@phdthesis{Zulawski2013,
  author    = {Zulawski, Monika Anna},
  title     = {Die Rolle der Phosphorylierung in der Regulation pflanzlicher Proteine},
  address   = {Potsdam},
  pages     = {160 S.},
  year      = {2013},
  language  = {de}
}
@article{ZhangPaijmansChangetal.2013,
  author    = {Zhang, Hucai and Paijmans, Johanna L. A. and Chang, Fengqin and Wu, Xiaohong and Chen, Guangjie and Lei, Chuzhao and Yang, Xiujuan and Wei, Zhenyi and Bradley, Daniel G. and Orlando, Ludovic and O'Connor, Terry and Hofreiter, Michael},
  title     = {Morphological and genetic evidence for early Holocene cattle management in northeastern China},
  series = {Nature Communications},
  volume    = {4},
  journal   = {Nature Communications},
  number    = {6},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2041-1723},
  doi       = {10.1038/ncomms3755},
  pages     = {7},
  year      = {2013},
  abstract  = {The domestication of cattle is generally accepted to have taken place in two independent centres: around 10,500 years ago in the Near East, giving rise to modern taurine cattle, and two millennia later in southern Asia, giving rise to zebu cattle. Here we provide firmly dated morphological and genetic evidence for early Holocene management of taurine cattle in northeastern China. We describe conjoining mandibles from this region that show evidence of oral stereotypy, dated to the early Holocene by two independent C-14 dates. Using Illumina high-throughput sequencing coupled with DNA hybridization capture, we characterize 15,406 bp of the mitogenome with on average 16.7-fold coverage. Phylogenetic analyses reveal a hitherto unknown mitochondrial haplogroup that falls outside the known taurine diversity. Our data suggest that the first attempts to manage cattle in northern China predate the introduction of domestic cattle that gave rise to the current stock by several thousand years.},
  language  = {en}
}
@phdthesis{Zauber2013,
  author    = {Zauber, Henrik},
  title     = {A systems biology driven approach for analyzing lipid protein interactions in sterol biosynthesis mutants},
  address   = {Potsdam},
  pages     = {126 S.},
  year      = {2013},
  language  = {en}
}
@article{ZarattiniMuraKetmaier2013,
  author    = {Zarattini, Paola and Mura, Graziella and Ketmaier, Valerio},
  title     = {Intra-specific variability in the thirteen known populations of the fairy shrimp Chirocephalus ruffoi (Crustacea: Anostraca) - resting egg morphometrics and mitochondrial DNA reveal decoupled patterns of deep divergence},
  series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica},
  volume    = {713},
  journal   = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica},
  number    = {1},
  publisher = {Springer},
  address   = {Dordrecht},
  issn      = {0018-8158},
  doi       = {10.1007/s10750-013-1487-8},
  pages     = {19 -- 34},
  year      = {2013},
  abstract  = {Chirocephalus ruffoi is a fairy shrimp endemic to the Italian peninsula, where it is known only from thirteen high mountain locations. Twelve of these are in the Northern Apennines while the thirteenth is about 700 km away in the Calabrian Apennines (Southern Italy). We quantified degree of genetic divergence within the species by sequencing a fragment of the mitochondrial DNA encoding for Cytochrome Oxidase I. We then combined genetic data with the re-analysis of two different datasets on the morphometrics of the resting eggs (cysts) produced by the species as an adaptation to survive seasonal droughts. Genetic data revealed profound divergence; we identified four clusters of haplotypes within the species phylogeography, three in the Northern Apennines and one in the Calabrian Apennines with most of the genetic variation (a parts per thousand 70\%) being apportioned among haplogroups. We found high variability in cyst morphometrics, especially in cyst size and height of the spines ornamenting the surface. Genetic and morphometric data are decoupled suggesting that cyst morphology is either under selection or a plastic trait. We, therefore, caution against using cyst morphology for taxonomic purposes in anostracans.},
  language  = {en}
}
@article{ZakharovaNikoloskiKoseska2013,
  author    = {Zakharova, A. and Nikoloski, Zoran and Koseska, Aneta},
  title     = {Dimensionality reduction of bistable biological systems},
  series = {Bulletin of mathematical biology : official journal of the Society for Mathematical Biology},
  volume    = {75},
  journal   = {Bulletin of mathematical biology : official journal of the Society for Mathematical Biology},
  number    = {3},
  publisher = {Springer},
  address   = {New York},
  issn      = {0092-8240},
  doi       = {10.1007/s11538-013-9807-8},
  pages     = {373 -- 392},
  year      = {2013},
