Biology subjects

Tian, X.-J.

Publications and source records attributed to Tian, X.-J..

6 recordsLinked to original sources

bioRxiv2025

Integrating Recombinase-Based Feedback and Feedforward Control for Optimal Resource Decoupling

Resource competition disrupts circuit modularity by introducing unintended coupling between otherwise independent gene modules, thereby compromising genetic circuit function. While various control strategies have been explored, their complexity or limited efficacy has hindered broader application. Here, we present the Re-NF-FF-Controller, a recombinase-based strategy that integrates negative feedback and feedforward regulation via promoter flipping to mitigate resource competition. Computational modeling and experimental validation demonstrate that Re-NF-FF-Controller effectively reduces resource coupling, ensuring robust gene expression and modularity. Moreover, its tunability allows for performance optimization through straightforward adjustments of recombinase enzyme levels. This strategy offers a versatile and easily implementable solution for designing reliable synthetic biological systems. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/653855v1_ufig1.gif" ALT="Figure 1"> View larger version (15K): org.highwire.dtl.DTLVardef@6b960forg.highwire.dtl.DTLVardef@148bc3borg.highwire.dtl.DTLVardef@3df13borg.highwire.dtl.DTLVardef@a865f2_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2021

Emergent Oscillation Induced by Nutrient-Modulating Growth Feedback

Growth feedback, the inherent coupling between the synthetic gene circuit and the host cell growth, could significantly change the circuit behaviors. Previously, a diverse array of emerged behaviors, such as growth bistability, enhanced ultrasensitivity, and topology-dependent memory loss, were reported to be induced by growth feedback. However, the influence of the growth feedback on the circuit functions remains underexplored. Here, we reported an unexpected oscillatory behavior of a self-activation gene circuit induced by nutrient-modulating growth feedback. Specifically, after dilution of the activated self-activation switch into the fresh medium with moderate nutrient, its gene expression first decreases as the cell grows and then shows a significant overshoot before it reaches the steady states, leading to oscillation dynamics. Fitting the data with a coarse-grained model suggests a nonmonotonic growth-rate regulation on gene production rate. The underlying mechanism of the oscillation was demonstrated by a molecular mathematical model, which includes the ribosome allocation towards gene production, cell growth, and cell maintenance. Interestingly, the model predicted a counterintuitive dependence of oscillation amplitude on the nutrition level, where the highest peak was found in the medium with a moderate nutrient but was not observed in rich nutrient. We experimentally verified this prediction by tuning the nutrient level in the culture medium. We did not observe significant oscillatory behavior for toggle switch, suggesting that the emergence of oscillatory behavior depends on circuit network topology. Our results demonstrated a new nonlinear emergent behavior mediated by growth feedback, which depends on the ribosome allocation between gene circuit and cell growth.

synthetic biology↗

bioRxiv2019

Topology-Dependent Interference of Synthetic Gene Circuits by Growth Feedback

Growth-mediated feedback between synthetic gene circuits and host organisms leads to diverse emerged behaviors, including growth bistability and enhanced ultrasensitivity. However, the range of possible impacts of growth feedback on different gene circuits remains underexplored. Here, we mathematically and experimentally demonstrated that growth feedback affects the functions of memory gene circuits in a network topology-dependent way. Specifically, the memory of the self-activation circuit is quickly lost due to the fast growth-mediated dilution of the circuit products. Decoupling of growth feedback reveals its memory, manifested by its hysteresis property across a broad range of stimulus. On the contrary, the toggle switch is more refractory to the growth-mediated dilution and can retrieve its memory after the fast-growth phase. The underlying principle lies in the different dependence of active and repressive regulations in these circuits on the growth-mediated dilution. Our results unveil the topology-dependent mechanism on how growth-mediated feedback influences the behaviors of gene circuits.

synthetic biology↗

bioRxiv2017

Rapid, modular, and cost-effective generation of donor DNA constructs for CRISPR-based gene knock-in

CRISPR-based gene knock-in at endogenous sites is desirable in multiple fields such as quantitative studies of signal transduction pathways and gene regulation, synthetic biology, and disease modeling. Contrasting the knock-out procedure, a key step of CRISPR knock-in procedure relies on the homology-directed repairing (HDR) process that requires a donor construct as repair template. Therefore, it is desirable to generate a series of donor DNA constructs efficiently and cost-effectively. In this study, we developed a general Gibson assembly procedure that combines strengths of a Modular Overlap-Directed Assembly with Linkers (MODAL) strategy and a restriction enzyme based hierarchical framework. This procedure also allows fusing sgRNAs to the constructs for enhanced homology-directed repairing efficiency. Experimental tests on multiple constructs achieved from 3-8 folds of increase in assembly efficiency to high yield of constructs that failed to make with conventional Gibson assembly. The modularized procedure is simple, fast and cost-effective while making multiple constructs, and a computer package is provided for customized design.

molecular biology↗

bioRxiv2017

Targeting temporal dynamics of microenvironmental factors halts tumor migration and alleviates effects of dynamic tumor heterogeneity

Targeting microenvironmental factors that foster migratory cell phenotypes is a promising strategy for halting tumor migration. However, lack of mechanistic understanding of the process impedes pharmaceutical drug development. Using a novel 3D microtumor model with tight control over tumor size, we recapitulated tumor size-induced hypoxic microenvironment and emergence of migratory phenotypes in epithelial T47D breast microtumors as well as those of patient-derived primary metastatic breast cancer cells, mesothelioma cells and lung cancer xenograft cells (PDX). The microtumor models from various patient-derived tumor cells and PDX cells revealed upregulation of tumor secretome, matrix metalloproteinase-9 (MMP9), fibronectin (FN), and soluble E-cadherin (sE-CAD) consistent with the clinically reported elevated levels of FN and MMP9 in the patient breast tumors compared to healthy mammary gland. We further showed that the tumor secretome induces migratory phenotype in non-hypoxic, non-migratory small microtumors. Subsequent mathematical model analysis identified a two-stage microtumor progression and migration mechanism, i.e., hypoxia induces migratory phenotype in the early initialization stage, which then becomes self-sustained through positive feedback loop established among the secretome. Both computational and experimental studies showed that inhibition of tumor secretome effectively halts microtumor migration despite tumor heterogeneity, while inhibition of the hypoxia is effective only within a time window and is compromised by tumor-to-tumor variation of the growth dynamics, supporting our notion that hypoxia initiates migratory phenotypes but does not sustain it. In summary, we show that targeting temporal dynamics of evolving microenvironments during tumor progression can halt and bypass major hurdle of tumor heterogeneity.

cancer biology↗

bioRxiv2017

Cells Interpret Temporal Information From TGF-β Through A Nested Relay Mechanism

The detection and transmission of the temporal quality of intracellular and extracellular signals is an essential cellular mechanism. It remains largely unexplored how cells interpret the duration information of a stimulus. In this paper, through an integrated quantitative and computational approach we demonstrate that crosstalk among multiple TGF-{beta} activated pathways forms a relay from SMAD to GLI1 that initializes and maintains SNAILl expression, respectively. This transaction is smoothed and accelerated by another temporal switch from elevated cytosolic GSK3 enzymatic activity to reduced nuclear GSK3 enzymatic activity. The intertwined network places SNAIL1 as a key integrator of information from TGF-{beta} signaling subsequently distributed through upstream divergent pathways; essentially cells generate a transient or sustained expression of SNAIL1 depending on TGF-{beta} duration. Other signaling pathways may use similar network structure to encode duration information.

systems biology↗