Genome-wide identification and analysis of expression pattern of REVEILLE transcription factors in castor (Ricinus communis L.)

Wei Xue,Zhang Jixing,Wang Nan,Sun Mengdi,Ding Xue,Xu Hui,Yu Xiumin,Yue Wenran,Huo Hongyan,Yu Lili,Wang Xiaoyu 한국원예학회 2024 Horticulture, Environment, and Biotechnology Vol.65 No.3

REVEILLE (RVEs) transcription factors play an important role in regulating circadian clock, plant growth and development, and stress responses. While RVEs have been identifi ed in various plant species, comprehensive genome exploration and analysis of RVEs in castor ( Ricinus communis L.) have not been previously reported. In this study, we identifi ed RcRVEs in the castor genome through sequence alignment and conducted an analysis encompassing gene structures, protein motifs, physicochemical properties, transcription patterns under cold stress, diff erent tissues, and diurnal rhythm. A total of fi ve RcRVEs were pinpointed in the castor genome. Evolutionary tree analysis categorized these RcRVEs into three distinct groups, implying that diff erent RcRVEs may fulfi ll distinct biological functions. Furthermore, several abiotic stresses and hormone-responsive cis -acting elements were found in the promoters of the RcRVEs . RNA-sequencing (RNA-seq) analysis revealed that RcRVE1 and RcRVE7 were induced by cold stress and exhibited upregulation over time, indicating their involvement in regulating cold adaptation in castor plants. Five RcRVEs have notably higher expression levels in leaves compared to other tissues. The expression of all RcRVEs displayed diurnal rhythms under light/dark cycles. This study provides valuable insights into the potential functions of RcRVEs in regulating castor’s growth and development, and responses to cold stress.

Discovery of novel glycoside hydrolases from C-glycoside-degrading bacteria using sequence similarity network analysis

Wei Bin,Wang Ya-Kun,Yu Jin-Biao,Wang Si-Jia,Yu Yan-Lei,Xu Xue-Wei,Wang Hong 한국미생물학회 2021 The journal of microbiology Vol.59 No.10

C-Glycosides are an important type of natural product with significant bioactivities, and the C-glycosidic bonds of C-glycosides can be cleaved by several intestinal bacteria, as exemplified by the human faeces-derived puerarin-degrading bacterium Dorea strain PUE. However, glycoside hydrolases in these bacteria, which may be involved in the C-glycosidic bond cleavage of C-glycosides, remain largely unknown. In this study, the genomes of the closest phylogenetic neighbours of five puerarin-degrading intestinal bacteria (including Dorea strain PUE) were retrieved, and the protein-coding genes in the genomes were subjected to sequence similarity network (SSN) analysis. Only four clusters of genes were annotated as glycoside hydrolases and observed in the genome of D. longicatena DSM 13814T (the closest phylogenetic neighbour of Dorea strain PUE); therefore, genes from D. longicatena DSM 13814T belonging to these clusters were selected to overexpress recombinant proteins (CG1, CG2, CG3, and CG4) in Escherichia coli BL21(DE3). In vitro assays indicated that CG4 efficiently cleaved the O-glycosidic bond of daidzin and showed moderate β-D-glucosidase and β-D-xylosidase activity. CG2 showed weak activity in hydrolyzing daidzin and pNP- β-D-fucopyranoside, while CG3 was identified as a highly selective and efficient α-glycosidase. Interestingly, CG3 and CG4 could be selectively inhibited by daidzein, explaining their different performance in kinetic studies. Molecular docking studies predicted the molecular determinants of CG2, CG3, and CG4 in substrate selectivity and inhibition propensity. The present study identified three novel and distinctive glycoside hydrolases, highlighting the potential of SSN in the discovery of novel enzymes from genomic data.

