Comparison of methods for library construction and short read annotation of shellfish viral metagenomes

Hong‑Ying Wei,Sheng Huang,Jiang‑Yong Wang,Fang Gao,Jing‑Zhe Jiang 한국유전학회 2018 Genes & Genomics Vol.40 No.3

The emergence and widespread use of high-throughput sequencing technologies have promoted metagenomic studies on environmental or animal samples. Library construction for metagenome sequencing and annotation of the produced sequence reads are important steps in such studies and influence the quality of metagenomic data. In this study, we collected some marine mollusk samples, such as Crassostrea hongkongensis, Chlamys farreri, and Ruditapes philippinarum, from coastal areas in South China. These samples were divided into two batches to compare two library construction methods for shellfish viral metagenome. Our analysis showed that reverse-transcribing RNA into cDNA and then amplifying it simultaneously with DNA by whole genome amplification (WGA) yielded a larger amount of DNA compared to using only WGA or WTA (whole transcriptome amplification). Moreover, higher quality libraries were obtained by agarose gel extraction rather than with AMPure bead size selection. However, the latter can also provide good results if combined with the adjustment of the filter parameters. This, together with its simplicity, makes it a viable alternative. Finally, we compared three annotation tools (BLAST, DIAMOND, and Taxonomer) and two reference databases (NCBI’s NR and Uniprot’s Uniref). Considering the limitations of computing resources and data transfer speed, we propose the use of DIAMOND with Uniref for annotating metagenomic short reads as its running speed can guarantee a good annotation rate. This study may serve as a useful reference for selecting methods for Shellfish viral metagenome library construction and read annotation.

Identification of a Methyltransferase Encoded by Gene ste16 and Its Function in Ebosin Biosynthesis of Streptomyces sp. 139

Hong-Guan Xie,Yong-Gang Bao,Li-ping Bai,Jun-Jie Shan,Rong Jiang,Yang Zhang,Lian-Hong Guo,Ren Zhang,Yuan Li 한국미생물학회 2009 The journal of microbiology Vol.47 No.2

Streptomyces sp. 139 generates a novel exopolysaccharide (EPS) designated as Ebosin, which exerts an antagonistic effect on IL-1R in vitro and anti-rheumatic arthritis activity in vivo. A ste gene cluster for Ebosin biosynthesis consisting of 27 ORFs was previously identified in our laboratory. In this paper, ste16 was expressed in Escherichia coli BL21 and the recombinant protein was purified, which has the ability to catalyze the transfer of the methyl group from S-adenosylmethionine (AdoMet) to dTDP-4-keto-6-deoxy-D-glucos, which was thus identified as a methyltransferase. In order to determine the function of ste16 in Ebosin biosynthesis, the gene was disrupted with a double crossover via homologous recombination. The monosaccharide composition of EPS-m generated by the mutant strain Streptomyces sp. 139 (ste16-) was found to differ from that of Ebosin. The IL-1R antagonist activity of EPS-m was markedly lower than that of Ebosin. These experimental results have shown that the ste16 gene codes for a methyltransferase which is involved in Ebosin biosynthesis.

Radiological gastrostomy: A comparative analysis of different image-guided methods

Hong-Tao Hu,Hang Yuan,Chen-Yang Guo,Quan-Jun Yao,Xiang Geng,Hong-Tao Cheng,Jun-Li Ma,Yan Zhao,Li Jiang,Yu-Qing Zhao,Hai-Liang Li 소화기인터벤션의학회 2021 Gastrointestinal Intervention Vol.10 No.2

