Effects of Supplementary Composts on Microbial Communities and Rice Productivity in Cold Water Paddy Fields

( Kai Zhi Xie ),( Pei Zhi Xu ),( Shao Hai Yang ),( Yu Sheng Lu ),( Rui Ping Jiang ),( Wen Jie Gu ),( Wen Ying Li ),( Li Li Sun ) 한국미생물 · 생명공학회 2015 Journal of microbiology and biotechnology Vol.25 No.5

Cold water paddy field soils are relatively unproductive, but can be ameliorated by supplementing with inorganic fertilizer from animal waste-based composts. The yield of two rice cultivars was significantly raised by providing either chicken manure or cow dung-based compost. The application of these composts raised the soil pH as well as both the total nitrogen and ammonium nitrogen content, which improved the soil’s fertility and raised its nitrification potential. The composts had a measurable effect on the abundance of nitrogencycling- related soil microbes, as measured by estimating the copy number of various bacterial and archaeal genes using quantitative real-time PCR. The abundance of ammonia oxidizing archaea and bacteria was markedly encouraged by the application of chicken manure-based compost. Supplementation with the composts helped promote the availability of soil nitrogen in the cold water paddy field, thereby improving the soil’s productivity and increasing the yield of the rice crop.

The Interactive Modeling Method of Virtual City Scene Based on Building Codes

( Wei-long Ding ),( Xiao-jie Zhu ),( Bin Xu ),( Yan Xu ),( Kai Chen ),( Zang-xin Wan ) 한국인터넷정보학회 2021 KSII Transactions on Internet and Information Syst Vol.15 No.1

For higher-level requirements of urban planning and management and the recent development of "digital earth" and "digital city", it is urgent to establish protocols for the construction of three-dimensional digital city models. However, some problems still exist in the digital technology of the three-dimensional city model, such as insufficient precision of the three-dimensional model, not optimizing the scene and not considering the constraints of building codes. In view of those points, a method to interactively simulate a virtual city scene based on building codes is proposed in this paper. Firstly, some constraint functions are set up to restrict the models to adhere to the building codes, and an improved directional bounding box technique is utilized to solve the problem that geometric objects may intersect in a virtual city scene. The three-dimensional model invocation strategy is designed to convert two-dimensional layouts to a three-dimensional urban scene. A Leap Motion hardware device is used to interactively place the 3D models in a virtual scene. Finally, the design and construction of the three-dimensional scene are completed by using Unity3D. The experiment shows that this method can simulate urban virtual scenes that strictly adhere to building codes in a virtual scene of the city environment, but also provide information and decision-making functions for urban planning and management.

Plant Virome Analysis by the Deep Sequencing of Small RNAs of Fritillaria thunbergii var. chekiangensis and the Rapid Identification of Viruses

Lu-xi Chen,Hang-kai Pan,Yu-tian Tao,Dang Yang,Hui-min Deng,Kai-jie Xu,Wen-bin Chen,Jun-min Li 한국식물병리학회 2022 Plant Pathology Journal Vol.38 No.5

Thunberg fritillary (Fritillaria thunbergii), a perennial used in traditional Chinese herbal medicine, is a members of the family Liliaceae. The degeneration of germplasm is a severe problem in the production of Fritillaria thunbergii var. chekiangensis. However, no information about viral infections of F. thunbergii var. chekiangensis has been reported. In this study, we sequenced the small RNAs of F. thunbergii var. chekiangensis from leaves and bulbs, and viruses were identified using a phylogenetic analysis and BLAST search for sequence. In addition, multiplex reverse transcriptase-polymerase chain reaction (RT-PCR) was used to rapidly detect viruses in this variety. Our study first reported that five viruses infected F. thunbergii var. chekiangensis. Among them, fritillary virus Y (FVY), lily mottle virus (LMoV), Thunberg fritillary mosaic virus (TFMV), and hop yellow virus (HYV) had been reported in F. thunbergii, while apple stem grooving virus was first reported in the genus Fritillaria. A multiplex RT-PCR method was developed to rapidly test the four viruses FVY, LMoV, TFMV, and HYV in F. thunbergii var. chekiangensis. Our results provide a better understanding of the infection of F. thunbergii var. chekiangensis by viruses and a basic reference for the better design of suitable control measures.

