Biology subjects

Can, A.

Publications and source records attributed to Can, A..

8 recordsLinked to original sources

bioRxiv2026

Genomic and Kinetic Modeling Involving Nanoparticle-Mediated Delivery of a Novel Chitinase Enzyme to Outpace Tuta absoluta Damage

The tomato leafminer, Tuta absoluta, poses a severe global agricultural threat due to its rapid leaf-mining behavior and swift development of resistance to conventional chemical pesticides. While microbial chitinases are potent biopesticides, their field efficacy is limited by environmental degradation and the short exposure window before larvae penetrate leaf tissues. This study evaluates a stimuli-responsive, controlled-release nanobiopesticide system utilizing a novel chitinase from newly characterized Serratia marcescens GBS19. A 61.1 kDa chitinase (GBS19_ChiA) was heterologously expressed in Escherichia coli and purified to a specific activity of 215.01 U/mg. The enzyme was immobilized onto starch-coated silica nanoparticles designed for target-triggered release via host alpha-amylase. Genomic profiling and R-based kinetic modeling were integrated to evaluate the efficacy of purified and immobilized forms against T. absoluta. Immobilization enhanced thermal and pH stability, with the nanocarrier maintaining 85% activity over 10 weeks. In larval bioassays, immobilization increased mortality from 21.9% to 59.4% (5000 U/mL) by day 3, reaching 62.5% by day 6. Genomic analysis identified an expansive secretome and a Type VI Secretion System (T6SS), characterizing GBS19 as a multi-pronged pathogen. Kinetic modeling established that while immobilized enzymes are effective, the 2.5-hour exposure time on T. absoluta requires the synergistic action of chitinases (ChiA/B/C) to reach the lethal desiccation threshold before larvae establish protective mines. Starch-coated silica nanoparticles significantly improve chitinase stability and delivery. However, overcoming the rapid penetration of T. absoluta necessitates a whole-cell or multi-enzyme synergistic approach to outpace larval behavioural defences.

biochemistry↗

bioRxiv2026

Multidimensional Characterization of Novel Phage UCB24 Targeting Erwinia amylovora

This study evaluates the novel bacteriophage UCB24 as an eco-friendly biocontrol agent against Erwinia amylovora, the bacterial pathogen responsible for fire blight. Following purification, UCB24 was characterized for its optimal multiplicity of infection (MOI), infection kinetics, and environmental stability across diverse pH and temperature ranges. Microtitration assays and scanning electron microscopy (SEM) confirmed distinct morphology of the phage and its potent capacity to disrupt E. amylovora biofilms. Whole-genome sequencing and phylogenetic profiling identified UCB24 as a genetically distinct relative of four known phages. Furthermore, protein-protein interaction analyses revealed a strong binding affinity between the phage lysin and the hosts N-acetylmuramic-acid 6-phosphate etherase, uncovering the precise molecular mechanism driving targeted host destruction. In vivo plant trials demonstrated exceptional protective efficacy in Apple cv. Gala (88.61%) and Quince cv. Esme (81.37%), significantly outperforming traditional copper treatments under severe baseline pathogen pressure. Consequently, UCB24 represents a highly effective and sustainable biopesticide for managing fire blight in susceptible orchard ecosystems.

microbiology↗

bioRxiv2025

The Specific Genetic Markers to Diagnose Xanthomonads Infecting Pepper and Tomato Plants

We have improved a marker system to examine the genetic diversity in Xanthomonads species by using whole genome sequence analysis and repetitive regions in the bacterial genome. Specifically, we amplified microsatellite regions using PCR, and the resulting fragments were digested with specific enzymes. These fragment profiles served as molecular markers. Consequently, a more precise marker for bacterial identification was developed by combining the microsatellite and RFLP methods to differentiate Xanthomonads species. In Addition, we analysed the ancestral ordering of various Xanthomonas species genomes available in NCBI using Progressive Mauve Alignment. The data revealed unique collinear regions characteristic of Xanthomonas species. These regions were also associated with cut genomic fragments used as markers, enabling the discrimination of Xanthomonas species infecting tomato and pepper. We propose that these findings contribute to understanding the genetic diversity of Xanthomonas and rapidly diagnosis.

