Kung, Y.-C. | Search bioRxiv

bioRxiv2023

Four-dimensional omics data reveals ribosome heterogeneity, regulation of translation efficacy, and nonsense-mediated decay in the differentiation of spermatocyte to round spermatid.

A protein expression is regulated by transcription, translation, and sequential processing. However, well correlated RNA and protein abundance just only proportionate 40%, and even poorer when cell was stressed, differentiated, or tumorigenic transformed. Here, we discovered spermatocyte (SP) differentiated to round spermatid (RS) had equal regulation extent which may related to ribosomal behavior alteration. The change of ribosome occupancy was related to SP and RS specific function in spermatogenesis. Interactome of functional ribosome in SP and RS revealed the activated ribosome in SP but stalled and nonsense-mediated decay (NMD) associated ribosome in RS. Functional ribosomes of RS occupied 5untranslated regions (5UTR) of SP specific transcripts and correlated its RNA and protein downregulation. These findings suggested a branched NMD pathway was activated in RS to eliminate SP specific transcripts and keep them from being translated. Our discovery suggested the heterogeneity of ribosomal interactome may play an important role in spermatogenesis.

molecular biology↗

bioRxiv2022

Integrated Diffusion Image Operator (iDIO): A tool for automated configuration and processing of diffusion MRI data

The preprocessing of diffusion magnetic resonance imaging (dMRI) data involves numerous steps, including the corrections for head motion, susceptibility distortion, low signal-to-noise ratio, and signal drifting. Researchers or clinical practitioners often need to configure different preprocessing steps depending on disparate image acquisition schemes, which increases the technical threshold for dMRI analysis for non-expert users. This could cause disparities in data processing approaches and thus hinder the comparability between studies. To make the dMRI data processing steps transparent and adapt to various dMRI acquisition schemes for researchers, we propose a semi-automated pipeline tool for dMRI named integrated Diffusion Image Operator or iDIO. This pipeline integrates features from a wide range of advanced dMRI software tools and targets at providing a one-click solution for dMRI data analysis, via automatic configuration for a set of optimal processing steps based on the image header of the input data. Additionally, the pipeline provides options for post-processing, such as estimation of diffusion tensor metrics and whole-brain tractography-based connectomes reconstruction using common brain atlases. The iDIO pipeline also outputs an easy-to-interpret quality control report to facilitate users to assess the data quality. To keep the transparency of data processing, the execution log and all the intermediate images produced in the iDIOs workflow are accessible. The goal of iDIO is to reduce the barriers for clinical or non-specialist users to adopt the state-of-art dMRI processing steps.

neuroscience↗