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113 results on '"Cherry, Joel"'

1. An Automated Scientist to Design and Optimize Microbial Strains for the Industrial Production of Small Molecules

Author

Singh, Amoolya H., primary, Kaufmann-Malaga, Benjamin B., additional, Lerman, Joshua A., additional, Dougherty, Daniel P., additional, Zhang, Yang, additional, Kilbo, Alexander L., additional, Wilson, Erin H., additional, Ng, Chiam Yu, additional, Erbilgin, Onur, additional, Curran, Kate A., additional, Reeves, Christopher D., additional, Hung, John E., additional, Mantovani, Simone, additional, King, Zachary A., additional, Ayson, Marites J., additional, Denery, Judith R., additional, Lu, Chia-Wei, additional, Norton, Phillip, additional, Tran, Carol, additional, Platt, Darren M., additional, Cherry, Joel R., additional, Chandran, Sunil S., additional, and Meadows, Adam L., additional

Published
2023
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4. Challenging the workhorse: Comparative analysis of eukaryotic micro‐organisms for expressing monoclonal antibodies

Author

Jiang, Hanxiao, Horwitz, Andrew A., Wright, Chapman, Tai, Anna, Znameroski, Elizabeth A., Tsegaye, Yoseph, Warbington, Hailley, Bower, Benjamin S., Alves, Christina, Co, Carl, Jonnalagadda, Kanvasri, Platt, Darren, Walter, Jessica M., Natarajan, Venkatesh, Ubersax, Jeffrey A., Cherry, Joel R., and Love, J. Christopher

Subjects
recombinant protein expression, Antibodies, Monoclonal, alternate expression systems, Article, Recombinant Proteins, Engineering Science of Biological Systems, ARTICLES, Eukaryotic Cells, Metabolic Engineering, antibody, yeast expression systems, Immunologic Factors, Technology, Pharmaceutical, genome engineering, Biotechnology
Abstract

For commercial protein therapeutics, Chinese hamster ovary (CHO) cells have an established history of safety, proven capability to express a wide range of therapeutic proteins and high volumetric productivities. Expanding global markets for therapeutic proteins and increasing concerns for broadened access of these medicines has catalyzed consideration of alternative approaches to this platform. Reaching these objectives likely will require an order of magnitude increase in volumetric productivity and a corresponding reduction in the costs of manufacture. For CHO‐based manufacturing, achieving this combination of targeted improvements presents challenges. Based on a holistic analysis, the choice of host cells was identified as the single most influential factor for both increasing productivity and decreasing costs. Here we evaluated eight wild‐type eukaryotic micro‐organisms with prior histories of recombinant protein expression. The evaluation focused on assessing the potential of each host, and their corresponding phyla, with respect to key attributes relevant for manufacturing, namely (a) growth rates in industry‐relevant media, (b) adaptability to modern techniques for genome editing, and (c) initial characterization of product quality. These characterizations showed that multiple organisms may be suitable for production with appropriate engineering and development and highlighted that yeast in general present advantages for rapid genome engineering and development cycles., In this work, we present a comparative study of the potential of eight different eukaryotic microorganisms (yeasts, fungi, diatom, and protozoan) as alternative hosts for the expression of recombinant biopharmaceuticals. The study assesses the suitability of these hosts in a ‘head‐to‐head’ manner that would allow direct comparisons of their tractability for high‐density cultivation, engineering with advanced genome editing tools (CRISPR/Cas9), and the molecular attributes of recombinant antibodies expressed in the tractable hosts.

