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.

Partial gasification of coal in a fluidized bed reactor: Comparison of a laboratory and pilot scale reactors

Rui Xiao,Laihong Shen,Mingyao Zhang,Baosheng Jin,Yuanquan Xiong,Yufeng Duan,Zhaoping Zhong,Xiaoping Chen,Yaji Huang,Hongcang Zhou 한국화학공학회 2007 Korean Journal of Chemical Engineering Vol.24 No.1

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>

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.

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>

Molecular Dynamics Simulation to Investigate the Rake Angle Effects on Nanometric Cutting of Single Crystal Ni3Al

Rui-cheng Feng,Yong-nian Qi,Zong-xiao Zhu,Wen-yuan Song,Hai-yan Li,Mao-mao Wang,Zhi-yuan Rui,Feng-shou Gu 한국정밀공학회 2020 International Journal of Precision Engineering and Vol.21 No.4

Molecular dynamics, an eff ective method to gain an insight into nanometric behaviour of materials, was employed to studythe nano-cutting behaviour of single crystal Ni 3 Al in nanometric scale. In this paper, comparisons were made for compressive/tensile stress, subsurface damage and surface roughness with three rake angles of a diamond tool. Subsurface damage waspartitioned by region and studied with work hardening in detail. A model for precise characterization of surface roughnesswas established with consideration of local surface fl uctuation. Simulation results showed that the chip thickness increasedas rake angle changed from negative to positive, and the boundary formed between tensile and compressive stress was inconsistent with the glide direction of stacking fault. Subsurface damage decreased as the increase of rake angle, and regularglide planes of stacking faults were found in front of the cutting tool. Further, the pinned dissociated 1/2 < 110 > superpartialdislocation with anti-phase boundary was demonstrated. The model was tested and characterized by implanted pits onperfect surface. Results showed that surface roughness can be well characterized, and an evident discrepancy was observedamong three rake angles, especially for 30° rake angle, which showed an distinct smooth surface compared with the others.

Thermal-balanced integral model for pyrolysis and ignition of wood

Rui Xiao,Dekui Shen,Mengxiang Fang,Wanki Chow 한국화학공학회 2013 Korean Journal of Chemical Engineering Vol.30 No.1

The pyrolysis and ignition of wood is of great importance to understand the initial stage of combustion,helping control the occurrence and spread of unwanted building and forestry fires. The development of a thermal-balanced model is introduced for examining the analytical relationship between the ignition time and external heat flux. The critical heat flux, one of the important fire-retardant characteristics of combustible solid, is determined from a correlation study between the ignition time and external heat flux. One of the thermal-balanced integral models, considering the effect of surface heat losses, average absorptivity and moisture content, is employed to give the prediction of surface temperature rise, ignition time and ignition temperature of the Aspen. The results show that the model readily and satisfactorily predicts ignition temperature and ignition time of wood with different moisture contents.

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.