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.

Thermal Immune NiGermanide for High Performance Ge MOSFETs on Ge-on- Si Substrate Utilizing <tex> $ \hbox{Ni}_{0.95}\hbox{Pd}_{0.05}$</tex> Alloy

Ying-Ying Zhang,Jungwoo Oh,In-Shik Han,Zhun Zhong,Shi-Guang Li,Soon-Yen Jung,Kee-Young Park,Hong-Sik Shin,Won-Ho Choi,Hyuk-Min Kwon,Wei-Yip Loh,Majhi, P.,Jammy, R.,Hi-Deok Lee IEEE 2009 IEEE transactions on electron devices Vol.56 No.2

<P>Highly thermally stable Ni germanide technology for high performance germanium metal-oxide-semiconductor field-effect transistors (Ge MOSFETs) is proposed, utilizing Pd incorporation into Ni germanide. The proposed Ni germanide shows not only the improvement of thermal stability but also the reduction of hole barrier height, which can improve the device on-current by reducing the Ni germanide to p+ source/drain contact resistance. The proposed Ni germanide showed a stable sheet resistance of up to 500 degrees C 30-min postgermanidation annealing due to the suppression of agglomeration and oxidation of Ni germanide and the diffusion of Ni and Ge atoms by the incorporated Pd. Therefore, the proposed Ni0.95Pd0.05, alloy could be promising for the high mobility Ge MOSFET applications.</P>

Constituents from Zhuyeqing Liquor with hepatoprotective effect on alcohol-induced HepaG 2 toxicity

Hong-Ying Gao,Guo-Yu Li,Hang-Yu Wang,Jian Huang,Xiao-Wei Du,Ying Han,Li-Fei Wang,Jin-Hui Wang 대한약학회 2015 Archives of Pharmacal Research Vol.38 No.5

An unprecedented new skeleton compound (1R,10R, 11S)-10,11-dimethyl-4-formyl-2,9-dioxa-bicyclo [5.4.0]undeca-4,6-dien-3-one (1), monoterpenoids and monoterpeneglycoside picrocrocinic ester (2), epijasminoside B (3) and 60 -O-(3-methoxyl-4-hydroxyl-coumaroyl)-epijasminoside B (4),along with 26 known compounds, were obtained fromZhuyeqing Liquor. These compounds were identified mainlyby analyzing their NMR, HR-ESI–MS and CD data. The isolatedcompounds were screened against alcohol induced HepaG2 toxicity for hepatoprotective assay. Compounds 10, 19,21 and 26 displayed the highest potency against alcoholinduced HepaG 2 toxicity with the cell viability ratio 41.21,56.91, 67.69 and 70.32 % respectively.

Enhancing mucosal immunity in mice by recombinant adenovirus expressing major epitopes of porcine circovirus-2 capsid protein delivered with cytosine-phosphate-guanosine oligodeoxynucleotides

Hong-tao Chang,Xiu-yuan He,Yu-Feng Liu,Lu Chen,Quan-hai Guo,Qiu-ying Yu,Jun Zhao,Xin-wei Wang,Xia Yang,Chuan-qing Wang 대한수의학회 2014 Journal of Veterinary Science Vol.15 No.3

A recombinant replication-defective adenovirus expressingthe major epitopes of porcine circovirus-2 (PCV-2) capsidprotein (rAd/Cap/518) was previously constructed and shownto induce mucosal immunity in mice following intranasaldelivery. In the present study, immune responses induced byintranasal immunization with a combination of rAd/Cap/518and cytosine-phosphate-guanosine oligodeoxynucleotides(CpG ODN) were evaluated in mice. The levels ofPCV-2-specific IgG in serum and IgA in saliva, lung, andintestinal fluids were significantly higher in the groupimmunized with rAd/Cap/518 and CpG ODN than animalsimmunized with rAd/Cap/518 alone. The frequencies ofIL-2-secreting CD4+ T cells and IFN-γ-producing CD8+ T cellswere significantly higher in the combined immunizationgroup than mice immunized with rAd/Cap/518 alone. Thefrequencies of CD3+, CD3+CD4+CD8−, and CD3+CD4−CD8+T cells in the combined immunization group were similar tothat treated with CpG ODN alone, but significantly higherthan mice that did not receive CpG ODN. PCV-2 load afterchallenge in the combined immunization group wassignificantly lower than that in the phosphate-buffered salineplacebo group and approximately 7-fold lower in the grouptreated with CpG ODN alone. These results indicate thatrAd/Cap/518 combined with CpG ODN can enhance systemicand local mucosal immunity in mice, and represent apromising synergetic mucosal vaccine against PCV-2.

