Xudong Zhang

2 months ago | nature.com | Junchao Shi |Yunfang Zhang |Yun Li |Liwen Zhang |Xudong Zhang |Qi Chen | +2 more

Small noncoding RNAs (sncRNAs) are a diverse group of RNAs including small interfering RNAs, microRNAs, PIWI-interacting RNAs and RNAs derived from structured RNAs such as transfer RNAs, ribosomal RNAs and others. These sncRNAs have varied termini and RNA modifications, which can interfere with adaptor ligation and reverse transcription during cDNA library construction, hindering detection of many types of sncRNA by standard small RNA sequencing methods. To address this limitation, PANDORA sequencing introduces a refined methodology. The procedure includes sequential enzymatic treatments of size-selected RNAs with T4PNK and AlkB, which effectively circumvent the challenges presented by the ligation-blocking termini and reverse transcription-blocking RNA modifications, followed by tailored small RNA library construction protocols and deep sequencing. The obtained datasets are analyzed with the SPORTS pipeline, which can comprehensively analyze various types of sncRNA beyond the traditionally studied classes, to include those derived from various parental RNAs (for example, from transfer RNA and ribosomal RNA), as well as output the locations on the parental RNA from which these sncRNAs are derived. The entire protocol takes ~7 d, depending on the sample size and sequencing turnaround time. PANDORA sequencing provides a transformative tool to further our understanding of the expanding small RNA universe and to explore the uncharted functions of sncRNAs. This Protocol describes optimized procedures for purification and sequencing of small noncoding RNAs from a variety of samples to characterize these diverse RNA species and map them to the parental RNAs from which they originate.

Dec 22, 2024 | mdpi.com | Xudong Zhang

3. Results 3.1. Publication Volume and Citation TrendsAs shown in , this study focuses on journal articles published between 2005 and 2024, and the research on photovoltaic landscapes can be roughly divided into three phases (): (1) initial development stage (2005–2008). During this period, research on photovoltaic landscapes was still in its nascent stage, with fewer than 100 articles published annually. (2) Stable growth stage (2009–2020).

Sep 14, 2024 | scienceopen.com | Xudong Zhang |Qi Xu

Record: foundAbstract: foundArticle: foundIs Open Access Author(s): , , Publication date (Electronic): Keywords: , , , , There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience. Since August 2023, Japan has discharged some eight rounds of Fukushima nuclear-contaminated water, totaling some 62,800 tons.

Jul 17, 2024 | journals.plos.org | Yu Chi Liu |Lichao Wei |Xudong Zhang |Chuhua Liu

Loading metrics Open Access Peer-reviewedResearch Article Citation: Liu Y, Liu C, Wei L, Zhang X, Liu Q, Bai J, et al. (2024) Additional organic and bacterium fertilizer input regulated soybean root architecture and dry matter distribution for a sustainable yield in the semi-arid Region of China. PLoS ONE 19(7): e0305836.

Jun 25, 2024 | nature.com | Xudong Zhang

AbstractEfficient semantic segmentation of large-scale point cloud scenes is a fundamental and essential task for perception or understanding the surrounding 3d environments. However, due to the vast amount of point cloud data, it is always a challenging to train deep neural networks efficiently and also difficult to establish a unified model to represent different shapes effectively due to their variety and occlusions of scene objects.