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.

Dynamic simulation and control of a triple column process for dimethyl carbonate- methanol separation

Hong-Mei Wei,Qiang Gao,Wei-zhou Jiao,Wei Wei 한국화학공학회 2022 Korean Journal of Chemical Engineering Vol.39 No.12

Separation of dimethyl carbonate/methanol azeotropic mixture by using pressure-swing distillation processhas been a hot-point in the study of the synthesis process of dimethyl carbonate by urea methanolysis method. Thisstudy updates the work of the writers (Ind.Eng.Chem.Res,2013,52,11463-11478), which explores the dynamic controlstructure of the three-column separation dimethyl carbonate (DMC)/methanol (MeOH) process from an actual pilotplant. At first, the conventional DMC/MeOH separation process in the pilot test of the DMC synthesis process throughalcoholysis of urea was described in detail. Then an optimized control structure for the entire DMC/MeOH separationunit was obtained by implementing a general heuristic design procedure. An economic analysis was performed to evaluatethe optimized process. Finally, three dynamic control schemes were proposed and evaluated with several large disturbances,an improved control scheme CS3, using the multiplier blocks “QR1/F1” and “RR1” in T1, “QR1/F1” and “R/F”in both T2 and T3, outperformed CS1 and CS2 by maintaining the product specification in each column.

hMSH2 and nm23 Expression in Sporadic Colorectal Cancer and its Clinical Significance

Wu, Hong-Wei,Gao, Li-Dong,Wei, Guang-Hui Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.3

Objective: To study the expression of the mismatch repair proteins hMSH2 and nm23 in sporadic colorectal cancer, determine any inter-relationship, and further investigate any clinical significance. Methods: Expression of hMSH2 and nm23 proteins was assessed in 87 colorectal cancer tissues by SP immunohistochemistry, with analysis of survival using follow-up data. Results: In the sporadic colorectal cancer tissues, nm23 protein expression appeared independent of the histological type (P>0.05), but correlated with the invasion depth and lymphatic metastasis (P<0.05). In contrast, hMSH2 protein expression was not significantly correlated with these clinicopathologic features (P>0.05), although it positively correlated with that of nm23 protein in the sporadic colorectal cancers (rs=0.635, P<0.05). Combined expression of the two was found to be related with invasion depth, lymphatic metastasis and prognosis of sporadic colorectal cancer (P<0.05). Conclusion: nm23 protein level was related with the degree of malignancy, and could be used as an index to predict the invasion and metastasis potential. The expression of hMSH2 protein is positively correlated that of nm23 protein, and the combined expression of the two has certain guiding significance for the prognosis of sporadic colorectal cancer.

The Cyclic Peptide Ecumicin Targeting ClpC1 Is Active against <i>Mycobacterium tuberculosis In Vivo</i>

Gao, Wei,Kim, Jin-Yong,Anderson, Jeffrey R.,Akopian, Tatos,Hong, Seungpyo,Jin, Ying-Yu,Kandror, Olga,Kim, Jong-Woo,Lee, In-Ae,Lee, Sun-Young,McAlpine, James B.,Mulugeta, Surafel,Sunoqrot, Suhair,Wang, American Society for Microbiology 2015 Antimicrobial Agents and Chemotherapy Vol.59 No.2

<P>Drug-resistant tuberculosis (TB) has lent urgency to finding new drug leads with novel modes of action. A high-throughput screening campaign of >65,000 actinomycete extracts for inhibition of <I>Mycobacterium tuberculosis</I> viability identified ecumicin, a macrocyclic tridecapeptide that exerts potent, selective bactericidal activity against <I>M. tuberculosis</I> <I>in vitro</I>, including nonreplicating cells. Ecumicin retains activity against isolated multiple-drug-resistant (MDR) and extensively drug-resistant (XDR) strains of <I>M. tuberculosis</I>. The subcutaneous administration to mice of ecumicin in a micellar formulation at 20 mg/kg body weight resulted in plasma and lung exposures exceeding the MIC. Complete inhibition of <I>M. tuberculosis</I> growth in the lungs of mice was achieved following 12 doses at 20 or 32 mg/kg. Genome mining of lab-generated, spontaneous ecumicin-resistant <I>M. tuberculosis</I> strains identified the ClpC1 ATPase complex as the putative target, and this was confirmed by a drug affinity response test. ClpC1 functions in protein breakdown with the ClpP1P2 protease complex. Ecumicin markedly enhanced the ATPase activity of wild-type (WT) ClpC1 but prevented activation of proteolysis by ClpC1. Less stimulation was observed with ClpC1 from ecumicin-resistant mutants. Thus, ClpC1 is a valid drug target against <I>M. tuberculosis</I>, and ecumicin may serve as a lead compound for anti-TB drug development.</P>

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.

