239 results on '"Hung-Yi Wu"'
Search Results
52. Accounting for Phase Drifts in SSVEP-Based BCIs by Means of Biphasic Stimulation.
- Author
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Hung-Yi Wu, Po-Lei Lee, Hsiang-Chih Chang, and Jen-Chuen Hsieh
- Published
- 2011
- Full Text
- View/download PDF
53. Innovation capital indicator assessment of Taiwanese Universities: A hybrid fuzzy model application.
- Author
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Hung-Yi Wu, Jui-Kuei Chen, and I-Shuo Chen
- Published
- 2010
- Full Text
- View/download PDF
54. A fuzzy MCDM approach for evaluating banking performance based on Balanced Scorecard.
- Author
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Hung-Yi Wu, Gwo-Hshiung Tzeng, and Yi-Hsuan Chen
- Published
- 2009
- Full Text
- View/download PDF
55. Diversity and pathogenicity of Colletotrichum species causing strawberry anthracnose in Taiwan and description of a new species, Colletotrichum miaoliense sp. nov
- Author
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Ting-Hsuan Hung, Hiran A. Ariyawansa, Chia-Lin Chung, Pei-Che Chung, Yen-Wen Wang, Hsien-Pin Hu, Shean-Shong Tzean, and Hung-Yi Wu
- Subjects
0301 basic medicine ,Population ,Genes, Fungal ,Taiwan ,lcsh:Medicine ,Biology ,Microbiology ,Fragaria ,Article ,03 medical and health sciences ,0302 clinical medicine ,Intergenic region ,Colletotrichum ,Internal transcribed spacer ,education ,DNA, Fungal ,lcsh:Science ,Phylogeny ,Plant Diseases ,education.field_of_study ,Multidisciplinary ,Virulence ,fungi ,lcsh:R ,Fungal genetics ,Fungi ,Genetic Variation ,food and beverages ,biology.organism_classification ,Plant disease ,Plant Leaves ,Horticulture ,030104 developmental biology ,Fruit ,Potato dextrose agar ,lcsh:Q ,Pathogens ,030217 neurology & neurosurgery - Abstract
Strawberry is a small fruit crop with high economic value. Anthracnose caused by Colletotrichum spp. poses a serious threat to strawberry production, particularly in warm and humid climates, but knowledge of pathogen populations in tropical and subtropical regions is limited. To investigate the diversity of infectious agents causing strawberry anthracnose in Taiwan, a disease survey was conducted from 2010 to 2018, and Colletotrichum spp. were identified through morphological characterization and multilocus phylogenetic analysis with internal transcribed spacer, glyceraldehyde 3-phosphate dehydrogenase, chitin synthase, actin, beta-tubulin, calmodulin, and the intergenic region between Apn2 and MAT1-2-1 (ApMAT). Among 52 isolates collected from 24 farms/nurseries in Taiwan, a new species, Colletotrichum miaoliense sp. nov. (6% of all isolates), a species not previously known to be associated with strawberry, Colletotrichum karstii (6%), and three known species, Colletotrichum siamense (75%), Colletotrichum fructicola (11%), and Colletotrichum boninense (2%), were identified. The predominant species C. siamense and C. fructicola exhibited higher mycelial growth rates on potato dextrose agar and caused larger lesions on wounded and non-wounded detached strawberry leaves. Colletotrichum boninense, C. karstii, and C. miaoliense only caused lesions on wounded leaves. Understanding the composition and biology of the pathogen population will help in disease management and resistance breeding.
- Published
- 2020
56. Construction of polycistronic baculovirus surface display vectors to express the PCV2 Cap(d41) protein and analysis of its immunogenicity in mice and swine
- Author
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Chi-Young Wang, Ching-Dong Chang, Yu-Kang Chang, Hung-Jen Liu, Wei-Ru Huang, Jyun-Yi Li, Kuo Pin Chuang, Wei-Chen Yang, Brent L. Nielsen, Hung-Yi Wu, Ya-Yi Chen, National Chung Hsing University, National Pingtung University of Science and Technology, and Brigham Young University (BYU)
- Subjects
0301 basic medicine ,Circovirus ,Cellular immunity ,Swine ,Protein subunit ,030106 microbiology ,Genetic Vectors ,Sus scrofa ,law.invention ,03 medical and health sciences ,Mice ,Viral Proteins ,Immune system ,Immunogenicity, Vaccine ,law ,Animals ,Circoviridae Infections ,IFN-γ ,cellular immune response ,Swine Diseases ,[SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health ,lcsh:Veterinary medicine ,General Veterinary ,biology ,Cap protein ,Immunogenicity ,virus neutralization test ,Virology ,baculovirus surface display vectors ,CD4+ T cells ,3. Good health ,Specific Pathogen-Free Organisms ,PCV2 ,Titer ,030104 developmental biology ,4Cap(d41) vaccine ,biology.protein ,Recombinant DNA ,lcsh:SF600-1100 ,Antibody ,[SDV.IMM.VAC]Life Sciences [q-bio]/Immunology/Vaccinology ,Baculoviridae ,CD8 ,Research Article - Abstract
To increase expression levels of the PCV2 Cap(d41) protein, novel baculovirus surface display vectors with multiple expression cassettes were constructed to create recombinant baculoviruses BacSC-Cap(d41), BacDD-2Cap(d41), BacDD-3Cap(d41), and BacDD-4Cap(d41). Our results reveal that the recombinant baculovirus BacDD-4Cap(d41) was able to express the highest levels of Cap(d41) protein. Optimum conditions for expressing the PCV2 Cap(d41) protein were determined, and our results show that 107 of Sf-9 infected with the recombinant baculovirus BacDD-4Cap(d41) at an MOI of 5 for 3 days showed the highest level of protein expression. Mice immunized with the 4Cap(d41) vaccine which was prepared from the recombinant baculovirus-infected cells (107) elicited higher ELISA titers compared to the Cap (d41) vaccine. The 4Cap(d41) vaccine could elicit anti-PCV2 neutralizing antibodies and IFN-γ in mice, as confirmed by virus neutralization test and IFN-γ ELISA. Moreover, the swine lymphocyte proliferative responses indicated that the 4Cap(d41) vaccine was able to induce a clear cellular immune response. Flow cytometry analysis showed that the percentage of CD4+ T cells and CD4+/CD8+ ratio was increased significantly in SPF pigs immunized with the 4Cap(d41) vaccine. Importantly, the 4Cap(d41) vaccine induced an IFN-γ response, further confirming that its effect is through cellular immunity in SPF pigs. An in vivo challenge study revealed that the 4Cap(d41) and the commercial vaccine groups significantly reduce the viral load of vaccinated pigs as compared with the CE negative control group. Taken together, we have successfully developed a 4Cap(d41) vaccine that may be a potential subunit vaccine for preventing the disease associated with PCV2 infections.
- Published
- 2020
57. The Human Tumor Atlas Network: Charting Tumor Transitions across Space and Time at Single-Cell Resolution
- Author
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Orit Rozenblatt-Rosen, Aviv Regev, Philipp Oberdoerffer, Tal Nawy, Anna Hupalowska, Jennifer E. Rood, Orr Ashenberg, Ethan Cerami, Robert J. Coffey, Emek Demir, Li Ding, Edward D. Esplin, James M. Ford, Jeremy Goecks, Sharmistha Ghosh, Joe W. Gray, Justin Guinney, Sean E. Hanlon, Shannon K. Hughes, E. Shelley Hwang, Christine A. Iacobuzio-Donahue, Judit Jané-Valbuena, Bruce E. Johnson, Ken S. Lau, Tracy Lively, Sarah A. Mazzilli, Dana Pe’er, Sandro Santagata, Alex K. Shalek, Denis Schapiro, Michael P. Snyder, Peter K. Sorger, Avrum E. Spira, Sudhir Srivastava, Kai Tan, Robert B. West, Elizabeth H. Williams, Denise Aberle, Samuel I. Achilefu, Foluso O. Ademuyiwa, Andrew C. Adey, Rebecca L. Aft, Rachana Agarwal, Ruben A. Aguilar, Fatemeh Alikarami, Viola Allaj, Christopher Amos, Robert A. Anders, Michael R. Angelo, Kristen Anton, Jon C. Aster, Ozgun Babur, Amir Bahmani, Akshay Balsubramani, David Barrett, Jennifer Beane, Diane E. Bender, Kathrin Bernt, Lynne Berry, Courtney B. Betts, Julie Bletz, Katie Blise, Adrienne Boire, Genevieve Boland, Alexander Borowsky, Kristopher Bosse, Matthew Bott, Ed Boyden, James Brooks, Raphael Bueno, Erik A. Burlingame, Qiuyin Cai, Joshua Campbell, Wagma Caravan, Hassan Chaib, Joseph M. Chan, Young Hwan Chang, Deyali Chatterjee, Ojasvi Chaudhary, Alyce A. Chen, Bob Chen, Changya Chen, Chia-hui Chen, Feng Chen, Yu-An Chen, Milan G. Chheda, Koei Chin, Roxanne Chiu, Shih-Kai Chu, Rodrigo Chuaqui, Jaeyoung Chun, Luis Cisneros, Graham A. Colditz, Kristina Cole, Natalie Collins, Kevin Contrepois, Lisa M. Coussens, Allison L. Creason, Daniel Crichton, Christina Curtis, Tanja Davidsen, Sherri R. Davies, Ino de Bruijn, Laura Dellostritto, Angelo De Marzo, David G. DeNardo, Dinh Diep, Sharon Diskin, Xengie Doan, Julia Drewes, Stephen Dubinett, Michael Dyer, Jacklynn Egger, Jennifer Eng, Barbara Engelhardt, Graham Erwin, Laura Esserman, Alex Felmeister, Heidi S. Feiler, Ryan C. Fields, Stephen Fisher, Keith Flaherty, Jennifer Flournoy, Angelo Fortunato, Allison Frangieh, Jennifer L. Frye, Robert S. Fulton, Danielle Galipeau, Siting Gan, Jianjiong Gao, Long Gao, Peng Gao, Vianne R. Gao, Tim Geiger, Ajit George, Gad Getz, Marios Giannakis, David L. Gibbs, William E. Gillanders, Simon P. Goedegebuure, Alanna Gould, Kate Gowers, William Greenleaf, Jeremy Gresham, Jennifer L. Guerriero, Tuhin K. Guha, Alexander R. Guimaraes, David Gutman, Nir Hacohen, Sean Hanlon, Casey R. Hansen, Olivier Harismendy, Kathleen A. Harris, Aaron Hata, Akimasa Hayashi, Cody Heiser, Karla Helvie, John M. Herndon, Gilliam Hirst, Frank Hodi, Travis Hollmann, Aaron Horning, James J. Hsieh, Shannon Hughes, Won Jae Huh, Stephen Hunger, Shelley E. Hwang, Heba Ijaz, Benjamin Izar, Connor A. Jacobson, Samuel Janes, Reyka G. Jayasinghe, Lihua Jiang, Brett E. Johnson, Bruce Johnson, Tao Ju, Humam Kadara, Klaus Kaestner, Jacob Kagan, Lukas Kalinke, Robert Keith, Aziz Khan, Warren Kibbe, Albert H. Kim, Erika Kim, Junhyong Kim, Annette Kolodzie, Mateusz Kopytra, Eran Kotler, Robert Krueger, Kostyantyn Krysan, Anshul Kundaje, Uri Ladabaum, Blue B. Lake, Huy Lam, Rozelle Laquindanum, Ashley M. Laughney, Hayan Lee, Marc Lenburg, Carina Leonard, Ignaty Leshchiner, Rochelle Levy, Jerry Li, Christine G. Lian, Kian-Huat Lim, Jia-Ren Lin, Yiyun Lin, Qi Liu, Ruiyang Liu, William J.R. Longabaugh, Teri Longacre, Cynthia X. Ma, Mary Catherine Macedonia, Tyler Madison, Christopher A. Maher, Anirban Maitra, Netta Makinen, Danika Makowski, Carlo Maley, Zoltan Maliga, Diego Mallo, John Maris, Nick Markham, Jeffrey Marks, Daniel Martinez, Robert J. Mashl, Ignas Masilionais, Jennifer Mason, Joan Massagué, Pierre Massion, Marissa Mattar, Richard Mazurchuk, Linas Mazutis, Eliot T. McKinley, Joshua F. McMichael, Daniel Merrick, Matthew Meyerson, Julia R. Miessner, Gordon B. Mills, Meredith Mills, Suman B. Mondal, Motomi Mori, Yuriko Mori, Elizabeth Moses, Yael Mosse, Jeremy L. Muhlich, George F. Murphy, Nicholas E. Navin, Michel Nederlof, Reid Ness, Stephanie Nevins, Milen Nikolov, Ajit Johnson Nirmal, Garry Nolan, Edward Novikov, Brendan O’Connell, Michael Offin, Stephen T. Oh, Anastasiya Olson, Alex Ooms, Miguel Ossandon, Kouros Owzar, Swapnil Parmar, Tasleema Patel, Gary J. Patti, Itsik Pe'er, Tao Peng, Daniel Persson, Marvin Petty, Hanspeter Pfister, Kornelia Polyak, Kamyar Pourfarhangi, Sidharth V. Puram, Qi Qiu, Álvaro Quintanal-Villalonga, Arjun Raj, Marisol Ramirez-Solano, Rumana Rashid, Ashley N. Reeb, Mary Reid, Adam Resnick, Sheila M. Reynolds, Jessica L. Riesterer, Scott Rodig, Joseph T. Roland, Sonia Rosenfield, Asaf Rotem, Sudipta Roy, Charles M. Rudin, Marc D. Ryser, Maria Santi-Vicini, Kazuhito Sato, Deborah Schrag, Nikolaus Schultz, Cynthia L. Sears, Rosalie C. Sears, Subrata Sen, Triparna Sen, Alex Shalek, Jeff Sheng, Quanhu Sheng, Kooresh I. Shoghi, Martha J. Shrubsole, Yu Shyr, Alexander B. Sibley, Kiara Siex, Alan J. Simmons, Dinah S. Singer, Shamilene Sivagnanam, Michal Slyper, Artem Sokolov, Sheng-Kwei Song, Austin Southard-Smith, Avrum Spira, Janet Stein, Phillip Storm, Elizabeth Stover, Siri H. Strand, Timothy Su, Damir Sudar, Ryan Sullivan, Lea Surrey, Mario Suvà, Nadezhda V. Terekhanova, Luke Ternes, Lisa Thammavong, Guillaume Thibault, George V. Thomas, Vésteinn Thorsson, Ellen Todres, Linh Tran, Madison Tyler, Yasin Uzun, Anil Vachani, Eliezer Van Allen, Simon Vandekar, Deborah J. Veis, Sébastien Vigneau, Arastoo Vossough, Angela Waanders, Nikhil Wagle, Liang-Bo Wang, Michael C. Wendl, Robert West, Chi-yun Wu, Hao Wu, Hung-Yi Wu, Matthew A. Wyczalkowski, Yubin Xie, Xiaolu Yang, Clarence Yapp, Wenbao Yu, Yinyin Yuan, Dadong Zhang, Kun Zhang, Mianlei Zhang, Nancy Zhang, Yantian Zhang, Yanyan Zhao, Daniel Cui Zhou, Zilu Zhou, Houxiang Zhu, Qin Zhu, Xiangzhu Zhu, Yuankun Zhu, and Xiaowei Zhuang
- Subjects
Cell ,Genomics ,Computational biology ,Tumor initiation ,Biology ,Article ,General Biochemistry, Genetics and Molecular Biology ,Metastasis ,03 medical and health sciences ,Atlases as Topic ,0302 clinical medicine ,Neoplasms ,Tumor Microenvironment ,medicine ,Humans ,Precision Medicine ,030304 developmental biology ,0303 health sciences ,Atlas (topology) ,Cancer ,medicine.disease ,3. Good health ,Human tumor ,Cell Transformation, Neoplastic ,medicine.anatomical_structure ,Single-Cell Analysis ,Single point ,030217 neurology & neurosurgery - Abstract
Crucial transitions in cancer-including tumor initiation, local expansion, metastasis, and therapeutic resistance-involve complex interactions between cells within the dynamic tumor ecosystem. Transformative single-cell genomics technologies and spatial multiplex in situ methods now provide an opportunity to interrogate this complexity at unprecedented resolution. The Human Tumor Atlas Network (HTAN), part of the National Cancer Institute (NCI) Cancer Moonshot Initiative, will establish a clinical, experimental, computational, and organizational framework to generate informative and accessible three-dimensional atlases of cancer transitions for a diverse set of tumor types. This effort complements both ongoing efforts to map healthy organs and previous large-scale cancer genomics approaches focused on bulk sequencing at a single point in time. Generating single-cell, multiparametric, longitudinal atlases and integrating them with clinical outcomes should help identify novel predictive biomarkers and features as well as therapeutically relevant cell types, cell states, and cellular interactions across transitions. The resulting tumor atlases should have a profound impact on our understanding of cancer biology and have the potential to improve cancer detection, prevention, and therapeutic discovery for better precision-medicine treatments of cancer patients and those at risk for cancer.
