@article{YildizLeimkuehler2021,
  author    = {Yildiz, Tugba and Leimk{\"u}hler, Silke},
  title     = {TusA is a versatile protein that links translation efficiency to cell division in Escherichia coli},
  series = {Journal of bacteriology},
  volume    = {203},
  journal   = {Journal of bacteriology},
  number    = {7},
  publisher = {American Society for Microbiology},
  address   = {Washington},
  issn      = {1098-5530},
  doi       = {10.1128/JB.00659-20},
  pages     = {20},
  year      = {2021},
  abstract  = {To enable accurate and efficient translation, sulfur modifications are introduced posttranscriptionally into nucleosides in tRNAs. The biosynthesis of tRNA sulfur modifications involves unique sulfur trafficking systems for the incorporation of sulfur atoms in different nucleosides of tRNA. One of the proteins that is involved in inserting the sulfur for 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)U34) modifications in tRNAs is the TusA protein. TusA, however, is a versatile protein that is also involved in numerous other cellular pathways. Despite its role as a sulfur transfer protein for the 2-thiouridine formation in tRNA, a fundamental role of TusA in the general physiology of Escherichia coli has also been discovered. Poor viability, a defect in cell division, and a filamentous cell morphology have been described previously for tusA-deficient cells. In this report, we aimed to dissect the role of TusA for cell viability. We were able to show that the lack of the thiolation status of wobble uridine (U-34) nucleotides present on Lys, Gln, or Glu in tRNAs has a major consequence on the translation efficiency of proteins; among the affected targets are the proteins RpoS and Fis. Both proteins are major regulatory factors, and the deregulation of their abundance consequently has a major effect on the cellular regulatory network, with one consequence being a defect in cell division by regulating the FtsZ ring formation. <br /> IMPORTANCE More than 100 different modifications are found in RNAs. One of these modifications is the mnm(5)s(2)U modification at the wobble position 34 of tRNAs for Lys, Gln, and Glu. The functional significance of U34 modifications is substantial since it restricts the conformational flexibility of the anticodon, thus providing translational fidelity. We show that in an Escherichia coli TusA mutant strain, involved in sulfur transfer for the mnm(5)s(2)U34 thio modifications, the translation efficiency of RpoS and Fis, two major cellular regulatory proteins, is altered. Therefore, in addition to the transcriptional regulation and the factors that influence protein stability, tRNA modifications that ensure the translational efficiency provide an additional crucial regulatory factor for protein synthesis.},
  language  = {en}
}
@article{YoshidaJonesEllneretal.2003,
  author    = {Yoshida, Takehito and Jones, Laura E. and Ellner, Stephen P. and Fussmann, Gregor F. and Hairston, Jr. and Nelson, G.},
  title     = {Rapid evolution drives ecological dynamics in a predator-prey system},
  year      = {2003},
  abstract  = {Ecological and evolutionary dynamics can occur on similar timescales. However, theoretical predictions of how rapid evolution can affect ecological dynamics are inconclusive and often depend on untested model assumptions. Here we report that rapid prey evolution in response to oscillating predator density affects predator-prey (rotifer-algal) cycles in laboratory microcosms. Our experiments tested explicit predictions from a model for our system that allows prey evolution. We verified the predicted existence of an evolutionary tradeoff between algal competitive ability and defence against consumption, and examined its effects on cycle dynamics by manipulating the evolutionary potential of the prey population. Single-clone algal cultures (lacking genetic variability) produced short cycle periods and typical quarter-period phase lags between prey and predator densities, whereas multi-clonal (genetically variable) algal cultures produced long cycles with prey and predator densities nearly out of phase, exactly as predicted. These results confirm that prey evolution can substantially alter predator-prey dynamics, and therefore that attempts to understand population oscillations in nature cannot neglect potential effects from ongoing rapid evolution.},
  language  = {en}
}
@article{YuKoflerHaeusleretal.2001,
  author    = {Yu, Tien-Shin and Kofler, Heike and H{\"a}usler, Rainer E. and Hille, Diana and Fl{\"u}gge, Ulf-Ingo and Zeeman, Samuel C. and Smith, Alison M. and Kossmann, Jens and Lloyd, James R. and Ritte, Gerhard and Steup, Martin and Lue, Wei-Ling and Chen, Jychian and Weber, Andreas P. M.},
