studies indicate that an individuals pain experience can be robustly predicted from distributed patterns of brain activity. Two brain decoders have notably been associated respectively with the nociceptive and cognitive aspects of pain experience, the Neurologic Pain Signature (NPS) and the Stimulus-Intensity Independent Pain Signature (SIIPS). Yet, we still do not know if these brain patterns are also causally related to pain experience. To evaluate this possibility, we used high-field (7-Tesla) fMRI to test whether humans can alter their pain experience by bidirectionally modulating their pain-related brain activity in decoded neurofeedback paradigm. In a double-blind design, participants were trained to up- and down-regulate the NPS or the SIIPS. Our results indicate that participants can achieve bidirectional control of both signatures. NPS expression reliably increased during pain stimulation and covaried with both stimulus intensity and subjective ratings. In contrast, SIIPS expression did not show consistent stimulus-locked effects in the primary analyses. Importantly, reduction in pain rating was specific for SIIPS-training, whereas NPS has failed to show any consistent behavioral effect. Based on these preliminary findings, we hereby preregister a follow-up study, with specified rationale, hypotheses, experimental design, and analysis protocols.

neuroscience↗

bioRxiv2025

Oligotrophy and organic carbon dissipation as trophic strategy in chernozem rare and uncultured taxa

Soil microbial communities harbor vast phylogenetic diversity, yet the functional ecology of rare and uncultured taxa remains poorly understood. These low-abundance microorganisms may employ specialized trophic strategies enabling their persistence in resource-limited environments. This study examined whether established oligotrophy markers could effectively characterize and differentiate the ecophysiology of rare and uncultured bacteria recovered from diverse Russian soil metagenomes. A total of 31 soil samples (chernozems, fluvisols, solonetz, solonchak, kastanozems, and leptosols) were collected from protected natural areas in the Rostov Region, Russia. Shotgun metagenomic sequencing was performed, and 246 metagenome-assembled genomes (MAGs) were recovered through assembly and binning. Genomic and functional traits associated with oligotrophy - including genome size, predicted generation time, ribosomal RNA operon copy number, two-component signaling systems, chemotaxis proteins, and carbohydrate-active enzymes - were analyzed. Metabolic capabilities for C1-compound oxidation, benzoyl-CoA pathway utilization, organosulfonate metabolism, and atmospheric trace gas scavenging were annotated. Principal component analysis was employed to cluster MAGs based on ecological strategy. MAGs spanned 18 bacterial phyla, with genome sizes ranging from 0.58-11.6 Mb and predicted doubling times from 0.6-15.6 hours. Six statistically significant clusters were identified, corresponding to distinct life-history strategies: fast-growing generalists, hydrogenotrophs, C1-compound specialists, polysaccharide degraders, aromatic compound degraders, and minimal-genome specialists. Oligotrophic lifestyles were confidently inferred for Methylomirabilota, Krumholzibacteriota, and Eisenbacteria MAGs, characterized by slow growth, reliance on low-molecular-weight carbon dissipation, and reduced regulatory complexity. Copiotrophic strategies were associated with Myxococcota, Bacteroidota, Gammaproteobacteria, and Verrucomicrobiota, which exhibited large genomes, rapid doubling times, extensive two-component systems, and high carbohydrate-active enzyme abundances. Combined analysis of genome size, generation time, regulatory system complexity, chemotaxis capacity, and substrate utilization pathways provides a robust framework for inferring trophic strategies of uncultured soil bacteria. Oligotrophy among rare taxa is characterized by adaptation to low-molecular-weight carbon dissipation, atmospheric trace gas oxidation, representing ecological strategies that enable persistence in nutrient-limited soil microhabitats.

microbiology↗

bioRxiv2024

Urban microbial communities shift towards carotenoid-producing species under constant anthropogenic stress

During years of investigating soil microbial communities, our research group consistently observed a predominance of carotenoid-producing microbes - characteristically pigmented in hues typical of carotenoids - in urban soil samples, as compared to those from recreational, rural, or non-urban areas. To validate this observation as non-random and to explore the ecological role of carotenoid-producing microorganisms in urban soils, we conducted a series of experiments. Additionally, we extended our study to other components of the urban ecosystem that may harbor and transfer microbial communities, including dust and snow samples. Through ecological monitoring, we assessed the proportion of culturable carotenoid-producing bacteria in those samples. It was found that in urban soils >60% of the isolates are pigmented, and in natural soils only about 30% exhibit carotenoid pigmentation. For snow and dust samples, all sites have shown pigmented bacteria predominance. Further, we analyzed both the physiological traits of individual isolates and the broader characteristics of entire culturomes (comprising all isolates from a single aliquot plated onto Petri dishes). Metagenomic analysis of the culturome washes was also performed to provide deeper insights into the microbial communities present. Metagenome of urban isolates clearly show elevated biodiversity of carotenoid biosynthesis genes and carotenoid-producing taxa, as compared to metagenome of natural habitat. In this study, Flavobacterium was identified as the most abundant pigmented genus of urban settings. Based on data obtained in this work, and similar literature data on urban microbial communities, we propose that the unique combination of environmental factors in urban settings fosters the selective enrichment of carotenoid-producing microorganisms. Finally, we offer a model to explain this selective process.

microbiology↗

bioRxiv2023

Sulfur cycle microbiota in extremely contaminated Technosol with ongoing pedogenesis: culture-dependent and metagenomic approach