- Published
- 2020
58. Structure-Based Stabilization of Non-native Protein–Protein Interactions of Coronavirus Nucleocapsid Proteins in Antiviral Drug Design
- Author
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Hung-Yi Wu, Yong Sheng Wang, Ching-Ming Chien, U-Ser Jeng, Kylene Kehn-Hall, Shih-Chao Lin, Chung-ke Chang, Ming-Hon Hou, Jia-Ning Hsu, and Shan-Meng Lin
- Subjects
Indoles ,Viral protein ,Protein domain ,Computational biology ,Plasma protein binding ,Crystallography, X-Ray ,medicine.disease_cause ,Antiviral Agents ,01 natural sciences ,Article ,Protein–protein interaction ,Hydrophobic effect ,03 medical and health sciences ,Alkaloids ,Protein Domains ,Chlorocebus aethiops ,Drug Discovery ,medicine ,Animals ,Coronavirus Nucleocapsid Proteins ,Protein oligomerization ,Amino Acid Sequence ,Vero Cells ,030304 developmental biology ,0303 health sciences ,Virtual screening ,Chemistry ,Drug discovery ,Nucleocapsid Proteins ,0104 chemical sciences ,Molecular Docking Simulation ,010404 medicinal & biomolecular chemistry ,Drug Design ,Middle East Respiratory Syndrome Coronavirus ,Molecular Medicine ,Protein Multimerization ,Hydrophobic and Hydrophilic Interactions ,Sequence Alignment ,Protein Binding - Abstract
Structure-based stabilization of protein–protein interactions (PPIs) is a promising strategy for drug discovery. However, this approach has mainly focused on the stabilization of native PPIs, and non-native PPIs have received little consideration. Here, we identified a non-native interaction interface on the three-dimensional dimeric structure of the N-terminal domain of the MERS-CoV nucleocapsid protein (MERS-CoV N-NTD). The interface formed a conserved hydrophobic cavity suitable for targeted drug screening. By considering the hydrophobic complementarity during the virtual screening step, we identified 5-benzyloxygramine as a new N protein PPI orthosteric stabilizer that exhibits both antiviral and N-NTD protein-stabilizing activities. X-ray crystallography and small-angle X-ray scattering showed that 5-benzyloxygramine stabilizes the N-NTD dimers through simultaneous hydrophobic interactions with both partners, resulting in abnormal N protein oligomerization that was further confirmed in the cell. This unique approach based on the identification and stabilization of non-native PPIs of N protein could be applied toward drug discovery against CoV diseases.
- Published
- 2020
59. In Vitro and in Planta Evaluation of Trichoderma asperellum TA as a Biocontrol Agent Against Phellinus noxius, the Cause of Brown Root Rot Disease of Trees
- Author
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Li-yu D. Liu, Yi-Ting Xiao, Hao Chou, Ting-Ting Li, Chia-Lin Chung, Jyh-Nong Tsai, Hung-Yi Wu, and Der-Syh Tzeng
- Subjects
0106 biological sciences ,0301 basic medicine ,Rhizosphere ,Phellinus noxius ,biology ,technology, industry, and agriculture ,food and beverages ,Wilting ,Plant Science ,Eriobotrya ,biology.organism_classification ,01 natural sciences ,Potting soil ,Plant disease ,03 medical and health sciences ,medicine.drug_formulation_ingredient ,Horticulture ,030104 developmental biology ,Trichoderma ,medicine ,Root rot ,Agronomy and Crop Science ,010606 plant biology & botany - Abstract
Brown root rot (BRR), caused by the white rot fungus Phellinus noxius, is an epidemic disease of diverse broadleaved and coniferous tree species in many tropical and subtropical regions. Flooding and trenching control measures are difficult to implement, and chemical controls can have an adverse impact on ecosystems. Previous studies have provided in vitro evidence for the potential use of Trichoderma spp. for biocontrol of BRR. Here, we analyzed the in vitro antagonistic and mycoparasitic abilities of four Trichoderma spp. isolates against four P. noxius isolates in dual culture and Ficus microcarpa wood blocks. A convenient inoculation system based on root inoculation of a highly susceptible loquat (Eriobotrya japonica) with P. noxius-colonized wheat-oat grains was developed to examine the effect of Trichoderma treatment in planta. Preventive application of Trichoderma asperellum TA, the isolate showing high antagonistic activity in vitro, was effective in preventing and delaying the wilting of P. noxius-inoculated loquat cuttings in greenhouse trials. To understand the specific niche in which T. asperellum TA interacts with P. noxius, KOH-aniline blue fluorescence microscopy was used to investigate the colonization of loquat roots by P. noxius and/or T. asperellum TA. Dilution plating assays were also conducted to quantify Trichoderma populations in the rhizosphere and potting mix. T. asperellum TA was able to robustly establish in the rhizosphere and potting mix but with scarce root penetration limited to the superficial layer. We discuss the timing and strategy for applying antagonistic Trichodema sp. on living trees or in BRR-infested areas for BRR management.
- Published
- 2019
60. Discovery of a Celecoxib Binding Site on Prostaglandin E Synthase (PTGES) with a Cleavable Chelation-Assisted Biotin Probe
- Author
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Christina M. Woo, Hope A. Flaxman, David K. Miyamoto, Jinxu Gao, and Hung-Yi Wu
- Subjects
0301 basic medicine ,Biotin ,Prostaglandin ,Photoaffinity Labels ,Prostaglandin E synthase ,01 natural sciences ,Biochemistry ,03 medical and health sciences ,chemistry.chemical_compound ,Binding site ,Chelating Agents ,Prostaglandin-E Synthases ,Binding Sites ,Cyclooxygenase 2 Inhibitors ,biology ,Photoaffinity labeling ,010405 organic chemistry ,General Medicine ,Small molecule ,0104 chemical sciences ,Cell biology ,030104 developmental biology ,chemistry ,Membrane protein ,Celecoxib ,Molecular Probes ,Prostaglandins ,biology.protein ,Molecular Medicine ,lipids (amino acids, peptides, and proteins) ,Signal transduction ,Signal Transduction - Abstract
The coxibs are a subset of nonsteroidal anti-inflammatory drugs (NSAIDs) that primarily target cyclooxygenase-2 (COX-2) to inhibit prostaglandin signaling and reduce inflammation. However, mechanisms to inhibit other members of the prostaglandin signaling pathway may improve selectivity and reduce off-target toxicity. Here, we report a novel binding site for celecoxib on prostaglandin E synthase (PTGES), which is an enzyme downstream of COX-2 in the prostaglandin signaling pathway, using a cleavable chelation-assisted biotin probe 6. Evaluation of the multifunctional probe 6 revealed significantly improved tagging efficiencies attributable to the embedded picolyl functional group. Application of the probe 6 within the small molecule interactome mapping by photoaffinity labeling (SIM-PAL) platform using photo-celecoxib as a reporter for celecoxib identified PTGES and other membrane proteins in the top eight enriched proteins from A549 cells. Four binding sites to photo-celecoxib were mapped by the probe 6, including a binding site with PTGES. The binding interaction with PTGES was validated by competitive displacement with celecoxib and licofelone, which is a known PTGES inhibitor, and was used to generate a structural model of the interaction. The identification of photo-celecoxib interactions with membrane proteins, including the direct binding site on the membrane protein PTGES, will inform further functional followup and the design of new selective inhibitors of the prostaglandin signaling pathway.
- Published
- 2019
61. Pose-Guided And Style-Transferred Face Reenactment
- Author
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Hung-Yi Wu and Gee-Sern Jison Hsu
- Subjects
Face (sociological concept) ,Psychology ,Visual arts ,Style (sociolinguistics) - Published
- 2021
62. Newcastle disease virus-induced caspase-independent apoptosis pathway in BHK-21 cells
- Author
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Chen-Wei Wang, Tzu-Chieh Lin, Wen-Ling Shih, Sheng-Chang Chung, Hung-Yi Wu, Chia-Ying Lin, and Duangsuda Thongchan
- Subjects
Caspase-Independent Apoptosis ,viruses ,Biology ,biology.organism_classification ,Virology ,Newcastle disease ,Virus - Abstract
Background: Newcastle disease virus (NDV) is an important virus for humans. It is highly lethal in fowl and is newly identified as an oncolytic virus for cancer treatment. In vivo, NDV induces spleen, thymus, bursa, and mesenteric gland cell apoptosis, thereby causing immunosuppression. In vitro , NDV can induce apoptosis by caspase-dependent pathways including the mitochondria-mediated pathway and death receptor-mediated pathway. Methods: In this study, the major materials were baby hamster kidney (BHK-21) cells, NDV virus ( Miyadera strain; 10 3.8 TCID 50 /μl), and pan-caspase inhibiter Z-Val-Ala-DL-Asp-fluoromethylketone (z-VAD-fmk). All of the experiments used a viral infection MOI of 1. Apoptosis was confirmed using DNA fragmentation and TUNEL assay. Finally, the apoptosis-independent pathway was confirmed by western blot analysis and immunofluorescence. Results: In this study, we differentiate between the caspase group and caspase inhibition group (added 100 µM pan-caspase inhibitor [z-VAD-fmk]) in BHK-21 cells treated with NDV at 0, 12, and 24 h. In the DNA fragmentation and TUNEL assays, the apoptosis appears at 12 h and apoptosis increases over time, regardless of caspase or not. In protein level determination, the antiapoptotic protein Bcl-2 decreased over time, which is the opposite of how the proapoptotic proteins Bax, cytochrome C, Mst3, and AIF behaved. Further, using western blot and immunofluorescent staining, we checked the AIF and Endo G translocation from the mitochondria (cytoplasmic) to the nucleus. In addition to apoptosis, we found that NDV treatment of BHK-21 cells decreased actin, regardless of caspase. The actin always decreased in the NDV-treated BHK-21 cells at 12 and 24 h. Conclusions: NDV-mediated BHK-21 cell apoptosis mechanisms involve complex pathway; when in the normal state, the caspase-dependent pathway is main apoptosis pathway; when the caspase is suppressed, the BHK-21 can switch on the caspase-independent pathway by AIF, Endo G, or Mst3 to allow apoptosis to continue.
