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.

A novel design method for improving collapse resistances of multi-story steel frames with unequal spans using steel braces

Zheng Tan,Wei-hui Zhong,Bao Meng,Shi-chao Duan,Hong-chen Wang3,Xing-You Yao,Yu-hui Zheng 국제구조공학회 2023 Steel and Composite Structures, An International J Vol.47 No.2

The bearing capacities resisted by the two-bay beams of multi-story planar frames with unequal spans under column removal scenarios differ considerably owing to the asymmetric stress on the left and right beams connected to the failed column and cause the potential for beams with larger span-to-depth ratios to be unable to exert effectively, which is disadvantageous for resisting the vertical load in unequal-span frame structures. To address this problem, the structural measure of adding braces to the weak bays of multi-story unequal-span frames was proposed, with the objective of achieving a coordinated stress state in two-bay beams with unequal spans, thereby improving the collapse resistance of unequal-span frame structures. Before conducting the numerical simulation, the modeling methods were verified by previous experimental results of two multi-story planar frames with and without steel braces. Thereafter, the effects of the tensile and compressive braces on the collapse behavior of the frame structures were elucidated. Then, based on the mechanical action laws of the braces throughout the collapse process, a detailed design method for improving the collapse resistance of unequal-span frame structures was proposed. Finally, the proposed design method was verified by using sufficient example models, and the results demonstrated that the design method has good application prospects and high practical value.

Analysis of Indoleamine 2-3 Dioxygenase (IDO) and EGFR Co-expression in Breast Cancer Tissue by Immunohistochemistry

Bi, Wei-Wei,Zhang, Wei-Hua,Yin, Gui-Hua,Luo, Hong,Wang, Shou-Qin,Wang, Hongran,Li, Chao,Yan, Wei-Qun,Nie, De-Zhi Asian Pacific Journal of Cancer Prevention 2014 Asian Pacific journal of cancer prevention Vol.15 No.14

Background: To determine the amount of co-expression of IDO and EGFR in breast cancer patients. Materials and Methods:In order to obtain the distribution of co-expression of IDO and EGFR in breast cancer, we tested 110 breast cancer paraffin tissue blocks with immunohistochemical methods. Then we investigated the relationship between the diagnostic and pathologic characteristics (tumor size, lymph node status, histologic grade, the gene expression of ER, PR, HER2, p53, Ki67 and PCNA) with the situation of co-expression of IDO and EGFR by reviewing the medical records of 32 breast cancer patients. Results: Among 110 breast cancers, 32 cases demonstrated IDO and EGFR co-expression (29.1%), IDO and EGFR synchronous co-expression being found in 19.1% and asynchronous in 10.0%. Conclusions: IDO and EGFR were co-expressed in breast cancer, including synchronous and asynchronous co-expression. The results suggest that considering IDO and EGFR as two indicators for breast cancer treatment or prognosis analysis provides a potential option of individual treatment for the portion of breast cancer patients with co-expression of IDO and EGFR.

RING Finger Proteins Are Involved in the Progression of Barrett Esophagus to Esophageal Adenocarcinoma: A Preliminary Study

( Xing Wei Wang ),( Wei Wei ),( Wei Qiang Wang ),( Xiao Yan Zhao ),( Hong Guo ),( Dian Chun Fang ) 대한소화기학회 2014 Gut and Liver Vol.8 No.5

Background/Aims: To investigate the differential expression of RING finger (RNF) proteins in Barrett esophagus (BE) and esophageal adenocarcinoma (EAC). Methods: The differential expression of RNFs in normal esophagus (NE), BE, and EAC was screened using microarray assay. Real-time quantitative polymerase chain reaction (PCR), tissue microarray assay, and Western blot analysis were independently performed to detect the mRNA and protein expression of screened RNFs. Results: The expression of nine RNFs in the BE or EAC was 2-fold higher than those in NE. Among these proteins, the RNF32 and RNF121 expression in BE was 20.3-fold and 16.4-fold higher, respectively, than that in NE, and the expression of RNF24, RNF130, RNF141, RNF139, RNF11, RNF14, and RNF159 was upregulated more than 2-fold compared with NE. The expression of nine RNFs was not only upregulated in the EAC but was also positively related to the RNF expression in BE. The PCR results also indicated increased expression of these RNFs in BE and EAC compared to NE. Furthermore, the mRNA expression of all RNFs, except for RNF141 in EAC, was dramatically higher than those in the BE. Similar results were also obtained from the Western blot analysis. Conclusions: A total of nine RNFs play critical roles in the progression of BE to EAC. (Gut Liver 2014;8:487-494)

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.

