@article{LaiDohertyMuellerRoeberetal.2012, author = {Lai, Alvina Grace and Doherty, Colleen J. and M{\"u}ller-R{\"o}ber, Bernd and Kay, Steve A. and Schippers, Jos H. M. and Dijkwel, Paul P.}, title = {CIRCADIAN CLOCK-ASSOCIATED 1 regulates ROS homeostasis and oxidative stress responses}, series = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {109}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, number = {42}, publisher = {National Acad. of Sciences}, address = {Washington}, issn = {0027-8424}, doi = {10.1073/pnas.1209148109}, pages = {17129 -- 17134}, year = {2012}, abstract = {Organisms have evolved endogenous biological clocks as internal timekeepers to coordinate metabolic processes with the external environment. Here, we seek to understand the mechanism of synchrony between the oscillator and products of metabolism known as Reactive Oxygen Species (ROS) in Arabidopsis thaliana. ROS-responsive genes exhibit a time-of-day-specific phase of expression under diurnal and circadian conditions, implying a role of the circadian clock in transcriptional regulation of these genes. Hydrogen peroxide production and scavenging also display time-of-day phases. Mutations in the core-clock regulator, CIRCADIAN CLOCK ASSOCIATED 1 (CCA1), affect the transcriptional regulation of ROS-responsive genes, ROS homeostasis, and tolerance to oxidative stress. Mis-expression of EARLY FLOWERING 3, LUX ARRHYTHMO, and TIMING OF CAB EXPRESSION 1 affect ROS production and transcription, indicating a global effect of the clock on the ROS network. We propose CCA1 as a master regulator of ROS homeostasis through association with the Evening Element in promoters of ROS genes in vivo to coordinate time-dependent responses to oxidative stress. We also find that ROS functions as an input signal that affects the transcriptional output of the clock, revealing an important link between ROS signaling and circadian output. Temporal coordination of ROS signaling by CCA1 and the reciprocal control of circadian output by ROS reveal a mechanistic link that allows plants to master oxidative stress responses.}, language = {en} } @article{XiaCaoDaietal.2012, author = {Xia, Haiyan and Cao, Yun and Dai, Xiaoman and Marelja, Zvonimir and Zhou, Di and Mo, Ran and Al-Mahdawi, Sahar and Pook, Mark A. and Leimk{\"u}hler, Silke and Rouault, Tracey A. and Li, Kuanyu}, title = {Novel Frataxin Isoforms May Contribute to the Pathological Mechanism of Friedreich Ataxia}, series = {PLOS ONE}, volume = {7}, journal = {PLOS ONE}, number = {10}, publisher = {PUBLIC LIBRARY SCIENCE}, address = {SAN FRANCISCO}, issn = {1932-6203}, doi = {10.1371/journal.pone.0047847}, pages = {11}, year = {2012}, abstract = {Friedreich ataxia (FRDA) is an inherited neurodegenerative disease caused by frataxin (FXN) deficiency. The nervous system and heart are the most severely affected tissues. However, highly mitochondria-dependent tissues, such as kidney and liver, are not obviously affected, although the abundance of FXN is normally high in these tissues. In this study we have revealed two novel FXN isoforms (II and III), which are specifically expressed in affected cerebellum and heart tissues, respectively, and are functional in vitro and in vivo. Increasing the abundance of the heart-specific isoform III significantly increased the mitochondrial aconitase activity, while over-expression of the cerebellum-specific isoform II protected against oxidative damage of Fe-S cluster-containing aconitase. Further, we observed that the protein level of isoform III decreased in FRDA patient heart, while the mRNA level of isoform II decreased more in FRDA patient cerebellum compared to total FXN mRNA. Our novel findings are highly relevant to understanding the mechanism of tissue-specific pathology in FRDA.}, language = {en} } @article{BojahrHerzogSchicketal.2012, author = {Bojahr, Andre and Herzog, Marc and Schick, Daniel and Vrejoiu, Ionela and Bargheer, Matias}, title = {Calibrated real-time detection of nonlinearly propagating strain waves}, series = {Physical review : B, Condensed matter and materials physics}, volume = {86}, journal = {Physical review : B, Condensed matter and materials physics}, number = {14}, publisher = {American Physical Society}, address = {College Park}, issn = {1098-0121}, doi = {10.1103/PhysRevB.86.144306}, pages = {5}, year = {2012}, abstract = {Epitaxially grown metallic oxide transducers support the generation of ultrashort strain pulses in SrTiO3 (STO) with high amplitudes up to 0.5\%. The strain amplitudes are calibrated by real-time measurements of the lattice deformation using ultrafast x-ray diffraction. We determine the speed at which the strain fronts propagate by broadband picosecond ultrasonics and conclude that, above a strain level of approx. 