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.

Fast Transient Buck Converter Using a Hysteresis PWM Controller

Yong-Xiao Liu,Jin-Bin Zhao,Ke-Qing Qu 전력전자학회 2013 JOURNAL OF POWER ELECTRONICS Vol.13 No.6

In this paper, a fast transient buck converter using hysteresis PWM control is presented. The proposed control method is based on hysteresis control of the capacitor C voltage. This offers a faster transient response to meet the challenges of the power supply requirements for fast dynamic input and load changes. It also provides better stability and solves the compensation problem of the error amplifier in conversional voltage PWM control. Finally, the steady-state and dynamic operation of the proposed control method are analyzed and verified by simulation and experimental results.

A Novel Mannose-binding Tuber Lectin from Typhonium divaricatum (L.) Decne (family Araceae) with Antiviral Activity Against HSV-II and Anti-proliferative Effect on Human Cancer Cell Lines

( Yong Ting Luo ),( Xiao Chao Xu ),( Ji Wei Liu ),( Jian Li ),( Yi Sheng Sun ),( Zhen Liu ),( Jin Zhi Liu ),( Els Van Damme ),( Jan Balzarini ),( Jin Ku Bao ) 생화학분자생물학회 2007 BMB Reports Vol.40 No.3

Molecular characterization and expression analysis of putative odorant carrier proteins in Adelphocoris lineolatus

Yong Xiao,Liang Sun,Qi Wang,Qiang Zhang,Shao-Hua Gu,Adel Khashaveh,Ze-Wen Liu,Yong-Jun Zhang 한국응용곤충학회 2018 Journal of Asia-Pacific Entomology Vol.21 No.3

The alfalfa plant bug Adelphocoris lineolatus (Goeze) (Hemiptera: Miridae), a serious pest of several agricultural crops, is extremely attracted by flowering plants to perform season host switching. Generally, chemoreception of A. lineolatus plays a crucial role in detecting food sources, locating mates and oviposition sites. In addition, odorant carrier proteins are believed to participate in the initial chemical communication and perception in insects. In this work, we identified 31 putative odorant carrier protein genes from the antennal transcriptomes of A. lineolatus, including 17 new odorant binding proteins (OBPs), 10 new chemosensory proteins (CSPs) and four Niemann-Pick type C2 proteins (NPC2s). Phylogenetic analysis demonstrated that the OBP and CSP genes from four mirid bug species (A. lineolatus, Adelphocoris suturalis, Apolygus lucorum and Lygus lineolaris) had a relatively close evolutionary relationship. Regular patterns and key conserved motifs of OBPs and CSPs in Hemiptera insects are also identified by using Multiple EM for Motif Elicitation (MEME) tool. Tissue expression profiles analysis showed that nine of the 17 OBPs, 10 CSPs and two of the four NPC2s were primarily or uniquely expressed in the adult antennae suggesting their putative roles in chemoreception. Our study provides the first insight into the roles of odorant carrier proteins in chemoreception of A. lineolatus, which will help to facilitate biological functions of odorant carrier proteins and develop novel insect behavioral regulation strategy

Effect of gelatin nano-coating containing Gardenia pigment on the preservation of pork slices

Yong Liu,Zi-Hao Liu,Chang-Qi Luo,Chun-Tao Xiao,Wen-Yu Zhou,Wen-Jin Xie 한국식품과학회 2022 Food Science and Biotechnology Vol.31 No.4

The nano-coating composed of gelatin and Gardenia pigment (GP) was successfully prepared and showed strong antioxidant activity. The average particle sizes of the nano-coating containing 0.1% and 0.3% GP were 269.58 and 394.13 nm, respectively. The pork slices uncoated and coated with the nano-coating were preserved at 4 C for 15 days. The pork slices’ pH, total volatile basic nitrogen (TVB-N), total viable counts (TVC), water-bind- ing capacity (WHC), and thiobarbituric acid reactive sub- stances (TBARS) were measured to assess the preservation effect of the nano-coating. The results showed that the pork coated with the nano-coating had lower pH, TVC, TVB-N, TBARS, and higher WHC, significantly different (p \ 0.05) than the uncoated pork. It is suggested that the proposed nano-coating can be used to effectively improve the pork’s quality and shelf life during refrigeration storage.