molecular biology↗

bioRxiv2024

Pesticide degradation capacity of a novel strain belonging to Serratia sarumanii (GBS19) with its genomic profile

The use of pesticides in agricultural pest control and the potential for biological degradation of these chemicals are significant factors in environmental conservation. Sustainable pest control strategies should prioritize the preservation of non-target organisms and the maintenance of soil ecosystem dynamics. Initiation from this point, this study aimed to identify microorganisms capable of pesticide biodegradation commonly used in our regions intensive agricultural fields. The microorganism with the broadest degradation spectrum was identified in vitro studies, and whole-genome sequence analyses indicated that some genomic regions were able to degrade pesticides, which was also confirmed with LC-MS analysis. Detailed genomic analyses linked to allele sequence definitions for ribosomal MLST have classified this strain as Serratia sarumanii under the Serratia genus. Moreover, our findings showed that the introduction of this microorganism can stimulate the degradation of certain pesticides in the environment while, interestingly, simultaneously enhancing the potency of low concentrations of some other pesticides through a synergistic effect. To validate of GBS19 biodegradation capacity, additional studies carried out on 25 pesticide active chemicals using LC-MS chromatographic analysis revealed that the Serratia sarumanii GBS19 strain is able to biodegrade some active compounds of various pesticides (fludioxonil, fenhexamid, pyrimethanil, and spirodiclofen) by up to 54%, 52%, 46%, and 23%, respectively. These results highlight the degrative properties of our prominent original strain as a gene pool which can be put into practice by transforming into competent strain using recombinant DNA technology.

genomics↗

bioRxiv2024

Unveiling Novel Biocontrol Strategies: Serratia marcescens chiA Gene Against Myzus persicae

BackgroundMicroorganisms produce a diverse array of enzymes with potential applications in biological control and pest management. Among these enzymes, chitinase stands out due to its safety for non-target organisms and the environment. Chitinase enzymes play a crucial role in breaking down chitin, which serves as a critical component in insect exoskeletons and fungal cell walls. As a result, they emerge as valuable tools for managing both agricultural pests and pathogens. ResultsThe chiA gene region of Serratia marcescens GBS19 was successfully amplified via PCR and cloned into expression vectors. The resulting chiA protein was expressed and purified through His-tag affinity chromatography. The purified chiA enzyme exhibited optimal activity at 40 {degrees}C and pH 5. The insecticidal properties of the purified chiA enzyme were tested against the agricultural pest Myzus persicae, revealing an LD50 value of 15,804 ppm. Comparative analysis with ref_seq chiA enzymes demonstrated that our purified enzyme shows 98.93% similarity, indicating a high degree of conservation and likely functional similarity. Bioinformatics modelling highlighted a strong binding affinity (-4.10 kcal/mol) between the enzyme and chitin, which was also confirmed with modelled chitin layer and enzyme interaction. ConclusionThe study underscores the potential of S. marcescens GBS19 chitinase as an effective and environmentally safe biocontrol agent. The chiA enzyme exhibits promising insecticidal properties, specifically against M. persicae, and its strong binding affinity to chitin supports its effectiveness. Given its safety for non-target organisms and the environment, S. marcescens GBS19 chitinase holds significant promise as a tool for integrated pest management, contributing to sustainable agricultural practices using directed recombinant DNA technology.

molecular biology↗

bioRxiv2024

Exploring the genome-wide expression level of the bacterial strain belonging to Bacillus safensis (MM19) against Phomopsis viticola

