1
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Hsu CT, Chiu CC, Hsiao PY, Lin CY, Cheng S, Lin YC, Yang YL, Wu FH, Harn HJ, Lin SZ, Lin CS. Transgene-free CRISPR/Cas9-mediated gene editing through protoplast-to-plant regeneration enhances active compounds in Salvia miltiorrhiza. Plant Biotechnol J 2024. [PMID: 38174833 DOI: 10.1111/pbi.14285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 12/11/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Affiliation(s)
- Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chi-Chou Chiu
- Institute of Tropical Plant Sciences and Microbiology, National Cheng Kung University, Tainan, Taiwan
| | - Pao-Yuan Hsiao
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Yu Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Sychyi Cheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yao-Cheng Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Yu-Liang Yang
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan, Taiwan
| | - Fu-Hui Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
| | - Horng-Jyh Harn
- Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
- Department of Pathology, Hualien Tzu Chi Hospital and Tzu Chi University, Hualien, Taiwan
| | - Shinn-Zong Lin
- Bioinnovation Center, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
- Department of Neurosurgery, Hualien Tzu Chi Hospital, Hualien, Taiwan
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan
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2
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Lee CC, Hwang JI, Chang KH, Lin YC, Chao CC, Cheng TF, Chen YC, Hsueh KC. Comparison of contrast-enhanced ultrasonography and MRI results obtained by expert and novice radiologists indicating short-term response after transarterial chemoembolisation for hepatocellular carcinoma. Clin Radiol 2024; 79:e73-e79. [PMID: 37914602 DOI: 10.1016/j.crad.2023.09.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 08/21/2023] [Accepted: 09/21/2023] [Indexed: 11/03/2023]
Abstract
AIM To evaluate inter-reader agreement between novice and expert radiologists in assessing contrast-enhanced ultrasonography (CEUS) and magnetic resonance imaging (MRI) images for detecting viable tumours with different sizes after conventional transarterial chemoembolisation (cTACE). MATERIALS AND METHODS This prospective study included patients who had less than five hepatomas and who underwent cTACE. Hepatomas with one or two feeding arteries were selected as target lesions. CEUS and MRI were performed within 1 week after cTACE to evaluate viable tumours. RESULTS The expert group had higher kappa values in evaluating all tumour sizes via CEUS compared with MRI. The novice group had similar kappa values. In patients with tumours measuring ≤3 cm, the expert group had higher kappa values in reading CEUS compared with MRI images; however, in the novice group, the kappa value was lower in evaluating CEUS compared with MRI images. In patients with tumours measuring >3 cm, the expert and novice groups had good to excellent kappa values. The confidence level of the two groups in reading MRI images was high; however, the novice group had a lower confidence level. CONCLUSION CEUS is a convenient, cost-effective, and easy to apply imaging tool that can help interventionists perform early detection of viable hepatocellular carcinoma post-TACE. It has a higher inter-rater agreement in interpreting CEUS images compared with MRI images among expert radiologists even when they are extremely familiar with post-cTACE MRI images. In novice radiologists, there may be a learning curve to achieve good consistency in CEUS interpretation.
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Affiliation(s)
- C-C Lee
- Division of Interventional Radiology, Department of Medical Imaging, Tungs' Taichung Metroharbor Hospital, Taichung 43503, Taiwan
| | - J-I Hwang
- Division of Interventional Radiology, Department of Medical Imaging, Tungs' Taichung Metroharbor Hospital, Taichung 43503, Taiwan; Department of Radiology, National Defense Medical Center, Taipei 11490, Taiwan
| | - K-H Chang
- Department of Medical Research, Tungs' Taichung Metroharbor Hospital, Taichung Taiwan; Center for General Education, China Medical University, Taichung 404, Taiwan; General Education Center, Jen-Teh Junior College of Medicine, Nursing and Management, Miaoli 356, Taiwan; Department of Life Sciences and Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 40227, Taiwan
| | - Y C Lin
- Division of Interventional Radiology, Department of Medical Imaging, Tungs' Taichung Metroharbor Hospital, Taichung 43503, Taiwan
| | - C C Chao
- Division of Interventional Radiology, Department of Medical Imaging, Tungs' Taichung Metroharbor Hospital, Taichung 43503, Taiwan
| | - T-F Cheng
- Division of Interventional Radiology, Department of Medical Imaging, Tungs' Taichung Metroharbor Hospital, Taichung 43503, Taiwan
| | - Y-C Chen
- Division of Interventional Radiology, Department of Medical Imaging, Tungs' Taichung Metroharbor Hospital, Taichung 43503, Taiwan; Department of Medical Research, Tungs' Taichung Metroharbor Hospital, Taichung Taiwan
| | - K-C Hsueh
- Division of Interventional Radiology, Department of Medical Imaging, Tungs' Taichung Metroharbor Hospital, Taichung 43503, Taiwan; Division of General Surgery, Department of Surgery, Tungs' Taichung Metroharbor Hospital, Taichung 43503, Taiwan; Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung, 40227, Taiwan.
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3
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Huang CJ, Wu TL, Zheng PX, Ou JY, Ting CL, Lin YC. Complete Genome Sequence Resource of Pectobacterium colocasium Strain F1-1 that Causes Soft Rot Disease of Taro. Plant Dis 2023:PDIS09222198A. [PMID: 36451306 DOI: 10.1094/pdis-09-22-2198-a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Pectobacterium colocasium is a recently named, narrow-host-range phytopathogenic bacterium causing soft rot of taro (Colocasium esculenta). It is found on the Chinese mainland and the island of Taiwan. Taro is a domesticated crop with a long history of cultivation in Taiwan and the Pacific islands. However, not much was known about Pectobacterium spp. from taro, especially from the islands in the Pacific. Herein, we report a high-quality, completely annotated genome sequence of P. colosacium strain F1-1. The 4,816,345 bp genome, which was assembled with Illumina and Nanopore reads with 217× and 311× coverage, respectively, consists of one chromosome and no plasmid. This completely circularized genome will aid future studies in comparative genomics, evolution, and pathogenicity of P. colocasium. This genome resource will also be helpful for developing strategies to control P. colocasium in taro.[Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
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Affiliation(s)
- Chien-Jui Huang
- Department of Plant Medicine, National Chiayi University, Chiayi 600355, Taiwan
| | - Ting-Li Wu
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Po-Xing Zheng
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Jheng-Yang Ou
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Chao-Ling Ting
- Crop Improvement Division, Miaoli District Agricultural Research and Extension Station, Council of Agriculture, Executive Yuan, Guannan, Miaoli 363201, Taiwan
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
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4
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Barchenger DW, Hsu YM, Ou JY, Lin YP, Lin YC, Balendres MAO, Hsu YC, Schafleitner R, Hanson P. Whole genome resequencing and complementation tests reveal candidate loci contributing to bacterial wilt (Ralstonia sp.) resistance in tomato. Sci Rep 2022; 12:8374. [PMID: 35589778 PMCID: PMC9120091 DOI: 10.1038/s41598-022-12326-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 04/07/2022] [Indexed: 01/19/2023] Open
Abstract
Tomato (Solanum lycopersicum) is one of the most economically important vegetable crops worldwide. Bacterial wilt (BW), caused by the Ralstonia solanacearum species complex, has been reported as the second most important plant pathogenic bacteria worldwide, and likely the most destructive. Extensive research has identified two major loci, Bwr-6 and Bwr-12, that contribute to resistance to BW in tomato; however, these loci do not completely explain resistance. Segregation of resistance in two populations that were homozygous dominant or heterozygous for all Bwr-6 and Bwr-12 associated molecular markers suggested the action of one or two resistance loci in addition to these two major QTLs. We utilized whole genome sequence data analysis and pairwise comparison of six BW resistant and nine BW susceptible tomato lines to identify candidate genes that, in addition to Bwr-6 and Bwr-12, contributed to resistance. Through this approach we found 27,046 SNPs and 5975 indels specific to the six resistant lines, affecting 385 genes. One sequence variant on chromosome 3 captured by marker Bwr3.2dCAPS located in the Asc (Solyc03g114600.4.1) gene had significant association with resistance, but it did not completely explain the resistance phenotype. The SNP associated with Bwr3.2dCAPS was located within the resistance gene Asc which was inside the previously identified Bwr-3 locus. This study provides a foundation for further investigations into new loci distributed throughout the tomato genome that could contribute to BW resistance and into the role of resistance genes that may act against multiple pathogens.
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Affiliation(s)
| | - Yu-Ming Hsu
- CNRS, INRAE, Institute of Plant Sciences Paris-Saclay (IPS2), Univ Evry, Université Paris-Saclay, 91405, Orsay, France
| | - Jheng-Yang Ou
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | | | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Mark Angelo O Balendres
- Institute of Plant Breeding, College of Agriculture and Food Science, University of the Philippines Los Baños, Los Baños, Laguna, Philippines
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5
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Lin CS, Hsu CT, Yuan YH, Zheng PX, Wu FH, Cheng QW, Wu YL, Wu TL, Lin S, Yue JJ, Cheng YH, Lin SI, Shih MC, Sheen J, Lin YC. DNA-free CRISPR-Cas9 gene editing of wild tetraploid tomato Solanum peruvianum using protoplast regeneration. Plant Physiol 2022; 188:1917-1930. [PMID: 35088855 PMCID: PMC8968427 DOI: 10.1093/plphys/kiac022] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/10/2021] [Indexed: 05/24/2023]
Abstract
Wild tomatoes (Solanum peruvianum) are important genomic resources for tomato research and breeding. Development of a foreign DNA-free clustered regularly interspaced short palindromic repeat (CRISPR)-Cas delivery system has potential to mitigate public concern about genetically modified organisms. Here, we established a DNA-free CRISPR-Cas9 genome editing system based on an optimized protoplast regeneration protocol of S. peruvianum, an important resource for tomato introgression breeding. We generated mutants for genes involved in small interfering RNAs biogenesis, RNA-DEPENDENT RNA POLYMERASE 6 (SpRDR6), and SUPPRESSOR OF GENE SILENCING 3 (SpSGS3); pathogen-related peptide precursors, PATHOGENESIS-RELATED PROTEIN-1 (SpPR-1) and PROSYSTEMIN (SpProSys); and fungal resistance (MILDEW RESISTANT LOCUS O, SpMlo1) using diploid or tetraploid protoplasts derived from in vitro-grown shoots. The ploidy level of these regenerants was not affected by PEG-Ca2+-mediated transfection, CRISPR reagents, or the target genes. By karyotyping and whole genome sequencing analysis, we confirmed that CRISPR-Cas9 editing did not introduce chromosomal changes or unintended genome editing sites. All mutated genes in both diploid and tetraploid regenerants were heritable in the next generation. spsgs3 null T0 regenerants and sprdr6 null T1 progeny had wiry, sterile phenotypes in both diploid and tetraploid lines. The sterility of the spsgs3 null mutant was partially rescued, and fruits were obtained by grafting to wild-type (WT) stock and pollination with WT pollen. The resulting seeds contained the mutated alleles. Tomato yellow leaf curl virus proliferated at higher levels in spsgs3 and sprdr6 mutants than in the WT. Therefore, this protoplast regeneration technique should greatly facilitate tomato polyploidization and enable the use of CRISPR-Cas for S. peruvianum domestication and tomato breeding.
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Affiliation(s)
| | - Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Hsuan Yuan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Po-Xing Zheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Fu-Hui Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Qiao-Wei Cheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
| | - Yu-Lin Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Ting-Li Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei 115, Taiwan
- Biotechnology Research Center in Southern Taiwan, Academia Sinica, Tainan 711, Taiwan
| | - Steven Lin
- Institute of Biochemistry, Academia Sinica, Taipei 115, Taiwan
| | - Jin-Jun Yue
- Research Institute of Subtropical Forestry, Chinese Academy of Forestry, Hangzhou 311, China
| | - Ying-Huey Cheng
- Plant Pathology Division, Taiwan Agricultural Research Institute, Taichung 413, Taiwan
| | - Shu-I Lin
- Department of Horticulture and Landscape Architecture, National Taiwan University, Taipei 106, Taiwan
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6
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Hsu CT, Yuan YH, Lin YC, Lin S, Cheng QW, Wu FH, Sheen J, Shih MC, Lin CS. Efficient and Economical Targeted Insertion in Plant Genomes via Protoplast Regeneration. CRISPR J 2021; 4:752-760. [PMID: 34569819 PMCID: PMC9639242 DOI: 10.1089/crispr.2021.0045] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Versatile genome editing can be facilitated by the insertion of DNA sequences into specific locations. Current protocols involving CRISPR and Cas proteins rely on low efficiency homology-directed repair or non-homologous end joining with modified double-stranded DNA oligonucleotides as donors. Our simple protocol eliminates the need for expensive equipment, chemical and enzymatic donor DNA modification, or plasmid construction by using polyethylene glycol-calcium to deliver non-modified single-stranded DNA oligonucleotides and CRISPR-Cas9 ribonucleoprotein into protoplasts. Plants regenerated via edited protoplasts achieved targeted insertion frequencies of up to 50% in Nicotiana benthamiana and 13.6% in rapid cycling Brassica oleracea without antibiotic selection. Using a 60 nt donor containing 27 nt in each homologous arm, 6/22 regenerated N. benthamiana plants showed targeted insertions, and one contained a precise insertion of a 6 bp HindIII site. The inserted sequences were transmitted to the next generation and invite the possibility of future exploration of versatile genome editing by targeted DNA insertion in plants.
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Affiliation(s)
- Chen-Tran Hsu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan; Harvard Medical School, Boston, Massachusetts, USA
| | - Yu-Hsuan Yuan
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan; Harvard Medical School, Boston, Massachusetts, USA
| | - Yao-Cheng Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan; Harvard Medical School, Boston, Massachusetts, USA
| | - Steven Lin
- Institute of Biological Chemistry, Academia Sinica, Taipei, Taiwan; Harvard Medical School, Boston, Massachusetts, USA
| | - Qiao-Wei Cheng
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan; Harvard Medical School, Boston, Massachusetts, USA
| | - Fu-Hui Wu
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan; Harvard Medical School, Boston, Massachusetts, USA
| | - Jen Sheen
- Department of Molecular Biology and Centre for Computational and Integrative Biology, Massachusetts General Hospital, Boston, Massachusetts, USA; and Harvard Medical School, Boston, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Ming-Che Shih
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan; Harvard Medical School, Boston, Massachusetts, USA
| | - Choun-Sea Lin
- Agricultural Biotechnology Research Center, Academia Sinica, Taipei, Taiwan; Harvard Medical School, Boston, Massachusetts, USA
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7
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Huang CJ, Wu TL, Zheng PX, Ou JY, Ni HF, Lin YC. Comparative Genomic Analysis Uncovered Evolution of Pathogenicity Factors, Horizontal Gene Transfer Events, and Heavy Metal Resistance Traits in Citrus Canker Bacterium Xanthomonas citri subsp. citri. Front Microbiol 2021; 12:731711. [PMID: 34557177 PMCID: PMC8453159 DOI: 10.3389/fmicb.2021.731711] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 08/18/2021] [Indexed: 12/30/2022] Open
Abstract
Background: Worldwide citrus production is severely threatened by Asiatic citrus canker which is caused by the proteobacterium Xanthomonas citri subsp. citri. Foliar sprays of copper-based bactericides are frequently used to control plant bacterial diseases. Despite the sequencing of many X. citri strains, the genome diversity and distribution of genes responsible for metal resistance in X. citri subsp. citri strains from orchards with different management practices in Taiwan are not well understood. Results: The genomes of three X. citri subsp. citri strains including one copper-resistant strain collected from farms with different management regimes in Taiwan were sequenced by Illumina and Nanopore sequencing and assembled into complete circular chromosomes and plasmids. CRISPR spoligotyping and phylogenomic analysis indicated that the three strains were located in the same phylogenetic lineages and shared ∼3,000 core-genes with published X. citri subsp. citri strains. These strains differed mainly in the CRISPR repeats and pathogenicity-related plasmid-borne transcription activator-like effector (TALE)-encoding pthA genes. The copper-resistant strain has a unique, large copper resistance plasmid due to an unusual ∼40 kbp inverted repeat. Each repeat contains a complete set of the gene cluster responsible for copper and heavy metal resistance. Conversely, the copper sensitive strains carry no metal resistance genes in the plasmid. Through comparative analysis, the origin and evolution of the metal resistance clusters was resolved. Conclusion: Chromosomes remained constant among three strains collected in Taiwan, but plasmids likely played an important role in maintaining pathogenicity and developing bacterial fitness in the field. The evolution of pathogenicity factors and horizontal gene transfer events were observed in the three strains. These data suggest that agricultural management practices could be a potential trigger for the evolution of citrus canker pathogens. The decrease in the number of CRISPR repeats and pthA genes might be the result of adaptation to a less stressful environment. The metal resistance genes in the copper resistant X. citri strain likely originated from the Mauritian strain not the local copper-resistant X. euvesicatoria strain. This study highlights the importance of plasmids as 'vehicles' for exchanging genetic elements between plant pathogenic bacteria and contributing to bacterial adaptation to the environment.
