Biology subjects

Shinoda, T.

Publications and source records attributed to Shinoda, T..

4 recordsLinked to original sources

bioRxiv2026

Ice drives the emergence of functional protocells

A defining feature of living systems is the high local concentration of diverse molecular components within membrane-bounded compartments. How did such an organization arise de novo, without complex molecular machinery or pre-existing cellular structures that could template their own reproduction? Prebiotic environments may have provided the physical driving forces needed to bring dispersed molecular components together and organize them into functional compartments. Here, we show that a freeze-thaw (FT) process can couple molecular concentration, the formation of cell-sized membrane compartments, and the activation of a biochemical system. In situ imaging showed that chemically diverse solutes and membrane material were co-concentrated within ice-confined liquid regions during slow freezing. Subsequent slow thawing gave rise to cell-sized giant vesicles that capture the concentrated molecules. Crucially, we show that these sequential processes can assemble a multicomponent transcription-translation system (PURE system) within vesicle compartments, enabling protein synthesis from diluted mixtures with little or no detectable activity in bulk solution. By demonstrating that functional cellular organization can emerge from otherwise inactive molecular components, our study suggests that environmental FT processes provide a physical route for the transition from chemical to biological organization, with implications for the emergence of life on Earth and beyond.

synthetic biology↗

bioRxiv2026

Inward thickening of embryonic neuron-packing brain walls: Mechanical integrity via curvature-associated inner-surface contractility

Despite recent explorations of tissue-level epithelial morphogenesis, how the embryonic brain wall, an epithelial derivative unique in its extensive cellular stratification coupled with epithelial-cell heightening to [~]0.5 mm, achieves thickening is unknown. Furthermore, the role of the inner curvature of the wall in this process remains unclear. Thus, whether the apically concave dorsal cerebral (pallial) wall thickens inward, not only outward as previously thought, was examined in culture and in vivo. The pallial wall in the midembryonic period, but not the earlier pallial wall, thickened inward at a pace equivalent to that of neuronal accumulation, which was found via stress-release tests to proceed in a compressive manner. The inhibition of actomyosin-mediated contraction of the inner/apical surface prevented the pallium from thickening, while inducing apical-surface buckling, suggesting the necessity of this inward thickening to actively avoid overcrowding. In contrast, inward bulging of the apically convex ganglionic eminence occurs more passively via pushing of the low-actomyosin apical surface by the constituent cells.

developmental biology↗

bioRxiv2025

Compositional selection of phospholipid compartments in icy environments drives the inheritance of encapsulated genetic information

The lipid world hypothesis proposes that both intracellular components and the chemical composition of the membrane compartment carry heritable information that contributes to protocellular fitness. However, there are few experimental demonstrations of membrane compositional selection and no study has shown that phospholipids--the primary membrane components of modern cells--can support selection of this type. As lipid compartments generally grow in size before fission, faster-growing compartments should enjoy a selective advantage that favors both the membrane itself and the contents it hosts. When situated in icy environments undergoing cycles of freezing and thawing (F/T), we found that the growth of phospholipid vesicles depends on their phospholipid composition: Vesicles with more unsaturated bonds in the acyl chain showed higher growth efficiency. When vesicles composed of lipids with either one or two unsaturated bonds were mixed and subjected to F/T cycles, a selective enrichment of the lipid with two unsaturated bonds was observed. Moreover, selection acting on lipid composition was propagated to the encapsulated genetic material, which was also enriched while selectively neutral. We conclude that phospholipid composition can be a direct target of selection for grown vesicles under an icy environment leading to indirect but concurrent enrichment of compartmentalized genetic molecules.

synthetic biology↗

bioRxiv2019

Dorsal-to-ventral neocortical expansion is physically primed by ventral streaming of early embryonic preplate neurons

Mammalian neocortex exhibits a disproportionally \"luxurious\" representation of somatotopies in its lateral region, which depends on dorsal-to-ventral expansion of the pallium during development. Despite recent studies elucidating the molecular mechanisms underlying the cortical arealization/patterning, we know very little about how the cortex expands ventrally and the nature of the underlying force-generating events. We found that neurons born earliest (at embryonic day 10 [E10]) in the mouse pallium migrated ventrally and then extended corticofugal axons, which together formed a morphogenetic flow of the preplate that persists until E13. These neurons exerted pulling and pushing forces at the process and the soma, respectively. Ablation of these E10-born neurons attenuated both deflection of radial glial fibers (by E13) and extension of the cortical plate (by E14), which should occur ventrally, and subsequently shrank the postnatal neocortical map dorsally. This previously unrecognized preplate stream physically primes neocortical expansion and somatotopic map formation.

neuroscience↗