中央研究院 生物化學研究所

研究領域與專長

Autophagy, Organelle damage responses, cell imaging, optogenetics.

see http://www.ibc.sinica.edu.tw/yang/

We develop and apply optogenetic schemes to perform quatitative measurements within single cells. We currently study the two following inter-related processes within the mammalian system:

細胞自噬 (Autophagy)

Cells utilize autophagosomal membranes to engulf cellular materials (from lipids, proteins, metabolites, entire organelles, to intruding pathogens) for autophagic degradation, and defective autophagy is implicated in a wide range diseases (e.g., neurodegenerative diseases, cancer, and aging).

How do cells determine the exact number of autophagosomes that needs to be generated at one time? How do they know precisely when and where autophagosome biogenesis should take place? We investigate questions related to how cells quantitatively tune their autophagosome biogenesis. The answers will provide insights on how autophagy can be utilized for medical interventions.

胞器損傷修復機制 (Organelle damage responses)

Our cells require a healthy pool of organelles to function- they therefore need to respond to organelle damages actively to survive. Gaining insights on how the various organelle damage responses work is attractive to us, as it permits the eventual manipulation of these pathways for extending cellular lifespan. We work toward this goal by combining organelle-specific dyes and targeted illumination to quantitatively elicit organelle dysfunction, and monitor cells’ reactions to this damage. The scheme we use allows one to designate the types of organelles targeted, and also controls the location as well as the extent and degree of the organelle damage that is applied.

學經歷

• 1997 – 2003   博士, 生物物理, 伊利諾州立大學香檳分校
• 1993 – 1997   學士, 物理系, 臺灣大學

• 2022 – 迄今   研究員, 中研院生化所
• 2014 – 2022   副研究員, 中研院生化所
• 2008 – 2014   助研究員, 中研院生化所
• 2003 – 2007   博士後研究員, 哈佛大學化學系

主要著作

A cryo-electron tomography workflow reveals protrusion-mediated shedding on injured plasma membrane. 
Mageswaran SK, Yang WY (corresponding author), Chakrabarty Y, Oikonomou CM, Jensen GJ 
Science Advances (2021)

Hsc70/Stub1 promotes the removal of individual oxidatively stressed peroxisomes. 
Chen BC, Chang YJ, Lin S, and Yang WY 
Nature Communications (2020)

Vesicular transport mediates the uptake of cytoplasmic proteins into mitochondria in Drosophila melanogaster. 
Chen PL, Huang KT, Cheng CY, Li JC, Chan HY, Lin TY, Su MP, Yang WY, Chang HC, Wang HD, and Chen CH 
Nature Communications (2020)

Omegasome-proximal PtdIns(4,5)P2 couples F-actin mediated mitoaggregate disassembly with autophagosome formation during mitophagy. 
Hsieh CW and Yang WY 
Nature Communications (2019)

Triggering mitophagy with photosensitizers. 
Hsieh CW and Yang WY 
Methods in Molecular Biology (2019)

Assays to monitor lysophagy. 
Chu YC, Hung YH, and Yang WY 
Methods in Enzymology (2017)

Bit-by-bit autophagic removal of parkin-labelled mitochondria. 
Yang JY and Yang WY 
Nature Communications (2013)

Spatiotemporally controlled induction of autophagy-mediated lysosome turnover. 
Hung YH, Chen LMW, Yang JY, and Yang WY 
Nature Communications (2013)

Spatiotemporally controlled initiation of Parkin-mediated mitophagy within single cells. 
Yang JY and Yang WY 
Autophagy (2011)

Site-Specific Two-Color Protein Labeling for FRET Studies Using Split Inteins. 
Yang JY and Yang WY 
Journal of the American Chemical Society (2009)

著作列表

1. Chen BH, (Yang WY)*  (2023-05)  Journal of visualized experiments : JoVE  (195), e65010  "Monitoring Stub1-Mediated Pexophagy."
   
