In silico Discovery of Genes Expressed in Liver, Kidney, Spleen and Small Intestine of Pigs

Pan, Zengxiang,Liu, Honglin,Chen, Jie,Xu, Dan,Jiang, Zhihua,Xie, Zhuang Asian Australasian Association of Animal Productio 2005 Animal Bioscience Vol.18 No.2

An in silico approach was developed to survey the genes expressed in four internal organs of pig: liver, kidney, spleen and small intestine. The major procedures of the approach included: (1) BLAST searching against GenBank "est_others" database using human cDNA sequences as queries to screen the porcine orthologous expressed sequence tags (ESTs), (2) classifying the porcine ESTs records by resources according to certain criteria and (3) analyzing data for ESTs specifically expressed in each organ. In order to do so, four Java programs were developed. Based on the ESTs available in the GenBank database, it was found that there were at least 2,100 genes expressed in these four organs, including 128 in the liver, 81 in the kidney, 780 in the spleen, and 1,423 in the small intestine respectively (a few genes co-expressed in these tissues). Gene expression patterns, such as co-expressed genes, preferentially expressed genes and basic active genes were also compared and characterized among these organs. This study provides a comprehensive model on how to use the bioinformatics approach and Genbank databases to facilitate the discovery of new genes in livestock species.

QTL mapping and identification of candidate genes for cold tolerance at the germination stage in wild rice

Pan Ying-Hua,Nong Bao-Xuan,Chen Lei,Yang Xing-Hai,Xia Xiu-Zhong,Zhang Zong-Qiong,Qing Dong-Jin,Gao Ju,Huang Cheng-Cui,Li Dan-Ting,Deng Guo-Fu 한국유전학회 2023 Genes & Genomics Vol.45 No.7

Background Cold damage stress significantly affects rice growth (germination and seedling) and causes serious losses in yield in temperate and high-altitude areas around the globe. Objective This study aimed to explore the cold tolerance (CT) locus of rice and create new cold-tolerant germplasm. We constructed a chromosome segment substitution line (CSSL) with strong CT and fine mapped quantitative trait loci (QTLs) associated with CT by performing the whole-genome resequencing of CSSL with phenotypes under cold treatment. Methods A chromosome CSSL, including 271 lines from a cross between the cold-tolerant wild rice Y11 (Oryza rufipogon Griff.) and the cold-sensitive rice variety GH998, was developed to map QTLs conferring CT at the germination stage. The whole-genome resequencing was performed on CSSL for mapping QTLs of associated with CT at the germination stage. Results A high-density linkage map of the CSSLs was developed using the whole-genome resequencing of 1484 bins. The QTL analysis using 615,466 single-nucleotide polymorphisms (SNPs) led to the identification of 2 QTLs related to germination rate at low-temperature on chromosome 8 (qCTG-8) and chromosome 11 (qCTG-11). The qCTG-8 and qCTG-11 explained 14.55% and 14.31% of the total phenotypic variation, respectively. We narrowed down qCTG-8 and qCTG-11 to 195.5 and 78.83-kb regions, respectively. The expression patterns of important candidate genes in different tissues, and of RNA-sequencing (RNA-seq) in CSSLs, were identified based on gene sequences in qCTG-8 and qCTG-11 cold-induced expression analysis. LOC_Os08g01120 and LOC_Os08g01390 were identified as candidate genes in qCTG-8, and LOC_Os11g32880 was identified as a candidate gene in qCTG-11. Conclusions This study demonstrated a general method that could be used to identify useful loci and genes in wild rice and aid in the future cloning of candidate genes of qCTG-8 and qCTG-11. The CSSLs with strong CT were supported for breeding cold-tolerant rice varieties.

Development and Evaluation of a Duplex Real-Time PCR Assay With a Novel Internal Standard for Precise Quantification of Plasma DNA

Dan Chen,Shi-yang Pan,Erfu Xie,Li Gao,Huaguo Xu,Wenying Xia,Ting Xu,Peijun Huang 대한진단검사의학회 2017 Annals of Laboratory Medicine Vol.37 No.1