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Affiliation(s)
- Chien-Jui Huang
- Department of Plant Medicine, National Chiayi University, Chiayi, Taiwan
| | - Ting-Li Wu
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Po-Xing Zheng
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Jheng-Yang Ou
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
| | - Hui-Fang Ni
- Department of Plant Protection, Chiayi Agricultural Experiment Station, Taiwan Agricultural Research Institute, Chiayi, Taiwan
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
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8
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Lin YC, Chou SH, Hsueh WJ. Tunable light absorption of graphene using topological interface states. Opt Lett 2020; 45:4369-4372. [PMID: 32796960 DOI: 10.1364/ol.397738] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
A tunable light absorption of graphene using topological interface states (TISs) is presented. The monolayer graphene is embedded in the interface of asymmetric topological photonic crystals (ATPCs). A strong absorption phenomenon occurs by the excitation of TISs. It is found that the absorption spectra are intensively dependent on the chemical potential of graphene and the periodic number of the ATPCs. Furthermore, the absorption can be rapidly switched in a slight variation of chemical potential, which is modulated by the applied gate voltage on graphene. This study not only opens up a new approach for enhancing light-monolayer graphene interactions, but also provides for practical applications in high absorption optoelectronic devices. This strong absorption phenomenon is different from those in Fabry-Perot resonators, nano-cavities photonic crystal, and traditional topological photonic crystals (TPCs).
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9
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Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin YC, Xu Q, Chen LJ, Yoshida K, Fujiwara S, Wang ZW, Zhang YQ, Mitsuda N, Wang M, Liu GH, Pecoraro L, Huang HX, Xiao XJ, Lin M, Wu XY, Wu WL, Chen YY, Chang SB, Sakamoto S, Ohme-Takagi M, Yagi M, Zeng SJ, Shen CY, Yeh CM, Luo YB, Tsai WC, Van de Peer Y, Liu ZJ. Author Correction: The Apostasia genome and the evolution of orchids. Nature 2020; 583:E30. [PMID: 32681116 PMCID: PMC7608229 DOI: 10.1038/s41586-020-2524-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Ke-Wei Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium.,VIB Center for Plant Systems Biology, 9052, Gent, Belgium
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium.,VIB Center for Plant Systems Biology, 9052, Gent, Belgium
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shan-Ce Niu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Jie-Yu Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China.,College of Forestry, South China Agricultural University, Guangzhou, 510640, China
| | - Yao-Cheng Lin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium.,VIB Center for Plant Systems Biology, 9052, Gent, Belgium.,Biotechnology Center in Southern Taiwan, Agricultural Biotechnology Research Center, Academia Sinica, 741, Tainan, Taiwan
| | - Qing Xu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Li-Jun Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Kouki Yoshida
- Technology Center, Taisei Corporation, Nase-cho 344-1, Totsuka-ku, Yokohama, Kanagawa, 245-0051, Japan
| | - Sumire Fujiwara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8562, Japan
| | - Zhi-Wen Wang
- PubBio-Tech Services Corporation, Wuhan, 430070, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8562, Japan
| | - Meina Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Guo-Hui Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Lorenzo Pecoraro
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Hui-Xia Huang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Xin-Ju Xiao
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Min Lin
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Xin-Yi Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China
| | - Wan-Lin Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China.,Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan
| | - You-Yi Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Song-Bin Chang
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8562, Japan
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki, 305-8562, Japan.,Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Masafumi Yagi
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki, 305-8519, Japan
| | - Si-Jin Zeng
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China.,College of Forestry, South China Agricultural University, Guangzhou, 510640, China
| | - Ching-Yu Shen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Chuan-Ming Yeh
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama, 338-8570, Japan
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan.,Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701, Taiwan
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Gent, Belgium.,VIB Center for Plant Systems Biology, 9052, Gent, Belgium.,Department of Genetics, Genomics Research Institute, Pretoria, 0028, South Africa
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen, 518114, China. .,College of Forestry, South China Agricultural University, Guangzhou, 510640, China. .,College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, 350002, China. .,The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen, 518055, China.
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10
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Lin YC, Yan HT. Media Freedom is the Primary Culprit for Depressive Disorders: A Cross-National Analysis. Eur J Public Health 2019. [DOI: 10.1093/eurpub/ckz187.102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Abstract
Background
There has been much speculation about social environments causing an epidemic of depression. The objectives of this study are to examine how media freedom influences prevalence of depressive disorders. A direct effect of free media is great levels of information complexity causing poor mental health. Two indirect effects are that media freedom facilitates modernization, which is associated with competition-related stress, and government investment in social protection, which impedes the person’s ability to manage stress.
Methods
The study used a cross-sectional analysis on determinants of prevalence of depressive disorders in 2015 covering 98 democratic countries. Media freedom was measured as the degree to which a country allows the freedom of news and information of print media, television, and radio broadcasting (0-100: least to most free). Control variables were then added, including GDP per capita growth, population density, country latitude, and religious affiliations. Further, a mediation analysis was applied to test if there is a causal pathway that links the degrees of media freedom and the levels of economic development or/and social protection to prevalence of depression.
Results
We found that an increase in the score of media freedom by 10 resulted in a 0.20 percentage point increase in prevalence of depressive disorders (%) (0.20, CI = 0.10-0.30). Our theoretical expectations were still confirmed when this study examined the relationship for each year between 2011 and 2014 (e.g. in 2014, 0.19, CI = 0.09-0.29), used an alternative index of media freedom from a practitioners’ view (0.17, CI = 0.02-0.32), or measured each country’s level of internet and digital media freedom (0.30, CI = 0.10-0.49). Further, a mediation test showed that 39.88% and 21.38% of the total effect was mediated through the economic and social pathway respectively.
Conclusions
The findings suggest that great levels of media freedom matter in increasing prevalence of depression.
Key messages
Great levels of media freedom matter in increasing prevalence of depression. There are direct and two indirect effects of media freedom on prevalence of depression.
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Affiliation(s)
- Y C Lin
- Chinese Medicine Department, China Medical University Hospital, Taichung City, Taiwan
| | - H T Yan
- Department of Government, University of Essex, Colchester, UK
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11
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Chiang JY, Fu CM, Lin YC, Ku BW, Hsu SU, Wu CK, Lin LY, Lin JL, Chiang FT, Juang JM. P1880Entropy-based algorithm for atrial fibrillation detection using photoplethysomgraphic signal recorded by a smart watch. Eur Heart J 2019. [DOI: 10.1093/eurheartj/ehz748.0628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
Atrial fibrillation (AF) is the most common arrhythmia, and its paroxysmal and short duration nature makes its detection challenging. The most important limitation of current smartwatches is that patients need to touch to the sensor of the watch to record signals when patients feel discomfort. We developed a wearable smart watch and evaluated its accuracy to differentiate AF from sinus rhythm, which can continuously detecting heart rhythm without hand touching the device.
Methods and results
A wearable smart watch with PPG sensor and electrocardiogram (ECG) recording function was used for signal acquisition. A total 399 patients with a mean age of 67 years old were enrolled in the study, of whom 237 (81.5%) were male, and 101 have been diagnosed with AF. Pulse wave extracted from the green light spectrum of the signal and ECG were recorded for about 10 minutes for each patient. Pulse-to-pulse intervals (PPI) were automatically identified. All ECG signals were verified by two cardiologists. The correlation between R-to-R interval on ECG and PPI were excellent, with a correlation coefficient R >0.99 (p<0.05). An entropy-based algorithm which combined Shannon entropy of successive difference of PPI and sample entropy of PPI was used to discriminate between AF and sinus rhythm. This method had high sensitivity and specificity (96% and 98%, respectively), the area under receiver operating characteristic curve reached 0.98.
Conclusions
We developed an entropy-based algorithm for AF detection with PPG signal recorded by a wearable smart watch. This algorithm discriminates AF from sinus rhythm accurately. This advance in technology overcomes an important clinical obstacle and can increase the AF detection rate tremendously.
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Affiliation(s)
- J Y Chiang
- National Taiwan University Hospital, Internal medicine, Taipei, Taiwan
| | - C M Fu
- MediaTek Inc, Taipei, Taiwan
| | - Y C Lin
- MediaTek Inc, Taipei, Taiwan
| | - B W Ku
- MediaTek Inc, Taipei, Taiwan
| | - S U Hsu
- MediaTek Inc, Taipei, Taiwan
| | - C K Wu
- MediaTek Inc, Taipei, Taiwan
| | - L Y Lin
- National Taiwan University Hospital, Division of Cardiology, Department of Internal Medicine, Taipei, Taiwan
| | - J L Lin
- National Taiwan University Hospital, Division of Cardiology, Department of Internal Medicine, Taipei, Taiwan
| | - F T Chiang
- National Taiwan University Hospital, Division of Cardiology, Department of Internal Medicine, Taipei, Taiwan
| | - J M Juang
- National Taiwan University Hospital, Division of Cardiology, Department of Internal Medicine, Taipei, Taiwan
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12
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Li MY, Ye J, Huang ZY, Lin YC, Liu AH, Li LP, Chen J, Wang YP. [Clinical analysis of five cases of autism spectrum disorder complicated with epilepsy with chromosome copy number variation]. Zhonghua Yi Xue Za Zhi 2019; 99:2615-2618. [PMID: 31510723 DOI: 10.3760/cma.j.issn.0376-2491.2019.33.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To explore the clinical features and genetic causes of autism spectrum disorder (ASD) patients with epilepsy. Methods: The clinical data of five patients with ASD and epilepsy admitted to Xuanwu Hospital between September 2017 and September 2018 were collected, including medical history, intelligence level, developmental level, physical examination, neuroimaging and electroencephalogram. High-throughput whole-genome sequencing was applied to five patients and their parents. Results: Of five patients, four were male and one was female. All five patients had mild mental retardation, and one patient had significant growth retardation and craniofacial deformity. The average epilepsy onset age was 6.3 years old (7 months to 16 years). The main epileptic type was tonic-clonic seizure with abnormal EEG results. All patients have a favorable response to anti-epileptic drugs. Whole-exome sequencing (WES) revealed copy number variation in all 5 patients. Among them, 3 cases were reported to be pathogenic, and 2 cases were not reported (chromosome 16p13.3 duplication and chromosome 21q22.3 deletion). Conclusions: The results of current study support that autism spectrum disorders with seizures is often associated with copy number variations, such as Williams-Beuren region duplication syndrome, chromosome 15q11.2 duplication syndrome and chromosome 15q11.2 deletion syndrome. We reported two novel copy number variations (chromosome 16p13.3 duplication and chromosome 21q22.3 deletion) in two autism spectrum disorder patients with epileptic seizures.
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Affiliation(s)
- M Y Li
- Department of Neurology, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
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13
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Rodrigues AS, Chaves I, Costa BV, Lin YC, Lopes S, Milhinhos A, Van de Peer Y, Miguel CM. Small RNA profiling in Pinus pinaster reveals the transcriptome of developing seeds and highlights differences between zygotic and somatic embryos. Sci Rep 2019; 9:11327. [PMID: 31383905 PMCID: PMC6683148 DOI: 10.1038/s41598-019-47789-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2018] [Accepted: 07/24/2019] [Indexed: 02/07/2023] Open
Abstract
Regulation of seed development by small non-coding RNAs (sRNAs) is an important mechanism controlling a crucial phase of the life cycle of seed plants. In this work, sRNAs from seed tissues (zygotic embryos and megagametophytes) and from somatic embryos of Pinus pinaster were analysed to identify putative regulators of seed/embryo development in conifers. In total, sixteen sRNA libraries covering several developmental stages were sequenced. We show that embryos and megagametophytes express a large population of 21-nt sRNAs and that substantial amounts of 24-nt sRNAs were also detected, especially in somatic embryos. A total of 215 conserved miRNAs, one third of which are conifer-specific, and 212 high-confidence novel miRNAs were annotated. MIR159, MIR171 and MIR394 families were found in embryos, but were greatly reduced in megagametophytes. Other families, like MIR397 and MIR408, predominated in somatic embryos and megagametophytes, suggesting their expression in somatic embryos is associated with in vitro conditions. Analysis of the predicted miRNA targets suggests that miRNA functions are relevant in several processes including transporter activity at the cotyledon-forming stage, and sulfur metabolism across several developmental stages. An important resource for studying conifer embryogenesis is made available here, which may also provide insightful clues for improving clonal propagation via somatic embryogenesis.
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Affiliation(s)
- Andreia S Rodrigues
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Inês Chaves
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Bruno Vasques Costa
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
- INESC-ID, Instituto Superior Técnico, Universidade de Lisboa, Rua Alves Redol 9, Lisboa, 1000-029, Portugal
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan and Agricultural Biotechnology Research Center, Academia Sinica, Tainan, Taiwan
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Susana Lopes
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Ana Milhinhos
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal
| | - Yves Van de Peer
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Private bag X20, Pretoria, 0028, South Africa
| | - Célia M Miguel
- iBET, Instituto de Biologia Experimental e Tecnológica, Apartado 12, 2781-901, Oeiras, Portugal.
- Instituto de Tecnologia Química e Biológica António Xavier, Universidade Nova de Lisboa (ITQB NOVA), Av. República, 2780-157, Oeiras, Portugal.
- BioISI - Biosystems & Integrative Sciences Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
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14
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Borgers K, Ou JY, Zheng PX, Tiels P, Van Hecke A, Plets E, Michielsen G, Festjens N, Callewaert N, Lin YC. Reference genome and comparative genome analysis for the WHO reference strain for Mycobacterium bovis BCG Danish, the present tuberculosis vaccine. BMC Genomics 2019; 20:561. [PMID: 31286858 PMCID: PMC6615170 DOI: 10.1186/s12864-019-5909-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 06/17/2019] [Indexed: 11/20/2022] Open
Abstract
BACKGROUND Mycobacterium bovis bacillus Calmette-Guérin (M. bovis BCG) is the only vaccine available against tuberculosis (TB). In an effort to standardize the vaccine production, three substrains, i.e. BCG Danish 1331, Tokyo 172-1 and Russia BCG-1 were established as the WHO reference strains. Both for BCG Tokyo 172-1 as Russia BCG-1, reference genomes exist, not for BCG Danish. In this study, we set out to determine the completely assembled genome sequence for BCG Danish and to establish a workflow for genome characterization of engineering-derived vaccine candidate strains. RESULTS By combining second (Illumina) and third (PacBio) generation sequencing in an integrated genome analysis workflow for BCG, we could construct the completely assembled genome sequence of BCG Danish 1331 (07/270) (and an engineered derivative that is studied as an improved vaccine candidate, a SapM KO), including the resolution of the analytically challenging long duplication regions. We report the presence of a DU1-like duplication in BCG Danish 1331, while this tandem duplication was previously thought to be exclusively restricted to BCG Pasteur. Furthermore, comparative genome analyses of publicly available data for BCG substrains showed the absence of a DU1 in certain BCG Pasteur substrains and the presence of a DU1-like duplication in some BCG China substrains. By integrating publicly available data, we provide an update to the genome features of the commonly used BCG strains. CONCLUSIONS We demonstrate how this analysis workflow enables the resolution of genome duplications and of the genome of engineered derivatives of the BCG Danish vaccine strain. The BCG Danish WHO reference genome will serve as a reference for future engineered strains and the established workflow can be used to enhance BCG vaccine standardization.
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Affiliation(s)
- Katlyn Borgers
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Jheng-Yang Ou
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, 74145 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 74145 Taiwan
| | - Po-Xing Zheng
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, 74145 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 74145 Taiwan
| | - Petra Tiels
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Annelies Van Hecke
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Evelyn Plets
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Gitte Michielsen
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Nele Festjens
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Nico Callewaert
- VIB-UGhent Center for Medical Biotechnology, Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
- Department of Biochemistry and Microbiology, Ghent University; Technologiepark-Zwijnaarde 71, 9052 Ghent, Belgium
| | - Yao-Cheng Lin
- Biotechnology Center in Southern Taiwan, Academia Sinica, Tainan, 74145 Taiwan
- Agricultural Biotechnology Research Center, Academia Sinica, Tainan, 74145 Taiwan
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15
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Abstract
We report a 49-year-old woman who presented with a hypertensive crisis and acute heart failure and reduced left ventricular systolic function. An abdominal ultrasonography revealed a huge lobulated heterogeneous mass at the lower pole of the right kidney and a mass over the left suprarenal area, which were further delineated by magnetic resonance imaging. The patient underwent laparoscopic right radical nephrectomy and left adrenalectomy. Histopathological analysis confirmed the diagnoses of clear cell renal cell carcinoma of the right kidney with metastasis to the lung; and atypical pheochromocytoma of the left adrenal gland. Target therapy was initiated, which resulted in stabilization of the patient's tumors and the recovery of her heart function. To avoid a delayed diagnosis and catastrophic outcome, clinicians should consider such rare causes of acute decompensated heart failure.
