Biology subjects

Saikia, A.

Publications and source records attributed to Saikia, A..

3 recordsLinked to original sources

bioRxiv2026

Gene Expansion and Regulatory Rewiring Shape Sex-Biased Evolution of the Mouse Submandibular Gland Secretome

Background Mammalian saliva plays essential roles in digestion, immunity, and host-microbiome interactions, yet its protein composition varies widely across species and sexes. This diversity makes saliva a powerful model to study evolution of gene expression. Here, we compared mouse and human salivary glands at the genomic, transcriptomic, and proteomic levels to understand how saliva composition evolves. Results We found that evolution of gene expression in mouse salivary glands is driven by rapid gene turnover and sexual dimorphism. In the submandibular and sublingual glands, 68% and 73% of expression from genes encoding secreted proteins derives from lineage-specific genes that lack one-to-one human orthologs. This contrasts the prevailing view that gene expression is largely conserved across tissues and highlights saliva as an unusually dynamic system of molecular evolution. Mouse submandibular gland shows striking sexual dimorphism, with 1537 tissue specific sex-biased genes, 3.8 times higher than in the liver (p<0.001), a classic model of sex-biased expression. We also identified sex-specific expression of glycosylation genes associated with differential Muc19 sialylation. These results suggest that sexual dimorphism in mouse saliva arises from both transcriptional differences in secreted proteins and sex-specific post-translational modifications. Further, differentially expressed genes in submandibular gland cluster in genomic regions shaped by recent gene duplication, such as the kallikrein gene cluster, a mouse-specific expansion that accounts for ~16.4% of male-biased submandibular gland expression. Our analyses suggest that this bias arises through regulatory changes that are expanded by gene duplication, including the spread of a testosterone-associated regulatory motif and the expansion of a shared chromatin domain that promotes coordinated gene regulation. Conclusions Together, our results reveal that lineage-specific genes disproportionately shape the mouse salivary transcriptome and that gene duplication and regulatory rewiring contribute to the rapid evolution of sex-biased expression in the submandibular gland. We describe a novel mechanism through which lineage-specific gene duplication and regulatory rewiring drive rapid, sex-specific evolution of the mammalian saliva. Our findings support saliva as an evolutionarily dynamic system and are consistent with developmental systems drift, whereby similar phenotypes across species may be maintained despite substantial divergence in their underlying gene-regulatory programs.

evolutionary biology↗

bioRxiv2025

Consistency in floral volatiles impacts plant-pollinator interactions in the face of environmental change in the Eastern Himalayas

Floral scents are an important mediator of many plant-pollinator interactions. However, environmental and ecological change could affect the synthesis and emission of volatile chemicals that constitute floral scents, potentially influencing pollinator perception of scents. We investigated the effects of elevation and warming on the floral scents of multiple co-occurring alpine meadow plant species along an elevational gradient in the Eastern Himalayas (3000 - 4000 masl). We also investigated pollinator responses in the same locations using 3-D printed floral models that replicated the differing volatile constituents. Finally, we assessed how pollinator preferences changed with variations in elevation, flowering season and location. We found that elevation and in-situ warming using Open Top Chambers (OTC) led to significant intraspecific variation in the composition of floral scents, both in terms of quality and quantity of volatiles released. Nevertheless, conspecific floral scents across elevations were more similar to each other than to other species. Cafeteria assays using artificial floral models revealed that pollinator preferences were driven by a small number of volatiles (p-cymene, 2-pentylfuran and -pinene), but these preferences were abolished in a novel plant-pollinator community where the same floral volatiles were not detected. Our results suggest that the local odourscape established by the floral community present plays a key role in plant-pollinator interactions. This emphasizes the need to incorporate ecological impacts such as changes in community into climate change analyses to understand the long-term impacts of human activity on co-evolutionary relationships like pollination. Significance StatementFloral scents are important for most plant-pollinator interactions, and can be affected by environmental factors like elevation and temperature. Our study shows that elevation and simulated in situ warming change the composition of floral scents, yet scents from the same species were more similar to each other across elevations and temperatures than to other species. Further, pollinator preferences to these scents replicated in artificial models persisted in spite of variation in temperature and elevation, but not in a novel plant-pollinator community containing floral species not releasing those volatiles. This emphasizes the need to incorporate factors such as floral community composition into our understanding of the long-term impacts of climate change and human activity on co-evolutionary relationships like pollination.

ecology↗

bioRxiv2021

Mapping the peptide binding groove of MHC class I

An essential element of adaptive immunity is the selective binding of peptide antigens by major histocompatibility complex (MHC) class I proteins and their presentation to cytotoxic T lymphocytes on the cell surface. Using native mass spectrometry, we here analyze the binding of peptides to an empty disulfide-stabilized HLA-A*02:01 molecule. This novel approach allows us to examine the binding properties of diverse peptides. The unique stability of our MHC class I even enables us to determine the binding affinity of complexes, which are suboptimally loaded with truncated or charge-reduced peptides. Notably, a unique erucamide adduct decouples affinity analysis from peptide identity alleviating issues usually attributed to clustering during electrospray ionization. We discovered that two anchor positions at the binding surface between MHC and peptide can be stabilized independently and further identify the contribution of other peptidic amino acids on the binding. We propose this as an alternative, likely universally applicable method to artificial prediction tools to estimate the binding strength of peptides to MHC class I complexes quickly and efficiently. This newly described MHC class I-peptide binding affinity quantitation represents a much needed orthogonal, independent approach to existing computational affinity predictions and has the potential to eliminate binding affinity biases and thus accelerate drug discovery in infectious diseases, autoimmunity, vaccine design, and cancer immunotherapy.

biophysics↗