The effects of codon usage on the formation of secondary structures of nucleocapsid protein of peste des petits ruminants virus

Xiao‑xia Ma,Yi‑ning Wang,Xiao‑an Cao,Xue‑rui Li,Yong‑sheng Liu,Jian‑hua Zhou,Xue‑peng Cai 한국유전학회 2018 Genes & Genomics Vol.40 No.9

The nucleocapsid (N) protein of peste des petits ruminants virus (PPRV) with a conserved amino acid usage pattern plays an important role in viral replication. The primary objective of this study was to estimate roles of synonymous codon usages of PPRV N gene and tRNA abundances of host in the formation of secondary structure of N protein. The potential effects of synonymous codon usages of N gene and tRNA abundances of host on shaping different folding units (α-helix, β-strand and the coil) in N protein were estimated, based on the information about the modeling secondary structure of PPRV N protein. The synonymous codon usage bias was found in different folding units in PPRV N protein. To better understand the role of translation speed caused by variant tRNA abundances in shaping the specific folding unit in N protein, we modeled the changing trends of tRNA abundance at the transition boundaries from one folding unit to another folding unit (β-strand → coil, coil → β-strand, α-helix → coil, coil → α-helix). The obvious fluctuations of tRNA abundance were identified at the two transition boundaries (β-strand → coil and coil → β-strand) in PPRV N protein. Our findings suggested that viral synonymous codon usage bias and cellular tRNA abundance variation might have potential effects on the formation of secondary structure of PPRV N protein.

Insect-specific microRNA involved in the development of the silkworm Bombyx mori

Yong Zhang,Xue Zhou,Xie Ge,Jiang-Hao Jiang,Mu-Wang Li,Shi-Hai Jia,Xiao-Nan Yang,Yun-Chao Kan,Xue-Xia Miao,Guo-Ping Zhao,Fei Li,Yong-Ping Huang 한국응용곤충학회 2009 한국응용곤충학회 학술대회논문집 Vol.2009 No.10

MicroRNAs (miRNAs) are endogenous non-coding genes that participate in post-transcription regulation by either degrading mRNA or blocking its translation. It is considered to be very important in regulating insect development and metamorphosis. Insects are the largest group of animals and are extremely valuable in biological and agriculture research. Insects are also important pests to human health and agriculture, and efforts are necessary protect both humans and plants from disease and damage. Despite their importance, insects lag behind mammals, nematodes, and plants in miRNA research. At present, only 279 insect miRNAs have been identified from Drosophila melanogaster, Anopheles gambiae, Apis mellifera, Bombyx mori, and D. pseudoobscura in miRBase, and most of these miRNAs were computationally predicted without experimental validation. Functional analysis of insect miRNAs has only been conducted in D. melanogaster.

Study of the Correlation of Plasma Resonance and the Refractive Index to Dielectric Dispersion in the Complex Plane

Xiao-Yong Zhou,Yan Shen,Er-Tao Hu,Jian-Bo Chen,Yuan Zhao,Ming-Yu Sheng,Jing Li,Yu-Xiang Zheng,Hai-Bin Zhao,Liang-Yao Chen,Wei Li,Xun-Ya Jiang,이영백,David W. Lynch 한국광학회 2013 Current Optics and Photonics Vol.17 No.1

Based on the dispersive feature of the dielectric function of noble metals and the wave vector conservation in physics, both the plasma effect and the complex refractive index, which are profoundly correlated to the complex dielectric function and permeability, have been studied and analyzed. The condition to induce a bulk or a surface plasma in the visible region will not be satisfied, and there will be one solution for the real and the imaginary parts of the refractive index, restricting it only to region I of the complex plane. The results given in this work will aid in understanding the properties of light transmission at the metal/dielectric interface as characterized by the law of refraction in nature.

