Taiwan International Graduate Program - Molecular and Biological Agricultural Sciences

Taiwan International Graduate Program (TIGP) in Molecular and Biological Agricultural Sciences (MBAS) graduate program of Academia Sinica focuses on both basic and applied research in bio-agricultural sciences, aiming to create new platform technologies and innovative systems with potential industrial applications in biotechnology. A key priority of the program is to promote translational research by advancing breakthrough findings in basic research into experimental projects with the potential to be transformed into practical platform technologies or industrial applications for agriculture. Beyond fostering groundbreaking research, the program emphasizes networking opportunities and provides information systems to support the communication and technological needs of the agricultural and biotechnology industries in Taiwan and globally.

HIGHLIGHTS

Keat Ying Chan, Ching-Cher Sanders Yan, Hsiao-Yuh Roan, Shao-Chun Hsu, Tzu-Lun Tseng, Chung-Der Hsiao, Chao-Ping Hsu, Chen-Hui Chen* (2022) Skin cells undergo asynthetic fission to expand body surfaces in zebrafish. Nature. (https://doi.org/10.1038/s41586-022-04641-0) (IF: 64.8)

As an animal’s surface area expands during development, skin cell populations must quickly respond to maintain sufficient epithelial coverage. Despite much progress in understanding of skin cell behaviours in vivo, it remains unclear how cells collectively act to satisfy coverage demands at an organismic level. Here we created a multicolour cell membrane tagging system, palmskin, to monitor the entire population of superficial epithelial cells (SECs) in developing zebrafish larvae. Using time-lapse imaging, we found that many SECs readily divide on the animal body surface; during a specific developmental window, a single SEC can produce a maximum of four progeny cells over its lifetime on the surface of the animal. Remarkably, EdU assays, DNA staining and hydroxyurea treatment showed that these terminally differentiated skin cells continue splitting despite an absence of DNA replication, causing up to 50% of SECs to exhibit reduced genome size. On the basis of a simple mathematical model and quantitative analyses of cell volumes and apical surface areas, we propose that ‘asynthetic fission’ is used as an efficient mechanism for expanding epithelial coverage during rapid growth. Furthermore, global or local manipulation of body surface growth affects the extent and mode of SEC division, presumably through tension-mediated activation of stretch-activated ion channels. We speculate that this frugal yet flexible mode of cell proliferation might also occur in contexts other than zebrafish skin expansion.

Cell division is a fundamental process for life. Besides mitosis in somatic cells and meiosis in germ cells, we discovered a variant form of cell division in live zebrafish larvae that accounts for a drastic increase of cell number during development.

TIGP 20th Certificate Conferral Ceremony

Congratulations to the TIGP-MBAS Graduation Awardees!

Sanjay Prasad Selvaraj, Ju-Chun Chang, Karukuvelraja Raja, Jing-Ting Zhu, Prakash Kishore Hazam, Wen-Chun Lin, Jung-Ren Huang, Tsung-Lin Li, Jyh-Yih Chen (2025). Novel self-assembled antimicrobial peptide Pardaxin hydrogel as a functional biomaterial for food packaging and preservation. Chemical Engineering Journal, 170727. https://doi.org/10.1016/j.cej.2025.170727 (IF: 13.2)

Our work addresses the urgent challenge of food spoilage and antimicrobial resistance (AMR), which together contribute to the loss of over 1.3 billion tons of food globally each year. Conventional chemical preservatives and packaging materials face increased scrutiny due to toxicity, environmental impact, and ineffectiveness against drug-resistant strains. There is a pressing need for easy-to-synthesize, biocompatible, sustainable, and functional antimicrobial materials in the food sector. In this study, we report a self-assembled antimicrobial peptide (SA-AMP) hydrogel derived from Pardaxin. Unlike conventional antimicrobial hydrogels that require chemical crosslinkers or loaded bioactives, our system spontaneously assembles into a nanofibrillar β-sheet-rich hydrogel under physiological conditions, driven entirely by non-covalent interactions. This minimalistic design results in a crosslinker-free, injectable, shear-thinning, and biodegradable matrix with remarkable antimicrobial properties. Pardaxin hydrogel was found to be non-toxic, exhibiting intrinsic antimicrobial activity against foodborne and drug-resistant pathogens, through a ‘trap-and-kill’ mechanism. Digestibility studies demonstrated enzymatic degradation of released peptides post-ingestion, enabling a tunable “on/off” antimicrobial function that ensures food safety without adverse effects. Food application was demonstrated in chicken meat and milk preservation models, where the hydrogel showed excellent coating stability, protective effects against S. putrefaciens and UV barrier properties. Our work is the first to apply a self-assembled AMP hydrogel as a direct antimicrobial coating in food systems, establishing a completely new material class for food preservation that unites principles from nanotechnology, and functional biomaterials. This approach directly tackles the limitations of conventional preservatives and passive packaging, and offers a highly tunable, scalable, and environmentally responsible alternative.

