A hybrid strategy for comprehensive annotation of the protein coding genes in prokaryotic genome

Jia-Feng Yu,Jing Guo,Qing-Bin Liu,Yue Hou,Ke Xiao,Qing-Li Chen,Ji-Hua Wang,Xiao Sun 한국유전학회 2015 Genes & Genomics Vol.37 No.4

Protein coding gene annotation errors in prokaryotic genomes are accumulating continually in bioinformatics databases, while the update rate of genome annotation can not keep up with the explosive increasing genome sequences in most cases. Hence it is critical to manually rectify the genome annotation errors. In this paper, a hybrid strategy by combing the gene ab initio predicting programs and the over annotated gene re-annotation programs is proposed for re-annotation of the protein coding genes in prokaryotic genomes. Based on this strategy, the protein coding genes in Geobacter sulfurreducens PCA is comprehensively re-annotated. As a consequence, 16 hypothetical genes are annotated as non-coding sequences and 104 missing genes are retrieved as protein coding genes. Subsequent function analysis and sequences analysis show that the predicting results are much reliable and robust. Further application to other genomes show that this work can provide alternative tools for later post-process of prokaryotic genome annotations.

Prevalence and Molecular Characterization of Echinococcus granulosus sensu stricto in Northern Xinjiang, China

Baoping Guo,Zhuangzhi Zhang,Xueting Zheng,Yongzhong Guo,Li Zhao,Ren Cai,Bingjie Wang,Mei Yang,Xi Shou,Wenbao Zhang,Bin Jia 대한기생충학ㆍ열대의학회 2019 The Korean Journal of Parasitology Vol.57 No.2

Echinococcus granulosus is an important zoonotic parasite globally causing cystic echinococcosis (CE) in hu- mans and animals. In this study, prevalence of CE and variation of cox1 gene sequence were analyzed with isolates E. granulosus collected from different areas in northern Xinjiang, China. The survey showed that 3.5% of sheep and 4.1% of cattle were infected with CE. Fragment of cox1 was amplified from all the positive sheep and cattle samples by PCR. In addition, 26 positive samples across the 4 areas were included. The isolates were all E. granulosus sensu stricto (s.s.) containing 15 haplotypes (Hap1-15), and clustered into 2 genotypes, G1 (90.1%, 91/101) and G3 (9.9%, 10/101). Hap1 was the most common haplotype (48.5%, 49/101). Hap9 were found in humans samples, indicating that sheep and cattle reservoir human CE. It is indicate that E. granulosus may impact on control of CE in livestock and humans in the region.

Intensity-Modulated Radiotherapy versus Three-Dimensional Conformal Radiotherapy in Definitive Chemoradiotherapy for Cervical Esophageal Squamous Cell Carcinoma: Comparison of Survival Outcomes and Toxicities

Nai-Bin Chen,Bo Qiu,Jun Zhang,Meng-Yun Qiang,Yu-Jia Zhu,Bin Wang,Jin-Yu Guo,Ling-Zhi Cai,Shao-Min Huang,Meng-Zhong Liu,Qun Li,Yong-Hong Hu,Qi-Wen Li,Hui Liu 대한암학회 2020 Cancer Research and Treatment Vol.52 No.1

Purpose The purpose of this study was to compare the survival and toxicities in cervical esophageal squamous cell carcinoma (CESCC) treated by concurrent chemoradiothrapy with either three-dimensional conformal radiotherapy (3D-CRT) or intensity-modulated radiotherapy (IMRT) techniques. Materials and Methods A total of 112 consecutive CESCC patients were retrospectively reviewed. 3D-CRT and IMRT groups had been analyzed by propensity score matching method, with sex, age, Karnofsky performance status, induction chemotherapy, and tumor stage well matched. The Kaplan- Meier method and Cox proportional hazards model were used for overall survival (OS) and progression-free survival (PFS). Toxicities were compared between two groups by Fisher exact test. Results With a median follow-up time of 34.9 months, the 3-year OS (p=0.927) and PFS (p=0.859) rate was 49.6% and 45.8% in 3D-CRT group, compared with 54.4% and 42.8% in IMRT group. The rates of grade ! 3 esophagitis, grade ! 2 pneumonitis, esophageal stricture, and hemorrhage were comparable between two groups, while the rate of tracheostomy dependence was much higher in IMRT group than 3D-CRT group (14.3% vs.1.8%, p=0.032). Radiotherapy technique (hazard ratio [HR], 0.09; 95% confidence interval [CI], 0.01 to 0.79) and pretreatment hoarseness (HR, 0.12; 95% CI 0.02 to 0.70) were independently prognostic of tracheostomy dependence. Conclusion No survival benefits had been observed while comparing IMRT versus 3D-CRT in CESCC patients. IMRT with fraction dose escalation and pretreatment hoarseness were considered to be associated with a higher risk for tracheostomy dependence. Radiation dose escalation beyond 60 Gy should be taken into account carefully when using IMRT with hypofractionated regimen.

