Browsing by Subject "ACCURATE MASS"

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  • Daly, Paul; Peng, Mao; Mitchell, Hugh D.; Kim, Young-Mo; Ansong, Charles; Brewer, Heather; de Gijsel, Peter; Lipton, Mary S.; Markillie, Lye Meng; Nicora, Carrie D.; Orr, Galya; Wiebenga, Ad; Hilden, Kristiina S.; Kabel, Mirjam A.; Baker, Scott E.; Makela, Miia R.; de Vries, Ronald P. (2020)
    Saprobic fungi, such as Aspergillus niger, grow as colonies consisting of a network of branching and fusing hyphae that are often considered to be relatively uniform entities in which nutrients can freely move through the hyphae. In nature, different parts of a colony are often exposed to different nutrients. We have investigated, using a multi-omics approach, adaptation of A. niger colonies to spatially separated and compositionally different plant biomass substrates. This demonstrated a high level of intra-colony differentiation, which closely matched the locally available substrate. The part of the colony exposed to pectin-rich sugar beet pulp and to xylan-rich wheat bran showed high pectinolytic and high xylanolytic transcript and protein levels respectively. This study therefore exemplifies the high ability of fungal colonies to differentiate and adapt to local conditions, ensuring efficient use of the available nutrients, rather than maintaining a uniform physiology throughout the colony.
  • Daly, Paul; Lopez, Sara Casado; Peng, Mao; Lancefield, Christopher S.; Purvine, Samuel O.; Kim, Young-Mo; Zink, Erika M.; Dohnalkova, Alice; Singan, Vasanth R.; Lipzen, Anna; Dilworth, David; Wang, Mei; Ng, Vivian; Robinson, Errol; Orr, Galya; Baker, Scott E.; Bruijnincx, Pieter C. A.; Hilden, Kristiina S.; Grigoriev, Igor V.; Mäkelä, Miia R.; de Vries, Ronald P. (2018)
    White-rot fungi, such as Dichomitus squalens, degrade all wood components and inhabit mixed-wood forests containing both soft- and hardwood species. In this study, we evaluated how D. squalens responded to the compositional differences in softwood [guaiacyl (G) lignin and higher mannan content] and hardwood [syringyl/guaiacyl (S/G) lignin and higher xylan content] using semi-natural solid cultures. Spruce (softwood) and birch (hardwood) sticks were degraded by D. squalens as measured by oxidation of the lignins using 2D-NMR. The fungal response as measured by transcriptomics, proteomics and enzyme activities showed a partial tailoring to wood composition. Mannanolytic transcripts and proteins were more abundant in spruce cultures, while a proportionally higher xylanolytic activity was detected in birch cultures. Both wood types induced manganese peroxidases to a much higher level than laccases, but higher transcript and protein levels of the manganese peroxidases were observed on the G-lignin rich spruce. Overall, the molecular responses demonstrated a stronger adaptation to the spruce rather than birch composition, possibly because D. squalens is mainly found degrading softwoods in nature, which supports the ability of the solid wood cultures to reflect the natural environment.