  title     = {The Arabidopsis sex1 mutant is defective in the R1 protein, a general regulator of starch degradation in plants, and not in the chloroplast hexose transporter},
  issn      = {1040-4651},
  year      = {2001},
  language  = {en}
}
@article{YuWuNowaketal.2019,
  author    = {Yu, Yanjun and Wu, Shenjie and Nowak, Jacqueline and Wang, Guangda and Han, Libo and Feng, Zhidi and Mendrinna, Amelie and Ma, Yinping and Wang, Huan and Zhang, Xiaxia and Tian, Juan and Dong, Li and Nikoloski, Zoran and Persson, Staffan and Kong, Zhaosheng},
  title     = {Live-cell imaging of the cytoskeleton in elongating cotton fibres},
  series = {Nature plants},
  volume    = {5},
  journal   = {Nature plants},
  number    = {5},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {2055-026X},
  doi       = {10.1038/s41477-019-0418-8},
  pages     = {498 -- 504},
  year      = {2019},
  abstract  = {Cotton (Gossypium hirsutum) fibres consist of single cells that grow in a highly polarized manner, assumed to be controlled by the cytoskeleton(1-3). However, how the cytoskeletal organization and dynamics underpin fibre development remains unexplored. Moreover, it is unclear whether cotton fibres expand via tip growth or diffuse growth(2-4). We generated stable transgenic cotton plants expressing fluorescent markers of the actin and microtubule cytoskeleton. Live-cell imaging revealed that elongating cotton fibres assemble a cortical filamentous actin network that extends along the cell axis to finally form actin strands with closed loops in the tapered fibre tip. Analyses of F-actin network properties indicate that cotton fibres have a unique actin organization that blends features of both diffuse and tip growth modes. Interestingly, typical actin organization and endosomal vesicle aggregation found in tip-growing cell apices were not observed in fibre tips. Instead, endomembrane compartments were evenly distributed along the elongating fibre cells and moved bi-directionally along the fibre shank to the fibre tip. Moreover, plus-end tracked microtubules transversely encircled elongating fibre shanks, reminiscent of diffusely growing cells. Collectively, our findings indicate that cotton fibres elongate via a unique tip-biased diffuse growth mode.},
  language  = {en}
}
@article{YuanHouBarlowetal.2019,
  author    = {Yuan, Jun-Xia and Hou, Xin-Dong and Barlow, Axel and Preick, Michaela and Taron, Ulrike H. and Alberti, Federica and Basler, Nikolas and Deng, Tao and Lai, Xu-Long and Hofreiter, Michael and Sheng, Gui-Lian},
  title     = {Molecular identification of late and terminal Pleistocene Equus ovodovi from northeastern China},
  series = {PLOS ONE},
  volume    = {14},
  journal   = {PLOS ONE},
  number    = {5},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0216883},
  pages     = {12},
  year      = {2019},
  abstract  = {The extant diversity of horses (family Equidae) represents a small fraction of that occurring over their evolutionary history. One such lost lineage is the subgenus Sussemionus, which is thought to have become extinct during the Middle Pleistocene. However, recent molecular studies and morphological analysis have revealed that one of their representatives, E. ovodovi, did exist in Siberia during the Late Pleistocene. Fossil materials of E. ovodovi have thus far only been found in Russia. In this study, we extracted DNA from three equid fossil specimens excavated from northeastern China dated at 12,770-12,596, 29,525-28,887 and 40,201-38,848 cal. yBP, respectively, and retrieved three near-complete mitochondrial genomes from the specimens. Phylogenetic analyses cluster the Chinese haplotypes together with previously published Russian E. ovodovi, strongly supporting the assignment of these samples to this taxon. The molecular identification of E. ovodovi in northeastern China extends the known geographical range of this fossil species by several thousand kilometers to the east. The estimated coalescence time of all E. ovodovi haplotypes is approximately 199 Kya, with the Chinese haplotypes coalescing approximately 130 Kya. With a radiocarbon age of 12,770-12,596 cal. yBP, the youngest sample in this study represents the first E. ovodovi sample dating to the terminal Pleistocene, moving the extinction date of this species forwards considerably compared to previously documented fossils. Overall, comparison of our three mitochondrial genomes with the two published ones suggests a genetic diversity similar to several extant species of the genus Equus.},
  language  = {en}
}
@article{YuanShengPreicketal.2020,
  author    = {Yuan, Junxia and Sheng, Guilian and Preick, Michaela and Sun, Boyang and Hou, Xindong and Chen, Shungang and Taron, Ulrike Helene and Barlow, Axel and Wang, Linying and Hu, Jiaming and Deng, Tao and Lai, Xulong and Hofreiter, Michael},