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Affiliation(s)
- H H Chen
- School of Medicine, National Defense Medical Center, Taipei, Taiwan
| | - S T Wu
- Division of Urology, Department of Surgery, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - Y C Lin
- Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
| | - C S Lin
- Division of Cardiology, Department of Internal Medicine, Tri-Service General Hospital, National Defense Medical Center, Taipei, Taiwan
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16
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Leng XR, Ye J, Zhou QL, Qi XH, Dong YH, Zhang LP, Zhang YF, Wang YP, Li LP, Lin YC. [Clinical features and gene analysis of TBC1D24 gene mutation related early-onset focal myoclonic epilepsy]. Zhonghua Yi Xue Za Zhi 2018; 98:445-449. [PMID: 29429257 DOI: 10.3760/cma.j.issn.0376-2491.2018.06.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Objective: To investigate the clinical features and genetic characteristics of patients with TBC1D24 gene mutation related early-onset focal myoclonic epilepsy. Methods: Clinical data of 3 patients with TBC1D24 gene mutation related early-onset focal myoclonic epilepsy of Xuanwu Hospital from November 2016 to June 2017 was collected and analyzed.Candidate gene mutations were screened by second generation sequencing. Results: Among the 3 patients, 1 was male and 2 were females.Seizure onset age was 4 months, 3 years and 5 years after birth respectively. Two patients had family history of epilepsy.They all had prolonged episodes of focal myoclonus. Two patients had mental retardation.Scalp electroencephalograms (EEG) was recorded in all 3 cases and myoclonic seizures were captured.The ictal EEGs were normal in all cases. In one patient, the ictal EEG of generalized seizure showed alpha rhythm originating from left fronto-central region. Brain magnetic resonance imaging (MRI) was normal in 2 patients. Abnormal signal was found bilaterally in cerebellum in 1 patient. The gene screening showed that two patients carried compound heterozygous mutation of TBC1D24 gene and one carried homozygous mutation, all of which were de novo mutations.All the patients were treated with multiple antiepileptic drugs (AEDs) and seizures were uncontrolled in 2 patients. One patient was followed up for 10 months without recurrence. Conclusions: TBC1D24 gene related early-onset focal myoclonic epilepsy is clinically characterized by early onset, prolonged focal myoclonus which relieved with sleep, mental retardation and poor response to AEDs.The interictal and ictal EEG usually show normal. Genetic analysis can assist in diagnosis and genetic counseling.
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Affiliation(s)
- X R Leng
- Department of Pediatrics, Xuanwu Hospital, Capital Medical University, Beijing 100053, China
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17
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Lin YC, Chang YH. Poor appetite and long-term risk of falls among middle-aged and older adults: A longitudinal study. Eur J Public Health 2018. [DOI: 10.1093/eurpub/cky214.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- YC Lin
- Department of Chinese Medicine, China Medical University Hospital, Taichung City, Taiwan
| | - YH Chang
- Department of Public Health, China Medical University, Taichung City, Taiwan
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18
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Lin YC, Tsou CH, Hsueh WJ. Ultra-slow light in one-dimensional Cantor photonic crystals. Opt Lett 2018; 43:4120-4123. [PMID: 30160731 DOI: 10.1364/ol.43.004120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 07/26/2018] [Indexed: 06/08/2023]
Abstract
Ultra-slow light and complete transmission properties in one-dimensional Cantor photonic crystals are presented. In contrast to traditional dielectric photonic crystals, the proposed structure has large group delay, slower group velocity, and a high quality factor within the same layers and materials. This study shows that larger than 1 μs group delay and slower than 1 m/s group velocity are achieved in the fifth-order Cantor photonic crystal with 52.75 μm length. This ultra-slow-light structure is very promising for application in advanced slow-light devices. A high quality factor of 109 and multiband filters with complete transmission can also be obtained by using this approach.
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19
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Petrov NV, Nalegaev SS, Belashov AV, Shevkunov IA, Putilin SE, Lin YC, Cheng CJ. Time-resolved inline digital holography for the study of noncollinear degenerate phase modulation. Opt Lett 2018; 43:3481-3484. [PMID: 30067690 DOI: 10.1364/ol.43.003481] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 06/08/2018] [Indexed: 06/08/2023]
Abstract
Recent works demonstrated that digital time-resolved holography is the prospective approach to study nonlinear light-matter interaction processes. In this Letter, we present a straightforward inline holographic approach for studying degenerate phase modulation induced by an inclined collimated pump beam in the isotropic sample. The method is based on a minimization of the difference between experimentally acquired data and simulated inline holograms obtained from a numerical model of pump-probe interaction in optical nonlinear media. A sophisticated experimental data processing algorithm is implemented to provide high sensitivity and a signal-to-noise ratio eligible for soft interaction with a collimated pump beam. The integral phase shift determined by our method can be used to estimate the nonlinear refractive index and the relaxation time for material with a low damage threshold. We validated our approach for the case of soda-lime and BK7 glasses.
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20
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Chen W, Wang S, Zhang HX, Ruan D, Xia WG, Cui YY, Zheng CT, Lin YC. Optimization of dietary zinc for egg production and antioxidant capacity in Chinese egg-laying ducks fed a diet based on corn-wheat bran and soybean meal. Poult Sci 2018; 96:2336-2343. [PMID: 28339968 DOI: 10.3382/ps/pex032] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2016] [Accepted: 02/24/2017] [Indexed: 11/20/2022] Open
Abstract
The aim of this study was to evaluate the effect of zinc supplementation on productive performance and antioxidant status in laying ducks. Five-hundred-four laying ducks were divided into 7 treatments, each containing 6 replicates of 12 ducks. The ducks were caged individually and fed a corn-soybean meal and wheat bran basal diet (37 mg Zn/kg) or the basal diet supplemented with 15, 30, 45, 60, 75, or 90 mg Zn/kg (as zinc sulfate). During the early laying period of 10 d (daily egg production <80%), egg production, daily egg mass, and FCR increased quadratically with increasing dietary Zn levels (P < 0.05). The highest egg production and daily egg weight were obtained when 30 or 45 mg Zn/kg diet was supplemented, with lowest FCR. Similarly, the highest egg production and daily egg mass were observed in the group supplemented with 30 or 45 mg Zn/kg during the peak laying period of the subsequent 120 d (daily egg production >80%). Average egg weight and feed intake did not differ among the groups of graded Zn supplementation.The egg quality was not affected by dietary Zn, including the egg shape index, Haugh unit, yolk color score, egg composition, and shell thickness. The activities of plasma activities of total superoxide dismutase (T-SOD) and glutathione peroxidase (GSH-PX) increased in a quadratic manner (P < 0.001) with increasing supplemental Zn. Plasma concentration of Zn increased quadratically (P < 0.05) as dietary Zn increased. The hepatic activity of Cu/Zn-SOD and GSH-PX increased quadratically (P < 0.05) with increasing dietary Zn. Plasma Zn concentrations were positively correlated with activities of T-SOD (P < 0.05), and positively with plasma Cu. Plasma concentration of reduced glutathione was correlated with plasma Cu. In conclusion, supplementation of Zn at 30 or 45 mg/kg to a corn-wheat bran and soybean basal diet may improve the productive performance and enhance the antioxidant capacity.
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Affiliation(s)
- W Chen
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China.,Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China.,Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China.,Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
| | - S Wang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China.,Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China.,Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China.,Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
| | - H X Zhang
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China.,Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China.,Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China.,Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
| | - D Ruan
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China.,Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China.,Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China.,Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
| | - W G Xia
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China.,Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China.,Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China.,Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
| | - Y Y Cui
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China.,Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China.,Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China.,Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
| | - C T Zheng
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China.,Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China.,Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China.,Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
| | - Y C Lin
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China.,State Key Laboratory of Livestock and Poultry Breeding, Guangzhou 510640, China.,Key Laboratory of Animal Nutrition and Feed Science in South China, Ministry of Agriculture, Guangzhou 510640, China.,Guangdong Public Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China.,Guangdong Key Laboratory of Animal Breeding and Nutrition, Guangzhou 510640, China
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21
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Wingfield BD, Berger DK, Steenkamp ET, Lim HJ, Duong TA, Bluhm BH, de Beer ZW, De Vos L, Fourie G, Naidoo K, Olivier N, Lin YC, Van de Peer Y, Joubert F, Crampton BG, Swart V, Soal N, Tatham C, van der Nest MA, van der Merwe NA, van Wyk S, Wilken PM, Wingfield MJ. IMA Genome-F 8: Draft genome of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens and Ophiostoma ips. IMA Fungus 2017; 8:385-396. [PMID: 29242781 PMCID: PMC5729718 DOI: 10.5598/imafungus.2017.08.02.10] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2017] [Accepted: 11/09/2017] [Indexed: 11/29/2022] Open
Abstract
The genomes of Cercospora zeina, Fusarium pininemorale, Hawksworthiomyces lignivorus, Huntiella decipiens, and Ophiostoma ips are presented in this genome announcement. Three of these genomes are from plant pathogens and otherwise economically important fungal species. Fusarium pininemorale and H. decipiens are not known to cause significant disease but are closely related to species of economic importance. The genome sizes range from 25.99 Mb in the case of O. ips to 4.82 Mb for H. lignivorus. These genomes include the first reports of a genome from the genus Hawksworthiomyces. The availability of these genome data will allow the resolution of longstanding questions regarding the taxonomy of these species. In addition these genome sequences through comparative studies with closely related organisms will increase our understanding of how these species or close relatives cause disease.
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Affiliation(s)
- Brenda D. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Dave K. Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Emma T. Steenkamp
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Hye-Jin Lim
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Tuan A. Duong
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Burton H. Bluhm
- Department of Plant Pathology, University of Arkansas, Fayetteville, USA
| | - Z. Wilhelm de Beer
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Lieschen De Vos
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - G. Fourie
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Kershney Naidoo
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Nicky Olivier
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Yao-Cheng Lin
- VIB Department of Plant Systems Biology, Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- VIB Department of Plant Systems Biology, Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Genetics, Genomics Research Institute, University of Pretoria, Pretoria, South Africa
| | - Fourie Joubert
- Centre for Bioinformatics and Computational Biology, Department of Biochemistry, University of Pretoria, Pretoria, South Africa
| | - Bridget G. Crampton
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Velushka Swart
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria, South Africa
| | - Nicole Soal
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Catherine Tatham
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Magriet A. van der Nest
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Nicolaas A. van der Merwe
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Stephanie van Wyk
- Department of Microbiology and Plant Pathology, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - P. Markus Wilken
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
| | - Michael J. Wingfield
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, Pretoria 0002, South Africa
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22
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Shi YK, Wang L, Han BH, Li W, Yu P, Liu YP, Ding CM, Song X, Ma ZY, Ren XL, Feng JF, Zhang HL, Chen GY, Han XH, Wu N, Yao C, Song Y, Zhang SC, Song W, Liu XQ, Zhao SJ, Lin YC, Ye XQ, Li K, Shu YQ, Ding LM, Tan FL, Sun Y. First-line icotinib versus cisplatin/pemetrexed plus pemetrexed maintenance therapy for patients with advanced EGFR mutation-positive lung adenocarcinoma (CONVINCE): a phase 3, open-label, randomized study. Ann Oncol 2017; 28:2443-2450. [PMID: 28945850 DOI: 10.1093/annonc/mdx359] [Citation(s) in RCA: 181] [Impact Index Per Article: 25.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND Icotinib has been previously shown to be non-inferior to gefitinib in non-selected advanced non-small-cell lung cancer patients when given as second- or further-line treatment. In this open-label, randomized, phase 3 CONVINCE trial, we assessed the efficacy and safety of first-line icotinib versus cisplatin/pemetrexed plus pemetrexed maintenance in lung adenocarcinoma patients with epidermal growth factor receptor (EGFR) mutation. PATIENTS AND METHODS Eligible participants were adults with stage IIIB/IV lung adenocarcinoma and exon 19/21 EGFR mutations. Participants were randomly allocated (1 : 1) to receive oral icotinib or 3-week cycle of cisplatin plus pemetrexed for up to four cycles; non-progressive patients after four cycles were maintained with pemetrexed until disease progression or intolerable toxicity. The primary end point was progression-free survival (PFS) assessed by independent response evaluation committee. Other end points included overall survival (OS) and safety. RESULTS Between January 2013 and August 2014, 296 patients were randomized, and 285 patients were treated (148 to icotinib, 137 to chemotherapy). Independent response evaluation committee-assessed PFS was significantly longer in the icotinib group (11.2 versus 7.9 months; hazard ratio, 0.61, 95% confidence interval 0.43-0.87; P = 0.006). No significant difference for OS was observed between treatments in the overall population or in EGFR-mutated subgroups (exon 19 Del/21 L858R). The most common grade 3 or 4 adverse events (AEs) in the icotinib group were rash (14.8%) and diarrhea (7.4%), compared with nausea (45.9%), vomiting (29.2%), and neutropenia (10.9%) in the chemotherapy group. AEs (79.1% versus 94.2%; P < 0.001) and treatment-related AEs (54.1% versus 90.5%; P < 0.001) were significantly fewer in the icotinib group than in the chemotherapy group. CONCLUSIONS First-line icotinib significantly improves PFS of advanced lung adenocarcinoma patients with EGFR mutation with a tolerable and manageable safety profile. Icotinib should be considered as a first-line treatment for this patient population.
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Affiliation(s)
- Y K Shi
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing.
| | - L Wang
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - B H Han
- Department of Pulmonology, Shanghai Chest Hospital, Shanghai
| | - W Li
- Department of Oncology, The First Hospital Affiliated to Jilin University, Changchun
| | - P Yu
- Department of Lung Cancer Medical Oncology, Sichuan Cancer Hospital, Chengdu
| | - Y P Liu
- Department of Medical Oncology, The First Hospital of China Medical University, Shenyang
| | - C M Ding
- Department of Respiratory Medicine, The Fourth Hospital of Hebei Medical University, Shijiazhuang
| | - X Song
- Department of Respiratory Medicine, Shanxi Provincial Tumor Hospital, Taiyuan
| | - Z Y Ma
- Department of Oncology, Henan Cancer Hospital, Zhengzhou
| | - X L Ren
- Department of Respiratory Medicine, Xijing Hospital, The Fourth Military Medical University, Xi'an
| | - J F Feng
- Department of Oncology, Jiangsu Cancer Hospital, Nanjing
| | - H L Zhang
- Department of Oncology, Tangdu Hospital, The Fourth Military Medical University, Xi'an
| | - G Y Chen
- Department of Medical Oncology, The Affiliated Tumor Hospital of Harbin Medical University, Harbin
| | - X H Han
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - N Wu
- Department of Imaging Diagnosis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - C Yao
- Department of Biostatistics, Peking University Clinical Research Institute, Beijing
| | - Y Song
- Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing
| | - S C Zhang
- Department of Medical Oncology, Beijing Chest Hospital, Capital Medical University, Beijing
| | - W Song
- Department of Radiology, Peking Union Medical College Hospital, Beijing
| | - X Q Liu
- Department of Pulmonary Oncology, The 307th Hospital of Chinese People's Liberation Army, Beijing
| | - S J Zhao
- Department of Imaging Diagnosis, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
| | - Y C Lin
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou
| | - X Q Ye
- Department of Respiratory Diseases, The Second Affiliated Hospital of Nanchang University, Nanchang
| | - K Li
- Department of Thoracic Oncology, Tianjin Medical University Cancer Institute and Hospital, Tianjin
| | - Y Q Shu
- Department of Oncology, Jiangsu Provincial Hospital, Nanjing
| | - L M Ding
- Betta Pharmaceuticals Co., Ltd, Hangzhou, China
| | - F L Tan
- Betta Pharmaceuticals Co., Ltd, Hangzhou, China
| | - Y Sun
- Department of Medical Oncology, Beijing Key Laboratory of Clinical Study on Anticancer Molecular Targeted Drugs, National Cancer Center/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing
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23
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Zhang GQ, Liu KW, Li Z, Lohaus R, Hsiao YY, Niu SC, Wang JY, Lin YC, Xu Q, Chen LJ, Yoshida K, Fujiwara S, Wang ZW, Zhang YQ, Mitsuda N, Wang M, Liu GH, Pecoraro L, Huang HX, Xiao XJ, Lin M, Wu XY, Wu WL, Chen YY, Chang SB, Sakamoto S, Ohme-Takagi M, Yagi M, Zeng SJ, Shen CY, Yeh CM, Luo YB, Tsai WC, Van de Peer Y, Liu ZJ. The Apostasia genome and the evolution of orchids. Nature 2017; 549:379-383. [PMID: 28902843 PMCID: PMC7416622 DOI: 10.1038/nature23897] [Citation(s) in RCA: 212] [Impact Index Per Article: 30.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/07/2017] [Indexed: 12/15/2022]
Abstract
WebComparing the whole genome sequence of Apostasia shenzhenica with transcriptome and genome data from five orchid subfamilies permits the reconstruction of an ancestral gene toolkit, providing insight into orchid origins, evolution and diversification. Around 10 per cent of flowering plant species are orchids, with a broad diversity in both morphology and lifestyle. Apostasia is one of the earliest-diverging genera of Orchidaceae. To study the evolution and diversity of Orchidaceae, Zhong-Jian Liu, Yves Van de Peer and colleagues sequenced the genome of Apostasia shenzhenica, a self-pollinating species found in southeast China. The authors also report improved genomes for two species of Epidendroideae, Phalaenopsis equestris and Dendrobium catenatum, as well as transcriptome analysis of representatives of subfamilies of Orchidaceae. Their analyses provide insights into orchid origins, genome evolution, adaptation and diversification. Constituting approximately 10% of flowering plant species, orchids (Orchidaceae) display unique flower morphologies, possess an extraordinary diversity in lifestyle, and have successfully colonized almost every habitat on Earth1,2,3. Here we report the draft genome sequence of Apostasia shenzhenica4, a representative of one of two genera that form a sister lineage to the rest of the Orchidaceae, providing a reference for inferring the genome content and structure of the most recent common ancestor of all extant orchids and improving our understanding of their origins and evolution. In addition, we present transcriptome data for representatives of Vanilloideae, Cypripedioideae and Orchidoideae, and novel third-generation genome data for two species of Epidendroideae, covering all five orchid subfamilies. A. shenzhenica shows clear evidence of a whole-genome duplication, which is shared by all orchids and occurred shortly before their divergence. Comparisons between A. shenzhenica and other orchids and angiosperms also permitted the reconstruction of an ancestral orchid gene toolkit. We identify new gene families, gene family expansions and contractions, and changes within MADS-box gene classes, which control a diverse suite of developmental processes, during orchid evolution. This study sheds new light on the genetic mechanisms underpinning key orchid innovations, including the development of the labellum and gynostemium, pollinia, and seeds without endosperm, as well as the evolution of epiphytism; reveals relationships between the Orchidaceae subfamilies; and helps clarify the evolutionary history of orchids within the angiosperms.
