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Sia, C. Y.

Publications and source records attributed to Sia, C. Y..

2 recordsLinked to original sources

Circadian and circatidal oscillations of clock gene expression in brains of Eurydice pulchra and Parhyale hawaiensis.

Intertidal organisms, such as the crustaceans Eurydice pulchra and Parhyale hawaiensis, express daily and tidal rhythms of physiology and behaviour to adapt to their temporally complex environments. Although the molecular-genetic basis of the circadian clocks driving daily rhythms in terrestrial animals is well understood, the nature and mechanism of the circatidal clocks driving tidal rhythms remain a mystery. Using in situ hybridisation, we identified discrete clusters of [~]60 putative "clock" cells co-expressing canonical circadian clock genes with comparable distributions across the protocerebrum of E. pulchra and P. hawaiensis brains. In tidally rhythmic, field-collected E. pulchra sampled under a light:dark (LD) cycle, the expression of period (per) and cryptochrome 2 (cry2) exhibited daily rhythms in particular cell groups (e.g., medioposterior cells) whereas timeless (tim) showed 12-hour rhythms in others (e.g., medial cells). In tidally rhythmic laboratory-reared P. hawaiensis, previously entrained to 12.4-hour cycles of agitation under LD and sampled under continuous darkness, several cell groups (e.g., medioposterior cells) exhibited circadian expression of per and cry2. In contrast, dorsal-lateral cells in the protocerebrum exhibited robust [~]12-hour, i.e., circatidal, rhythms of per and cry2, phased to the prior tidal agitation but not the prior LD. In P. hawaiensis exhibiting daily behaviour under LD without tidal agitation, robust daily rhythms of per and cry2 expression were evident in medioposterior and other cells whereas expression in dorsal-lateral cells was not rhythmic, underlining their intrinsic tidal periodicity. These results implicate canonical circadian mechanisms in circatidal time-keeping and reveal conserved brain networks as potential neural substrates for the generation of interactive daily and tidal rhythms appropriate to intertidal habitats.

neuroscience↗

Spatially tuneable multi-omics sequencing using light-driven combinatorial barcoding of molecules in tissues

Mapping the molecular identities and functions of cells within their spatial context is key to understanding the complex interplay within and between tissue neighbourhoods. A wide range of methods have recently enabled spatial profiling of cellular anatomical contexts, some offering single-cell resolution. These use different barcoding schemes to encode either the location or the identity of target molecules. However, all these technologies face a trade-off between spatial resolution, depth of profiling, and scalability. Here, we present Barcoding by Activated Linkage of Indexes (BALI), a method that uses light to write combinatorial spatial molecular barcodes directly onto target molecules in situ, enabling multi-omic profiling by next generation sequencing. A unique feature of BALI is that the user can define the number, size, and shape, and resolution of the spatial locations to be interrogated, with the potential to profile millions of distinct regions with subcellular precision. As a proof of concept, we used BALI to capture the transcriptome, chromatin accessibility, or both simultaneously, from distinct areas of the mouse brain in single tissue sections, demonstrating strong concordance with publicly available datasets. BALI therefore combines high spatial resolution, high throughput, histological compatibility, and workflow accessibility to enable powerful spatial multi-omic profiling.

genomics↗