  title     = {Mitochondrial genomes of Late Pleistocene caballine horses from China belong to a separate clade},
  series = {Quaternary science reviews : the international multidisciplinary research and review journal},
  volume    = {250},
  journal   = {Quaternary science reviews : the international multidisciplinary research and review journal},
  publisher = {Elsevier},
  address   = {Amsterdam [u.a.]},
  issn      = {0277-3791},
  doi       = {10.1016/j.quascirev.2020.106691},
  pages     = {8},
  year      = {2020},
  abstract  = {There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E. dalianensis and E. przewalskii specimens excavated from Late Pleistocene strata in northeastern China. Phylogenetic analyses revealed that caballoid horses were divided into two subclades: the New World and the Old World caballine horse subclades. The Old World caballine horses comprise of two deep phylogenetic lineages, with modern and ancient Equus caballus and modern E. przewalskii forming lineage I, and the individuals in this study together with one Yakut specimen forming lineage II. Our results indicate that Chinese Late Pleistocene caballoid horses showed a closer relationship to other Eurasian caballine horses than that to Pleistocene horses from North America. In addition, phylogenetic analyses suggested a close relationship between E. dalianensis and the Chinese fossil E. przewalskii, in agreement with previous researches based on morphological analyses. Interestingly, E. dalianensis and the fossil E. przewalskii were intermixed rather than split into distinct lineages, suggesting either that gene flow existed between these two species or that morphology-based species assignment of palaeontological specimens is not always correct. Moreover, Bayesian analysis showed that the divergence time between the New World and the Old World caballoid horses was at 1.02 Ma (95\% CI: 0.86-1.24 Ma), and the two Old World lineages (I \& II) split at 0.88 Ma (95\% CI: 0.69-1.13 Ma), which indicates that caballoid horses seem to have evolved into different populations in the Old World soon after they migrated from North America via the Bering Land Bridge. Finally, the TMRCA of E. dalianensis was estimated at 0.20 Ma (95\% CI: 0.15-0.28 Ma), and it showed a relative low genetic diversity compared with other Equus species.},
  language  = {en}
}
@article{YuryevKascheIgnatovaetal.2010,
  author    = {Yuryev, Ruslan and Kasche, Volker and Ignatova, Zoya and Galunsky, Boris},
  title     = {Improved A. faecalis penicillin amidase mutant retains the thermodynamic and pH stability of the wild type enzyme},
  issn      = {1572-3887},
  doi       = {10.1007/s10930-010-9238-4},
  year      = {2010},
  abstract  = {Penicillin amidase from Alacaligenes faecalis is an attractive biocatalyst for hydrolysis of penicillin G for production of 6-aminopenicillanic acid, which is used in the synthesis of semi-synthetic beta-lactam antibiotics. Recently a mutant of this enzyme with extended C-terminus of the A-chain comprising parts of the connecting linker peptide was constructed. Its turnover number for the hydrolysis of penicillin G was 140 s(-1), about twice of the value for the wild-type enzyme (80 s(-1)). At the same time the specificity constant was improved about three-fold. The wild- type and the mutant enzymes showed similar pH stability suggesting that the linker peptide fragment covalently attached to the A-chain does not alter the electrostatic interactions in the protein core. Although the global stability of A. faecalis wild-type enzyme and the T206GS213G variant does not differ, the presence of the linker fragment stabilizes the domains interface, as evidenced by the monophasic transition of the mutant enzyme from folded to unfolded state during urea-induced denaturation. The high stability and activity of the mutant enzyme provides a rationale to use it as a biocatalyst in the industrial processes, where the enzyme must be more robust to fluctuations in the operational conditions.},
  language  = {en}
}
@article{ZabihiGraffSchumacheretal.2018,
  author    = {Zabihi, Fatemeh and Graff, Patrick and Schumacher, Fabian and Kleuser, Burkhard and Hedtrich, Sarah and Haag, Rainer},
  title     = {Synthesis of poly(lactide-co-glycerol) as a biodegradable and biocompatible polymer with high loading capacity for dermal drug delivery},
  series = {Nanoscale},
  volume    = {10},
  journal   = {Nanoscale},
  number    = {35},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {2040-3364},
  doi       = {10.1039/c8nr05536j},
  pages     = {16848 -- 16856},
  year      = {2018},
