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.

Identification of candidate odorant‐degrading enzyme genes in the antennal transcriptome of Aphidius gifuensis

Kang Zhi‐Wei,Liu Fang‐Hua,Xu Yong‐Yu,Cheng Jia‐Hui,Lin Xiao‐Li,Jing Xiang‐Feng,Tian Hong‐Gang,Liu Tong‐Xian 한국곤충학회 2021 Entomological Research Vol.51 No.1

Odorant‐degrading enzymes (ODEs) have been found in insect antennae and play a critical role in signal chemical degradation once the message is conveyed. Significant progress has been made in characterizing ODEs in a variety of pests but very little is known in their natural enemies. We have carried out an antennae‐ and sex‐specific transcriptome of Aphidius gifuensis, a natural enemy of aphid, to identify the candidate ODEs. Based on the antennae‐ and sex‐specific transcriptome, a total of 100 putative ODEs were identified including one aldehyde oxidase (AOX), four alcohol dehydrogenases (ADs), eight UDP‐glucuronosyltransferases (UGTs), 45 cytochrome P450 (P450s), nine glutathione S‐transferases (GSTs) and 40 carboxylesterases (CCEs or CXEs). Additionally, we used RT‐qPCR to determine the expression profiles of these genes in tissues of both sexes. Based on the phylogenic analysis and tissue‐expression patterns, AgifEstE4, AgifCXE3, AgifCCE4, AgifCCE7, and AgifCCE18 were suggested as key ODEs in A. gifuensis. In addition, the female or male specifically enriched genes, such as AgifCCE17, AgifEstB1, AgifCYP18a1, AgifUGT2C2, were also considered to involve in the chemosensory processing in A. gifuensis. This study not only identified the candidate ODEs in A. gifuensis but also provided source for further exploration of the molecular mechanisms of chemical signal transductions in A. gifuensis, as well as other hymenopteran species.

Clinical Profles and Short-Term Outcomes of Acute Disseminated Encephalomyelitis in Adult Chinese Patients

Hong-Qi Yang,Wen-Cong Zhao,Wei-Min Yang,Yong-Li Li,Zhi-Kun Sun,Shuai Chen,Wei Li,Jian-Jun Ma 대한신경과학회 2016 Journal of Clinical Neurology Vol.12 No.3

Background and PurposezzAcute disseminated encephalomyelitis (ADEM) is an infammatory demyelinating disorder that predominantly afects children. Previous studies have mostly involved children in Western developed countries. MethodszzTis study retrospectively reviewed the clinical profles of ADEM in adult Chinese patients. ResultszzADEM occurred during summer and autumn in about two-thirds of the 42 included patients. Prior infection was found in fve patients and no preimmunization was recorded. Te most frequent clinical presentations were alterations in consciousness (79%) and behavior changes (69%), followed by motor defcits (64%) and fever (50%). About one-quarter (26%) of the patients showed positive results for oligoclonal bands, and about half of them exhibited increases in the IgG index and 24-hour IgG synthesis rate. Magnetic resonance imaging showed white- and gray-matter lesions in 83% and 23% of the patients, respectively. Steroids were the main treatment, and full recovery occurred in 62% of the patients, with residual focal neurological defcits recorded in a few patients. Afer a mean follow-up period of 3.4 years, two patients exhibited recurrence and one patient exhibited a multiphasic course. One patient was diagnosed with multiple sclerosis (MS). ConclusionszzWith the exception of the seasonal distribution pattern and prior vaccine rate, the clinical profles of ADEM in adult Chinese patients are similar to those in pediatric populations. No specifc markers are available for distinguishing ADEM from MS at the initial presentation. Careful clinical evaluations, cerebrospinal fuid measurements, and neuroradiological examinations with long-term follow-up will aid the correct diagnosis of ADEM.

