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.

Diagnostic Significance of Apparent Diffusion Coefficient Values with Diffusion Weighted MRI in Breast Cancer: a Meta-Analysis

Sun, Jiang-Hong,Jiang, Li,Guo, Fei,Zhang, Xiu-Shi Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.19

Aims: Apparent diffusion coefficient (ADC) values of nodes in diffusion-weighted imaging (DWI) are widely used in differentiating metastatic from non-metastatic lymph nodes. The purpose of this meta-analysis was to demonstrate whether DWI could contribute to the precise diagnosis of breast cancer (BC) with and without lymph node metastasis (LNM). Materials and Methods: English and Chinese electronic databases were searched for relevant studies followed by a comprehensive literature search. Two reviewers independently assessed the methodological quality of the included trials based on the quality assessment of diagnostic accuracy studies (QUADAS). Summary odds ratios (ORs) and corresponding 95% confidence intervals (95% CIs) were calculated. Results: Final analysis of 624 BC subjects (patients with LNM = 254, patients without LNM = 370) were incorporated into the current meta-analysis from 9 eligible cohort studies. Combined ORs of ADCs suggested that ADC values in BC patients without LNM were higher than in patients with LNM (OR=0.56, 95%CI: 0.11-1.01, p=0.015). Subgroup analysis stratified by country indicated a low ADC value in BC patients with LNM rather than those without LNM among Chinese (OR=1.27, 95%CI: 0.89-1.66, p<0.001), Italians (OR=0.75, 95%CI: 0.13-1.38, p=0.018), and Egyptians (OR=1.27, 95%CI: 0.71-1.84, p<0.001). The findings of subgroup analysis by MRI machine type revealed that ADC values from diffusion MRI may be potential diagnostic indicators for BC using Non-Philips 1.5T (OR=1.10, 95%CI: 0.84-1.36, p<0.001). Conclusions: The main findings of our meta-analysis demonstrated that increased signal intensity on DWI and decreased signals on ADC are helpful in diagnosis of BC patients with or without LNM. DWI could therefore be an important imaging investigation in patients suspected of BC.

EST-SSRs characterization and in-silico alignments with linkage map SSR loci in Grape (Vitis L.) genome

Hong Huang,Xia Xu,Xiaoqin Yang,Shuang Liang,Jiao Wu,Jiang Lu 한국유전학회 2012 Genes & Genomics Vol.34 No.1

11,581 grape (Vitis L.) EST-SSRs were produced and characterized from a total of 381,609 grape ESTs. Among the EST-SSRs, the tri repeat (5,560, 45.4%) represented the most abundant class of microsatellites in grape EST. Most of grape EST-SSR motifs fall within 18-24 bps in length. The EST-SSRs tri- repeats occurred a higher percentage in 5'-end (59.3%) than in 3'-end (48.3%). And EST-SSR tri- repeats had abundant codon repeats for putative amino acid runs as Proline, Arginine in grape ESTs. To better utilizing these markers, 142 of newly developed and validated EST SSR loci as well as 223 linkage map SSR loci were in silico aligned and mapped in grape genome. The orders of these SSR loci in the chromosomal physical locations and in the linkage groups were compared, and about twenty linkage map loci positions were switched or rearranged in grape genome. The EST-SSR markers extended the linkage map in grape genome. The method of in silico mapping reported in this study provided an initial collection for grape mapping resources. This approach offers great opportunities to understand the genetic variations in nucleotide sequences differences in physical map,and genetic recombination in linkage maps, as well as benefits for markers enrichment in a specific grape genome region for fine mapping or QTL mapping.

외국인 유학생 유치 정책에 대한 연구 및 제언

홍강 金泉大學 2018 논문집 Vol.39 No.-

Over 200,000 foreign students have arrived. The government started the policy of attracting people in the early 2000s. There are many achievements, but there are problems such as competition for competition, illegal stay. This study understands the policy of attracting and searching for development direction. This study first described the research purpose. Second, I introduced the status of foreign student stay. It started at 5,000, but now it has achieved great results. The government has launched many policies to attract talented workers. The 2020 budget for the "Invitation Program for Foreign Scholars Invited by the Government" is 200 billion won. The Study Korea Project started in 2001. The initial goal is 50,000, but now it is 200,000. The government has started the foreign student enrollment and management capacity certification system for the management of international students. And started policies for international student employment and start-up. Finally, I described my researchers' ideas. Implement policies consistently. Create an international student management system. Expand support policy to help employment and start-up. This study sought to describe policies and directions for attracting foreign students. This study helps attract foreign students and plan policies.

Comparison of developmental and reproductive biology inwing diphenic Anaphothrips obscurus (Thysanoptera: Thripidae)

Hong-Xue Jiang,Su-Huan Niu,Xiao-Wei Li,Xiao-Chen Zhang,Ji-Nian Feng 한국응용곤충학회 2015 Journal of Asia-Pacific Entomology Vol.18 No.4

Anaphothrips obscurus (Müller) is a cosmopolitan pest feeding on cereal crops and grasses. This species exhibits wing polyphenism. Differences in the life history traits of female macropterous and brachypterous A. obscurus were compared in the laboratory for this study. Experiments were performed in climate chambers set at 20 and 25 ± 1 °C, 60 ± 10% RH under a 16 L:8D photoperiod. The duration of total pre-adult stage, adult preoviposition period and total pre-oviposition period of macropterous morphs were significantly longer than in the brachypterous morphs both at 20 and 25 °C. No significant differenceswere found in adult longevity, survival rate or total fecundity between the twowingmorphs,while early fecunditywas significantly higher for brachypterous females compared with that for macropterous females at two temperatures.

