Biology subjects

Bhamidipati, P. S.

Publications and source records attributed to Bhamidipati, P. S..

4 recordsLinked to original sources

bioRxiv2026

A novel reaction-diffusion architecture for engineering self-organized patterns in mammalian cells

Reaction-diffusion circuits generate self-organized spatial patterns through local activation and long-range inhibition, but synthetic implementations in mammalian cells have been limited by the differential-diffusion requirement. Here, we introduce a novel architecture, juxtacrine activation with paracrine inhibition (JAPI), where the activator propagates through cell-cell contacts rather than diffusion. We demonstrate mathematically and numerically that JAPI accesses the same patterning regimes as classical diffusion-based circuits with one fewer free parameter. We then engineer compact synNotch-based JAPI circuits in mammalian fibroblasts and demonstrate their sufficiency for self-organized patterning through tunable, size-limited signal propagation. Functionalized to spatially control morphogen secretion, these circuits perturb feather bud formation on adjacent embryonic chicken epidermis. Finally, we develop a library-based approach to explore coupled, dual-JAPI circuits with tunable cross-inhibition, enabling programmable interactions between patterns and access to a broad morphospace of spatial states. Together, JAPI provides a compact, modular platform for programming self-organized multicellular patterning. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=97 SRC="FIGDIR/small/727552v1_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@fae8c9org.highwire.dtl.DTLVardef@c8eddborg.highwire.dtl.DTLVardef@177d08corg.highwire.dtl.DTLVardef@11cc952_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Designing biochemical circuits with tree search

Discovering biochemical circuits that exhibit a desired behavior is an outstanding problem in biological engineering. The traditional approach of enumerating every possible circuit topology becomes intractable for circuits with more than four components due to combinatorial scaling of the search space. Here, we use Monte Carlo Tree Search (MCTS), a reinforcement learning (RL) algorithm, to optimize circuit topology for a target phenotype by approaching circuit design as a sequence of assembly decisions. Our RL-based design framework, which we call CircuiTree, efficiently and comprehensively finds robust designs for three-component oscillators by prioritizing sparsity. CircuiTree can also infer candidate network motifs from its search results, producing similar results to enumeration. Using parallel MCTS, we scale this workflow up to five components and find that highly fault-tolerant designs use a novel strategy, which we call motif multiplexing. Multiplexed circuits contain many overlapping network motifs that each activate in different mutational scenarios, in one case lending robustness to four out of five single-gene deletions. Overall, CircuiTree provides the first scalable computational platform for designing biochemical circuits.

systems biology↗

bioRxiv2022

Control of spatio-temporal patterning via cell density in a multicellular synthetic gene circuit

A major goal in synthetic development is to design and construct gene regulatory circuits that control the patterning and morphogenesis of synthetic multicellular structures. In natural development, an interplay between mechanical and chemical communication shapes the dynamics of gene regulatory circuits that underlie patterning and morphogenesis. However, for synthetic gene circuits, how the non-genetic properties of the growth environment impact circuit behavior remains poorly understood. Here, we describe an occurrence of mechano-chemical coupling in synthetic contact-dependent synNotch patterning circuits demonstrating that cell density modulates the transduction of signal between a sender and receiver cell. By exploiting density-dependent signaling, we construct multicellular signal propagation circuits with synNotch and control the patterning outcome both temporally and spatially via cell density gradients established in vitro via plating or small-molecule mediated modulation of proliferation. Our work demonstrates that synthetic gene circuits can be critically impacted by their context, providing an alternate means for programming multi-cellular circuit patterning outcomes.

synthetic biology↗

bioRxiv2019

Comparative transcriptomics reveal distinct patterns of gene expression conservation through vertebrate embryogenesis

Despite lifes diversity, studies of variation across animals often remind us of our shared evolutionary past. Abundant genome sequencing over the last ~25 years reveals remarkable conservation of genes and recent analyses of gene regulatory networks illustrate that not only genes but entire pathways are conserved, reused, and elaborated in the evolution of diversity. Predating these discoveries, 19th-century embryologists observed that though morphology at birth varies tremendously, certain stages of embryogenesis appear remarkably similar across vertebrates. Specifically, while early and late stages are variable across species, anatomy of mid-stages embryos (the phylotypic stage) is conserved. This model of vertebrate development and diversification has found mixed support in recent analyses comparing gene expression across species possibly owing to differences across studies in species, embryonic stages, and gene sets compared. Here we perform a comparative analysis using 186 microarray and RNA-seq expression data sets covering embryogenesis in six vertebrate species spanning ~420 million years of evolution. We use an unbiased clustering approach to group stages of embryogenesis by transcriptomic similarity and ask whether gene expression similarity of clustered embryonic stages deviates from the null hypothesis of no relationship between timing and diversification. We use a phylogenetic comparative approach to characterize expression conservation pattern (i.e., early conservation, hourglass, inverse hourglass, late conservation, or no relationship) of each gene at each evolutionary node. Across vertebrates, we find an enrichment of genes exhibiting early conservation, hourglass, late conservation patterns and a large depletion of gene exhibiting no distinguishable pattern of conservation in both microarray and RNA-seq data sets. Enrichment of genes showing patterned conservation through embryogenesis indicates diversification of embryogenesis may be temporally constrained. However, the circumstances (e.g., gene groups, evolutionary nodes, species) under which each pattern emerges remain unknown and require both broad evolutionary sampling and systematic examination of embryogenesis across species.

evolutionary biology↗