- Published
- 2021
63. Labeling Preferences of Diazirines with Protein Biomolecules
- Author
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Andrew C. Huang, Lyn H. Jones, Giovanni Muncipinto, Christina M. Woo, Hung-Yi Wu, Matthew T Labenski, and Alexander V West
- Subjects
Proteome ,Protein Conformation ,Photoaffinity Labels ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Catalysis ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Protein structure ,Humans ,Reactivity (chemistry) ,Amino Acids ,Alkyl ,chemistry.chemical_classification ,Binding Sites ,Photoaffinity labeling ,Chemistry ,Biomolecule ,Voltage-Dependent Anion Channel 1 ,Proteins ,General Chemistry ,Diazonium Compounds ,Hydrogen-Ion Concentration ,Combinatorial chemistry ,0104 chemical sciences ,Amino acid ,Diazomethane ,Diazirine ,Diazo - Abstract
Diazirines are widely used in photoaffinity labeling (PAL) to trap noncovalent interactions with biomolecules. However, design and interpretation of PAL experiments is challenging without a molecular understanding of the reactivity of diazirines with protein biomolecules. Herein, we report a systematic evaluation of the labeling preferences of alkyl and aryl diazirines with individual amino acids, single proteins, and in the whole cell proteome. We find that alkyl diazirines exhibit preferential labeling of acidic amino acids in a pH-dependent manner that is characteristic of a reactive alkyl diazo intermediate, while the aryl-fluorodiazirine labeling pattern reflects reaction primarily through a carbene intermediate. From a survey of 32 alkyl diazirine probes, we use this reactivity profile to rationalize why alkyl diazirine probes preferentially enrich highly acidic proteins or those embedded in membranes and why probes with a net positive charge tend to produce higher labeling yields in cells and in vitro. These results indicate that alkyl diazirines are an especially effective chemistry for surveying the membrane proteome and will facilitate design and interpretation of biomolecular labeling experiments with diazirines.
- Published
- 2021
64. A Binding Site Hotspot Map of the FKBP12–Rapamycin–FRB Ternary Complex by Photoaffinity Labeling and Mass Spectrometry-Based Proteomics
- Author
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Hope A. Flaxman, Christina M. Woo, Chia-Fu Chang, Carter H. Nakamoto, and Hung-Yi Wu
- Subjects
Models, Molecular ,Proteomics ,Binding Sites ,Photoaffinity labeling ,Stereochemistry ,Chemistry ,TOR Serine-Threonine Kinases ,Molecular Conformation ,Photoaffinity Labels ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Small molecule ,Mass Spectrometry ,Catalysis ,0104 chemical sciences ,chemistry.chemical_compound ,Colloid and Surface Chemistry ,Proteome ,Diazirine ,Binding site ,Small molecule binding ,Ternary complex - Abstract
Structural characterization of small molecule binding site hotspots within the global proteome is uniquely enabled by photoaffinity labeling (PAL) coupled with chemical enrichment and unbiased analysis by mass spectrometry (MS). MS-based binding site maps provide structural resolution of interaction sites in conjunction with identification of target proteins. However, binding site hotspot mapping has been confined to relatively simple small molecules to date; extension to more complex compounds would enable the structural definition of new binding modes in the proteome. Here, we extend PAL and MS methods to derive a binding site hotspot map for the immunosuppressant rapamycin, a complex macrocyclic natural product that forms a ternary complex with the proteins FKBP12 and FRB. Photo-rapamycin was developed as a diazirine-based PAL probe for rapamycin, and the FKBP12-photo-rapamycin-FRB ternary complex formed readily in vitro. Photoirradiation, digestion, and MS analysis of the ternary complex revealed a McLafferty rearrangement product of photo-rapamycin conjugated to specific surfaces on FKBP12 and FRB. Molecular modeling based on the binding site map revealed two distinct conformations of complex-bound photo-rapamycin, providing a 5.0 Å distance constraint between the conjugated residues and the diazirine carbon and a 9.0 Å labeling radius for the diazirine upon photoactivation. These measurements may be broadly useful in the interpretation of binding site measurements from PAL. Thus, in characterizing the ternary complex of photo-rapamycin by MS, we applied binding site hotspot mapping to a macrocyclic natural product and extracted precise structural measurements for interpretation of PAL products that may enable the discovery of new binding sites in the "undruggable" proteome.
- Published
- 2019
65. Interaction of coronavirus nucleocapsid protein with the 5′‐ and 3′‐ends of the coronavirus genome is involved in genome circularization and negative‐strand RNA synthesis
- Author
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Tsung-Lin Tsai, Hung-Yi Wu, Chen-Yu Lo, Chao-Nan Lin, and Ching Hung Lin
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0301 basic medicine ,replication ,Negative strand ,coronavirus ,genome circularization ,Genome, Viral ,Virus Replication ,medicine.disease_cause ,Biochemistry ,Genome ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Animals ,Coronavirus Nucleocapsid Proteins ,Nucleotide ,RNA, Messenger ,Molecular Biology ,Bovine coronavirus ,Coronavirus ,Coronavirus, Bovine ,chemistry.chemical_classification ,RNA-Binding Proteins ,RNA ,Original Articles ,Cell Biology ,Nucleocapsid Proteins ,Molecular biology ,cis‐acting element ,Dissociation constant ,030104 developmental biology ,chemistry ,(−)‐strand synthesis ,030220 oncology & carcinogenesis ,RNA, Viral ,Original Article ,Cattle ,Trans-acting ,Poly A ,nucleocapsid protein - Abstract
Synthesis of the negative‐strand ((−)‐strand) counterpart is the first step of coronavirus (CoV) replication; however, the detailed mechanism of the early event and the factors involved remain to be determined. Here, using bovine coronavirus (BCoV)‐defective interfering (DI) RNA, we showed that (a) a poly(A) tail with a length of 15 nucleotides (nt) was sufficient to initiate efficient (−)‐strand RNA synthesis and (b) substitution of the poly(A) tail with poly(U), (C) or (G) only slightly decreased the efficiency of (−)‐strand synthesis. The findings indicate that in addition to the poly(A) tail, other factors acting in trans may also participate in (−)‐strand synthesis. The BCoV nucleocapsid (N) protein, an RNA‐binding protein, was therefore tested as a candidate. Based on dissociation constant (Kd) values, it was found that the binding affinity between N protein, but not poly(A)‐binding protein, and the 3′‐terminal 55 nt plus a poly(A), poly(U), poly(C) or poly(G) tail correlates with the efficiency of (−)‐strand synthesis. Such an association was also evidenced by the binding affinity between the N protein and 5′‐ and 3′‐terminal cis‐acting elements important for (−)‐strand synthesis. Further analysis demonstrated that N protein can act as a bridge to facilitate interaction between the 5′‐ and 3′‐ends of the CoV genome, leading to circularization of the genome. Together, the current study extends our understanding of the mechanism of CoV (−)‐strand RNA synthesis through involvement of N protein and genome circularization and thus may explain why the addition of N protein in trans is required for efficient CoV replication., In the initial stage of coronavirus (CoV) (−)‐strand RNA synthesis, binding of the CoV N protein to the 5′‐ and 3′‐terminal structures of (+)‐strand CoV genome leads to circularization of the genome, serving as a platform to recruit cellular proteins and viral replicase proteins including RNA‐dependent RNA polymerase. This then initiates (−)‐strand RNA synthesis.
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- 2019
66. The R&D efficiency of the Taiwanese semiconductor industry
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I-Shuo Chen, Ching-Fan Chien, Hung-Yi Wu, and Jui-Kuei Chen
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Return on assets ,Future studies ,Earnings per share ,Applied Mathematics ,020208 electrical & electronic engineering ,010401 analytical chemistry ,02 engineering and technology ,D optimal ,Condensed Matter Physics ,01 natural sciences ,0104 chemical sciences ,Semiconductor industry ,0202 electrical engineering, electronic engineering, information engineering ,Data envelopment analysis ,Business ,Electrical and Electronic Engineering ,Instrumentation ,Industrial organization - Abstract
The aim of the study is to explore the Research and Design (R&D) efficiency of the semiconductor industry in Taiwan from a patent perspective. Six evaluation indices are selected as inputs (total assets, staff numbers, and R&D expenditure) and outputs (return on assets (ROA), earnings per share (EPS), and patent number), and then the 4-year annual data of the listed 42 semiconductor companies of the semiconductor industry in Taiwan are obtained. The Data Envelopment Analysis (DEA) is utilized for the efficiency computation among 42 semiconductor companies. Based on the research results, recommendations for semiconductor companies and suggestions for future studies are provided.
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- 2019
67. Quantification of gas-assisted evaporation in minichannels with negative wall superheats
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Hung-Yi Wu, Chin Pan, and Ben-Ran Fu
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Fluid Flow and Transfer Processes ,Convection ,Flow visualization ,Materials science ,Mechanical Engineering ,Heat transfer enhancement ,Condensation ,Evaporation ,02 engineering and technology ,Mechanics ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,01 natural sciences ,010305 fluids & plasmas ,Volumetric flow rate ,Boiling ,0103 physical sciences ,Heat transfer ,0210 nano-technology - Abstract
The present study quantifies the gas-assisted evaporation of ethanol in two parallel minichannels with negative wall superheats using helium as the auxiliary gas. At the exit of minichannels, an innovative gas–liquid separation and vapor condensation device is designed to measure the ethanol evaporated. The experimental results demonstrate that both the gas-assisted evaporation and mixing effects are significant mechanisms responsible for the significant enhancement of heat transfer with the introduction of helium gas in ethanol flow. For the present study, the maximum heat transfer enhancement of 275% is demonstrated under the condition of ethanol flow rate of 0.028 m/s, helium flow rate of 0.833 m/s, and wall superheat of −3.2 °C. Under such a condition, the gas-assisted evaporation contributes about 40% of total heat transfer rate. Flow visualization and exit quality measurement reveal that the phase change mechanism is dominated by convective evaporation in the region with negative wall superheat, while it is dominated by convective boiling under the conditions with positive wall superheat. The evaporation efficiency increases with decrease in ethanol flow rate, increases in helium flow rate and wall superheat. An empirical correlation for the evaporation efficiency is, thus, developed.
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- 2019
68. A HYBRID MULTI-CRITERIA DECISION ANALYSIS APPROACH FOR ENVIRONMENTAL PERFORMANCE EVALUATION: AN EXAMPLE OF THE TFT-LCD MANUFACTURERS IN TAIWAN
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Hung-Yi Wu, Hung-Shu Wu, and August Tsai
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Environmental Engineering ,Liquid-crystal display ,law ,Thin-film transistor ,Computer science ,Management, Monitoring, Policy and Law ,Multiple-criteria decision analysis ,Pollution ,Reliability engineering ,law.invention - Published
- 2019
69. Stable pH Suppresses Defense Signaling and is the Key to Enhance Agrobacterium-Mediated Transient Expression in Arabidopsis Seedlings
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Erh-Min Lai, Hung-Yi Wu, Manda Yu, Yi-Chieh Wang, and Po-Yuan Shih
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0106 biological sciences ,0301 basic medicine ,Agrobacterium ,Mutant ,Arabidopsis ,Plant Immunity ,lcsh:Medicine ,Peptide Elongation Factor Tu ,01 natural sciences ,Article ,03 medical and health sciences ,Transformation, Genetic ,Bacterial Proteins ,Gene Expression Regulation, Plant ,Gene expression ,lcsh:Science ,MAMP ,Plant Diseases ,Regulation of gene expression ,Multidisciplinary ,biology ,Arabidopsis Proteins ,Chemistry ,fungi ,lcsh:R ,Hydrogen-Ion Concentration ,Plants, Genetically Modified ,biology.organism_classification ,Cell biology ,030104 developmental biology ,Agrobacterium tumefaciens ,Seedlings ,bacteria ,Calcium ,lcsh:Q ,Signal transduction ,Signal Transduction ,010606 plant biology & botany - Abstract
Agrobacterium-mediated transient expression is a powerful analysis platform for diverse plant gene functional studies, but the mechanisms regulating the expression or transformation levels are poorly studied. Previously, we developed a highly efficient and robust Agrobacterium-mediated transient expression system, named AGROBEST, for Arabidopsis seedlings. In this study, we found that AGROBEST could promote the growth of agrobacteria as well as inhibit the host immunity response. When the factor of agrobacterial growth is minimized, maintaining pH at 5.5 with MES buffer was the key to achieving optimal transient expression efficiency. The expression of plant immunity marker genes, FRK1 and NHL10, was suppressed in the pH-buffered medium as compared with non-buffered conditions in Col-0 and an efr-1 mutant lacking the immunity receptor EFR recognizing EF-Tu, a potent pathogen- or microbe-associated molecular pattern (PAMP or MAMP) of A. tumefaciens. Notably, such immune suppression could also occur in Arabidopsis seedlings without Agrobacterium infection. Furthermore, the PAMP-triggered influx of calcium ions was compromised in the pH-buffered medium. We propose that the enhanced transient expression efficiency by stable pH was due to inhibiting calcium ion uptake and subsequently led to suppressing immunity against Agrobacterium.