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Affiliation(s)
- Guo-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Ke-Wei Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Rolf Lohaus
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Shan-Ce Niu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jie-Yu Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,College of Forestry, South China Agricultural University, Guangzhou 510640, China
| | - Yao-Cheng Lin
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium
| | - Qing Xu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Li-Jun Chen
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Kouki Yoshida
- Technology Center, Taisei Corporation, Nase-cho 344-1, Totsuka-ku, Yokohama, Kanagawa 245-0051, Japan
| | - Sumire Fujiwara
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Zhi-Wen Wang
- PubBio-Tech Services Corporation, Wuhan 430070, China
| | - Yong-Qiang Zhang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Nobutaka Mitsuda
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Meina Wang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Guo-Hui Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Lorenzo Pecoraro
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Hui-Xia Huang
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Xin-Ju Xiao
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Min Lin
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Xin-Yi Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China
| | - Wan-Lin Wu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan
| | - You-Yi Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Song-Bin Chang
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Shingo Sakamoto
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan
| | - Masaru Ohme-Takagi
- Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology (AIST), Central 6, Higashi 1-1-1, Tsukuba, Ibaraki 305-8562, Japan.,Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Masafumi Yagi
- NARO Institute of Floricultural Science (NIFS), 2-1 Fujimoto, Tsukuba, Ibaraki 305-8519, Japan
| | - Si-Jin Zeng
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,College of Forestry, South China Agricultural University, Guangzhou 510640, China
| | - Ching-Yu Shen
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Chuan-Ming Yeh
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura-ku, Saitama 338-8570, Japan
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan 701, Taiwan.,Department of Life Sciences, National Cheng Kung University, Tainan 701, Taiwan.,Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan 701, Taiwan
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Gent, Belgium.,VIB Center for Plant Systems Biology, 9052 Gent, Belgium.,Department of Genetics, Genomics Research Institute, Pretoria 0028, South Africa
| | - Zhong-Jian Liu
- Shenzhen Key Laboratory for Orchid Conservation and Utilization, The National Orchid Conservation Center of China and The Orchid Conservation and Research Center of Shenzhen, Shenzhen 518114, China.,College of Forestry, South China Agricultural University, Guangzhou 510640, China.,College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou 350002, China.,The Center for Biotechnology and BioMedicine, Graduate School at Shenzhen, Tsinghua University, Shenzhen 518055, China
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24
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Christie N, Myburg AA, Joubert F, Murray SL, Carstens M, Lin YC, Meyer J, Crampton BG, Christensen SA, Ntuli JF, Wighard SS, Van de Peer Y, Berger DK. Systems genetics reveals a transcriptional network associated with susceptibility in the maize-grey leaf spot pathosystem. Plant J 2017; 89:746-763. [PMID: 27862526 DOI: 10.1111/tpj.13419] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/29/2016] [Revised: 10/20/2016] [Accepted: 11/04/2016] [Indexed: 05/20/2023]
Abstract
We used a systems genetics approach to elucidate the molecular mechanisms of the responses of maize to grey leaf spot (GLS) disease caused by Cercospora zeina, a threat to maize production globally. Expression analysis of earleaf samples in a subtropical maize recombinant inbred line population (CML444 × SC Malawi) subjected in the field to C. zeina infection allowed detection of 20 206 expression quantitative trait loci (eQTLs). Four trans-eQTL hotspots coincided with GLS disease QTLs mapped in the same field experiment. Co-expression network analysis identified three expression modules correlated with GLS disease scores. The module (GY-s) most highly correlated with susceptibility (r = 0.71; 179 genes) was enriched for the glyoxylate pathway, lipid metabolism, diterpenoid biosynthesis and responses to pathogen molecules such as chitin. The GY-s module was enriched for genes with trans-eQTLs in hotspots on chromosomes 9 and 10, which also coincided with phenotypic QTLs for susceptibility to GLS. This transcriptional network has significant overlap with the GLS susceptibility response of maize line B73, and may reflect pathogen manipulation for nutrient acquisition and/or unsuccessful defence responses, such as kauralexin production by the diterpenoid biosynthesis pathway. The co-expression module that correlated best with resistance (TQ-r; 1498 genes) was enriched for genes with trans-eQTLs in hotspots coinciding with GLS resistance QTLs on chromosome 9. Jasmonate responses were implicated in resistance to GLS through co-expression of COI1 and enrichment of genes with the Gene Ontology term 'cullin-RING ubiquitin ligase complex' in the TQ-r module. Consistent with this, JAZ repressor expression was highly correlated with the severity of GLS disease in the GY-s susceptibility network.
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Affiliation(s)
- Nanette Christie
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, Department of Biochemistry, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Alexander A Myburg
- Department of Genetics, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Fourie Joubert
- Centre for Bioinformatics and Computational Biology, Genomics Research Institute, Department of Biochemistry, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Shane L Murray
- Centre for Proteomic and Genomic Research, 0A Anzio Rd, Observatory, Cape Town, 7925, South Africa
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa
| | - Maryke Carstens
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Yao-Cheng Lin
- Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
| | - Jacqueline Meyer
- Centre for Proteomic and Genomic Research, 0A Anzio Rd, Observatory, Cape Town, 7925, South Africa
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Bridget G Crampton
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Shawn A Christensen
- Center for Medical, Agricultural, and Veterinary Entomology, United States Department of Agriculture, Agricultural Research Service, Chemistry Research Unit, Gainesville, FL, 32608, USA
| | - Jean F Ntuli
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa
| | - Sara S Wighard
- Department of Molecular and Cell Biology, University of Cape Town, Private Bag, Rondebosch, 7701, South Africa
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium
- Department of Genetics, Genomics Research Institute, University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
| | - Dave K Berger
- Department of Plant and Soil Sciences, Forestry and Agricultural Biotechnology Institute (FABI), Genomics Research Institute (GRI), University of Pretoria, Private Bag X20, Pretoria, 0028, South Africa
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Wang SY, Chen SC, Lin YC, Kuo YC, Chen JY, Kao CM. Acidification and sulfide formation control during reductive dechlorination of 1,2-dichloroethane in groundwater: Effectiveness and mechanistic study. Chemosphere 2016; 160:216-229. [PMID: 27376861 DOI: 10.1016/j.chemosphere.2016.06.066] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 03/21/2016] [Accepted: 06/17/2016] [Indexed: 06/06/2023]
Abstract
To enhance the reductive dechlorination of 1,2-dichloroethane (DCA) in groundwater, substrate injection may be required. However, substrate biodegradation causes groundwater acidification and sulfide production, which inhibits the bacteria responsible for DCA dechlorination and results in an odor problem. In the microcosm study, the effectiveness of the addition of ferrous sulfate (FS), desulfurization slag (DS), and nanoscale zero-valent iron (nZVI) on acidification and sulfide control was studied during reductive dechlorination of DCA, and the emulsified substrate (ES) was used as the substrate. Up to 94% of the sulfide was removed with FS and DS addition (0.25 wt%) (initial DCA concentration = 13.5 mg/L). FS and DS amendments resulted in the formation of a metal sulfide, which reduced the hydrogen sulfide concentration as well as the subsequent odor problem. Approximately 96% of the DCA was degraded under reductive dechlorination with nZVI or DS addition using ES as the substrate. In microcosms with nZVI or DS addition, the sulfide concentration was reduced to less than 15 μg/L. Acidification can be controlled via hydroxide ions production after nZVI oxidation and reaction of free CaO (released from DS) with water, which enhanced DCA dechlorination. The quantitative polymerase chain reaction results confirmed that the microcosms with nZVI added had the highest Dehalococcoides population (up to 2.5 × 10(8) gene copies/g soil) due to effective acidification control. The α-elimination mechanism was the main abiotic process, and reductive dechlorination dominated by Dehalococcides was the biotic mechanism that resulted in DCA removal. More than 22 bacterial species were detected, and dechlorinating bacteria existed in soils under alkaline and acidic conditions.
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Affiliation(s)
- S Y Wang
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - S C Chen
- Department of Life Sciences, National Central University, Chung-Li, Taiwan
| | - Y C Lin
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
| | - Y C Kuo
- Formosa Petrochemical Co., Kaohsiung, Taiwan
| | - J Y Chen
- Formosa Petrochemical Co., Kaohsiung, Taiwan
| | - C M Kao
- Institute of Environmental Engineering, National Sun Yat-Sen University, Kaohsiung, Taiwan
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Luo HY, Li YH, Wang W, Wang ZQ, Yuan X, Ma D, Wang FH, Zhang DS, Lin DR, Lin YC, Jia J, Hu XH, Peng JW, Xu RH. Single-agent capecitabine as maintenance therapy after induction of XELOX (or FOLFOX) in first-line treatment of metastatic colorectal cancer: randomized clinical trial of efficacy and safety. Ann Oncol 2016; 27:1074-1081. [PMID: 26940686 DOI: 10.1093/annonc/mdw101] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 02/17/2016] [Indexed: 02/05/2023] Open
Abstract
BACKGROUND The optimal strategy of maintenance therapy for patients with mCRC is controversial. This study was to evaluate the efficacy and safety of maintenance therapy with capecitabine versus observation following inductive chemotherapy in patients with metastatic colorectal cancer. PATIENTS AND METHODS In this randomized, open-label, multicenter, phase III trial, patients who received 18-24 weeks of induction chemotherapy with XELOX or FOLFOX and achieved disease control were randomly assigned centrally (1:1) to receive maintenance therapy of capecitabine or only observation until disease progression. The primary end point was progression-free survival (PFS) from randomization; the secondary end points included overall survival (OS), PFS from induction treatment (PFS2) and safety. Analyses were done by intention to treat. This trial is registered with ClinicalTrials.gov, number NCT02027363. RESULTS Between 30 July 2010 and 15 September 2013, 274 patients were enrolled in the study from 11 sites in China and randomly assigned to maintenance group (n = 136) or observation group (n = 138). Clinicopathological characteristics were balanced in two groups. The median follow-up time from randomization was 29.0 months [interquartile range (IQR) 21-36 months]. The primary end point of PFS was statistically significantly longer in capecitabine maintenance group than in observation group {6.43 [95% confidence interval (CI) 5.26-7.71] versus 3.43 (2.83-4.16) months, HR 0.54 (0.42-0.70), P < 0.001}. The median OS of capecitabine maintenance group was longer than that of observation group, but not statistically significant [25.63 (22.46-27.80) versus 23.30 (19.68-26.92) months; HR 0.85 (0.64-1.11), P = 0.2247]. Similar safety profiles were observed in both arms. The most common grade 3 or 4 toxicities in capecitabine maintenance group versus observation group were neutropenia, hand-foot syndrome, and mucositis. CONCLUSIONS Maintenance therapy with a single agent of capecitabine can be considered an appropriate option following the induction of XELOX or FOLFOX in mCRC patients with acceptable toxicities. CLINICAL TRIALS NUMBER NCT02027363.
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Affiliation(s)
- H Y Luo
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou
| | - Y H Li
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou
| | - W Wang
- Department of Medical Oncology, The First People's Hospital of Foshan, Guangzhou
| | - Z Q Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou
| | - X Yuan
- Department of Medical Oncology, Huizhou Central Hospital, Huizhou
| | - D Ma
- Department of Medical Oncology, Guangdong General Hospital, Guangzhou
| | - F H Wang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou
| | - D S Zhang
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou
| | - D R Lin
- Department of Medical Oncology, Jiangmen Central Hospital, Jiangmen
| | - Y C Lin
- Department of Medical Oncology, Cancer Hospital of Shantou University Medical College, Shantou
| | - J Jia
- Department of Medical Oncology, Dongguan People's Hospital, Dongguan
| | - X H Hu
- Department of Medical Oncology, Tumor Hospital of Guangxi Medical University, Nanning
| | - J W Peng
- Department of Medical Oncology, Zhongshan People's Hospital, Zhongshan, China
| | - R H Xu
- Department of Medical Oncology, Sun Yat-sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou.
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Hsiao J, Yuan TY, Tsai MS, Lu CY, Lin YC, Lee ML, Lin SW, Chang FC, Liu Pimentel H, Olive C, Coito C, Shen G, Young M, Thorne T, Lawrence M, Magistri M, Faghihi MA, Khorkova O, Wahlestedt C. Upregulation of Haploinsufficient Gene Expression in the Brain by Targeting a Long Non-coding RNA Improves Seizure Phenotype in a Model of Dravet Syndrome. EBioMedicine 2016; 9:257-277. [PMID: 27333023 PMCID: PMC4972487 DOI: 10.1016/j.ebiom.2016.05.011] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/02/2016] [Accepted: 05/09/2016] [Indexed: 02/07/2023] Open
Abstract
Dravet syndrome is a devastating genetic brain disorder caused by heterozygous loss-of-function mutation in the voltage-gated sodium channel gene SCN1A. There are currently no treatments, but the upregulation of SCN1A healthy allele represents an appealing therapeutic strategy. In this study we identified a novel, evolutionary conserved mechanism controlling the expression of SCN1A that is mediated by an antisense non-coding RNA (SCN1ANAT). Using oligonucleotide-based compounds (AntagoNATs) targeting SCN1ANAT we were able to induce specific upregulation of SCN1A both in vitro and in vivo, in the brain of Dravet knock-in mouse model and a non-human primate. AntagoNAT-mediated upregulation of Scn1a in postnatal Dravet mice led to significant improvements in seizure phenotype and excitability of hippocampal interneurons. These results further elucidate the pathophysiology of Dravet syndrome and outline a possible new approach for the treatment of this and other genetic disorders with similar etiology.
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Affiliation(s)
- J Hsiao
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - T Y Yuan
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - M S Tsai
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University Hospital, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen-Ai Rd., Taipei 100, Taiwan
| | - C Y Lu
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan
| | - Y C Lin
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - M L Lee
- Dep. Clinical Laboratory Science and Medical Biotechnology, National Taiwan University Hospital, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - S W Lin
- Department of Clinical Laboratory Sciences and Medical Biotechnology, National Taiwan University Hospital, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen-Ai Rd., Taipei 100, Taiwan; Department of Laboratory Medicine, National Taiwan University Hospital, College of Medicine, National Taiwan University, No. 7, Chung-Shan S. Rd., Taipei 100, Taiwan; Center for Genomic Medicine, National Taiwan University, No. 7, Chung-Shan S. Rd., Taipei 100, Taiwan
| | - F C Chang
- Department of Veterinary Medicine, School of Veterinary Medicine, National Taiwan University, No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan; Graduate Institute of Brain and Mind Sciences, College of Medicine, National Taiwan University, No. 1, Sec. 1, Jen-Ai Rd., Taipei 100, Taiwan; Graduate Institute of Acupuncture Science, College of Chinese Medicine, China Medical University, Taichung, Taiwan
| | - H Liu Pimentel
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - C Olive
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - C Coito
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - G Shen
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - M Young
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - T Thorne
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - M Lawrence
- RxGen, 100 Deepwood Drive, Hamden, CT 06517, USA
| | - M Magistri
- Center for Therapeutic Innovation and the Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami 33136, FL, USA
| | - M A Faghihi
- Center for Therapeutic Innovation and the Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami 33136, FL, USA
| | - O Khorkova
- OPKO Health Inc., 10320 USA Today Way, Miramar, FL 33025, USA
| | - C Wahlestedt
- Center for Therapeutic Innovation and the Department of Psychiatry and Behavioral Sciences, University of Miami Miller School of Medicine, 1501 NW 10th Avenue, Miami 33136, FL, USA.