Concurrent Engineering Based Collaborative Design Under Network Environment

Jiang Gongliang,Huang Hong-Zhong,Fan Xianfeng,Miao Qiang,Ling Dan The Korean Society of Mechanical Engineers 2006 JOURNAL OF MECHANICAL SCIENCE AND TECHNOLOGY Vol.20 No.10

Concurrent Engineering (CE) is a popular method employed in product development. It treats the whole product design process by the consideration of product quality, cost, rate of progress, and demands of customers. The development of computer and network technologies provides a strong support to the realization of CE in practice. Aiming at the characteristics of CE and network collaborative design, this paper built network collaborative design system frame. Through the analysis of the network collaborative design modes based on CE, this paper provided a novel network collaborative design integration model. This model can integrate the product design information, design process, and knowledge. Intelligent collaboration was considered in the proposed model. The study showed that the proposed model considered main factors such as information, knowledge, and design process in collaborative design. It has potential application in CE fields.

A new role of substance P as an injury-inducible messenger for mobilization of CD29⁺ stromal-like cells

Hong, Hyun Sook,Lee, Jungsun,Lee, EunAh,Kwon, Young Sam,Lee, Eunkyung,Ahn, Woosung,Jiang, Mei Hua,Kim, Jae Chan,Son, Youngsook Nature Publishing Group 2009 Nature medicine Vol.15 No.4

Tissue injury may create a specific microenvironment for inducing the systemic participation of stromal-like cells in the repair process. Here we show that substance P is an injury-inducible factor that acts early in the wound healing process to induce CD29<SUP>+</SUP> stromal-like cell mobilization. Likewise, mobilization of such cells also occurs in uninjured mice, rats and rabbits if substance P is intravenously injected. Upon further characterization these substance P–mobilized CD29<SUP>+</SUP> cells were found to be similar to stromal cells from a number of connective tissues, including bone marrow (that is, bone marrow stromal cells, or BMSCs). Both substance P injection and transfusion of autologously derived substance P–mobilized CD29<SUP>+</SUP> cells from uninjured rabbits accelerated wound healing in an alkali burn model. Also, epithelial engraftment of the transfused cells into the injured tissue occurred during the wound healing. Finally, using human BMSCs as a test population, we show that substance P stimulates transmigration, cell proliferation, activation of the extracellular signal–related kinases (Erk) 1 and 2 and nuclear translocation of β-catenin in vitro. This finding highlights a previously undescribed function of substance P as a systemically acting messenger of injury and a mobilizer of CD29<SUP>+</SUP> stromal-like cells to participate in wound healing.

Molecular Cloning and Characterization of a New C-type Lysozyme Gene from Yak Mammary Tissue

Jiang, Ming Feng,Hu, Ming Jun,Ren, Hong Hui,Wang, Li Asian Australasian Association of Animal Productio 2015 Animal Bioscience Vol.28 No.12

Milk lysozyme is the ubiquitous enzyme in milk of mammals. In this study, the cDNA sequence of a new chicken-type (c-type) milk lysozyme gene (YML), was cloned from yak mammary gland tissue. A 444 bp open reading frames, which encodes 148 amino acids (16.54 kDa) with a signal peptide of 18 amino acids, was sequenced. Further analysis indicated that the nucleic acid and amino acid sequences identities between yak and cow milk lysozyme were 89.04% and 80.41%, respectively. Recombinant yak milk lysozyme (rYML) was produced by Escherichia coli BL21 and Pichia pastoris X33. The highest lysozyme activity was detected for heterologous protein rYML5 (M = 1,864.24 U/mg, SD = 25.75) which was expressed in P. pastoris with expression vector $pPICZ{\alpha}A$ and it clearly inhibited growth of Staphylococcus aureus. Result of the YML gene expression using quantitative polymerase chain reaction showed that the YML gene was up-regulated to maximum at 30 day postpartum, that is, comparatively high YML can be found in initial milk production. The phylogenetic tree indicated that the amino acid sequence was similar to cow kidney lysozyme, which implied that the YML may have diverged from a different ancestor gene such as cow mammary glands. In our study, we suggest that YML be a new c-type lysozyme expressed in yak mammary glands that plays a role as host immunity.

Quantitative trait loci for cold tolerance of rice recombinant inbred lines in low temperature environments

Jiang, Wenzhu,Jin, Yong-Mei,Lee, Joohyun,Lee, Kang-Ie,Piao, Rihua,Han, Longzhi,Shin, Jin-Chul,Jin, Rong-De,Cao, Tiehua,Pan, Hong-Yu,Du, Xinglin,Koh, Hee-Jong Springer-Verlag 2011 Molecules and cells Vol.32 No.6

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.