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- 2018
70. Community Evaluation of Glycoproteomics Informatics Solutions Reveals High-Performance Search Strategies of SerumN- andO-Glycopeptide Data
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Wantao Ying, Josef M. Penninger, Yehia Mechref, Gun Wook Park, Weiqian Cao, Morten Thaysen-Andersen, Jingfu Zhao, Rebeca Kawahara, Radoslav Goldman, Kai-Hooi Khoo, Mingqi Liu, Marcus Hoffmann, Nicolle H. Packer, Benjamin L. Schulz, Erdmann Rapp, Enes Sakalli, Miloslav Sanda, Yingwei Hu, Hui Zhang, Jonas Nilsson, Doron Kletter, Sriram Neelamegham, Nathan Edwards, Cassandra L. Pegg, Pengyuan Yang, Jong Shin Yoo, Hung-Yi Wu, Daniel Kolarich, Adam Pap, Robert J. Chalkley, Georgy Sofronov, Benjamin L. Parker, Terry Nguyen-Khuong, Kai Cheng, Yong Zhang, Bo Meng, Nichollas E. Scott, Benoit Liquet-Weiland, Joseph Zaia, Sergey Y. Vakhrushev, Markus Pioch, Johannes Stadlmann, Toan K. Phung, Marshall Bern, Christina M. Woo, Katalin F. Medzihradszky, Stuart M. Haslam, Giuseppe Palmisano, Anastasia Chernykh, Göran Larson, Matthew S F Choo, Jin Young Kim, Yifan Huang, and Kathirvel Alagesan
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Profiling (computer programming) ,Software ,Computer science ,business.industry ,Informatics ,Human proteome project ,business ,Community evaluation ,Data science ,Tandem mass spectrum ,Glycoproteomics - Abstract
Glycoproteome profiling (glycoproteomics) is a powerful yet analytically challenging research tool. The complex tandem mass spectra generated from glycopeptide mixtures require sophisticated analysis pipelines for structural determination. Diverse software aiding the process have appeared, but their relative performance remains untested. Conducted through the HUPO Human Proteome Project – Human Glycoproteomics Initiative, this community study, comprising both developers and users of glycoproteomics software, evaluates the performance of informatics solutions for system-wide glycopeptide analysis. Mass spectrometry-based glycoproteomics datasets from human serum were shared with all teams. The relative team performance forN- andO-glycopeptide data analysis was comprehensively established and validated through orthogonal performance tests. Excitingly, several high-performance glycoproteomics informatics solutions were identified. While the study illustrated that significant informatics challenges remain, as indicated by a high discordance between annotated glycopeptides, lists of high-confidence (consensus) glycopeptides were compiled from the standardised team reports. Deep analysis of the performance data revealed key performance-associated search variables and led to recommendations for improved “high coverage” and “high accuracy” glycoproteomics search strategies. This study concludes that diverse software for comprehensive glycopeptide data analysis exist, points to several high-performance search strategies, and specifies key variables that may guide future software developments and assist informatics decision-making in glycoproteomics.
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- 2021
71. Investigation of Avian polyomavirusand Psittacine beakand Feather disease virusin parrots in Taiwan
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Hung-Yi Wu
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PCR ,Taiwan ,PBFDV ,APV ,Psittacine Birds - Abstract
The Thai Journal of Veterinary Medicine, 51, 2, 239
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- 2021
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72. Labeling Preferences of Diazirines with Protein Biomolecules
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Alexander West, Giovanni Muncipinto, Hung-Yi Wu, Andrew Huang, Matthew T. Labenski, and Christina Woo
- Abstract
Diazirines are widely used in photoaffinity labeling (PAL) to trap non-covalent interactions with biomolecules. However, design and interpretation of PAL experiments is challenging without a molecular understanding of the reactivity of diazirines with protein biomolecules. Here, we report a systematic evaluation of the labeling preferences of alkyl and aryl diazirines with individual amino acids, single proteins, and in the whole cell proteome. We find that aryl-fluorodiazirines react primarily through a carbene intermediate, while alkyl diazirines generate a reactive alkyl diazo intermediate on route to the carbene. The generation of a reactive diazo intermediate leads to preferential labeling of acidic amino acids in a pH-dependent manner. From a survey of 32 alkyl diazirine probes, we use this reactivity profile to rationalize why these probes preferentially enrich highly acidic proteins or those embedded in membranes and why probes with a net positive-charge tend to produce higher labeling yields. These results indicate that alkyl diazirines are an especially effective chemistry for surveying the membrane proteome, and will facilitate probe design and interpretation of biomolecular labeling experiments with diazirines.
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- 2020
73. Correlation between goose circovirus and goose parvovirus with gosling feather loss disease and goose broke feather disease in southern Taiwan
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Chiu Huang Ting, Shyh Shyan Liu, Chen Wei Wang, Yang Chieh Huang, Hung-Yi Wu, Shao Yu Peng, and Chia Ying Lin
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Circovirus ,Veterinary medicine ,animal structures ,040301 veterinary sciences ,polymerase chain reaction ,Taiwan ,Disease ,Virus ,law.invention ,0403 veterinary science ,Parvoviridae Infections ,03 medical and health sciences ,Goose ,law ,Parvovirinae ,biology.animal ,Geese ,Pathology ,Prevalence ,Animals ,Circoviridae Infections ,Polymerase chain reaction ,Poultry Diseases ,030304 developmental biology ,0303 health sciences ,General Veterinary ,biology ,Parvovirus ,goose disease ,parvovirus ,04 agricultural and veterinary sciences ,Feathers ,biology.organism_classification ,Feather ,visual_art ,visual_art.visual_art_medium ,Original Article ,Viral load - Abstract
Background Goslings in several Taiwanese farms experienced gosling feather loss disease (GFL) at 21-35 days and goose broke feather disease (GBF) at 42-60 days. The prevalence ranges from a few birds to 500 cases per field. It is estimated that about 12,000 geese have been infected, the morbidity is 70-80% and the mortality is 20-30%. Objectives This study aims to investigate the pathogens that cause GFL and GBF. Focus on the study of the correlation between goose circovirus (GoCV) and goose parvovirus (GPV) with the goose feather loss in southern Taiwan. Furthermore, a phylogenetic tree was established to align the differences between southern and northern Taiwan and compare with virus strains from China and Europe. Methods Samples were collected from animal hospitals. Molecular and microscopy diagnostics were used to examine 92 geese. Specific quantitative polymerase chain reaction (Q-PCR) assays are performed to evaluate GPV and GoCV viral loads and simultaneously evaluated the feather loss conditions in geese with the scoring method. Results High prevalence of GoCV and GPV infection in geese showing signs of GFL and GBF. Inclusion body was detected in the feather follicles and Lieberkuhn crypt epithelial cells. The Q-PCR showed the high correlation between feather loss and viruses during 3rd-5th week. However, the infection was not detected using the same test in 60 healthy geese. Conclusions Thus, GFL and GBF appear to be significantly closely related to GoCV and GPV. The geese feathers showed increasing recovery after being quarantined and disinfected.
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- 2020
74. First Report of
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Hung-Yi, Wu, Chi-Yun, Tsai, Yi-Mei, Wu, Hiran Anjana, Ariyawansa, Chia-Lin, Chung, and Pei-Che, Chung
- Abstract
For the past 30 years, the most predominant strawberry cultivar in Taiwan has been 'Taoyuan No. 1', which produces fruit with rich flavor and aroma but is highly susceptible to anthracnose (Chung et al. 2019). Because epidemics of anthracnose became more destructive, farmers switched to an anthracnose-tolerant cultivar 'Xiang-Shui' (~50% and ~80% of the cultivation area in 2018 and 2019, respectively). Since 2018, severe leaf blight and crown rot symptoms have been observed all year in 'Xiang-Shui' in Miaoli, Nantou, Hsinchu, Taipei, Taoyuan, and Chiayi Counties. The disease became more prevalent and severe during 2019 to 2020 and caused up to 30% plant loss after transplanting. Symptoms appeared as brown necrotic lesions with black acervuli on leaves, slightly sunken dark-brown necrosis on stolons, and sunken reddish-brown necrosis on fruit. The diseased crown tissue showed marbled reddish-brown necrosis with a dark-brown margin, and plants with severe crown rot usually showed reddish-brown discoloration on leaves (the leaves initially turned reddish-brown between the veins and could become entirely scorched at later stages). To isolate the causal agent, small fragments of diseased leaves, crowns, stolons, and fruits were surface-disinfested with 0.5% sodium hypochlorite for 30 seconds, rinsed with sterile water then placed on 1.5% water agar. Single hyphal tips extended from tissues were transferred to potato dextrose agar and cultured for 7 days at 25°C under a 12-h/12-h photoperiod. Total 20 isolates were obtained from diseased leaves, crowns, stolons, and fruits. Colonies were white with cottony aerial mycelium, irregular margins, and black acervuli distributed in concentric rings. Conidia were fusiform to ellipsoid (five cells) with one basal appendage and three or four (usually three) apical appendages. From colony and conidial morphology, the causal agent was identified as
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- 2020
75. Effects of Coronavirus Persistence on the Genome Structure and Subsequent Gene Expression, Pathogenicity and Adaptation Capability
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Shan Chia Ou, Tsung Lin Tsai, Chen Yu Lo, Cheng Yao Yang, Meilin Wang, Hung-Yi Wu, and Ching Hung Lin
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Gene Expression Regulation, Viral ,0301 basic medicine ,Transcription, Genetic ,viruses ,030106 microbiology ,coronavirus ,Genome, Viral ,Regulatory Sequences, Ribonucleic Acid ,Biology ,medicine.disease_cause ,Genome ,Article ,genome structure ,Cell Line ,Betacoronavirus ,03 medical and health sciences ,Transcription (biology) ,Gene expression ,virus fitness ,medicine ,Animals ,Humans ,pathogenicity ,RNA, Messenger ,lcsh:QH301-705.5 ,Coronavirus ,Bovine coronavirus ,Subgenomic mRNA ,Coronavirus, Bovine ,Genetics ,SARS-CoV-2 ,Computational Biology ,virus diseases ,General Medicine ,persistence ,030104 developmental biology ,lcsh:Biology (General) ,Regulatory sequence ,Cell culture ,gene expression ,RNA, Viral ,Cattle ,Coronavirus Infections - Abstract
Coronaviruses are able to establish persistence. However, how coronaviruses react to persistence and whether the selected viruses have altered their characteristics remain unclear. In this study, we found that the persistent infection of bovine coronavirus (BCoV), which is in the same genus as SARS-COV-2, led to alterations of genome structure, attenuation of gene expression, and the synthesis of subgenomic mRNA (sgmRNA) with a previously unidentified pattern. Subsequent analyses revealed that the altered genome structures were associated with the attenuation of gene expression. In addition, the genome structure at the 5&prime, terminus and the cellular environment during the persistence were responsible for the sgmRNA synthesis, solving the previously unanswered question regarding the selection of transcription regulatory sequence for synthesis of BCoV sgmRNA 12.7. Although the BCoV variants (BCoV-p95) selected under the persistence replicated efficiently in cells without persistent infection, its pathogenicity was still lower than that of wild-type (wt) BCoV. Furthermore, in comparison with wt BCoV, the variant BCoV-p95 was not able to efficiently adapt to the challenges of alternative environments, suggesting wt BCoV is genetically robust. We anticipate that the findings derived from this fundamental research can contribute to the disease control and treatments against coronavirus infection including SARS-CoV-2.
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- 2020
76. The Impacts of Antivirals on the Coronavirus Genome Structure and Subsequent Pathogenicity, Virus Fitness and Antiviral Design
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Meilin Wang, Hung-Yi Wu, Tsung Lin Tsai, Cheng Yao Yang, Shan Chia Ou, Ching Hung Lin, and Chen Yu Lo
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0301 basic medicine ,antiviral drug ,medicine.drug_class ,viruses ,030106 microbiology ,coronavirus ,Medicine (miscellaneous) ,remdesivir ,Biology ,medicine.disease_cause ,spike protein ,Article ,General Biochemistry, Genetics and Molecular Biology ,Virus ,genome structure ,03 medical and health sciences ,medicine ,pathogenicity ,innate immunity ,lcsh:QH301-705.5 ,Coronavirus ,Bovine coronavirus ,Genetics ,Innate immune system ,Wild type ,Pathogenicity ,030104 developmental biology ,lcsh:Biology (General) ,biology.protein ,Antiviral drug ,Antibody - Abstract
With the global threat of SARS-CoV-2, much effort has been focused on treatment and disease control. However, how coronaviruses react to the treatments and whether the surviving viruses have altered their characteristics are also unanswered questions with medical importance. To this end, bovine coronavirus (BCoV), which is in the same genus as SARS-CoV-2, was used as a test model and the findings were as follows. With the treatment of antiviral remdesivir, the selected BCoV variant with an altered genome structure developed resistance, but its pathogenicity was not increased in comparison to that of wild type (wt) BCoV. Under the selection pressure of innate immunity, the genome structure was also altered, however, neither resistance developed nor pathogenicity increased for the selected BCoV variant. Furthermore, both selected BCoV variants showed a better efficiency in adapting to alternative host cells than wt BCoV. In addition, the previously unidentified feature that the spike protein was a common target for mutations under different antiviral treatments might pose a problem for vaccine development because spike protein is a common target for antibody and vaccine designs. The findings derived from this fundamental research may contribute to the disease control and treatments against coronaviruses, including SARS-CoV-2.
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- 2020
77. Genetic sequence changes related to the attenuation of avian infectious bronchitis virus strain TW2575/98
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Cheng-Ta Tsai, Hung-Yi Wu, and Ching-Ho Wang
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animal structures ,040301 veterinary sciences ,Infectious bronchitis virus ,Virulence ,RNA-dependent RNA polymerase ,Genome, Viral ,Virus Replication ,Virus ,0403 veterinary science ,03 medical and health sciences ,Virology ,Genetic variation ,Genetics ,3' Untranslated Regions ,Molecular Biology ,030304 developmental biology ,Infectivity ,chemistry.chemical_classification ,0303 health sciences ,Base Sequence ,biology ,Genetic Variation ,Genomics ,04 agricultural and veterinary sciences ,General Medicine ,biology.organism_classification ,Amino acid ,Viral replication ,chemistry ,Avian infectious bronchitis virus ,Coronavirus Infections - Abstract
The attenuated avian infectious bronchitis virus (IBV), derived from a wild strain (TW2575/98w) in chicken embryos after 75 passages, is designed as a commercial vaccine strain (TW2575/98vac) to control the disease in Taiwan. The differences in viral infectivity, replication efficiency, and genome sequences between TW2575/98w and TW2575/98vac were determined and compared. TW2575/98vac caused earlier death of chicken embryos and had higher viral replication efficiency. Thirty amino acid substitutions resulting from 44 mutated nucleotides in the viral genome were found in TW2575/98vac. All of the molecular variations lead to attenuation, found in TW2575/98, were not observed consistently in the other IBVs (TW2296/95, Ark/Ark-DPI/81, the Massachusetts strain, GA98/CWL0470/98, and CK/CH/LDL/97I) and vice versa. After further comparisons and evaluations from three aspects: (1) longitudinal analysis on the timing of variations appeared in specific homologous strain passages, (2) horizontal evaluations with the amino acid changes between wild and vaccine strains among the other 5 IBVs, and (3) inspection on alterations in the chemical characteristics of substituted amino acid residues in viral proteins, four amino acid substitutions [V342D in p87, S1493P and P2025S in HD1, as well as F2308Y in HD1(P41)] were selected as highly possible candidates for successful TW2575/98w attenuation. Our findings imply that molecular variations, which contribute to the successful attenuation of different IBVs, are diverse and not restricted to a fixed pattern or specific amino acid substitutions in viral proteins. In addition, four amino acid changes within the replicase gene-encoded proteins might be associated with TW2575/98 virus virulence.