0.2\%, the compressive and tensile strain components travel at considerably different sound velocities, indicating nonlinear wave behavior. Simulations based on an anharmonic linear-chain model are in excellent accord with the experimental findings and show how the spectrum of coherent phonon modes changes with time.}, language = {en} } @article{UusiHeikkilaBoeckenhoffWolteretal.2012, author = {Uusi-Heikkila, Silva and Boeckenhoff, Linda and Wolter, Christian and Arlinghaus, Robert}, title = {Differential Allocation by Female Zebrafish (Danio rerio) to Different-Sized Males - An Example in a Fish Species Lacking Parental Care}, series = {PLOS ONE}, volume = {7}, journal = {PLOS ONE}, number = {10}, publisher = {PUBLIC LIBRARY SCIENCE}, address = {SAN FRANCISCO}, issn = {1932-6203}, doi = {10.1371/journal.pone.0048317}, pages = {7}, year = {2012}, abstract = {Organisms allocate resources to reproduction in response to the costs and benefits of current and future reproductive opportunities. According to the differential allocation hypothesis, females allocate more resources to high-quality males. We tested whether a fish species lacking parental care (zebrafish, Danio rerio) expresses male size-dependent differential allocation in monogamous spawning trials. In addition, we tested whether reproductive allocation by females is affected by previous experience of different-quality males, potentially indicating plasticity in mate choice. To that end, females were conditioned to large, small or random-sized males (controls) for 14 days to manipulate females\’ expectations of the future mate quality. Females showed a clear preference for large males in terms of spawning probability and clutch size independent of the conditioning treatment. However, when females experienced variation in male size (random-sized conditioning treatment) they discriminated less against small males compared to females conditioned to large and small males. This might suggest that differential allocation and size-dependent sexual selection is of less relevance in nature than revealed in the present laboratory study.}, language = {en} } @article{GoetzeGrecoMitricetal.2012, author = {Goetze, Jan P. and Greco, Claudio and Mitric, Roland and Bonacic-Koutecky, Vlasta and Saalfrank, Peter}, title = {BLUF Hydrogen network dynamics and UV/Vis spectra: A combined molecular dynamics and quantum chemical study}, series = {JOURNAL OF COMPUTATIONAL CHEMISTRY}, volume = {33}, journal = {JOURNAL OF COMPUTATIONAL CHEMISTRY}, number = {28}, publisher = {WILEY-BLACKWELL}, address = {HOBOKEN}, issn = {0192-8651}, doi = {10.1002/jcc.23056}, pages = {2233 -- 2242}, year = {2012}, abstract = {Blue light sensing using flavin (BLUF) protein photoreceptor domains change their hydrogen bond network after photoexcitation. To explore this phenomenon, BLUF domains from R. sphaeroides were simulated using Amber99 molecular dynamics (MD). Five starting configurations were considered, to study different BLUF proteins (AppA/BlrB), Trp conformations (Win/Wout), structure determination (X-ray/NMR), and finally, His protonation states. We found dependencies of the hydrogen bonds on almost all parameters. Our data show an especially strong correlation of the Trp position and hydrogen bonds involving Gln63. The latter is in some contradiction to earlier results (Obanayama et al., Photochem. Photobiol. 2008, 84 10031010). Possible origins and implications are discussed. Our calculations support conjectures that Gln63 is more flexible with Trp104 in Win position. Using snapshots from MD and time-dependent density functional theory, UV/vis spectra for the chromophore were determined, which account for molecular motion of the protein under ambient conditions. In accord with experiment, it is found that the UV/vis spectra of BLUF bound flavin are red-shifted and thermally broadened for all calculated p ? p* transitions, relative to gas phase flavin at T = 0 K. However, differences in the spectra between the various BLUF configurations cannot be resolved with the present approach. (c) 2012 Wiley Periodicals, Inc.