Biology subjects

Li-Byarlay, H.

Publications and source records attributed to Li-Byarlay, H..

10 recordsLinked to original sources

bioRxiv2026

Coordinated neural, metabolic and muscular transcriptomic signatures associated with mite-biting behavior in honeybees (Apis mellifera L.)

Biting behavior is an important natural defense mechanism in honeybees (Apis mellifera) against Varroa destructor. Significant variation in this behavior exists across genetic lines of honeybees, with certain colonies exhibiting higher mite-biting activity than others. Selective breeding for enhanced biting behavior provides a promising strategy for sustainable mite control and colony resilience. However, successful implementation of such breeding programs requires a comprehensive understanding of the genomic mechanism underlying this trait. In this study, RNA-seq analysis of mandible transcriptomes of 1-day and 8-day old worker honeybees from high mite biting (HB) and low mite biting (LB) colonies were performed. A total of 9,345 genes (97.30%) showed a significant differential expression between LB and HB honeybees across different ages (one-way ANOVA, FDR < 0.05). Comparison of LB vs. HB workers collected on day 1 detected 166 down-regulated and 403 up-regulated genes, whereas workers collected on day 8 identified 82 down-regulated and 46 up-regulated genes. Furthermore, the Weighted Gene Coexpression Network Analysis (WGCNA) exhibited the brown and yellow modules with significantly higher expression in HB compared with LB on both day 1 (FC = 1.52, FDR = 0.0019 and FC = 1.47, FDR = 2.7 x 10-4, respectively) and day 8 (FC = 1.27, FDR = 0.056 and FC = 1.16, FDR = 0.073, respectively). Gene Ontology (GO) enrichment analysis identified over-representation of biological processes involved in muscle contraction, chitin binding, neural signaling, oxidative phosphorylation, neuron development, electron transport chain, mitochondrial ATP synthesis, stress response, sensory perception and metabolic processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways analysis identified significant enrichment of various pathways including oxidative phosphorylation, cytoskeleton-related pathways, carbon metabolism, motor proteins, ribosome-associated pathways, and citrate cycle (TCA cycle). The present findings demonstrate mite-biting behavior is associated with coordinated activation of neural, energetic and muscular system rather than a single molecular mechanism. These findings provide a basis to improve honeybee health, enhance resistance to Varroa and other ectoparasite, and eventually support sustainable beekeeping and agricultural pollination systems.

genomics↗

bioRxiv2026

Spatiotemporal variation in honeybee (Apis mellifera L.) virome composition across landscape types and seasons

Honeybees face increasing threats from biotic stress of viral pathogens that can severely impact colony health and contribute to global colony decline. However, comprehensive studies of biotic stress and composition of bee viruses across different environmental contexts and seasons remain scarce. This study aims to characterize and compare the diversity, abundance and composition of the Apis mellifera L. virome across three different landscapes (conventional, organic, and roadside) and seasonal gradients (early vs. late season) to better understand how environmental and temporal factors affect viral communities in honeybees. A. mellifera were collected from three different habitats (conventional farm, organic farm, and roadside habitat) during the spring and summer of 2024. Total RNA was extracted individually from whole honeybees and mRNA libraries were prepared, which were subsequently used for sequencing on an Illumina NovaSeq X Plus platform using paired-end 150 bp reads. Several bacteriophages, putative novel viruses, plant-, insect- and bee-associated viruses were detected in the honeybee viromes including Sacbrood virus, Black queen cell virus, Deformed wing virus-B (previously known as Varroa destructor virus-1) and Deformed wing virus. Furthermore, both habitat types and seasons influence viral abundance as majority of detected viruses showed higher abundance in the conventional farm and late season samples. The present findings provide novel insights into the ecological and seasonal dynamics of honeybee-virus interactions and contribute to strategies for improving honeybee health and resilience.