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- 2020
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78. Engineering a Proximity-Directed O-GlcNAc Transferase for Selective Protein O-GlcNAcylation in Cells
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Stephanie Tang, Timothy R. O’Meara, Chanat Aonbangkhen, Christina M. Woo, Jeffrey A. Naftaly, Daniel H. Ramirez, and Hung-Yi Wu
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0301 basic medicine ,Glycosylation ,Proteome ,Recombinant Fusion Proteins ,Proteomics ,N-Acetylglucosaminyltransferases ,Protein Engineering ,01 natural sciences ,Biochemistry ,Article ,03 medical and health sciences ,chemistry.chemical_compound ,Humans ,010405 organic chemistry ,HEK 293 cells ,General Medicine ,Protein engineering ,Single-Domain Antibodies ,0104 chemical sciences ,Cell biology ,Glycoproteomics ,Tetratricopeptide ,030104 developmental biology ,HEK293 Cells ,chemistry ,alpha-Synuclein ,Molecular Medicine ,Target protein ,Protein Processing, Post-Translational - Abstract
O-Linked β-N-acetylglucosamine (O-GlcNAc) is a monosaccharide that plays an essential role in cellular signaling throughout the nucleocytoplasmic proteome of eukaryotic cells. Strategies for selectively increasing O-GlcNAc levels on a target protein in cells would accelerate studies of this essential modification. Here, we report a generalizable strategy for introducing O-GlcNAc into selected target proteins in cells using a nanobody as a proximity-directing agent fused to O-GlcNAc transferase (OGT). Fusion of a nanobody that recognizes GFP (nGFP) or a nanobody that recognizes the four-amino acid sequence EPEA (nEPEA) to OGT yielded nanobody-OGT constructs that selectively delivered O-GlcNAc to a series of tagged target proteins (e.g., JunB, cJun, and Nup62). Truncation of the tetratricopeptide repeat domain as in OGT(4) increased selectivity for the target protein through the nanobody by reducing global elevation of O-GlcNAc levels in the cell. Quantitative chemical proteomics confirmed the increase in O-GlcNAc to the target protein by nanobody-OGT(4). Glycoproteomics revealed that nanobody-OGT(4) or full-length OGT produced a similar glycosite profile on the target protein JunB and Nup62. Finally, we demonstrate the ability to selectively target endogenous α-synuclein for O-GlcNAcylation in HEK293T cells. These first proximity-directed OGT constructs provide a flexible strategy for targeting additional proteins and a template for further engineering of OGT and the O-GlcNAc proteome in the future. The use of a nanobody to redirect OGT substrate selection for glycosylation of desired proteins in cells may further constitute a generalizable strategy for controlling a broader array of post-translational modifications in cells.
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- 2020
79. Cryo-RALib -- a modular library for accelerating alignment in cryo-EM
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Hung-Yi Wu, I-Ping Tu, Huei-Lun Siao, Cheng-Yu Hung, Szu-Chi Chung, and Wei-Hau Chang
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FOS: Computer and information sciences ,Computer science ,business.industry ,Image and Video Processing (eess.IV) ,Electrical Engineering and Systems Science - Image and Video Processing ,Python (programming language) ,Modular design ,Quantitative Biology - Quantitative Methods ,Field (computer science) ,Computational science ,Visualization ,Statistical classification ,Signal-to-noise ratio ,Computer Science - Distributed, Parallel, and Cluster Computing ,FOS: Biological sciences ,Container (abstract data type) ,Benchmark (computing) ,FOS: Electrical engineering, electronic engineering, information engineering ,Distributed, Parallel, and Cluster Computing (cs.DC) ,business ,computer ,Quantitative Methods (q-bio.QM) ,computer.programming_language - Abstract
With the enhancement of algorithms, cryo-EM has become the most efficient technique to solve structures of molecules. Take a recent event for example, after the outbreak of COVID-19 in January, the first structure of 2019-nCoV Spike trimer was published in March using cryo-EM, which has provided crucial medical insight for developing vaccines. The enabler behind this efficiency is the GPU-accelerated computation which shortens the whole analysis process to 12 days. However, the data characteristics include strong noise, huge dimension, large sample size and high heterogeneity with unknown orientations have made analysis very challenging. Though, the popular GPU-accelerated Bayesian approach has been shown to be successful in 3D refinement. It is noted that the traditional method based on multireference alignment may better differentiate subtle structure differences under low signal to noise ratio (SNR). However, a modular GPU-acceleration package for multireference alignment is still lacking in the field. In this work, a modular GPU-accelerated alignment library called Cryo-RALib is proposed. The library contains both reference-free alignment and multireference alignment that can be widely used to accelerate state-of-the-art classification algorithms. In addition, we connect the cryo-EM image analysis with the python data science stack which enables users to perform data analysis, visualization and inference more easily. Benchmark on the TaiWan Computing Cloud container, our implementation can accelerate the computation by one order of magnitude. The library has been made publicly available at this https URL.
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- 2020
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80. Epinecidin-1 Protects against Methicillin Resistant Staphylococcus aureus Infection and Sepsis in Pyemia Pigs
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Bor Chyuan Su, Han Ning Huang, Chieh Yu Pan, Hung Yi Wu, and Jyh-Yih Chen
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antimicrobial peptide (AMP) ,Serum albumin ,Pharmaceutical Science ,MRSA ,medicine.disease_cause ,Microbiology ,Sepsis ,03 medical and health sciences ,Drug Discovery ,medicine ,Pharmacology, Toxicology and Pharmaceutics (miscellaneous) ,Blood urea nitrogen ,030304 developmental biology ,0303 health sciences ,biology ,030306 microbiology ,business.industry ,C-reactive protein ,epinecidin-1 ,biochemical phenomena, metabolism, and nutrition ,Antimicrobial ,medicine.disease ,Methicillin-resistant Staphylococcus aureus ,pyemia pigs ,Toxicity ,biology.protein ,Vancomycin ,business ,medicine.drug - Abstract
Methicillin resistant Staphylococcus aureus (MRSA) may be found on the skin, nose, and throats of long-term hospitalized patients. While MRSA infections are usually minor, serious infections and death may occur in immunocompromised or diabetic patients, or after exposure of MRSA to blood. This report demonstrates that the antimicrobial peptide (AMP) epinecidin-1 (Epi-1) efficiently protects against MRSA infection in a pyemia pig model. We first found that Epi-1 exhibits bactericidal activity against MRSA. Next, pharmacokinetic analysis revealed that Epi-1 was stable in serum for 4 h after injection, followed by a gradual decrease. This pharmacokinetic profile suggested Epi-1 may bind serum albumin, which was confirmed in vitro. Harmful effects were not observed for doses up to 100 mg/kg body weight in pigs. When Epi-1 was supplied as a curative agent 30 min post-infection, MRSA-induced abnormalities in blood uric acid (UA), blood urea nitrogen (BUN), creatine (CRE), GOT, and GPT levels were restored to normal levels. We further showed that the bactericidal activity of Epi-1 was higher than that of the antibiotic drug vancomycin. Epi-1 significantly decreased MRSA counts in the blood, liver, kidney, heart, and lungs of infected pigs. Elevated levels of serum C reactive protein (CRP), proinflammatory cytokine IL6, IL1&beta, and TNF&alpha, were also attenuated by Epi-1 treatment. Moreover, the MRSA genes, enterotoxin (et)-A, et-B, intrinsic methicillin resistance A (mecA), and methicillin resistance factor A (femA), were significantly reduced or abolished in MRSA-infected pigs after treatment with Epi-1. Hematoxylin and eosin staining of heart, liver, lung, and kidney sections indicated that Epi-1 attenuated MRSA toxicity in infected pigs. A survival study showed that the pyemia pigs infected with MRSA alone died within a week, whereas the pigs post-treated with 2.5 mg/kg Epi-1 were completely protected against death. The present investigation, thus, demonstrates that Epi-1 effectively protects pyemia pigs against pathogenic MRSA without major toxic side effects.
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- 2019
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81. Epinecidin-1 Protects against Methicillin Resistant
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Han-Ning, Huang, Chieh-Yu, Pan, Bor-Chyuan, Su, Hung-Yi, Wu, and Jyh-Yih, Chen
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Fish Proteins ,Methicillin-Resistant Staphylococcus aureus ,Dose-Response Relationship, Drug ,Swine ,antimicrobial peptide (AMP) ,epinecidin-1 ,MRSA ,biochemical phenomena, metabolism, and nutrition ,Staphylococcal Infections ,Article ,Anti-Bacterial Agents ,Disease Models, Animal ,C-Reactive Protein ,Vancomycin ,Sepsis ,pyemia pigs ,Animals ,Antimicrobial Cationic Peptides - Abstract
Methicillin resistant Staphylococcus aureus (MRSA) may be found on the skin, nose, and throats of long-term hospitalized patients. While MRSA infections are usually minor, serious infections and death may occur in immunocompromised or diabetic patients, or after exposure of MRSA to blood. This report demonstrates that the antimicrobial peptide (AMP) epinecidin-1 (Epi-1) efficiently protects against MRSA infection in a pyemia pig model. We first found that Epi-1 exhibits bactericidal activity against MRSA. Next, pharmacokinetic analysis revealed that Epi-1 was stable in serum for 4 h after injection, followed by a gradual decrease. This pharmacokinetic profile suggested Epi-1 may bind serum albumin, which was confirmed in vitro. Harmful effects were not observed for doses up to 100 mg/kg body weight in pigs. When Epi-1 was supplied as a curative agent 30 min post-infection, MRSA-induced abnormalities in blood uric acid (UA), blood urea nitrogen (BUN), creatine (CRE), GOT, and GPT levels were restored to normal levels. We further showed that the bactericidal activity of Epi-1 was higher than that of the antibiotic drug vancomycin. Epi-1 significantly decreased MRSA counts in the blood, liver, kidney, heart, and lungs of infected pigs. Elevated levels of serum C reactive protein (CRP), proinflammatory cytokine IL6, IL1β, and TNFα were also attenuated by Epi-1 treatment. Moreover, the MRSA genes, enterotoxin (et)-A, et-B, intrinsic methicillin resistance A (mecA), and methicillin resistance factor A (femA), were significantly reduced or abolished in MRSA-infected pigs after treatment with Epi-1. Hematoxylin and eosin staining of heart, liver, lung, and kidney sections indicated that Epi-1 attenuated MRSA toxicity in infected pigs. A survival study showed that the pyemia pigs infected with MRSA alone died within a week, whereas the pigs post-treated with 2.5 mg/kg Epi-1 were completely protected against death. The present investigation, thus, demonstrates that Epi-1 effectively protects pyemia pigs against pathogenic MRSA without major toxic side effects.
- Published
- 2019
82. Author Correction: Community evaluation of glycoproteomics informatics solutions reveals high-performance search strategies for serum glycopeptide analysis
- Author
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Rebeca Kawahara, Anastasia Chernykh, Kathirvel Alagesan, Marshall Bern, Weiqian Cao, Robert J. Chalkley, Kai Cheng, Matthew S. Choo, Nathan Edwards, Radoslav Goldman, Marcus Hoffmann, Yingwei Hu, Yifan Huang, Jin Young Kim, Doron Kletter, Benoit Liquet, Mingqi Liu, Yehia Mechref, Bo Meng, Sriram Neelamegham, Terry Nguyen-Khuong, Jonas Nilsson, Adam Pap, Gun Wook Park, Benjamin L. Parker, Cassandra L. Pegg, Josef M. Penninger, Toan K. Phung, Markus Pioch, Erdmann Rapp, Enes Sakalli, Miloslav Sanda, Benjamin L. Schulz, Nichollas E. Scott, Georgy Sofronov, Johannes Stadlmann, Sergey Y. Vakhrushev, Christina M. Woo, Hung-Yi Wu, Pengyuan Yang, Wantao Ying, Hui Zhang, Yong Zhang, Jingfu Zhao, Joseph Zaia, Stuart M. Haslam, Giuseppe Palmisano, Jong Shin Yoo, Göran Larson, Kai-Hooi Khoo, Katalin F. Medzihradszky, Daniel Kolarich, Nicolle H. Packer, and Morten Thaysen-Andersen
- Subjects
Computational platforms and environments ,Glycobiology ,Cell Biology ,Author Correction ,GLICOSÍDEOS ,Molecular Biology ,Biochemistry ,Software ,Research data ,Biotechnology - Published
- 2021
83. Effects of cytoplasts from Taiwan native yellow cattle on the cellular antioxidant ability of cloned Holstein cattle and their offspring
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Piyawit Kesorn, Shyh-Shyan Liu, Jai-Wei Lee, Jyh-Cherng Ju, Hung-Yi Wu, Perng-Chih Shen, Hsi-Hsun Wu, and Shao-Yu Peng
- Subjects
0301 basic medicine ,Cytoplasm ,Hot Temperature ,Antioxidant ,Offspring ,Cloning, Organism ,medicine.medical_treatment ,Oxidative phosphorylation ,Mitochondrion ,Biology ,Cytoplast ,Antioxidants ,Oxidative Phosphorylation ,03 medical and health sciences ,Food Animals ,Stress, Physiological ,medicine ,Animals ,Small Animals ,Fibroblast ,Cell Nucleus ,Genetics ,Equine ,0402 animal and dairy science ,Gene Expression Regulation, Developmental ,Ear ,04 agricultural and veterinary sciences ,Fibroblasts ,040201 dairy & animal science ,Molecular biology ,030104 developmental biology ,medicine.anatomical_structure ,Coenzyme Q – cytochrome c reductase ,Cattle ,Animal Science and Zoology - Abstract
We previously demonstrated that the cellular thermotolerance of cloned cattle produced by combination of ooplasm (o) derived from Taiwan native yellow cattle (Y) and the donor (d) nucleus derived from Holstein (H) cattle (Yo-Hd) transmits to their offspring (Yo-Hd-F1). In the present study, the responses of mitochondria in these cloned cattle and their offspring after heat shock were investigated to elucidate influence of cytoplasmic input (i.e., ooplasm) during the course of heat stress. After heat shock, oxidative phosphorylation proteins (Complex III and IV) of ear fibroblast cells with Y-originated cytoplasm (including Y, Yo-Hd, and Yo-Hd-F1 cattle) were significantly greater (P 0.05) than those of ear fibroblast cells with H-originated cytoplasm (including H, Ho-Hd, and Ho-Hd-F1 cattle). However, the expressions of Complex I and Complex II protein in heat shocked cells derived from Yo-Hd-F1 cattle were significantly (P 0.05) higher than those of cell derived from cattle with the H-cytoplasm. The catalase (CAT) expression in heat shocked ear fibroblast cells derived from Yo-Hd and Yo-Hd-F1 cattle were significantly (P 0.05) higher than that of cells derived from Ho-Hd-F1 cattle. However, the level of glutathione peroxidase (GPx) expression was higher (P 0.05) in ear fibroblast cells with Y-originated cytoplasm compared to cells with H-originated cytoplasm. In conclusion, the expression of proteins involved in mitochondrial oxidative phosphorylation and antioxidant enzymes after heat shock was increased in ear fibroblast cells from cattle with Y-originated cytoplasm, which can be transmitted to their offspring.