}, language = {en} } @article{JeonMonneJavanainenetal.2012, author = {Jeon, Jae-Hyung and Monne, Hector Martinez-Seara and Javanainen, Matti and Metzler, Ralf}, title = {Anomalous diffusion of phospholipids and cholesterols in a lipid bilayer and its origins}, series = {Physical review letters}, volume = {109}, journal = {Physical review letters}, number = {18}, publisher = {American Physical Society}, address = {College Park}, issn = {0031-9007}, doi = {10.1103/PhysRevLett.109.188103}, pages = {5}, year = {2012}, abstract = {Combining extensive molecular dynamics simulations of lipid bilayer systems of varying chemical compositions with single-trajectory analyses, we systematically elucidate the stochastic nature of the lipid motion. We observe subdiffusion over more than 4 orders of magnitude in time, clearly stretching into the submicrosecond domain. The lipid motion depends on the lipid chemistry, the lipid phase, and especially the presence of cholesterol. We demonstrate that fractional Langevin equation motion universally describes the lipid motion in all phases, including the gel phase, and in the presence of cholesterol. The results underline the relevance of anomalous diffusion in lipid bilayers and the strong effects of the membrane composition.}, language = {en} } @article{ZuoGandhiArndtetal.2012, author = {Zuo, Zhili and Gandhi, Neha S. and Arndt, Katja Maren and Mancera, Ricardo L.}, title = {Free energy calculations of the interactions of c-Jun-based synthetic peptides with the c-Fos protein}, series = {Biopolymers}, volume = {97}, journal = {Biopolymers}, number = {11}, publisher = {Wiley-Blackwell}, address = {Hoboken}, issn = {0006-3525}, doi = {10.1002/bip.22099}, pages = {899 -- 909}, year = {2012}, abstract = {The c-Fosc-Jun complex forms the activator protein 1 transcription factor, a therapeutic target in the treatment of cancer. Various synthetic peptides have been designed to try to selectively disrupt the interaction between c-Fos and c-Jun at its leucine zipper domain. To evaluate the binding affinity between these synthetic peptides and c-Fos, polarizable and nonpolarizable molecular dynamics (MD) simulations were conducted, and the resulting conformations were analyzed using the molecular mechanics generalized Born surface area (MM/GBSA) method to compute free energies of binding. In contrast to empirical and semiempirical approaches, the estimation of free energies of binding using a combination of MD simulations and the MM/GBSA approach takes into account dynamical properties such as conformational changes, as well as solvation effects and hydrophobic and hydrophilic interactions. The predicted binding affinities of the series of c-Jun-based peptides targeting the c-Fos peptide show good correlation with experimental melting temperatures. This provides the basis for the rational design of peptides based on internal, van der Waals, and electrostatic interactions.}, language = {en} } @article{HahnHoldt2012, author = {Hahn, Simone and Holdt, Hans-J{\"u}rgen}, title = {Extraction of hexachloroplatinate from hydrochloric acid solutions with phosphorylated hexane-1,6-diyl polymers}, series = {Reactive \& functional polymers}, volume = {72}, journal = {Reactive \& functional polymers}, number = {11}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1381-5148}, doi = {10.1016/j.reactfunctpolym.2012.08.004}, pages = {878 -- 888}, year = {2012}, abstract = {A series of diols (diethylene glycol, triethylene glycol, butane-1,4-diol and hexane-1,6-diol) were immobilized onto Merrifield resin and subsequently phosphorylated with dialkyl chlorophosphate (alkyl = Me, Et, Bu). The resins bearing hexane-1,6-diyl groups exhibited very good extraction abilities in regard to precious metal chloro complexes like platinum(IV), palladium(II) and rhodium(III). In batch experiments, more than 98\% of Pt(IV) is extracted even when the metal and the hydrochloric acid concentration is enhanced significantly. Elution can be achieved with a solution of 0.5 mol L-1 thiourea in 0.1 mol L-1 hydrochloric acid. In the presence of other noble metals, platinum(IV) is preferentially bound. The extraction yield decreases in slightly acidic solution in the following order: Pt(IV)approximate to Pd(II)>Rh(III) and changes with increasing hydrochloric acid concentration to Pt(IV)>Pd(II)>> Rh(III). At different ratios of metal and acid, the temperature has nearly no influence on the platinum extraction. On slightly acidic media, the extraction of rhodium decreases by 30\% when the temperature is increased from 10 degrees C to 40 degrees C. When the acid and metal concentration is enhanced, the palladium extraction decreases by 7-9\%, depending on the resin.