Analysis of the Genome Sequence of Strain GiC-126 of Gloeostereum incarnatum with Genetic Linkage Map

( Wan-zhu Jiang ),( Fang-jie Yao ),( Ming Fang ),( Li-xin Lu ),( You-min Zhang ),( Peng Wang ),( Jing-jing Meng ),( Jia Lu ),( Xiao-xu Ma ),( Qi He ),( Kai-sheng Shao ),( Asif Ali Khan ),( Yun-hui Wei 한국균학회 2021 Mycobiology Vol.49 No.4

Gloeostereum incarnatum has edible and medicinal value and was first cultivated and domesticated in China. We sequenced the G. incarnatum monokaryotic strain GiC-126 on an Illumina HiSeq X Ten system and obtained a 34.52-Mb genome assembly sequence that encoded 16,895 predicted genes. We combined the GiC-126 genome with the published genome of G. incarnatum strain CCMJ2665 to construct a genetic linkage map (GiC-126 genome) that had 10 linkage groups (LGs), and the 15 assembly sequences of CCMJ2665 were integrated into 8 LGs. We identified 1912 simple sequence repeat (SSR) loci and detected 700 genes containing 768 SSRs in the genome; 65 and 100 of them were annotated with gene ontology (GO) terms and KEGG pathways, respectively. Carbohydrate-active enzymes (CAZymes) were identified in 20 fungal genomes and annotated; among them, 144 CAZymes were annotated in the GiC-126 genome. The A mating-type locus (MAT-A) of G. incarnatum was located on scaffold885 at 38.9 cM of LG1 and was flanked by two homeodomain (HD1) genes, mip and beta-fg. Fourteen segregation distortion markers were detected in the genetic linkage map, all of which were skewed toward the parent GiC-126. They formed three segregation distortion regions (SDR1-SDR3), and 22 predictive genes were found in scaffold1920 where three segregation distortion markers were located in SDR1. In this study, we corrected and updated the genomic information of G. incarnatum. Our results will provide a theoretical basis for fine gene mapping, functional gene cloning, and genetic breeding the follow-up of G. incarnatum.

Cyanidin-3-Glucoside-Rich Extract from Chinese Bayberry Fruit Protects Pancreatic b Cells and Ameliorates Hyperglycemia in Streptozotocin-Induced Diabetic Mice

Chong-De Sun,Bo Zhang,Jiu-Kai Zhang,Chang-Jie Xu,Yu-Lian Wu,Xian Li,Kun-Song Chen 한국식품영양과학회 2012 Journal of medicinal food Vol.15 No.3

Chinese bayberry fruit is a rich source of anthocyanins, especially cyanidin-3-glucoside (C3G). The present study investigated the protective effects of C3G-rich bayberry fruit extract (CRBFE) against pancreatic b cells against oxidative stress–induced injury as well as its hypoglycemic effect in diabetic mice. Bayberry extract from ‘‘Biqi’’ was used for both in vitro and in vivo testing because of its high C3G content and high antioxidant capacity. Pretreatment of b cells with CRBFE (containing 0.5 lmol/L C3G) prevented cell death, increased cellular viability, and decreased mitochondrial reactive oxygen species production and cell necrosis induced by 800 or 1200 lmol/L H2O2. CRBFE dose-ependently up-regulated pancreatic duodenal homeobox 1 gene expression, contributing to increased insulin-like growth factor II gene transcript levels and insulin protein in INS-1 cells. In addition, adminitration of CRBFE (150 lg of C3G/10 g of body weight twice per day)significantly reduced blood glucose in streptozotocin-induced diabetic ICR mice and increased the glucose tolerance in an oral glucose tolerance test (P < .05). Such results indicated that CRBFE might be useful in prevention and control of diabetes mellitus and diabetes-associated complications.