Yu Wu, Hsin-Yi Chang, Chih-Hang Wu, Erh-Min Lai, Chih-Horng Kuo* (2025). Comparative transcriptomics reveals context- and strain-specific regulatory programmes of Agrobacterium during plant colonization. Microbial Genomics, 11(8):001485. https://www.microbiologyresearch.org/content/journal/mgen/10.1099/mgen.0.001485

Agrobacterium is a genus of plant-associated bacteria capable of transferring DNA into host genomes to induce tumourigenesis. The process has been primarily studied in a few model strains, particularly C58, and developed into Agrobacterium-mediated transformation for genetic manipulation. However, the diversity of wild-type strains and their context-specific regulatory responses remains poorly characterized. Here, we evaluated five wild-type strains and identified 1D1108 as superior in tumourigenesis on legumes and transient transformation in Nicotiana benthamiana. Under in vitro virulence induction with acetosyringone, we identified 126 differentially expressed genes (DEGs) in 1D1108. Although the number of DEGs was comparable to those in C58 and the legume isolate 1D1609 under the same condition, only 22 DEGs, primarily within the vir regulon, were conserved, indicating extensive divergence among these Agrobacterium strains. Leaf infiltration of N. benthamiana revealed 1,134 DEGs specifically regulated in planta for 1D1108. These included genes involved in attachment, virulence regulation, type IV pilus, succinoglycan biosynthesis and diverse nutrient transporters, providing new evidence on expression regulation during colonization. Comparative analyses of in planta transcriptomes with C58 and Pseudomonas syringae DC3000 revealed distinct secretion systems required for pathogenesis, namely, type IV for Agrobacterium and type III for Pseudomonas, and only ~5–19% of DEGs were conserved. These limited transcriptomic overlaps underscore the importance of studying gene expression in strains and conditions directly relevant to the biological context, rather than relying on model systems. Together, this work reveals how environmental and host-associated cues shape transcriptional responses in plant-associated bacteria.

Negi A, Yadav BG, Kuo CW, Hazam PK, Lin WC, Teh OK, Chen JY. A Deep-Sea probiotic platform: Dual-function biopreservation for aquaculture immunomodulation and meat shelf-life extension. Innovative Food Science & Emerging Technologies. 2025 Jul 2:104107. https://doi.org/10.1016/j.ifset.2025.104107

Two major challenges in the food industry include antibiotic overuse in aquaculture and reliance on synthetic preservatives to increase meat shelf-life. To address these challenges, we developed a dual-function platform using Lactococcus lactis L25_4, isolated from 312-m depth in Taiwan's Taimali region. As a feed additive, L. lactis L25_4 significantly enhanced Litopenaeus vannamei (whiteleg shrimp) survival against Vibrio vulnificus infection by modulating gut microbiota (e.g., enriching Rhodobacteraceae and Streptococcaceae and inhibiting Desulfovibrionaceae and Klebsiella) and improving gut membrane integrity. It also upregulated immune genes (e.g., HSP70, Lysozyme C, SOD and Tollo) and increased short chain fatty acids (SCFAs) levels in the shrimp intestinal region. Transcriptomic and microbiome analyses revealed immune priming and stress mitigation, with Spearman correlations linking beneficial bacteria to enhanced gut integrity and immune activation. The cell-free supernatant (CFS) of L. lactis L25_4 was incorporated into a chitosan-based hydrogel and applied as a surface coating on raw pork meat. Samples were inoculated with Shewanella putrefaciens (106 CFU/mL), a known meat spoilage bacterium, and the CFS–chitosan hydrogel inhibited bacterial growth by >99 % for up to 5 days at 4°C compared to untreated controls, as confirmed by CFU enumeration and Cryo-SEM imaging. L. lactis L25_4 demonstrated functional stability across aquaculture and chilled meat systems, supporting its dual application in biopreservation. By integrating multi-omics, biopolymer engineering, and pathogen inhibition assays, we present a scalable, nature-derived alternative to antibiotics and synthetic preservatives. This work advanced food science via a validated, application-ready platform aligned with One Health principles and offers a paradigm shift in sustainable biopreservation technologies.