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Ranade SS, Lin YC, Van de Peer Y, García-Gil MR. Comparative in silico analysis of SSRs in coding regions of high confidence predicted genes in Norway spruce (Picea abies) and Loblolly pine (Pinus taeda). BMC Genet 2015; 16:149. [PMID: 26706685 PMCID: PMC4691297 DOI: 10.1186/s12863-015-0304-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 12/10/2015] [Indexed: 11/24/2022] Open
Abstract
Background Microsatellites or simple sequence repeats (SSRs) are DNA sequences consisting of 1–6 bp tandem repeat motifs present in the genome. SSRs are considered to be one of the most powerful tools in genetic studies. We carried out a comparative study of perfect SSR loci belonging to class I (≥20) and class II (≥12 and <20 bp) types located in coding regions of high confidence genes in Picea abies and Pinus taeda. SSRLocator was used to retrieve SSRs from the full length CDS of predicted genes in both species. Results Trimers were the most abundant motifs in class I followed by hexamers in Picea abies, while trimers and hexamers were equally abundant in Pinus taeda class I SSRs. Hexamers were most frequent within class II SSRs followed by trimers, in both species. Although the frequency of genes containing SSRs was slightly higher in Pinus taeda, SSR counts per Mbp for class I was similar in both species (P-value = 0.22); while for class II SSRs, it was significantly higher in Picea abies (P-value = 0.00009). AT-rich motifs were higher in abundance than the GC-rich motifs, within class II SSRs in both the species (P-values = 10−9 and 0). With reference to class I SSRs, AT-rich and GC-rich motifs were detected with equal frequency in Pinus taeda (P-value = 0.24); while in Picea abies, GC-rich motifs were detected with higher frequency than the AT-rich motifs (P-value = 0.0005). Conclusions Our study gives a comparative overview of the genome SSRs composition based on high confidence genes in the two recently sequenced and economically important conifers and, also provides information on functional molecular markers that can be applied in genetic studies in Pinus and Picea species. Electronic supplementary material The online version of this article (doi:10.1186/s12863-015-0304-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sonali Sachin Ranade
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden.
| | - Yao-Cheng Lin
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium.
| | - Yves Van de Peer
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052, Ghent, Belgium. .,Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028, South Africa. .,Bioinformatics Institute Ghent, Ghent University, 9052, Ghent, Belgium.
| | - María Rosario García-Gil
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, SE-901 83, Umeå, Sweden.
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Sundell D, Mannapperuma C, Netotea S, Delhomme N, Lin YC, Sjödin A, Van de Peer Y, Jansson S, Hvidsten TR, Street NR. The Plant Genome Integrative Explorer Resource: PlantGenIE.org. New Phytol 2015; 208:1149-56. [PMID: 26192091 DOI: 10.1111/nph.13557] [Citation(s) in RCA: 162] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/19/2015] [Accepted: 06/08/2015] [Indexed: 05/18/2023]
Abstract
Accessing and exploring large-scale genomics data sets remains a significant challenge to researchers without specialist bioinformatics training. We present the integrated PlantGenIE.org platform for exploration of Populus, conifer and Arabidopsis genomics data, which includes expression networks and associated visualization tools. Standard features of a model organism database are provided, including genome browsers, gene list annotation, Blast homology searches and gene information pages. Community annotation updating is supported via integration of WebApollo. We have produced an RNA-sequencing (RNA-Seq) expression atlas for Populus tremula and have integrated these data within the expression tools. An updated version of the ComPlEx resource for performing comparative plant expression analyses of gene coexpression network conservation between species has also been integrated. The PlantGenIE.org platform provides intuitive access to large-scale and genome-wide genomics data from model forest tree species, facilitating both community contributions to annotation improvement and tools supporting use of the included data resources to inform biological insight.
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Affiliation(s)
- David Sundell
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden
| | - Chanaka Mannapperuma
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden
| | - Sergiu Netotea
- Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden
| | - Nicolas Delhomme
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden
| | - Yao-Cheng Lin
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Andreas Sjödin
- Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden
- Department of Chemistry, Umeå University, SE-907 81, Umeå, Sweden
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Hatfield Campus, 0028, Pretoria, South Africa
| | - Stefan Jansson
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden
| | - Torgeir R Hvidsten
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, 1432, Ås, Norway
| | - Nathaniel R Street
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-907 81, Umeå, Sweden
- Computational Life Science Cluster (CLiC), Umeå University, SE-907 81, Umeå, Sweden
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Delhomme N, Sundström G, Zamani N, Lantz H, Lin YC, Hvidsten TR, Höppner MP, Jern P, Van de Peer Y, Lundeberg J, Grabherr MG, Street NR. Serendipitous Meta-Transcriptomics: The Fungal Community of Norway Spruce (Picea abies). PLoS One 2015; 10:e0139080. [PMID: 26413905 PMCID: PMC4586145 DOI: 10.1371/journal.pone.0139080] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 09/09/2015] [Indexed: 11/18/2022] Open
Abstract
After performing de novo transcript assembly of >1 billion RNA-Sequencing reads obtained from 22 samples of different Norway spruce (Picea abies) tissues that were not surface sterilized, we found that assembled sequences captured a mix of plant, lichen, and fungal transcripts. The latter were likely expressed by endophytic and epiphytic symbionts, indicating that these organisms were present, alive, and metabolically active. Here, we show that these serendipitously sequenced transcripts need not be considered merely as contamination, as is common, but that they provide insight into the plant’s phyllosphere. Notably, we could classify these transcripts as originating predominantly from Dothideomycetes and Leotiomycetes species, with functional annotation of gene families indicating active growth and metabolism, with particular regards to glucose intake and processing, as well as gene regulation.
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Affiliation(s)
- Nicolas Delhomme
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
| | - Görel Sundström
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Neda Zamani
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Henrik Lantz
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Bioinformatics Infrastructure for Life Sciences (BILS), Uppsala, Sweden
| | - Yao-Cheng Lin
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Ghent, Belgium
| | - Torgeir R. Hvidsten
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- Department of Chemistry, Biotechnology and Food Science, Norwegian University of Life Sciences, Ås, Norway
| | - Marc P. Höppner
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Bioinformatics Infrastructure for Life Sciences (BILS), Uppsala, Sweden
| | - Patric Jern
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
| | - Yves Van de Peer
- Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics (Ghent University), Ghent, Belgium
- Genomics Research Institute, University of Pretoria, Pretoria, South Africa
| | - Joakim Lundeberg
- School of Biotechnology, Science for Life Laboratory, KTH Royal Institute of Technology, Solna, Sweden
| | - Manfred G. Grabherr
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Bioinformatics Infrastructure for Life Sciences (BILS), Uppsala, Sweden
| | - Nathaniel R. Street
- Department of Plant Physiology, Umeå Plant Science Centre, Umeå University, Umeå, Sweden
- * E-mail:
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Lin YC, Hu WY. P-73 Develop a culturally oriented advance care planning intervention model for community older adults in taiwan – a study protocol. BMJ Support Palliat Care 2015. [DOI: 10.1136/bmjspcare-2015-000978.203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Ghorbani S, Lin YC, Parizot B, Fernandez A, Njo MF, Van de Peer Y, Beeckman T, Hilson P. Expanding the repertoire of secretory peptides controlling root development with comparative genome analysis and functional assays. J Exp Bot 2015; 66:5257-5269. [PMID: 26195730 PMCID: PMC4526923 DOI: 10.1093/jxb/erv346] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plant genomes encode numerous small secretory peptides (SSPs) whose functions have yet to be explored. Based on structural features that characterize SSP families known to take part in postembryonic development, this comparative genome analysis resulted in the identification of genes coding for oligopeptides potentially involved in cell-to-cell communication. Because genome annotation based on short sequence homology is difficult, the criteria for the de novo identification and aggregation of conserved SSP sequences were first benchmarked across five reference plant species. The resulting gene families were then extended to 32 genome sequences, including major crops. The global phylogenetic pattern common to the functionally characterized SSP families suggests that their apparition and expansion coincide with that of the land plants. The SSP families can be searched online for members, sequences and consensus (http://bioinformatics.psb.ugent.be/webtools/PlantSSP/). Looking for putative regulators of root development, Arabidopsis thaliana SSP genes were further selected through transcriptome meta-analysis based on their expression at specific stages and in specific cell types in the course of the lateral root formation. As an additional indication that formerly uncharacterized SSPs may control development, this study showed that root growth and branching were altered by the application of synthetic peptides matching conserved SSP motifs, sometimes in very specific ways. The strategy used in the study, combining comparative genomics, transcriptome meta-analysis and peptide functional assays in planta, pinpoints factors potentially involved in non-cell-autonomous regulatory mechanisms. A similar approach can be implemented in different species for the study of a wide range of developmental programmes.
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Affiliation(s)
- Sarieh Ghorbani
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Yao-Cheng Lin
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Boris Parizot
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Ana Fernandez
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Maria Fransiska Njo
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria 0028, South Africa
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - Pierre Hilson
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, Saclay Plant Sciences, INRA, route de Saint-Cyr, 78026 Versailles, France
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Pi TW, Lin YH, Fanchiang YT, Chiang TH, Wei CH, Lin YC, Wertheim GK, Kwo J, Hong M. In-situ atomic layer deposition of tri-methylaluminum and water on pristine single-crystal (In)GaAs surfaces: electronic and electric structures. Nanotechnology 2015; 26:164001. [PMID: 25824203 DOI: 10.1088/0957-4484/26/16/164001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The electronic structure of single-crystal (In)GaAs deposited with tri-methylaluminum (TMA) and water via atomic layer deposition (ALD) is presented with high-resolution synchrotron radiation core-level photoemission and capacitance-voltage (CV) characteristics. The interaction of the precursor atoms with (In)GaAs is confined at the topmost surface layer. The Ga-vacant site on the GaAs(111)A-2 × 2 surface is filled with Al, thereby effectively passivating the As dangling bonds. The As-As dimers on the GaAs(001)-2 × 4 surface are entirely passivated by one cycle of TMA and water. The presumed layerwise deposition fails to happen in GaAs(001)-4 × 6. In In0.20Ga0.80As(001)-2 × 4, the edge row As atoms are partially bonded with the Al, and one released methyl then bonds with the In. It is suggested that the unpassivated surface and subsurface atoms cause large frequency dispersions in CV characteristics under the gate bias. We also found that the (In)GaAs surface is immune to water in ALD. However, the momentary exposure of it to air (less than one minute) introduces significant signals of native oxides. This indicates the necessity of in situ works of high κ/(In)GaAs-related experiments in order to know the precise interfacial atomic bonding and thus know the electronic characteristics. The electric CV measurements of the ALD-Al2O3 on these (In)GaAs surfaces are correlated with their electronic properties.
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Affiliation(s)
- T W Pi
- National Synchrotron Radiation Research Center, Hsinchu 30076, Taiwan
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De La Torre AR, Lin YC, Van de Peer Y, Ingvarsson PK. Genome-wide analysis reveals diverged patterns of codon bias, gene expression, and rates of sequence evolution in picea gene families. Genome Biol Evol 2015; 7:1002-15. [PMID: 25747252 PMCID: PMC4419791 DOI: 10.1093/gbe/evv044] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The recent sequencing of several gymnosperm genomes has greatly facilitated studying the evolution of their genes and gene families. In this study, we examine the evidence for expression-mediated selection in the first two fully sequenced representatives of the gymnosperm plant clade (Picea abies and Picea glauca). We use genome-wide estimates of gene expression (>50,000 expressed genes) to study the relationship between gene expression, codon bias, rates of sequence divergence, protein length, and gene duplication. We found that gene expression is correlated with rates of sequence divergence and codon bias, suggesting that natural selection is acting on Picea protein-coding genes for translational efficiency. Gene expression, rates of sequence divergence, and codon bias are correlated with the size of gene families, with large multicopy gene families having, on average, a lower expression level and breadth, lower codon bias, and higher rates of sequence divergence than single-copy gene families. Tissue-specific patterns of gene expression were more common in large gene families with large gene expression divergence than in single-copy families. Recent family expansions combined with large gene expression variation in paralogs and increased rates of sequence evolution suggest that some Picea gene families are rapidly evolving to cope with biotic and abiotic stress. Our study highlights the importance of gene expression and natural selection in shaping the evolution of protein-coding genes in Picea species, and sets the ground for further studies investigating the evolution of individual gene families in gymnosperms.
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Affiliation(s)
| | - Yao-Cheng Lin
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Systems Biology, VIB, and Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium Genomics Research Institute, University of Pretoria, South Africa
| | - Pär K Ingvarsson
- Department of Ecology and Environmental Science, Umeå University, Sweden Umeå Plant Science Centre, Umeå, Sweden
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Lin YC, Su KW, Huang KF, Chen YF. Pattern formation of second harmonic conical waves in a nonlinear medium with extended defect structure. Opt Express 2014; 22:27859-27868. [PMID: 25402028 DOI: 10.1364/oe.22.027859] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
We experimentally demonstrate the propagation of the conical second harmonic fields generated from a nonlinear crystal with extended defects to investigate their pattern formation. The generated second harmonic waves are found to be the interference of multiple Bessel-like beams that originate from distinct longitudinal layers inside the crystal. To reconstruct the experimental results, we model the individual Bessel-like beam to be the superposition of an ensemble of identical decentered Gaussian waves with random phases. We present that the randomness of the phases leads the Bessel-like beams to show wave profiles with different extent of localization. Moreover, we use the coherent superposition of the developed wave functions with a phase factor to manifest the interference of multiple Bessel-like beams. The relative phases among the Bessel-like beams are shown to be closely related to the near and far-field patterns. With the experimental observations and the theoretical model, the relative phases are decided to successfully reconstruct the propagation characteristics of the multiple Bessel-like beams.
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An FP, Balantekin AB, Band HR, Beriguete W, Bishai M, Blyth S, Butorov I, Cao GF, Cao J, Chan YL, Chang JF, Chang LC, Chang Y, Chasman C, Chen H, Chen QY, Chen SM, Chen X, Chen X, Chen YX, Chen Y, Cheng YP, Cherwinka JJ, Chu MC, Cummings JP, de Arcos J, Deng ZY, Ding YY, Diwan MV, Draeger E, Du XF, Dwyer DA, Edwards WR, Ely SR, Fu JY, Ge LQ, Gill R, Gonchar M, Gong GH, Gong H, Grassi M, Gu WQ, Guan MY, Guo XH, Hackenburg RW, Han GH, Hans S, He M, Heeger KM, Heng YK, Hinrichs P, Hor YK, Hsiung YB, Hu BZ, Hu LM, Hu LJ, Hu T, Hu W, Huang EC, Huang H, Huang XT, Huber P, Hussain G, Isvan Z, Jaffe DE, Jaffke P, Jen KL, Jetter S, Ji XP, Ji XL, Jiang HJ, Jiao JB, Johnson RA, Kang L, Kettell SH, Kramer M, Kwan KK, Kwok MW, Kwok T, Lai WC, Lau K, Lebanowski L, Lee J, Lei RT, Leitner R, Leung A, Leung JKC, Lewis CA, Li DJ, Li F, Li GS, Li QJ, Li WD, Li XN, Li XQ, Li YF, Li ZB, Liang H, Lin CJ, Lin GL, Lin PY, Lin SK, Lin YC, Ling JJ, Link JM, Littenberg L, Littlejohn BR, Liu DW, Liu H, Liu JL, Liu JC, Liu SS, Liu YB, Lu C, Lu HQ, Luk KB, Ma QM, Ma XY, Ma XB, Ma YQ, McDonald KT, McFarlane MC, McKeown RD, Meng Y, Mitchell I, Monari Kebwaro J, Nakajima Y, Napolitano J, Naumov D, Naumova E, Nemchenok I, Ngai HY, Ning Z, Ochoa-Ricoux JP, Olshevski A, Patton S, Pec V, Peng JC, Piilonen LE, Pinsky L, Pun CSJ, Qi FZ, Qi M, Qian X, Raper N, Ren B, Ren J, Rosero R, Roskovec B, Ruan XC, Shao BB, Steiner H, Sun GX, Sun JL, Tam YH, Tang X, Themann H, Tsang KV, Tsang RHM, Tull CE, Tung YC, Viren B, Vorobel V, Wang CH, Wang LS, Wang LY, Wang M, Wang NY, Wang RG, Wang W, Wang WW, Wang X, Wang YF, Wang Z, Wang Z, Wang ZM, Webber DM, Wei HY, Wei YD, Wen LJ, Whisnant K, White CG, Whitehead L, Wise T, Wong HLH, Wong SCF, Worcester E, Wu Q, Xia DM, Xia JK, Xia X, Xing ZZ, Xu JY, Xu JL, Xu J, Xu Y, Xue T, Yan J, Yang CC, Yang L, Yang MS, Yang MT, Ye M, Yeh M, Yeh YS, Young BL, Yu GY, Yu JY, Yu ZY, Zang SL, Zeng B, Zhan L, Zhang C, Zhang FH, Zhang JW, Zhang QM, Zhang Q, Zhang SH, Zhang YC, Zhang YM, Zhang YH, Zhang YX, Zhang ZJ, Zhang ZY, Zhang ZP, Zhao J, Zhao QW, Zhao Y, Zhao YB, Zheng L, Zhong WL, Zhou L, Zhou ZY, Zhuang HL, Zou JH. Search for a light sterile neutrino at Daya Bay. Phys Rev Lett 2014; 113:141802. [PMID: 25325631 DOI: 10.1103/physrevlett.113.141802] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2014] [Indexed: 06/04/2023]
Abstract
A search for light sterile neutrino mixing was performed with the first 217 days of data from the Daya Bay Reactor Antineutrino Experiment. The experiment's unique configuration of multiple baselines from six 2.9 GW(th) nuclear reactors to six antineutrino detectors deployed in two near (effective baselines 512 m and 561 m) and one far (1579 m) underground experimental halls makes it possible to test for oscillations to a fourth (sterile) neutrino in the 10(-3) eV(2)<|Δm(41)(2) |< 0.3 eV(2) range. The relative spectral distortion due to the disappearance of electron antineutrinos was found to be consistent with that of the three-flavor oscillation model. The derived limits on sin(2) 2θ(14) cover the 10(-3) eV(2) ≲ |Δm(41)(2)| ≲ 0.1 eV(2) region, which was largely unexplored.
