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.

Is it innovation or conservation?

Xiao, Rui,Kim, Namsoon(김남순) 한남대학교 교육연구소 2015 교육연구 Vol.22 No.-

그 동안 외국어 교육에서 과업중심 교수법 (Task-based Approach)은 학습자들의 의사소통 능력을 증진시킬 수 있는 매우 효과적인 교수법으로 널리 사용되어 왔다. 학습자 중심의, 진정성 있는 의사소통, 언어의 사용 경험을 중시하는 과업중심 교수법은 과업의 목적을 달성하기 위하여, 학습자가 자연스럽게 목표언어를 사용하면서 자연스럽게 의사소통 능력을 증진시킬 수 있는 장점이 있다. 이 연구는 외국어로서의 중국어교육 분야에서 과업중심 교수법과 관련된 연구현황을 분석하여 그 타당성과 효용성을 조사하고, 장래 방향을 조명하는 것을 목표로 하고 있다. 연구 대상은 중국에 소재하는 대학에서 2000년부터 2015년까지 외국어로서의 중국어교육 분야에서 출간된--과업중심 교수법울 다룬--대학원 학위논문이며, 이와 관련하여, 총 35편의 논문이 수집되고 분석되었다. 연구결과, 대다수의 논문들이 과업중심 방법의 이론과 실천 방향을 소개하는 데에 초점을 맞추고 있었고, 효용성을 증명할 수 있는 질적 및 양적 연구는 극소수에 불과하였다. 앞으로도 외국어로서의 중국어 교육에서 학습자들의 의사소통 능력을 증진시킬 수 있는 효과적인 과업중심 교수법이 더욱 요구되고 있다. 이에 따라서, 과업중심 교수법의 효과성을 증명할 수 있는 더욱 많은 질적 및 양적 연구가 개발되고, 그에 따른 후속 연구가 필요하다. Task-based approach (TBA), a teaching approach widely used in second language teaching and learning, intends to develop students’ communicative ability in their target language. In this student-centered language teaching, students are stimulated to learn by doing and using their target language through fulfilling authentic communicative tasks. The purposes of this study are to examine the trends of using TBA in Chinese language teaching and to provide insights to the teaching of Chinese language for future use. Total of thirty-five graduate theses were examined in the study. Results of the study indicated that the previous research has dealt mostly with theories and introduction of TBA to be used in the field of Chinese language teaching. It was suggested that more research studies are needed through both quantitative and qualitative research studies.

Characterization of the bovine endogenous retrovirus beta3 genome.

Xiao, Rui,Kim, Juhyun,Choi, Hojun,Park, Kwangha,Lee, Hoontaek,Park, Chankyu Korean Society for Molecular Biology 2008 Molecules and cells Vol.25 No.1

<P>We recently used degenerate PCR and locus-specific PCR methods to identify the endogenous retroviruses (ERV) in the bovine genome. Using the ovine ERV classification system, the bovine ERVs (BERVs) could be classified into four families. Here, we searched the most recently released bovine genome database with the partial nucleotide sequence of the pro/pol region of the BERV beta3 family. This allowed us to obtain and analyze the complete genome of BERV beta3. The BERV beta3 genome is 7666 nucleotides long and has the typical retroviral organization, namely, 5'-long terminal repeat (LTR)-gag-pro-pol-env-LTR-3'. The deduced open reading frames for gag, pro, pol and env of BERV Beta en- code 507, 271, 879 and 603 amino acids, respectively. BERV beta3 showed little amino acid similarity to other betaretroviruses. Phylogenetic analysis showed that it clusters with HERV-K. This is the first report describing the genetic structure and sequence of an entire BERV.</P>

Identification and Classification of Endogenous Retroviruses in Cattle

Xiao, Rui,Park, Kwangha,Lee, Hoontaek,Kim, Jinhoi,Park, Chankyu American Society for Microbiology 2008 Journal of virology Vol.82 No.1

<B>ABSTRACT</B><P>The aim of this study was to identify the endogenous retrovirus (ERV) sequences in a bovine genome. We subjected bovine genomic DNA to PCR with degenerate or ovine ERV (OERV) family-specific primers that aimed to amplify the retroviral <I>pro/pol</I> region. Sequence analysis of 113 clones obtained by PCR revealed that 69 were of retroviral origin. On the basis of the OERV classification system, these clones from degenerate PCR could be divided into the β3, γ4, and γ9 families. PCR with OERV family-specific primers revealed an additional ERV that was classified into the bovine endogenous retrovirus (BERV) γ7 family. In conclusion, here we report the results of a genome scale study of the BERV. Our study shows that the ERV family expansion in cattle may be somewhat limited, while more diverse family members of ERVs have been reported from other artiodactyls, such as pigs and sheep.</P>