  abstract  = {Time hierarchies, arising as a result of interactions between system's components, represent a ubiquitous property of dynamical biological systems. In addition, biological systems have been attributed switch-like properties modulating the response to various stimuli across different organisms and environmental conditions. Therefore, establishing the interplay between these features of system dynamics renders itself a challenging question of practical interest in biology. Existing methods are suitable for systems with one stable steady state employed as a well-defined reference. In such systems, the characterization of the time hierarchies has already been used for determining the components that contribute to the dynamics of biological systems. However, the application of these methods to bistable nonlinear systems is impeded due to their inherent dependence on the reference state, which in this case is no longer unique. Here, we extend the applicability of the reference-state analysis by proposing, analyzing, and applying a novel method, which allows investigation of the time hierarchies in systems exhibiting bistability. The proposed method is in turn used in identifying the components, other than reactions, which determine the systemic dynamical properties. We demonstrate that in biological systems of varying levels of complexity and spanning different biological levels, the method can be effectively employed for model simplification while ensuring preservation of qualitative dynamical properties (i.e., bistability). Finally, by establishing a connection between techniques from nonlinear dynamics and multivariate statistics, the proposed approach provides the basis for extending reference-based analysis to bistable systems.},
  language  = {en}
}
@article{YarmanScheller2013,
  author    = {Yarman, Aysu and Scheller, Frieder W.},
  title     = {Coupling biocatalysis with molecular imprinting in a biomimetic sensor},
  series = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition},
  volume    = {52},
  journal   = {Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker ; International edition},
  number    = {44},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1433-7851},
  doi       = {10.1002/anie.201305368},
  pages     = {11521 -- 11525},
  year      = {2013},
  language  = {en}
}
@article{XuWollenbergerQianetal.2013,
  author    = {Xu, Xuan and Wollenberger, Ursula and Qian, Jing and Lettau, Katrin and Jung, Christiane and Liu, Songqin},
  title     = {Electrochemically driven biocatalysis of the oxygenase domain of neuronal nitric oxide synthase in indium tin oxide nanoparticles/polyvinyl alcohol nanocomposite},
  series = {Bioelectrochemistry : an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry ; official journal of the Bioelectrochemical Society},
  volume    = {94},
  journal   = {Bioelectrochemistry : an international journal devoted to electrochemical aspects of biology and biological aspects of electrochemistry ; official journal of the Bioelectrochemical Society},
  number    = {47},
  publisher = {Elsevier},
  address   = {Lausanne},
  issn      = {1567-5394},
  doi       = {10.1016/j.bioelechem.2013.04.005},
  pages     = {7 -- 12},
  year      = {2013},
  abstract  = {Nitric oxide synthase (NOS) plays a critical role in a number of key physiological and pathological processes. Investigation of electron-transfer reactions in NOS would contribute to a better understanding of the nitric oxide (NO) synthesis mechanism. Herein, we describe an electrochemically driven catalytic strategy, using a nanocomposite that consisted of the oxygenase domain of neuronal NOS (D290nNOSoxy), indium tin oxide (ITO) nanopartides and polyvinyl alcohol (PVA). Fast direct electron transfer between electrodes and D290nNOSoxy was observed with the heterogeneous electron transfer rate constant (k(er)) of 154.8 +/- 0.1 s(-1) at the scan rate of 5 V s(-1). Moreover, the substrate IV-hydroxy-L-arginine (NHA) was used to prove the concept of electrochemically driven biocatalysis of D290nNOSoxy. In the presence of the oxygen cosubstrate and tetrahydrobiopterin (BH4) cofactor, the addition of NHA caused the decreases of both oxidation current at + 0.1 V and reduction current at potentials ranging from -0.149 V to -0.549 V vs Ag/AgCl. Thereafter, a series of control experiments such as in the absence of BH4 or D290nNOSoxy were performed. All the results demonstrated that D290nNOSoxy biocatalysis was successfully driven by electrodes in the presence of BH4 and oxygen. This novel bioelectronic system showed potential for further investigation of NOS and biosensor applications. (C) 2013 Elsevier B.V. All rights reserved.},
  language  = {en}
}
@article{WisselManackBrainin2013,
  author    = {Wissel, J{\"o}rg and Manack, Aubrey and Brainin, Michael},
  title     = {Toward an epidemiology of poststroke spasticity},
  series = {Neurology : official journal of the American Academy of Neurology},
  volume    = {80},
  journal   = {Neurology : official journal of the American Academy of Neurology},
  number    = {1},
  publisher = {Lippincott Williams \& Wilkins},
  address   = {Philadelphia},
  issn      = {0028-3878},