ecology↗

bioRxiv2025

Oxidative Stress in two pollinators from Different Landscapes based on different pesticide residue profiles

Oxidative stress (OX) is a state of imbalance between antioxidants and reactive oxygen species, which are the byproducts of oxidative phosphorylation in the mitochondria. Different landscapes: conventional, organic, and roadside use different pesticides and pest control management practices pest control. The roadside landscape is a control for minimum application of herbicides and management. Two important pollinators, honey bees (Apis mellifera) and small carpenter bees (Ceratina calcarata) are studied here for their abiotic stress from different landscape. It is unknown whether the differences in these landscapes affect the oxidative stress of these two pollinators. Conventional farms offer the most exposure to pesticides, which have been related to increased stress levels. We hypothesized that honey bees and small carpenter bees (SCB) from conventional farms would experience the highest levels of OX. Results from the lipid assay indicated that honey bees and SCB of organic and roadside landscapes experienced the lowest and highest OX levels. The results of the protein carbonyl assay indicated a significant difference found between conventional and organic bees (p < 0.05), based on Tukeys post-hoc test. Previous research has shown that feral bees have a tolerance to high stress levels. The same could be true of honey bees and SCB from roadside landscapes, where the conditions imitate natural habitats. Organic farms use naturally derived pesticides and moderate management practices, likely contributing to their lower levels. Examining how these pollinators are affected by different farm landscapes can reveal the benefits and detriments of their corresponding management practices. This will lead to streamlined practices that are healthier for pollinators.

physiology↗

bioRxiv2025

Developmental and Environmental Stability of Candidate Reference Genes in the Wild Bee Ceratina calcarata

Quantitative real-time PCR (RT-qPCR) is a widely used method for measuring gene expression, but its accuracy depends on the use of stable reference genes for data normalization. In this study, we evaluated the expression stability of seven candidate reference genes (RPS18, RPS5, RPL32, RPL8, EF-1, {beta}-Actin, and GAPDH) in the small carpenter bee Ceratina calcarata across developmental stages (larvae, pupae, adults) and different landscape environments (conventional farms, organic farms, and roadside sites). Using four analytical algorithms, GeNorm, NormFinder, BestKeeper, and the comparative {Delta}Ct method, we identified RPS18 and RPL8 as the most stable reference genes under varying biological and environmental conditions. These findings were further supported by RefFinder, which integrates results from all algorithms. Our study provides the first validated reference genes for C. calcarata, enabling more accurate and reproducible gene expression analysis in this ecologically important wild bee species. This work will support future research in pollinator biology, environmental stress responses, and conservation genomics.

genomics↗

bioRxiv2025

Comparative Virome Profiling and Discovery of Novel Viruses in Managed and Wild Bees using RNA-seq

Insect pollinators face growing challenges from viral pathogens that may contribute to population declines, yet comparative data on virome composition in managed versus wild bees remain limited. Using RNA-Seq-based metatranscriptomic analysis, we compared the virome of Apis mellifera L. and Ceratina calcarata Robertson collected from agricultural and non-agricultural landscapes. We identified multiple known bee pathogens including Black Queen Cell Virus and Deformed Wing Virus in A. mellifera, and discovered three novel insect viruses--two iflaviruses and one entomopoxvirus--associated with C. calcarata. Notably, one novel iflavirus was identified in A. mellifera. Our findings reveal species- and landscape-specific viral prevalence, highlight viral diversity beyond canonical bee pathogens, and provide genomic resources for future functional studies. These data offer new insights into virus-host dynamics and underscore the utility of virome profiling in understanding pollinator health at the molecular level.

genomics↗

bioRxiv2023

Synergistic effects of multiple pesticides on the flight ability of honey bees (Apis cerana F.)