Stability Analysis and Dynamic Output Feedback Control for Nonlinear T-S Fuzzy System with Multiple Subsystems and Normalized Membership Functions

Wei Zheng,Zhi-Ming Zhang,Hong-Bin Wang,Hong-Rui Wang,Peng-Heng Yin 제어·로봇·시스템학회 2018 International Journal of Control, Automation, and Vol.16 No.6

This paper addresses the stability analysis and dynamic output-feedback control problems for a class of nonlinear Takagi-Sugeno (T-S) fuzzy systems with multiple subsystems and normalized membership functions. First, the switching control law of the membership function is proposed based on the membership function for the nonlinear T-S fuzzy subsystems. Secondly, the relaxation parameter is introduced into this switching control law to guarantee a minimal dwell time between two consecutive switching. Then, based on the proposed switching control law of the membership function and relaxation parameter, the dynamic output feedback controller with the estimate algorithm is designed to estimate the attraction domain. By introducing the new switched Lyapunov-Krasovskii functional, it can be seen that the solutions of the resultant closed-loop system converge to an adjustable bounded region. Compared with the previous works, the developed controller in this paper is flexible and smooth, which only uses the system output. And the results are further extended to the mobile robot case and the chemical process case. Finally, two simulation examples are performed to show the effectiveness of the theoretical results.

New Cytotoxic Sulfated Saponins from the Starfish Certonardoa semiregularis

Wang Wei Hong,Jang Hyo Jin,Hong Jong Ki,Lee Chong Ok,Bae Song Ja,Shin Sook,Jung Jee H. The Pharmaceutical Society of Korea 2005 Archives of Pharmacal Research Vol.28 No.3

Two new sulfated saponins designated as certonardosides P$_{2}$ and I$_{3}$ (1 and 2) were isolated from the brine shrimp active fraction of the MeOH extract of the starfish Certonardoa semiregularis. The structures were determined on the basis of spectral analysis. Compounds 1 and 2 were tested for cytotoxicity against five human tumor cell lines (A549, SK-OV-3, SK-MEL-2, XF498, and HCT15), and compound 1 displayed significant cytotoxicity against the SK-MEL-2 skin cancer cell.

DNA Microarray Probe Preparation by Gel Isolation Nested PCR

Wang, Hong-Min,Ma, Wen-li,Huang, Hai,Xiao, Wei-Wei,Wang, Yan,Zheng, Wen-Ling Korean Society for Biochemistry and Molecular Biol 2004 Journal of biochemistry and molecular biology Vol.37 No.3

To develop a simplified method that can rapidly prepare DNA microarray probes in a massive scale, a lambda phage genomic DNA-fragments library was constructed for the microarray-probes collection. Four methods of DNA band recovery from the first PCR products were tested and compared. The DNA microarray probes were collected by a novel method of nested PCR that was mediated by gel isolation of the first PCR products. This method was named GIN-PCR. The probes that were prepared by this GIN-PCR technique were used as subjects to fabricate a DNA microarray. The results showed that a wooden toothpick was superior to the other 3 methods, since this technique can steadily transfer the DNA bands as the template of the second PCR after the first PCR. A group of probes were successfully collected and DNA microarrays were constructed using these probes. Hybridization results demonstrated that this technique of DNA recovery and probe preparation was rapid, efficient, and effective. We developed a cost-effective and less labor-intensive method for DNA microarray probe preparation by nested PCR that is mediated by wooden toothpick transfer of the DNA bands in the gel after electrophoresis.

Carboxymethyl Flavonoids and A Monoterpene Glucoside from Selaginella moellendorffii

Hong-Sheng Wang,Ling Sun,Yue-Hu Wang,Ya-Na Shi,Gui-Hua Tang,Fu-Wei Zhao,Hong-Mei Niu,Chun-Lin Long,Ling Li 대한약학회 2011 Archives of Pharmacal Research Vol.34 No.8

A new dihydroflavone, 5-carboxymethyl-7,4'-dihydroxyflavonone (1), and its glucoside 5-carboxymethyl-7,4'-dihydroxyflavonone-7-O-β-D-glucopyranoside (2), and one new monoterpene glucoside, (4Z,6E)-2,7-dimethyl-8-hydroxyocta-4,6-dienoic acid 8-O-β-D-glucopyranoside (3), were isolated from the whole plants of Selaginella moellendorffii. Their structures were determined by spectroscopic methods and chemical transformation. Compound 2 was evaluated for the ability to enhance glucose consumption in normal and insulin-resistant L6 muscle cells induced by high concentrations of insulin and glucose. Glucose consumption in insulin-resistant cells (but not in normal cells) was increased 15.2 ± 3.3% (p < 0.01) by compound 2 at a concentration of 0.1 μM in the presence of insulin (1 nM).

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.