TY  - JOUR
A1  - Grunzel, Petra
A1  - Pilarek, Maciej
A1  - Steinbrueck, Doerte
A1  - Neubauer, Antje
A1  - Brand, Eva
A1  - Kumke, Michael Uwe
A1  - Neubauer, Peter
A1  - Krause, Mirja
T1  - Mini-scale cultivation method enables expeditious plasmid production in Escherichia coli
JF  - Biotechnology journal : systems & synthetic biology, nanobiotech, medicine
N2  - 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.
KW  - Escherichia coli
KW  - High-cell-density culture
KW  - Miniaturized cultivations
KW  - Optical oxygen sensor
KW  - Plasmid DNA production
Y1  - 2014
U6  - https://doi.org/10.1002/biot.201300177
SN  - 1860-6768
SN  - 1860-7314
VL  - 9
IS  - 1
SP  - 128
EP  - 136
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - BOOK
A1  - Berndt, Klaus-Peter
A1  - Neubauer, Manfred
A1  - Parnow, Klaus
T1  - Videos zur Umweltbildung : Teil 1 Biotope aus 2. Hand : Der Torstich ; Frühjahrsblüher. Biochorin : Der Baumstumpf ; [Begleitheft]
Y1  - 1994
PB  - Univ.
CY  - Potsdam
ER  - 
TY  - GEN
A1  - Berndt, Klaus-Peter
A1  - Neubauer, Manfred
A1  - Parnow, Klaus
T1  - Videos zur Umweltbildung : Teil 2 Pflanzen am Wasser ; [Videokasette]
Y1  - 1994
PB  - Univ.
CY  - Potsdam
ER  - 
TY  - GEN
A1  - Berndt, Klaus-Peter
A1  - Neubauer, Manfred
A1  - Parnow, Klaus
T1  - Videos zur Umweltbildung : Teil 2 Pflanzen am Wasser ; [Begleitheft]
Y1  - 1994
PB  - Univ.
CY  - Potsdam
ER  - 
TY  - GEN
A1  - Berndt, Klaus-Peter
A1  - Neubauer, Manfred
A1  - Parnow, Klaus
T1  - Videos zur Umweltbildung : Teil 1 Biotope aus 2. Hand : Der Torstich ; Frühjahrsblüher. Biochorin : Der Baumstumpf ; [Videokasette]
Y1  - 1994
PB  - Univ.
CY  - Potsdam
ER  - 
TY  - JOUR
A1  - Gutschmann, Björn
A1  - Simões, Matilde Maldonado
A1  - Schiewe, Thomas
A1  - Schröter, Edith S.
A1  - Münzberg, Marvin
A1  - Neubauer, Peter
A1  - Bockisch, Anika
A1  - Riedel, Sebastian Lothar Stefan
T1  - Continuous feeding strategy for polyhydroxyalkanoate production from solid waste animal fat at laboratory- and pilot-scale
JF  - Microbial biotechnology / Society for Applied Microbiology
N2  - 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.
Y1  - 2022
U6  - https://doi.org/10.1111/1751-7915.14104
SN  - 1751-7915
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Avcilar-Kucukgoze, Irem
A1  - Bartholomäus, Alexander
A1  - Varela, Juan A. Cordero
A1  - Kaml, Robert Franz-Xaver
A1  - Neubauer, Peter
A1  - Budisa, Nediljko
A1  - Ignatova, Zoya
T1  - Discharging tRNAs: a tug of war between translation and detoxification in Escherichia coli
JF  - Nucleic acids research
N2  - 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.
Y1  - 2016
U6  - https://doi.org/10.1093/nar/gkw697
SN  - 0305-1048
SN  - 1362-4962
VL  - 44
SP  - 8324
EP  - 8334
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Masigol, Hossein
A1  - Khodaparast, Seyed Akbar
A1  - Mostowfizadeh-Ghalamfarsa, Reza
A1  - Rojas-Jimenez, Keilor
A1  - Woodhouse, Jason Nicholas
A1  - Neubauer, Darshan
A1  - Grossart, Hans-Peter
T1  - Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran
JF  - Aquatic Ecology
N2  - 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.
KW  - Achlya
KW  - Saprolegnia
KW  - aquatic ecosystems
KW  - carbon cycling
KW  - polymer degradation
KW  - Saprolegniaceae
KW  - Achlyaceae
Y1  - 2020
U6  - https://doi.org/10.1007/s10452-019-09745-w
SN  - 1573-5125
SN  - 1386-2588
VL  - 54
IS  - 1
SP  - 323
EP  - 336
PB  - Springer Science
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Masigol, Hossein
A1  - Khodaparast, Seyed Akbar
A1  - Woodhouse, Jason Nicholas
A1  - Rojas Jiménez, Keilor
A1  - Fonvielle, Jeremy Andre
A1  - Rezakhani, Forough
A1  - Mostowfizadeh-Ghalamfarsa, Reza
A1  - Neubauer, Darshan
A1  - Goldhammer, Tobias
A1  - Grossart, Hans-Peter
T1  - The contrasting roles of aquatic fungi and oomycetes in the degradation and transformation of polymeric organic matter
JF  - Limnology and oceanography
N2  - 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.
Y1  - 2019
SN  - 0024-3590
SN  - 1939-5590
VL  - 64
IS  - 6
SP  - 2662
EP  - 2678
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - GEN
A1  - Masigol, Hossein
A1  - Khodaparast, Seyed Akbar
A1  - Mostowfizadeh-Ghalamfarsa, Reza
A1  - Rojas-Jimenez, Keilor
A1  - Woodhouse, Jason Nicholas
A1  - Neubauer, Darshan
A1  - Grossart, Hans-Peter
T1  - Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran
T2  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - 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.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 1395 
KW  - Achlya
KW  - Saprolegnia
KW  - aquatic ecosystems
KW  - carbon cycling
KW  - polymer degradation
KW  - Saprolegniaceae
KW  - Achlyaceae
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-515820
SN  - 1866-8372
IS  - 1
ER  -