- Published
- 2017
84. First Report of Xanthomonas fragariae Causing Angular Leaf Spot on Strawberry (Fragaria × ananassa) in Taiwan
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Hung-Yi Wu, Nai-Chun Lin, Pei-Che Chung, Qiao-Juan Lai, Yi-Mei Wu, and Chia-Lin Chung
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Horticulture ,Bacterial disease ,biology ,Spots ,Inoculation ,Leaf spot ,Plant Science ,PEST analysis ,Cultivar ,biology.organism_classification ,Fragaria ,Agronomy and Crop Science ,Xanthomonas fragariae - Abstract
Angular leaf spot of strawberry, considered an A2 quarantine pest by the European and Mediterranean Plant Protection Organization (EPPO 2019), is an important bacterial disease in many regions. Since 2017, symptoms similar to angular leaf spot were observed in several strawberry cultivars including 'Taoyuan No. 1' and 'Xiang-Shui'. Early symptoms were angular, water-soaked lesions on the abaxial leaf surface, and later, reddish-brown irregular spots and coalesced lesions developed on the adaxial surface. In the humid conditions, sticky bacterial ooze exuding from lesions was observed. To isolate the causal agent, leaves showing water-soaked lesions were surface sterilized, cut into small pieces and soaked in 5 ml sterile water for at least 15 min. The supernatant from the cut-up pieces was serially diluted followed by spreading on sucrose peptone agar (SPA) (Hayward 1960). After incubating at 20°C for 4-5 days, single colonies grown on SPA were transferred to a new SPA plate and cultured at 20°C until colonies appeared. The yellow, glossy and mucoid colonies, which resembled the colony morphology of Xanthomonas fragariae, were selected as candidates for further confirmation. First, bacterial DNA of four candidate isolates, B001, B003 and B005 from Miaoli County and B004 from Taoyuan City, was PCR amplified with X. fragariae-specific primers: XF9/XF12 (Roberts et al. 1996) and 245A/B and 295A/B (Pooler et al. 1996). All four isolates could be detected by XF9/XF12 primer. Furthermore, isolates B003 and B004 could be detected by both 245A/B and 295A/B primers, while B001 and B005 could be detected by 295A/B only. Next, DNA gyrase subunit B (gyrB) was PCR amplified with the primers XgyrB1F/XgyrB1R (Young et al. 2008). The gyrB sequences of these four isolates were deposited in GenBank with accession numbers MT754942 to MT754945. The gyrB phylogenetic tree was constructed based on Bayesian inference analysis and maximum likelihood analysis. The gyrB sequences of the four isolates from Taiwan clustered in the clade containing the type strain of X. fragariae ICMP5715, indicating that they belong to X. fragariae. B001 and B005 formed a sub-group separated from B003 and B004, suggesting genetic differences between these isolates. To fulfill Koch's postulates, the abaxial surface of strawberry leaves were syringe infiltrated (KJP Silva et al., 2017) or wounded inoculated (Wang et al., 2017) with bacterial suspensions (final OD600 = 1.0-2.0) prepared from colonies of B001 and B003 washed from SPA plates. Inoculated plants were enclosed in a plastic bag (> 90% RH) at 25/20°C (day/night) under a 12-h/12-h photoperiod. After 7-14 days, water-soaked lesions similar to those observed in the field were developed on all inoculated leaves. The bacteria were successfully re-isolated from lesions of inoculated leaves and confirmed by specific primers XF9/XF12, 245A/B and 295A/B. We also found that the disease commonly occurs in the strawberry fields/nurseries with sprinkler irrigation during winter or early spring, and was particularly serious in the windward side or near riverside. To our knowledge, this is the first report of X. fragariae causing angular leaf spot on strawberry in Taiwan. Currently, the disease only occurs severely in certain regions, but establishment of effective management strategies will be needed to prevent spreading of this disease and potential economic loss in the future.
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- 2021
85. RecA-SSB Interaction Modulates RecA Nucleoprotein Filament Formation on SSB-Wrapped DNA
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Hung-Yi Wu, Chih-Hao Lu, and Hung-Wen Li
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0301 basic medicine ,DNA, Bacterial ,Mutant ,lcsh:Medicine ,Biology ,DNA-binding protein ,Article ,Protein filament ,03 medical and health sciences ,chemistry.chemical_compound ,stomatognathic system ,Recombinase ,Escherichia coli ,Nucleotide ,skin and connective tissue diseases ,lcsh:Science ,chemistry.chemical_classification ,Multidisciplinary ,030102 biochemistry & molecular biology ,Escherichia coli Proteins ,lcsh:R ,Molecular biology ,eye diseases ,Nucleoprotein ,DNA-Binding Proteins ,Rec A Recombinases ,stomatognathic diseases ,030104 developmental biology ,Nucleoproteins ,chemistry ,Tethered particle motion ,Biophysics ,bacteria ,lcsh:Q ,DNA - Abstract
E. coli RecA recombinase catalyzes the homology pairing and strand exchange reactions in homologous recombinational repair. RecA must compete with single-stranded DNA binding proteins (SSB) for single-stranded DNA (ssDNA) substrates to form RecA nucleoprotein filaments, as the first step of this repair process. It has been suggested that RecA filaments assemble mainly by binding and extending onto the free ssDNA region not covered by SSB, or are assisted by mediators. Using the tethered particle motion (TPM) technique, we monitored individual RecA filament assembly on SSB-wrapped ssDNA in real-time. Nucleation times of the RecA E38K nucleoprotein filament assembly showed no apparent dependence among DNA substrates with various ssDNA gap lengths (from 60 to 100 nucleotides) wrapped by one SSB in the (SSB)65 binding mode. Our data have shown an unexpected RecA filament assembly mechanism in which a RecA-SSB-ssDNA interaction exists. Four additional pieces of evidence support our claim: the nucleation times of the RecA assembly varied (1) when DNA substrates contained different numbers of bound SSB tetramers; (2) when the SSB wrapping mode conversion is induced; (3) when SSB C-terminus truncation mutants are used; and (4) when an excess of C-terminal peptide of SSB is present. Thus, a RecA-SSB interaction should be included in discussing RecA regulatory mechanism.
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- 2017
86. Pigeon circovirus infection in disqualified racing pigeons from Taiwan
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Shinn-Shyong Tsai, Duangsuda Thongchan, Rupak Khatri-Chhetri, Yen-Li Huang, Omir Adrian Castaneda, and Hung-Yi Wu
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Circovirus ,0301 basic medicine ,medicine.medical_specialty ,Pathology ,040301 veterinary sciences ,Taiwan ,Pigeon circovirus ,chemical and pharmacologic phenomena ,Inclusion bodies ,0403 veterinary science ,03 medical and health sciences ,Food Animals ,parasitic diseases ,medicine ,Animals ,Bursa of Fabricius ,Circoviridae Infections ,Cloning, Molecular ,Columbidae ,Gizzard ,Phylogeny ,Base Sequence ,General Immunology and Microbiology ,biology ,Bird Diseases ,food and beverages ,hemic and immune systems ,04 agricultural and veterinary sciences ,biology.organism_classification ,Virology ,Basophilic ,030104 developmental biology ,DNA, Viral ,Animal Science and Zoology ,Histopathology ,psychological phenomena and processes - Abstract
Pigeons (Columba livia) infected with pigeon circovirus (PiCV) have been reported worldwide. The present study diagnosed PiCV infection in tissue samples of disqualified racing pigeons in Taiwan, using molecular and microscopy diagnostics. Among the 164 dead pigeons examined, 96.95% (159/164) tested positive for PiCV. Severe histopathological lesions, with characteristic inclusions, were observed in various organs of the PiCV-infected pigeons. Multiglobular basophilic intranuclear and intracytoplasmic inclusion bodies were found in the bursa of Fabricius and non-lymphoid tissues. The present study identified, for the first time, the presence of inclusion bodies in the thyroid gland, oesophagus, gizzard, and in the third eyelid of circovirus-infected pigeons. The presence of inclusion bodies in the third eyelid and mucosa of the gizzard was confirmed by transmission electron microscopy. A high detection rate of PiCV and some severe lesions evident in disqualified racing pigeons, as well as PiCV sequences in this study were highly similar with those detected in European countries suggesting an epidemiological association possibly due to imported pigeons.
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- 2017
87. A RETROSPECTIVE STUDY OF PATHOLOGICAL FINDINGS IN ENDANGERED FORMOSAN PANGOLINS (MANIS PENTADACTYLA PENTADACTYLA) FROM SOUTHEASTERN TAIWAN
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Kurtis Jai-Chyi Pei, Hung-Yi Wu, Tsung-Chou Chang, Yen-Li Huang, Rupak Khatri-Chhetri, and Nabin Khatri-Chhetri
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Pathology ,medicine.medical_specialty ,biology ,040301 veterinary sciences ,business.industry ,Interstitial nephritis ,Pangolin ,04 agricultural and veterinary sciences ,Hyperplasia ,medicine.disease ,biology.organism_classification ,Cerebral edema ,0403 veterinary science ,Gross examination ,03 medical and health sciences ,0302 clinical medicine ,Manis pentadactyla ,030220 oncology & carcinogenesis ,Ventriculitis ,medicine ,business ,Pathological - Abstract
Formosan pangolin, a sub-species of Chinese pangolin is a critically endangered insectivorous mammal found only in Taiwan. Pathological studies are helpful in the diagnosis and investigation of wildlife diseases. Pathological findings in pangolins have not been well documented. The present paper reports the pathological findings of 14 free-ranging Formosan pangolins. External injuries and superficial wounds (6/14) were common finding in gross examination and were mostly found in the legs. Respiratory system (78%, 11/14) lesions included interstitial pneumonia, atelectasis and emphysema. Hepatic changes (43%, 6/14) included necrosis, bile duct hyperplasia, lipidosis and extensive hepatocyte degeneration. Parasites were detected in 57% of pangolins (8/14) studied and included both endoparasites and ectoparasites. Urinary system (21%, 3/14) lesions were interstitial nephritis and nephrolithiasis. Brain lesions were found in three pangolins and included cerebral edema and hemorrhage and ventriculitis. Additional pathological lesions included thyroid gland hyperplasia and left ventricular hypertrophy. The presented pathological findings can aid in the understanding of diseases of pangolins and will contribute knowledge to future investigations on diseases of pangolins.
