Biology subjects

Ahmed, A. C.

Publications and source records attributed to Ahmed, A. C..

3 recordsLinked to original sources

bioRxiv2025

RESCUE: recovery of idiosyncratic expression patterns in spatial transcriptomics

Spatial transcriptomics (ST) enables gene expression profiling while preserving the spatial architecture of intact tissue. Analyzing ST data often proceeds by first extracting cell-level information, typically through cell segmentation or cell-type deconvolution. However, a critical oversight has been that a substantial portion of molecular expression is systematically lost or unannotated by these methods. This lost expression can arise from diverse and biologically important sources like fragile or underrepresented cell types, subcellular structures like neurites, and extracellular expression. These omissions can result in biased analyses and incorrect or incomplete biological interpretations. We describe a new computational method, RESCUE, that can recover the unattributed spatial expression patterns missed by existing ST analysis methods and enable robust inference even when reference is incomplete. We validate RESCUE using MERFISH data from the honey bee brain and apply it to multiple ST datasets to demonstrate how it can reveal novel insights into complex tissue biology.

bioinformatics↗

bioRxiv2025

Social evolution and absence of olfactory function in larval honey bees

Social evolution made larval honey bees dependent on adult colony members for feeding. We therefore predicted they have diminished olfactory capabilities, and based on organismal resource conservation theory, also have downregulated olfactory receptor (OR) gene expression. Behavioral assays demonstrated that larvae cannot find food via olfaction and expressed very low levels of Orco, an essential gene for OR function. By contrast, larvae showed higher expression of Ir25a, an essential gene for multiple forms of sensory perception including gustation. These results suggest larvae rely on taste for feeding. In addition, considering that adult bees use OR-based olfaction extensively, they demonstrate strong developmental regulation of the OR system. Comparative transcriptomics of social and non-social insects further highlight the role of social evolution in shaping this sensory trait.

evolutionary biology↗

bioRxiv2023

Gut microbes contribute to variation in foraging intensity in the honey bee, Apis mellifera.

Gut microbiomes are increasingly recognized for mediating diverse biological aspects of their hosts, including complex behavioral phenotypes. While many studies have reported that experimental disruptions to the gut microbiome result in atypical host behavior, studies that address how gut microbes contribute to adaptive behavioral trait variation are rare. Eusocial insects represent a powerful model to test this, due to their simple microbiomes and complex division of labor characterized by colony-level variation in behavioral phenotypes. While previous studies report correlational differences in gut microbiome associated with division of labor, here, we provide evidence that gut microbes play a causal role in defining differences in foraging behavior between honey bees. Gut microbial community structure consistently differed between hive-based nurse bees and bees that leave the hive to forage for floral resources. These differences were associated with variation in the abundance of individual microbes, including Bifidobacterium asteroides, Bombilactobacillus mellis, and Lactobacillus melliventris. Manipulations of colony demography and individual foraging experience suggested that differences in microbiome composition were associated with task experience. Moreover, single microbe inoculations with B. asteroides, B. mellis, and L. melliventris caused changes in foraging intensity. These results demonstrate that gut microbes contribute to division of labor in a social insect, and support a role of gut microbes in modulating host behavioral phenotypic variation.

animal behavior and cognition↗