IntroductionRhizobacteria has the suppression ability to compete with pathogenic microorganisms and help for plant immunity and defense mechanism. Their growth and survival in rhizosphere ensure biological balance in favor of the host plant. MethodsIn our study, with agar diffusion assays, we found a rhizobacterium species belonging to Bacillus safensis, which can significantly suppress Phomopsis viticola. To elucidate the antagonistic mechanism, genome-wide gene expression profiling of B. safensis (strain MM19) was performed in the presence and absence of P. viticola. We used RNA-seq analysis to obtain a comprehensive overview of the responsive B. safensis whole gene expression classified according to biological and metabolic process to P. viticola concomitant growth in liquid culture. ResultsThe differential gene expression profiles of B. safensis (MM19) revealed significantly increased expression of prominent genes related to thiamine biosynthesis involving various metabolites and enzymes that play role in the suppression of mycelium growth and pathogen inhibition. Correspondingly, the expression of three major genes (HOG1, FUS3, SGI) involving in the virulence of P. viticola was followed using qPCR analysis. HOG1 was the highest expressed gene in the pathogen when it co-cultivated with MM19. Based on these findings, we performed molecular docking and dynamics analysis to explore the interaction between HOG1 and thiamine, besides expression of network analysis constructed using Cytoscape. DiscussionThe results proved that the functional genomic data related to thiamine biosynthesis and corresponding pathways ensure a priming role in the antagonistic behavior of B. safensis (MM19) against P. viticola as a supporter for plant immunity.

microbiology↗

bioRxiv2024

VENTRAL HIPPOCAMPAL AND BASOLATERAL AMYGDALAR INPUTS TO DEEP, BUT NOT SUPERFICIAL LAYERS OF MEDIAL PREFRONTAL CORTEX UNDERLIE STRESS SUSCEPTIBILITY

Stress response is essential for adapting to an ever-changing environment. However, the mechanisms that render some individuals susceptible to stress are poorly understood. While chronic stress is known to induce dendritic atrophy and spine loss in medial prefrontal cortex (mPFC), its impact on synapses made by long-range projections terminating on the mPFC remains unknown. Here, we labeled synapses on male mouse mPFC dendrites formed by ventral hippocampus (VH), basolateral amygdala (BLA) and ventral tegmental area (VTA) long-range afferents using different-colored eGRASP constructs. We obtained multispectral 3D-images of the mPFC covering all cortical laminae, and automatically segmented the dendrites and synapses. In layer II/III, the relative abundances and spatial organizations of VH-mPFC and BLA-mPFC synapses changed similarly in stress resilient (SR) and stress susceptible (SS) mice when compared to stress naive (SN) mice. In layers Vb and VI, on the other hand, the percentage of BLA-mPFC increased and that of VH-mPFC decreased only in SS mice. Moreover, the distances of VH synapses to their corresponding closest BLA synapses decreased and the distances of BLA synapses to their corresponding closest VH synapses increased in the SS group. Consistently, the percentage of single dendritic segments receiving input from multiple brain regions increased in the SS group, suggesting that long-range synaptic inputs to deep layers of mPFC were disorganized in SS mice. Our findings demonstrate afferent- and lamina-specific differential reorganization of synapses between different stress phenotypes, suggesting specific roles for different long-range projections in mediating the stress response.

neuroscience↗

bioRxiv2019

Glyoxal Does Not Preserve Cellular Proteins as Accurately as PFA: A Microscopical Survey of Epitopes

Chemical fixation is one of the most critical steps to retaining cellular targets as naturally as possible. Recent developments in microscopy allow sophisticated detection and measuring techniques with which spatio-temporal molecular alterations is conceivable. Here, we document the fixation competence of glyoxal (Gly), a less-toxic dialdehyde molecule, and paraformaldehyde (PFA) side-by-side (with or without Triton-X 100 permealization) in live- and fixed-cell preparations including human stem cells, spermatozoa, mouse oocytes/embryos using super-resolution microscopy. Although Gly seemed to act faster than PFA, catastrophic consequences were found not acceptable, especially in oocytes and embryos. Due to cell lysate and immunocytochemistry surveys, it was obvious that PFA is superior to Gly in retaining cellular proteins in situ with little/no background staining. In many samples, PFA revealed more reliable and consistent results regarding the protein quantity and cellular localization corresponding to previously defined patterns in the literature. Although the use of Gly is beneficial as indicated by previous reports, we concluded that it does not meet the requirement for proper fixation, at least for the tested cell types and proteins.

cell biology↗