Background: Circulating levels of cell-free DNA increase in many pathologic conditions. However, notable discrepancies in the quantitative analysis of cell-free DNA from a large number of laboratories have become a considerable pitfall, hampering its clinical application. Methods: We designed a novel recombinant DNA fragment that could be applied as an internal standard in a newly developed and validated duplex real-time PCR assay for the quantitative analysis of total cell-free plasma DNA, which was tested in 5,442 healthy adults and 200 trauma patients. Results: Compared with two traditional methods, this novel assay showed a lower detection limit of 0.1 ng/mL, lower intra- and inter-assay CVs, and higher accuracy in the recovery test. The median plasma DNA concentration of healthy males (20.3 ng/mL, n=3,092) was significantly higher than that of healthy females (16.1 ng/mL, n=2,350) (Mann-Whitney two-sample rank sum test, P<0.0001). The reference intervals of plasma DNA concentration were 0-45.8 ng/mL and 0-52.5 ng/mL for healthy females and males, respectively. The plasma DNA concentrations of the majority of trauma patients (96%) were higher than the upper normal cutoff values and were closely related to the corresponding injury severity scores (R2=0.916, P<0.0001). Conclusions: This duplex real-time PCR assay with a new internal standard could eliminate variation and allow for more sensitive, repeatable, accurate, and stable quantitative measurements of plasma DNA, showing promising application in clinical diagnosis.

Optimization of a Synthesis Process for Octenylsuccinic Anhydride Modified Gum Arabic

Jingna Pan,LEIYANG,Dan Qiu 한국식품과학회 2015 Food Science and Biotechnology Vol.24 No.1

Gum arabic (GA) was esterified using octenylsuccinic anhydride (OSA) in an aqueous solution. HPLC was used to analyze the bound OS content (%OS) after esterification, and total OS content (%OStotal) results from HPLC were in agreement with titration results. The effects of temperature, reaction time, pH value, and GA concentration on the %OS value were determined using single factor experiments. Temperature, time, and pH were used for further optimization. Process parameters for preparation of octenylsuccinic anhydride modified gum arabic (OS-GA) were optimized using response surface methodology (RSM). The theoretical optimum conditions were a temperature of 37.9oC, a reaction time of 116.4 min, and a pH of the reaction system=7.99. Under optimum conditions, the %OS value of OS-GA was 2.07%.

Selecting the Optimal Hidden Layer of Extreme Learning Machine Using Multiple Kernel Learning

( Wentao Zhao Pan Li ),( Qiang Liu Dan Liu ),( Xinwang Liu ) 한국인터넷정보학회 2018 KSII Transactions on Internet and Information Syst Vol.12 No.12

Extreme learning machine (ELM) is emerging as a powerful machine learning method in a variety of application scenarios due to its promising advantages of high accuracy, fast learning speed and easy of implementation. However, how to select the optimal hidden layer of ELM is still an open question in the ELM community. Basically, the number of hidden layer nodes is a sensitive hyperparameter that significantly affects the performance of ELM. To address this challenging problem, we propose to adopt multiple kernel learning (MKL) to design a multi-hidden-layer-kernel ELM (MHLK-ELM). Specifically, we first integrate kernel functions with random feature mapping of ELM to design a hidden-layer-kernel ELM (HLK-ELM), which serves as the base of MHLK-ELM. Then, we utilize the MKL method to propose two versions of MHLK-ELMs, called sparse and non-sparse MHLK-ELMs. Both two types of MHLK-ELMs can effectively find out the optimal linear combination of multiple HLK-ELMs for different classification and regression problems. Experimental results on seven data sets, among which three data sets are relevant to classification and four ones are relevant to regression, demonstrate that the proposed MHLK-ELM achieves superior performance compared with conventional ELM and basic HLK-ELM.

Phospholipid and Fatty Acid Composition in Leaves and Roots of Ten Autumn Chrysanthemum Cultivars Grown at Low Temperature

Yan Li,Yonghua Li,Pan Yang,Hua’ao Zhang,Dan He 한국원예학회 2017 Horticulture, Environment, and Biotechnology Vol.58 No.4

The objective of this study was to evaluate the relationship between cold hardiness and phospholipid andfatty acid content in leaves and roots of chrysanthemum, and to explore cold resistance mechanisms of chrysanthemumin order to provide a theoretical basis for selecting and breeding a new cold-resistant cultivar. We analyzed thephospholipid and fatty acid components in leaves and roots of 10 autumn chrysanthemum cultivars including sixearly-flowering cultivars and four late-flowering cultivars. We determined the content of phosphatidyl ethanolamine(PE), phosphatidyl choline (PC), phosphatidyl serine (PS), phosphatidyl glycerol (PG), myristic acid (C14:0), palmiticacid (C16:0), stearic acid (C18:0), docosanoic acid (C22:0), oleic acid (C18:1), linoleic acid (C18:2), and linolenic acid(C18:3) in leaves and roots of chrysanthemum seedlings grown at 16C and 5C. The cultivars had different responsesto low temperature that included changes in the cell membrane composition in leaves and roots. The main phospholipidin leaves and roots of chrysanthemum was PE, and the main saturated fatty acid was palmitic acid. Amongunsaturated fatty acids, linolenic acid was found in leaves, whereas oleic acid and linoleic acid were present in theroots. Based on the unsaturated fatty acid content and the ratio of unsaturated to saturated fatty acids in leaves, theearly-flowering cultivars ‘Tan Xiang Shi Zi’ and ‘Tong Que Chun Shen’ and the late-flowering cultivars ‘Guan DongXin Xia’ and ‘Yun Long Feng Wu’ were classified as strongly cold tolerant, while the early-flowering cultivar ‘JinFeng Ling’ and the late-flowering cultivar ‘Mo Bao’ were weakly cold tolerant.