Associations of Single Nucleotide Polymorphisms in miR-146a, miR-196a, miR-149 and miR-499 with Colorectal Cancer Susceptibility

Du, Wei,Ma, Xue-Lei,Zhao, Chong,Liu, Tao,Du, Yu-Liang,Kong, Wei-Qi,Wei, Ben-Ling,Yu, Jia-Yun,Li, Yan-Yan,Huang, Jing-Wen,Li, Zi-Kang,Liu, Lei Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.2

Background: MicroRNAs (miRNAs) are an abundant class of endogenous small non-coding RNAs of 20-25 nucleotides in length that function as negative gene regulators. MiRNAs play roles in most biological processes, as well as diverse human diseases including cancer. Recently, many studies investigated the association between SNPs in miR-146a rs2910164, miR-196a2 rs11614913, miR-149 rs229283, miR-499 rs3746444 and colorectal cancer (CRC), which results have been inconclusive. Methodology/Principal Findings: PubMed, EMBASE, CNKI databases were searched with the last search updated on November 5, 2013. For miR-196a2 rs11614913, a significantly decreased risk of CRC development was observed under three genetic models (dominant model: OR = 0.848, 95%CI: 0.735-0.979, P = 0.025; recessive model: OR = 0.838, 95%CI: 0.721-0.974, P = 0.021; homozygous model: OR = 0.754, 95%CI: 0.627-0.907, P = 0.003). In the subgroup analyses, miR-$196a2^*T$ variant was associated with a significantly decreased susceptibility of CRC (allele model: OR = 0.839, 95%CI: 0.749-0.940, P = 0.000; dominant model: OR = 0.770, 95%CI: 0.653-0.980, P = 0.002; recessive model: OR = 0.802, 95%CI: 0.685-0.939, P = 0.006; homozygous model: OR = 0.695, 95%CI: 0.570-0.847, P = 0.000). As for miR-149 rs2292832, the two genetic models (recessive model: OR = 1.199, 95% CI 1.028-1.398, P = 0.021; heterozygous model: OR = 1.226, 95% CI 1.039-1.447, P = 0.013) demonstrated increased susceptibility to CRC. On subgroup analysis, significantly increased susceptibility of CRC was found in the genetic models (recessive model: OR = 1.180, 95% CI 1.008-1.382, P = 0.040; heterozygous model: OR = 1.202, 95% CI 1.013-1.425, P = 0.013) in the Asian group. Conclusions: These findings supported that the miR-196a2 rs11614913 and miR-149 rs2292832 polymorphisms may contribute to susceptibility to CRC.

Identification of Novel Subregions of LOH in Gastric Cancer and Analysis of the HIC1 and TOB1 Tumor Suppressor Genes in These Subregions

Jingcui Yu,Songbin Fu,Peng Liu,Xiaobo Cui,Yu Sui,Guohua Ji,Rongwei Guan,Donglin Sun,Wei Ji,Fangli Liu,An Liu,Yuzhen Zhao,Yang Yu,Yan Jin,Jing Bai,Jingshu Geng,Yingwei Xue,Jiping Qi,Ki-Young Lee 한국분자세포생물학회 2011 Molecules and cells Vol.32 No.1

Previously, we identified 3 overlapping regions showing loss of heterozygosity (LOH, R_1-R_3 from 11 to 30 cM) on chromosome 17 in 45 primary gastric cancers (GCs). The data indicated the presence of tumor suppressor genes (TSGs) on chromosome 17 involved in GC. Among the putative TSGs in these regions, HIC1 (in SR_1) and TOB1 (in SR_3) remain to be examined in GC. By immunohistochemistry (IHC), methylation-specific PCR (MSP) and western blot, we evaluated the expression and regulation status for HIC1 and TOB1 protein in GC. We narrowed down the deletion intervals on chromosome 17 and defined five smaller LOH subregions, SR_1-SR_5 (0.54 to 3.42 cM), in GC. We found that HIC1 had downregulated expression in 86% (91/106) and was methylated in 87% (26/30) of primary GCs. Of the primary GCs showing downregulation of HIC1 protein, 75% (18/24) had methylated HIC1 gene. TOB1 was either absent or expressed at reduced levels in 75% (73/97) of the GC samples. In addition, a general reduction was found in total and the ratio of unphosphorylated to phosphorylated TOB1 protein levels in the differentiated GC cell lines. Further analysis revealed significant simultaneous downregulation of both HIC1 and TOB1 protein in GC tissue microarray samples (67%, 52/78) and in primary GCs (65%, 11/17). These results indicate that silencing of HIC1 and TOB1 expression is a common occurrence in GC and may contribute to the development and progression of the disease.