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Affiliation(s)
- F P An
- Institute of Modern Physics, East China University of Science and Technology, Shanghai
| | | | - H R Band
- University of Wisconsin, Madison, Wisconsin, USA
| | - W Beriguete
- Brookhaven National Laboratory, Upton, New York, USA
| | - M Bishai
- Brookhaven National Laboratory, Upton, New York, USA
| | - S Blyth
- Department of Physics, National Taiwan University, Taipei
| | - I Butorov
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - G F Cao
- Institute of High Energy Physics, Beijing
| | - J Cao
- Institute of High Energy Physics, Beijing
| | - Y L Chan
- Chinese University of Hong Kong, Hong Kong
| | - J F Chang
- Institute of High Energy Physics, Beijing
| | - L C Chang
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | - Y Chang
- National United University, Miao-Li
| | - C Chasman
- Brookhaven National Laboratory, Upton, New York, USA
| | - H Chen
- Institute of High Energy Physics, Beijing
| | | | - S M Chen
- Department of Engineering Physics, Tsinghua University, Beijing
| | - X Chen
- Chinese University of Hong Kong, Hong Kong
| | - X Chen
- Institute of High Energy Physics, Beijing
| | - Y X Chen
- North China Electric Power University, Beijing
| | - Y Chen
- Shenzhen University, Shenzhen
| | - Y P Cheng
- Institute of High Energy Physics, Beijing
| | | | - M C Chu
- Chinese University of Hong Kong, Hong Kong
| | | | - J de Arcos
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois, USA
| | - Z Y Deng
- Institute of High Energy Physics, Beijing
| | - Y Y Ding
- Institute of High Energy Physics, Beijing
| | - M V Diwan
- Brookhaven National Laboratory, Upton, New York, USA
| | - E Draeger
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois, USA
| | - X F Du
- Institute of High Energy Physics, Beijing
| | - D A Dwyer
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - W R Edwards
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - S R Ely
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - J Y Fu
- Institute of High Energy Physics, Beijing
| | - L Q Ge
- Chengdu University of Technology, Chengdu
| | - R Gill
- Brookhaven National Laboratory, Upton, New York, USA
| | - M Gonchar
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - G H Gong
- Department of Engineering Physics, Tsinghua University, Beijing
| | - H Gong
- Department of Engineering Physics, Tsinghua University, Beijing
| | - M Grassi
- Institute of High Energy Physics, Beijing
| | - W Q Gu
- Shanghai Jiao Tong University, Shanghai
| | - M Y Guan
- Institute of High Energy Physics, Beijing
| | - X H Guo
- Beijing Normal University, Beijing
| | | | - G H Han
- College of William and Mary, Williamsburg, Virginia, USA
| | - S Hans
- Brookhaven National Laboratory, Upton, New York, USA
| | - M He
- Institute of High Energy Physics, Beijing
| | - K M Heeger
- University of Wisconsin, Madison, Wisconsin, USA and Department of Physics, Yale University, New Haven, Connecticut, USA
| | - Y K Heng
- Institute of High Energy Physics, Beijing
| | - P Hinrichs
- University of Wisconsin, Madison, Wisconsin, USA
| | - Y K Hor
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia, USA
| | - Y B Hsiung
- Department of Physics, National Taiwan University, Taipei
| | - B Z Hu
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | - L M Hu
- Brookhaven National Laboratory, Upton, New York, USA
| | - L J Hu
- Beijing Normal University, Beijing
| | - T Hu
- Institute of High Energy Physics, Beijing
| | - W Hu
- Institute of High Energy Physics, Beijing
| | - E C Huang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - H Huang
- China Institute of Atomic Energy, Beijing
| | | | - P Huber
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia, USA
| | - G Hussain
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Z Isvan
- Brookhaven National Laboratory, Upton, New York, USA
| | - D E Jaffe
- Brookhaven National Laboratory, Upton, New York, USA
| | - P Jaffke
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia, USA
| | - K L Jen
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | - S Jetter
- Institute of High Energy Physics, Beijing
| | - X P Ji
- School of Physics, Nankai University, Tianjin
| | - X L Ji
- Institute of High Energy Physics, Beijing
| | - H J Jiang
- Chengdu University of Technology, Chengdu
| | | | - R A Johnson
- Department of Physics, University of Cincinnati, Cincinnati, Ohio, USA
| | - L Kang
- Dongguan University of Technology, Dongguan
| | - S H Kettell
- Brookhaven National Laboratory, Upton, New York, USA
| | - M Kramer
- Lawrence Berkeley National Laboratory, Berkeley, California, USA and Department of Physics, University of California, Berkeley, California, USA
| | - K K Kwan
- Chinese University of Hong Kong, Hong Kong
| | - M W Kwok
- Chinese University of Hong Kong, Hong Kong
| | - T Kwok
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - W C Lai
- Chengdu University of Technology, Chengdu
| | - K Lau
- Department of Physics, University of Houston, Houston, Texas, USA
| | - L Lebanowski
- Department of Engineering Physics, Tsinghua University, Beijing
| | - J Lee
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - R T Lei
- Dongguan University of Technology, Dongguan
| | - R Leitner
- Charles University, Faculty of Mathematics and Physics, Prague
| | - A Leung
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - J K C Leung
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - C A Lewis
- University of Wisconsin, Madison, Wisconsin, USA
| | - D J Li
- University of Science and Technology of China, Hefei
| | - F Li
- Institute of High Energy Physics, Beijing and Chengdu University of Technology, Chengdu
| | - G S Li
- Shanghai Jiao Tong University, Shanghai
| | - Q J Li
- Institute of High Energy Physics, Beijing
| | - W D Li
- Institute of High Energy Physics, Beijing
| | - X N Li
- Institute of High Energy Physics, Beijing
| | - X Q Li
- School of Physics, Nankai University, Tianjin
| | - Y F Li
- Institute of High Energy Physics, Beijing
| | - Z B Li
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - H Liang
- University of Science and Technology of China, Hefei
| | - C J Lin
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - G L Lin
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | - P Y Lin
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | - S K Lin
- Department of Physics, University of Houston, Houston, Texas, USA
| | - Y C Lin
- Chengdu University of Technology, Chengdu
| | - J J Ling
- Brookhaven National Laboratory, Upton, New York, USA and Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - J M Link
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia, USA
| | - L Littenberg
- Brookhaven National Laboratory, Upton, New York, USA
| | - B R Littlejohn
- Department of Physics, University of Cincinnati, Cincinnati, Ohio, USA
| | - D W Liu
- Department of Physics, University of Houston, Houston, Texas, USA
| | - H Liu
- Department of Physics, University of Houston, Houston, Texas, USA
| | - J L Liu
- Shanghai Jiao Tong University, Shanghai
| | - J C Liu
- Institute of High Energy Physics, Beijing
| | - S S Liu
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - Y B Liu
- Institute of High Energy Physics, Beijing
| | - C Lu
- Joseph Henry Laboratories, Princeton University, Princeton, New Jersey, USA
| | - H Q Lu
- Institute of High Energy Physics, Beijing
| | - K B Luk
- Lawrence Berkeley National Laboratory, Berkeley, California, USA and Department of Physics, University of California, Berkeley, California, USA
| | - Q M Ma
- Institute of High Energy Physics, Beijing
| | - X Y Ma
- Institute of High Energy Physics, Beijing
| | - X B Ma
- North China Electric Power University, Beijing
| | - Y Q Ma
- Institute of High Energy Physics, Beijing
| | - K T McDonald
- Joseph Henry Laboratories, Princeton University, Princeton, New Jersey, USA
| | | | - R D McKeown
- College of William and Mary, Williamsburg, Virginia, USA and California Institute of Technology, Pasadena, California, USA
| | - Y Meng
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia, USA
| | - I Mitchell
- Department of Physics, University of Houston, Houston, Texas, USA
| | | | - Y Nakajima
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - J Napolitano
- Department of Physics, College of Science and Technology, Temple University, Philadelphia, Pennsylvania, USA
| | - D Naumov
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - E Naumova
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - I Nemchenok
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - H Y Ngai
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - Z Ning
- Institute of High Energy Physics, Beijing
| | - J P Ochoa-Ricoux
- Lawrence Berkeley National Laboratory, Berkeley, California, USA and Instituto de Física, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - A Olshevski
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - S Patton
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - V Pec
- Charles University, Faculty of Mathematics and Physics, Prague
| | - J C Peng
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - L E Piilonen
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia, USA
| | - L Pinsky
- Department of Physics, University of Houston, Houston, Texas, USA
| | - C S J Pun
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - F Z Qi
- Institute of High Energy Physics, Beijing
| | - M Qi
- Nanjing University, Nanjing
| | - X Qian
- Brookhaven National Laboratory, Upton, New York, USA
| | - N Raper
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, New York, USA
| | - B Ren
- Dongguan University of Technology, Dongguan
| | - J Ren
- China Institute of Atomic Energy, Beijing
| | - R Rosero
- Brookhaven National Laboratory, Upton, New York, USA
| | - B Roskovec
- Charles University, Faculty of Mathematics and Physics, Prague
| | - X C Ruan
- China Institute of Atomic Energy, Beijing
| | - B B Shao
- Department of Engineering Physics, Tsinghua University, Beijing
| | - H Steiner
- Lawrence Berkeley National Laboratory, Berkeley, California, USA and Department of Physics, University of California, Berkeley, California, USA
| | - G X Sun
- Institute of High Energy Physics, Beijing
| | - J L Sun
- China General Nuclear Power Group, Shenzhen
| | - Y H Tam
- Chinese University of Hong Kong, Hong Kong
| | - X Tang
- Institute of High Energy Physics, Beijing
| | - H Themann
- Brookhaven National Laboratory, Upton, New York, USA
| | - K V Tsang
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - R H M Tsang
- California Institute of Technology, Pasadena, California, USA
| | - C E Tull
- Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Y C Tung
- Department of Physics, National Taiwan University, Taipei
| | - B Viren
- Brookhaven National Laboratory, Upton, New York, USA
| | - V Vorobel
- Charles University, Faculty of Mathematics and Physics, Prague
| | - C H Wang
- National United University, Miao-Li
| | - L S Wang
- Institute of High Energy Physics, Beijing
| | - L Y Wang
- Institute of High Energy Physics, Beijing
| | - M Wang
- Shandong University, Jinan
| | - N Y Wang
- Beijing Normal University, Beijing
| | - R G Wang
- Institute of High Energy Physics, Beijing
| | - W Wang
- College of William and Mary, Williamsburg, Virginia, USA and Sun Yat-Sen (Zhongshan) University, Guangzhou
| | | | - X Wang
- College of Electronic Science and Engineering, National University of Defense Technology, Changsha
| | - Y F Wang
- Institute of High Energy Physics, Beijing
| | - Z Wang
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Z Wang
- Institute of High Energy Physics, Beijing
| | - Z M Wang
- Institute of High Energy Physics, Beijing
| | - D M Webber
- University of Wisconsin, Madison, Wisconsin, USA
| | - H Y Wei
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Y D Wei
- Dongguan University of Technology, Dongguan
| | - L J Wen
- Institute of High Energy Physics, Beijing
| | | | - C G White
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois, USA
| | - L Whitehead
- Department of Physics, University of Houston, Houston, Texas, USA
| | - T Wise
- University of Wisconsin, Madison, Wisconsin, USA
| | - H L H Wong
- Lawrence Berkeley National Laboratory, Berkeley, California, USA and Department of Physics, University of California, Berkeley, California, USA
| | - S C F Wong
- Chinese University of Hong Kong, Hong Kong
| | - E Worcester
- Brookhaven National Laboratory, Upton, New York, USA
| | - Q Wu
- Shandong University, Jinan
| | - D M Xia
- Institute of High Energy Physics, Beijing
| | - J K Xia
- Institute of High Energy Physics, Beijing
| | - X Xia
- Shandong University, Jinan
| | - Z Z Xing
- Institute of High Energy Physics, Beijing
| | - J Y Xu
- Chinese University of Hong Kong, Hong Kong
| | - J L Xu
- Institute of High Energy Physics, Beijing
| | - J Xu
- Beijing Normal University, Beijing
| | - Y Xu
- School of Physics, Nankai University, Tianjin
| | - T Xue
- Department of Engineering Physics, Tsinghua University, Beijing
| | - J Yan
- Xi'an Jiaotong University, Xi'an
| | - C C Yang
- Institute of High Energy Physics, Beijing
| | - L Yang
- Dongguan University of Technology, Dongguan
| | - M S Yang
- Institute of High Energy Physics, Beijing
| | | | - M Ye
- Institute of High Energy Physics, Beijing
| | - M Yeh
- Brookhaven National Laboratory, Upton, New York, USA
| | - Y S Yeh
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | - B L Young
- Iowa State University, Ames, Iowa, USA
| | - G Y Yu
- Nanjing University, Nanjing
| | - J Y Yu
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Z Y Yu
- Institute of High Energy Physics, Beijing
| | | | - B Zeng
- Chengdu University of Technology, Chengdu
| | - L Zhan
- Institute of High Energy Physics, Beijing
| | - C Zhang
- Brookhaven National Laboratory, Upton, New York, USA
| | - F H Zhang
- Institute of High Energy Physics, Beijing
| | - J W Zhang
- Institute of High Energy Physics, Beijing
| | | | - Q Zhang
- Chengdu University of Technology, Chengdu
| | - S H Zhang
- Institute of High Energy Physics, Beijing
| | - Y C Zhang
- University of Science and Technology of China, Hefei
| | - Y M Zhang
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Y H Zhang
- Institute of High Energy Physics, Beijing
| | - Y X Zhang
- China General Nuclear Power Group, Shenzhen
| | - Z J Zhang
- Dongguan University of Technology, Dongguan
| | - Z Y Zhang
- Institute of High Energy Physics, Beijing
| | - Z P Zhang
- University of Science and Technology of China, Hefei
| | - J Zhao
- Institute of High Energy Physics, Beijing
| | - Q W Zhao
- Institute of High Energy Physics, Beijing
| | - Y Zhao
- North China Electric Power University, Beijing and College of William and Mary, Williamsburg, Virginia, USA
| | - Y B Zhao
- Institute of High Energy Physics, Beijing
| | - L Zheng
- University of Science and Technology of China, Hefei
| | - W L Zhong
- Institute of High Energy Physics, Beijing
| | - L Zhou
- Institute of High Energy Physics, Beijing
| | - Z Y Zhou
- China Institute of Atomic Energy, Beijing
| | - H L Zhuang
- Institute of High Energy Physics, Beijing
| | - J H Zou
- Institute of High Energy Physics, Beijing
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Ranade SS, Lin YC, Zuccolo A, Van de Peer Y, García-Gil MDR. Comparative in silico analysis of EST-SSRs in angiosperm and gymnosperm tree genera. BMC Plant Biol 2014; 14:220. [PMID: 25143005 PMCID: PMC4160553 DOI: 10.1186/s12870-014-0220-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/05/2014] [Indexed: 05/24/2023]
Abstract
BACKGROUND Simple Sequence Repeats (SSRs) derived from Expressed Sequence Tags (ESTs) belong to the expressed fraction of the genome and are important for gene regulation, recombination, DNA replication, cell cycle and mismatch repair. Here, we present a comparative analysis of the SSR motif distribution in the 5'UTR, ORF and 3'UTR fractions of ESTs across selected genera of woody trees representing gymnosperms (17 species from seven genera) and angiosperms (40 species from eight genera). RESULTS Our analysis supports a modest contribution of EST-SSR length to genome size in gymnosperms, while EST-SSR density was not associated with genome size in neither angiosperms nor gymnosperms. Multiple factors seem to have contributed to the lower abundance of EST-SSRs in gymnosperms that has resulted in a non-linear relationship with genome size diversity. The AG/CT motif was found to be the most abundant in SSRs of both angiosperms and gymnosperms, with a relative increase in AT/AT in the latter. Our data also reveals a higher abundance of hexamers across the gymnosperm genera. CONCLUSIONS Our analysis provides the foundation for future comparative studies at the species level to unravel the evolutionary processes that control the SSR genesis and divergence between angiosperm and gymnosperm tree species.