Fast Transient Buck Converter Using a Hysteresis PWM Controller

Liu, Yong-Xiao,Zhao, Jin-Bin,Qu, Ke-Qing The Korean Institute of Power Electronics 2013 JOURNAL OF POWER ELECTRONICS Vol.13 No.6

In this paper, a fast transient buck converter using hysteresis PWM control is presented. The proposed control method is based on hysteresis control of the capacitor C voltage. This offers a faster transient response to meet the challenges of the power supply requirements for fast dynamic input and load changes. It also provides better stability and solves the compensation problem of the error amplifier in conversional voltage PWM control. Finally, the steady-state and dynamic operation of the proposed control method are analyzed and verified by simulation and experimental results.

Effect of CXCR4 and CD133 Co-expression on the Prognosis of Patients with Stage II~III Colon Cancer

Li, Xiao-Feng,Guo, Xiao-Guang,Yang, Yong-Yan,Liu, Ai-Yong Asian Pacific Journal of Cancer Prevention 2015 Asian Pacific journal of cancer prevention Vol.16 No.3

Background: To explore the relationship between CXCR4, CD133 co-expression and clinicopathological features as well as prognosis of patients with phase II~III colon cancer. Materials and Methods: Forty-nine paraffin-embedded samples of tumor tissue and epithelial tissue adjacent to cancer were collected from patients with colon cancer undergoing radical surgery in Baotou Cancer Hospital from January, 2010 to June, 2011. CXCR4 and CD133 expression was detected using immunohistochemistry and its relationship with clinicopathological features and the 3-year survival rate was analyzed. Results: In the tumor tissue and colonic epithelial tissue adjacent to cancer, the positive expression rates of CXCR4 were respectively 61.2% (30/49) and 8.16% (4/49), while those of CD133 being 36.7% (18/49) and 6.12% (3/49). CXCR4 and CD133 expression in tumor tissue was not related to patient age, gender, primary focal sites, tumor size, TNM staging, histological type, tumor infiltration depth and presence or absence of lymphatic metastasis, but CXCR4 and CD133 co-expression was associated with TNM staging and lymphatic metastasis. The 3-year survival rate of patients with CXCR4 and CD133 co-expression was 27.3% (3/11), and that of the remainderwas 76.3% (29/38), the difference being significant ($X^2=7.0206$, p=0.0081). Conclusions: CXCR4 and CD133 co-expression may be a risk factor for poor prognosis of patients with stage II~III colon cancer.

8q24 rs4242382 Polymorphism is a Risk Factor for Prostate Cancer among Multi-Ethnic Populations: Evidence from Clinical Detection in China and a Meta-analysis

Zhao, Cheng-Xiao,Liu, Ming,Xu, Yong,Yang, Kuo,Wei, Dong,Shi, Xiao-Hong,Yang, Fan,Zhang, Yao-Guang,Wang, Xin,Liang, Si-Ying,Zhao, Fan,Zhang, Yu-Rong,Wang, Na-Na,Chen, Xin,Sun, Liang,Zhu, Xiao-Quan,Yuan Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.19

