@article{GrunzelPilarekSteinbruecketal.2014,
  author    = {Grunzel, Petra and Pilarek, Maciej and Steinbrueck, Doerte and Neubauer, Antje and Brand, Eva and Kumke, Michael Uwe and Neubauer, Peter and Krause, Mirja},
  title     = {Mini-scale cultivation method enables expeditious plasmid production in Escherichia coli},
  series = {Biotechnology journal : systems \& synthetic biology, nanobiotech, medicine},
  volume    = {9},
  journal   = {Biotechnology journal : systems \& synthetic biology, nanobiotech, medicine},
  number    = {1},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1860-6768},
  doi       = {10.1002/biot.201300177},
  pages     = {128 -- 136},
  year      = {2014},
  abstract  = {The standard procedure in the lab for plasmid isolation usually involves a 2-mL, 16 h over-night cultivation in 15-mL bioreaction tubes in LB medium. This is time consuming, and not suitable for high-throughput applications. This study shows that it is possible to produce plasmid DNA (pDNA) in a 1.5-mL microcentrifuge tube with only 100 L cultivation volume in less than 7 h with a simple protocol. Compared with the standard LB cultivation for pDNA production reaching a final pDNA concentration range of 1.5-4 mu g mL(-1), a 6- to 10-fold increase in plasmid concentration (from 10 up to 25 mu g mL(-1) cultivation volume) is achieved using an optimized medium with an internal substrate delivery system (EnBase (R)). Different strains, plasmids, and the applicability of different inoculation tools (i.e. different starting ODs) were compared, demonstrating the robustness of the system. Additionally, dissolved oxygen was monitored in real time online, indicating that under optimized conditions oxygen limitation can be avoided. We developed a simple protocol with a significantly decreased procedure time, enabling simultaneous handling of more samples, while a consistent quality and a higher final pDNA concentration are ensured.},
  language  = {en}
}
@book{BerndtNeubauerParnow1994,
  author    = {Berndt, Klaus-Peter and Neubauer, Manfred and Parnow, Klaus},
  title     = {Videos zur Umweltbildung : Teil 1 Biotope aus 2. Hand : Der Torstich ; Fr{\"u}hjahrsbl{\"u}her. Biochorin : Der Baumstumpf ; [Begleitheft]},
  publisher = {Univ.},
  address   = {Potsdam},
  pages     = {32 S.},
  year      = {1994},
  language  = {de}
}
@misc{BerndtNeubauerParnow1994,
  author    = {Berndt, Klaus-Peter and Neubauer, Manfred and Parnow, Klaus},
  title     = {Videos zur Umweltbildung : Teil 2 Pflanzen am Wasser ; [Videokasette]},
  publisher = {Univ.},
  address   = {Potsdam},
  year      = {1994},
  language  = {de}
}
@misc{BerndtNeubauerParnow1994,
  author    = {Berndt, Klaus-Peter and Neubauer, Manfred and Parnow, Klaus},
  title     = {Videos zur Umweltbildung : Teil 2 Pflanzen am Wasser ; [Begleitheft]},
  publisher = {Univ.},
  address   = {Potsdam},
  pages     = {51 S.},
  year      = {1994},
  language  = {de}
}
@misc{BerndtNeubauerParnow1994,
  author    = {Berndt, Klaus-Peter and Neubauer, Manfred and Parnow, Klaus},
  title     = {Videos zur Umweltbildung : Teil 1 Biotope aus 2. Hand : Der Torstich ; Fr{\"u}hjahrsbl{\"u}her. Biochorin : Der Baumstumpf ; [Videokasette]},
  publisher = {Univ.},
  address   = {Potsdam},
  year      = {1994},
  language  = {de}
}
@article{AvcilarKucukgozeBartholomaeusVarelaetal.2016,
  author    = {Avcilar-Kucukgoze, Irem and Bartholom{\"a}us, Alexander and Varela, Juan A. Cordero and Kaml, Robert Franz-Xaver and Neubauer, Peter and Budisa, Nediljko and Ignatova, Zoya},
  title     = {Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli},
  series = {Nucleic acids research},
  volume    = {44},
  journal   = {Nucleic acids research},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0305-1048},
  doi       = {10.1093/nar/gkw697},
  pages     = {8324 -- 8334},
  year      = {2016},
  abstract  = {Translation is a central cellular process and is optimized for speed and fidelity. The speed of translation of a single codon depends on the concentration of aminoacyl-tRNAs. Here, we used microarray-based approaches to analyze the charging levels of tRNAs in Escherichia coli growing at different growth rates. Strikingly, we observed a non-uniform aminoacylation of tRNAs in complex media. In contrast, in minimal medium, the level of aminoacyl-tRNAs is more uniform and rises to approximately 60\%. Particularly, the charging level of tRNA(Ser), tRNA(Cys), tRNA(Thr) and tRNA(His) is below 50\% in complex medium and their aminoacylation levels mirror the degree that amino acids inhibit growth when individually added to minimal medium. Serine is among the most toxic amino acids for bacteria and tRNAs(Ser) exhibit the lowest charging levels, below 10\%, at high growth rate although intracellular serine concentration is plentiful. As a result some serine codons are among the most slowly translated codons. A large fraction of the serine is most likely degraded by L-serine-deaminase, which competes with the seryl-tRNA-synthetase that charges the tRNAs(Ser). These results indicate that the level of aminoacylation in complex media might be a competition between charging for translation and degradation of amino acids that inhibit growth.},
  language  = {en}
}
@article{MasigolKhodaparastMostowfizadehGhalamfarsaetal.2020,
  author    = {Masigol, Hossein and Khodaparast, Seyed Akbar and Mostowfizadeh-Ghalamfarsa, Reza and Rojas-Jimenez, Keilor and Woodhouse, Jason Nicholas and Neubauer, Darshan and Grossart, Hans-Peter},
