Shuai Liu

Tongji Hospital

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Ding Ai

Tianjin Medical University

Roland Foisner

Max Perutz Labs

Ling Liu

Tianjin University

Shanshan Tian

Tianjin Medical University

Zhi Yao

Second Hospital of Shandong University

Qi Zhang

Third Affiliated Hospital of Sun Yat-sen University

Jihui Hao

Tianjin Medical University Cancer Institute and Hospital

Kai Zhang

Shanghai Jiao Tong University

Rui Guo

Beijing University of Chemical Technology

Qiushi Guo

Tianjin Medical University Cancer Institute and Hospital

Cooperative Institutions

Tianjin Medical University

Shanghai Jiao Tong University

Tianjin Medical University Cancer Institute and Hospital

Chinese Academy of Medical Sciences & Peking Union Medical College

Ministry of Education of the People's Republic of China

Tianjin Medical University General Hospital

Chinese Academy of Sciences

Fudan University

Sun Yat-sen University

Ministry of Agriculture and Rural Affairs

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Analysis of epigenetic chromatin modification during mitosis in rice

Indian Journal of Genetics and Plant Breeding (The) (2016)

Rui Guo Chao Xue Shuai Liu Yong Zhou Mingliang Zhang

DNA methylation and histone modification are two important types of epigenetic modification. In this study, we analyzed the dynamic changes and chromosomal localizations of four different epigenetic modifications, DNA 5-MeC, H3K4me3, H3K9me2, and H3S10Ph, during mitosis in rice. The results showed that signals from DNA 5-MeC and H3K4me3 were distributed in the heterochromatin and euchromatin regions respectively, but no obvious signals from H3K9me2 were detected. There were no significant changes noticed in these three modification patterns at different phases during mitosis. However, the H3S10Ph, which was mainly distributed in the centromeric regions, showed dynamic changes during mitosis that occurred mainly at prophase and anaphase but not at interphase and telophase.

10.5958/0975-6906.2016.00004.3

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[Application of eight-probe fluorescence in situ hybridization and R-banding karyotype analysis for the diagnosis of acute lymphoblastic leukemia].

PubMed (2016)

Ding Zhao Shuai Liu Zhenxin Guo Rui Li

To assess the value of eight-probe fluorescence in situ hybridization (FISH) and R-banding karyotype analysis for the diagnosis of acute lymphoblastic leukemia (ALL).With the eight-probe FISH (using probes for MYC, P16, E2A, CHIC2/D10Z1/D17Z1, TEL/AMLl, MLL, BCR/ABL1, and IGH) and R-banding karyotype analysis, 237 cases of ALL were analyzed.Cytogenetic changes were detected in 135 (56.96%) of all cases, which have involved MYC, P16, E2A, CHIC2/D10Z1/D17Z1, TEL/AMLl, MLL, BCR/ABL1, and IGH polyploidies. R-banding karyotype analysis has only detected abnormalities in 48 of such cases, in addition with 14 abnormalities missed by the FISH probes, which have given a total positive rate of 26.16%. The detection rate of the two methods has differed significantly(P<0.05).Compared with the R-banding karyotype analysis, the eight-probe FISH is more accurate and efficient. Diagnosis of cytogenetic abnormalities for children with ALL using the combined method can provide a basis for evaluation of prognosis as well as personalized therapy.

10.3760/cma.j.issn.1003-9406.2016.01.003

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Additional file 1 of LAP2α preserves genome integrity through assisting RPA deposition on damaged chromatin

Figshare (2022)

Kaiwen Bao Qi Zhang Shuai Liu Nan Song Qiushi Guo

Additional file 1: Table S1. SILAC-based quantitative mass spectrometry analysis of RPA1-containing protein complexes.

Deposition

10.6084/m9.figshare.19254555

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Molecular characterization and ligand binding specificity of the PDZ domain-containing protein GIPC3 from Schistosoma japonicum

Parasites & Vectors (2012)

Yi Mu Haiming Huang Shuai Liu Pengfei Cai Youhe Gao

Abstract Background Schistosomiasis is a serious global health problem that afflicts more than 230 million people in 77 countries. Long-term mass treatments with the only available drug, praziquantel, have caused growing concerns about drug resistance. PSD-95/Dlg/ZO-1 (PDZ) domain-containing proteins are recognized as potential targets for the next generation of drug development. However, the PDZ domain-containing protein family in parasites has largely been unexplored. Methods We present the molecular characteristics of a PDZ domain-containing protein, GIPC3, from Schistosoma japonicum (SjGIPC3) according to bioinformatics analysis and experimental approaches. The ligand binding specificity of the PDZ domain of SjGIPC3 was confirmed by screening an arbitrary peptide library in yeast two-hybrid (Y2H) assays. The native ligand candidates were predicted by Tailfit software based on the C-terminal binding specificity, and further validated by Y2H assays. Results SjGIPC3 is a single PDZ domain-containing protein comprised of 328 amino acid residues. Structural prediction revealed that a conserved PDZ domain was presented in the middle region of the protein. Phylogenetic analysis revealed that SjGIPC3 and other trematode orthologues clustered into a well-defined cluster but were distinguishable from those of other phyla. Transcriptional analysis by quantitative RT-PCR revealed that the SjGIPC3 gene was relatively highly expressed in the stages within the host, especially in male adult worms. By using Y2H assays to screen an arbitrary peptide library, we confirmed the C-terminal binding specificity of the SjGIPC3-PDZ domain, which could be deduced as a consensus sequence, -[SDEC]-[STIL]-[HSNQDE]-[VIL]*. Furthermore, six proteins were predicted to be native ligand candidates of SjGIPC3 based on the C-terminal binding properties and other biological information; four of these were confirmed to be potential ligands using the Y2H system. Conclusions In this study, we first characterized a PDZ domain-containing protein GIPC3 in S. japonicum . The SjGIPC3-PDZ domain is able to bind both type I and II ligand C-terminal motifs. The identification of native ligand will help reveal the potential biological function of SjGIPC3. These data will facilitate the identification of novel drug targets against S. japonicum infections.

