Biology subjects

Chai, A.

Publications and source records attributed to Chai, A..

5 recordsLinked to original sources

bioRxiv2025

Larval seedboxes: a modular and effective tool for scaling coral reef restoration

Natural recovery of degraded coral reefs is constrained by low larval recruitment, limiting restoration at ecologically meaningful scales. While propagule-based approaches have proven effective in plant-dominated systems, scaling larval restoration for sessile invertebrates like corals remains challenging. Traditional coral larval methods rely on net enclosures, restricting impact to small areas (<75 m2). We developed and tested a modular, passive larval delivery system - the larval seedbox - to overcome these spatial constraints. Each unit (600 x 500 x 300 mm; 11 kg) enables delayed release of competent larvae near the benthos, enhancing substrate encounter rates over broader areas. At Lizard Island (Great Barrier Reef), five seedboxes delivered [~]14 million larvae across [~]2 ha of degraded reef. Larval release coincided with slack currents to facilitate local retention and subsequent dispersal. Settlement was assessed on 234 tiles placed in concentric arrays around each seedbox. After 48 hours, 85% of tiles had settlers (up to 1,041 per tile), with mean densities 24-times greater than background levels. Enhanced settlement was directly quantified across >470 m2, with spatial modelling estimating >3,000 m2 via tidally driven dispersal. The larval seedbox enables unrestrained, scalable coral larval seeding and represents a practical advance toward broad-scale reef restoration.

ecology↗

bioRxiv2025

The influence of larval retention on coral recruitment

Marine broadcast spawners typically exhibit bipartite life-histories with distinct pelagic larvae and benthic phases. The transition between phases shapes benthic populations, but the rate of larval arrival to a reef is largely unknown due to challenges in accurately measuring supply. Once larvae arrive to a reef, reduced current flow and velocity, facilitate the transition from the water column to the benthos for inefficient swimming larvae. Yet, for coral reefs characterised by complex hydrodynamics and tides, slack current conditions typically last 1.5-3 hours and it remains unclear if such short retention periods drive significant recruitment. This study mechanistically examined the effects of water retention on the settlement of coral larvae from the water column to the benthos and subsequent longer-term recruitment over 15-months. Brief periods of slack currents (<3-hours) retained larvae in unconstrained larval supply treatments, resulting in settlement rates 40-times higher than natural, background rates. Constrained and longer retention of larvae under nets for 2.5- and 24-hours resulted in 4-7-times higher initial settlement than the unconstrained treatment and 305-times higher than background rates. However, after 15-months, similar numbers of surviving recruits were observed across all larval supply treatments, highlighting the effects of density-dependent population regulation. Observations from recruitment tiles show survival rates of coral recruits after 15-months were low (<0.25), even though gregarious settlement behaviour and settlement close to tile edges improved survival. In contrast, observations from the natural substrate show survival rates were 2.5-3.5-times higher than tiles after 15-months, indicating density-independent survival due to optimal niche space and less space limitation. Therefore, when larval supply is high and gregarious behaviour prominent, key vital rates including recruitment and mortality derived from settlement tiles are likely overestimated, as substrate and microhabitat properties between tiles and natural reef environment vary. Overall, our study highlights the prominent role of slack current conditions and local retention of larvae in facilitating the supply-to-settlement transition, and how this interacts with density-dependent processes post-settlement. Our findings underscore the need to investigate how the interaction strengths of pre-and post-settlement processes modulate early coral recovery to best model recovery trajectories for conservation and restoration prioritisation.

ecology↗

bioRxiv2024

FAST-STEM: A human pluripotent stem cell engineering toolkit for rapid design-build-test-learn development of human cell-based therapeutic devices