Understanding the microbial communities involved in the global sulfur cycle is crucial for comprehending key biogeochemical processes on Earth. However, most studies tend to focus on marine ecosystems, while investigations into the terrestrial sulfur cycle are scarce. In this study, we employed culture-dependent techniques and metagenomics to characterize sulfur-cycling microbiota in extremely contaminated soils. We analyzed shotgun and amplicon sequencing data to assess taxonomical diversity, metagenome-assembled genomes (MAGs) for functional diversity, and also calculated the most probable numbers (MPN) of sulfur-oxidizing and sulfate-reducing bacteria based on culture-dependent data. Our taxonomic profiling, using both shotgun and amplicon data, revealed a high diversity of sulfur cycle bacteria, which was found to be dependent on pH levels. Additionally, our findings confirmed recent modelling of specific taxa biogeographical distribution, such as the sulfur-reducing Mesotoga. Using a functional metagenomics approach, we identified non-canonical taxa involved in dissimilatory sulfur metabolism (e.g., sulfate-reducing acidobacteria and members of the Binatota phylum), and canonical taxa engaged in various oxidative, reductive, and organosulfur transformations (e.g., sulfur-oxidizing alpha-, beta-, and gammaproteobacteria). Furthermore, we discovered that multiple taxa in the studied Technosol encoded different enzymes capable of sulfite transformation and the removal of sulfite from various organosulfonate molecules, thus contributing to the cryptic cycling of sulfur compounds. Estimated MPNs of sulfur-oxidizing bacteria aligned with our shotgun and amplicon data, while those of sulfate-reducing bacteria contradicted functional metagenomic findings. Based on our overall analysis, we support the idea that sulfate-reducers belong to the rare biosphere in soil. We suggest that they behave differently in soils compared to aquatic habitats due to the high taxonomic diversity along with low absolute abundance. Our findings unveil a diverse and unique community of sulfur-metabolizing bacteria that has evolved in soil under severe technogenic pollution, high bulk sulfur content, and fluctuating redox states.

microbiology↗

bioRxiv2022

Behavioral and neurochemical effects of novel N-Benzyl-2-phenylethylamine derivatives in adult zebrafish

Serotonergic hallucinogenic drugs potently affect human brain and behavior, and have recently emerged as potentially promising agents in psychopharmacotherapy. Complementing rodent studies, zebrafish (Danio rerio) is a powerful animal model for screening neuroactive drugs, including serotonergic agents. Here, we test ten different N-Benzyl-2-phenylethylamine (NBPEA) derivatives with the 2,4- and 3,4-dimethoxy substitutions in the phenethylamine moiety and the - OCH3, -OCF3, -F, -Cl and -Br substitutions in the ortho position of phenyl ring of N-benzyl fragment, assessing their behavioral and neurochemical effects in adult zebrafish. Overall, substitutions in N-benzyl fragment primarily affected zebrafish locomotion, and in phenethylamine moiety - anxiety-like behavior, also modulating brain serotonin and/or dopamine turnover. We also identified several behavioral clusters, including anxiogenic/hypolocomotor (24H-NBF, 24H-NBOMe and 34H-NBF), behaviorally inert (34H-NBBr, 34H-NBCl and 34H- NBOMe), anxiogenic/hallucinogenic-like (24H-NBBr, 24H-NBCl and 24H-NBOMe(F)), and anxiolytic/hallucinogenic-like (34H-NBOMe(F)) agents. The 24H-NBOMe(F) and 34H-NBOMe(F) also reduced despair-like behavior in zebrafish. The artificial intelligence-driven phenotyping supports association of multiple compounds with NMDA antagonists and/or MDMA, supporting their potential hallucinogenic-like properties, as well as other valuable psychoactive effects. In silico functional molecular activity modelling also supports existing of similarities between studied NBPEAs drugs, MDMA, and ketamine. Functional analysis implicates potential involvement of serotonin release stimulating activity, calcium channel (voltage-sensitive) activity, some serotonin receptors activity and variety of psychiatric and neurologic disorders treatments activities. Overall, we report potent neuroactive properties of several novel synthetic N-benzylphenylethylamines in an in vivo vertebrate model system (zebrafish), raising the possibility of their potential use in clinical practice.

neuroscience↗

bioRxiv2021

Modulation of behavioral and hippocampal transcriptomic responses in rat prolonged chronic unpredictable stress model by fluoxetine, eicosapentaenoic acid and lipopolysaccharide

Animal models are widely used to study stress-induced affective disorders and associated with them neuroinflammation and other neuroimmune processes. Here, we examined rat behavioral and hippocampal transcriptomic responses to prolonged chronic unpredictable stress (PCUS), as well as following a 4-week treatment with a classical antidepressant fluoxetine, an anti-inflammatory agent eicosapentaenoic acid (EPA), a pro-inflammatory agent lipopolysaccharide (LPS) and their combinations. Overall, PCUS evoked an anxiety-like behavioral phenotype in rats (corrected by chronic fluoxetine alone or combined with other drugs), EPA was anxiolytic and LPS promoted anxiety in this model. PCUS evoked pronounced transcriptomic responses in rat hippocampi, including >200 differentially expressed genes. While pharmacological manipulations did not affect hippocampal gene expression markedly, Gpr6, Drd2 and Adora2a were downregulated in stressed rats treated with fluoxetine+EPA, suggesting G protein-coupled receptor 6, dopamine D2 receptor and adenosine A2A receptor as potential evolutionarily conserved targets in chronic stress. Overall, these findings support the validity of rat PCUS paradigm as a useful tool to study stress-related affective pathologies and calls for further research probing how various conventional and novel drugs modulate behavioral and neurotranscriptomic biomarkers of chronic stress.

neuroscience↗