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- 2017
88. Antimicrobial peptide Epinecidin-1 promotes complete skin regeneration of methicillin-resistant Staphylococcus aureus-infected burn wounds in a swine model
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Han-Ning Huang, Chieh-Yu Pan, Jyh-Yih Chen, and Hung-Yi Wu
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0301 basic medicine ,Fish Proteins ,Keratinocytes ,Methicillin-Resistant Staphylococcus aureus ,antimicrobial peptide ,Swine ,medicine.medical_treatment ,030106 microbiology ,Staphylococcal infections ,medicine.disease_cause ,Microbiology ,03 medical and health sciences ,In vivo ,medicine ,Animals ,Humans ,Cells, Cultured ,Skin ,integumentary system ,business.industry ,Staphylococcal Infections ,medicine.disease ,Antimicrobial ,Methicillin-resistant Staphylococcus aureus ,Anti-Bacterial Agents ,HaCaT ,030104 developmental biology ,Cytokine ,Oncology ,Epinecidin-1 ,Staphylococcus aureus ,Wound Infection ,Wound healing ,business ,Burns ,Research Paper ,Antimicrobial Cationic Peptides - Abstract
// Han-Ning Huang 1, * , Chieh-Yu Pan 2, * , Hung-Yi Wu 3 , Jyh-Yih Chen 1 1 Marine Research Station, Institute of Cellular and Organismic Biology, Academia Sinica, Jiaushi, Ilan, Taiwan 2 Department and Graduate Institute of Aquaculture, National Kaohsiung Marine University, Kaohsiung, Taiwan 3 Department of Veterinary Medicine, College of Veterinary Medicine, National Pingtung University of Science and Technology, Neipu, Taiwan * These authors have contributed equally to this work Correspondence to: Hung-Yi Wu, email: wuhy@mail.npust.edu.tw Jyh-Yih Chen, email: zoocjy@gate.sinica.edu.tw Keywords: antimicrobial peptide, Epinecidin-1, methicillin-resistant Staphylococcus aureus Abbreviations: Epi-1, Epinecidin 1; MRSA, Methicillin-resistant Staphylococcus aureus ; SA, Staphylococcus aureus ; CRP, C-reactive protein Received: October 12, 2016 Accepted: January 16, 2017 Published: February 03, 2017 ABSTRACT This report shows that the antimicrobial peptide (AMP) Epinecidin-1 (Epi-1) efficiently heals MRSA-infected heat burn injuries and provides protection from infection in a pig model. The presence of an optimal level of Epi-1 induces cell proliferation by promoting cell cycle progression through an increase in S-phase cells. Epi-1 also induces proliferation to cover the wounded region in an in vitro cell proliferation assay using immortalized human epithelial HaCaT cells. Next, the in vivo wound healing efficiency of Epi-1 was tested in heat-burned pig skin infected with MRSA under in vivo conditions. Treatment of the injury with Epi-1 for 1 h at six hours post-infection completely healed the wound within 25 days. Conversely, the injury in the untreated control was not healed 25 days post-infection. Histological staining of wound sections with H&E showed that Epi-1 enhanced vascularization and increased epithelial activities in the wound region. Neutrophil recruitment to the wounded region in the Epi-1-treated sections was visualized by Giemsa staining. Additionally, Masson’s trichrome staining of wound sections confirmed that Epi-1 enhanced extracellular collagen compound formation. The induction of sepsis-associated blood C-reactive protein (CRP) and the pro-inflammatory cytokine IL-6 in response to MRSA infection was also suppressed in pigs that received Epi-1. Taken together, the results demonstrate that the biomaterial Epi-1 heals wounds through increasing epithelial cell proliferation, vascularization, and the formation of collagen and controls MRSA infection-mediated sepsis in pigs.
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- 2017
89. Cellular thermotolerance is inheritable from Holstein cattle cloned with ooplasts of Taiwan native yellow cattle
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Shyh-Shyan Liu, Piyawit Kesorn, Jai-Wei Lee, Perng-Chih Shen, Hsi-Hsun Wu, Hung-Yi Wu, Shao-Yu Peng, and Jyh-Cherng Ju
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0301 basic medicine ,Cytoplasm ,Mitochondrial DNA ,Proteases ,Hot Temperature ,Offspring ,Somatic cell ,Cloning, Organism ,Gene Expression Regulation, Enzymologic ,03 medical and health sciences ,Food Animals ,Stress, Physiological ,medicine ,Animals ,Small Animals ,Caspase ,bcl-2-Associated X Protein ,biology ,Equine ,0402 animal and dairy science ,Gene Expression Regulation, Developmental ,Ear ,04 agricultural and veterinary sciences ,Fibroblasts ,medicine.disease ,040201 dairy & animal science ,Molecular biology ,Lymphoma ,030104 developmental biology ,Proto-Oncogene Proteins c-bcl-2 ,Apoptosis ,Caspases ,biology.protein ,Cattle ,Animal Science and Zoology - Abstract
We have previously demonstrated that the somatic cells from cattle cloned with Holstein (H) donor cells and Taiwan native yellow cattle (Y) ooplasm (Yo-Hd) had better thermotolerance than those from cattle cloned with both Holstein donor cells and ooplasm (Ho-Hd). The present study aimed to investigate whether the cellular thermotolerance of these cloned cattle is transmissible to their offspring (Ho-Hd-F1 and Yo-Hd-F1). Thermotolerance of ear fibroblasts derived from these cloned cattle and their offspring were analyzed. Polymorphisms in mitochondrial DNA (mtDNA) D-loop of ear fibroblasts derived from Yo-Hd and Yo-Hd-F1 indicated that the cytoplasm is originated from Bos indicus (Y). After heat shock, the apoptotic rates, B-cell lymphoma 2-associated X protein/B-cell lymphoma 2 ratios, and relative expression levels of cysteine-aspartic proteases (caspases)-3, -8, and -9 of ear fibroblasts with Y-originated cytoplasm (including Y, Yo-Hd, and Yo-Hd-F1) were lower (P
- Published
- 2017
90. Exploring benchmark corporations in the semiconductor industry based on efficiency
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Chia-Han Tsai, Hung-Yi Wu, Rih-Wei Ye, I-Shuo Chen, and Jui-Kuei Chen
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Marketing ,Finance ,050208 finance ,Information Systems and Management ,business.industry ,Strategy and Management ,Corporate governance ,05 social sciences ,Enterprise value ,Computer Science Applications ,Intellectual capital ,Semiconductor industry ,Management of Technology and Innovation ,0502 economics and business ,Data envelopment analysis ,Benchmark (computing) ,Business ,050203 business & management ,Industrial organization - Abstract
The aim of this study is to explore benchmark corporations in the semiconductor industry based on efficiency. In this study, perspectives of intellectual capital and corporate governance are taken into account for the input data, whereas firm value is considered as the output data. Data envelope analysis (DEA), including CCR and BCC models, is utilized to ensure that the benchmark standards are precisely selected. Based on the result, suggestions for both semiconductor corporations and future research are provided at the end of this article.
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- 2017
91. Fishing pressure occurs down to the lower mesophotic coral ecosystem in Lyudao, Taiwan
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Hung-Yi Wu, Ming-Jay Ho, Shiahn-Wern Shyue, Chao-Yang Kuo, Chaolun Allen Chen, and Ming-Shiou Jeng
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Fishery ,Geography ,Coral ,Fishing ,Ecosystem ,Marine protected area - Published
- 2020
92. Surveillance of ticks and associated pathogens in free-ranging Formosan pangolins ( Manis pentadactyla pentadactyla )
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Nabin Khatri-Chhetri, Kurtis Jai-Chyi Pei, Hsien-Chun Liao, Han-Chun Shih, Chen-Chih Chen, Hung-Yi Wu, Rupak Khatri-Chhetri, Hsi-Chieh Wang, and Ching-Min Sun
- Subjects
Male ,Nymph ,0301 basic medicine ,Veterinary medicine ,Ixodidae ,030231 tropical medicine ,Population ,Taiwan ,Tick ,Southeast asian ,Microbiology ,03 medical and health sciences ,0302 clinical medicine ,Manis pentadactyla ,parasitic diseases ,Animals ,education ,Mammals ,education.field_of_study ,biology ,Pangolin ,Amblyomma testudinarium ,bacterial infections and mycoses ,biology.organism_classification ,Tick Infestations ,030104 developmental biology ,Infectious Diseases ,Population Surveillance ,Insect Science ,Haemaphysalis hystricis ,Female ,Parasitology - Abstract
Chinese pangolins are critically endangered insectivorous mammals distributed in several South and Southeast Asian countries. In recent years, there has been an increase in spread of tick-borne diseases in both humans and animals worldwide. Currently, limited information is available on ticks and associated pathogens infesting pangolins. The objective of the present study was to survey ticks and associated pathogens in the Formosan pangolin population in Southeastern Taiwan. Free-ranging Formosan pangolins captured during ecological survey were examined for the presence of ticks. DNA extracted from these ticks was used to identify the tick species and also to detect the tick-borne pathogens, by molecular methods. In the present study, we found 25% (13/52) of pangolins captured during 2012-2014 infested with ixodid ticks. A total of 21 ticks were collected and 3 species were identified: Haemaphysalis hystricis (14/21), Haemaphysalis formosensis (2/21) and Amblyomma testudinarium (5/21). We detected four different tick-borne pathogens, where one was identical to Anaplasma sp. strain An.H1446 while others showed close resemblance to Rickettsia conorii subsp. caspia A-167, Ehrlichia sp. TC251-2 and Cytauxzoon spp., respectively. The present study is the first survey of ticks infesting the free-ranging Chinese pangolins and pathogens harboured by these ticks. This information is important to know the diversity of ticks and tick-borne pathogens, and its conservation significance to pangolins and other sympatric wildlife. Important future step should be regular surveillance of ticks and tick-borne diseases at human-domestic animals-wildlife interface, which can provide a useful insight into the dynamics of these pathogens and can help control and prevent outbreak of zoonoses.
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- 2016
93. Discovery of a celecoxib binding site on PTGES with a cleavable chelation-assisted biotin probe
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Christina M. Woo, Hope A. Flaxman, Jinxu Gao, Hung-Yi Wu, and David K. Miyamoto
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genetic structures ,biology ,Chemistry ,Prostaglandin ,Prostaglandin E synthase ,Small molecule ,Cell biology ,chemistry.chemical_compound ,Membrane protein ,Biotin ,biology.protein ,lipids (amino acids, peptides, and proteins) ,Binding site ,Signal transduction ,Licofelone - Abstract
The coxibs are a subset of non-steroidal anti-inflammatory drugs (NSAIDs) that primarily target cyclooxygenase-2 (COX-2) to inhibit prostaglandin signaling and reduce inflammation. However, mechanisms to inhibit other members of the prostaglandin signaling pathway may improve selectivity and reduce off-target toxicity. Here, we report a novel binding site for celecoxib on prostaglandin E synthase (PTGES), an enzyme downstream of COX-2 in the prostaglandin signaling pathway, using a cleavable chelation-assisted biotin probe 6. Evaluation of the multi-functional probe 6 revealed significantly improved tagging efficiencies attributable to the embedded picolyl functional group. Application of the probe 6 within the small molecule interactome mapping by photo-affinity labeling (SIM-PAL) platform using photo-celecoxib as a reporter for celecoxib identified PTGES and other membrane proteins in the top eight enriched proteins from A549 cells. Carbonic anhydrase 12, a known protein target of celecoxib, was also enriched. Four binding sites to photo-celecoxib were additionally mapped by the probe 6, including a binding site with PTGES. The binding interaction with PTGES was validated by competitive displacement with celecoxib and known PTGES inhibitor licofelone. The binding site of photo-celecoxib on PTGES enabled the development of a structural model of the interaction and will inform the design of new selective inhibitors of the prostaglandin signaling pathway.
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- 2019
94. In Vitro and in Planta Evaluation of
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Hao, Chou, Yi-Ting, Xiao, Jyh-Nong, Tsai, Ting-Ting, Li, Hung-Yi, Wu, Li-Yu D, Liu, Der-Syh, Tzeng, and Chia-Lin, Chung
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Trichoderma ,Biological Control Agents ,Basidiomycota ,Antibiosis ,In Vitro Techniques ,Ecosystem ,Plant Diseases ,Trees - Abstract
Brown root rot (BRR), caused by the white rot fungus
- Published
- 2019
95. Gene Variations in Cis-Acting Elements between the Taiwan and Prototype Strains of Porcine Epidemic Diarrhea Virus Alter Viral Gene Expression
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Chen-Chang Su, Hung-Yi Wu, Chen-Yu Lo, Tsung-Lin Tsai, Chao-Nan Lin, Ching-Chi Hsieh, Hui-Wen Chang, and Ching-Houng Lin
- Subjects
cis-acting element ,0301 basic medicine ,Untranslated region ,lcsh:QH426-470 ,medicine.disease_cause ,Article ,03 medical and health sciences ,Transcription (biology) ,Gene expression ,Genetics ,medicine ,Genetics(clinical) ,Gene ,Genetics (clinical) ,porcine epidemic diarrhea virus ,Coronavirus ,biology ,nucleotide composition ,biology.organism_classification ,lcsh:Genetics ,030104 developmental biology ,Regulatory sequence ,gene evolution ,gene expression ,Porcine epidemic diarrhea virus ,Sequence motif - Abstract
In 2013, the outbreak of porcine epidemic diarrhea (PED) in Taiwan caused serious economic losses. In this study, we examined whether the variations of the cis-acting elements between the porcine epidemic diarrhea virus (PEDV) Taiwan (TW) strain and the prototype strain CV777 alter gene expression. For this aim, we analyzed the variations of the cis-acting elements in the 5′ and 3′ untranslated regions (UTRs) between the PEDV TW, CV777, and other reference strains. We also determined the previously unidentified transcription regulatory sequence (TRS), a sequence motif required for coronavirus transcription, and found that a nucleotide deletion in the TW strain, in comparison with CV777 strain, immediately downstream of the leader core sequence alters the identity between the leader TRS and the body TRS. Functional analyses using coronavirus defective interfering (DI) RNA revealed that such variations in cis-acting elements for the TW strain compared with the CV777 strain have an influence on the efficiency of gene expression. The current data show for the first time the evolution of PEDV in terms of cis-acting elements and their effects on gene expression, and thus may contribute to our understanding of recent PED outbreaks worldwide.
