Biology subjects

Ho, C.-K.

Publications and source records attributed to Ho, C.-K..

4 recordsLinked to original sources

bioRxiv2025

RamanOmics Decodes Spatial Vibrational-Molecular Architecture and Rewiring in Aging and Repair

Aging and tissue repair involve multilayered and spatially heterogeneous remodeling across transcriptional, biochemical, and cellular dimensions, yet prevailing definitions rely on isolated molecular markers that obscure how biochemical and transcriptional states co-evolve in tissues. Here we present RamanOmics, a multimodal framework that integrates single-nucleus RNA sequencing (snRNA-seq), spatial transcriptomics, and label-free Raman imaging to map the spatial vibrational-biochemical and molecular architecture of aging and senescence directly in intact tissues. Applied to mouse lung and skin, RamanOmics generates spatially resolved biochemical-molecular maps revealing tissue-specific programs: lung senescent cells are enriched for extracellular matrix (ECM) remodeling and TGF-{beta} signaling (Serpine1, Dab2, Igfbp7), whereas skin senescence is dominated by keratinization and barrier homeostasis modules (Krt10, Lor, Sbsn). Across tissues, we identify a conserved branched-chain fatty-acid-linked biochemical profile and Raman signature (1131-1135 cm-{superscript 1}) that robustly marks p21 senescent cells. To unify these layers, we develop a machine learning derived "multimodal barcode" that quantitatively integrates biochemical and transcriptional features, enabling non-destructive identification of senescence in situ. In a wound-healing model, RamanOmics further reveals coordinated reactivation of barrier-repair programs in senescent cells, marked by upregulation of Krt10, Lor, Sbsn, Sfn, and Dmkn together with matching increases in lipid-associated Raman signatures, confirming biological generalizability beyond steady-state aging. By directly integrating gene programs to spatial vibrational-biochemical states, RamanOmics provides a general framework and resource for scalable, multimodal profiling of cellular states.

systems biology↗

bioRxiv2024

Effects of local and landscape factors on paddy field arthropod diversity: from species to communities

Agricultural landscapes are dynamic mosaics where environmental conditions vary across spatial scales. Identifying the spatial scales of environmental variables relevant to biodiversity is therefore essential for safeguarding biodiversity and the ecosystem services they provide. Although species richness is a useful aggregate metric the captures the responses of biodiversity as a whole, few studies have examined how species-specific responses to environmental variables give rise to community-level patterns. Failure to account for the heterogeneity in species responses may undermine potential processes that structure biodiversity. In this study, we sampled paddy-field inhabiting arthropods across the first growing season and examined how local (organic farming, water depth, and crop height) and landscape factors (forest cover and connectivity) affect their abundance and distribution. We built a spatio-temporally explicit joint species distribution model (JSDM) to answer three main questions. 1) How do species differ in their response to local and landscapes factors. 2) Can trophic guild explain the variation in species responses to environmental covariates, and 3) How do species-specific responses scale-up to structure species richness at the community-level? Our results show that the mean importance of environmental covariates was low overall (mean R2 = 0.21), suggesting the prevalence of stochasticity in structuring species abundances. However, environmental importance varied substantially across species (highest R2 = 0.87 and lowest R2 = 0.01) and that trophic guild explained only approximately 15% of species responses, which indicates high idiosyncrasy in species responses both within and among guilds. At the community-level, we found that species richness responds negligibly to local factors while increasing with forest cover at the landscape scale. The importance of each environmental covariate was reflected by the variability of species responses. Lastly, we found no evidence of dispersal limitation in structuring species abundances. Taken together, our study suggests that many paddy field arthropods exhibit transient dynamics and that environmental effects are highly species-specific, even within the same trophic guild. Most importantly, our study highlights the need to understand biodiversity from the species level to understand the processes that structure them in dynamic mosaic landscapes.

ecology↗

bioRxiv2022

Multiple climate change factors jointly increased the competitiveness of a C4 grass against its C3 competitor

C3 and C4 plants are the two major terrestrial plant groups that respond differently to temperature, water, and CO2. Although much research has focused on the individual effect of warming, water availability, and elevated CO2 on biomass production and competitive interactions between C3 and C4 plants, the joint effects of these factors remain underexplored. We grew naturally co-occurring C3 (Oplismenus composites) and C4 (Paspalum conjugatum) grass under three temperature warming scenarios (control, +2{degrees}C, and +4{degrees}C), two water supply intervals (normal 2 days vs. prolonged 7 days [drought]), and two CO2 concentrations (ambient 400 ppm vs. elevated 800 ppm) in growth chambers and measured their above- and below-ground dry biomass in monoculture and mixture to quantify their biomass performances and competitive responses. Warming and elevated CO2 together enhanced the above- and/or below-ground biomass of both C3 and C4 grass. Moreover, temperature, water, and CO2 interacted to increase the below-ground biomass of the C4 grass. Surprisingly, the C3 grass performed worse under interspecific competition (mixture biomass) relative to intraspecific competition (monoculture biomass) at elevated CO2 compared to ambient CO2, while the reverse is true for the C4 grass. Furthermore, the C4 grass was most competitive against the C3 grass under simultaneous 4{degrees}C warming, drought, and elevated CO2. Taken together, our results suggest that the competitive balance could potentially shift in favor of C4 plants under the projected temperature warming, increased drought frequencies, and rising atmospheric CO2, with an increase in C4 relative abundance in future plant communities.

ecology↗

bioRxiv2020

Benefit of Drought on an Herbivore of Herbaceous Plants: Enemy Free Space and Reduced Competition

Plants grow under reduced water availability can have divergent effects on insect herbivores, in some instances producing benefits to them. However, the forces mediating these positive impacts remain mostly unclear. We conducted a manipulative field study using a specialist herbivore Pieris rapae, and its host plant, Rorippa indica, in two populations to identify how water availability impacts overall plant quality and multitrophic interactions. We observed that R. indica growing under low water availability led to higher survival of P. rapae larvae. The increase in survival of eggs and larvae was related to the reduced abundance of other herbivores and natural enemies. Water availability had differential impacts on members of the herbivore community through changes in plant quality. Low water availability decreased the quality of R. indica to most herbivores as indicated by reduced abundance in the field and decreased relative growth rate in feeding assays. In contrast, the performance of P. rapae larvae were not affected by differences in sympatric R. indica grown under different water availability. These results indicate that local P. rapae possess some physiological adaptation to overcome fluctuations in host quality. Our findings illustrate that reduced water availability is beneficial to a specialist herbivore, but detrimental to most other herbivores. Our work highlights the complex roles of the arthropod communities associated with plants in determining the impacts of water availability on insect herbivores.

ecology↗