Inhibition of cancer cell growth and migration by dihydroxynaphthyl aryl ketones

Wei Xiong,Yun-Feng Li,Shan Liu,Ting Chen,Hong-Tao Zhang,Zhi-Bin Yang,Ying-Ying Ding,De-Pei Gao,Guan-Shun Wang,Jian Dong,Jian Dong 대한독성 유전단백체 학회 2016 Molecular & cellular toxicology Vol.12 No.4

Dihydroxynaphthyl aryl ketones 1-5 exhibit activity as tubulin polymerization inhibitors by targeting the colchicine binding site of microtubules making them potential anticancer drugs. Therefore, analogues 1-5 have been evaluated for their cytotoxic activity against the cancer cell lines DU-145 (prostate), T24 (bladder) and MCF-7 (breast). notable differences in biological activity were observed for compounds 1-5, most likely related to the nature of the aryl substituent bonded to the carbonyl group. among the tested compounds, only compound 5 showed selectivity for cancer cells over healthy, non-transformed cells. T24 cancer cells treated with compound 5 presented a concentration-dependent decrease in cell proliferation and a loss of migration ability. The cytotoxicity of compounds 1-5 on the selected cell-based assays is discussed in terms of it lipophilicity and polarizability parameters.

RESEARCH PAPERS : Effect of Impeller Blade Number on KLa in Mechanically Agitated Vessels

(Wei Ming Lu),(Hong Zhang Wu),(Cheng Ying Chou) 한국화학공학회 1999 Korean Journal of Chemical Engineering Vol.16 No.5

Effects of impeller blade number on gas dispersion and mass transfer rate were thoroughly investigated for mechanically agitated vessels equipped with 2-, 4-, 6- and 8-straight blades disk turbine impellers. The results show that under the same rotational speed, the impeller with more blades always can disperse gas more effectively, which induces a higher value of $lt;K_La$gt;. However, with the same total power consumption, the 4-blade impeller can obtain a higher $lt;K_La$gt; value than the 6- and 8-blade impellers under a lower gassing rate condition (Q-g$lt;0.5vvm), but if Q_g) exceeds 0.5vvm, the 6-blade impeller will perform better than the 4- and 8- blade impellers. To examine the results obtained from the single impeller systems, the same approach is applied to measure $lt;K_La$gt; values for the triple stage 6-blade impeller system (3×6) and quadruple stage 4-blade impeller system (4×4). From the experimental results, it can be found that the 4×4 system gives higher $lt;K_La$gt; value than the 3×6 system under gas completely dispersed conditions. By correlating $lt;K_La$gt; with n_b, N and V_s, the following correlation can be given as: $lt;K_La$gt; = 0.00119n^(0.62)_bN^(1.56)V^(0.4)_s $lt;K_La$gt; = 0.0297n^(0.1)_b(P_s/V)^(0.34)V^(0.48)_s These two correlations can also be used to evaluate the mass transfer coefficient of each impeller region for the multiple impeller systems and the deviation is always less than 10%.

Radiofrequency Ablation Combined with Transcatheter Arterial Chemoembolization Therapy Versus Surgical Resection for Hepatocellular Carcinoma within the Milan Criteria: A Meta-Analysis

Wei-dong Wang,Li-hua Zhang,Jia-Yan Ni,Xiong-ying Jiang,Dong Chen,Yao-ting Chen,Hong-liang Sun,Jiang-hong Luo,Lin-feng Xu 대한영상의학회 2018 Korean Journal of Radiology Vol.19 No.4

Objective: To meta-analytically compare combined transarterial chemoembolization (TACE) plus radiofrequency ablation (RFA) and surgical resection (SR) for the treatment of hepatocellular carcinoma (HCC) within the Milan criteria. Materials and Methods: PubMed, Medline, Embase, and Cochrane Library were searched for studies comparing these two therapies that were published between January 2006 and August 2017. Overall survival rate (OS), recurrence-free survival rate (RFS), major complications and the average length of hospital stay were compared between these two therapies. Metaanalytic pooled odds ratio (OR) was calculated using TACE plus RFA as the base category. Results: Seven case-control studies and one randomized trial were identified. Meta-analytic results revealed that, compared with SR, TACE plus RFA had significantly higher 1-year OS (OR for survival = 0.50, p = 0.009) and lower major complications (OR = 1.88, p = 0.02) after therapy. Three studies reported on the length of hospital stay. The average length ± standard deviation reported in individual studies for SR and TACE plus RFA groups was 19.8 ± 8.4 days and 7.4 ± 2.2 days, respectively; 18.7 ± 4.9 days and 11.5 ± 6.9 days, respectively; and 16.6 ± 6.7 days and 8.5 ± 4.1 days, respectively (p < 0.0001 for all studies). Three or 5-year OS and 1-, 3-, or 5-year RFS did not significantly differ between the two therapies. Conclusion: Combined TACE plus RFA may be an alternative to SR for the treatment of patients with HCC within Milan the criteria. Non-randomized design in most of the original studies was a limitation.