Published
2019

8. Challenging the workhorse: Comparative analysis of eukaryotic micro‐organisms for expressing monoclonal antibodies

Author

Koch Institute for Integrative Cancer Research at MIT, Jiang, Hanxiao, Horwitz, Andrew A, Wright, Chapman, Tai, Anna, Znameroski, Elizabeth A, Tsegaye, Yoseph, Warbington, Hailley, Bower, Benjamin S, Alves, Christina, Co, Carl, Jonnalagadda, Kanvasri, Platt, Darren, Walter, Jessica M, Natarajan, Venkatesh, Ubersax, Jeffrey A, Cherry, Joel R, Love, J Christopher, Koch Institute for Integrative Cancer Research at MIT, Jiang, Hanxiao, Horwitz, Andrew A, Wright, Chapman, Tai, Anna, Znameroski, Elizabeth A, Tsegaye, Yoseph, Warbington, Hailley, Bower, Benjamin S, Alves, Christina, Co, Carl, Jonnalagadda, Kanvasri, Platt, Darren, Walter, Jessica M, Natarajan, Venkatesh, Ubersax, Jeffrey A, Cherry, Joel R, and Love, J Christopher

Abstract

© 2019 The Authors. Biotechnology and Bioengineering Published by Wiley Periodicals, Inc. For commercial protein therapeutics, Chinese hamster ovary (CHO) cells have an established history of safety, proven capability to express a wide range of therapeutic proteins and high volumetric productivities. Expanding global markets for therapeutic proteins and increasing concerns for broadened access of these medicines has catalyzed consideration of alternative approaches to this platform. Reaching these objectives likely will require an order of magnitude increase in volumetric productivity and a corresponding reduction in the costs of manufacture. For CHO-based manufacturing, achieving this combination of targeted improvements presents challenges. Based on a holistic analysis, the choice of host cells was identified as the single most influential factor for both increasing productivity and decreasing costs. Here we evaluated eight wild-type eukaryotic micro-organisms with prior histories of recombinant protein expression. The evaluation focused on assessing the potential of each host, and their corresponding phyla, with respect to key attributes relevant for manufacturing, namely (a) growth rates in industry-relevant media, (b) adaptability to modern techniques for genome editing, and (c) initial characterization of product quality. These characterizations showed that multiple organisms may be suitable for production with appropriate engineering and development and highlighted that yeast in general present advantages for rapid genome engineering and development cycles.

Published
2021

24. Recent advances in synthetic biology for engineering isoprenoid production in yeast

Author

Vickers, Claudia E., Williams, Thomas C., Peng, Bingyin, Cherry, Joel, Vickers, Claudia E., Williams, Thomas C., Peng, Bingyin, and Cherry, Joel

Abstract

Isoprenoids (terpenes/terpenoids) have many useful industrial applications, but are often not produced at industrially viable level in their natural sources. Synthetic biology approaches have been used extensively to reconstruct metabolic pathways in tractable microbial hosts such as yeast and re-engineer pathways and networks to increase yields. Here we review recent advances in this field, focusing on central carbon metabolism engineering to increase precursor supply, re-directing carbon flux for production of C10, C15, or C20 isoprenoids, and chemical decoration of high value diterpenoids (C20). We also overview other novel synthetic biology strategies that have potential utility in yeast isoprenoid pathway engineering. Finally, we address the question of what is required in the future to move the field forwards.

Published
2017

25. Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: structure and function of a large, enigmatic family

Author

Harris, Paul V., Welner, Ditte, McFarland, K.C., Re, Edward, Poulsen, Jens-Christian Navarro, Brown, Kimberly, Salbo, Rune, Hanshu Ding, Vlasenko, Elena, Merino, Sandy, Feng Xu, Cherry, Joel, Larsen, Sine, and Leggio, Leila Lo

Subjects
Catalysis -- Analysis, Cellulose -- Chemical properties, Alcohol -- Chemical properties, Alcohol, Denatured -- Chemical properties, Glycosides -- Chemical properties, Hydrolases -- Chemical properties, Enzymes -- Chemical properties, Biological sciences, Chemistry
Abstract

The structural and functional studies on the enigmatic family of glycoside hydrolase 61 (GH61) that catalyze cellulose and hemicellulose hydrolysis are presented. The total protein loading required to hydrolyze lignocellulosic biomass could be reduced to 2-fold by incorporating the gene for one GH61 protein into a commercial Trichoderma reesei strain producing high levels of cellulolytic enzymes.