Genetic diversity and population structure of the amylolytic yeast Saccharomycopsis fibuligera associated with Baijiu fermentation in China

Wang Ju-Wei,Han Pei-Jie,Han Da-Yong,Zhou Sen,Li Kuan,He Peng-Yu,Zhen Pan,Yu Hui-Xin,Liang Zhen-Rong,Wang Xue-Wei,Bai Feng-Yan 한국미생물학회 2021 The journal of microbiology Vol.59 No.8

The amylolytic yeast Saccharomycopsis fibuligera is a predominant species in starters and the early fermentation stage of Chinese liquor (Baijiu). However, the genetic diversity of the species remains largely unknown. Here we sequenced the genomes of 97 S. fibuligera strains from different Chinese Baijiu companies. The genetic diversity and population structure of the strains were analyzed based on 1,133 orthologous genes and the whole genome single nucleotide polymorphisms (SNPs). Four main lineages were recognized. One lineage contains 60 Chinese strains which are exclusively homozygous with relatively small genome sizes (18.55–18.72 Mb) and low sequence diversity. The strains clustered in the other three lineages are heterozygous with larger genomes (21.85–23.72 Mb) and higher sequence diversity. The genomes of the homozygous strains showed nearly 100% coverage with the genome of the reference strain KPH12 and the sub-genome A of the hybrid strain KJJ81 at the above 98% sequence identity level. The genomes of the heterozygous strains showed nearly 80% coverage with both the sub-genome A and the whole genome of KJJ81, suggesting that the Chinese heterozygous strains are also hybrids with nearly 20% genomes from an unidentified source. Eighty-three genes were found to show significant copy number variation between different lineages. However, remarkable lineage specific variations in glucoamylase and α-amylase activities and growth profiles in different carbon sources and under different environmental conditions were not observed, though strains exhibiting relatively high glucoamylase activity were mainly found from the homozygous lineage.

Cloning and Characterization of a β-Glucosidase from Marine Microbial Metagenome with Excellent Glucose Tolerance

( Wei Fang ),( Bao Lin Sun ),( Yu Zhi Hong ),( Ze Min Fang ),( Juan Juan Liu ),( Hui Peng ),( Xue Cheng Zhang ),( Ya Zhong Xiao ) 한국미생물 · 생명공학회 2010 Journal of microbiology and biotechnology Vol.20 No.9

Prepartum body condition score affects milk yield, lipid metabolism, and oxidation status of Holstein cows

Wei Zhao,Xue Chen,Jun Xiao,Xiao Hui Chen,Xue Feng Zhang,Tao Wang,Yu Guo Zhen,Gui Zin Qin 아세아·태평양축산학회 2019 Animal Bioscience Vol.32 No.12

Objective: This study aimed to investigate the effects of prepartum body condition score (BCS) on the milk yield, lipid metabolism, and oxidative status of Holstein cows. Methods: A total of 112 multiparous Holstein cows were divided into 4 groups according to the BCS at 21 days before calving: medium BCS (3.0 to 3.25, MBCS), high BCS (3.5 to 3.75, HBCS), higher BCS (4.0 to 4.25, HerBCS), and highest BCS (4.5 to 5.0, HestBCS). Blood samples were collected on 21, 14, and 7 days before calving (precalving), on the calving day (calving), and on 7, 14, and 21 days after calving (postcalving). The indices of lipid metabolism and oxidative status were analyzed using bovine-specific enzyme-linked immunosorbent assay kit. Colostrum were taken after calving and analyzed by a refractometer and milk analyzer. The individual milk yield was recorded every 3 days. Results: The density and levels of immune globulin and lactoprotein of colostrum from Holstein cows in the HestBCS group were the highest (p<0.05). These animals not only had the highest (p<0.05) levels of serum non-esterified fatty acids and beta-hydroxybutyrate, but also had the highest (p<0.05) levels of malondialdehyde, superoxide dismutase, catalase, vitamin A, and vitamin E. In addition, greater (p<0.05) BCS loss was observed in the HestBCS cows. Conclusion: This study demonstrates that the milk yield, lipid metabolism, and oxidative status of Holstein cows are related to prepartum BCS and BCS loss during the transition period. HestBCS cows are more sensitive to oxidative stress and suffer greater loss of BCS after calving, whereas the MBCS animals had better milk yield performance.