Expression and Localization of the spermatogenesis-related gene, Znf230, in mouse testis and spermatozoa during postnatal development

( Hong Xia Song ),( Dan Su Pan Lu ),( Ji Yun Yang ),( Wei Zhang ),( Yuan Yang ),( Yun Qiang Liu ),( Si Zhong Zhang ) 생화학분자생물학회 2008 BMB Reports Vol.41 No.9

Identification of qRT-PCR reference genes for Chilo suppressalis (Walker) during parasitism by Cotesia chilonis (Matsumura)

Zi-Lan Li,Dan-Dan Pan,Ming-Xing Lu,Yu-zhou Dua 한국응용곤충학회 2020 Journal of Asia-Pacific Entomology Vol.23 No.1

Quantitative real-time RT-PCR is highly sensitive approach for identifying and studying genes that function in various biochemical and cellular processes. Choosing the proper reference genes is a necessary step in ensuring the accuracy of results obtained with qRT-PCR. Herein, we evaluate the expression stability of nine potential reference genes in Chilo suppressalis parasitized by Cotesia chilonis. Stability was analyzed using the ΔCt method, geNorm, NormFinder, and BestKeeper, and our results show that the combination of TUB, EF1 and NADHD was optimal for normalizing expression. The transcription of target genes Hsp60 and CAT in C. suppressalis during parasitism was used to evaluate reference genes, and the results varied depending on the gene selected for normalization. Therefore, it is imperative to choose the proper reference genes to estimate target gene expression accurately in a given experiment. This study provides insights on gene expression in C. suppressalis and is especially relevant to further experiments that explore the effectiveness of C. chilonis in biological control.

움직임 동사와 선-영역 위상간 관련성에 관한 연구

조미영 ( Mi-young Cho ),송단 ( Dan Song ),최준호 ( Jun-ho Choi ),김원필 ( Won-pil Kim ),김판구 ( Pan-koo Kim ) 한국정보처리학회 2004 한국정보처리학회 학술대회논문집 Vol.11 No.1

비디오 데이터베이스에서 움직임 정보를 가지고 있는 이동객체에 대한 모델링은 크게 두 가지 측면 즉, 공간적 혹은 시간적 관계성에 의해 다루어진다. 공간적 관계에서 위상 관계는 근접 그래프에 의한 모델링이 대부분이며, 이를 이용한 내용 기반 비디오 검색에서 자연어 형태의 질의어는 정형화된 위상 관계 표현으로 변환하는 과정을 거친다. 그러나 이 과정에서 위상 관계 표현이 인간이 사용하는 언어의 의미를 정확히 반영하는지는 알 수 없다. 이에 본 논문에서는 위상 관계 표현과 인간이 사용하는 움직임 동사간 의미의 차이를 줄이기 위해 위상 관계 표현과 실제 움직임 동사간의 매칭에 대해 연구했다.

Background Error Statistics for Aerosol Variables from WRF/Chem Predictions in Southern California

Zengliang Zang,Zilong Hao,Xiaobin Pan,Zhijin Li,Dan Chen,Li Zhang,Qinbin Li 한국기상학회 2015 Asia-Pacific Journal of Atmospheric Sciences Vol.51 No.2

Background error covariance (BEC) is crucial in data assimilation. This paper addresses the multivariate BEC associated with black carbon, organic carbon, nitrates, sulfates, and other constituents of aerosol species. These aerosol species are modeled and predicted using the Model for Simulating Aerosol Interactions and Chemistry scheme (MOSAIC) in the Weather Research and Forecasting/Chemistry (WRF/Chem) model at a resolution of 4 km in Southern California. The BEC is estimated from the differences between the 36-hour and 12-hour forecasts using the NMC method. The results indicated that the maximum background error standard deviation is associated with nitrate and is larger than that of black carbon, organic carbon, and sulfate. The horizontal and vertical scale of the correlation of nitrate is much smaller than that of other species. A significant cross-correlation is found between the species of black carbon and organic carbon. The cross-correlations between nitrate and other variables are relatively smaller and exhibit a relatively smaller length scale. Single observation data assimilation experiments are performed to illustrate the effect of the BEC on analysis increments.