Background: Evidence supporting an association between the 8q24 rs4242382-A polymorphism and prostate cancer (PCa) risk has been reported in North American and Europe populations, though data from Asian populations remain limited. We therefore investigated this association by clinical detection in China, and meta-analysis in Asian, Caucasian and African-American populations. Materials and Methods: Blood samples and clinical information were collected from ethnically Chinese men from Northern China with histologically-confirmed PCa (n=335) and from age-matched normal controls (n=347). The 8q24 (rs4242382) gene polymorphism was genotyped by polymerase chain reaction-high-resolution melting analysis. We initially analyzed the associations between the risk allele and PCa and clinical covariates. A meta-analysis was then performed using genotyping data from a total of 1,793 PCa cases and 1,864 controls from our study and previously published studies in American and European populations, to determine the association between PCa and risk genotype. Results: The incidence of the risk allele was higher in PCa cases than controls (0.222 vs 0.140, $P=7.3{\times}10^{-5}$), suggesting that the 8q24 rs4242382-A polymorphism was associated with PCa risk in Chinese men. The genotypes in subjects were in accordance with a dominant genetic model (ORadj=2.03, 95%CI: 1.42-2.91, $Padj=1.1{\times}10^{-4}$). Presence of the risk allele rs4242382-A at 8q24 was also associated with clinical covariates including age at diagnosis ${\geq}65$ years, prostate specific antigen >10 ng/ml, Gleason score <8, tumor stage and aggressive PCa, compared with the non-risk genotype ($P=4.6{\times}10^{-5}-3.0{\times}10^{-2}$). Meta-analysis confirmed the association between 8q24 rs4242382-A polymorphism and PCa risk (OR=1.62, 95%CI: 1.39-1.88, $P=1.0{\times}10^{-5}$) across Asian, Caucasian and African American populations. Conclusions: The replicated data suggest that the 8q24 rs4242382-A variation might be associated with increased PCa susceptibility in Asian, Caucasian and African American populations. These results imply that this polymorphism may be a useful risk biomarker for PCa in multi-ethnic populations.

Meta-analysis of Circulating Tumor Cells as a Prognostic Marker in Lung Cancer

Ma, Xue-Lei,Xiao, Zhi-Lan,Liu, Lei,Liu, Xiao-Xiao,Nie, Wen,Li, Ping,Chen, Nian-Yong,Wei, Yu-Quan Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.4

Introduction: Recent studies have shown that circulating tumor cells (CTCs) play potential roles as diagnostic and prognostic biomarkers with various cancer types. The aim of this study was to comprehensively and quantitatively summarize the evidence for the use of CTCs to predict the survival outcome of lung cancer patients. Materials and Methods: Relevant literature was identified using Medline and EMBASE. Patients' clinical characteristics, overall survival (OS) and progression-free survival (PFS) together with CTC positive rates at different time points (before, during and after treatment) were extracted. A meta-analysis was performed to clarify the prognostic role of CTCs and the correlation between the CTC appearance and clinical characteristics. Results: A total of 12 articles containing survival outcomes and clinical characteristics and 15 articles containing only clinical characteristics were included for the global meta-analysis. The hazard ratio (HR) for OS predicted by pro-treatment CTCs was 2.61 [1.82, 3.74], while the HR for PFS was 2.37 [1.41, 3.99]. The HR for OS predicted by post-treatment CTCs was 4.19 [2.92, 6.00], while the HR for PFS was 4.97 [3.05, 8.11]. Subgroup analyses were conducted according to histological classification and detection method. Odds ratio (OR) showed the appearance of pro-treatment CTCs correlated with the lymph node status, distant metastasis, and TNM staging, while post-treatment CTCs correlated with TNM staging only. Conclusion: Detection of CTCs in the peripheral blood indicates a poor prognosis in patients with lung cancer.

Two New Species in the Family Cunninghamellaceae from China

( Heng Zhao ),( Jing Zhu ),( Tong-kai Zong ),( Xiao-ling Liu ),( Li-ying Ren ),( Qing Lin ),( Min Qiao ),( Yong Nie ),( Zhi-dong Zhang ),( Xiao-yong Liu ) 한국균학회 2021 Mycobiology Vol.49 No.2

The species within the family Cunninghamellaceae are widely distributed and produce important metabolites. Morphological studies along with a molecular phylogeny based on the internal transcribed spacer (ITS) and large subunit (LSU) of ribosomal DNA revealed two new species in this family from soils in China, that is, Absidia ovalispora sp. nov. and Cunninghamella globospora sp. nov. The former is phylogenetically closely related to Absidia koreana, but morphologically differs in sporangiospores, sporangia, sporangiophores, columellae, collars, and rhizoids. The latter is phylogenetically closely related to Cunninghamella intermedia, but morphologically differs in sporangiola and colonies. They were described and illustrated.