  abstract  = {Due to the low cutaneous bioavailability of tacrolimus (TAC), penetration enhancers are used to improve its penetration into the skin. However, poor loading capacity, non-biodegradability, toxicity, and in some cases inefficient skin penetration are challenging issues that hamper their applications for the dermal TAC delivery. Here we present poly(lactide-co-glycerol) (PLG) as a water soluble, biodegradable, and biocompatible TAC-carrier with high loading capacity (14.5\% w/w for TAC) and high drug delivery efficiencies into the skin. PLG was synthesized by cationic ring-opening copolymerization of a mixture of glycidol and lactide and showed 35 nm and 300 nm average sizes in aqueous solutions before and after loading of TAC, respectively. Delivery experiments on human skin, quantified by fluorescence microscopy and LC-MS/MS, showed a high ability for PLG to deposit Nile red and TAC into the stratum corneum and viable epidermis of skin in comparison with Protopic (R) (0.03\% w/w, TAC ointment). The cutaneous distribution profile of delivered TAC proved that 80\%, 16\%, and 4\% of the cutaneous drug level was deposited in the stratum corneum, viable epidermis, and upper dermis, respectively. TAC delivered by PLG was able to efficiently decrease the IL-2 and TSLP expressions in human skin models. Taking advantage of the excellent physicochemical and biological properties of PLG, it can be used for efficient dermal TAC delivery and potential treatment of inflammatory skin diseases.},
  language  = {en}
}
@article{ZaccheusBroekerLundborgetal.2012,
  author    = {Zaccheus, Mona V. and Br{\"o}ker, Nina Kristin and Lundborg, Magnus and Uetrecht, Charlotte and Barbirz, Stefanie and Widmalm, Goran},
  title     = {Structural studies of the O-antigen polysaccharide from Escherichia coli TD2158 having O18 serogroup specificity and aspects of its interaction with the tailspike endoglycosidase of the infecting bacteriophage HK620},
  series = {Carbohydrate research},
  volume    = {357},
  journal   = {Carbohydrate research},
  number    = {8},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0008-6215},
  doi       = {10.1016/j.carres.2012.05.022},
  pages     = {118 -- 125},
  year      = {2012},
  abstract  = {We have analyzed the O-antigen polysaccharide of the previously uncharacterized Escherichia coli strain TD2158 which is a host of bacteriophage HK620. This bacteriophage recognizes and cleaves the polysaccharide with its tailspike protein (TSP). The polysaccharide preparation as well as oligosaccharides obtained from HK620TSP endoglycosidase digests were analyzed with NMR spectroscopy. Additionally, sugar analysis was performed on the O-antigen polysaccharide and MALDI-TOF MS was used in oligosaccharide analysis. The present study revealed a heterogeneous polysaccharide with a hexasaccharide repeating unit of the following structure: alpha-D-Glcp-(1 -> 6) vertical bar vertical bar 2)-alpha-L-Rhap-(1 -> 6)-alpha-D-Glcp-(1 -> 4)-alpha-D-Galp-(1 -> 3)-alpha-D-GlcpNAc- (1 ->vertical bar beta-D-Glcp/beta-D-GlcpNAc-(1 -> 3) A repeating unit with a D-GlcNAc substitution of D-Gal has been described earlier as characteristic for serogroup O18A1. Accordingly, we termed repeating units with D-Glc substitution at D-Gal as O18A2. NMR analyses of the polysaccharide confirmed that O18A1- and O18A2-type repeats were present in a 1:1 ratio. However, HK620TSP preferentially bound the D-GlcNAc- substituted O18A1-type repeating units in its high affinity binding pocket with a dissociation constant of 140 mu M and disfavored the O18A2-type having a beta-D-Glcp-(1 -> 3)-linked group. As a result, in hexasaccharide preparations, O18A1 and O18A2 repeats were present in a 9: 1 ratio stressing the clear preference of O18A1- type repeats to be cleaved by HK620TSP.},
  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{ZancolliBakerBarlowetal.2016,
  author    = {Zancolli, Giulia and Baker, Timothy G. and Barlow, Axel and Bradley, Rebecca K. and Calvete, Juan J. and Carter, Kimberley C. and de Jager, Kaylah and Owens, John Benjamin and Price, Jenny Forrester and Sanz, Libia and Scholes-Higham, Amy and Shier, Liam and Wood, Liam and W{\"u}ster, Catharine E. and W{\"u}ster, Wolfgang},
  title     = {Is Hybridization a Source of Adaptive Venom Variation in Rattlesnakes? A Test, Using a Crotalus scutulatus x viridis Hybrid Zone in Southwestern New Mexico},
  series = {Toxins},
  volume    = {8},
  journal   = {Toxins},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2072-6651},
  doi       = {10.3390/toxins8060188},
  pages     = {16},
  year      = {2016},
