Biology subjects

Zhang, H.-W.

Publications and source records attributed to Zhang, H.-W..

3 recordsLinked to original sources

bioRxiv2024

Postharvest partial dehydration of blueberries enhanced blueberry wine aroma via upregulating phenylalanine metabolism and terpene biosynthesis

Postharvest partial dehydration of blueberries can enhance blueberry wine aroma, while the underlying mechanisms remain unclear. In this study, the key odor-active volatiles in blueberry wines fermented from dehydrated blueberries (30% weight loss) were identified via aroma extract dilution analysis. Results showed that increased levels of phenylalanine-derived compounds such as phenylethanol, and terpenes such as linalool and geraniol, primarily led to the enhancement of sweet, floral and fruity aromas of blueberry wines. Postharvest partial dehydration increased the contents of these compounds, which could be linked to the upregulation of VcGOT2 and VcPAR involved in phenylalanine metabolism, and the upregulation of VcDXS, VcHDR and VcTPS involved in terpene biosynthesis. Notably, the upregulated VcTPS encoded a monoterpene synthase responsible for producing linalool. These findings provided insight into the impact of postharvest dehydration on phenylalanine and terpene metabolism in blueberries, offering a reference for improving blueberry wine aroma through postharvest partial dehydration techniques.

biochemistry↗

bioRxiv2023

A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex

De novo DNA methylation in plants relies on transcription elongation of RNA polymerase V (Pol V) along with KTF1 and SPT4, which produces long non-coding RNAs for recruitment and assembly of DNA methylation machinery. Here, we report a cryo-EM structure of the KTF1-bound Pol V transcription elongation complex. The structure reveals conformation of the structure motifs in the active site of Pol V that accounts for its inferior RNA-extension ability. The structure further reveals structural features of Pol V that prevent it from interacting with the general transcription factors of Pol II and Pol IV. The KOW5 domain of KTF1 binds near the RNA exit channel of Pol V, where it provides a scaffold for the proposed recruitment of Argonaute proteins to initiate the assembly of DNA methylation machinery. The structure provides insight into the Pol V transcription elongation and the role of KTF1 during Pol V transcription-coupled DNA methylation.

biochemistry↗

bioRxiv2016

Accurate prediction of human essential genes using only nucleotide composition and association information

Three groups recently identified essential genes in human cancer cell lines using wet experiments, and these genes are of high values. Herein, we improved the widely used Z curve method by creating a {lambda}-interval Z curve, which considered interval association information. With this method and recursive feature elimination technology, a computational model was developed to predict human gene essentiality. The 5-fold cross-validation test based on our benchmark dataset obtained an area under the receiver operating characteristic curve (AUC) of 0.8814. For the rigorous jackknife test, the AUC score was 0.8854. These results demonstrated that the essentiality of human genes could be reliably reflected by only sequence information. However, previous classifiers in three eukaryotes can gave satisfactory prediction only combining sequence with other features. It is also demonstrated that although the information contributed by interval association is less than adjacent nucleotides, this information can still play an independent role. Integrating the interval information into adjacent ones can significantly improve our classifiers prediction capacity. We re-predicted the benchmark negative dataset by Pheg server (https://cefg.uestc.edu.cn/Pheg), and 118 genes were additionally predicted as essential. Among them, 21 were found to be homologues in mouse essential genes, indicating that at least a part of the 118 genes were indeed essential, however previous experiments overlooked them. As the first available server, Pheg could predict essentiality for anonymous gene sequences of human. It is also hoped the {lambda}-interval Z curve method could be effectively extended to classification issues of other DNA elements.

bioinformatics↗