Rapid Identification of Bifidobacteria in Dairy Products by Gene-targeted Species-specific PCR Technique and DGGE

Hong, Wei-Shung,Chen, Ming-Ju Asian Australasian Association of Animal Productio 2007 Animal Bioscience Vol.20 No.12

In this paper, a rapid and reliable gene-targeted species-specific polymerase chain reaction (PCR) technique based on a two-step process was established to identify bifidobacteria in dairy products. The first step was the PCR assay for genus Bifidobacterium with genus specific primers followed by the second step, which identified the species level with species-specific primer mixtures. Ten specific primer pairs, designed from nucleotide sequences of the 16-23S rRNA region, were developed for the Bifidobacterium species including B. angulatum, B. animalis, B. bifidum, B. breve, B. catenulatum, B. infantis, B. longum, B. minimum, B. subtile, and B. thermophilum. This technique was applied to the identification of Bifidobacterium species isolated from 6 probiotic products, and four different Bifidobacterium spp. (B. bifidum, B. longum, B. infantis, and B. breve) were identified. The findings indicated that the 16S-23S rDNA gene-targeted species-specific PCR technique is a simple and reliable method for identification of bifidobacteria in probiotic products. PCR combined with Denaturing Gradient Gel Electrophoresis (DGGE) for identification of the bifidobacteria was also evaluated and compared with the gene-targeted species-specific technique. Results indicated that for fermented milk products consistency was found for both species-specific PCR and PCR-DGGE in detecting species. However, in some lyophilized products, the bands corresponding to these species were not visualized in the DGGE profile but the specific PCR gave a positive result.

Synthesis of 2,5-Disubstituted Pyrrolidines from N-Alkenyl and Alkynyl N-Benzoyloxysulfonamides Catalyzed by (CuOTf)2・C6H6

Wei-Min Liu,Zhen-Hong Liu,Wei-Wen Cheong,Lu-Yi Teo Priscilla,Yongxin Li,Koichi Narasaka 대한화학회 2010 Bulletin of the Korean Chemical Society Vol.31 No.3

A new synthetic method of 2,5-disubstituted pyrrolidines is developed by the cyclization of unsaturated N-benzoyloxysulfonamides by (CuOTf)2·C6H6 in refluxing dichloroethane. Various N-4- and N-5-alkenyl and alkynyl N-benzoyloxysulfonamides are cyclized to give pyrrolidines. The cyclization proceeds via addition of sulfonamidoyl radicals to intramolecular unsaturated bonds or allylic hydrogen abstraction with the radical intermediates.

Blind Source Separation of Instantaneous Mixture of Delayed Sources Using High-Order Taylor Approximation

Wei Zhao,Zhi-Gang Yuan,Yue-hong Shen,Yufan Cao,Yimin Wei,Pengcheng Xu,Wei Jian 한국전자통신연구원 2015 ETRI Journal Vol.37 No.4

This paper deals with the problem of blind source separation (BSS), where observed signals are a mixture of delayed sources. In reference to a previous work, when the delay time is small such that the first-order Taylor approximation holds, delayed observations are transformed into an instantaneous mixture of original sources and their derivatives, for which an extended second-order blind identification (SOBI) approach is used to recover sources. Inspired by the results of this previous work, we propose to generalize its first-order Taylor approximation to suit higher-order approximations in the case of a large delay time based on a similar version of its extended SOBI. Compared to SOBI and its extended version for a first-order Taylor approximation, our method is more efficient in terms of separation quality when the delay time is large. Simulation results verify the performance of our approach under different time delays and signal-to-noise ratio conditions, respectively.

