TY  - GEN
A1  - Hoffmann, Stefan A.
A1  - Wohltat, Christian
A1  - Müller, Kristian M.
A1  - Arndt, Katja Maren
T1  - A user-friendly, low-cost turbidostat with versatile growth rate estimation based on an extended Kalman filter
N2  - For various experimental applications, microbial cultures at defined, constant densities are highly advantageous over simple batch cultures. Due to high costs, however, devices for continuous culture at freely defined densities still experience limited use. We have developed a small-scale turbidostat for research purposes, which is manufactured from inexpensive components and 3D printed parts. A high degree of spatial system integration and a graphical user interface provide user-friendly operability. The used optical density feedback control allows for constant continuous culture at a wide range of densities and offers to vary culture volume and dilution rates without additional parametrization. Further, a recursive algorithm for on-line growth rate estimation has been implemented. The employed Kalman filtering approach based on a very general state model retains the flexibility of the used control type and can be easily adapted to other bioreactor designs. Within several minutes it can converge to robust, accurate growth rate estimates. This is particularly useful for directed evolution experiments or studies on metabolic challenges, as it allows direct monitoring of the population fitness.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 390 
Y1  - 2017
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-403406
ER  - 
TY  - GEN
A1  - Azuma, Yusuke
A1  - Kükenshöner, Tim
A1  - Ma, Guangyong
A1  - Yasunaga, Jun-ichiro
A1  - Imanishi, Miki
A1  - Tanaka, Gen
A1  - Nakase, Ikuhiko
A1  - Maruno, Takahiro
A1  - Kobayashi, Yuji
A1  - Arndt, Katja Maren
A1  - Matsuoka, Masao
A1  - Futaki, Shiroh
T1  - Controlling leucine-zipper partner recognition in cells through modification of a–g interactions
N2  - By focusing on the a–g interactions, successful design and selection were accomplished to obtain a leucine-zipper segment that discriminates the appropriate partner over another that provides very similar patterns of electrostatic interactions.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 276 
Y1  - 2016
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-98758
ER  - 
TY  - GEN
A1  - Baumann, Tobias
A1  - Arndt, Katja Maren
A1  - Müller, Kristian M.
T1  - Directional cloning of DNA fragments using deoxyinosine-containing oligonucleotides and endonuclease V
T2  - Postprints der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe
N2  - Background: DNA fragments carrying internal recognition sites for the restriction endonucleases intended for cloning into a target plasmid pose a challenge for conventional cloning.

Results: A method for directional insertion of DNA fragments into plasmid vectors has been developed. The target sequence is amplified from a template DNA sample by PCR using two oligonucleotides each containing a single deoxyinosine base at the third position from the 5' end. Treatment of such PCR products with endonuclease V generates 3' protruding ends suitable for ligation with vector fragments created by conventional restriction endonuclease reactions.

Conclusions: The developed approach generates terminal cohesive ends without the use of Type II restriction endonucleases, and is thus independent from the DNA sequence. Due to PCR amplification, minimal amounts of template DNA are required. Using the robust Taq enzyme or a proofreading Pfu DNA polymerase mutant, the method is applicable to a broad range of insert sequences. Appropriate primer design enables direct incorporation of terminal DNA sequence modifications such as tag addition, insertions, deletions and mutations into the cloning strategy. Further, the restriction sites of the target plasmid can be either retained or removed.
T3  - Zweitveröffentlichungen der Universität Potsdam : Mathematisch-Naturwissenschaftliche Reihe - 983 
KW  - cohesive ends
KW  - DNA cleavage
KW  - genetic vectors
KW  - modified primers
KW  - molecular methods
KW  - polymerase chain reaction
KW  - recombinant Escherichia coli
KW  - restriction enzymes
Y1  - 2020
U6  - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:517-opus4-431085
SN  - 1866-8372
IS  - 983
ER  -