TY - JOUR A1 - Hoffmann, Stefan A. A1 - Hao, Nan A1 - Shearwin, Keith E. A1 - Arndt, Katja Maren T1 - Characterizing transcriptional interference between converging genes in bacteria JF - ACS synthetic biology N2 - Antisense transcription is common in naturally occurring genomes and is increasingly being used in synthetic genetic circuitry as a tool for gene expression control. Mutual influence on the expression of convergent genes can be mediated by antisense RNA effects and by transcriptional interference (TI). We aimed to quantitatively characterize long-range TI between convergent genes with untranslated intergenic spacers of increasing length. After controlling for antisense RNA-mediated effects, which contributed about half of the observed total expression inhibition, the TI effect was modeled. To achieve model convergence, RNA polymerase processivity and collision resistance were assumed to be modulated by ribosome trailing. The spontaneous transcription termination rate in regions of untranslated DNA was experimentally determined. Our modeling suggests that an elongating RNA polymerase with a trailing ribosome is about 13 times more likely to resume transcription than an opposing RNA polymerase without a trailing ribosome, upon head-on collision of the two. KW - gene regulation KW - antisense transcription KW - transcriptional interference KW - mathematical modeling KW - Escherichia coli Y1 - 2019 U6 - https://doi.org/10.1021/acssynbio.8b00477 SN - 2161-5063 VL - 8 IS - 3 SP - 466 EP - 473 PB - American Chemical Society CY - Washington ER - TY - JOUR A1 - Hoffmann, Bernd A1 - Kahmen, Ansgar A1 - Cernusak, Lucas A. A1 - Arndt, Stefan K. A1 - Sachse, Dirk T1 - Abundance and distribution of leaf wax n-alkanes in leaves of Acacia and Eucalyptus trees along a strong humidity gradient in northern Australia JF - Organic geochemistry : the international journal for rapid publication of current research in organic geochemistry and biochemistry N2 - Environmental parameters such as rainfall, temperature and relative humidity can affect the composition of higher plant leaf wax. The abundance and distribution of leaf wax biomarkers, such as long chain n-alkanes, in sedimentary archives have therefore been proposed as proxies reflecting climate change. However, a robust palaeoclimatic interpretation requires a thorough understanding of how environmental changes affect leaf wax n-alkane distributions in living plants. We have analysed the concentration and chain length distribution of leaf wax n-alkanes in Acacia and Eucalyptus species along a 1500 km climatic gradient in northern Australia that ranges from subtropical to arid. We show that aridity affected the concentration and distribution of n-alkanes for plants in both genera. For both Acacia and Eucalyptus n-alkane concentration increased by a factor of ten to the dry centre of Australia, reflecting the purpose of the wax in preventing water loss from the leaf. Furthermore, Acacian-alkanes decreased in average chain length (ACL) towards the arid centre of Australia, whereas Eucalyptus ACL increased under arid conditions. Our observations demonstrate that n-alkane concentration and distribution in leaf wax are sensitive to hydroclimatic conditions. These parameters could therefore potentially be employed in palaeorecords to estimate past environmental change. However, our finding of a distinct response of n-alkane ACL values to hydrological changes in different taxa also implies that the often assumed increase in ACL under drier conditions is not a robust feature for all plant species and genera and as such additional information about the prevalent vegetation are required when ACL values are used as a palaeoclimate proxy. Y1 - 2013 U6 - https://doi.org/10.1016/j.orggeochem.2013.07.003 SN - 0146-6380 VL - 62 IS - 9 SP - 62 EP - 67 PB - Elsevier CY - Oxford ER - TY - JOUR A1 - Mazumder, Mostafizur A1 - Brechun, Katherine E. A1 - Kim, Yongjoo B. A1 - Hoffmann, Stefan A. A1 - Chen, Yih Yang A1 - Keiski, Carrie-Lynn A1 - Arndt, Katja Maren A1 - McMillen, David R. A1 - Woolley, G. Andrew T1 - An Escherichia coli system for evolving improved light-controlled DNA-binding proteins JF - Protein engineering design & selection N2 - Light-switchable proteins offer numerous opportunities as tools for manipulating biological systems with exceptional degrees of spatiotemporal control. Most designed light-switchable proteins currently in use have not been optimised using the randomisation and