PDZ domain

10.1186/1756-3305-5-227

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Community Analysis of Endophytic Bacteria from the Seeds of the Medicinal Plant Panax notoginseng

Journal of Agricultural Science (2017)

Shuai Liu Dinghua Li Xiuming Cui Limei Chen Nian Hongjuan

Panax notoginseng is a traditional Chinese medicine. The roots of P. notoginseng can be used for treatment of diseases and raw materials in Chinese medicinal products. High yield and quality roots require cultivation in shade and humid conditions for 3 years. The long period cultivation makes P. notoginseng vulnerable to infect by pathogens. So control diseases are vital for the high yield and quality of P. notoginseng. The seed is the carrier systems of many probiotics and pathogens. To explore the indigenous bacterial community diversity, the endophytic bacteria from the seeds of the medicinal plant P. notoginseng were isolated and identified using traditional cultivation methods in combination with molecular technique. A total of 137 endophytic bacteria strains were isolated. The 16S rDNA of these strains was amplified and subjected to amplified ribosomal DNA restriction analysis (ARDRA) with restriction enzyme HaeIII. All the isolated strains were grouped into 9 OTUs (Operational Taxonomic Units) on the basis of the similarity of the ARDRA band profiles. Each representative strain of 9 OTUs was selected for sequencing. r-proteobacteria was the most dominant group among the isolates (98.5%), containing eight genera. Pseudomonas was the most dominant genus (58 of 135 isolates), whose isolates occurred in the seeds collected from all three places. The second dominant genus was Enterobacter (20.7%), followed by uncultured bacterium (14.8%) and Stenotrophomonas (10.4%). Among the six areas sampled, endophytic bacteria in the seeds collected from Panlong of Yanshan exhibited species diversity and contained the most isolates. These results suggest an abundant diversity of bacterial community within the seeds of P. notoginseng. These data provide insights into monitoring the seed health and disease outbreak during seeding.

Panax notoginseng

Stenotrophomonas

HaeIII

Pantoea

10.5539/jas.v9n2p37

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Additional file 3 of LAP2α preserves genome integrity through assisting RPA deposition on damaged chromatin

Figshare (2022)

Kaiwen Bao Qi Zhang Shuai Liu Nan Song Qiushi Guo

Additional file 3: Table S2. Mass spectrometry analysis of LAP2α-containing protein complexes.

10.6084/m9.figshare.19254561

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Elena Semino & Zsófia Demjén (eds.), The Routledge handbook of metaphor and language. London & New York: Routledge, 2017. Pp. xvii + 540.

Journal of Linguistics (2018)

Shuai Liu Wei Zhang

An abstract is not available for this content so a preview has been provided. Please use the Get access link above for information on how to access this content.

Content (measure theory)

10.1017/s0022226718000026

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Effects of NPK Fertilization on Photosynthetic Characteristics and Nutrients of Pecan at the Seedling Stage

Journal of soil science and plant nutrition (2021)

Junping Liu Wenjing Chen Hankun Wang Fangren Peng Mengyun Chen

10.1007/s42729-021-00533-w

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Preparation and application of centromere-specific protein CENH3 antibody in rice.

Zhongguo shuidao kexue (2017)

Chao Xue Rong Zhang Rui Guo Shuai Liu Xiaoyu Liu

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Diversified Application of Barcoded PLATO (PLATO-BC) Platform for Identification of Protein Interactions

Genomics Proteomics & Bioinformatics (2019)

Weili Kong Tsuyoshi Hayashi Guillaume Fiches Qikai Xu Mamie Z. Li

Abstract Proteins usually associate with other molecules physically to execute their functions. Identifying these interactions is important for the functional analysis of proteins. Previously, we reported the parallel analysis of translated ORFs (PLATO) to couple ribosome display of full-length ORFs with affinity enrichment of mRNA/protein/ribosome complexes for the “bait” molecules, followed by the deep sequencing analysis of mRNA. However, the sample processing, from extraction of precipitated mRNA to generation of DNA libraries, includes numerous steps, which is tedious and may cause the loss of materials. Barcoded PLATO (PLATO-BC), an improved platform was further developed to test its application for protein interaction discovery. In this report, we tested the antisera-antigen interaction using serum samples from patients with inclusion body myositis (IBM). Tripartite motif containing 21 (TRIM21) was identified as a potentially new IBM autoantigen. We also expanded the application of PLATO-BC to identify protein interactions for JQ1, single ubiquitin peptide, and NS5 protein of Zika virus. From PLATO-BC analyses, we identified new protein interactions for these “bait” molecules. We demonstrate that Ewing sarcoma breakpoint region 1 (EWSR1) binds to JQ1 and their interactions may interrupt the EWSR1 association with acetylated histone H4. RIO kinase 3 (RIOK3), a newly identified ubiquitin-binding protein, is preferentially associated with K63-ubiquitin chain. We also find that Zika NS5 protein interacts with two previously unreported host proteins, par-3 family cell polarity regulator (PARD3) and chromosome 19 open reading frame 53 (C19orf53), whose attenuated expression benefits the replication of Zika virus. These results further demonstrate that PLATO-BC is capable of identifying novel protein interactions for various types of “bait” molecules.

ORFS

10.1016/j.gpb.2018.12.010

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Citations (9)