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Zhou Q, Sun P, Xiong HM, Xie J, Zhu GY, Tantillo DJ, Huang AC. Insight into neofunctionalization of 2,3-oxidosqualene cyclases in B,C-ring-opened triterpene biosynthesis in quinoa. New Phytol 2024; 241:764-778. [PMID: 37904576 DOI: 10.1111/nph.19345] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Accepted: 10/04/2023] [Indexed: 11/01/2023]
Abstract
Bioactive triterpenes feature complex fused-ring structures, primarily shaped by the first-committed enzyme, 2,3-oxidosqualene cyclases (OSCs) in plant triterpene biosynthesis. Triterpenes with B,C-ring-opened skeletons are extremely rare with unknown formation mechanisms, harbouring unchartered chemistry and biology. Here, through mining the genome of Chenopodium quinoa followed by functional characterization, we identified a stress-responsive and neofunctionalized OSC capable of generating B,C-ring-opened triterpenes, including camelliol A and B and the novel (-)-quinoxide A as wax components of the specialized epidermal bladder cells, namely the quinoxide synthase (CqQS). Protein structure analysis followed by site-directed mutagenesis identified key variable amino acid sites underlying functional interconversion between pentacyclic β-amyrin synthase (CqbAS1) and B,C-ring-opened triterpene synthase CqQS. Mutation of one key residue (N612K) in even evolutionarily distant Arabidopsis β-amyrin synthase could generate quinoxides, indicating a conserved mechanism for B,C-ring-opened triterpene formation in plants. Quantum computation combined with docking experiments further suggests that conformations of conserved W613 and F413 of CqQS might be key to selectively stabilizing intermediate carbocations towards B,C-ring-opened triterpene formation. Our findings shed light on quinoa triterpene skeletal diversity and mechanisms underlying B,C-ring-opened triterpene biosynthesis, opening avenues towards accessing their chemistry and biology and paving the way for quinoa trait engineering and quality improvement.
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Affiliation(s)
- Qian Zhou
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Peng Sun
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Hao-Ming Xiong
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, 999078, China
| | - Jiali Xie
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
| | - Guo-Yuan Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau, 999078, China
| | - Dean J Tantillo
- Department of Chemistry, University of California, Davis, CA, 95616, USA
| | - Ancheng C Huang
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, SUSTech-PKU Institute of Plant and Food Science, Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, Guangdong, 518055, China
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Lin HC, de Ulzurrun GVD, Chen SA, Yang CT, Tay RJ, Iizuka T, Huang TY, Kuo CY, Gonçalves AP, Lin SY, Chang YC, Stajich JE, Schwarz EM, Hsueh YP. Key processes required for the different stages of fungal carnivory by a nematode-trapping fungus. PLoS Biol 2023; 21:e3002400. [PMID: 37988381 PMCID: PMC10662756 DOI: 10.1371/journal.pbio.3002400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 10/24/2023] [Indexed: 11/23/2023] Open
Abstract
Nutritional deprivation triggers a switch from a saprotrophic to predatory lifestyle in soil-dwelling nematode-trapping fungi (NTF). In particular, the NTF Arthrobotrys oligospora secretes food and sex cues to lure nematodes to its mycelium and is triggered to develop specialized trapping devices. Captured nematodes are then invaded and digested by the fungus, thus serving as a food source. In this study, we examined the transcriptomic response of A. oligospora across the stages of sensing, trap development, and digestion upon exposure to the model nematode Caenorhabditis elegans. A. oligospora enacts a dynamic transcriptomic response, especially of protein secretion-related genes, in the presence of prey. Two-thirds of the predicted secretome of A. oligospora was up-regulated in the presence of C. elegans at all time points examined, and among these secreted proteins, 38.5% are predicted to be effector proteins. Furthermore, functional studies disrupting the t-SNARE protein Sso2 resulted in impaired ability to capture nematodes. Additionally, genes of the DUF3129 family, which are expanded in the genomes of several NTF, were highly up-regulated upon nematode exposure. We observed the accumulation of highly expressed DUF3129 proteins in trap cells, leading us to name members of this gene family as Trap Enriched Proteins (TEPs). Gene deletion of the most highly expressed TEP gene, TEP1, impairs the function of traps and prevents the fungus from capturing prey efficiently. In late stages of predation, we observed up-regulation of a variety of proteases, including metalloproteases. Following penetration of nematodes, these metalloproteases facilitate hyphal growth required for colonization of prey. These findings provide insights into the biology of the predatory lifestyle switch in a carnivorous fungus and provide frameworks for other fungal-nematode predator-prey systems.