Impact of fatty liver on long-term outcomes in chronic hepatitis B: a systematic review and matched analysis of individual patient data meta-analysis

Yu Jun Wong,Vy H. Nguyen,Hwai-I Yang,Jie Li,Michael Huan Le,Wan-Jung Wu,Nicole Xinrong Han,Khi Yung Fong,Elizabeth Chen,Connie Wong,Fajuan Rui,Xiaoming Xu,Qi Xue,Xin Yu Hu,Wei Qiang Leow,George Boon-B 대한간학회 2023 Clinical and Molecular Hepatology(대한간학회지) Vol.29 No.3

Background/Aims: Chronic hepatitis B (CHB) and fatty liver (FL) often co-exist, but natural history data of this dual condition (CHB-FL) are sparse. Via a systematic review, conventional meta-analysis (MA) and individual patient-level data MA (IPDMA), we compared liver-related outcomes and mortality between CHB-FL and CHB-no FL patients. Methods: We searched 4 databases from inception to December 2021 and pooled study-level estimates using a random- effects model for conventional MA. For IPDMA, we evaluated outcomes after balancing the two study groups with inverse probability treatment weighting (IPTW) on age, sex, cirrhosis, diabetes, ALT, HBeAg, HBV DNA, and antiviral treatment. Results: We screened 2,157 articles and included 19 eligible studies (17,955 patients: 11,908 CHB-no FL; 6,047 CHB-FL) in conventional MA, which found severe heterogeneity (I2=88–95%) and no significant differences in HCC, cirrhosis, mortality, or HBsAg seroclearance incidence (P=0.27–0.93). IPDMA included 13,262 patients: 8,625 CHB-no FL and 4,637 CHB-FL patients who differed in several characteristics. The IPTW cohort included 6,955 CHB-no FL and 3,346 CHB-FL well-matched patients. CHB-FL patients (vs. CHB-no FL) had significantly lower HCC, cirrhosis, mortality and higher HBsAg seroclearance incidence (all P≤0.002), with consistent results in subgroups. CHB-FL diagnosed by liver biopsy had a higher 10-year cumulative HCC incidence than CHB-FL diagnosed with non-invasive methods (63.6% vs. 4.3%, P<0.0001). Conclusions: IPDMA data with well-matched CHB patient groups showed that FL (vs. no FL) was associated with significantly lower HCC, cirrhosis, and mortality risk and higher HBsAg seroclearance probability.

A Case of Extranodal Natural Killer/T-Cell Lymphoma, Nasal Type with Dermatomyositis

( Yu Gong ),( Ke Xue ),( Yifan Hu ),( Rong Wei ),( Yeqiang Liu ),( Hua Cao ),( Yuling Shi ) 대한피부과학회 2021 Annals of Dermatology Vol.33 No.2

The Entropy-Based Hop Scheme for Influence Maximization in Dynamic Social Networks

Yu Jianyong,Liu Zekun,Liang Wei,Han Xue,Xiong Neal N. 한국컴퓨터산업협회 2023 Human-centric Computing and Information Sciences Vol.13 No.-

The influence maximization that selects the nodes to maximize the influence spread has been becoming a hot research topic. The classical algorithms based on static network are difficult to solve it in dynamic network where nodes and edges are updated all the time. In this paper, we propose a novel hop approach based on information entropy, which selects the optimal set according to the local topology information while activation probability calculated by improved hop approach in dynamic linear threshold model. This study uses the information entropy to get the unique threshold to reflect the heterogeneity of nodes. In consideration of a node that attempts to activate its neighbors in a static snapshot, the improved hop approach is used to update only the activation probabilities of nodes affected by newly added activation nodes in set of activated nodes. This paper also proves and deduces the relevant theorems and formulas in proposed method. The effectiveness of our method is demonstrated by comparing experiments with five selection algorithms on three real datasets. Through five different sets of experiments, it can be found that our method can get the best results in terms of influence spread and speed of propagation with specified budget.