  abstract  = {Venomous snakes often display extensive variation in venom composition both between and within species. However, the mechanisms underlying the distribution of different toxins and venom types among populations and taxa remain insufficiently known. Rattlesnakes (Crotalus, Sistrurus) display extreme inter-and intraspecific variation in venom composition, centered particularly on the presence or absence of presynaptically neurotoxic phospholipases A2 such as Mojave toxin (MTX). Interspecific hybridization has been invoked as a mechanism to explain the distribution of these toxins across rattlesnakes, with the implicit assumption that they are adaptively advantageous. Here, we test the potential of adaptive hybridization as a mechanism for venom evolution by assessing the distribution of genes encoding the acidic and basic subunits of Mojave toxin across a hybrid zone between MTX-positive Crotalus scutulatus and MTX-negative C. viridis in southwestern New Mexico, USA. Analyses of morphology, mitochondrial and single copy-nuclear genes document extensive admixture within a narrow hybrid zone. The genes encoding the two MTX subunits are strictly linked, and found in most hybrids and backcrossed individuals, but not in C. viridis away from the hybrid zone. Presence of the genes is invariably associated with presence of the corresponding toxin in the venom. We conclude that introgression of highly lethal neurotoxins through hybridization is not necessarily favored by natural selection in rattlesnakes, and that even extensive hybridization may not lead to introgression of these genes into another species.},
  language  = {en}
}
@article{ZaplataNhabangaStalmansetal.2020,
  author    = {Zaplata, Markus Klemens and Nhabanga, Abel and Stalmans, Marc and Volpers, Thomas and Burkart, Michael and Sperfeld, Erik},
  title     = {Grasses cope with high-contrast ecosystem conditions in the large outflow of the Banhine wetlands, Mozambique},
  series = {African journal of ecology},
  volume    = {59},
  journal   = {African journal of ecology},
  number    = {1},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0141-6707},
  doi       = {10.1111/aje.12820},
  pages     = {190 -- 203},
  year      = {2020},
  abstract  = {Ecosystems with highly pulsed water supply must be better understood as climate change may increase frequency and severity of intense storms, droughts and floods. Here we collected data over 3 years (2016-2018) in the episodic wetland outflow channel (Aluize), Banhine National Park, in which the system state changed from dry to wet to dry. Field sampling included vegetation records, small-scale vegetation zoning, the seed bank and water and soil quality. The same main plant species were found in both dry and wet conditions across the riverbed of the outflow channel. We found only very few diaspores of plants in the soil after prolonged drought. In the subsequent flooded state, we examined very dense vegetation on the water surface, which was dominated by the gramineous species Paspalidium obtusifolium. This species formed a compact floating mat that was rooted to the riverbed. The Cyperaceae Bolboschoenus glaucus showed high clonal growth in the form of root tubers, which likely serve as important food reservoir during drought. Soil and water analyses do not indicate a limitation by nutrients. We outline how resident people may change the plant community structure with an increasing practice of setting fire to the meadows in the dried-up riverbed to facilitate plant regrowth as food for their livestock.},
  language  = {en}
}
@article{ZappaSchlafferBroccaetal.2022,
  author    = {Zappa, Luca and Schlaffer, Stefan and Brocca, Luca and Vreugdenhil, Mariette and Nendel, Claas and Dorigo, Wouter},
  title     = {How accurately can we retrieve irrigation timing and water amounts from (satellite) soil moisture?},
  series = {International journal of applied earth observation and geoinformation},
  volume    = {113},
  journal   = {International journal of applied earth observation and geoinformation},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {1569-8432},
  doi       = {10.1016/j.jag.2022.102979},
  pages     = {12},
  year      = {2022},
  abstract  = {While ensuring food security worldwide, irrigation is altering the water cycle and generating numerous environmental side effects. As detailed knowledge about the timing and the amounts of water used for irrigation over large areas is still lacking, remotely sensed soil moisture has proved potential to fill this gap. However, the spatial resolution and revisit time of current satellite products represent a major limitation to accurately estimating irrigation. This work aims to systematically quantify their impact on the retrieved irrigation information, hence assessing the value of satellite soil moisture for estimating irrigation timing and water amounts. In a real-world experiment, we modeled soil moisture using actual irrigation and meteorological data, obtained from farmers and weather stations, respectively. Modeled soil moisture was compared against various remotely sensed products differing in terms of