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Affiliation(s)
- Sonali Sachin Ranade
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
| | - Yao-Cheng Lin
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
| | - Andrea Zuccolo
- />Istituto di Genomica Applicata, Via J. Linussio 51, 33100 Udine, Italy
- />Institute of Life Sciences, Scuola Superiore Sant’Anna, 56127 Pisa, Italy
| | - Yves Van de Peer
- />Department of Plant Systems Biology (VIB) and Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, 9052 Ghent, Belgium
- />Genomics Research Institute, University of Pretoria, Hatfield Campus, Pretoria, 0028 South Africa
| | - María del Rosario García-Gil
- />Umeå Plant Science Centre (UPSC), Department of Forest Genetics and Plant Physiology, Swedish University of Agricultural Sciences, SE-901-83 Umeå, Sweden
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Boone M, Lin YC, Meuris L, Lemmens I, Van Roy N, Soete A, Reumers J, Moisse M, Plaisance S, Drmanac R, Chen J, Speleman F, Lambrechts D, Van de Peer Y, Tavernier J, Callewaert N. Genome dynamics of the human embryonic kidney 293 (HEK293) lineage in response to cell biology manipulations. N Biotechnol 2014. [DOI: 10.1016/j.nbt.2014.05.1775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Tanigawa S, Lee CH, Lin CS, Ku CC, Hasegawa H, Qin S, Kawahara A, Korenori Y, Miyamori K, Noguchi M, Lee LH, Lin YC, Lin CLS, Nakamura Y, Jin C, Yamaguchi N, Eckner R, Hou DX, Yokoyama KK. Erratum: Jun dimerization protein 2 is a critical component of the Nrf2/MafK complex regulating the response to ROS homeostasis. Cell Death Dis 2014. [PMCID: PMC4123110 DOI: 10.1038/cddis.2014.322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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An FP, Balantekin AB, Band HR, Beriguete W, Bishai M, Blyth S, Brown RL, Butorov I, Cao GF, Cao J, Carr R, Chan YL, Chang JF, Chang Y, Chasman C, Chen HS, Chen HY, Chen SJ, Chen SM, Chen XC, Chen XH, Chen Y, Chen YX, Cheng YP, Cherwinka JJ, Chu MC, Cummings JP, de Arcos J, Deng ZY, Ding YY, Diwan MV, Draeger E, Du XF, Dwyer DA, Edwards WR, Ely SR, Fu JY, Ge LQ, Gill R, Gonchar M, Gong GH, Gong H, Gornushkin YA, Gu WQ, Guan MY, Guo XH, Hackenburg RW, Hahn RL, Han GH, Hans S, He M, Heeger KM, Heng YK, Hinrichs P, Hor Y, Hsiung YB, Hu BZ, Hu LJ, Hu LM, Hu T, Hu W, Huang EC, Huang HX, Huang HZ, Huang XT, Huber P, Hussain G, Isvan Z, Jaffe DE, Jaffke P, Jetter S, Ji XL, Ji XP, Jiang HJ, Jiao JB, Johnson RA, Kang L, Kettell SH, Kramer M, Kwan KK, Kwok MW, Kwok T, Lai WC, Lai WH, Lau K, Lebanowski L, Lee J, Lei RT, Leitner R, Leung A, Leung JKC, Lewis CA, Li DJ, Li F, Li GS, Li QJ, Li WD, Li XN, Li XQ, Li YF, Li ZB, Liang H, Lin CJ, Lin GL, Lin SK, Lin YC, Ling JJ, Link JM, Littenberg L, Littlejohn BR, Liu DW, Liu H, Liu JC, Liu JL, Liu SS, Liu YB, Lu C, Lu HQ, Luk KB, Ma QM, Ma XB, Ma XY, Ma YQ, McDonald KT, McFarlane MC, McKeown RD, Meng Y, Mitchell I, Nakajima Y, Napolitano J, Naumov D, Naumova E, Nemchenok I, Ngai HY, Ngai WK, Ning Z, Ochoa-Ricoux JP, Olshevski A, Patton S, Pec V, Peng JC, Piilonen LE, Pinsky L, Pun CSJ, Qi FZ, Qi M, Qian X, Raper N, Ren B, Ren J, Rosero R, Roskovec B, Ruan XC, Shao BB, Steiner H, Sun GX, Sun JL, Tam YH, Tanaka HK, Tang X, Themann H, Trentalange S, Tsai O, Tsang KV, Tsang RHM, Tull CE, Tung YC, Viren B, Vorobel V, Wang CH, Wang LS, Wang LY, Wang LZ, Wang M, Wang NY, Wang RG, Wang W, Wang WW, Wang X, Wang YF, Wang Z, Wang Z, Wang ZM, Webber DM, Wei H, Wei YD, Wen LJ, Whisnant K, White CG, Whitehead L, Wise T, Wong HLH, Wong SCF, Worcester E, Wu Q, Xia DM, Xia JK, Xia X, Xing ZZ, Xu J, Xu JL, Xu JY, Xu Y, Xue T, Yan J, Yang CG, Yang L, Yang MS, Ye M, Yeh M, Yeh YS, Young BL, Yu GY, Yu JY, Yu ZY, Zang SL, Zhan L, Zhang C, Zhang FH, Zhang JW, Zhang QM, Zhang SH, Zhang YC, Zhang YH, Zhang YM, Zhang YX, Zhang ZJ, Zhang ZP, Zhang ZY, Zhao J, Zhao QW, Zhao YB, Zheng L, Zhong WL, Zhou L, Zhou ZY, Zhuang HL, Zou JH. Spectral measurement of electron antineutrino oscillation amplitude and frequency at Daya Bay. Phys Rev Lett 2014; 112:061801. [PMID: 24580686 DOI: 10.1103/physrevlett.112.061801] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/24/2013] [Indexed: 06/03/2023]
Abstract
A measurement of the energy dependence of antineutrino disappearance at the Daya Bay reactor neutrino experiment is reported. Electron antineutrinos (ν¯(e)) from six 2.9 GW(th) reactors were detected with six detectors deployed in two near (effective baselines 512 and 561 m) and one far (1579 m) underground experimental halls. Using 217 days of data, 41 589 (203 809 and 92 912) antineutrino candidates were detected in the far hall (near halls). An improved measurement of the oscillation amplitude sin(2)2θ(13)=0.090(-0.009)(+0.008) and the first direct measurement of the ν¯(e) mass-squared difference |Δm(ee)2|=(2.59(-0.20)(+0.19))×10(-3) eV2 is obtained using the observed ν¯(e) rates and energy spectra in a three-neutrino framework. This value of |Δm(ee)2| is consistent with |Δm(μμ)2| measured by muon neutrino disappearance, supporting the three-flavor oscillation model.
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Affiliation(s)
- F P An
- Institute of High Energy Physics, Beijing and East China University of Science and Technology, Shanghai
| | | | - H R Band
- University of Wisconsin, Madison, Wisconsin
| | - W Beriguete
- Brookhaven National Laboratory, Upton, New York
| | - M Bishai
- Brookhaven National Laboratory, Upton, New York
| | - S Blyth
- Department of Physics, National Taiwan University, Taipei
| | - R L Brown
- Brookhaven National Laboratory, Upton, New York
| | - I Butorov
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - G F Cao
- Institute of High Energy Physics, Beijing
| | - J Cao
- Institute of High Energy Physics, Beijing
| | - R Carr
- California Institute of Technology, Pasadena, California
| | - Y L Chan
- Chinese University of Hong Kong, Hong Kong
| | - J F Chang
- Institute of High Energy Physics, Beijing
| | - Y Chang
- National United University, Miao-Li
| | - C Chasman
- Brookhaven National Laboratory, Upton, New York
| | - H S Chen
- Institute of High Energy Physics, Beijing
| | - H Y Chen
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | | | - S M Chen
- Department of Engineering Physics, Tsinghua University, Beijing
| | - X C Chen
- Chinese University of Hong Kong, Hong Kong
| | - X H Chen
- Institute of High Energy Physics, Beijing
| | - Y Chen
- Shenzhen Univeristy, Shenzhen
| | - Y X Chen
- North China Electric Power University, Beijing
| | - Y P Cheng
- Institute of High Energy Physics, Beijing
| | | | - M C Chu
- Chinese University of Hong Kong, Hong Kong
| | | | - J de Arcos
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois
| | - Z Y Deng
- Institute of High Energy Physics, Beijing
| | - Y Y Ding
- Institute of High Energy Physics, Beijing
| | - M V Diwan
- Brookhaven National Laboratory, Upton, New York
| | - E Draeger
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois
| | - X F Du
- Institute of High Energy Physics, Beijing
| | - D A Dwyer
- Lawrence Berkeley National Laboratory, Berkeley, California
| | - W R Edwards
- Lawrence Berkeley National Laboratory, Berkeley, California and Department of Physics, University of California, Berkeley, California
| | - S R Ely
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - J Y Fu
- Institute of High Energy Physics, Beijing
| | - L Q Ge
- Chengdu University of Technology, Chengdu
| | - R Gill
- Brookhaven National Laboratory, Upton, New York
| | - M Gonchar
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - G H Gong
- Department of Engineering Physics, Tsinghua University, Beijing
| | - H Gong
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Y A Gornushkin
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - W Q Gu
- Shanghai Jiao Tong University, Shanghai
| | - M Y Guan
- Institute of High Energy Physics, Beijing
| | - X H Guo
- Beijing Normal University, Beijing
| | | | - R L Hahn
- Brookhaven National Laboratory, Upton, New York
| | - G H Han
- College of William and Mary, Williamsburg, Virginia
| | - S Hans
- Brookhaven National Laboratory, Upton, New York
| | - M He
- Institute of High Energy Physics, Beijing
| | - K M Heeger
- Department of Physics, Yale University, New Haven, Connecticut
| | - Y K Heng
- Institute of High Energy Physics, Beijing
| | - P Hinrichs
- University of Wisconsin, Madison, Wisconsin
| | - Yk Hor
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia
| | - Y B Hsiung
- Department of Physics, National Taiwan University, Taipei
| | - B Z Hu
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | - L J Hu
- Beijing Normal University, Beijing
| | - L M Hu
- Brookhaven National Laboratory, Upton, New York
| | - T Hu
- Institute of High Energy Physics, Beijing
| | - W Hu
- Institute of High Energy Physics, Beijing
| | - E C Huang
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - H X Huang
- China Institute of Atomic Energy, Beijing
| | - H Z Huang
- University of California, Los Angeles, California
| | | | - P Huber
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia
| | - G Hussain
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Z Isvan
- Brookhaven National Laboratory, Upton, New York
| | - D E Jaffe
- Brookhaven National Laboratory, Upton, New York
| | - P Jaffke
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia
| | - S Jetter
- Institute of High Energy Physics, Beijing
| | - X L Ji
- Institute of High Energy Physics, Beijing
| | - X P Ji
- School of Physics, Nankai University, Tianjin
| | - H J Jiang
- Chengdu University of Technology, Chengdu
| | | | - R A Johnson
- Department of Physics, University of Cincinnati, Cincinnati, Ohio
| | - L Kang
- Dongguan University of Technology, Dongguan
| | - S H Kettell
- Brookhaven National Laboratory, Upton, New York
| | - M Kramer
- Lawrence Berkeley National Laboratory, Berkeley, California and Department of Physics, University of California, Berkeley, California
| | - K K Kwan
- Chinese University of Hong Kong, Hong Kong
| | - M W Kwok
- Chinese University of Hong Kong, Hong Kong
| | - T Kwok
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - W C Lai
- Chengdu University of Technology, Chengdu
| | - W H Lai
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | - K Lau
- Department of Physics, University of Houston, Houston, Texas
| | - L Lebanowski
- Department of Engineering Physics, Tsinghua University, Beijing
| | - J Lee
- Lawrence Berkeley National Laboratory, Berkeley, California
| | - R T Lei
- Dongguan University of Technology, Dongguan
| | - R Leitner
- Charles University, Faculty of Mathematics and Physics, Prague
| | - A Leung
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - J K C Leung
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - C A Lewis
- University of Wisconsin, Madison, Wisconsin
| | - D J Li
- University of Science and Technology of China, Hefei
| | - F Li
- Institute of High Energy Physics, Beijing
| | - G S Li
- Shanghai Jiao Tong University, Shanghai
| | - Q J Li
- Institute of High Energy Physics, Beijing
| | - W D Li
- Institute of High Energy Physics, Beijing
| | - X N Li
- Institute of High Energy Physics, Beijing
| | - X Q Li
- School of Physics, Nankai University, Tianjin
| | - Y F Li
- Institute of High Energy Physics, Beijing
| | - Z B Li
- Sun Yat-Sen (Zhongshan) University, Guangzhou
| | - H Liang
- University of Science and Technology of China, Hefei
| | - C J Lin
- Lawrence Berkeley National Laboratory, Berkeley, California
| | - G L Lin
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | - S K Lin
- Department of Physics, University of Houston, Houston, Texas
| | - Y C Lin
- Chengdu University of Technology, Chengdu
| | - J J Ling
- Brookhaven National Laboratory, Upton, New York
| | - J M Link
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia
| | | | - B R Littlejohn
- Department of Physics, University of Cincinnati, Cincinnati, Ohio
| | - D W Liu
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois and Department of Physics, University of Houston, Houston, Texas
| | - H Liu
- Department of Physics, University of Houston, Houston, Texas
| | - J C Liu
- Institute of High Energy Physics, Beijing
| | - J L Liu
- Shanghai Jiao Tong University, Shanghai
| | - S S Liu
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - Y B Liu
- Institute of High Energy Physics, Beijing
| | - C Lu
- Joseph Henry Laboratories, Princeton University, Princeton, New Jersey
| | - H Q Lu
- Institute of High Energy Physics, Beijing
| | - K B Luk
- Lawrence Berkeley National Laboratory, Berkeley, California and Department of Physics, University of California, Berkeley, California
| | - Q M Ma
- Institute of High Energy Physics, Beijing
| | - X B Ma
- North China Electric Power University, Beijing
| | - X Y Ma
- Institute of High Energy Physics, Beijing
| | - Y Q Ma
- Institute of High Energy Physics, Beijing
| | - K T McDonald
- Joseph Henry Laboratories, Princeton University, Princeton, New Jersey
| | | | - R D McKeown
- College of William and Mary, Williamsburg, Virginia
| | - Y Meng
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia
| | - I Mitchell
- Department of Physics, University of Houston, Houston, Texas
| | - Y Nakajima
- Lawrence Berkeley National Laboratory, Berkeley, California
| | - J Napolitano
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, New York
| | - D Naumov
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - E Naumova
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - I Nemchenok
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - H Y Ngai
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - W K Ngai
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - Z Ning
- Institute of High Energy Physics, Beijing
| | | | - A Olshevski
- Joint Institute for Nuclear Research, Dubna, Moscow Region
| | - S Patton
- Lawrence Berkeley National Laboratory, Berkeley, California
| | - V Pec
- Charles University, Faculty of Mathematics and Physics, Prague
| | - J C Peng
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois
| | - L E Piilonen
- Center for Neutrino Physics, Virginia Tech, Blacksburg, Virginia
| | - L Pinsky
- Department of Physics, University of Houston, Houston, Texas
| | - C S J Pun
- Department of Physics, The University of Hong Kong, Pokfulam, Hong Kong
| | - F Z Qi
- Institute of High Energy Physics, Beijing
| | - M Qi
- Nanjing University, Nanjing
| | - X Qian
- Brookhaven National Laboratory, Upton, New York and California Institute of Technology, Pasadena, California
| | - N Raper
- Department of Physics, Applied Physics, and Astronomy, Rensselaer Polytechnic Institute, Troy, New York
| | - B Ren
- Dongguan University of Technology, Dongguan
| | - J Ren
- China Institute of Atomic Energy, Beijing
| | - R Rosero
- Brookhaven National Laboratory, Upton, New York
| | - B Roskovec
- Charles University, Faculty of Mathematics and Physics, Prague
| | - X C Ruan
- China Institute of Atomic Energy, Beijing
| | - B B Shao
- Department of Engineering Physics, Tsinghua University, Beijing
| | - H Steiner
- Lawrence Berkeley National Laboratory, Berkeley, California and Department of Physics, University of California, Berkeley, California
| | - G X Sun
- Institute of High Energy Physics, Beijing
| | - J L Sun
- China Guangdong Nuclear Power Group, Shenzhen
| | - Y H Tam
- Chinese University of Hong Kong, Hong Kong
| | - H K Tanaka
- Brookhaven National Laboratory, Upton, New York
| | - X Tang
- Institute of High Energy Physics, Beijing
| | - H Themann
- Brookhaven National Laboratory, Upton, New York
| | | | - O Tsai
- University of California, Los Angeles, California
| | - K V Tsang
- Lawrence Berkeley National Laboratory, Berkeley, California
| | - R H M Tsang
- California Institute of Technology, Pasadena, California
| | - C E Tull
- Lawrence Berkeley National Laboratory, Berkeley, California
| | - Y C Tung
- Department of Physics, National Taiwan University, Taipei
| | - B Viren
- Brookhaven National Laboratory, Upton, New York
| | - V Vorobel
- Charles University, Faculty of Mathematics and Physics, Prague
| | - C H Wang
- National United University, Miao-Li
| | - L S Wang
- Institute of High Energy Physics, Beijing
| | - L Y Wang
- Institute of High Energy Physics, Beijing
| | - L Z Wang
- North China Electric Power University, Beijing
| | - M Wang
- Shandong University, Jinan
| | - N Y Wang
- Beijing Normal University, Beijing
| | - R G Wang
- Institute of High Energy Physics, Beijing
| | - W Wang
- College of William and Mary, Williamsburg, Virginia
| | | | - X Wang
- College of Electronic Science and Engineering, National University of Defense Technology, Changsha
| | - Y F Wang
- Institute of High Energy Physics, Beijing
| | - Z Wang
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Z Wang
- Institute of High Energy Physics, Beijing
| | - Z M Wang
- Institute of High Energy Physics, Beijing
| | - D M Webber
- University of Wisconsin, Madison, Wisconsin
| | - H Wei
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Y D Wei
- Dongguan University of Technology, Dongguan
| | - L J Wen
- Institute of High Energy Physics, Beijing
| | | | - C G White
- Department of Physics, Illinois Institute of Technology, Chicago, Illinois
| | - L Whitehead
- Department of Physics, University of Houston, Houston, Texas
| | - T Wise
- University of Wisconsin, Madison, Wisconsin
| | - H L H Wong
- Lawrence Berkeley National Laboratory, Berkeley, California and Department of Physics, University of California, Berkeley, California
| | - S C F Wong
- Chinese University of Hong Kong, Hong Kong
| | - E Worcester
- Brookhaven National Laboratory, Upton, New York
| | - Q Wu
- Shandong University, Jinan
| | - D M Xia
- Institute of High Energy Physics, Beijing
| | - J K Xia
- Institute of High Energy Physics, Beijing
| | - X Xia
- Shandong University, Jinan
| | - Z Z Xing
- Institute of High Energy Physics, Beijing
| | - J Xu
- Beijing Normal University, Beijing
| | - J L Xu
- Institute of High Energy Physics, Beijing
| | - J Y Xu
- Chinese University of Hong Kong, Hong Kong
| | - Y Xu
- School of Physics, Nankai University, Tianjin
| | - T Xue
- Department of Engineering Physics, Tsinghua University, Beijing
| | - J Yan
- Xi'an Jiaotong University, Xi'an
| | - C G Yang
- Institute of High Energy Physics, Beijing
| | - L Yang
- Dongguan University of Technology, Dongguan
| | - M S Yang
- Institute of High Energy Physics, Beijing
| | - M Ye
- Institute of High Energy Physics, Beijing
| | - M Yeh
- Brookhaven National Laboratory, Upton, New York
| | - Y S Yeh
- Institute of Physics, National Chiao-Tung University, Hsinchu
| | | | - G Y Yu
- Nanjing University, Nanjing
| | - J Y Yu
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Z Y Yu
- Institute of High Energy Physics, Beijing
| | | | - L Zhan
- Institute of High Energy Physics, Beijing
| | - C Zhang
- Brookhaven National Laboratory, Upton, New York
| | - F H Zhang
- Institute of High Energy Physics, Beijing
| | - J W Zhang
- Institute of High Energy Physics, Beijing
| | | | - S H Zhang
- Institute of High Energy Physics, Beijing
| | - Y C Zhang
- University of Science and Technology of China, Hefei
| | - Y H Zhang
- Institute of High Energy Physics, Beijing
| | - Y M Zhang
- Department of Engineering Physics, Tsinghua University, Beijing
| | - Y X Zhang
- China Guangdong Nuclear Power Group, Shenzhen
| | - Z J Zhang
- Dongguan University of Technology, Dongguan
| | - Z P Zhang
- University of Science and Technology of China, Hefei
| | - Z Y Zhang
- Institute of High Energy Physics, Beijing
| | - J Zhao
- Institute of High Energy Physics, Beijing
| | - Q W Zhao
- Institute of High Energy Physics, Beijing
| | - Y B Zhao
- Institute of High Energy Physics, Beijing
| | - L Zheng
- University of Science and Technology of China, Hefei
| | - W L Zhong
- Institute of High Energy Physics, Beijing
| | - L Zhou
- Institute of High Energy Physics, Beijing
| | - Z Y Zhou
- China Institute of Atomic Energy, Beijing
| | - H L Zhuang
- Institute of High Energy Physics, Beijing
| | - J H Zou
- Institute of High Energy Physics, Beijing
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Chen W, Lv YT, Zhang HX, Ruan D, Wang S, Lin YC. Developmental specificity in skeletal muscle of late-term avian embryos and its potential manipulation. Poult Sci 2013; 92:2754-64. [PMID: 24046424 DOI: 10.3382/ps.2013-03099] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Unlike the mammalian fetus, development of the avian embryo is independent of the maternal uterus and is potentially vulnerable to physiological and environmental stresses close to hatch. In contrast to the fetus of late gestation in mammals, skeletal muscle in avian embryos during final incubation shows differential developmental characteristics: 1) muscle mobilization (also called atrophy) is selectively enhanced in the type II fibers (pectoral muscle) but not in the type I fibers (biceps femoris and semimembranosus muscle), involving activation of ubiquitin-mediated protein degradation and suppression of S6K1-mediated protein translation; 2) the proliferative activity of satellite cells is decreased in the atrophied muscle of late-term embryos but enhanced at the day of hatch, probably preparing for the postnatal growth. The mobilization of muscle may represent an adaptive response of avian embryos to external (environmental) or internal (physiological) changes, considering there are developmental transitions both in hormones and requirements for glycolytic substrates from middle-term to late-term incubation. Although the exact mechanism triggering muscle fiber atrophy is still unknown, nutritional and endocrine changes may be of importance. The atrophied muscle fiber recovers as soon as feed and water are available to the hatchling. In ovo feeding of late-term embryos has been applied to improve the nutritional status and therein enhances muscle development. Similarly, in ovo exposure to higher temperature or green light during the critical period of muscle development are also demonstrated to be potential strategies to promote pre- and posthatch muscle growth.
