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.

Effects of temperature on the development, reproduction and population growth of Anaphothrips obscurus (Thysanoptera: Thripidae)

Hong-Xue Jiang,Xiao-Chen Zhang,Su-Huan Niu,Ji-Nian Feng 한국응용곤충학회 2016 Journal of Asia-Pacific Entomology Vol.19 No.4

Anaphothrips obscurus is a cosmopolitan pest feeding on cereals and other grasses. The effects of constant temperatures on the biology of A. obscurus are notwell known. Laboratory studieswere conducted to assess the effects of temperature on the development, survival, longevity, fecundity and population parameter of A. obscurus at six constant temperatures (15, 20, 25, 30, 32, 35 °C). The hatchability was the lowest at 15 °C, the highest at 25 °C and no eggs hatched at 35 °C. Developmental rates increased linearly as the temperature increased. The lower developmental threshold temperaturewas 10.6 °C and 200 degree-dayswere required to complete development from egg to adult. Adult longevity decreased with increasing temperature, and ranged from 68.87 d at 15 °C to 16.41 d at 32 °C. The highest total fecundity occurred at 20 °Cwith 162 eggs per female. The temperature-dependent total fecundity, age-specific oviposition rate, and age-specific survival rate models were described. The intrinsic rate of increase (rm) was significantly higher at 30 and 32 °C (0.239 and 0.250) than at other temperatures. This study suggests that optimal developmental and reproductive temperatures for A. obscurus ranges between 25 and 30 °C and this may help this species adapt to warmer areas and widen its distribution and potential for damage in response to global warming. These findings will also be useful in developing monitoring programs, population dynamic models, and timing of control measures for A. obscurus.

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.

ACOUSTIC CLASSIFICATION OF URBAN PUBLIC UNDERGROUND SPACES

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

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.

Alginate-Coated Thiolated Chitosan Microspheres for an Oral Drug Delivery System In Vitro

Jiang, Hu Lin,Arote, Rohidas B.,Quan, Ji Shan,Yoo, Mi Kyong,Kim, You Kyoung,Kim, In Yong,Hong, Zhong Shan,Lee, Hong Gu,Jin, Xun,Choi, Yun Jaie,Cho, Chong Su Trans Tech Publications, Ltd. 2007 Key Engineering Materials Vol.342 No.-

<P>Thiolated polymers have been studied by many researchers because of the mucoadhesive properties of thiol group. Alginate is a natural and biocompatible polymer that has been widely used in drug delivery. In this study, thiolated chitosan microspheres (TCMs) were prepared by ionic gelation process with tripolyphosphate and then, the bovine growth hormone (BGH) was loaded as a model drug. Finally, the BGH-loaded TCMs (BTCMs) were coated with alginate to improve the stability in gastrointestinal (GI) track. The alginate-coated BTCMs (ABTCMs) were observed as spherical shapes. The average particle sizes of ABTCMs were 6.97±0.55 -m and the sizedistribution was shown uniformly. Release of BGH from ABTCMs was decreased by coating with alginate and increased rapidly with the change in medium pH from 1.2 to 7.4. Results indicate that the ABTCMs have a potential as a drug carrier for oral drug delivery.</P>

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.

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.

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.

The Prognostic Value of CD8+ and CD45RO+ T Cells Infiltration and Beclin1 Expression Levels for Early Postoperative Cholangitis of Biliary Atresia Patients after Kasai Operation

Hong Jiang,Pengfei Gao,Huadong Chen,Zhihai Zhong,Man Shu,Zhichong Zhang,Jinbiao She,Juncheng Liu 대한의학회 2018 Journal of Korean medical science Vol.33 No.30

Background: Postoperative cholangitis is a common but severe complication after Kasai portoenterostomy for biliary atresia (BA). This study aimed to identify its prognostic factors Methods: Two sets of liver paraffin-embedded tissue samples were collected from BA patients who received Kasai portoenterostomy (n = 25 and n = 31, respectively). Patients were divided into non-cholangitis and cholangitis groups. The infiltration of CD4+ , CD8+ , CD45RO+ , CD68+ cells and expression of Beclin1 were quantitatively evaluated in immunohistochemical analysis. Results: Cholangitis group had a significantly lower CD8+ T cell infiltration but a higher CD45RO+ cell infiltration, and a lower Beclin1 level than non-cholangitis group (all P < 0.01). Multivariate logistic regression analysis indicated that infiltration of CD8+ cells (odds ratio [OR], 0.112; 95% confidence interval [CI], 0.022–0.577) and CD45RO+ cells (OR, 3.88; 95% CI, 1.37–11.03), and Beclin1 level (OR, 0.088; 95% CI, 0.018–0.452) were independent influence factors for early postoperative cholangitis. Receiver operating characteristic (ROC) analysis showed that area under ROC curve (AUROC) values for CD8+ cells, CD45RO+ cells and Beclin1 were 0.857, 0.738 and 0.900, respectively. Conclusion: Our findings demonstrated the CD8+ cells, CD45RO+ cells and Beclin1 level possessed the prognostic value for early postoperative cholangitis following Kasai operation, which may be helpful to develop new prevention and treatment strategies for postoperative cholangitis.