Evolutionary and functional implications of 3′ untranslated region length of mRNAs by comprehensive investigation among four taxonomically diverse metazoan species

Wei Wang,Dong‑hui Fang,Jia Gan,Yi Shi,Hui Tang,Huai Wang,Mao‑zhong Fu,Jun Yi 한국유전학회 2019 Genes & Genomics Vol.41 No.7

Background In eukaryotic organisms, it has been well acknowledged that 3′ untranslated regions (3′ UTRs) of mRNA are actively involved in post-transcriptional regulations of gene expression. Although both shortening and lengthening of 3′ UTRs of specific candidate genes were explicitly documented to have functional consequences, landscape of 3′ UTR lengths in relation to evolutionary dynamics and biological meanings remains to be elucidated when large-scale data become available. Objectives The primary objective of this study was to revealed different inter- and intra-species patterns on length distribution of 3′ UTRs in comparison with 5′ UTRs and coding regions. Methods In the present study, we investigated 3′ UTR lengths in a highly curated set of 57,135 mRNA sequences among four well-studied and taxonomically diverse metazoan species (fruit fly, zebrafish, mouse and human). Results The average length ratio of 3′–5′ UTRs considerably increased from fruit fly (twofold) to human (fivefold). Moreover, genes can be characterized by the obviously different patterns of evolutionary change on 3′ UTR lengths. By utilizing the Gene Ontology annotations, genes with differential lengths of 3′ UTRs were suggested to have the divergent functional implications. In human, we further revealed that ubiquitously transcribed genes had higher median lengths of 3′ UTRs than the genes of tissue-restricted expressions. Conclusion We conducted a comprehensive analysis and provided an overview regarding 3′ UTRs biology of mRNAs in animals, whereas the mechanistic explanations of 3′ UTRs length variation in correlation to regulation of gene expression still remain to be further studied.

Recent Progress in HER2 Associated Breast Cancer

Wang, Wei-Jia,Lei, Yuan-Yuan,Mei, Jin-Hong,Wang, Chun-Liang Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.7

Breast cancer is the most common cancer worldwide among women and the second most common cancer. Approximately 15-23% of breast cancers over-express human epidermal growth factor receptor2 (HER2), a 185-kDa transmembrane tyrosine kinase, which is mainly found at the cell surface of tumor cells. HER2-positive breast cancer, featuring amplification of HER2/neu and negative expression of ER and PR, has the three following characteristics: rapid tumor growth, lower survival rate, and better response to adjuvant therapies. Clinically, it is notable for its role in a pathogenesis that is associated with increased disease recurrence and acts as a worse prognosis. At the same time, it represents a good target for anti-cancer immunotherapy despite the prevalence of drug resistance. New treatments are a major topic of research, and a brighter future can be expected. This review discusses the role of HER2 in breast cancer, therapeutic modalities available and prognostic factors.

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.

Genetic structure of six cattle populations revealed by transcriptomewide SNPs and gene expression

Wei Wang,Huai Wang,Hui Tang,Jia Gan,Changgeng Shi,Qing Lu,Donghui Fang,Jun Yi,Maozhong Fu 한국유전학회 2018 Genes & Genomics Vol.40 No.7

There are abundant cattle breeds/populations in China, and the systematic discovery of genomic variants is essential for performing the marker assisted selection and conservation of genetic resources. In the present study, we employed whole transcriptome sequencing (RNA-Seq) technology for revealing genetic structure among six Chinese cattle populations according to transcriptome-wide SNPs and gene expression. A total of 68,094 variants consisting of 61,754 SNPs and 6340 InDels were detected and widely distributed among all chromosomes, by which the clear patterns of population structures were revealed. We also found the significantly differential density of variant distribution among genes. Additionally, we totally assembled 15,992 genes and detected obvious differences on the expression profiles among populations. In contrast to genomic variants, the measure of gene expression levels failed to support the expected population structure. Here, we provided a global landscape on the differential expression genes among these cattle populations.

Effects of Transition-Metal Ions on the Morphology and Electrochemical Properties of δ-MnO2 for Supercapacitors

Jia-Wei Wang,Ya Chen,Bai-Zhen Chen 대한금속·재료학회 2014 METALS AND MATERIALS International Vol.20 No.6