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Affiliation(s)
- Hung-Che Lin
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | | | - Sheng-An Chen
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Ching-Ting Yang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Rebecca J. Tay
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Tomoyo Iizuka
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Tsung-Yu Huang
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - Chih-Yen Kuo
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
| | - A. Pedro Gonçalves
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Siou-Ying Lin
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
| | - Yu-Chu Chang
- Department of Biochemistry and Molecular Cell Biology, School of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Jason E. Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, California, United States of America
| | - Erich M. Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York, United States of America
| | - Yen-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, Nankang, Taipei, Taiwan
- Molecular and Cell Biology, Taiwan International Graduate Program, Academia Sinica and Graduate Institute of Life Sciences, National Defense Medical Center, Taipei, Taiwan
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Reilly DK, Schwarz EM, Muirhead CS, Robidoux AN, Narayan A, Doma MK, Sternberg PW, Srinivasan J. Transcriptomic profiling of sex-specific olfactory neurons reveals subset-specific receptor expression in Caenorhabditis elegans. Genetics 2023; 223:iyad026. [PMID: 36801937 PMCID: PMC10319972 DOI: 10.1093/genetics/iyad026] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Revised: 12/23/2022] [Accepted: 02/13/2023] [Indexed: 02/20/2023] Open
Abstract
The nematode Caenorhabditis elegans utilizes chemosensation to navigate an ever-changing environment for its survival. A class of secreted small-molecule pheromones, termed ascarosides, play an important role in olfactory perception by affecting biological functions ranging from development to behavior. The ascaroside #8 (ascr#8) mediates sex-specific behaviors, driving avoidance in hermaphrodites and attraction in males. Males sense ascr#8 via the ciliated male-specific cephalic sensory (CEM) neurons, which exhibit radial symmetry along dorsal-ventral and left-right axes. Calcium imaging studies suggest a complex neural coding mechanism that translates stochastic physiological responses in these neurons to reliable behavioral outputs. To test the hypothesis that neurophysiological complexity arises from differential expression of genes, we performed cell-specific transcriptomic profiling; this revealed between 18 and 62 genes with at least twofold higher expression in a specific CEM neuron subtype vs both other CEM neurons and adult males. These included two G protein-coupled receptor (GPCR) genes, srw-97 and dmsr-12, that were specifically expressed in nonoverlapping subsets of CEM neurons and whose expression was confirmed by GFP reporter analysis. Single CRISPR-Cas9 knockouts of either srw-97 or dmsr-12 resulted in partial defects, while a double knockout of both srw-97 and dmsr-12 completely abolished the attractive response to ascr#8. Together, our results suggest that the evolutionarily distinct GPCRs SRW-97 and DMSR-12 act nonredundantly in discrete olfactory neurons to facilitate male-specific sensation of ascr#8.