Background: Radiographic guided percutaneous gastrostomy has become a safe and effective enteral nutrition method for patients who can not eat by mouth. Fluoroscopy, computed tomography (CT) and cone-beam CT have been routinely used clinically. The aim of this study was to compare the advantages and disadvantages of percutaneous gastrostomy using different radiographic guided methods. Methods: We retrospectively analyzed the clinical data of 538 patients undergoing percutaneous gastrostomy in our department. According to the image guidance method used in gastrostomy, the patients were divided into groups A by fluoroscopy guidance, group B by fluoroscopy combined with C-arm CT guidance, and group C with the whole process CT guidance. The gastrostomy success rate, complication rate, procedure time, and patient radiation dose were analyzed in the three groups. Results: Among 538 patients, 534 were successful and the success rates are 94.3%, 99.3%, and 100% in group A, B, and C, respectively (P > 0.05). There were 3 cases occurred postoperative bleeding as serious adverse events and transferred to surgical gastrostomy. The minor complications include local infection, hyperplasia of granulation tissue, tube obstruction or prolapse, and local pain of the ostomy. The minor complication rates were 10.5%, 10.4%, and 7.7% in group A, B, and C, respectively (P > 0.05). The average procedure time was 25.57 ± 5.99 minutes, 29.01 ± 6.63 minutes, and 45.47 ± 8.98 minutes, respectively (χ2 = 87.98, P < 0.001). The average radiation dosage was 27.30 ± 19.27 mGy, 145.07 ± 106.08 mGy, and 2,590.26 ± 1,088.22 mGy, respectively (χ2 = 204.44, P < 0.001). Conclusion: There were no significant differences in the success rates and complication rates of gastrostomy under the three guiding methods. For difficult cases, CT-guided gastrostomy may be a very useful supplemental method.

ACOUSTIC CLASSIFICATION OF URBAN PUBLIC UNDERGROUND SPACES

Hong Jiang,Hong Jin,Jian Kang 한국소음진동공학회 2008 한국소음진동공학회 국제학술대회논문집 Vol.2008 No.7

Feedback in Interpreter Training

Hong Jiang 한국통역번역학회 2011 통역과 번역 Vol.13 No.1

Interpreting is a complex skill, involving many sub-skills. For students to acquire the skills and develop from a novice to a journeyman, feedback is one important component of the training process. This presentation hopes to explore the relationship of feedback and skill development, the various forms of feedback and how they can be effectively used to contribute to students’ learning process.

Detection and Prognostic Analysis of Serum Protein Expression in Esophageal Squamous Cell Cancer

Jiang, Hong,Wang, Xiao-Hong,Yu, Xin-Min,Zheng, Zhi-Guo Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.4

Objective: To assess differences in serum proteins in esophageal squamous cell carcinoma patients. Methods: 144 esophageal squamous cell carcinoma patients and 50 healthy volunteers were included in this study, with surface-enhanced laser desorption-ionization time-of-flight mass spectrometry and weak cation exchange magnetic beads. Follow-up allowed the relations between serum proteins and prognosis to be analyzed. Results: A total of 93 protein peaks were detected (molecular weight range: 1500-30000), 10 demonstrating statistically significant differences. There were no differences in protein peaks between 92 patients with a survival more than 2 years and 52 patients with survival less than 2 years. There were two significantly different protein peaks between 45 stage II patients with a survival more than 2 years and 14 stage II patients with survival less than 2 years. There was one significantly different protein peak between 22 stage III patients with a survival more than 2 years and 29 stage III patients with survival less than 2 years. Conclusion: Differences of serum proteins in esophageal squamous cell carcinoma are related to prognosis of patients. The protein fingerprint can be helpful for clinical diagnosis and treatment.

A flow rate on-line monitoring method for piezoelectric pump based on self-sensing circuit

Hong Jiang,Guohui Wu,Lipeng He,Yuecheng Wang,Dianbin Hu,Zheng Zhang,Guangming Cheng 대한기계학회 2022 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.36 No.5

This paper presents a new flow rate monitoring method for a piezoelectric micropump based on a self-sensing circuit. Utilizing the voltage generated by the secondary direct piezoelectric effect as the sensing voltage, a soft sensor of the piezoelectric actuator can be implemented onto the piezoelectric micropump. A bridge-type circuit is proposed as the selfsensing circuit, the piezoelectric micropump is fabricated with a circular piezoelectric actuator, the characteristics of the self-sensing voltage and the flow rate are experimentally investigated under different excitation voltages and frequencies. The results show that the method can accurately determine optimal frequency of the micropump (100 Hz, 280 Hz), and for a fixed frequency of 100 Hz and a voltage range of 50-180 V, the correlation between the self-sensing voltage and the flow rate is 0.9732. As a result, the method demonstrated in this paper allows precise monitoring of the flow rate of the piezoelectric micropump without using external sensors.