ELECTRIC-FIELD DEPENDENCE OF MOLECULAR CONFORMATIONS OBSERVED BY USING SCANNING TUNNELING MICROSCOPY

XIAO JING MA,RUI ZHANG,YONG TAO SHEN,XIAO HUI QIU,YAN LIAN YANG,CHEN WANG 성균관대학교(자연과학캠퍼스) 성균나노과학기술원 2008 NANO Vol.3 No.2

We review the progress in observation of electrically induced conformational changes of a range of single molecules and molecular assemblies using scanning tunneling microscopy (STM). Recent results using species with optical active functional groups and supramolecular structures confirmed the previously observed effects that the cholesterol molecules with soft linkers have the conformational bistability when switching the bias polarity, while no discernable changes were observed for the mesogen molecules, containing rigid linking units. In addition, it was also observed that the linker units could have appreciable impacts on the assembling characteristics.

Highly synergic adsorption and photocatalytic degradation of walnut shell biochar/NiCr-layered double hydroxides composite for Methyl orange

Xiao-fang Li,Rui-xian Li,Ke-xin Wang,Xiao-qiang Feng 한국공업화학회 2023 Journal of Industrial and Engineering Chemistry Vol.126 No.-

Methyl orange (MO) is a kind of azo dye, and will do great harm to the ecological environment. Alleviating this problem by removing MO is crucial role to prevent harmful damage to the environment. In this paper, NiCr layered double hydroxides (LDH) were prepared through hydrothermal method andthen modified with different mass rations of walnut shell biochar. The structure and properties ofbiochar/NiCr-LDH composites were analyzed by Fourier transform infrared spectroscopy (FT-IR), powderX-ray diffraction (XRD), field emission scanning electron microscopy (FE-SEM) coupled with energy dispersespectroscopy (EDS), and X-ray photoelectron spectroscopy (XPS). Moreover, the adsorption andphotocatalytic degradation behavior of composites on anionic dye MO were investigated. Characterization results indicated that NiCr-LDH was perfectly synthesized and coated on the biochar. All the biochar/NiCr-LDH composites show enhanced adsorption and photodegradation performancefor MO dye compared with pure NiCr-LDH and biochar. When the biochar content was 22.3 wt.% andthe biochar/NiCr-LDH (S2) dosage was 1.0 mg/mL, the maximum removal amount of MO could reach100 % within 60 min at the natural pH, experimental data fitted well with the pseudo-second-orderkinetic and Freundlich isotherm model, and the maximum adsorption capacity of S2 was 108.2 mg/g. Besides, compared with NiCr-LDH, S2 also demonstrated wonderful photodegradation activity for MOunder visible-light irradiation, the rate constant of S2 (0.0173 min1) is about 1.5 times that of NiCr-LDH (0.0118 min1), and the enhanced performance can be due to the faster separation of electronholepairs, in which biochar acted as charge separation carriers. Meanwhile, the hydroxyl radical andsuperoxide radical played crucial roles in the dye photocatalytic degradation, and a possible photocatalyticdegradation mechanism was proposed. The excellent photocatalytic activity and stability makebiochar/NiCr-LDH an ideal photocatalyst to solve environmental crisis.

Structural Characterization of the Genome of BERV gamma4, the Most Abundant Endogenous Retrovirus Family in Cattle.

Xiao, Rui,Park, Kwangha,Oh, Younshin,Kim, Jinhoi,Park, Chankyu Korean Society for Molecular Biology 2008 Molecules and cells Vol.26 No.4

<P>The genome of replication-competent BERV gamma4 provirus, which is the most abundant ERV family in the bovine genome, was characterized in detail. The BERV gamma4 genome showed that BERV gamma4 harbors 8576 nucleotides and has the typical 5'-long terminal repeat (LTR)-gag-pro-pol-env-LTR-3'retroviral organization with a long leader region positioned before the gag open reading frame. Multiple sequences analysis showed that the nucleotide difference between 5' and 3' LTRs was 4.2% (mean value 0.042) in average, suggesting that the provirus formed at most 13.3 million years ago. Gag separated by a stop codon from pro-pol in the same reading frame, while env resides in another reading frame lacking of a functional surface domain. According to the current bovine genome sequence assembly, the full-length BERV gamma4 provirus sequences were only found in the chromosomes 1, 2, 6, 10, 15, 23, 26, 28, X, and unassigned, although the partial sequences almost evenly distributed in the entire bovine genome. This is the first detailed study describing the genome structure of BERV gamma4, the most abundant ERV family present in bovine genome. Combined with our recent reports on characterization of ERVs in bovine, this study will contribute to illuminate ERVs in the cattle of which no information was previously available.</P>