selection/screening approaches that are widely used in other areas of protein engineering. Here we report an approach for screening light-switchable DNA-binding proteins that relies on light-dependent repression of the transcription of a fluorescent reporter. We demonstrate that the method can be used to recover a known light-switchable DNA-binding protein from a random library. KW - directed evolution KW - fluorescent reporter KW - optogenetics Y1 - 2015 U6 - https://doi.org/10.1093/protein/gzv033 SN - 1741-0126 SN - 1741-0134 VL - 28 IS - 9 SP - 293 EP - 302 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Hoffmann, Stefan A. A1 - Kruse, Sabrina M. A1 - Arndt, Katja Maren T1 - Long-range transcriptional interference in E-coli used to construct a dual positive selection system for genetic switches JF - Nucleic acids research N2 - We have investigated transcriptional interference between convergent genes in E. coli and demonstrate substantial interference for inter-promoter distances of as far as 3 kb. Interference can be elicited by both strong σ70 dependent and T7 promoters. In the presented design, a strong promoter driving gene expression of a ‘forward’ gene interferes with the expression of a ‘reverse’ gene by a weak promoter. This arrangement allows inversely correlated gene expression without requiring further regulatory components. Thus, modulation of the activity of the strong promoter alters expression of both the forward and the reverse gene. We used this design to develop a dual selection system for conditional operator site binding, allowing positive selection both for binding and for non-binding to DNA. This study demonstrates the utility of this novel system using the Lac repressor as a model protein for conditional DNA binding, and spectinomycin and chloramphenicol resistance genes as positive selection markers in liquid culture. Randomized LacI libraries were created and subjected to subsequent dual selection, but mispairing IPTG and selection cues in respect to the wild-type LacI response, allowing the isolation of a LacI variant with a reversed IPTG response within three rounds of library generation and dual selection. Y1 - 2016 U6 - https://doi.org/10.1093/nar/gkw125 SN - 0305-1048 SN - 1362-4962 VL - 44 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR 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 JF - PLoS one 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. Y1 - 2017 U6 - https://doi.org/10.1371/JOURNAL.PONE.0181923 SN - 1932-6203 VL - 12 IS - 7 SP - 1 EP - 15 PB - PLoS CY - Lawrence, Kan. ER - 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 - JOUR A1 - Hoffmann, Stefan A. A1 - Wohltat, Christian A1 - Mueller, Kristian M. A1 - Arndt, Katja Maren T1 - A user-friendly, low-cost turbidostat with versatile growth rate estimation based on an extended Kalman filter JF - PLoS one 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. Y1 - 2017 U6 - https://doi.org/10.1371/journal.pone.0181923 SN - 1932-6203 VL - 12 SP - 5944 EP - 5952 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Weber, Michael H. A1 - Abu-Ayyash, Khalil A1 - Abueladas, Abdel-Rahman A1 - Agnon, Amotz A1 - Alasonati-Tašárová, Zuzana A1 - Al-Zubi, Hashim A1 - Babeyko, Andrey A1 - Bartov, Yuval A1 - Bauer, Klaus A1 - Becken, Michael A1 - Bedrosian, Paul A. A1 - Ben-Avraham, Zvi A1 - Bock, Günter A1 - Bohnhoff, Marco A1 - Bribach, Jens A1 - Dulski, Peter A1 - Ebbing, Joerg A1 - El-Kelani, Radwan J. A1 - Foerster, Andrea A1 - Förster, Hans-Jürgen A1 - Frieslander, Uri A1 - Garfunkel, Zvi A1 - Götze, Hans-Jürgen A1 - Haak, Volker A1 - Haberland, Christian A1 - Hassouneh, Mohammed A1 - Helwig, Stefan L. A1 - Hofstetter, Alfons A1 - Hoffmann-Rothe, Arne A1 - Jaeckel, Karl-Heinz A1 - Janssen, Christoph A1 - Jaser, Darweesh A1 - Kesten, Dagmar A1 - Khatib, Mohammed Ghiath A1 - Kind, Rainer A1 - Koch, Olaf A1 - Koulakov, Ivan A1 - Laske, Maria Gabi A1 - Maercklin, Nils T1 - Anatomy of the Dead Sea transform from lithospheric to microscopic scale N2 - Fault zones are the locations where motion of tectonic plates, often associated with earthquakes, is accommodated. Despite a rapid increase in the understanding of faults in the last decades, our knowledge of their geometry, petrophysical properties, and controlling processes remains incomplete. The central questions addressed here in our study of the Dead Sea Transform (DST) in the Middle East are as follows: (1) What are the structure and kinematics of a large fault zone? (2) What controls