δ-MnO2 materials doped with transition-metal cations (Zn, Co, and Ag) were successfully synthesized usinga hydrothermal technique. The structures and morphologies of the obtained oxides were analyzed using X-raydiffraction, scanning electron microscopy and Brunauer-Emmett-Teller measurements. Additionally, the electrochemicalproperties were evaluated through cyclic voltammetry, electrochemical impedance spectroscopyand galvanostatic cycling measurements. The results indicate that the pure and doped samples crystallize inthe δ form with a layered structure and that the Mn/Zn, Mn/Co and Mn/Ag molar ratios are all approximately1:0.09. Both the Zn-doped and pure MnO2 materials exhibit a petal-like morphology; however, the formerhas a higher specific surface area of up to 98.97m2 g1. Furthermore, the Zn-doped MnO2 exhibits a near-rectangularcyclic voltammetry (CV) curve with broad quasi-reversible redox peaks and a specific capacitance of182.9 F g−1 at a CV scan rate of 2mVs1. The Co-doped material exhibits a distinct spiny-fiber morphology, andthe electrochemical performance of this material is significantly worse than that of pure MnO2. The averageattenuation rate of the Ag-doped material is only 0.028% after 1000 cycles, which is lower than that of pureMnO2.

Halomonas alkalitolerans sp. nov., a Novel Moderately Halophilic Bacterium Isolated from Soda Meadow Saline Soil in Daqing, China

Shuang Wang,Qian Yang,Zhi-Hua Liu,Lei Sun,Dan Wei,Jun-Zheng Zhang,Jin-Zhu Song,Yun Wang,Jia Song,Jin-Xia Fan,Xian-Xin Meng,Wei Zhang 한국미생물학회 2011 The journal of microbiology Vol.49 No.1

A moderately halophilic bacterial strain 15-13^T, which was isolated from soda meadow saline soil in Daqing City, Heilongjiang Province, China, was subjected to a polyphasic taxonomic study. The cells of strain 15-13^T were found to be Gram-negative, rod-shaped, and motile. The required growth conditions for strain 15-13^T were: 1-23% NaCl (optimum, 7%), 10-50°C (optimum, 35°C), and pH 7.0-11.0 (optimum, pH 9.5). The predominant cellular fatty acids were C18:1 ω7c (60.48%) and C16:0 (13.96%). The DNA G+C content was 67.6 mol%. Phylogenetic analysis based on 16S rRNA gene sequence comparisons indicated that strain 15-13^T clustered within a branch comprising species of the genus Halomonas. The closest phylogenetic neighbor of strain 15-13^T was Halomonas pantelleriensis DSM 9661^T (98.9% 16S rRNA gene sequence similarity). The level of DNA-DNA relatedness between the novel isolated strain and H. pantelleriensis DSM 9661^T was 33.8%. On the basis of the phenotypic and phylogenetic data, strain 15-13^T represents a novel species of the genus Halomonas, for which the name Halomonas alkalitolerans sp. nov. is proposed. The type strain for this novel species is 15-13^T (=CGMCC 1.9129^T =NBRC 106539^T).

An Improved Method for Rapid Preparation of Oligodendrocytespecific Rabbit Polyclonal Antibody

Tao Wang,Wei Wang,Lintao Jia,Xin Bu,Fang Wang,Libo Yao,Bin Zhang 한국생물공학회 2011 Biotechnology and Bioprocess Engineering Vol.16 No.3

Antibodies are important tools in the study of protein function and diagnostic tests. However, traditional antiserum preparation requires a time-consuming immunization protocol and subsequent purification of polyclonal antibodies. In this study, a rapid and efficient method for polyclonal antibody preparation has been developed. Juxtanodin (JN) and silent information regulator-2 (Sirt2),both of which are oligodendrocyte-specific proteins, were used for antibody preparation. The N-terminal 170 amino acids of JN (JN170) and amino acids 231-351 of Sirt2 (Sirt2-121) were expressed as GST-tagged proteins from a pET-41a(+) vector in E. coli strain BL21 (DE3) cells. The fusion proteins were purified and used to immunize rabbits following both a traditional protocol, in which antigen was presented biweekly, and a modified rapid protocol, in which the immunization on day 1 was boosted on days 5and 28. ELISA, Western blot analysis and immunofluorescent staining showed that antibodies produced via the rapid protocol could recognize these two oligodendrocytespecific proteins in vitro and in the rat central nervous system (CNS), respectively, similar to those produced with the traditional protocol. Thus, our study provides a novel rapid method to prepare high specificity antibodies via a modified immunization protocol and subsequent antibody purification.