Adaptive Neural Tracking Control for Uncertain Switched Nonlinear Non-lower Triangular System with Disturbances and Dead-zone Input

Rui-Bing Li,Xiao-Mei Wang,Xiao-Mei Liu,Ben Niu,Dong Yang 제어·로봇·시스템학회 2020 International Journal of Control, Automation, and Vol.18 No.6

This work investigates the adaptive neural tracking control problem for a class of uncertain switched nonlinear non-lower triangular systems with disturbances and dead-zone input. First, radial basis function (RBF) neural networks (NNs) serve as a flexible tool to approximate the unknown nonlinear functions. Then during the controller design, the dynamic surface control (DSC) method is used to avoid the issue of "explosion of complexity", and only one adaptive law is adopted to reduce the computational burden. What’s more, a few classical mathematical approaches are used to handle the design difficulties caused by dead-zone input, and the proposed controller guarantees the closed-loop system signals are semi-globally uniform ultimate boundedness (SGUUB). Finally, a simulation example is given to illustrate the availability of the proposed control scheme.

Cold hardiness characteristic of the overwintering pupae of fall webworm Hyphantria cunea (Drury) (Lepidoptera: Arctiidae) in the northeast of China

Xiao-Rui Xu,Ming-Ming Zhu,Liang-Liang Li,Guang-Cai Zhang,Ye Zheng,Ting Li,Shou-Hui Sun 한국응용곤충학회 2015 Journal of Asia-Pacific Entomology Vol.18 No.1

The fallwebworm, Hyphantria cunea (Drury) (Lepidoptera: Arctiidae), is an invasive and important pest in China. Understanding the physiological–biochemical characteristics of the overwintering pupae is essential for its cold tolerance and potential distribution in the northeast of China. Results indicated that the supercooling point (SCP) of H. cunea overwintering pupae varied significantly among Jilin city (43°N, 126°E), Jilin Province, Shenyang (41.8°N, 123.4°E), Liaoning Province and Yingkou (40.39°N, 122.13°E), Liaoning Province. The average SCP in Jilin was the lowest (−23.49 ± 0.46 °C) in those of three areas. The water content in overwintering pupae had a significant positive correlation with the SCP (R = 0.848,P = 0.03). Contents of alanine (ALA) (26.00%), lysine (LYS) (30.51%) and arginine (ARG) (22.88%) in the overwintering pupae's hemolymph were higher than others. During the overwintering, the fat content in pupae's bodies decreased gradually. Analysis of variance (ANOVA) indicated that the content of trehalose in the body of H. cunea was remarkably different (P= 0.007) month by month, with the maximum in March (2.88 mg·mL−1) and the minimum (0.40 mg·mL−1) in November. Pearson's correlation test indicated that SCP had a significant negative correlation with the SOD enzyme activity (R = −0.850; P = 0.008). Thermal hysteresis activity (THA) of hemolymph was 0.68°C and 0.7–0.8°C for H. cunea pupae and larva, respectively, using differential scanning calorimetry, which suggests that the H. cunea can improve their cold tolerance through producing antifreeze proteins. These results could help us to predict the distribution of the H. cunea in the northeast of China.

Expression and Preliminary Functional Profiling of the let-7 Family during Porcine Ovary Follicle Atresia

Rui Cao,Wang Jun Wu,Xiao Long Zhou,Peng Xiao,Yi Wang,Honglin Liu 한국분자세포생물학회 2015 Molecules and cells Vol.38 No.4

Most follicles in the mammalian ovary undergo atresia. Granulosa cell apoptosis is a hallmark of follicle atresia. Our previous study using a microRNA (miRNA) microarray showed that the let-7 microRNA family was differentially expressed during follicular atresia. However, whether the let- 7 miRNA family members are related to porcine (Sus scrofa) ovary follicular apoptosis is unclear. In the current study, real-time quantitative polymerase chain reaction showed that the expression levels of let-7 family members in follicles and granulosa cells were similar to our microarray data, in which miRNAs let-7a, let-7b, let-7c, and let-7i were significantly decreased in early atretic and progressively atretic porcine ovary follicles compared with healthy follicles, while let-7g was highly expressed during follicle atresia. Furthermore, flow cytometric analysis and Hoechst33342 staining demonstrated that let-7g increased the apoptotic rate of cultured granulosa cells. In addition, let-7 target genes were predicted and annotated by TargetScan, PicTar, gene ontology and Kyoto encyclopedia of genes and genomes pathways. Our data provide new insight into the association between the let-7 miRNA family in granulosa cell programmed death.