A review on colorless and optically transparent polyimide films: Chemistry, process and engineering applications

Hong-jiang Ni,Jin-gang Liu,Zhen-he Wang,Shi-yong Yang 한국공업화학회 2015 Journal of Industrial and Engineering Chemistry Vol.28 No.-

Recent research and development of colorless and optically transparent polyimide (CPI) films have beenreviewed. CPI films possess both of the merits of conventional aromatic PI films and common polymeroptical film; thus have been widely investigated as components for microelectronic and optoelectronicfabrications. The current review coveres the latest research and development for CPI films, includingsynthesis chemistry, manufacturing process, and engineering applications. Especially, this reviewfocuses on the applications of CPI films as flexible substrates for optoelectrical devices, such as flexibleactive matrix organic light emitting display devices (AMOLEDs), flexible printing circuit boards (FPCBs),and flexible solar cells.

Radiological gastrostomy: A comparative analysis of different image-guided methods

Hong-Tao Hu,Hang Yuan,Chen-Yang Guo,Quan-Jun Yao,Xiang Geng,Hong-Tao Cheng,Jun-Li Ma,Yan Zhao,Li Jiang,Yu-Qing Zhao,Hai-Liang Li 소화기인터벤션의학회 2021 International journal of gastrointestinal interven Vol.10 No.2

Background: Radiographic guided percutaneous gastrostomy has become a safe and effective enteral nutrition method for patients who can not eat by mouth. Fluoroscopy, computed tomography (CT) and cone-beam CT have been routinely used clinically. The aim of this study was to compare the advantages and disadvantages of percutaneous gastrostomy using different radiographic guided methods. Methods: We retrospectively analyzed the clinical data of 538 patients undergoing percutaneous gastrostomy in our department. According to the image guidance method used in gastrostomy, the patients were divided into groups A by fluoroscopy guidance, group B by fluoroscopy combined with C-arm CT guidance, and group C with the whole process CT guidance. The gastrostomy success rate, complication rate, procedure time, and patient radiation dose were analyzed in the three groups. Results: Among 538 patients, 534 were successful and the success rates are 94.3%, 99.3%, and 100% in group A, B, and C, respectively (P > 0.05). There were 3 cases occurred postoperative bleeding as serious adverse events and transferred to surgical gastrostomy. The minor complications include local infection, hyperplasia of granulation tissue, tube obstruction or prolapse, and local pain of the ostomy. The minor complication rates were 10.5%, 10.4%, and 7.7% in group A, B, and C, respectively (P > 0.05). The average procedure time was 25.57 ± 5.99 minutes, 29.01 ± 6.63 minutes, and 45.47 ± 8.98 minutes, respectively (χ2 = 87.98, P < 0.001). The average radiation dosage was 27.30 ± 19.27 mGy, 145.07 ± 106.08 mGy, and 2,590.26 ± 1,088.22 mGy, respectively (χ2 = 204.44, P < 0.001). Conclusion: There were no significant differences in the success rates and complication rates of gastrostomy under the three guiding methods. For difficult cases, CT-guided gastrostomy may be a very useful supplemental method.

The infection status of anisakid larvae in marine fish and cephalopods from the Bohai Sea, China and their taxonomical consideration

Hong-Wei MA,Tai-Jing JIANG,Fu-Shi QUAN,Xiao-Guang CHEN,Hui-dong WANG,Yun-Shu ZHANG,Ming-Shan CUI,Wen-Yan ZHI,Dian-Chen JIANG 대한기생충학열대의학회 1997 The Korean Journal of Parasitology Vol.35 No.1