Overview
Background
Yosephine Gumulya has a degree in Food Technology (2004) from Bogor Agricultural University (Indonesia) and a Master of Biotechnology (2007) from Technical University Hamburg Harburg (Germany). She completed her PhD in 2010 at Max Planck Institute for Coal Research (Germany), where she learned how to mimic the natural evolution in laboratory and use this technique to generate novel enzymes for biotechnology applications. After spending 1.5 years working for food industry in Spain, in October 2012, she decided to pursue an academic career by doing postdoctoral research in the lab of Prof Elizabeth Gillam and A.Prof. Mikael Boden. Her research has focused on protein engineering and ancestral sequence reconstruction. This knowledge is essential for understanding the protein evolutionary histroy as well for creating robust yet promiscous enzymes for industrial applications.
Availability
- Dr Yosephine Gumulya is:
- Available for supervision
Qualifications
- Doctor of Philosophy of Natural Sciences, Ruhr University Bochum
Research interests
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Ancestral protein reconstruction
Hypothesising that the Earth was hot in ancient times, resurrecting ancestral proteins in the laboratory can generate robust proteins that useful for industrial applications.
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Protein Engineering / Directed evolution
Mimicking the natural evolution in the laboratory can create biocatalysts with suitable properties for industrial applications (e.g. selectivity, activity, stability)
Research impacts
A major limitation of industrial process development is the lack of robust enzymes with novel functions or suitable properties for industrial application. With laboratory-based methods (protein engineering and ancestral sequence reconstruction), we have generated stable yet promiscuous enzymes that can be used to generate drug metabolites. As a result, it will significantly speed up the drug development pipeline and, more importantly, reduce the cost of overall drug discovery process.
Works
Search Professor Yosephine Gumulya’s works on UQ eSpace
2018
Journal Article
In a quest for engineering acidophiles for biomining applications: Challenges and opportunities
Gumulya, Yosephine, Boxall, Naomi J., Khaleque, Himel N., Santala, Ville, Carlson, Ross P. and Kaksonen, Anna H. (2018). In a quest for engineering acidophiles for biomining applications: Challenges and opportunities. Genes, 9 (2) 116, 116-2. doi: 10.3390/genes9020116
2018
Journal Article
Effect of Binding on Enantioselectivity of Epoxide Hydrolase
Zaugg, Julian, Gumulya, Yosephine, Bodén, Mikael, Mark, Alan E and Malde, Alpeshkumar K (2018). Effect of Binding on Enantioselectivity of Epoxide Hydrolase. Journal of Chemical Information and Modeling, 58 (3), 630-640. doi: 10.1021/acs.jcim.7b00353
2018
Journal Article
Determinants of thermostability in the cytochrome P450 fold
Harris, Kurt L., Thomson, Raine E. S., Strohmaier, Silja J., Gumulya, Yosephine and Gillam, Elizabeth M. J. (2018). Determinants of thermostability in the cytochrome P450 fold. Biochimica et Biophysica Acta - Proteins and Proteomics, 1866 (1), 97-115. doi: 10.1016/j.bbapap.2017.08.003
2017
Journal Article
Learning epistatic interactions from sequence-activity data to predict enantioselectivity
Zaugg, Julian, Gumulya, Yosephine, Malde, Alpeshkumar K and Bodén, Mikael (2017). Learning epistatic interactions from sequence-activity data to predict enantioselectivity. Journal of computer-aided molecular design, 31 (12), 1085-1096. doi: 10.1007/s10822-017-0090-x
2017
Journal Article
Genetically programmed chiral organoborane synthesis
Jennifer Kan, S. B., Huang, Xiongyi, Gumulya, Yosephine, Chen, Kai and Arnold, Frances H. (2017). Genetically programmed chiral organoborane synthesis. Nature, 552 (7683), 132-136. doi: 10.1038/nature24996
2016
Journal Article
Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro' approach to protein engineering
Gumulya, Yosephine and Gillam, Elizabeth M. J. (2016). Exploring the past and the future of protein evolution with ancestral sequence reconstruction: the 'retro' approach to protein engineering. Biochemical Journal, 474 (1), 1-19. doi: 10.1042/BCJ20160507
2014
Book Chapter
Computational tools for directed evolution: a comparison of prospective and retrospective strategies
Zaugg, Julian, Gumulya, Yosephine, Gillam, Elizabeth M. J. and Bodén, Mikael (2014). Computational tools for directed evolution: a comparison of prospective and retrospective strategies. Directed evolution library creation: methods and protocols. (pp. 315-333) edited by Elizabeth M. J. Gillam, Janine N. Copp and David F. Ackerley. New York, NY, United States: Humana Press. doi: 10.1007/978-1-4939-1053-3_21