Pesticides cause risks in the environment for Asian honey bees (Apis cerana). Imidacloprid (I), chlorpyrifos (C) and glyphosate (G) are among the most-widely used pesticides in the world. It is not clear on how these pesticides and combination of them affect the flight ability of A. cerana. Here we utilized flight mills to show new results that acute treatment of individual pesticides, such as 0.2 ng/bees imidacloprid (20 L, 10 ng/g), 0.6 ng/bees chlorpyrifos (20 L, 30 ng/g) and 1.2 ng/bees glyphosate (20 L, 60 ng/g), had no effect on the flight ability of bees. However, forager bees showed a significantly decrease in the flying duration and flying distance when oral exposed to two or three these pesticides. This evidence indicated that two or three pesticides can produce synergistic changes in the flight ability and behavior of honeybees. Results showed a light on new understandings of complex effects and potential risks of these three pesticide on bee behavior including homing ability and food-collecting ability. Our results are key information to understand new synergistic potential among pesticide formulations and how they impair bee behavior. Table of Contents Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/541595v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@70e24dorg.highwire.dtl.DTLVardef@1195fb8org.highwire.dtl.DTLVardef@db5ad5org.highwire.dtl.DTLVardef@1287b51_HPS_FORMAT_FIGEXP M_FIG C_FIG

animal behavior and cognition↗

bioRxiv2021

THE LIFESPAN AND OXIDATIVE STRESS BETWEEN FERAL AND MANAGED HONEY BEE COLONIES

Molecular damage caused by oxidative stress may lead to organismal aging and resulted in acute mortality in organisms. Oxidative stress resistance and longevity are closely linked. Honey bees are the most important managed pollinator in agriculture but the long-term survival of honey bees is seriously threatened. Feral honey bee colonies displayed persistence to Varroa mites. However, it is unknown whether feral honey bees are stress-resistant or survive longer than managed bee populations. More work is needed to determine the impact of oxidative stress on honey bee health and survival. We used the paired colony design to determine the lifespan and levels of oxidative stress on worker bees from either a feral or a managed colony. Each pair of colonies shared similar foraging resources. Results exhibit longer survival time and lifespans of foragers in feral colonies than the managed colonies. The levels of oxidative stress from the lipid damage of feral colonies are higher than the managed colonies, indicating a tolerant mechanism not a repair mechanism to survive. Our study provided new insights into colony difference of physiology and oxidative stress resistance between feral honey bees and commercial stocks.

physiology↗

bioRxiv2020

Assessment and comparison of two different methods to extract nucleic acids from individual honey bees

The honey bee is an excellent model system to study behavior ecology, behavioral genetics, and sociogenomics. Nucleic acid based analyses enable a broad scope of research in functional genomics, disease diagnostics, mutant screening, and genetic breeding. Multiple levels of analysis lead to a more comprehensive understanding of the causes of phenotypic variation by integrating genomic variation, transcriptomic profiles, and epigenomic information. One limitation, however, is the sample preparation procedures to obtain high quality DNA and RNA simultaneously, particularly from small amounts of material, such as tissues of individual bees. We demonstrate that it is feasible to perform dual extractions of DNA and RNA from a single individual bee and compare the quality and quantity of the extracted nucleic acids using two different types of methods (column based versus ethanol precipitation). We obtained a higher yield of both DNA and RNA with one of the extraction methods over the other, although the quality of the DNA and RNA was not significantly different between methods. We describe here the first validated method for dual extraction of DNA and RNA specifically from individual honey bees.

molecular biology↗

bioRxiv2020

The defensive behavior of Indiana mite biting honeybees against Varroa destructor and the structure of mandibles