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- 2018
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96. Interplay between the Poly(A) Tail, Poly(A)-Binding Protein, and Coronavirus Nucleocapsid Protein Regulates Gene Expression of Coronavirus and the Host Cell
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Ching-Houng Lin, Chao-Nan Lin, Chen-Yu Lo, Hung-Yi Wu, and Tsung-Lin Tsai
- Subjects
0301 basic medicine ,Polyadenylation ,Immunoprecipitation ,viruses ,Immunology ,medicine.disease_cause ,Microbiology ,Poly(A)-Binding Proteins ,03 medical and health sciences ,chemistry.chemical_compound ,Virology ,Poly(A)-binding protein ,medicine ,Animals ,Coronavirus Nucleocapsid Proteins ,Humans ,Translation factor ,Coronavirus ,Coronavirus, Bovine ,Messenger RNA ,030102 biochemistry & molecular biology ,biology ,EIF4G ,EIF4E ,Nucleocapsid Proteins ,Cell biology ,Genome Replication and Regulation of Viral Gene Expression ,030104 developmental biology ,Eukaryotic Initiation Factor-4E ,HEK293 Cells ,chemistry ,Gene Expression Regulation ,Insect Science ,biology.protein ,Cattle ,Coronavirus Infections ,Eukaryotic Initiation Factor-4G ,Poly A - Abstract
In the present study, we investigated the roles of interactions among the poly(A) tail, coronavirus nucleocapsid (N) protein, and poly(A)-binding protein (PABP) in the regulation of coronavirus gene expression. Through dissociation constant (K(d)) comparison, we found that the coronavirus N protein can bind to the poly(A) tail with high affinity, establishing N protein as a PABP. A subsequent analysis with UV cross-linking and immunoprecipitation revealed that the N protein is able to bind to the poly(A) tail in infected cells. Further examination demonstrated that poly(A) tail binding by the N protein negatively regulates translation of coronaviral RNA and host mRNA both in vitro and in cells. Although the N protein can interact with PABP and eukaryotic initiation factor 4G (eIF4G), the poor interaction efficiency between the poly(A)-bound N protein and eIF4E may explain the observed decreased translation efficiency. In addition to interaction with translation factor eIF4G, the N protein is able to interact with coronavirus nonstructural protein 9 (nsp9), a replicase protein required for replication. The study demonstrates interactions among the poly(A) tail, N protein, and PABP both in vitro and in infected cells. Of the interactions, binding of the poly(A) tail to N protein decreases the interaction efficiency between the poly(A) tail and eIF4E, leading to translation inhibition. The poly(A)-dependent translation inhibition by N protein has not been previously demonstrated and thus extends our understanding of coronavirus gene expression. IMPORTANCE Gene expression in coronavirus is a complicated and dynamic process. In this study, we demonstrated that coronavirus N protein is able to bind to the poly(A) tail with high affinity, establishing N protein as a PABP. We also show how the interplay between coronavirus 3′ poly(A) tail, PABP, and N protein regulates gene expression of the coronavirus and host cell. Of the interactions, poly(A) tail binding by the N protein negatively regulates translation, and to our knowledge, this inhibition of translation by binding of the N protein to poly(A) tail has not been previously studied. Accordingly, the study provides fundamental molecular details regarding coronavirus infection and expands our knowledge of coronavirus gene expression.
- Published
- 2018
97. First Report of Neopestalotiopsis rosae Causing Leaf Blight and Crown Rot on Strawberry in Taiwan
- Author
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Pei-Che Chung, Hung-Yi Wu, Chia-Lin Chung, Yi-Mei Wu, Hiran A. Ariyawansa, and Chi-Yun Tsai
- Subjects
Stolon ,fungi ,Crown (botany) ,food and beverages ,Plant Science ,Biology ,Conidium ,Spore ,Horticulture ,Blight ,Potato dextrose agar ,Cultivar ,Agronomy and Crop Science ,Mycelium - Abstract
For the past 30 years, the most predominant strawberry cultivar in Taiwan has been 'Taoyuan No. 1', which produces fruit with rich flavor and aroma but is highly susceptible to anthracnose (Chung et al. 2019). Because epidemics of anthracnose became more destructive, farmers switched to an anthracnose-tolerant cultivar 'Xiang-Shui' (~50% and ~80% of the cultivation area in 2018 and 2019, respectively). Since 2018, severe leaf blight and crown rot symptoms have been observed all year in 'Xiang-Shui' in Miaoli, Nantou, Hsinchu, Taipei, Taoyuan, and Chiayi Counties. The disease became more prevalent and severe during 2019 to 2020 and caused up to 30% plant loss after transplanting. Symptoms appeared as brown necrotic lesions with black acervuli on leaves, slightly sunken dark-brown necrosis on stolons, and sunken reddish-brown necrosis on fruit. The diseased crown tissue showed marbled reddish-brown necrosis with a dark-brown margin, and plants with severe crown rot usually showed reddish-brown discoloration on leaves (the leaves initially turned reddish-brown between the veins and could become entirely scorched at later stages). To isolate the causal agent, small fragments of diseased leaves, crowns, stolons, and fruits were surface-disinfested with 0.5% sodium hypochlorite for 30 seconds, rinsed with sterile water then placed on 1.5% water agar. Single hyphal tips extended from tissues were transferred to potato dextrose agar and cultured for 7 days at 25°C under a 12-h/12-h photoperiod. Total 20 isolates were obtained from diseased leaves, crowns, stolons, and fruits. Colonies were white with cottony aerial mycelium, irregular margins, and black acervuli distributed in concentric rings. Conidia were fusiform to ellipsoid (five cells) with one basal appendage and three or four (usually three) apical appendages. From colony and conidial morphology, the causal agent was identified as Neopestalotiopsis sp. (Maharachchikumbura et al. 2014). The internal transcribed spacer (ITS) region, β-tubulin (TUB), and translation elongation factor 1-alpha (TEF-1α) of three isolates (ML1664 from diseased crown tissue collected in Hsinchu County; ML2147 and ML2411 from diseased leaves collected in Miaoli County) were sequenced (GenBank nos. MT469940 to MT469948). All three isolates clustered with the ex-type strain of Neopestalotiopsis rosae in the multilocus (ITS+TUB+TEF-1α) phylogenetic tree. To fulfill Koch's postulates, spore suspensions of ML1664 and ML2147 at 1×106 conidia/mL were used to spray-inoculate 'Xiang-Shui' seedlings at the 3 to 4 leaf stage until run-off (two trials, five seedlings per trial). Inoculated plants were put in a plastic bag (> 90% RH) at 25°C under a 12-h/12-h photoperiod. After 10-14 days, 80% of inoculated plants showed leaf or crown symptoms similar to those in the field. Control plants sprayed with sterile water showed no symptoms (4-5 seedlings per trial). The fungi were re-isolated from necrotic lesions with 100% frequency (n ≥ 3 isolates per trial), and morphological characters and ITS sequences were identical to the original ones. This is the first report of N. rosae causing leaf blight and crown rot in strawberry in Taiwan. N. rosae and N. clavispora have been reported as new threats to strawberry in several other countries (Rebollar-Alviter 2020; Gilardi 2019). Clarification of the pathogen provides a basis for developing strategies to control the emerging disease. Further studies are needed to evaluate the resistance/susceptibility of major strawberry cultivars and the fungicide sensitivity of the pathogen.
- Published
- 2021
98. Detection of Strawberry Diseases Using a Convolutional Neural Network
- Author
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Max T. Hou, Pei-Che Chung, Quoc Hung Phan, Hung-Yi Wu, Jer-Liang Andrew Yeh, and Jia-Rong Xiao
- Subjects
0106 biological sciences ,Plant Science ,Biology ,01 natural sciences ,Convolutional neural network ,Article ,convolution neural network ,lcsh:Botany ,Blight ,Transplanting ,Ecology, Evolution, Behavior and Systematics ,Training period ,Ecology ,strawberry diseases ,business.industry ,Deep learning ,04 agricultural and veterinary sciences ,Fragaria ,lcsh:QK1-989 ,Horticulture ,image recognition ,040103 agronomy & agriculture ,0401 agriculture, forestry, and fisheries ,Artificial intelligence ,business ,Powdery mildew ,010606 plant biology & botany - Abstract
The strawberry (Fragaria ×, ananassa Duch.) is a high-value crop with an annual cultivated area of ~500 ha in Taiwan. Over 90% of strawberry cultivation is in Miaoli County. Unfortunately, various diseases significantly decrease strawberry production. The leaf and fruit disease became an epidemic in 1986. From 2010 to 2016, anthracnose crown rot caused the loss of 30&ndash, 40% of seedlings and ~20% of plants after transplanting. The automation of agriculture and image recognition techniques are indispensable for detecting strawberry diseases. We developed an image recognition technique for the detection of strawberry diseases using a convolutional neural network (CNN) model. CNN is a powerful deep learning approach that has been used to enhance image recognition. In the proposed technique, two different datasets containing the original and feature images are used for detecting the following strawberry diseases&mdash, leaf blight, gray mold, and powdery mildew. Specifically, leaf blight may affect the crown, leaf, and fruit and show different symptoms. By using the ResNet50 model with a training period of 20 epochs for 1306 feature images, the proposed CNN model achieves a classification accuracy rate of 100% for leaf blight cases affecting the crown, leaf, and fruit, 98% for gray mold cases, and 98% for powdery mildew cases. In 20 epochs, the accuracy rate of 99.60% obtained from the feature image dataset was higher than that of 1.53% obtained from the original one. This proposed model provides a simple, reliable, and cost-effective technique for detecting strawberry diseases.
- Published
- 2020
99. COMMINUTED FRACTURE OF RIGHT TARSAL BONES WITH OLD CALLUS FORMATION IN A SLAUGHTERED PIG
- Author
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Tien-Huan Hsu, Chia-Lin Ho, Kuan-Sheng Chen, Cheng-Chung Lin, Julia Chu-Ning Hsu, Hao-Kai Chang, and Hung-Yi Wu
- Subjects
0301 basic medicine ,medicine.medical_specialty ,Callus formation ,business.industry ,0402 animal and dairy science ,Tarsal Joint ,04 agricultural and veterinary sciences ,Anatomy ,040201 dairy & animal science ,Bone remodeling ,Surgery ,Tarsal Bone ,03 medical and health sciences ,Skin Abscess ,030104 developmental biology ,medicine.anatomical_structure ,medicine ,Hock ,Fourth metatarsal bone ,Calcaneus ,business - Abstract
An enlarged and hard right hind limb of a condemned lame pig from a local slaughterhouse was submitted to National Chung Hsing University for pathological examination on 29 May 2015. Gross examination revealed brush burn and skin abscess. The radiography of the affected foot showed enlarged hock joint, collapsed tarsal joint with bony proliferation, and a soft tissue mass extending from the lateral to the tarsal bones. After the sample was split between the third and fourth metatarsal bone longitudinally, the calcaneus, talus, and the fourth tarsal bone were shown to be broken and damaged. Histopathological findings were as follows. First, the fractured bones showed the formation of callus and multiple small bone fragments were found. Second, osteoclasts and osteogenesis with bone remodeling were discovered at the edge of the bone fragments. Third, the skin abscess showed well-encapsulated clumps of bacteria and cellular debris. Trueperella pyogenes was identified from skin abscess and bone marrow. We speculate that the neglected fractures might have been related to crush injury inflicted by a sow or possible damage caused by the floor of the crate. This case highlights the importance of maintaining a high standard of animal welfare and once a lesion has occurred in food-producing animals, medication or elimination should be considered to avoid the long-term suffering of the animals.
- Published
- 2016
100. Improved cellular thermotolerance in cloned Holstein cattle derived with cytoplasts from a thermotolerant breed
- Author
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Hung-Yi Wu, Shyh-Shyan Liu, Jai-Wei Lee, Hung Li, and Perng-Chin Shen
- Subjects
Patient-Specific Modeling ,0301 basic medicine ,Hot Temperature ,Cloning, Organism ,Apoptosis ,Biology ,Cytoplast ,03 medical and health sciences ,Animal science ,Food Animals ,Stress, Physiological ,Heat shock protein ,Animals ,Small Animals ,Equine ,0402 animal and dairy science ,Gene Expression Regulation, Developmental ,Ear ,Embryo ,04 agricultural and veterinary sciences ,Fibroblasts ,040201 dairy & animal science ,Molecular biology ,Breed ,030104 developmental biology ,Cytoplasm ,Caspases ,Somatic cell nuclear transfer ,Cattle ,Animal Science and Zoology ,Purebred - Abstract
The objective of this study was to compare the thermotolerance of ear fibroblasts derived from various SCNT cattle. Specimens were produced from cloned embryos that had been reconstructed using donor cells (d) from the same Holstein cow (Hd) and the ooplasm (o) from Holstein cattle (Ho) or Taiwan yellow cattle (Yo). Polymorphism in the D-loop region of mitochondrial DNA in ear fibroblasts derived from SCNT cattle reconstructed with the Y ooplasm and H donor cells (SCNT-Yo-Hd) indicates that the cytoplasm originated from Bos indicus. The rates of apoptosis in heat-shocked ear fibroblasts derived from SCNT-Yo-Hd cattle (1.9%) and purebred Y cattle (1.5%) were significantly (P < 0.05) lower than those of cells derived from SCNT cattle reconstructed with the H ooplasm (SCNT-Ho-Hd: 3.4%), donor cells (4.0%), and purebred Holstein (4.1%) cattle. At the protein level, the relative abundances of apoptosis-inducing factor, B cell lymphoma 2-associated X protein, endonuclease G, cytochrome c, cysteinyl aspartate-specific proteinases 3, 8 and 9 in ear fibroblasts derived from SCNT-Yo-Hd cattle were significantly (P < 0.05) lower than those of cells derived from SCNT-Ho-Hd cattle after heat shock. In contrast, the relative abundances of heat shock proteins 27, 70 and B cell lymphoma 2 in ear fibroblasts derived from SCNT-Yo-Hd cattle were higher (P < 0.05) than those of fibroblasts derived from SCNT-Ho-Hd cattle. Moreover, heat-shocked ear fibroblasts derived from SCNT-Yo-Hd cattle have a significantly (P < 0.05) lower percentage of apoptosis-inducing factor-positive nuclei than do heat-shocked ear fibroblasts derived from SCNT-Ho-Hd cattle (11.1% vs. 18.5%). Taken together, these results report that ear fibroblasts derived from SCNT cattle reconstructed using the Y ooplasm are more thermotolerant than ear fibroblasts derived from SCNT cattle reconstructed using the H ooplasm. This is an indication that the cytoplasm may be a major determinant of thermal sensitivity in bovine ear fibroblasts.
- Published
- 2016
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