2012
Journal Article
Many pathways in laboratory evolution can lead to improved enzymes: How to escape from local minima
Gumulya, Yosephine, Sanchis, Joaquin and Reetz, Manfred T. (2012). Many pathways in laboratory evolution can lead to improved enzymes: How to escape from local minima. ChemBioChem, 13 (7), 1060-1066. doi: 10.1002/cbic.201100784
2011
Journal Article
Enhancing the thermal robustness of an enzyme by directed evolution: least favorable starting points and inferior mutants can map superior evolutionary Pathways
Gumulya, Yosephine and Reetz, Manfred T. (2011). Enhancing the thermal robustness of an enzyme by directed evolution: least favorable starting points and inferior mutants can map superior evolutionary Pathways. ChemBioChem, 12 (16), 2502-2510. doi: 10.1002/cbic.201100412
2010
Journal Article
Increasing the stability of an enzyme toward hostile organic solvents by directed evolution based on iterative saturation mutagenesis using the B-FIT method
Reetz, Manfred T., Soni, Pankaj, Fernandez, Layla, Gumulya, Yosephine and Carballeira, Jose D. (2010). Increasing the stability of an enzyme toward hostile organic solvents by directed evolution based on iterative saturation mutagenesis using the B-FIT method. Chemical Communications, 46 (45), 8657-8658. doi: 10.1039/c0cc02657c
2010
Journal Article
Iterative saturation mutagenesis accelerates laboratory evolution of enzyme stereoselectivity: rigorous comparison with traditional methods
Reetz, Manfred T., Prasad, Shreenath, Carballeira, Jose D., Gumulya, Yosephine and Bocola, Marco (2010). Iterative saturation mutagenesis accelerates laboratory evolution of enzyme stereoselectivity: rigorous comparison with traditional methods. Journal of the American Chemical Society, 132 (26), 9144-9152. doi: 10.1021/ja1030479
2010
Journal Article
An efficient method for mutant library creation in Pichia pastoris useful in directed evolution
Fernandez, Layla, Jiao, Ning, Soni, Pankaj, Gumulya, Yosephine, De Oliveira, Luciana Gonzaga and Reetz, Manfred T. (2010). An efficient method for mutant library creation in Pichia pastoris useful in directed evolution. Biocatalysis and Biotransformation, 28 (2), 122-129. doi: 10.3109/10242420903505834
2008
Journal Article
Evaluation of the laccase from Myceliophthora thermophila as industrial biocatalyst for polymerization reactions
Hollmann, Frank, Gumulya, Yosephine, Toelle, Christoph, Liese, Andreas and Thum, Oliver (2008). Evaluation of the laccase from Myceliophthora thermophila as industrial biocatalyst for polymerization reactions. Macromolecules, 41 (22), 8520-8524. doi: 10.1021/ma801763t
2008
Journal Article
Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates
Sanchis, Joaquin, Fernandez, Layla, Carballeira, J. Daniel, Drone, Jullien, Gumulya, Yosephine, Hoebenreich, Horst, Kahakeaw, Daniel, Kille, Sabrina, Lohmer, Renate, Peyralans, Jerome J. -P., Podtetenieff, John, Prasad, Shreenath, Soni, Pankaj, Taglieber, Andreas, Wu, Sheng, Zilly, Felipe E. and Reetz, Manfred T. (2008). Improved PCR method for the creation of saturation mutagenesis libraries in directed evolution: application to difficult-to-amplify templates. Applied Microbiology and Biotechnology, 81 (2), 387-397. doi: 10.1007/s00253-008-1678-9
Funding
Current funding
Supervision
Availability
- Dr Yosephine Gumulya is:
- Available for supervision
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Supervision history
Current supervision
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Doctor Philosophy
Enhancing fermentations by smart starter culture selection
Associate Advisor
Other advisors: Professor Mark Turner
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Doctor Philosophy
Optimizing Mixed Gas Fermentation for Enhanced Biofuel Production
Associate Advisor
Other advisors: Dr James Heffernan, Professor Esteban Marcellin
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Doctor Philosophy
Tailoring fermentation cultures for plant-based dairy alternatives
Associate Advisor
Other advisors: Associate Professor Sangeeta Prakash, Professor Mark Turner
Completed supervision
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2019
Doctor Philosophy
Computational Modelling of Enzymes: Predicting and Understanding the Selectivity of an Epoxide Hydrolase
Associate Advisor
Other advisors: Professor Mikael Boden
Media
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