Paul Thomas Matsudaira

Receptor binding and tortuosity explain morphogen local-to-global diffusion coefficient transition

Shiwen Zhu, Yi Ting Loo, Sapthaswaran Veerapathiran, Tricia Y. J. Loo et autres

Morphogens are intercellular signaling molecules providing spatial information to cells in developing tissues to coordinate cell fate decisions. The spatial information is encoded within long-ranged concentration gradients of the morphogen. Direct measurement of morphogen dynamics in a range of systems suggests that …

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Receptor binding and tissue architecture explain the morphogen local-to-global mobility transition

Shiwen Zhu, Yi Ting Loo, Sapthaswaran Veerapathiran, Tricia Y. J. Loo et autres

ABSTRACT Morphogens are intercellular signaling molecules providing spatial information to cells in developing tissues to coordinate cell fate decisions. The spatial information is encoded within long-ranged concentration gradients of the morphogen. Direct measurement of morphogen dynamics in a range of systems suggests …

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Engineering a Hierarchy of Disorder: A New Route to Synthesize High‐Performance 3D Nanoporous All‐Carbon Materials**

Jong Hak Lee, N. Duane Loh, Zhen Yuan Yeo, Yong Kang Ong et autres

Abstract A new nanoporous amorphous carbon (NAC) structure that achieves both ultrahigh strength and high electrical conductivity, which are usually incompatible in porous materials is reported. By using modified spark plasma sintering, three amorphous carbon phases with different atomic bonding configurations are …

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A Collagen10a1 mutation disrupts cell polarity in a medaka model for metaphyseal chondrodysplasia type Schmid

Wen Hui Tan, Martin Rücklin, Daria Larionova, Tran Bich Ngoc et autres

Heterozygous mutations in COL10A1 lead to metaphyseal chondrodysplasia type Schmid (MCDS), a skeletal disorder characterized by epiphyseal abnormalities. Prior analysis revealed impaired trimerization and intracellular retention of mutant collagen type X alpha 1 chains as cause for elevated endoplasmic reticulum (ER) stress. …

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Coarse-Grained Model of Glycosaminoglycans for Biomolecular Simulations

Aishwary Tukaram Shivgan, Jan K. Marzinek, Alexander Krah, Paul Thomas Matsudaira et autres

Proteoglycans contain glycosaminoglycans (GAGs) which are negatively charged linear polymers made of repeating disaccharide units of uronic acid and hexosamine units. They play vital roles in numerous physiological and pathological processes, particularly in governing cellular communication and attachment. Depending on their sulfonation …

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A coarse-grained model of glycosaminoglycans for biomolecular simulations

Aishwary Tukaram Shivgan, Jan K. Marzinek, Alexander Krah, Paul Thomas Matsudaira et autres

Abstract Proteoglycans contain glycosaminoglycans (GAGs), negatively charged linear polymers made of repeating disaccharide units of uronic acid and hexosamine units. They play vital roles in numerous physiological and pathological processes, particularly governing cellular communication and attachment. Depending on their sulphonation state, acetylation, …

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Contributions of individual satellite cells to muscle regeneration assessed using a confetti mouse model

Hans Heemskerk, Narendra Suhas Jagannathan, N. Jannah M. Nasir, Binh Phu Nguyen et autres

Summary Insufficient regeneration is implicated in muscle pathologies, but much remains unknown about the regenerative output of individual muscle stem cells, called satellite cells (SCs). Prior work showed that individual SCs contribute to regeneration of more than one muscle fiber (“fiber-crossing”) after …

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Cell clusters containing intestinal stem cells, line the zebrafish intestine intervillus pocket

Sahar Tavakoli, Shiwen Zhu, Paul Thomas Matsudaira

In the mammalian intestine, stem cells (ISCs) replicate in basal crypts, translocate along the villus, and undergo cell death. This pattern of renewal occurs in the zebrafish intestine in which villi are elongated into villar ridges (VR) separated by intervillus pockets (IVP) …

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Strain maps characterize the symmetry of convergence and extension patterns during zebrafish gastrulation

Dipanjan Bhattacharya, Jun Zhong, Sahar Tavakoli, Alexandre Kabla et autres

During gastrulation of the zebrafish embryo, the cap of blastoderm cells organizes into the axial body plan of the embryo with left-right symmetry and head-tail, dorsal-ventral polarities. Our labs have been interested in the mechanics of early development and have investigated whether …

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Stall force does not affect the stalk coiling propagation of Vorticella convallaria

Sangjin Ryu, Paul Thomas Matsudaira

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A collagen10a1 mutation disrupts cell polarity and causes skeletal defects in a medaka model for Schmid Metaphyseal Chondrodysplasia

Wen Hui Tan, Bích Ngọc Trần, Daria Larionova, Bertie Joan van Heuven et autres

Background/Introduction:Computational anatomy (CA) approaches estimate a 'template' from a sample of images.This template is then used as a basis for statistical analysis to quantify structural differences among groups of interest.Purpose: In this work we aim to identify and quantify differences in 3D …

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Biochemical and structural characterization of a recombinant fibrinogen-related lectin from Penaeus monodon

Nongnuch Singrang, Sirasit Laophetsakunchai, Bích Ngọc Trần, Paul Thomas Matsudaira et autres

Abstract Fibrinogen-related lectins are carbohydrate-binding proteins of the innate immune system that recognize glycan structures on microbial surfaces. These innate immune lectins are crucial for invertebrates as they do not rely on adaptive immunity for pathogen clearance. Here, we characterize a recombinant …

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