Biology subjects

Villalobos, C.

Publications and source records attributed to Villalobos, C..

3 recordsLinked to original sources

bioRxiv2026

Gene circuit-driven amplified selection enables evolution of fast-growing Escherichia coli

The laboratory Escherichia coli K-12 strain has doubled no faster than [~]20 minutes for decades. This plateau could reflect a biophysical limit or simply the way batch culture selects on growth rate. Here we show it can be broken through amplified selection with a Red Queen gene circuit, which takes advantage of growth rate heterogeneity in monoclonal populations to selectively suppress slow-growing cells and creates a tunable mapping from intrinsic growth rate to survival. After 70 days ([~]1,000 generations) of amplified selection in MG1655+FHr and subsequent removal of the circuit, a top evolved clone (RQ70) reached a maximum specific growth rate of 2.61 h-{superscript 1} in shake-flask culture. This corresponds to a doubling time of 15.9 minutes, to our knowledge the shortest reported for E. coli K-12, against 18.1 minutes for evolved controls and 20.3 minutes for the ancestor. The gain came at the cost of a [~]3-fold increase in lag time, indicating that the 20-minute plateau is a multi-trait optimum under conventional batch selection rather than an absolute constraint. We argue that synthetic gene circuits can therefore reshape the evolutionary process itself, pushing performance beyond apparent physiological limits.

synthetic biology↗

bioRxiv2025

Actin Branching Regulates Cell Spreading and Force on Talin, but not Activation of YAP

Cells sense the mechanical properties of their environment through physical engagement and spreading, with high stiffness driving nuclear translocation of the mechanosensitive transcription factor YAP. Restriction of cell spread area or environmental stiffness both inhibit YAP activation and nuclear translocation. The Arp2/3 complex plays a critical role in polymerization of branched actin networks that drive cell spreading, protrusion, and migration. While YAP activation has been closely linked to cellular spreading, the specific role of actin branching in force buildup and YAP activation is unclear. To assess the role of actin branching in this process, we measured cell spreading, YAP nuclear translocation, force on the adhesion adaptor protein Talin (FRET tension sensor), and extracellular forces (traction force microscopy, TFM) in 3T3 cells with and without inhibition of actin branching. The results indicate that YAP activation still occurs when actin branching and cell spreading is reduced. Interestingly, while actin de-branching resulted in decreased force on talin, relatively little change in average traction stress was observed, highlighting the distinct difference between molecular level and cellular level force regulation of YAP. While cell spreading is a driver of YAP nuclear translocation, this is likely through indirect effects. Changes in cell spreading induced by actin branching inhibition do not significantly perturb YAP activation. Additionally, this work provides evidence that focal adhesion molecular forces are not a direct regulator of YAP activation.

bioengineering↗

bioRxiv2025

A Multi-Model Ensemble Reveals Soil Carbon Gains from Regenerative Practices in the U.S. Midwest Cropland

Process-based cropping systems models (CSMs) are key components of measurement, monitoring, reporting, and verification (MMRV) frameworks of carbon markets, but their application suffers from model-specific differences that keep any one model from working well across all combinations of soils, climates, crops, and agronomic practices at varying scales. Multi-model ensemble (MME), successfully used to quantify soil, management and climate impact on crop productivity, provide an opportunity to better estimate changes in soil organic carbon (SOC) outcomes for agronomic practices that have the potential to mitigate SOC loss at scale. We used an MME across 46 million hectares of US Midwest cropland at a resolution of 4- km2 to assess the aggregate ability of different regenerative practices to sequester SOC at this scale compared to their dynamic baselines. MME was validated with long-term experimental data and compared to its constituent CSMs, showing greater accuracy and lower uncertainty. The results show that adopting no-till combined with cover crops increased SOC stocks by 0.36 {+/-} 0.12 Mg ha-1 yr-1 aggregated across the entire U.S. Midwest cropland. At the regional scale, this corresponds to a net SOC gain of 16.4 Tg C yr-1 compared to business-as-usual baselines. These benefits are approximately halved when each management change is practiced individually, and the modest gains are only fully realized when continued over the long-term in soils with low initial carbon stock. Results demonstrate the power of MMEs run at high resolution for providing robust estimates of environmental outcomes following agricultural practice change, and for pinpointing locations for most effective intervention. This approach can alleviate many producer carbon market participation barriers and help address market issues while ultimately supporting large-scale regenerative agriculture initiatives.

ecology↗