Biology subjects

Chen, J.-H.

Publications and source records attributed to Chen, J.-H..

24 records · Page 2Linked to original sources

bioRxiv2020

Canonical Wnt signaling Is Involved in Anterior Regeneration of the Annelid Aeolosoma viride

Annelids are regenerative animals, but the underlying mechanisms await to be discovered. Because Wnt pathway is involved in animal regeneration to varying extents, we used Aeolosoma viride to interrogate whether and how this pathway plays a role in annelid anterior regeneration. We found that the expression of wnt4, {beta}-catenin and nuclear-localized {beta}-catenin protein were up-regulated during blastemal formation and down-regulated as anterior structures gradually reformed. Consistent with potential Wnt activities in the blastema, treatments with either Wnt pathway activator (azakenpaullone) or inhibitor (XAV939) inhibited head regeneration, which further supports a role of Wnt pathway during anterior regeneration. Detailed tissue-level examines demonstrated that wound closure and blastemal cell proliferation were impaired by over-activating the pathway, and that neuronal and musculature differentiation were affected under Wnt inhibition. Combined, gene expression and chemical inhibitor data suggest the presence of dynamic Wnt activities at different anterior regeneration stages: an initial low activity may be required for wound closure, and the following activation may signal blastemal formation and cell differentiation. In a nutshell, we propose that the canonical Wnt signaling regulates blastemal cellular responses during annelid regeneration.

developmental biology↗

bioRxiv2019

Quantitative Analysis of Trans-synaptic Protein Alignment

Nanoscale distribution of proteins and their relative positioning within a defined subcellular region are key to their physiological functions. Thanks to the super-resolution imaging methods, especially the single-molecule localization microscopy (SMLM), mapping the three-dimensional distribution of multiple proteins has been easier and more efficient than ever. In spite of the many tools available for efficient localization detection and image rendering, it has been a challenge to quantitatively analyze the 3D distribution and relative positioning of proteins in these SMLM data. Here, using the heterogeneously distributed synaptic proteins as examples, we describe in detail a series of analytical methods including detection of nanoscale density clusters, quantification of the trans-synaptic alignment between these protein densities, and automatic enface projection and averaging. These analyses were performed within customized Matlab routines and we make the full scripts available. The concepts behind these analytical methods and the scripts can be adapted for quantitative analysis of spatial organization of other macromolecular complexes.\n\nHighlightsO_LILocalization microscopy provides sufficient data for precise quantitative analysis.\nC_LIO_LIAn algorithm to identify local density peaks within a 3D localization cluster.\nC_LIO_LINew methods for quantitative analysis of trans-synaptic proteins alignment and enrichment.\nC_LIO_LIThese algorithms can be easily adapted to analysis of other subcellular organizations.\nC_LI

neuroscience↗

bioRxiv2018

General characterization of regeneration in Aeolosoma viride

Regeneration has long attracted scientists for its potential to restore lost, damaged or aged tissues and organs. A wide range of studies have conducted on different model organisms on both cellular and molecular levels. Current evidences suggest that a variety of regenerative strategies are developed and used by different species, and their regenerative strategies are highly correlated to their reproductive methods. Our present work focused on the freshwater annelid Aeolosoma viride, which reproduces by paratonic fission and is capable of complete regeneration. We found out that A. viride can regenerate both anterior and posterior end, even with only 3 segments remained. This process is characterized by epimorphosis that involves large amount of cell proliferation which drives the formation of blastema. Cell proliferation and regeneration successful ratio were significantly decreased when treated with microtubule inhibitor taxol or Avi-tubulin dsRNA, which confirmed that cell proliferation served as a key event during regeneration. Together, our data described the regenerative processes of A. viride, which includes high level of cell proliferation and the formation of blastema. Furthermore, our findings demonstrated A. viride as a potential model for the study of regeneration.

developmental biology↗

bioRxiv2018

Integrated systems biology and imaging of the smallest free-living eukaryote Ostreococcus tauri

Ostreococcus tauri is an ancient phototrophic microalgae that possesses favorable genetic and cellular characteristics for reductionist studies probing biosystem design and dynamics. Here multimodal bioimaging and multi-omics techniques were combined to interrogate O. tauri cellular changes in response to variations in bioavailable nitrogen and carbon ratios. Confocal microscopy, stimulated Raman scattering, and cryo-soft x-ray tomography revealed whole cell ultrastructural dynamics and composition while proteomic and lipidomic profiling captured changes at the molecular and macromolecular scale.\n\nDespite several energy dense long-chain triacylglycerol lipids showing more than 40-fold higher abundance under N deprivation, only a few proteins directly associated with lipid biogenesis showed significant expression changes. However, the entire pathway for starch granule biosynthesis was highly upregulated suggesting much of the cellular energy is preferentially directed towards starch over lipid accumulation. Additionally, three of the five most downregulated and five of the ten most upregulated proteins during severe nitrogen depletion were unnamed protein products that warrant additional biochemical analysis and functional annotation to control carbon transformation dynamics in this smallest eukaryote.

systems biology↗

bioRxiv2018

PSF correction in soft x-ray tomography

In this manuscript, we introduce a linear approximation of the forward model of soft x-ray tomography (SXT), such that the reconstruction is solvable by standard iterative schemes. This linear model takes into account the three-dimensional point spread function (PSF) of the optical system, which consequently enhances the reconstruction data. The feasibility of the model is demonstrated on both simulated and experimental data, based on theoretically estimated and experimentally measured PSFs.

cell biology↗

bioRxiv2018

Ostreococcus tauri is a high-lipid content green algae that extrudes clustered lipid droplets

Lipid droplet biogenesis, accumulation and secretion is an important field of research spanning biofuel feedstock production in algae and yeast to plant-microbe symbiosis or human metabolic disorders and other diseases. Here we evaluate the critical elements that influence lipid accumulation in the highly simplified and smallest known eukaryote Ostreococcus tauri and identify several conditions that satisfy its classification as an oleaginous green alga. In addition, these experiments revealed the release of excess lipids in pea-pod like structures where many dense lipid droplets are clustered in a linear fashion surrounded by an enveloping membrane which contrasts with known mechanisms from other eukaryotes. These results highlight the potential for Ostreococcus tauri to probe the evolution of lipid droplet dynamics as an emerging model organism with a compacted eukaryotic genome and also to impact lipid feedstock bioproduction applications either directly or using synthetic biology.\n\nOne Sentence SummaryThe smallest known eukaryote Ostreococcus tauri is oleaginous and sheds lipid droplets as pea-pod like membrane enclosed clusters.

cell biology↗