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| 1 | ALK,the Key Gene for Gelatinization Temperature,is a Modifier Gene for Gel Consistency in Rice显示文摘Gelatinization temperature(GT) is an important parameter in evaluating the cooking and eating quality of rice.Indeed,the phenotype,biochemistry and inheritance of GT have been widely studied in recent times.Previous map-based cloning revealed that GT was controlled by ALK gene,which encodes a putative soluble starch synthase II-3.Complementation vector and RNAi vector were constructed and transformed into Nipponbare mediated by Agrobacterium.Phenotypic and molecular analyses of transgenic lines provided direct evidence for ALK as a key gene for GT.Meanwhile,amylose content,gel consistency and pasting properties were also affected in transgenic lines.Two of four nonsynonymous single nucleotide polymorphisms in coding sequence of ALK were identified as essential for GT.Based on the single nucleotide polymorphisms(SNPs),two new sets of SNP markers combined with one cleaved amplified polymorphic sequence marker were developed for application in rice quality breeding. | Zhenyu Gao Dali Zeng Fangmin Cheng Zhixi Tian Longbiao Guo Yan Su Meixian Yan Hua Jiang Guojun Dong Yuchen Huang Bin Han Jiayang Li Qian Qian | 2011 | Journal of Integrative Plant Biology2011，53，9： | 13 |
| 2 | TSNAdb: A Database for Tumor-specific Neoantigens from Immunogenomics Data Analysis显示文摘Tumor-specific neoantigens have attracted much attention since they can be used as biomarkers to predict therapeutic effects of immune checkpoint blockade therapy and as potential targets for cancer immunotherapy. In this study, we developed a comprehensive tumor-specific neoantigen database(TSNAdb v1.0), based on pan-cancer immunogenomic analyses of somatic mutation data and human leukocyte antigen(HLA) allele information for 16 tumor types with 7748 tumor samples from The Cancer Genome Atlas(TCGA) and The Cancer Immunome Atlas(TCIA). We predicted binding affinities between mutant/wild-type peptides and HLA class I molecules by NetMHCpan v2.8/v4.0, and presented detailed information of 3,707,562/1,146,961 potential neoantigens generated by somatic mutations of all tumor samples. Moreover, we employed recurrent mutations in combination with highly frequent HLA alleles to predict potential shared neoantigens across tumor patients,which would facilitate the discovery of putative targets for neoantigen-based cancer immunotherapy.TSNAdb is freely available at http://biopharm.zju.edu.cn/tsnadb. | Jingcheng Wu Wenyi Zhao Binbin Zhou Zhixi Su Xun Gu Zhan Zhou Shuqing Chen | 2018 | Genomics, Proteomics & Bioinformatics2018，16，4： | 2 |
| 3 | Paralog-divergent Features May Help Reduce Off-target Effects of Drugs:Hints from Glucagon Subfamily Analysis显示文摘Side effects from targeted drugs remain a serious concern. One reason is the nonselective binding of a drug to unintended proteins such as its paralogs, which are highly homologous in sequences and have similar structures and drug-binding pockets. To identify targetable differences between paralogs, we analyzed two types(type-I and type-II) of functional divergence between two paralogs in the known target protein receptor family G-protein coupled receptors(GPCRs) at the amino acid level. Paralogous protein receptors in glucagon-like subfamily, glucagon receptor(GCGR) and glucagon-like peptide-1 receptor(GLP-1R), exhibit divergence in ligands and are clinically validated drug targets for type 2 diabetes. Our data showed that type-II amino acids were significantly enriched in the binding sites of antagonist MK-0893 to GCGR, which had a radical shift in physicochemical properties between GCGR and GLP-1R. We also examined the role of type-I amino acids between GCGR and GLP-1R. The divergent features between GCGR and GLP-1R paralogs may be helpful in their discrimination, thus enabling the identification of binding sites to reduce undesirable side effects and increase the target specificity of drugs. | Zhining Sa Jingqi Zhou Yangyun Zou Zhixi Su Xun Gu | 2017 | Genomics, Proteomics & Bioinformatics2017，15，4： | 0 |
| 4 | Multiple Excitation Wavelength Fluorescence Emission Spectra Technique for Discrimination of Phytoplankton显示文摘In vivo fluorescence methods are efficient tools for studying the distribution of phytoplankton in nature.Different algae species usually have different pigments with different ratios,which results in different fluorescence emission spectra.Based on multiple excitation wavelength fluorescence emission spectra,a discrimination technique is established in this study.The discrimination method,established by multivariate linear regression and weighted least-squares,was used to differentiate the samples cultured in the laboratory and collected from Jiaozhou Bay near Qingdao at the division level.The correctly discriminated samples were ≥ 86% for single algae samples,≥ 88% for simulatively mixed ones,≥ 91% for physically mixed ones and 100% for samples collected from Jiaozhou Bay.The result in this research is more definite for the physically mixed samples in the laboratory.The method described here can be employed to monitor the phytoplankton population in the marine environment. | HU Xupeng SU Rongguo ZHANG Fang WANG Xiulin WANG Hongtao ZHENG Zhixi | 2010 | Journal of Ocean University of China2010，9，1： | 0 |
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