Biology subjects

Wang, T.-C.

Publications and source records attributed to Wang, T.-C..

4 recordsLinked to original sources

bioRxiv2026

High-throughput stomatal phenotyping provides selection targets for stress-resilient wheat

Phenotyping stomatal traits and their developmental plasticity is time-consuming but holds potential to improve water use efficiency and photosynthesis for designing stress-tolerant crops under climate change. Here, we develop a robust, high-throughput pipeline for phenotyping 14 stomatal traits in winter wheat related to size, variation, maximum conductance, and spatial patterning. We (1) analyze over 25,000 images from 60 wheat cultivars grown in growth chamber, greenhouse, and field conditions; (2) investigate the impact of light, temperature, and reduced water and nitrogen supply on stomatal traits and their developmental plasticity across adaxial and abaxial surfaces; and (3) evaluate genetic diversity and breeding progress of stomatal traits. Stomatal traits were highly broad-sense heritable, were largely plastic in response to environmental conditions, and showed genotype-specific responses. Stomatal traits of third leaves under controlled environments with stable light and temperature conditions reliably captured the genetic variance of flag leaves under field conditions. Our data suggests that the upper leaf surface contributed more to transpiration and cooling through consistently higher stomatal density, area, and maximum conductance, while the lower surface facilitated CO2 diffusion via systematic proper patterning and spacing. Breeding maintains the genetic diversity of stomatal traits, and our pipeline facilitates breeders to target them to enhance water use efficiency in high-yielding modern cultivars.

plant biology↗

bioRxiv2025

Multi-omics investigation reveals molecular determinants of cancer cell evolution on soft extracellular matrix

Cancer cell adaptation to their physical tumor microenvironment is a key driver of malignancy. Recent experimental evolution experiments show that the soft extracellular matrix (ECM) can impose a selection pressure on genetically variable tumor populations. Over months of sustained culture, the selection pressure leads to enrichment of specific genetic variants with high fitness, but the mechanisms underlying the high fitness of these soft-selected clones are not fully understood. Here, we used a combination of RNA-seq, ATAC-seq, and RRBS-seq to compare soft-selected populations with non-selected ancestral populations cultured on soft ECM. We demonstrate that ancestral populations grown on soft ECM for short durations are characterized by a stressed cell state with low fitness marked by cell cycle arrest and distinct metabolic shifts, whereas sustained culture selects for a robust proliferative phenotype. Mechanistically, selected cells exhibit a silenced ancestral stress response through epigenetic modifications, characterized by reduced chromatin accessibility and de novo DNA methylation, including CDH1 promoter hypermethylation. This repressive landscape supports a high-fitness state defined by elevated MYBL2 and FAK levels. An in-silico mechanism-based model shows that these molecular differences, together with high YAP1 nuclear localization in soft-selected cells, are salient features of genetic clones capable of FAK upregulation. These findings uncover a coordinated genetic and epigenetic mechanism driving cancer cell evolution in mechanically soft microenvironments.

systems biology↗

bioRxiv2025

Blood-based Transcriptomics Reveal Sex- and Amyloid-Modulated Biology of Plasma pTau217 in Preclinical Alzheimer's Disease

Plasma pTau217, an emerging Alzheimers disease (AD) biomarker, may reflect a synaptic response to {beta}-amyloid (A{beta}) plaques before cortical tangle formation, but its broader biological correlates remain unclear. We sought to identify associations between whole blood gene expression and plasma pTau217, and to determine whether APOE{varepsilon}4, sex, and neocortical A{beta}-PET modify these associations in 724 participants from the Anti-Amyloid Treatment in Asymptomatic Alzheimers and accompanying LEARN studies (A4/LEARN, Agemean(SD)=72.2(4.6); 63%female). Of 20,621 genes tested (1,048 X-linked), none were directly associated with pTau217; one gene was moderated by APOE{varepsilon}4, 1,540 genes by A{beta}-PET, and 772 genes by both A{beta}-PET and sex. Over 100 of these significant associations were X-linked, supporting a role of the X chromosome in AD. Sex interactions were only observed in the presence of elevated A{beta}-PET. Our results underscore the complexity of molecular mechanisms that can be linked to plasma pTau217, particularly in the context of elevated A{beta}-PET.

neuroscience↗

bioRxiv2020

Deep-learning based denoising and reconstruction of super-resolution structured illumination microscopy images

Super-resolution structured illumination microscopy (SR-SIM) provides an up to two-fold enhanced spatial resolution of fluorescently labeled samples. The reconstruction of high quality SR-SIM images critically depends on patterned illumination with high modulation contrast. Noisy raw image data, e.g. as a result of low excitation power or low exposure times, result in reconstruction artifacts. Here, we demonstrate deep-learning based SR-SIM image denoising that results in high quality reconstructed images. A residual encoding-decoding convolution neural network (RED-Net) was used to successfully denoise computationally reconstructed noisy SR-SIM images. We also demonstrate the entirely deep-learning based denoising and reconstruction of raw SIM images into high-resolution SR-SIM images. Both image reconstruction methods prove to be very robust against image reconstruction artifacts and generalize very well over various noise levels. The combination of computational reconstruction and subsequent denoising via RED-Net shows very robust performance during inference after training even if the microscope settings change.

biophysics↗