  title     = {Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran},
  series = {Aquatic Ecology},
  volume    = {54},
  journal   = {Aquatic Ecology},
  number    = {1},
  publisher = {Springer Science},
  address   = {Dordrecht},
  issn      = {1573-5125},
  doi       = {10.1007/s10452-019-09745-w},
  pages     = {323 -- 336},
  year      = {2020},
  abstract  = {Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50\% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems.},
  language  = {en}
}
@misc{MasigolKhodaparastMostowfizadehGhalamfarsaetal.2020,
  author    = {Masigol, Hossein and Khodaparast, Seyed Akbar and Mostowfizadeh-Ghalamfarsa, Reza and Rojas-Jimenez, Keilor and Woodhouse, Jason Nicholas and Neubauer, Darshan and Grossart, Hans-Peter},
  title     = {Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran},
  series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {1},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-51582},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-515820},
  pages     = {16},
  year      = {2020},
  abstract  = {Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50\% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems.},
  language  = {en}
}
@article{MasigolKhodaparastWoodhouseetal.2019,
  author    = {Masigol, Hossein and Khodaparast, Seyed Akbar and Woodhouse, Jason Nicholas and Rojas Jim{\´e}nez, Keilor and Fonvielle, Jeremy Andre and Rezakhani, Forough and Mostowfizadeh-Ghalamfarsa, Reza and Neubauer, Darshan and Goldhammer, Tobias and Grossart, Hans-Peter},
  title     = {The contrasting roles of aquatic fungi and oomycetes in the degradation and transformation of polymeric organic matter},
  series = {Limnology and oceanography},
  volume    = {64},
  journal   = {Limnology and oceanography},
  number    = {6},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0024-3590},
  pages     = {2662 -- 2678},
  year      = {2019},
  abstract  = {Studies on the ecological role of fungi and, to a lesser extent, oomycetes, are receiving increasing attention, mainly due to their participation in the cycling of organic matter in aquatic ecosystems. To unravel their importance in humification processes, we isolated several strains of fungi and oomycetes from Anzali lagoon, Iran. We then performed taxonomic characterization by morphological and molecular methods, analyzed the ability to degrade several polymeric substrates, performed metabolic fingerprinting with Ecoplates, and determined the degradation of humic substances (HS) using liquid chromatography-organic carbon detection. Our analyses highlighted the capacity of aquatic fungi to better degrade a plethora of organic molecules, including complex polymers. Specifically, we were able to demonstrate not only the utilization of these complex polymers, but also the role of fungi in the production of HS. In contrast, oomycetes, despite some morphological and physiological similarities with aquatic fungi, exhibited a propensity toward opportunism, quickly benefitting from the availability of small organic molecules, while exhibiting sensitivity toward more complex polymers. Despite their contrasting roles, our study highlights the importance of both oomycetes and fungi in aquatic organic matter transformation and cycling with potential implications for the global carbon cycle.},
  language  = {en}
}
@article{GutschmannSimoesSchieweetal.2022,
  author    = {Gutschmann, Bj{\"o}rn and Sim{\~o}es, Matilde Maldonado and Schiewe, Thomas and Schr{\"o}ter, Edith S. and M{\"u}nzberg, Marvin and Neubauer, Peter and Bockisch, Anika and Riedel, Sebastian Lothar Stefan},
  title     = {Continuous feeding strategy for polyhydroxyalkanoate production from solid waste animal fat at laboratory- and pilot-scale},
  series = {Microbial biotechnology / Society for Applied Microbiology},
  journal   = {Microbial biotechnology / Society for Applied Microbiology},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {1751-7915},
  doi       = {10.1111/1751-7915.14104},
  pages     = {12},
  year      = {2022},
  abstract  = {Bioconversion of waste animal fat (WAF) to polyhydroxyalkanoates (PHAs) is an approach to lower the production costs of these plastic alternatives. However, the solid nature of WAF requires a tailor-made process development. In this study, a double-jacket feeding system was built to thermally liquefy the WAF to employ a continuous feeding strategy. During laboratory-scale cultivations with Ralstonia eutropha Re2058/pCB113, 70\% more PHA (45 g(PHA) L-1) and a 75\% higher space-time yield (0.63 g(PHA) L-1 h(-1)) were achieved compared to previously reported fermentations with solid WAF. During the development process, growth and PHA formation were monitored in real-time by in-line photon density wave spectroscopy. The process robustness was further evaluated during scale-down fermentations employing an oscillating aeration, which did not alter the PHA yield although cells encountered periods of oxygen limitation. Flow cytometry with propidium iodide staining showed that more than two-thirds of the cells were viable at the end of the cultivation and viability was even little higher in the scale-down cultivations. Application of this feeding system at 150-L pilot-scale cultivation yielded in 31.5 g(PHA) L-1, which is a promising result for the further scale-up to industrial scale.},
  language  = {en}
}