Reversibility and safety of KISS1 metastasis suppressor gene vaccine in immunocastration of ram lambs

Han, Yan-Guo,Liu, Gui-Qiong,Jiang, Xun-Ping,Xiang, Xing-Long,Huang, Yong-Fu,Nie, Bin,Zhao, Jia-Yu,Nabeel, Ijaz,Tesema, Birhanu Asian Australasian Association of Animal Productio 2018 Animal Bioscience Vol.31 No.6

Objective: The aim of this study was to investigate the reversibility and safety of KISS1 metastasis suppressor (KISS1) gene vaccine in immunocastration. Methods: Six eight-week old ram lambs were randomly divided into vaccinated and control groups. The vaccine (1 mg/ram lamb) was injected at weeks 0, 3, and 6 of the study. Blood samples were collected from the jugular vein before primary immunization and at weeks 2, 4, 6, 10, 14, 22, and 30 after primary immunization. All ram lambs were slaughtered at 38 weeks of age, and samples were collected. Results: The specific anti-KISS1 antibody titers in vaccinated animals were significantly higher and the serum testosterone level was significantly lower than those in the control groups from week 4 to 14 after primary immunization (p<0.05). No significant difference was observed at weeks 22 and 30 after the primary immunization. Similar results were also found for scrotal circumference, testicular weight, length, breadth, and spermatogenesis in seminiferous tubules in week 30 after primary immunization. KS (KISS1-hepatitis B surface antigen S) fusion fragment of KISS1 gene vaccine was not detected in host cell genomic DNA of 9 tissues of the vaccinated ram lambs by polymerase chain reaction. Conclusion: The effects of KISS1 gene vaccine in immunocastration were reversible and no integration events were recorded.

Electronic Structures and Optical Properties of CuSCN with Cu Vacancies

Wei Jin,Guo-Qing Yue,Fu-Shun Ke,Song Wu,Hai-Bin Zhao,Liang-Yao Chen,Song-You Wang,Yu Jia 한국물리학회 2012 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.60 No.8

Based on density functional theory (DFT) within the generalized gradient approximation (GGA) using the CASTEP code, we calculated the formation energy of a Cu vacancy, as well as the band structure and the optical properties of β-CuSCN with Cu vacancies. Removal a Cu atom from the 32-site and the 72-site supercell results in an enlargement of the band-gap and a slight relaxation in the lattice parameter. An accepter level above the valence band maximum is observed in the 32-site supercell with a Cu vacancy, which results in the onset of a small absorption pre-peak at 0.65 eV.

Sertad1 Induces Neurological Injury after Ischemic Stroke via the CDK4/p-Rb Pathway

Jianxiong Li,Bin Li,Yujie Bu,Hailin Zhang,Jia Guo,Jianping Hu,Yanfang Zhang 한국분자세포생물학회 2022 Molecules and cells Vol.45 No.4

SERTA domain-containing protein 1 (Sertad1) is upregulated in the models of DNA damage and Alzheimer’s disease, contributing to neuronal death. However, the role and mechanism of Sertad1 in ischemic/hypoxic neurological injury remain unclear. In the present study, our results showed that the expression of Sertad1 was upregulated in a mouse middle cerebral artery occlusion and reperfusion model and in HT22 cells after oxygen-glucose deprivation/reoxygenation (OGD/R). Sertad1 knockdown significantly ameliorated ischemia-induced brain infarct volume, neurological deficits and neuronal apoptosis. In addition, it significantly ameliorated the OGD/R-induced inhibition of cell viability and apoptotic cell death in HT22 cells. Sertad1 knockdown significantly inhibited the ischemic/hypoxic-induced expression of p-Rb, B-Myb, and Bim in vivo and in vitro. However, Sertad1 overexpression significantly exacerbated the OGD/R-induced inhibition of cell viability and apoptotic cell death and p-Rb, B-Myb, and Bim expression in HT22 cells. In further studies, we demonstrated that Sertad1 directly binds to CDK4 and the CDK4 inhibitor ON123300 restores the effects of Sertad1 overexpression on OGD/R-induced apoptotic cell death and p-Rb, B-Myb, and Bim expression in HT22 cells. These results suggested that Sertad1 contributed to ischemic/hypoxic neurological injury by activating the CDK4/p-Rb pathway.