spatio-temporal resolution to test the hypothesis that high-resolution observations can disclose the irrigation signal from individual fields while coarse-scale satellite products cannot. Then, in a synthetic experiment, we systematically investigated the effect of soil moisture spatial and temporal resolution on the accuracy of irrigation estimates. The analysis was further elaborated by considering different irrigation scenarios and by adding realistic amounts of random errors in the soil moisture time series. We show that coarse-scale remotely sensed soil moisture products achieve higher correlations with rainfed simulations, while high-resolution satellite observations agree significantly better with irrigated simulations, suggesting that high-resolution satellite soil moisture can inform on field-scale (similar to 40 ha) irrigation. A thorough analysis of the synthetic dataset showed that satisfactory results, both in terms of detection (F-score > 0.8) and quantification (Pearson's correlation > 0.8), are found for noise-free soil moisture observations either with a temporal sampling up to 3 days or if at least one-third of the pixel covers the irrigated field(s). However, irrigation water amounts are systematically underestimated for temporal samplings of more than one day, and decrease proportionally to the spatial resolution, i.e., coarsening the pixel size leads to larger irrigation underestimations. Although lower spatial and temporal resolutions decrease the detection and quantification accuracies (e.g., R between 0.6 and 1 depending on the irrigation rate and spatio-temporal resolution), random errors in the soil moisture time series have a stronger negative impact (Pearson R always smaller than 0.85). As expected, better performances are found for higher irrigation rates, i.e. when more water is supplied during an irrigation event. Despite the potentially large underestimations, our results suggest that high-resolution satellite soil moisture has the potential to track and quantify irrigation, especially over regions where large volumes of irrigation water are applied to the fields, and given that low errors affect the soil moisture observations.},
  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{ZaupaNeffePierceetal.2011,
  author    = {Zaupa, Alessandro and Neffe, Axel T. and Pierce, Benjamin F. and N{\"o}chel, Ulrich and Lendlein, Andreas},
  title     = {Influence of tyrosine-derived moieties and drying conditions on the formation of helices in gelatin},
  series = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences},
  volume    = {12},
  journal   = {Biomacromolecules : an interdisciplinary journal focused at the interface of polymer science and the biological sciences},
  number    = {1},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1525-7797},
  doi       = {10.1021/bm101029k},
  pages     = {75 -- 81},
  year      = {2011},
  abstract  = {The single and triple helical organization of protein chains strongly influences the mechanical properties of gelatin-based materials. A chemical method for obtaining different degrees of helical organization in gelatin is covalent functionalization, while a physical method for achieving the same goal is the variation of the drying conditions of gelatin solutions. Here we explored how the introduction of desaminotyrosine (DAT) and desaminotyrosyl tyrosine (DATT) linked to lysine residues of gelatin influenced the kinetics and thermodynamic equilibrium of the helicalization process of single and triple helices following different drying conditions. Drying at a temperature above. the helix-to-coil transition temperature of gelatin (T > T-c, called nu(short)) generally resulted in gelatins with relatively lower triple helical content (X-c,X-t = 1-2\%) than lower temperature drying (T < T-c, called nu(long)) (X-c,X-t = 8-10\%), where the DAT(T) functional groups generally disrupted helix formation. While different helical contents affected the thermal transition temperatures only slightly, the mechanical properties were strongly affected for swollen hydrogels (E = 4-13 kPa for samples treated by nu(long) and E = 120-700 kPa for samples treated by nu(short)). This study shows that side group functionalization and different drying conditions are viable options to control the helicalization and macroscopic properties of gelatin-based materials.},
  language  = {en}
}
@article{ZavorkaBlancoChaguacedaetal.2023,
  author    = {Zavorka, Libor and Blanco, Andreu and Chaguaceda, Fernando and Cucherousset, Julien and Killen, Shaun S. and Lienart, Camilla and Mathieu-Resuge, Margaux and Nemec, Pavel and Pilecky, Matthias and Scharnweber, Inga Kristin and Twining, Cornelia W. and Kainz, Martin J.},
  title     = {The role of vital dietary biomolecules in eco-evo-devo dynamics},