2. Lin CC, Yan J, Kapur MD, Norris KL, Hsieh CW, Huang D, Vitale N, Lim KL, Guan Z, Wang XF, Chi JT, (Yang WY), Yao TP  (2022-12)  EMBO Reports  23(12), e55191  "Parkin coordinates mitochondrial lipid remodeling to execute mitophagy"
   
3. Chang HY, (Yang WY)*  (2022-04)  IUBMB life  74(4), 361-370  "Golgi quality control and autophagy."
   
4. Muthusamy S, Jan HM, Hsieh MY, Mondal S, Liu WC, Ko YA, (Yang WY), Mong KT, Chen GC, Lin CH*  (2021-10)  Journal of biomedical science  28(1), 72  "Enhanced enzymatic production of cholesteryl 6\'-acylglucoside impairs lysosomal degradation for the intracellular survival of Helicobacter pylori."
   
5. Mageswaran SK, (Yang WY)*, Chakrabarty Y, Oikonomou CM, Jensen GJ  (2021-03)  Science Advances  7(13), eabc6345  "A cryo-electron tomography workflow reveals protrusion-mediated shedding on injured plasma membrane."
   
6. Klionsky DJ, Chen GC, Chen RH, (Yang WY) et al.  (2021-02)  Autophagy  17(1), 1-382  "Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)."
   
7. Chen BH, Chang YJ, Lin S, (Yang WY)*  (2020-10)  Nature Communications  11(1), 5267  "Hsc70/Stub1 promotes the removal of individual oxidatively stressed peroxisomes"
   
8. Chen PL, Huang KT, Cheng CY, Li JC, Chan HY, Lin TY, Su MP, (Yang WY), Chang HC, Wang HD, Chen CH  (2020-05)  Nature communications  11(1), 2592  "Vesicular transport mediates the uptake of cytoplasmic proteins into mitochondria in Drosophila melanogaster."
   
9. Hong MH, Lin WH, Weng IC, Hung YH, Chen HL, Chen HY, Chen P, Lin CH, (Yang WY), Liu FT  (2020-01)  Glycobiology  30(1), 36-48  "Intracellular galectins control cellular responses commensurate with cell surface carbohydrate composition."
   
10. Hsieh CW, (Yang WY)*  (2019-02)  Nature Communications  10(1), 969  "Omegasome-proximal PtdIns(4,5)P2 couples F-actin mediated mitoaggregate disassembly with autophagosome formation during mitophagy."
    
11. Chen YC, Cheng TH, Lin WL, Chen CL, (Yang WY), Blackstone C, Chang CR  (2019-01)  iScience  11, 305-317  "Srv2 Is a Pro-fission Factor that Modulates Yeast Mitochondrial Morphology and Respiration by Regulating Actin Assembly."
    
12. Hsieh CW, (Yang WY)*  (2019)  Methods in molecular biology  1880, 611-619  "Triggering Mitophagy with Photosensitizers."
    
13. Chu YP, Hung YH, Chang HY, (Yang WY)*  (2017)  Methods in enzymology  588, 231-244  "Assays to Monitor Lysophagy."
    
14. Chen BH, Yang HJ, Chou HY, Chen GC, (Yang WY)*  (2017)  Methods in molecular biology  1560, 231-236  "Staining of Lipid Droplets with Monodansylpentane."
    
15. Klionsky DJ, Chen GC, (Yang WY) et al.  (2016)  Autophagy  12(1), 1-222  "Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)."
    
16. (Yang WY)*  (2015)  Annals of the New York Academy of Sciences  1350, 48-51  "Optogenetic probing of mitochondrial damage responses."
    
17. Hsieh CW, Chu CH, Lee HM, and (Yang WY)*  (2015)  Scientific Reports  5, 10376  "Triggering mitophagy with far-red fluorescent photosensitizers."
    