Pre-operative Predictive Factors for Intra-operative Pathological Lymph Node Metastasis in Rectal Cancers

Gao, Chun,Li, Jing-Tao,Fang, Long,Wen, Si-Wei,Zhang, Lei,Zhao, Hong-Chuan Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.11

Background: A number of clinicopathologic factors have been found to be associated with pathological lymph node metastasis (pLNM) in rectal cancer; however, most of them can only be identified by expensive high resolution imaging or obtained after surgical treatment. Just like the Child-Turcotte-Pugh (CTP) and the model for end-stage liver disease (MELD) scores which have been widely used in clinical practice, our study was designed to assess the pre-operative factors which could be obtained easily to predict intra-operative pLNM in rectal cancer. Methods: A cohort of 469 patients who were treated at our hospital in the period from January 2003 to June 2011, and with a pathologically hospital discharge diagnosis of rectal cancer, were included. Clinical, laboratory and pathologic parameters were analyzed. A multivariate unconditional logistic regression model, areas under the curve (AUC), the Kaplan-Meier method (log-rank test) and the Cox regression model were used. Results: Of the 469 patients, 231 were diagnosed with pLNM (49.3%). Four variables were associated with pLNM by multivariate logistic analysis, age<60 yr (OR=1.819; 95% CI, 1.231-2.687; P=0.003), presence of abdominal pain or discomfort (OR=1.637; 95% CI, 1.052-2.547; P=0.029), absence of allergic history (OR=1.879; 95% CI, 1.041-3.392; P=0.036), and direct $bilirubin{\geq}2.60{\mu}mol/L$ (OR=1.540; 95% CI, 1.054-2.250; P=0.026). The combination of all 4 variables had the highest sensitivity (98.7%) for diagnostic performance. In addition, age<60 yr and direct $bilirubin{\geq}2.60{\mu}mol/L$ were found to be associated with prognosis. Conclusion: Age, abdominal pain or discomfort, allergic history and direct bilirubin were associated with pLNM, which may be helpful for preoperative selection.

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.

Study on the Hydrothermal Synthesis and Optical Properties of YVO4:Dy3+ Phosphor Powders

Hong-Tao Liu,Yan Liang,Xiao-Yong Gao,Sa Zhang,Xian-Wei Zhao,Xian-Mei Chen 한국물리학회 2013 THE JOURNAL OF THE KOREAN PHYSICAL SOCIETY Vol.63 No.8

YVO4:Dy3+ phosphor powders were synthesized by using the hydrothermal method under differentpH conditions. The crystallization, surface morphology, lattice vibration, optical properties,luminescent mechanism and influencing factors of the obtained YVO4:Dy3+ phosphor powders werecarefully studied and analyzed in detail. All of the YVO4:Dy3+ phosphor powders had tetragonalstructures, and the pH value had a significant impact on the surface morphology, structure andoptical properties of the synthesized samples. Strong acidic and alkali environments were favorablefor the crystallization of YVO4:Dy3+phosphor powders, and the YVO4:Dy3+ phosphor powderssynthesized under strong alkali environments had the best luminescent properties.

Novel SNPs in the bovine Transmembrane protein 18 gene, their linkage and their associations with growth traits in Nanyang cattle

Wei Ma,Yun Ma,Dong Liu,Yuan Gao,Xiao-mei Sun,Ai-min Li,Chun-lei Zhang,Hong Chen 한국유전학회 2012 Genes & Genomics Vol.34 No.6

Transmembrane protein 18 (TMEM18) gene is expressed in the central nervous system that has recently been linked to human obesity and body mass index (BMI) in genome wide association studies (GWAS). In this study, two novel single nucleotide polymorphisms (SNPs), g.3835 G > A (aa. Gly >Ser) and g.3865 A > G were detected in cattle TMEM18 gene by DNA sequencing. Polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) and forced PCR-RFLP methods were used to genotype the two SNPs in 1218 Chinese native cattle individuals. The association between novel SNPs and growth traits (especially on body weight and body height) in Nanyang cattle showed that individuals with GG genotype was higher than those with AA genotype at g.3835G>A locus (P < 0.05) in Nanyang cattle. Significant association also revealed that individuals of AA genotype at g. 3865 A>G locus were higher in terms of body weight, average daily gain, chest circunmference, body length (P < 0.05), body height and hucklebone width (P < 0.01) than GG genotypes in Nanyang cattle. Moreover, the effect of XspI-MluI combinations with growth traits in Nanyang cattle revealed that AAGG type had higher body weight, body length, chest circumference and average daily gain (P < 0.05)than GGAG in Nanyang cattle aged at 6 months.

Transactions : A Study on Varying Principle of Fiber Property in Pure Cotton Card Sliver Making Process

( Hong Wei Zhang ),( Dong Sheng Chen ),( Dong Mei Gao ),( Ya Bo Wan ) 한국의류산업학회 2006 Clothing Research Journal Vol.4 No.1