  pages     = {S13 -- S19},
  year      = {2013},
  abstract  = {Poststroke spasticity (PSS)-related disability is emerging as a significant health issue for stroke survivors. There is a need for predictors and early identification of PSS in order to minimize complications and maladaptation from spasticity. Reviewing the literature on stroke and upper motor neuron syndrome, spasticity, contracture, and increased muscle tone measured with the Modified Ashworth Scale and the Tone Assessment Scale provided data on the dynamic time course of PSS. Prevalence estimates of PSS were highly variable, ranging from 4\% to 42.6\%, with the prevalence of disabling spasticity ranging from 2\% to 13\%. Data on phases of the PSS continuum revealed evidence of PSS in 4\% to 27\% of those in the early time course (1-4 weeks poststroke), 19\% to 26.7\% of those in the postacute phase (1-3 months poststroke), and 17\% to 42.6\% of those in the chronic phase (>3 months poststroke). Data also identified key risk factors associated with the development of spasticity, including lower Barthel Index scores, severe degree of paresis, stroke-related pain, and sensory deficits. Although such indices could be regarded as predictors of PSS and thus enable early identification and treatment, the different measures of PSS used in those studies limit the strength of the findings. To optimize evaluation in the different phases of care, the best possible assessment of PSS would make use of a combination of indicators for clinical impairment, motor performance, activity level, quality of life, and patient-reported outcome measures. Applying these recommended measures, as well as increasing our knowledge of the physiologic predictors of PSS, will enable us to perform clinical and epidemiologic studies that will facilitate identification and early, multimodal treatment.},
  language  = {en}
}
@phdthesis{Winkler2013,
  author    = {Winkler, Andr{\´e}},
  title     = {Entstehung und ph{\"a}notyp anti - inflammatorischer IgG und ihre Verwendung zur Induktion von Toleranz in der Maus},
  address   = {Potsdam},
  pages     = {100 S.},
  year      = {2013},
  language  = {de}
}
@article{WinckArvidssonMauricioRianoPachonetal.2013,
  author    = {Winck, Flavia Vischi and Arvidsson, Samuel Janne and Mauricio Riano-Pachon, Diego and Hempel, Sabrina and Koseska, Aneta and Nikoloski, Zoran and Urbina Gomez, David Alejandro and Rupprecht, Jens and M{\"u}ller-R{\"o}ber, Bernd},
  title     = {Genome-wide identification of regulatory elements and reconstruction of gene regulatory networks of the green alga chlamydomonas reinhardtii under carbon deprivation},
  series = {PLoS one},
  volume    = {8},
  journal   = {PLoS one},
  number    = {11},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0079909},
  pages     = {16},
  year      = {2013},
  abstract  = {The unicellular green alga Chlamydomonas reinhardtii is a long-established model organism for studies on photosynthesis and carbon metabolism-related physiology. Under conditions of air-level carbon dioxide concentration [CO2], a carbon concentrating mechanism (CCM) is induced to facilitate cellular carbon uptake. CCM increases the availability of carbon dioxide at the site of cellular carbon fixation. To improve our understanding of the transcriptional control of the CCM, we employed FAIRE-seq (formaldehyde-assisted Isolation of Regulatory Elements, followed by deep sequencing) to determine nucleosome-depleted chromatin regions of algal cells subjected to carbon deprivation. Our FAIRE data recapitulated the positions of known regulatory elements in the promoter of the periplasmic carbonic anhydrase (Cah1) gene, which is upregulated during CCM induction, and revealed new candidate regulatory elements at a genome-wide scale. In addition, time series expression patterns of 130 transcription factor (TF) and transcription regulator (TR) genes were obtained for cells cultured under photoautotrophic condition and subjected to a shift from high to low [CO2]. Groups of co-expressed genes were identified and a putative directed gene-regulatory network underlying the CCM was reconstructed from the gene expression data using the recently developed IOTA (inner composition alignment) method. Among the candidate regulatory genes, two members of the MYB-related TF family, Lcr1 (Low-CO2 response regulator 1) and Lcr2 (Low-CO2 response regulator 2), may play an important role in down-regulating the expression of a particular set of TF and TR genes in response to low [CO2]. The results obtained provide new insights into the transcriptional control of the CCM and revealed more than 60 new candidate regulatory genes. Deep sequencing of nucleosome-depleted genomic regions indicated the presence of new, previously unknown regulatory elements in the C. reinhardtii genome. Our work can serve as a basis for future functional studies of transcriptional regulator genes and genomic regulatory elements in Chlamydomonas.},
  language  = {en}
}