Very recent clinical advances in stem cell derived tissue replacement and gene therapy, in addition to the rise of artificial intelligence-aided scientific discovery, have placed the possibility of sophisticated human cell-based therapies firmly within reach. However, development of such cells and testing of their engineered gene circuit components, has proven highly challenging, due to the need for generating stable cell lines for each design-build-test-learn engineering cycle. Current approaches to generating stable human induced pluripotent stem cell (hiPSC) lines are highly time-consuming and suffer from lack of control, poor integration efficiency, and limited functionality. Validation in clinically relevant stem cell derived tissues is also broadly lacking. Such drawbacks are prohibitive to repeatably conducting cutting-edge stem cell engineering with broad application within a realistic timeframe and will not scale with the future of regenerative medicine. We have developed FAST-STEM (Facile Accelerated Stem-cell Transgene integration with SynBio Tunable Engineering Modes), a hPSC engineering platform that drastically reduces the time to generate differentiation ready stem cell lines from several weeks to 5 days, exhibiting a ~612-fold improvement in transgene integration rate over previous methodologies. Additional FAST-STEM innovations include: (i) rapid and highly efficient transgene integration; (ii) copy number control; (iii) simultaneous or consecutive integration of multiple gene cassettes; (iv) library screen capability. In addition to this unique functional versatility, platform transportability and broad use case for stem cell-engineering was confirmed by differentiation into eight different cell types across nine different laboratories. This platform dramatically lowers the bar for integration of synthetic biology with regenerative medicine, enabling experiments which were previously deemed logistically impossible, thus paving the way for sophisticated human cell device development.

bioengineering↗

bioRxiv2021

Neural stem cells alter nucleocytoplasmic partitioning and accumulate nuclear polyadenylated transcripts during quiescence

Quiescence is a cellular state characterised by reversible cell-cycle arrest and diminished biosynthetic activity that protects against environmental insults, replicative exhaustion and proliferation-induced mutations1. Entry into and exit from this state controls development, maintenance and repair of tissues plus, in the adult central nervous system, generation of new neurons and thus cognition and mood2-4. Cancer stem cells too can undergo quiescence, which confers them resistance to current therapies5, 6. Despite clinical relevance, quiescence is poorly understood and is defined functionally given lack of molecular markers. Decrease of the most resource-intensive cellular process of protein synthesis is a feature of quiescence, controlled across species and cell types by inhibition of the Target of Rapamycin (TOR) pathway1, 7. Here, we combine Drosophila genetics and a mammalian model to show that altered nucleocytoplasmic partitioning and nuclear accumulation of polyadenylated RNAs are novel evolutionarily conserved hallmarks of quiescence regulation. Furthermore, nuclear accumulation of messenger RNA (mRNA) in quiescent NSCs (qNSCs) largely predicts protein downregulation, accounting for uncoupling between transcriptome and proteome in quiescence. These mechanisms provide a previously unappreciated regulatory layer to reducing protein synthesis in quiescent cells, whilst priming them for reactivation in response to appropriate cues.

developmental biology↗

bioRxiv2018

Spatiotemporally controlled genetic perturbation for efficient large-scale studies of cell non-autonomous effects

Studies in genetic model organisms have revealed much about the development and pathology of complex tissues. Most have focused on cell-intrinsic gene functions and mechanisms. Much less is known about how transformed, or otherwise functionally disrupted, cells interact with healthy ones towards a favorable or pathological outcome. This is largely due to technical limitations. We developed new genetic tools in Drosophila melanogaster that permit efficient multiplexed gain- and loss-of-function genetic perturbations with separable spatial and temporal control. Importantly, our novel tool-set is independent of the commonly used GAL4/UAS system, freeing the latter for additional, non-autonomous, genetic manipulations; and is built into a single strain, allowing one-generation interrogation of non-autonomous effects. Altogether, our design opens up efficient genome-wide screens on any deleterious phenotype. Specifically, we developed tools to study extrinsic effects on neural tumor growth but the strategy presented has endless applications within and beyond neurobiology, and in other model organisms.\n\nImpact statementA novel genetic strategy for induction of reproducible neural tumors (or any other deleterious phenotype) in a single Drosophila stock (applicable to other organisms).

developmental biology↗