Microstructures and nano mechanical properties of the metal tungsten film

Zhu Li-na,Li Guo-lu,Wang Hai-dou,Xu Bin-shi,Zhuang Da-ming,Liu Jia-jun 한국물리학회 2009 Current Applied Physics Vol.9 No.3

The W film was prepared on 1045 steel by magnetron sputtering, with the thickness of 2 ㎛, its surface and cross-section morphologies were investigated with SEM, and the phase structure was analyzed with XRD. X-ray stress determinator was utilized to measure its residual stress, and the nano-hardness and elastic modulus of the film were surveyed by nano-indentation tester. The results show that the surface of W film is very compact and smooth; the particles arranged regularly, the granularity of the thin film is about 1 ㎛. The microcracks, cavities and desquamation were not found in the film and interface, and the bonding between the W film and substrate is well. The XRD results showed that the W film had a body-centered cubic structure, the lattice constant: ɑ = 0.316 nm, the growth preferred orientations are (110) and (220). The compressive stress (-169 MPa) was found on the surface. The average nano-hardness and elastic modulus of W film are 15.22 GPa, 176.64 GPa, respectively, and the mechanical properties of W film are well. The W film was prepared on 1045 steel by magnetron sputtering, with the thickness of 2 ㎛, its surface and cross-section morphologies were investigated with SEM, and the phase structure was analyzed with XRD. X-ray stress determinator was utilized to measure its residual stress, and the nano-hardness and elastic modulus of the film were surveyed by nano-indentation tester. The results show that the surface of W film is very compact and smooth; the particles arranged regularly, the granularity of the thin film is about 1 ㎛. The microcracks, cavities and desquamation were not found in the film and interface, and the bonding between the W film and substrate is well. The XRD results showed that the W film had a body-centered cubic structure, the lattice constant: ɑ = 0.316 nm, the growth preferred orientations are (110) and (220). The compressive stress (-169 MPa) was found on the surface. The average nano-hardness and elastic modulus of W film are 15.22 GPa, 176.64 GPa, respectively, and the mechanical properties of W film are well.

Analysis of the Relationship between MHC-DRB1 Gene Polymorphism and Hydatidosis in Kazakh Sheep

Li, Ren-Yan,Jia, Bin,Zhang, Wen-Ju,Zhao, Zong-Sheng,Shi, Guo-Qing,Shen, Hong,Peng, Qiang,Lv, Li-Min,Zhou, Qi-Wei,Du, Ying-Chun Asian Australasian Association of Animal Productio 2010 Animal Bioscience Vol.23 No.9

The objective of this work was to analyze the relationship between ovine major histocompatibility complex (MHC) DRB1 gene polymorphism and genetic resistance to hydatidosis in Kazakh sheep. The Ovar (ovine MHC) class II DRB1 second exon was amplified by polymerase chain reaction (PCR) from DNA samples of 702 Kazakh sheep, including 302 sheep with hydatidosis and 400 health controls. PCR products were characterized by the restriction fragment length polymorphism (RFLP) technique using five restriction enzymes, i.e., MvaI, HaeIII, SacI, SacII and Hin1I, yielding 14 alleles and 28 genotypes. Comparing the frequency of genotypes in hydatidosis sheep with the control group, it was found that the genotype frequencies of MvaIbc, Hin1Iab, SacIIab, HaeIIIde, HaeIIIdf and HaeIIIdd in control sheep were significantly (p<0.01) higher than in hydatidosis sheep, indicating that a significant correlation existed between these genotypes and resistance to hydatidosis. Genotype frequencies of MvaIbb, SacIIaa, Hin1Ibb and HaeIIIef in sheep with hydatidosis were extremely significantly (p<0.01) higher than in the control group, and the genotype frequency of HaeIIIab was significantly higher (p<0.05), indicating that a marked correlation existed between these genotypes and susceptibility to hydatidosis. By way of analyzing haplotype with these resistant genotypes, the hydatidosis resistant haplotype MvaIbc-SacIIab-Hin1Iab of Kazakh sheep was screened out, and then verified through artificial hydatid infection in sheep. The results indicated that the infection rate of sheep with the resistant haplotype of hydatidosis was significantly lower (p<0.01) than without this resistant haplotype. It showed that the genic haplotype MvaIbc-SacIIab-Hin1Iab of Ovar-DRB1 exon 2 was the resistant haplotype of hydatidosis in Kazakh sheep.