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Affiliation(s)
- Douglas K Reilly
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY 14853, USA
| | - Caroline S Muirhead
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Annalise N Robidoux
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
- Department of Chemistry and Biochemistry, Worcester Polytechnic Institute, Worcester, MA 01605, USA
| | - Anusha Narayan
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Meenakshi K Doma
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Paul W Sternberg
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Jagan Srinivasan
- Department of Biology and Biotechnology, Worcester Polytechnic Institute, Worcester, MA 01605, USA
- Bioinformatics and Computational Biology Program, Worcester Polytechnic Institute, Worcester, MA 01605, USA
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Pavlović M, Kahrović E, Aranđelović S, Radulović S, Ilich PP, Grgurić-Šipka S, Ljubijankić N, Žilić D, Jurec J. Tumor selective Ru(III) Schiff bases complexes with strong in vitro activity toward cisplatin-resistant MDA-MB-231 breast cancer cells. J Biol Inorg Chem 2023; 28:263-284. [PMID: 36781474 DOI: 10.1007/s00775-023-01989-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2022] [Accepted: 01/24/2023] [Indexed: 02/15/2023]
Abstract
Novel ruthenium(III) complexes of general formula Na[RuCl2(L1-3-N,O)2] where L(1-3) denote deprotonated Schiff bases (HL1-HL3) derived from 5-substituted salicyladehyde and alkylamine (propyl- or butylamine) were prepared and characterized based on elemental analysis, mass spectra, infrared, electron spin/paramagnetic resonance (ESR/EPR) spectroscopy, and cyclovoltammetric study. Optimization of five isomers of complex C1 was done by DFT calculation. The interaction of C1-C3 complexes with DNA (Deoxyribonucleic acid) and BSA (Bovine serum albumin) was investigated by electron spectroscopy and fluorescence quenching. The cytotoxic activity of C1-C3 was investigated in a panel of four human cancer cell lines (K562, A549, EA.hy926, MDA-MB-231) and one human non-tumor cell line (MRC-5). Complexes displayed an apparent cytoselective profile, with IC50 values in the low micromolar range from 1.6 ± 0.3 to 23.0 ± 0.1 µM. Cisplatin-resistant triple-negative breast cancer cells MDA-MB-231 displayed the highest sensitivity to complexes, with Ru(III) compound containing two chlorides and two deprotonated N-propyl-5-chloro-salicylidenimine (hereinafter C1) as the most potent (IC50 = 1.6 µM), and approximately ten times more active than cisplatin (IC50 = 21.9 µM). MDA-MB-231 cells treated for 24 h with C1 presented with apoptotic morphology, as seen by acridine orange/ethidium bromide staining, while 48 h of treatment induced DNA fragmentation, and necrotic changes in cells, as seen by flow cytometry analysis. Drug-accumulation study by inductively coupled plasma mass spectrometry (ICP-MS) demonstrated markedly higher intracellular accumulation of C1 compared with cisplatin.
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Affiliation(s)
- Marijana Pavlović
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, Belgrade, Serbia
| | - Emira Kahrović
- Laboratory for Inorganic and Bioinorganic Chemistry, Department of Chemistry, Faculty of Science, University of Sarajevo, Zmaja od Bosne 33, 71 000, Sarajevo, Bosnia and Herzegovina.
| | - Sandra Aranđelović
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, Belgrade, Serbia
| | - Siniša Radulović
- Department of Experimental Oncology, Institute for Oncology and Radiology of Serbia, Pasterova 14, Belgrade, Serbia
| | - Predrag-Peter Ilich
- Department of Natural Sciences, Weissman School of Arts and Sciences, Baruch College/CUNY, New York City, NY, USA
| | - Sanja Grgurić-Šipka
- Faculty of Chemistry, University of Belgrade, Studentski Trg 12-16, Belgrade, Serbia
| | - Nevzeta Ljubijankić
- Laboratory for Inorganic and Bioinorganic Chemistry, Department of Chemistry, Faculty of Science, University of Sarajevo, Zmaja od Bosne 33, 71 000, Sarajevo, Bosnia and Herzegovina
| | - Dijana Žilić
- Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
| | - Jurica Jurec
- Ruđer Bošković Institute, Bijenička 54, Zagreb, Croatia
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Bhattacharya P, Chen J, Hoops S, Machi D, Lewis B, Venkatramanan S, Wilson ML, Klahn B, Adiga A, Hurt B, Outten J, Adiga A, Warren A, Baek YY, Porebski P, Marathe A, Xie D, Swarup S, Vullikanti A, Mortveit H, Eubank S, Barrett CL, Marathe M. Data-driven scalable pipeline using national agent-based models for real-time pandemic response and decision support. Int J High Perform Comput Appl 2023; 37:4-27. [PMID: 38603425 PMCID: PMC9596688 DOI: 10.1177/10943420221127034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/13/2024]
Abstract
This paper describes an integrated, data-driven operational pipeline based on national agent-based models to support federal and state-level pandemic planning and response. The pipeline consists of (i) an automatic semantic-aware scheduling method that coordinates jobs across two separate high performance computing systems; (ii) a data pipeline to collect, integrate and organize national and county-level disaggregated data for initialization and post-simulation analysis; (iii) a digital twin of national social contact networks made up of 288 Million individuals and 12.6 Billion time-varying interactions covering the US states and DC; (iv) an extension of a parallel agent-based simulation model to study epidemic dynamics and associated interventions. This pipeline can run 400 replicates of national runs in less than 33 h, and reduces the need for human intervention, resulting in faster turnaround times and higher reliability and accuracy of the results. Scientifically, the work has led to significant advances in real-time epidemic sciences.