}, language = {en} } @article{HartmannZimmermann2012, author = {Hartmann, Katharina and Zimmermann, Malte}, title = {Focus marking in Bura - semantic uniformity matches syntactic heterogeneity}, series = {Natural language \& linguistic theory}, volume = {30}, journal = {Natural language \& linguistic theory}, number = {4}, publisher = {Springer}, address = {Dordrecht}, issn = {0167-806X}, doi = {10.1007/s11049-012-9174-4}, pages = {1061 -- 1108}, year = {2012}, abstract = {The present article introduces a theory of (morpho-)syntactic focus marking on nominal categories in Bura, a Central Chadic SVO language spoken in the northeast of Nigeria. Our central claim is that the particle an plays a crucial role in the marking of subject and non-subject focus. We put forward a uniform analysis of an as a focus copula that selects for syntactic predicates of type < e,t > and a focused constituent of type < e >. This uniform semantic representation is transparently mapped onto different syntactic structures: In a clause with a focused subject, the focus copula appears between the subject in SpecTP and the predicative VP. On the other hand, syntactically focused non-subjects are fronted and appear in a bi-clausal cleft structure that contains the focus copula and a relative cleft-remnant. The non-uniform analysis of focus marking is further supported by the structure of predicative constructions, in which the focus copula separates the focused subject and the adjectival or nominal predicate. It is also shown that alternative unified analyses fail to account for the full range of Bura data. The latter part of the article provides an analysis of the Bura cleft construction. Based on syntactic and semantic evidence, we come to the conclusion that the clefted constituent is base-generated in its initial surface position, and that an empty operator moves within the relative clause. The article concludes with a brief discussion of the potential conceptual reasons behind the observed subject/non-subject asymmetry in Bura.}, language = {en} } @article{HesseJaschkeKanzleiteretal.2012, author = {Hesse, Deike and Jaschke, Alexander and Kanzleiter, Timo and Witte, Nicole and Augustin, Robert and Hommel, Angela and P{\"u}schel, Gerhard Paul and Petzke, Klaus-J{\"u}rgen and Joost, Hans-Georg and Schupp, Michael and Sch{\"u}rmann, Annette}, title = {GTPase ARFRP1 is essential for normal hepatic glycogen storage and insulin-like growth factor 1 secretion}, series = {Molecular and cellular biology}, volume = {32}, journal = {Molecular and cellular biology}, number = {21}, publisher = {American Society for Microbiology}, address = {Washington}, issn = {0270-7306}, doi = {10.1128/MCB.00522-12}, pages = {4363 -- 4374}, year = {2012}, abstract = {The GTPase ADP-ribosylation factor-related protein 1 (ARFRP1) is located at the trans-Golgi compartment and regulates the recruitment of Arf-like 1 (ARL1) and its effector golgin-245 to this compartment. Here, we show that liver-specific knockout of Arfrp1 in the mouse (Arfrp1(liv-/-)) resulted in early growth retardation, which was associated with reduced hepatic insulin-like growth factor 1 (IGF1) secretion. Accordingly, suppression of Arfrp1 in primary hepatocytes resulted in a significant reduction of IGF1 release. However, the hepatic secretion of IGF-binding protein 2 (IGFBP2) was not affected in the absence of ARFRP1. In addition, Arfrp1(liv-/-) mice exhibited decreased glucose transport into the liver, leading to a 50\% reduction of glycogen stores as well as a marked retardation of glycogen storage after fasting and refeeding. These abnormalities in glucose metabolism were attributable to reduced protein levels and intracellular retention of the glucose transporter GLUT2 in Arfrp1(liv-/-) livers. As a consequence of impaired glucose uptake into the liver, the expression levels of carbohydrate response element binding protein (ChREBP), a transcription factor regulated by glucose concentration, and its target genes (glucokinase and pyruvate kinase) were markedly reduced. Our data indicate that ARFRP1 in the liver is involved in the regulation of IGF1 secretion and GLUT2 sorting and is thereby essential for normal growth and glycogen storage.}, language = {en} }