Published
2010

27. Amalgamation of Synthetic Biology and Chemistry for High-Throughput Nonconventional Synthesis of the Antimalarial Drug Artemisinin

Author

Singh, Dharmendra, primary, McPhee, Derek, additional, Paddon, Christopher J., additional, Cherry, Joel, additional, Maurya, Ghanshyam, additional, Mahale, Ganesh, additional, Patel, Yogesh, additional, Kumar, Neeraj, additional, Singh, Subhash, additional, Sharma, Brajesh, additional, Kushwaha, Lavkesh, additional, Singh, Satinder, additional, and Kumar, Ashok, additional

Published
2017
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28. Spectroscopic characterization of the Leu513His variant of fungal laccase: effect of increased axial ligand interactions on the geometric and electronic structure of the type 1Cu site

Author

Palmer, Amy E., Szilagyi, Robert K., Cherry, Joel R., Jones, Aubrey, Xu, Feng, and Solomon, Edward I.

Subjects
Chemistry, Inorganic -- Research, Inorganic compounds -- Composition, Spectrum analysis -- Usage, Ligands -- Composition, Copper compounds -- Composition, Density functionals -- Usage, Reactivity (Chemistry) -- Analysis, Chemistry
Abstract

Research has been conducted on Leu513His variant of type 1Cu site in Myceliophthora thermophila laccase. The authors have investigated the electronic structure of this variant via the use of spectroscopic techniques and density functional calculations, and have concluded that Cu site's electronic structure correlate with the reactivity differences of the green His variant of blue wild-type fungal laccase.

Published
2003

29. Erratum: Community crystal gazing

Author

Acharya, Anu, primary, Bingham, Kate, additional, Bradner, Jay, additional, Burke, Wylie, additional, Charo, R Alta, additional, Cherry, Joel, additional, Choulika, André, additional, Coles, Tony, additional, Cook-Deegan, Robert, additional, Crook, Stanley T, additional, Díaz, Emilia, additional, Erickson, Brent, additional, Giddings, L Val, additional, Giwa, Sebastian Eriksson, additional, Greenwood, James C, additional, Gulati, Vishal, additional, Hall, Sam, additional, Harris, John, additional, Heywood, Jamie, additional, Hill, Colin, additional, Levin, Jeremy, additional, Mangubat, Adina, additional, Maraganore, John, additional, Mariggi, Giovanni, additional, Mazur, Barbara J, additional, McGuire, Amy L, additional, Moll, Nathalie, additional, Moreno, Jonathan, additional, Naughton, Gail, additional, Nelsen, Lita, additional, Osbourn, Jane, additional, Perez, Daniel, additional, Reed, John, additional, Schmidt, Eric, additional, Seyfert-Margolis, Vicki, additional, Stoffels, Paul, additional, Thorball, Jørgen, additional, O'Toole, Tara, additional, Vainu, Indrek, additional, van Deventer, Sander, additional, Zerhouni, Elias, additional, and Zohar, Daphne, additional

Published
2016
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30. Community crystal gazing

Author

Acharya, Anu, primary, Bingham, Kate, additional, Bradner, Jay, additional, Burke, Wylie, additional, Charo, R Alta, additional, Cherry, Joel, additional, Choulika, André, additional, Coles, Tony, additional, Cook-Deegan, Robert, additional, Crooke, Stanley T, additional, Díaz, Emilia, additional, Erickson, Brent, additional, Giddings, L Val, additional, Giwa, Sebastian Eriksson, additional, Greenwood, James C, additional, Gulati, Vishal, additional, Hall, Sam, additional, Harris, John, additional, Heywood, Jamie, additional, Hill, Colin, additional, Levin, Jeremy, additional, Mangubat, Adina, additional, Maraganore, John, additional, Mariggi, Giovanni, additional, Mazur, Barbara J, additional, McGuire, Amy L, additional, Moll, Nathalie, additional, Moreno, Jonathan, additional, Naughton, Gail, additional, Nelsen, Lita, additional, Osbourn, Jane, additional, Perez, Daniel, additional, Reed, John, additional, Schmidt, Eric, additional, Seyfert-Margolis, Vicki, additional, Stoffels, Paul, additional, Thorball, Jørgen, additional, O'Toole, Tara, additional, Vainu, Indrek, additional, van Deventer, Sander, additional, Zerhouni, Elias, additional, and Zohar, Daphne, additional