its structure and kinematics? (3) How does the DST compare to other plate boundary fault zones? The DST has accommodated a total of 105 km of left-lateral transform motion between the African and Arabian plates since early Miocene (similar to 20 Ma). The DST segment between the Dead Sea and the Red Sea, called the Arava/Araba Fault (AF), is studied here using a multidisciplinary and multiscale approach from the mu m to the plate tectonic scale. We observe that under the DST a narrow, subvertical zone cuts through crust and lithosphere. First, from west to east the crustal thickness increases smoothly from 26 to 39 km, and a subhorizontal lower crustal reflector is detected east of the AF. Second, several faults exist in the upper crust in a 40 km wide zone centered on the AF, but none have kilometer-size zones of decreased seismic velocities or zones of high electrical conductivities in the upper crust expected for large damage zones. Third, the AF is the main branch of the DST system, even though it has accommodated only a part (up to 60 km) of the overall 105 km of sinistral plate motion. Fourth, the AF acts as a barrier to fluids to a depth of 4 km, and the lithology changes abruptly across it. Fifth, in the top few hundred meters of the AF a locally transpressional regime is observed in a 100-300 m wide zone of deformed and displaced material, bordered by subparallel faults forming a positive flower structure. Other segments of the AF have a transtensional character with small pull-aparts along them. The damage zones of the individual faults are only 5-20 m wide at this depth range. Sixth, two areas on the AF show mesoscale to microscale faulting and veining in limestone sequences with faulting depths between 2 and 5 km. Seventh, fluids in the AF are carried downward into the fault zone. Only a minor fraction of fluids is derived from ascending hydrothermal fluids. However, we found that on the kilometer scale the AF does not act as an important fluid conduit. Most of these findings are corroborated using thermomechanical modeling where shear deformation in the upper crust is localized in one or two major faults; at larger depth, shear deformation occurs in a 20-40 km wide zone with a mechanically weak decoupling zone extending subvertically through the entire lithosphere. Y1 - 2009 UR - http://www.agu.org/journals/rg/ U6 - https://doi.org/10.1029/2008rg000264 SN - 8755-1209 ER - TY - JOUR A1 - Jay, Raphael M. A1 - Norell, Jesper A1 - Eckert, Sebastian A1 - Hantschmann, Markus A1 - Beye, Martin A1 - Kennedy, Brian A1 - Quevedo, Wilson A1 - Schlotter, William F. A1 - Dakovski, Georgi L. A1 - Minitti, Michael P. A1 - Hoffmann, Matthias C. A1 - Mitra, Ankush A1 - Moeller, Stefan P. A1 - Nordlund, Dennis A1 - Zhang, Wenkai A1 - Liang, Huiyang W. A1 - Kunnus, Kristian A1 - Kubicek, Katharina A1 - Techert, Simone A. A1 - Lundberg, Marcus A1 - Wernet, Philippe A1 - Gaffney, Kelly A1 - Odelius, Michael A1 - Föhlisch, Alexander T1 - Disentangling Transient Charge Density and Metal-Ligand Covalency in Photoexcited Ferricyanide with Femtosecond Resonant Inelastic Soft X-ray Scattering JF - The journal of physical chemistry letters N2 - Soft X-ray spectroscopies are ideal probes of the local valence electronic structure of photocatalytically active metal sites. Here, we apply the selectivity of time resolved resonant inelastic X-ray scattering at the iron L-edge to the transient charge distribution of an optically excited charge-transfer state in aqueous ferricyanide. Through comparison to steady-state spectra and quantum chemical calculations, the coupled effects of valence-shell closing and ligand-hole creation are experimentally and theoretically disentangled and described in terms of orbital occupancy, metal-ligand covalency, and ligand field splitting, thereby extending established steady-state concepts to the excited-state domain. pi-Back-donation is found to be mainly determined by the metal site occupation, whereas the ligand hole instead influences sigma-donation. Our results demonstrate how ultrafast resonant inelastic X-ray scattering can help characterize local charge distributions around catalytic metal centers in short-lived charge-transfer excited states, as a step toward future rationalization and tailoring of photocatalytic capabilities of transition-metal complexes. Y1 - 2018 U6 - https://doi.org/10.1021/acs.jpclett.8b01429 SN - 1948-7185 VL - 9 IS - 12 SP - 3538 EP - 3543 PB - American Chemical Society CY - Washington ER -