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Affiliation(s)
- Parantapa Bhattacharya
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Jiangzhuo Chen
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Stefan Hoops
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Dustin Machi
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Bryan Lewis
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | | | - Mandy L Wilson
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Brian Klahn
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Aniruddha Adiga
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Benjamin Hurt
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Joseph Outten
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Abhijin Adiga
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Andrew Warren
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Young Yun Baek
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Przemyslaw Porebski
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Achla Marathe
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
- Dept. of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Dawen Xie
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Samarth Swarup
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
| | - Anil Vullikanti
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
- Dept. of Computer Science, University of Virginia, Charlottesville, VA, USA
| | - Henning Mortveit
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
- Dept. of Eng. Systems and Environment, University of Virginia, Charlottesville, VA, USA
| | - Stephen Eubank
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
- Dept. of Public Health Sciences, University of Virginia, Charlottesville, VA, USA
| | - Christopher L Barrett
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
- Dept. of Computer Science, University of Virginia, Charlottesville, VA, USA
| | - Madhav Marathe
- Biocomplexity Institute and Initiative, University of Virginia, Charlottesville, VA, USA
- Dept. of Computer Science, University of Virginia, Charlottesville, VA, USA
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Vidal-Diez de Ulzurrun G, Lee YY, Stajich JE, Schwarz EM, Hsueh YP. Genomic analyses of two Italian oyster mushroom Pleurotus pulmonarius strains. G3 (Bethesda) 2021; 11:jkaa007. [PMID: 33585863 PMCID: PMC8022975 DOI: 10.1093/g3journal/jkaa007] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 12/14/2020] [Indexed: 11/14/2022]
Abstract
Pleurotus mushrooms are among the most cultivated fungi in the world and are highly valuable for food, medicine, and biotechnology industries. Furthermore, Pleurotus species are carnivorous fungi; they can rapidly paralyze and kill nematodes when nutrient-deprived. The predator-prey interactions between Pleurotus and nematodes are still widely unexplored. Moreover, the molecular mechanisms and the genes involved in the carnivorous behavior of Pleurotus mushrooms remain a mystery. We are attempting to understand the interactions between Pleurotus mushrooms and their nematode prey through genetic and genomic analyses. Two single spores (ss2 and ss5) isolated from a fruiting body of Pleurotus pulmonarius exhibited significant differences in growth and toxicity against nematodes. Thus, using PacBio long reads, we assembled and annotated two high-quality genomes for these two isolates of P. pulmonarius. Each of these assemblies contains 23 scaffolds, including 6 (ss2) and 8 (ss5) telomere-to-telomere scaffolds, and they are among the most complete assembled genomes of the Pleurotus species. Comparative analyses identified the genomic differences between the two P. pulmonarius strains. In sum, this work provides a genomic resource that will be invaluable for better understanding the Italian oyster mushroom P. pulmonarius.
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Affiliation(s)
| | - Yi-Yun Lee
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei 115, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
| | - Jason E Stajich
- Department of Microbiology and Plant Pathology, University of California, Riverside, 900 University Ave. Riverside, CA 92521, USA
| | - Erich M Schwarz
- Department of Molecular Biology and Genetics, Cornell University, Biotechnology 351, 526 Campus Road, Ithaca, NY 14853-2703, USA
| | - Yen-Ping Hsueh
- Institute of Molecular Biology, Academia Sinica, 128 Academia Road, Section 2, Nangang, Taipei 115, Taiwan
- Genome and Systems Biology Degree Program, National Taiwan University and Academia Sinica, Taipei, Taiwan
- Department of Biochemical Science and Technology, National Taiwan University No. 1, Sec. 4, Roosevelt Road, Taipei 106, Taiwan
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