Cloning and characterization of the cardiac-specific Lrrc10 promoter

( Xiong Wei Fan ),( Qing Yang ),( You Liang Wang ),( Yan Zhang ),( Jian Wang ),( Jia Jia Yuan ),( Yong Qing Li ),( Yue Qun Wang ),( Yun Deng ),( Wu Zhou Yuan ),( Xiao Yang Mo ),( Yong Qi Wan ),( Karen 생화학분자생물학회(구 한국생화학분자생물학회) 2011 BMB Reports Vol.44 No.2

Leucine-rich repeat containing protein 10 (LRRC10) is characterized as a cardiac-specific gene, suggesting a role in heart development and disease. A severe cardiac morphogenic defect in zebrafish morphants was recently reported but a contradictory result was found in mice, suggesting a more complicated molecular mechanism exists during mouse embryonic development. To elucidate how LRRC10 is regulated, we analyzed the 5`enhancer region approximately 3 kilo bases (kb) upstream of the Lrrc10 start site using luciferase reporter gene assays. Our characterization of the Lrrc10 promoter indicates it possesses complicated cis-and trans-acting elements. We show that GATA4 and MEF2C could both increase transcriptional activity of Lrrc10 promoter individually but that they do not act synergistically, suggesting that there exists a more complex regulation pattern. Surprisingly, knockout of Gata4 and Mef2c binding sites in the 5`enhancer region (-2,894/-2,889) didn`t change the transcriptional activity of the Lrrc10 promoter and the likely GATA4 binding site identified was located in a region only 100 base pair (bp) upstream of the promoter. Our data provides insight into the molecular regulation of Lrrc10 expression, which probably also contributes to its tissue-specific expression. [BMB reports 2011; 44(2): 123-128]

The NAD(P)H: Quinine Oxidoreductase 1 (NQO1) Gene 609 C>T Polymorphism is Associated with Gastric Cancer Risk: Evidence from a Case-control Study and a Meta-analysis

Hu, Wei-Guo,Hu, Jia-Jia,Cai, Wei,Zheng, Min-Hua,Zang, Lu,Wang, Zheng-Ting,Zhu, Zheng-Gang Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.5

The association between the NAD(P)H:quinone oxidoreductase 1 (NQO1) gene C609T polymorphism (rs1800566) and gastric cancer has been widely evaluated, but a definitive answer is so far lacking. We first conducted a case-control study to assess this association in a large Han Chinese population, and then performed a meta-analysis to further address this issue. Although our case-control association study indicated no significant difference in the genotype and allele distributions of C609T polymorphism between gastric cancer patients and controls, in the meta analysis involving 4,000 subjects, comparison of alleles 609T and 609C indicated a significantly increased risk (46%) for gastric cancer (95% confidence interval (95%CI) for odds ratio (OR)=1.20-1.79) in individuals with the T allele. The tendency was similar to the homozygote (OR=1.81, 95%CI: 1.16-2.84), dominant models (OR=1.41, 95%CI: 1.12-1.79), as well as recessive model (OR=1.58, 95%CI: 1.06-2.35). Stratified analysis by study design demonstrated stronger associations in population-based than in hospital-based studies. And ethnicity-based analysis demonstrated a significant association in Asians. We conclude that the NQO1 gene C609T polymorphism increases the risk for gastric cancer, especially in Asian populations.

SDSS J013127.34-032100.1: A NEWLY DISCOVERED RADIO-LOUD QUASAR AT <i>z</i> = 5.18 WITH EXTREMELY HIGH LUMINOSITY

Yi, Wei-Min,Wang, Feige,Wu, Xue-Bing,Yang, Jinyi,Bai, Jin-Ming,Fan, Xiaohui,Brandt, William N.,Ho, Luis C.,Zuo, Wenwen,Kim, Minjin,Wang, Ran,Yang, Qian,Zhang, Ju-jia,Wang, Fang,Wang, Jian-Guo,Ai, Yanl IOP Publishing 2014 ASTROPHYSICAL JOURNAL LETTERS - Vol.795 No.2

<P>Very few of the z > 5 quasars discovered to date have been radio-loud, with radio-to-optical flux ratios (radio-loudness parameters) higher than 10. Here we report the discovery of an optically luminous radio-loud quasar, SDSS J013127.34-032100.1 (J0131-0321 in short), at z = 5.18 +/- 0.01 using the Lijiang 2.4 m and Magellan telescopes. J0131-0321 has a spectral energy distribution consistent with that of radio-loud quasars. With an i-band magnitude of 18.47 and a radio flux density of 33 mJy, its radio-loudness parameter is similar to 100. The optical and near-infrared spectra taken by Magellan enable us to estimate its bolometric luminosity to be L-bol similar to 1.1 x 10(48) erg s(-1), approximately 4.5 times greater than that of the most distant quasar known to date. The black hole mass of J0131-0321 is estimated to be 2.7 x 10(9) M-circle dot, with an uncertainty up to 0.4 dex. Detailed physical properties of this high-redshift, radio-loud, potentially super-Eddington quasar can be probed in the future with more dedicated and intensive follow-up observations using multi-wavelength facilities.</P>