Tick-Borne Pathogens in Ixodid Ticks from Poyang Lake Region, Southeastern China

Wei Qing Zheng,Xue Nan Xuan,Ren Long Fu,Hui Ying Tao,Yang Qing Liu,Xiao Qing Liu,Dong Mei Li,Hong Mei Ma,Hai Ying Chen 대한기생충학열대의학회 2018 The Korean Journal of Parasitology Vol.56 No.6

Study on Thermodynamics of Three Kinds of Benzindocarbocyanine Dyes in Aqueous Methanol Solution

Wei Huang,Lan-Ying Wang,Yi-Le Fu,Ji-Quan Liu,You-Ni Tao,Fang-Li Fan,Gao-Hong Zhai,Zhen-Yi Wen 대한화학회 2009 Bulletin of the Korean Chemical Society Vol.30 No.3

Aggregation behavior of three kinds of benzindocarbocyanine dyes in aqueous methanol solution was studied by UV-Vis absorption spectrum. The results indicated that the three dyes all existed monomer-dimer equilibrium in aqueous methanol solution (concentration range 10−5 to 10−6 M) at 25.0~41.0 °C for Dye 1, 28.0~49.0 oC for Dye 2 and 26.0~47.0 °C for Dye 3. The fundamental property of the three dyes as the dimeric association constant KD, the dimeric free energy ΔGD, the dimeric entropy ΔSD, and the dimeric enthalpy ΔHD were determined. The ΔHD of three dyes: Dye 1, Dye 2 and Dye 3 was -42.5, -15.1 and -18.9 kJ/mol, respectively. The experimental observations were the subject of a theoretical study including the ground-state geometries which were fully optimized using DFT at B3LYP/6-31G level. The effect of dye molecule structure on ΔHD was discussed by theoretical calculations.

A Discovery of Low Hydraulic Resistance Channel Along Meridians

Wei-Bo Zhang,Yu-Ying Tian,Hong Li,Jia-He Tian,Ming-Fu Luo,Fa-Liang Xu,Guang-Jun Wang,Tao Huang,Yi-Hui Xu,Rui-Hong Wang 사단법인약침학회 2008 Journal of Acupuncture & Meridian Studies Vol.1 No.1

A hydro-mechanic model was put forward to study the fundamental nature of acupuncture meridians. The basic state of low hydraulic resistance was tested on humans and mini pigs using three methods. The first, a modified Guyton’s method, proved that there was lower hydraulic resistance on meridians compared with nonmeridians. The second scanning method involved a single pressure transducer that can find the lowest resistance point in tissue, and the third method used two transducers and provided a more stable measurement. Using the latter method, low hydraulic resistance points were found very close to low impedance points along meridians. The transmission of artificial interstitial fluid pressure waves was measured to examine their connection to the low resistance points, with the result that a good connection between the points was confirmed. This means the points form channels along the meridians that we refer to as low hydraulic resistance channels. The channel was imaged through isotopic tracing and a migration of isotope 99mTe could be found along the channel. The layer of the channel was detected by injecting Alcian blue and the track was found beneath the skin. All of the above experiments suggest the existence of a new type of channel in living tissues that has not yet been described in modern science, but coincides quite well with the Qi channel theory of traditional Chinese medicine. A hydro-mechanic model was put forward to study the fundamental nature of acupuncture meridians. The basic state of low hydraulic resistance was tested on humans and mini pigs using three methods. The first, a modified Guyton’s method, proved that there was lower hydraulic resistance on meridians compared with nonmeridians. The second scanning method involved a single pressure transducer that can find the lowest resistance point in tissue, and the third method used two transducers and provided a more stable measurement. Using the latter method, low hydraulic resistance points were found very close to low impedance points along meridians. The transmission of artificial interstitial fluid pressure waves was measured to examine their connection to the low resistance points, with the result that a good connection between the points was confirmed. This means the points form channels along the meridians that we refer to as low hydraulic resistance channels. The channel was imaged through isotopic tracing and a migration of isotope 99mTe could be found along the channel. The layer of the channel was detected by injecting Alcian blue and the track was found beneath the skin. All of the above experiments suggest the existence of a new type of channel in living tissues that has not yet been described in modern science, but coincides quite well with the Qi channel theory of traditional Chinese medicine.