Genetic linkage map construction and quantitative trait loci mapping of agronomic traits in Gloeostereum incarnatum

Jiang Wan-Zhu,Yao Fang-Jie,Lu Li-Xin,Fang Ming,Wang Peng,Zhang You-Min,Meng Jing-Jing,Lu Jia,Ma Xiao-Xu,He Qi,Shao Kai-Sheng 한국미생물학회 2021 The journal of microbiology Vol.59 No.1

Gloeostereum incarnatum is an edible medicinal mushroom widely grown in China. Using the whole genome of G. incarnatum, simple sequence repeat (SSR) markers were developed and synthetic primers were designed to construct its first genetic linkage map. The 1,048.6 cm map is composed of 10 linkage groups and contains 183 SSR markers. In total, 112 genome assembly sequences were anchored, representing 16.43 Mb and covering 46.41% of the genome. Selfing populations were used for quantitative trait loci (QTL) targeting, and the composite interval mapping method was used to co-localize the mycelium growth rate (potato dextrose agar and sawdust), growth period, yield and fruiting body length, and width and thickness. The 14 QTLs of agronomic traits had LOD values of 3.20–6.51 and contribution rates of 2.22– 13.18%. No linkage relationship was found between the mycelium growth rate and the growth period, but a linkage relationship was observed among the length, width and thickness of the fruiting bodies. Using NCBI’s BLAST alignment, the genomic sequences corresponding to the QTL regions were compared, and a TPR-like protein candidate gene was selected. Using whole-genome data, 138 candidate genes were found in four sequence fragments of two SSR markers located in the same scaffold. The genetic map and QTLs established in this study will aid in developing selective markers for agronomic traits and identifying corresponding genes, thereby providing a scientific basis for the further gene mapping of quantitative traits and the marker-assisted selection of functional genes in G. incarnatum breeding programs.

Clinicopathologic Characteristics and Prognoses for Multicentric Occurrence and Intrahepatic Metastasis in Synchronous Multinodular Hepatocellular Carcinoma Patients

Li, Shi-Lai,Su, Ming,Peng, Tao,Xiao, Kai-Yin,Shang, Li-Ming,Xu, Bang-Hao,Su, Zhi-Xiong,Ye, Xin-Ping,Peng, Ning,Qin, Quan-Lin,Chen, De-Feng,Chen, Jie,Li, Le-Qun Asian Pacific Journal of Cancer Prevention 2013 Asian Pacific journal of cancer prevention Vol.14 No.1

Background: Hepatocellular carcinoma (HCC) is one of the most common cancers worldwide, and the outcomes for patients are still poor. It is important to determine the original type of synchronous multinodular HCC for preoperative assessment and the choice of treatment therapy as well as for the prediction of prognosis after treatment. Aims: To analyze clinicopathologic characteristics and prognoses in patients with multicentric occurrence (MO) and intrahepatic metastasis (IM) of synchronous multinodular hepatocellular carcinoma (HCC). Methods: The study group comprised 42 multinodular HCC patients with a total of 112 nodules. The control group comprised 20 HCC patients with 16 single nodular HCC cases and 4 HCC cases with a portal vein tumor emboli. The mitochondrial DNA (mtDNA) D-loop region was sequenced, and the patients of the study group were categorized as MO or IM based on the sequence variations. Univariate and multivariate analyses were used to determine the important clinicopathologic characteristics in the two groups. Results: In the study group, 20 cases were categorized as MO, and 22 as IM, whereas all 20 cases in the control group were characterized as IM. Several factors significantly differed between the IM and MO patients, including hepatitis B e antigen (HBeAg), cumulative tumor size, tumor nodule location, cirrhosis, portal vein and/or microvascular tumor embolus and the histological grade of the primary nodule. Multivariate analysis further demonstrated that cirrhosis and portal vein and/or microvascular tumor thrombus were independent factors differentiating between IM and MO patients. The tumor-free survival time of the MO subjects was significantly longer than that of the IM subjects ($25.7{\pm}4.8$ months vs. $8.9{\pm}3.1$ months, p=0.017). Similarly, the overall survival time of the MO subjects was longer ($31.6{\pm}5.3$ months vs. $15.4{\pm}3.4$ months, p=0.024). The multivariate analysis further demonstrated that the original type (p=0.035) and Child-Pugh grade (p<0.001) were independent predictors of tumor-free survival time. Cirrhosis (p=0.011), original type (p=0.034) and Child-Pugh grade (p<0.001) were independent predictors of overall survival time. Conclusions: HBeAg, cumulative tumor size, tumor nodule location, cirrhosis, portal vein and/or microvascular tumor embolus and histological grade of the primary nodule are important factors for differentiating IM and MO. MO HCC patients might have a favorable outcome compared with IM patients.