DEPTOR Expression Negatively Correlates with mTORC1 Activity and Tumor Progression in Colorectal Cancer

Lai, Er-Yong,Chen, Zhen-Guo,Zhou, Xuan,Fan, Xiao-Rong,Wang, Hua,Lai, Ping-Lin,Su, Yong-Chun,Zhang, Bai-Yu,Bai, Xiao-Chun,Li, Yun-Feng Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.11

The mammalian target of rapamycin (mTOR) signaling pathway is upregulated in the pathogenesis of many cancers, including colorectal cancer (CRC). DEPTOR is an mTOR inhibitor whose expression is negatively regulated by mTOR. However, the role of DEPTOR in the development of CRC is not known. The aim of this study was to investigate the expression of DEPTOR and mTORC1 activity (P-S6) in a subset of CRC patients and determine their relation to tumor differentiation, invasion, nodal metastasis and disease-free survival. Here, Immunohistochemical expression of P-S6 (S235/236) and DEPTOR were evaluated in 1.5 mm tumor cores from 90 CRC patients and in 90 samples of adjacent normal mucosa by tissue microarray. The expression of P-S6 (S235/236) was upregulated in CRC, with the positive rate of P-S6 (S235/236) in CRC (63.3%) significantly higher than that in control tissues (36.7%, 30%) (p<0.05). P-S6 (S235/236) also correlated with high tumor histologic grade (p=0.002), and positive nodal metastasis (p=0.002). In contrast, the expression level of DEPTOR was correlated with low tumor histological grade (p=0.006), and negative nodal metastasis (p=0.001). Interestingly, P-S6 (S235/236) expression showed a significant negative association with the expression of DEPTOR in CRC (p=0.011, R= -0.279). However, upregulation of P-S6 (S235/236) (p=0.693) and downregulation of DEPTOR (p=0.331) in CRC were not significantly associated with overall survival. Thus, we conclude that expression of DEPTOR negatively correlates with mTORC1 activity and tumor progression in CRC. DEPTOR is a potential marker for prognostic evaluation and a target for the treatment of CRC.

Knockdown of LncRNAZFAS1 suppresses cell proliferation and metastasis in nonsmall cell lung cancer

Yong Zhou,Xiao-Wei Hu,Si-Jia Yang,Zhe Yu 한국통합생물학회 2020 Animal cells and systems Vol.24 No.2

To evaluate the effects of LncRNAZFAS1 on cell proliferation and tumor metastasis in non-small cell lung cancer (NSCLC), we detected the expression level of LncRNAZFAS1 in NSCLC-related tissues and cells. qRT-PCR results revealed that LncRNAZFAS1 in tumor tissues was significantly higher than that in normal lung tissue, especially significantly up-regulated in stage III / IV and in metastatic NSCLC tissues. LncRNAZFAS1 expression was dramatically up-regulated in 4 NSCLCrelated cells (A549, SPC-A1, SK-MES-1, and NCI-H1299), with having the highest expression level in A549 cells. Furthermore, we implemented a knockdown of LncRNAZFAS1 in A549 cells, and the results of CCK8 and Transwell assays suggested that knockdown of LncRNAZFAS1 significantly inhibited NSCLC cell proliferation and metastasis. Next, we constructed a tumor xenograft model to evaluate the effect of LncRNAZFAS1 on the NSCLC cell proliferation in vivo. The results indicated that knockdown of LncRNAZFAS1 dramatically inhibited A549 cells proliferation and repressed tumor growth. Additionally, knockdown of LncRNAZFAS1 drastically weakened the expressions of MMP2, MMP9 and Bcl-2 proteins, whereas noticeably strengthened the expression of BAX protein. Our results altogether suggest that knockdown of LncRNAZFAS1 has a negative effect on the proliferation and metastasis of NSCLC cell, which implying LncRNAZFAS1 is a potential unfavorable biomarker in patients with NSCLC.