The honey bee (Apis mellifera) is the most important managed pollinator to sustainable agriculture and our ecosystem. Yet managed honey bee colonies in the United States experience 30-40% losses annually. Among the many biotic stressors, the parasitic mite Varroa destructor is considered one of the main causes of colony losses. Bees mite-biting behavior has been selected as a Varroa-tolerant or Varroa-resistant trait in the state of Indiana for more than a decade. A survey of damaged mites from the bottom of a colony can be used as an extended phenotype to evaluate the mite-biting behavior of a colony. In this study, on average, 37% of mites sampled from the breeding stocks of 59 colonies of mite biters in Indiana were damaged or mutilated, which is significantly higher than the 19% of damaged mites found in commercial colonies in the southern United States. Indiana mite biter colonies had a higher proportion of damaged mites, although among the damaged mites, the number of missing legs was not significantly higher. In addition, the morphology of pollen-forager worker bee mandibles was compared by X-ray microcomputed tomography for six parameters in two populations, and a difference was detected in one parameter. Our results provide scientific evidence that potentially explains the defensive mechanism against Varroa mites: structural changes in the worker bee mandibles.

animal behavior and cognition↗

bioRxiv2020

Transcriptomic and epigenomic dynamics of honey bees in response to lethal IAPV viral infection

Honey bees (Apis mellifera L) suffer from many brood pathogens, including viruses. Despite considerable research, the molecular responses and dynamics of honey bee pupae to viral pathogens remain poorly understood. Israeli Acute Paralysis Virus (IAPV) is emerging as a model virus since its association with severe colony losses. Using worker pupae, we studied the transcriptomic and methylomic consequences of IAPV infection over three distinct time points after inoculation. Contrasts of gene expression and 5mC DNA methylation profiles between IAPV-infected and control individuals at these time points--corresponding to the pre-replicative (5 hr), replicative (20 hr), and terminal (48 hr) phase of infection--indicate that profound immune responses and distinct manipulation of host molecular processes accompany the lethal progression of this virus. We identify the temporal dynamics of the transcriptomic response to with more genes differentially expressed in the replicative and terminal phases than in the pre-replicative phase. However, the number of differentially methylated regions decreased dramatically from the pre-replicative to the replicative and terminal phase. Several cellular pathways experienced hyper- and hypo-methylation in the pre-replicative phase and later dramatically increased in gene expression at the terminal phase, including the MAPK, Jak-STAT, Hippo, mTOR, TGF-beta signaling pathways, ubiquitin mediated proteolysis, and spliceosome. These affected biological functions suggest that adaptive host responses to combat the virus are mixed with viral manipulations of the host to increase its own reproduction, all of which are involved in anti-viral immune response, cell growth, and proliferation. Comparative genomic analyses with other studies of viral infections of honey bees and fruit flies indicated that similar immune pathways are shared. Our results further suggest that dynamic DNA methylation responds to viral infections quickly, regulating subsequent gene activities. Our study provides new insights of molecular mechanisms involved in epigenetic that can serve as foundation for the long-term goal to develop anti-viral strategies for honey bees, the most important commercial pollinator. Author SummaryHoney bees, the most important managed pollinators, are experiencing unsustainable mortality. Israeli Acute Paralysis Virus (IAPV) causes economically important disease in honey bees, and it is emerging as a model system to study viral pathogen-host interactions in pollinators. The pupation stage is important for bee development but individuals are particularly vulnerable for parasitic mite infestations and viral infections. Currently, it is unclear how honey bee pupae respond to this virus. However, these responses, including gene expression and DNA methylomic changes, are critical to understand so that anti-viral genes can be identified and new anti-viral strategies be developed. Here, we use next-generation sequencing tools to reveal the dynamic changes of gene expression and DNA methylation as pupae succumb to IAPV infections after 5, 20, and 48 hours. We found that IAPV causes changes in regions of DNA methylation more at the beginning of infection than later. The activity of several common insect immune pathways are affected by the IAPV infections, as are some other fundamental biological processes. Expression of critical enzymes in DNA methylation are also induced by IAPV in a temporal manner. By comparing our results to other virus studies of honey bees and fruit flies, we identified common anti-viral immune responses. Thus, our study provides new insight on the genome responses of honey bees over the course of a fatal virus infection with theoretical and practical implications.

genomics↗