Herbal formula (Danggui Beimu Kushen Wan) for prostate disorders: a systematic review of classical literature

Hong Li,Andrew Hung,Angela Wei Hong Yang 한국한의학연구원 2019 Integrative Medicine Research Vol.8 No.4

Background: Danggui Beimu Kushen Wan (DBKW) was initially known for difficult urination in pregnancy and has been widely used for prostate disorders in modern days. This study aimed to comprehensively investigate the implications of DBKW in traditional evidence. Methods: The Encyclopedia of Traditional Chinese Medicine was searched to identify the ingredients, dosage, etiologies, pathogeneses, actions and indications related to DBKW documented in ancient books. Descriptive summary was provided to their characteristics. Results: A total of 41 texts in 36 classic books were included. Two etiologies and 10 pathogeneses were investigated. All the identified formulas contain Angelicae Sinensis Radix, Fritillariae Thunbergii Bulbus and Sophorae Flavescentis Radix with the ratio of 1:1:1. The treatment dosage is three to 10 pills each time. The primary indication of DBKW is difficult urination with heat stagnation. Nine included texts specified that this formula could also be used for male. Conclusion: Included classic literature has provided fundamental evidence for the management of difficult urination in female and male. Further studies should investigate its mechanisms of actions for difficult urination related conditions, such as prostate disorders.

A conjugated polyazine containing diketopyrrolopyrrole for ambipolar organic thin film transistors

Hong, Wei,Sun, Bin,Aziz, Hany,Park, Won-Tae,Noh, Yong-Young,Li, Yuning The Royal Society of Chemistry 2012 Chemical communications Vol.48 No.67

<P>A π-conjugated polyazine containing diketopyrrolopyrrole (DPP) moiety, PDBTAZ, is synthesized through a simple condensation polymerization. PDBTAZ is found to be a high-performance ambipolar semiconductor in organic thin film transistors (OTFTs), showing an electron mobility of up to 0.41 cm<SUP>2</SUP> V<SUP>−1</SUP> s<SUP>−1</SUP> and a hole mobility of up to 0.36 cm<SUP>2</SUP> V<SUP>−1</SUP> s<SUP>−1</SUP>.</P> <P>Graphic Abstract</P><P>A π-conjugated polyazine containing diketopyrrolopyrrole (DPP) moiety shows high-performance in ambipolar organic thin film transistors. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=c2cc33998f'> </P>

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.

Concurrent Weekly Docetaxel Chemotherapy in Combination with Radiotherapy for Stage III and IVA-B Nasopharyngeal Carcinoma

Wei, Wei-Hong,Cai, Xiu-Yu,Xu, Tao,Zhang, Guo-Yi,Wu, Yong-Feng,Feng, Wei-Neng,Lin, Li,Deng, Yan-Ming,Lu, Qiu-Xia,Huang, Zhe-Li Asian Pacific Journal of Cancer Prevention 2012 Asian Pacific journal of cancer prevention Vol.13 No.3

Background and Purpose: Cisplatin is the most common chemotherapeutic agent for loco-regionally advanced nasopharyngeal carcinoma (NPC); however, toxicity is a limiting factor for some patients. We retrospectively compared the efficacy and toxicity of weekly docetaxel-based and cisplatin-based concurrent chemoradiotherapy in loco-regionally advanced NPC. Methods and Materials: Eighty-four patients with Stage III and IVA-B NPCs, treated between 2007 and 2008, were retrospectively analyzed. Thirty received weekly docetaxel-based concurrent chemotherapy, and 43 were given weekly cisplatin-based concurrent chemotherapy. Radiotherapy was administered using a conventional technique (seven weeks, 2.0 Gy per fraction, total dose 70-74 Gy) with 6-8 Gy boosts for some patients with locally advanced disease. Results: Median follow-up time was 42.3 months (range, 8.6-50.8 months). There were no significant differences in the 3-year loco-regional failure-free survival (85.6% vs. 92.3%; p=0.264), distant failure-free survival (87.0% vs. 92.5%; p=0.171), progression-free survival (85.7% vs. 88.4%; p=0.411) or overall survival (86.5% vs. 92.5%, p=0.298) of patients treated concurrently with docetaxel or cisplatin. Severe toxicity was not common in either group. Conclusions: Weekly docetaxel-based concurrent chemoradiotherapy is potentially effective and has a tolerable toxicity; however, further investigations are required to determine if docetaxel is superior to cisplatin for advanced stage NPC.