Crosstalk between gut microbiota and Sirtuin-3 in colonic inflammation and tumorigenesis

Yong Zhang,Xiao-lan Wang,Min Zhou,Chao Kang,He-dong Lang,Meng-ting Chen,Suo-cheng Hui,Bin Wang,Man-tian Mi 생화학분자생물학회 2018 Experimental and molecular medicine Vol.50 No.-

Colorectal cancer (CRC) is a disease involving a variety of genetic and environmental factors. Sirtuin-3 (Sirt3) is expressed at a low level in cancer tissues of CRC, but it is unclear how Sirt3 modulates colonic tumorigenesis. In this study, we found that gut microbiota play a central role in the resistance to CRC tumor formation in wild-type (WT) mice through APC (Adenomatous Polyposis Coli)-mutant mouse microbiota transfer via Wnt signaling. We also found that Sirt3-deficient mice were hypersusceptible to colonic inflammation and tumor development through altered intestinal integrity and p38 signaling, respectively. Furthermore, susceptibility to colorectal tumorigenesis was aggravated by initial commensal microbiota deletion via Wnt signaling. Mice with Sirt3-deficient microbiota transfer followed by chemically induced colon tumorigenesis had low Sirt3 expression compared to WT control microbiome transfer, mainly due to a decrease in Escherichia/Shigella, as well as an increase in Lactobacillus reuteri and Lactobacillus taiwanensis. Collectively, our data revealed that Sirt3 is an anti-inflammatory and tumor-suppressing gene that interacts with the gut microbiota during colon tumorigenesis.

Triterpenoids and Sterones from the Stem Bark of Ailanthus altissima

Zhou, Xiao-Jiang,Xu, Min,Li, Xue-Song,Wang, Yue-Hu,Gao, Ye,Cai, Rui,Cheng, Yong-Xian Korean Chemical Society 2011 Bulletin of the Korean Chemical Society Vol.32 No.1

One new tirucallane-type triterpenoid, alianthusaltinin A (1), one new $C_{29}$ sterone, alianthaltone A (2), and 12 known compounds have been isolated from the stem bark of Ailanthus altissima. The structures of new compounds were identified by means of spectroscopic methods. Compound 3 was isolated from natural sources for the first time, and compounds 4, 5, and 9 were isolated from this plant for the first time.

Optimal Monochromatic Imaging of Spectral Computed Tomography Potentially Improves the Quality of Hepatic Vascular Imaging

Xiao-Ping Yin,Bu-Lang Gao,Cai-Ying Li,Huan Zhou,Liang Zhao,Ya-Ting Zheng,Yong-Xia Zhao 대한영상의학회 2018 Korean Journal of Radiology Vol.19 No.4

Objective: To investigate the efficiency of spectral computed tomography (CT) optimal monochromatic images in improving imaging quality of liver vessels. Materials and Methods: The imaging data of 35 patients with abdominal CT angiography were retrospectively analyzed. Hepatic arteries, portal veins, and hepatic veins were reconstructed with mixed energy (quality check, QC), 70 keV and optimal monochromatic mode. Comparative parameters were analyzed including CT value, image noise (IN), contrast-to-noise ratio (CNR), signal-to-noise ratio (SNR), and subjective qualitative analysis. Results: The optimal monochromatic value for assessment of the common hepatic artery, portal vein, and hepatic vein ranged between 49 keV and 53 keV, with a mean of 51 keV. There were statistically significant differences (p < 0.001) among the optimal monochromatic, 70 keV and QC images with regards to the hepatic vascular CT value, IN, CNR, SNR, and subjective qualitative score. CNR of the common hepatic artery in the optimal monochromatic, 70 keV and QC groups was 24.6 ± 10.9, 18.1 ± 8.3, and 11.6 ± 4.6, respectively (p < 0.001) with subjective scores of 4.7 ± 0.2, 4.0 ± 0.3, and 3.6 ± 0.4, respectively (p < 0.001). CNR of the hepatic portal vein was 6.9 ± 2.7, 4.3 ± 1.9, and 3.0 ± 2.1, respectively (p < 0.001) with subjective scores of 4.5 ± 0.3, 3.9 ± 0.4, and 3.3 ± 0.3, respectively (p < 0.001). CNR of the hepatic vein was 5.7 ± 2.3, 4.2 ± 1.9, and 2.7 ± 1.4, respectively with subjective scores of 4.3 ± 0.3, 3.8 ± 0.4, and 3.2 ± 0.3, respectively (p < 0.001). Conclusion: Optimal monochromatic images can lead to improvement in the imaging parameters and optimization of the image quality of the common hepatic artery, hepatic portal vein and hepatic vein compared with conventional mixed kV and with 70 keV datasets.