  series = {Trends in ecology and evolution},
  volume    = {38},
  journal   = {Trends in ecology and evolution},
  number    = {1},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {0169-5347},
  doi       = {10.1016/j.tree.2022.08.010},
  pages     = {72 -- 84},
  year      = {2023},
  abstract  = {The physiological dependence of animals on dietary intake of vitamins, amino acids, and fatty acids is ubiquitous. Sharp differences in the availability of these vital dietary biomolecules among different resources mean that consumers must adopt a range of strategies to meet their physiological needs. We review the emerging work on omega-3 long-chain polyunsaturated fatty acids, focusing predominantly on predator-prey interactions, to illustrate that trade-off between capacities to consume resources rich in vital biomolecules and internal synthesis capacity drives differences in phenotype and fitness of consumers. This can then feedback to impact ecosystem functioning. We outline how focus on vital dietary biomolecules in eco-eco-devo dynamics can improve our understanding of anthropogenic changes across multiple levels of biological organization.},
  language  = {en}
}
@article{ZbilutGiulianiColosimoetal.2004,
  author    = {Zbilut, J. P. and Giuliani, A. and Colosimo, A. and Mitchell, J. C. and Colafranceschi, M. and Marwan, Norbert and Webber, C. L. and Uversky, V. N.},
  title     = {Charge and hydrophobicity patterning along the sequence predicts the folding mechanism and aggregation of proteins : a computational approach},
  issn      = {1535-3893},
  year      = {2004},
  abstract  = {The presence of partially folded intermediates along the folding funnel of proteins has been suggested to be a signature of potentially aggregating systems. Many studies have concluded that metastable, highly flexible intermediates are the basic elements of the aggregation process. In a previous paper, we demonstrated how the choice between aggregation and folding behavior was influenced by hydrophobicity distribution patterning along the sequence, as quantified by recurrence quantification analysis (RQA) of the Myiazawa-Jernigan coded primary structures. In the present paper, we tried to unify the "partially folded intermediate" and "hydrophobicity/charge" models of protein aggregation verifying the ability of an empirical relation, developed for rationalizing the effect of different mutations on aggregation propensity of acyl-phosphatase and based on the combination of hydrophobicity RQA and charge descriptors, to discriminate in a statistically significant way two different protein populations: (a) proteins that fold by a process passing by partially folded intermediates and (b) proteins that do not present partially folded intermediates},
  language  = {en}
}
@article{ZeisigRudolphEueetal.1995,
  author    = {Zeisig, Reinhard and Rudolph, Michael and Eue, Ines and Arndt, Dietrich},
  title     = {Influence of hexadecylphosphocholine on the release of tumor necrosis factor and nitroxide from peritoneal macro phages in vitro},
  year      = {1995},
  language  = {en}
}
@article{ZeitlerYeAndreyevaetal.2019,
  author    = {Zeitler, Stefanie and Ye, Lian and Andreyeva, Aksana and Schumacher, Fabian and Monti, Juliana and N{\"u}rnberg, Bernd and Nowak, Gabriel and Kleuser, Burkhard and Reichel, Martin and Fejtova, Anna and Kornhuber, Johannes and Rhein, Cosima and Friedland, Kristina},
  title     = {Acid sphingomyelinase - a regulator of canonical transient receptor potential channel 6 (TRPC6) activity},
  series = {Journal of neurochemistry},
  volume    = {150},
  journal   = {Journal of neurochemistry},
  number    = {6},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0022-3042},
  doi       = {10.1111/jnc.14823},
  pages     = {678 -- 690},
  year      = {2019},
  abstract  = {Recent investigations propose the acid sphingomyelinase (ASM)/ceramide system as a novel target for antidepressant action. ASM catalyzes the breakdown of the abundant membrane lipid sphingomyelin to the lipid messenger ceramide. This ASM-induced lipid modification induces a local shift in membrane properties, which influences receptor clustering and downstream signaling. Canonical transient receptor potential channels 6 (TRPC6) are non-selective cation channels located in the cell membrane that play an important role in dendritic growth, synaptic plasticity and cognition in the brain. They can be activated by hyperforin, an ingredient of the herbal remedy St. John's wort for treatment of depression disorders. Because of their role in the context of major depression, we investigated the crosstalk between the ASM/ceramide system and TRPC6 ion channels in a pheochromocytoma cell line 12 neuronal cell model (PC12 rat pheochromocytoma cell