18. Yang JY, (Yang WY)*  (2013)  Nature Communications  4, 2428  "Bit-by-bit autophagic removal of parkin-labelled mitochondria"
    
19. Hung YH, Chen LMW, Yang JY, and (Yang WY)*  (2013)  Nature Communications  4, 2111  "Spatiotemporally controlled induction of autophagy-mediated lysosome turnover"
    
20. Klionsky DJ, Chen GC, (Yang WY) et al.  (2012)  Autophagy  8(4), 445-544  "Guidelines for the use and interpretation of assays for monitoring autophagy"
    
21. Yang HJ, Hsu CL, Yang JY, and (Yang WY)*  (2012)  PLoS One  7(3), e32693  "Monodansylpentane as a Blue-Fluorescent Lipid-Droplet Marker for Multi-Color Live-Cell Imaging"
    
22. Kuang E, Okumura CY, Sheffy-Levin S, Varsano T, Shu VC, Qi J, Niesman IR, Yang HJ, Lopez-Otin C, (Yang WY), Reed JC, Broday L, Nizet V, Ronai ZA  (2012)  PLoS genetics  8(10), e1003007  "Regulation of ATG4B Stability by RNF5 Limits Basal Levels of Autophagy and Influences Susceptibility to Bacterial Infection."
    
23. Yang JY and (Yang WY)*  (2011)  Autophagy  7(10), 1230-1238  "Spatiotemporally controlled initiation of Parkin-mediated mitophagy within single cells"
    
24. Yang JY and (Yang WY)*  (2009)  Journal of the American Chemical Society  131(33), 11644-11645  "Site-Specific Two-Color Protein Labeling for FRET Studies Using Split Inteins."
    
25. (Yang WY) and Gruebele M  (2006)  Biophysical Journal  90(8), 2930-2937  "Binary and ternary aggregation within tethered protein constructs"
    
26. Xie XS, Yu J and (Yang WY)  (2006)  Science  312(5771), 228-230  "Living cells as test tubes."
    
27. (Yang WY) and Gruebele M  (2005)  Philosophical Transactions of the Royal Society A-Mathematical Physical and Engineering Sciences  363(1827), 565-573  "Kinetic equivalence of the heat and cold structural transitions of lambda6-85"
    
28. Nan X, (Yang WY) and Xie XS  (2004-08)  Biophotonics International  11(8), 44-47  "CARS microscopy lights up lipids in living cells"
    
29. E. Larios, (W. Y. Yang), K. Schulten and M. Gruebele  (2004)  Chemical Physics  307, 217-225  "A similarity measure for partially folded proteins: application to unfolded and native-like conformational fluctuations"
    
30. (Yang WY) and Gruebele M  (2004)  Journal of the American Chemical Society  126, 7758-7759  "Detection-dependent kinetics probe folding landscape microstructure"
    
31. (Yang WY) and Gruebele M  (2004)  Biophysical Journal  87, 596-608  "Folding lambda-repressor at its speed limit"
    
32. (Yang WY), Pitera JW, Swopes WS and Gruebele M  (2004)  Journal of Molecular Biology  336, 241-251  "Heterogeneous folding of the trpzip hairpin: Full atom simulation and experiment"
    
33. (Yang WY) and Gruebele M  (2004)  Biochemistry  43(41), 13018-13025  "Rate-temperature relationships in lambda-repressor fragment lambda 6-85 folding."
    
34. (Yang WY), Gruebele M  (2003)  Nature  423(6936), 193-197  "Folding at the speed limit."
    
35. (Yang WY), Larios E and Gruebele M  (2003)  Journal of the American Chemical Society  125, 16220-16227  "On the extended beta-structure propensity of polypeptides at high temperatures"
    
36. (Yang WY), Prince RB, Sabelko J, Moore JS and Gruebele M  (2000)  Journal of the American Chemical Society  122, 3248-3249  "Transition from exponential to nonexponential kinetics during formation of a nonbiological helix"