Biology subjects

Yuksel, M.

Publications and source records attributed to Yuksel, M..

4 recordsLinked to original sources

bioRxiv2025

Host constraints on viral recombination and emergence

Recombination (including reassortment) is a salient force in viral evolution and has been implicated in the emergence of several zoonotic pathogens in humans. Viral recombination occurs during simultaneous infection of an individual host with multiple genotypes (co-infection). Thus, processes which affect the incidence of a disease in the host population affect how often viral genotypes recombine. We investigate whether and how host traits affect the realized rate of viral recombination using a mathematical model that makes feedbacks between viral evolution and host ecology (in particular, lifespan) explicit. Our main result is that viruses of host species that are short-lived tend to recombine more frequently than those of relatively long-lived hosts. This is because of differences in population density and, thus, the prevalence of (co-)infection at equilibrium. Using highly pathogenic avian influenza sequence data, we test the prediction that recombination is elevated in short-lived hosts. In agreement with this prediction, the magnitude of statistical associations between mutations on different segments of the flu genome increases with host body size, a proxy for lifespan. Similarly, estimates of the reassortment rate from phylogenetic network analyses decrease with body size. We discuss the implications of these findings for disease emergence. Subject categoryEvolution Subject areasevolution, health and disease and epidemiology, ecology

evolutionary biology↗

bioRxiv2025

CD20+ natural killer cells are polyfunctional, memory-like cells that are enriched in inflammatory disorders

While CD20 was initially characterized as a B cell-specific marker, its expression on memory T cells has expanded our understanding of this molecules distribution and function. Here, we identify a previously unrecognized CD20-expressing NK cell population and demonstrate its functional significance. CD56+CD20+ NK cells exhibit hallmarks of cellular activation, including elevated NKp46, CD69, and CD137 expression, enhanced proliferative capacity, and increased production of inflammatory cytokines (IFN-{gamma}, GM-CSF, TNF-, IL-10). Functional analyses revealed enhanced cytotoxicity against K562 targets, correlating with increased expression of cytolytic mediators including granzymes A, B, and K, perforin, FASL, and TRAIL. Single-cell transcriptional profiling demonstrated that MS4A1-expressing NK cells possess a distinct molecular signature characterized by elevated granzyme K expression and memory-like features. These cells preferentially localize to secondary lymphoid organs and accumulate in inflammatory tissues. Notably, CD56+CD20+ NK cells are enriched in multiple inflammatory conditions, including multiple sclerosis, autoimmune hepatitis, hepatitis B infection, hepatocellular carcinoma, and lung cancer. Treatment with rituximab depletes this population, suggesting potential therapeutic implications. Our findings establish CD20+ NK cells as a functionally distinct lymphocyte subset with enhanced effector capabilities and tissue-homing properties, providing new insights into immune regulation in inflammatory diseases. One Sentence SummaryOur study reveals expression of CD20 by NK cells, in relation with enhanced functionality, memory-like features, and inflammation.

immunology↗

bioRxiv2023

Hydraulic Conductivity of The Hemp Stems Under Water Stress

The hydraulic conductivity of hemp stems under water-stress conditions was investigated to assess the impact on water transport from the root to the leaves. Water-stress conditions induce embolism (cavitation) in xylem channels, thereby affecting water flow. The percentage loss of water transfer ability within the xylem channels can be represented by a vulnerability curve (VC). This study utilized an air injection technique to induce embolisms in the stem and measured the subsequent changes in hydraulic conductivity using a specialized measurement apparatus. The results revealed that the shape of the vulnerability curve for hemp was influenced by the xylem area, which is an atypical finding with no prior evidence in other plant species. The statistical analysis confirmed the significance of this effect (p-value=0.003 at 95% confidence intervals). Consequently, a non-traditional mathematical equation (simple power law) was developed to describe the relationship between pressure and xylem area. Furthermore, our findings demonstrated that hemp stems are more responsive to water stress compared to other plant species documented in previous literature. The minimum pressure (0.15 MPa) at which initial cavitation is observed and the maximum pressure ([~]2.4 MPa) at which all stem conductance is lost were among the lowest reported values, indicating that hemp growth may be significantly affected by deficit irrigation strategies. Thus, careful monitoring of the irrigation schedule is crucial, particularly for younger stems with smaller xylem cross-sectional areas. These insights into the hydraulic behavior of hemp can contribute to the development of improved irrigation strategies in agriculture, ultimately enhancing water-use efficiency and optimizing crop production. HighlightO_LIThe hydraulic conductivity of hemp stems under water-stress conditions was investigated to assess the impact on water transport from the root to the leaves. C_LIO_LIThe results revealed that the shape of the vulnerability curve for hemp was influenced by the xylem area, which is an atypical finding with no prior evidence in other plant species. C_LIO_LIOur findings demonstrated that hemp stems are more responsive to water stress compared to other plant species documented in previous literature. C_LIO_LIThe minimum pressure (0.15 MPa) at which initial cavitation is observed and the maximum pressure ([~]2.4 MPa) at which all stem conductance is lost were among the lowest reported values, indicating that hemp growth may be significantly affected by deficit irrigation strategies. C_LIO_LIThus, careful monitoring of the irrigation schedule is crucial, particularly for younger stems with smaller xylem cross-sectional areas. These insights into the hydraulic behavior of hemp can contribute to the development of improved irrigation strategies in agriculture, ultimately enhancing water-use efficiency and optimizing crop production. C_LI

cell biology↗

bioRxiv2020

Adaptive evolution of hybrid bacteria by horizontal gene transfer

Horizontal gene transfer is an important factor in bacterial evolution that can act across species boundaries. Yet, we know little about rate and genomic targets of cross-lineage gene transfer, and about its effects on the recipient organisms physiology and fitness. Here, we address these questions in a parallel evolution experiment with two Bacillus subtilis lineages of 7% sequence divergence. We observe rapid evolution of hybrid organisms: gene transfer swaps ~12% of the core genome in just 200 generations, and 60% of core genes are replaced in at least one population. By genomics, transcriptomics, fitness assays, and statistical modeling, we show that transfer generates adaptive evolution and functional alterations in hybrids. Specifically, our experiments reveal a strong, repeatable fitness increase of evolved populations in the stationary growth phase. By genomic analysis of the transfer statistics across replicate populations, we infer that selection on HGT has a broad genetic basis: 40% of the observed transfers are adaptive. At the level of functional gene networks, we find signatures of negative and positive selection, consistent with hybrid incompatibilities and adaptive evolution of network functions. Our results suggest that gene transfer navigates a complex cross-lineage fitness landscape, bridging epistatic barriers along multiple high-fitness paths. Significance statementIn a parallel evolution experiment, we probe lateral gene transfer between two Bacillus subtilis lineages close to the species boundary. We show that laboratory evolution by horizontal gene transfer can rapidly generate hybrid organisms with broad genomic and functional alterations. By combining genomics, transcriptomics, fitness assays and statistical modeling, we map the selective effects underlying gene transfer. We show that transfer takes place under genome-wide positive and negative selection, generating a net fitness increase in hybrids. The evolutionary dynamics efficiently navigates this fitness landscape, finding viable paths with increasing fraction of transferred genes.

evolutionary biology↗