Published
2016
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34. Stimulation of lignocellulosic biomass hydrolysis by proteins of glycoside hydrolase family 61: Structure and function of a large, enigmatic family

Author

Harris, Paul V, Welner, Ditte Hededam, McFarland, KC, Re, E, Poulsen, Jens-Christian Navarro, Brown, K, Salbo, Rune, Ding, H, Vlasenko, E, Marino, Sandy, Xu, F, Cherry, Joel, Larsen, Sine, Lo Leggio, Leila, Harris, Paul V, Welner, Ditte Hededam, McFarland, KC, Re, E, Poulsen, Jens-Christian Navarro, Brown, K, Salbo, Rune, Ding, H, Vlasenko, E, Marino, Sandy, Xu, F, Cherry, Joel, Larsen, Sine, and Lo Leggio, Leila

Published
2010

35. Use Cost Models to Guide R&D.

Author

BENJAMIN, KIRSTEN R., HILL, PAUL W., MEADOWS, ADAM L., SINGH, AMOOLYA H., and CHERRY, JOEL R.

Subjects
RESEARCH & development finance, COST, MATHEMATICAL models of economics, RESEARCH & development, COST control, INDUSTRIAL costs
Abstract

The article discusses the general recommendations and specific approaches used at Amyris Biotechnologies Inc., an integrated renewable products company, for the use of cost models to decision-making throughout research and development (R&D). It notes the creation of an R&D pipeline with predictable scale-down and scale-up fidelity. It also tackles the process of simplifying the cost model to emphasize major cost drivers that can be improved by strain and process changes.

Published
2016

40. Progress and Challenges in Enzyme Development for Biomass Utilization.

Author

Olsson, Lisbeth, Merino, Sandra T., and Cherry, Joel

Abstract

Enzymes play a critical role in the conversion of lignocellulosic waste into fuels and chemicals, but the high cost of these enzymes presents a significant barrier to commercialization. In the simplest terms, the cost is a function of the large amount of enzyme protein required to break down polymeric sugars in cellulose and hemicellulose to fermentable monomers. In the past 6 years, significant effort has been expended to reduce the cost by focusing on improving the efficiency of known enzymes, identification of new, more active enzymes, creating enzyme mixes optimized for selected pretreated substrates, and minimization of enzyme production costs. Here we describe advances in enzyme technology for use in the production of biofuels and the challenges that remain. [ABSTRACT FROM AUTHOR]

Published
2007
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43. Directed evolution of a fungal peroxidase

Author

Cherry, Joel R., primary, Lamsa, Michael H., additional, Schneider, Palle, additional, Vind, Jesper, additional, Svendsen, Allan, additional, Jones, Aubrey, additional, and Pedersen, Anders H., additional

Published
1999
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49. Introduction to Session 1B.

Author

McMillan, James D., Adney, William S., Mielenz, Jonathan R., Klasson, K. Thomas, Cherry, Joel R., and Gray, Kevin

Abstract

Enzymes are clearly recognized as a keystone technology for the production of fuels and chemicals from renewable feedstocks. Their specificity, performance under mild reaction conditions, and biodegradability make them ideally suited to widespread use in biorefineries around the world, and as the world puts greater and greater value on sustainable processes and environmentally friendly production methods, the further the development of enzyme technology grows in importance. This session focuses on the discovery, production, modification, and use of enzymes by bringing together 6 oral and 64 poster presentations describing the state of the art in enzyme technology. [ABSTRACT FROM AUTHOR]

Published
2006
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