Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis

Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis

Summary: Exophiala dermatitidis is a polyextremotolerant fungus with a small genome, thus suitable as a model system for melanogenesis and carotenogensis. A genome-scale model, iEde2091, is reconstructed to increase metabolic understanding and used in a shadow price analysis of pigments, as detailed...

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Main Authors: Wheaton L. Schroeder, Rajib Saha
Format: Article
Language:English
Published: Elsevier 2020-09-01
Series:STAR Protocols
Online Access:http://www.sciencedirect.com/science/article/pii/S2666166720300927
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spelling doaj-3c4d1074e3ae4d6c9dd9fac6f5fa594d2020-11-25T04:09:05ZengElsevierSTAR Protocols2666-16672020-09-0112100105Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidisWheaton L. Schroeder0Rajib Saha1Department of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68526, USA; Corresponding authorDepartment of Chemical and Biomolecular Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska 68526, USA; Corresponding authorSummary: Exophiala dermatitidis is a polyextremotolerant fungus with a small genome, thus suitable as a model system for melanogenesis and carotenogensis. A genome-scale model, iEde2091, is reconstructed to increase metabolic understanding and used in a shadow price analysis of pigments, as detailed here. Important to this reconstruction is OptFill, a recently developed alternative gap-filling method useful in the holistic and conservative reconstruction of genome-scale models of metabolism, particularly for understudied organisms like E. dermatitidis where gaps in metabolic knowledge are abundant.For complete details on the use and execution of this protocol, please refer to Schroeder and Saha (2020) and Schroeder et al. (2020).http://www.sciencedirect.com/science/article/pii/S2666166720300927
collection DOAJ
language English
format Article
sources DOAJ
author Wheaton L. Schroeder
Rajib Saha
spellingShingle Wheaton L. Schroeder
Rajib Saha
Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis
STAR Protocols
author_facet Wheaton L. Schroeder
Rajib Saha
author_sort Wheaton L. Schroeder
title Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis
title_short Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis
title_full Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis
title_fullStr Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis
title_full_unstemmed Protocol for Genome-Scale Reconstruction and Melanogenesis Analysis of Exophiala dermatitidis
title_sort protocol for genome-scale reconstruction and melanogenesis analysis of exophiala dermatitidis
publisher Elsevier
series STAR Protocols
issn 2666-1667
publishDate 2020-09-01
description Summary: Exophiala dermatitidis is a polyextremotolerant fungus with a small genome, thus suitable as a model system for melanogenesis and carotenogensis. A genome-scale model, iEde2091, is reconstructed to increase metabolic understanding and used in a shadow price analysis of pigments, as detailed here. Important to this reconstruction is OptFill, a recently developed alternative gap-filling method useful in the holistic and conservative reconstruction of genome-scale models of metabolism, particularly for understudied organisms like E. dermatitidis where gaps in metabolic knowledge are abundant.For complete details on the use and execution of this protocol, please refer to Schroeder and Saha (2020) and Schroeder et al. (2020).
url http://www.sciencedirect.com/science/article/pii/S2666166720300927
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