Phylogeny and molecular evolution of the DMC1 gene within the StH genome species in Triticeae (Poaceae)

Xiao-Li Wang,Xing Fan,Jian Zeng,Li-Na Sha,Hai-Qin Zhang,Hou-Yang Kang,Rui-Wu Yang,Li Zhang,Chun-Bang Ding,Yong-Hong Zhou 한국유전학회 2012 Genes & Genomics Vol.34 No.3

To estimate the phylogeny and molecular evolution of a single-copy nuclear disrupted meiotic cDNA (DMC1) gene within the StH genome species, two DMC1 homoeologous sequences were isolated from nearly all the sampled StH genome species and were analyzed with those from seven diploid taxa representing the St and H genomes in Triticeae. Sequence diversity patterns and genealogical analysis suggested that (1) there is a close relationship among North American StH genome species;(2) the DMC1 gene sequences of the StH genome species from North America and Eurasia are evolutionarily distinct;(3) the StH genome polyploids have higher levels of sequence diversity in the St genome homoeolog than the H genome homoeolog;(4) the DMC1 sequence may evolve faster in the polyploid species than in the diploids; (5) high dN and dN/dS values in the St genome within polyploid species could be caused by low selective constraints or AT-biased mutation pressure. Our result provides some insight on evolutionary dynamics of duplicate DMC1 gene, the polyploidization events and phylogeny of the StH genome species.

Increased retinoic acid signaling decreases lung metastasis in salivary adenoid cystic carcinoma by inhibiting the noncanonical Notch1 pathway

Zhou Meng-jiao,Yang Jia-jie,Ma Ting-yao,Feng Ge-xuan,Wang Xue-lian,Wang Li-Yong,Ge Yu-ze,Gao Ran,Hong-liang Liu,Shan Lin,Kong Lu,Chen Xiao-hong 생화학분자생물학회 2023 Experimental and molecular medicine Vol.55 No.-

MYB-NFIB fusion and NOTCH1 mutation are common hallmark genetic events in salivary gland adenoid cystic carcinoma (SACC). However, abnormal expression of MYB and NOTCH1 is also observed in patients without MYB-NFIB fusion and NOTCH1 mutation. Here, we explore in-depth the molecular mechanisms of lung metastasis through single-cell RNA sequencing (scRNA-seq) and exome target capture sequencing in two SACC patients without MYB-NFIB fusion and NOTCH1 mutation. Twenty-five types of cells in primary and metastatic tissues were identified via Seurat clustering and categorized into four main stages ranging from near-normal to cancer-based on the abundance of each cell cluster in normal tissue. In this context, we identified the Notch signaling pathway enrichment in almost all cancer cells; RNA velocity, trajectory, and sub-clustering analyses were performed to deeply investigate cancer progenitor-like cell clusters in primary tumor-associated lung metastases, and signature genes of progenitor-like cells were enriched in the “MYC_TARGETS_V2” gene set. In vitro, we detected the NICD1-MYB-MYC complex by co-immunoprecipitation (Co-IP) and incidentally identified retinoic acid (RA) as an endogenous antagonist of genes in the “MYC_TARGETS_V2” gene set. Following this, we confirmed that all-trans retinoic acid (ATRA) suppresses the lung metastasis of SACC by correcting erroneous cell differentiation mainly caused by aberrant NOTCH1 or MYB expression. Bioinformatic, RNA-seq, and immunohistochemical (IHC) analyses of primary tissues and metastatic lung tissues from patients with SACC suggested that RA system insufficiency partially promotes lung metastasis. These findings imply the value of the RA system in diagnosis and treatment.