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Affiliation(s)
- W Chen
- Institute of Animal Science, Guangdong Academy of Agricultural Sciences, Guangzhou 510640, China
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Yang SK, Tan N, Yan XM, Chen F, Long W, Lin YC. Thorium(IV) removal from aqueous medium by citric acid treated mangrove endophytic fungus Fusarium sp. #ZZF51. Mar Pollut Bull 2013; 74:213-219. [PMID: 23871201 DOI: 10.1016/j.marpolbul.2013.06.055] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2013] [Revised: 06/23/2013] [Accepted: 06/26/2013] [Indexed: 06/02/2023]
Abstract
Thorium(IV) biosorption is investigated by citric acid treated mangrove endophytic fungus Fussarium sp. #ZZF51 (CA-ZZF51) from South China Sea. The biosorption process was optimized at pH 4.5, equilibrium time 90 min, initial thorium(IV) concentration 50 mg L(-1) and adsorbent dose 0.6 g L(-1) with 90.87% of removal efficiency and 75.47 mg g(-1) of adsorption capacity, which is obviously greater than that (11.35 mg g(-1)) of the untreated fungus Fussarium sp. #ZZF51 for thorium(IV) biosorption under the condition of optimization. The experimental data are analyzed by using isotherm and kinetic models. Kinetic data follow the pseudo-second-order model and equilibrium data agree very well with the Langmuir model. In addition, FTIR analysis indicates that hydroxyl, amino, and carbonyl groups act as the important roles in the adsorption process.
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Affiliation(s)
- S K Yang
- School of Chemistry and Chemical Engineering, University of South China, Hengyang, Hunan 421001, China.
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Tseng LM, Hsu NC, Chen SC, Lu YS, Lin CH, Chang DY, Li H, Lin YC, Chang HK, Chao TC, Ouyang F, Hou MF. Distant metastasis in triple-negative breast cancer. Neoplasma 2013; 60:290-4. [PMID: 23373998 DOI: 10.4149/neo_2013_038] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Triple-negative breast cancer (TNBC) relapses more frequently than hormone receptor-positive subtypes and is often associated with poor outcomes. This retrospective study reviewed the pattern of distant metastasis with regard to survival in patients with TNBC. A total of 205 TNBC patients were analyzed. TNBC patients with lung metastases had the longest median post-metastatic OS (with 95% confidence interval) of 16.6 (10.3-22.9) months, followed by the bone, 16.3 (11.7-20.8) months, the liver, 8.9 (3.5-14.4) months, the pleura, 7.5 (2.8-12.3) months, and the brain, 4.3 (0.6-8.0) months. Kaplan-Meier plots indicated that TNBC patients with metastatic spread to brain, liver, and pleural had poorer post-metastatic OS rate than patients with lung metastases (p = 0.001, 0.004, and 0.029, respectively). Moreover, brain and liver metastases correlated significantly with poorer post-metastatic OS as compared to bone metastasis (p = 0.004 and 0.011, respectively). Route of first metastasis correlated significantly with survival of TNBC patients with brain metastases being the poorest survival indicator, followed by metastases to liver, pleura, bone, and lung.
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Affiliation(s)
- L M Tseng
- Department of Surgery, Taipei Veterans General Hospital, Taipei, Taiwan
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Lo YC, Chen WC, Huang WT, Lin YC, Liu MC, Kuo HW, Chuang JH, Yang JR, Liu MT, Wu HS, Yang CH, Chou JH, Chang FY. Surveillance of avian influenza A(H7N9) virus infection in humans and detection of the first imported human case in Taiwan, 3 April to 10 May 2013. Euro Surveill 2013. [DOI: 10.2807/ese.18.20.20479-en] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
On 3 April 2013, suspected and confirmed cases of influenza A(H7N9) virus infection became notifiable in the primary care sector in Taiwan, and detection of the virus became part of the surveillance of severe community-acquired pneumonia. On 24 April, the first imported case, reported through both surveillance systems, was confirmed in a man returning from China by sequencing from endotracheal aspirates after two negative throat swabs. Three of 139 contacts were ill and tested influenza A(H7N9)-negative.
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Affiliation(s)
- Y C Lo
- Centers for Disease Control, Taipei, Taiwan
| | - W C Chen
- Centers for Disease Control, Taipei, Taiwan
| | - W T Huang
- Centers for Disease Control, Taipei, Taiwan
| | - Y C Lin
- Centers for Disease Control, Taipei, Taiwan
| | - M C Liu
- Centers for Disease Control, Taipei, Taiwan
| | - H W Kuo
- Centers for Disease Control, Taipei, Taiwan
| | - J H Chuang
- Centers for Disease Control, Taipei, Taiwan
| | - J R Yang
- Centers for Disease Control, Taipei, Taiwan
| | - M T Liu
- Centers for Disease Control, Taipei, Taiwan
| | - H S Wu
- Centers for Disease Control, Taipei, Taiwan
| | - C H Yang
- Centers for Disease Control, Taipei, Taiwan
| | - J H Chou
- Centers for Disease Control, Taipei, Taiwan
| | - F Y Chang
- Centers for Disease Control, Taipei, Taiwan
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Lo YC, Chen WC, Huang WT, Lin YC, Liu MC, Kuo HW, Chuang JH, Yang JR, Liu MT, Wu HS, Yang CH, Chou JH, Chang FY. Surveillance of avian influenza A(H7N9) virus infection in humans and detection of the first imported human case in Taiwan, 3 April to 10 May 2013. Euro Surveill 2013; 18:20479. [PMID: 23725865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/02/2023] Open
Abstract
On 3 April 2013, suspected and confirmed cases of influenza A(H7N9) virus infection became notifiable in the primary care sector in Taiwan, and detection of the virus became part of the surveillance of severe community-acquired pneumonia. On 24 April, the first imported case, reported through both surveillance systems, was confirmed in a man returning from China by sequencing from endotracheal aspirates after two negative throat swabs. Three of 139 contacts were ill and tested influenza A(H7N9)-negative.
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Affiliation(s)
- Y C Lo
- Centers for Disease Control, Taipei, Taiwan
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46
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Van Bogaert INA, Holvoet K, Roelants SLKW, Li B, Lin YC, Van de Peer Y, Soetaert W. The biosynthetic gene cluster for sophorolipids: a biotechnological interesting biosurfactant produced byStarmerella bombicola. Mol Microbiol 2013; 88:501-9. [DOI: 10.1111/mmi.12200] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Inge N. A. Van Bogaert
- Laboratory of Industrial Biotechnology and Biocatalysis; Department of Biochemical and Microbial Technology; Ghent University; Coupure Links 653 B-9000 Ghent Belgium
| | - Kevin Holvoet
- Laboratory of Food Microbiology and Food Preservation; Department of Food Safety and Food Quality; Faculty of Bioscience Engineering; Ghent University; Coupure Links 653 B-9000 Ghent Belgium
- Research Group EnBiChem; Department of Industrial Engineering and Technology; University College West-Flanders (Howest); Graaf Karel de Goedelaan 5 B-8500 Kortrijk Belgium
| | - Sophie L. K. W. Roelants
- Laboratory of Industrial Biotechnology and Biocatalysis; Department of Biochemical and Microbial Technology; Ghent University; Coupure Links 653 B-9000 Ghent Belgium
| | - Bing Li
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Gent Belgium
| | - Yao-Cheng Lin
- Department of Plant Systems Biology; VIB; Technologiepark 927 9052 Gent Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics; Ghent University; Gent Belgium
- Department of Plant Systems Biology; VIB; Technologiepark 927 9052 Gent Belgium
| | - Wim Soetaert
- Laboratory of Industrial Biotechnology and Biocatalysis; Department of Biochemical and Microbial Technology; Ghent University; Coupure Links 653 B-9000 Ghent Belgium
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47
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Wang YY, Lin YC, Hung HC, Tien WY, Shieh TY. Polymorphisms in Kallikrein7 and 10 genes and oral cancer risks in Taiwan betel quid chewers and smokers. Oral Dis 2013; 19:824-32. [PMID: 23413953 DOI: 10.1111/odi.12072] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2012] [Revised: 11/02/2012] [Accepted: 01/08/2013] [Indexed: 01/25/2023]
Abstract
OBJECTIVES We investigated the association between mRNA levels, polymorphisms of Kallikrein7 (KLK7) and Kallikrein10 (KLK10), and the development of oral squamous cell carcinoma (OSCC). MATERIALS AND METHODS We recruited 217 OSCC patients and 138 healthy controls. All were men, betel quid chewers, cigarette smokers, and Minnan ethnicity. Genotyping was performed using a TaqMan probe genotyping assay. Gene expression levels were determined using real-time polymerase chain reactions (PCRs) for 20 pairs of cancerous and non-cancerous tissues. RESULTS Kallikrein10 rs3745535G>T polymorphisms were significantly associated with OSCC development [adjusted OR (AOR) = 1.62, 95% CI = 1.02-2.59], but KLK7 polymorphisms were not. The KLK7 rs10581213(wt/ins + ins/ins) genotypes were significantly associated with early-stage cancer (AOR = 0.34, 95% CI = 0.14-0.78), but KLK10 polymorphisms were not. Relative expression analysis indicated that an increase in KLK7 and KLK10 mRNA levels was found in cancerous tissues (2(-ΔΔCT) = 25.23 ± 8.85 and 10.89 ± 4.97, respectively). A significantly higher level of KLK7 was expressed in early-stage cancer with the rs10581213(wt/ins + ins/ins) genotypes, but there was no significant difference in the mRNA levels of KLK7 and KLK10 between early- and advanced-stage cancers. CONCLUSIONS This is the first correlation of OSCC with KLK10 rs3745535G>T polymorphisms. Early-stage OSCC and high KLK7 mRNA levels were correlated with the rs10581213(wt/ins + ins/ins) genotypes. More studies with large sample sizes are needed to verify our findings.
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Affiliation(s)
- Y Y Wang
- School of Dentistry, Kaohsiung Medical University, Kaohsiung, Taiwan
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Lin YH, Liu YS, Lin YC, Wei YS, Liao KS, Lee KR, Lai JY, Chen HM, Jean YC, Liu CY. Decoupling free-carriers contributions from oxygen-vacancy and cation-substitution in extrinsic conducting oxides. J Appl Phys 2013; 113:33706. [PMID: 23405036 PMCID: PMC3562333 DOI: 10.1063/1.4776781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2012] [Accepted: 01/02/2013] [Indexed: 06/01/2023]
Abstract
The intrinsic oxygen-vacancies and the extrinsic dopants are two major fundamental free-carrier sources for the extrinsic conducting oxides, such as Sn-doped In(2)O(3). Yet, the individual contributions of the above two free-carrier sources to the total carrier concentrations have never been unraveled. A carrier-concentration separation model is derived in this work, which can define the individual contributions to the total carrier concentration from the intrinsic oxygen-vacancies and the extrinsic dopants, separately. The individual contributions obtained from the present carrier-concentration separation model are verified by the two-state trapping model, photoluminescence, and positron annihilation lifetime (PAL) spectroscopy. In addition, the oxygen-vacancy formation energy of the Sn:In(2)O(3) thin film is determined to be 0.25 eV by PAL spectroscopy.
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Shao KT, Lai KC, Lin YC, Chen LS, Li HY, Hsu CH, Lee H, Hsu HW, Mai GS. Experience and Strategy of Biodiversity Data Integration in Taiwan. Data Sci J 2013. [DOI: 10.2481/dsj.wds-008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Akira A, Ohmura H, Uzumcu M, Araki T, Lin YC. Gossypol inhibits aromatase activity in cultured porcine granulosa cells. Theriogenology 2012; 41:1489-97. [PMID: 16727503 DOI: 10.1016/0093-691x(94)90200-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/1993] [Accepted: 03/08/1994] [Indexed: 11/25/2022]
Abstract
The present study investigated whether gossypol inhibited aromatase activity in cultured porcine granulosa cells. Aromatase activity was assayed by measuring (3)H-H(2)O released from [1beta-(3)H]-androstenedione. First, immature porcine granulosa cells were cultured with various doses of follicle stimulating hormone (FSH, 1 to 1000 ng/ml) for 1 to 5 d to determine optimal culture conditions for aromatase activity assay. Second, porcine granulosa cells were cultured with or without FSH in the presence or absence of gossypol. Gossypol, at 4 muM, significantly inhibited FSH-induced aromatase activity while showing no effect on basal aromatase activity. Gossypol did not inhibit cell proliferation during cell culture. These results suggest that gossypol inhibits aromatase activity by interfering with FSH induction of aromatase in cultured porcine granulosa cells.
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Affiliation(s)
- A Akira
- Laboratory of Reproductive Endocrinology Department of Veterinary Physiology and Pharmacology College of Veterinary Medicine The Ohio State University 1900 Coffey Road Columbus, OH 43210-1092 USA
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