Morphology and ultrastructure of the male reproductive system of the jewel wasp, Nasonia vitripennis (Walker) (Hymenoptera: Pteromalidae)

Nai-Yong Liu,Guo-XingWu,Sang-Zi Ze,Bin Yang,Jia-Ying Zhu 한국응용곤충학회 2017 Journal of Asia-Pacific Entomology Vol.20 No.2

The genital systems of insects are undoubtedly of great key for the success of mating and population reproduction. In the meantime,morphological and ultrastructural characteristics of the reproductive systems also provide valuable evidences for the studies of taxonomy, reproductive biology and evolutionary biology.More previously, the reproductive systemof female Nasonia vitripennis was already described. To complement the information of reproductive systems from this species, the male reproductive system was here dissected and characterized by light microscopy and transmission electron microscopy. Results showed that the system follows the pattern of most Hymenoptera species: paired testes with one follicle, deferent ducts, seminal vesicles, accessory glands and a fused ejaculatory duct ultimately connected to the external aedeagus. Histologically, the testes, seminal vesicles and accessory glands are all composed of three portions, all of which include epithelial and luminal regions. In addition, both lipidic inclusions and nuclei are presented in the three organs with variable sizes and shapes. Spermatozoa are observed in the testes and seminal vesicles, and also vary considerably in size and shape, suggesting different phases of spermatogenesis.Mitochondria are abundant in seminal vesicles and accessory glands. Notably, membranous inclusions and Golgi complexes are found only in seminal vesicles, whereas secretory granules are presented only in accessory glands, being indicative of organ or age specificity. Together, this study complements the information of the reproductive systems from N. vitripennis, and provides an extensive resource for taxonomy, reproductive biology and evolutionary biology.

Exosomal CircPRRX1 Enhances Doxorubicin Resistance in Gastric Cancer by Regulating MiR-3064-5p/PTPN14 Signaling

Shumin Wang,Mei Ping,Bin Song,Yarong Guo,Yuanfei Li,Junmei Jia 연세대학교의과대학 2020 Yonsei medical journal Vol.61 No.9

Purpose: Gastric cancer (GC) is a malignant tumor with a high mortality rate. Drug resistance is a major obstacle to GC therapy. This study aimed to investigate the role and mechanism of exosomal circPRRX1 in doxorubicin resistance in GC. Materials and Methods: HGC-27 and AGS cells were exposed to different doses of doxorubicin to construct doxorubicin-resistantcell lines. Levels of circPRRX1, miR-3064-5p, and nonreceptor tyrosine phosphatase 14 (PTPN14) were detected by quantitativereal-time PCR or Western blot assay. Then, 3-(4,5-dimethyl-2-thiazolyl)-2,5-diphenyl-2-H-tetrazolium bromide, transwell,and Western blot assays were used to explore the function of circPRRX1 in GC cells. Interactions among circPRRX1, miR-3064-5p,and PTPN14 were confirmed by dual-luciferase reporter assay. The in vivo function of circPRRX1 was analyzed in a xenograft tumormodel. Results: CircPRRX1 was highly expressed in doxorubicin-resistant GC cell lines. Knockdown of circPRRX1 reversed doxorubicinresistance in doxorubicin-resistant GC cells. Additionally, extracellular circPRRX1 was carried by exosomes to spread doxorubicinresistance. CircPRRX1 silencing reduced doxorubicin resistance by targeting miR-3064-5p or regulating PTPN14. In GC patients,high levels of circPRRX1 in serum exosomes were associated with poor responses to doxorubicin treatment. Moreover, depletionof circPRRX1 reduced doxorubicin resistance in vivo. Conclusion: CircPRRX1 strengthened doxorubicin resistance by modulating miR-3064-5p/PTPN14 signaling and might be atherapeutic target for GC patients.