Biology subjects

Sil, T.

Publications and source records attributed to Sil, T..

3 recordsLinked to original sources

bioRxiv2026

Probabilistic mouse-human brain correspondence by multimodal optimal transport

The mouse is the principal model for brain mechanism and disease, allowing experiments that cannot be performed in humans. However, findings often translate poorly because homologous regions differ in relative size and some human territories have no clear mouse counterpart. Here we present OTTER, which learns mouse-human brain correspondence as a probabilistic, parcel-resolution coupling using multimodal fused Gromov-Wasserstein optimal transport, integrating functional and structural connectivity with spatial position and curated homologies. OTTER recovers established homologues on a transcriptomic benchmark and preserves broad cross-species organisation along the cortical areal hierarchy. Applying the coupling to human functional connectivity reveals a graded decline in mouse-based reconstruction across evolutionarily expanded association cortex, with the lowest values in lateral prefrontal territory. Finally, the bidirectional map generates testable human predictions from mouse experiments and ranks mouse circuits corresponding to human clinical targets.

neuroscience↗

bioRxiv2026

De novo origin and evolution of an antimicrobial protein function

Antimicrobial peptides (AMPs) constitute key components of innate immunity across the tree of life. Canonical AMPs are typically translated as small proteins and secreted from host cells to act against microbes. However, cryptic AMP-like domains are also embedded within diverse proteins not classically associated with antimicrobial function. How such embedded AMPs first emerge and diversify remains unclear. Here we retrace the origin and evolution of the abundant mammalian protein lactoferrin and its embedded AMP, lactoferricin. By resurrecting extinct lactoferrin ancestors dating back to the earliest mammals, we identify a gradual enrichment of cationic and hydrophobic amino acids in the lactoferricin domain over time. These changes enabled ancient lactoferricin to first rupture bacterial membranes, an activity that was later enhanced in extant mammals conferring potent bactericidal activity against diverse bacteria. In addition, we find that recent natural selection within the lactoferricin domain has continued to modulate antimicrobial activity on recent evolutionary timescales. In particular, we pinpoint a single rapidly evolving site in lactoferricin among great apes that significantly enhances antimicrobial potency against major pathogenic bacteria. Together our study illustrates how novel immune protein functions can arise, evolve, and diversify to strengthen host defense against diverse microbial pathogens.

evolutionary biology↗

bioRxiv2021

Genome sequencing and assembly of Tinospora cordifolia (Giloy) plant

During the ongoing COVID-19 pandemic Tinospora cordifolia also known as Giloy gained immense popularity and use due to its immunity-boosting function and anti-viral properties. T. cordifolia is among the most important medicinal plants that has numerous therapeutic applications in health due to the production of a diverse array of secondary metabolites. Therefore, to gain genomic insights into the medicinal properties of T. cordifolia, the first genome sequencing was carried out using 10x Genomics linked read technology and the draft genome assembly comprised of 1.01 Gbp. This is also the first genome sequenced from the plant family Menispermaceae. We also performed the first genome size estimation for T. cordifolia and was found to be 1.13 Gbp. The deep sequencing of transcriptome from the leaf tissue was also performed followed by transcriptomic analysis to gain insights into the gene expression and functions. The genome and transcriptome assemblies were used to construct the gene set in T. cordifolia that resulted in 19,474 coding gene sequences. Further, the phylogenetic position of T. cordifolia was also determined through the construction of a genome-wide phylogenetic tree using 35 other dicot species and one monocot species as an outgroup species.

genomics↗