line). Ca2+ imaging experiments indicated that hyperforin-induced Ca2+ influx through TRPC6 channels is modulated by ASM activity. While antidepressants, known as functional inhibitors of ASM activity, reduced TRPC6-mediated Ca2+ influx, extracellular application of bacterial sphingomyelinase rebalanced TRPC6 activity in a concentration-related way. This effect was confirmed in whole-cell patch clamp electrophysiology recordings. Lipidomic analyses revealed a decrease in very long chain ceramide/sphingomyelin molar ratio after ASM inhibition, which was connected with changes in the abundance of TRPC6 channels in flotillin-1-positive lipid rafts as visualized by western blotting. Our data provide evidence that the ASM/ceramide system regulates TRPC6 channels likely by controlling their recruitment to specific lipid subdomains and thereby fine-tuning their physical properties.},
  language  = {en}
}
@article{ZellmerPfeilLasch1995,
  author    = {Zellmer, Sebastian and Pfeil, Wolfgang and Lasch, J{\"u}rgen},
  title     = {Interaction of phosphatidylcholine liposomes with the human stratum corneum},
  year      = {1995},
  language  = {en}
}
@article{ZengFrascaRumschoetteletal.2016,
  author    = {Zeng, Ting and Frasca, Stefano and Rumsch{\"o}ttel, Jens and Koetz, Joachim and Leimk{\"u}hler, Silke and Wollenberger, Ursula},
  title     = {Role of Conductive Nanoparticles in the Direct Unmediated Bioelectrocatalysis of Immobilized Sulfite Oxidase},
  series = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis},
  volume    = {28},
  journal   = {Electroanalysis : an international journal devoted to fundamental and practical aspects of electroanalysis},
  publisher = {Wiley-VCH},
  address   = {Weinheim},
  issn      = {1040-0397},
  doi       = {10.1002/elan.201600246},
  pages     = {2303 -- 2310},
  year      = {2016},
  language  = {en}
}
@article{ZengLeimkuehlerKoetzetal.2015,
  author    = {Zeng, Ting and Leimk{\"u}hler, Silke and Koetz, Joachim and Wollenberger, Ursula},
  title     = {Effective Electrochemistry of Human Sulfite Oxidase Immobilized on Quantum-Dots-Modified Indium Tin Oxide Electrode},
  series = {ACS applied materials \& interfaces},
  volume    = {7},
  journal   = {ACS applied materials \& interfaces},
  number    = {38},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1944-8244},
  doi       = {10.1021/acsami.5b06665},
  pages     = {21487 -- 21494},
  year      = {2015},
  abstract  = {The bioelectrocatalytic sulfite oxidation by human sulfite oxidase (hSO) on indium tin oxide (ITO) is reported, which is facilitated by functionalizing of the electrode surface with polyethylenimine (PEI)-entrapped CdS nanoparticles and enzyme. hSO was assembled onto the electrode with a high surface loading of electroactive enzyme. In the presence of sulfite but without additional mediators, a high bioelectrocatalytic current was generated. Reference experiments with only PEI showed direct electron transfer and catalytic activity of hSO, but these were less pronounced. The application of the polyelectrolyte-entrapped quantum dots (QDs) on ITO electrodes provides a compatible surface for enzyme binding with promotion of electron transfer. Variations of the buffer solution conditions, e.g., ionic strength, pH, viscosity, and the effect of oxygen, were studied in order to understand intramolecular and heterogeneous electron transfer from hSO to the electrode. The results are consistent with a model derived for the enzyme by using flash photolysis in solution and spectroelectrochemistry and molecular dynamic simulations of hSO on monolayer-modified gold electrodes. Moreover, for the first time a photoelectrochemical electrode involving immobilized hSO is demonstrated where photoexcitation of the CdS/hSO-modified electrode lead to an enhanced generation of bioelectrocatalytic currents upon sulfite addition. Oxidation starts already at the redox potential of the electron transfer domain of hSO and is greatly increased by application of a small overpotential to the CdS/hSO-modified ITO.},
  language  = {en}
}
@article{ZengLeimkuehlerWollenbergeretal.2017,
  author    = {Zeng, Ting and Leimk{\"u}hler, Silke and Wollenberger, Ulla and Fourmond, Vincent},
  title     = {Transient Catalytic Voltammetry of Sulfite Oxidase Reveals Rate Limiting Conformational Changes},
  series = {Journal of the American Chemical Society},
  volume    = {139},
  journal   = {Journal of the American Chemical Society},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {0002-7863},
  doi       = {10.1021/jacs.7b05480},
  pages     = {11559 -- 11567},
  year      = {2017},
  abstract  = {Sulfite oxidases are metalloenzymes that oxidize sulfite to sulfate at a molybdenum active site. In vertebrate sulfite oxidases, the electrons generated at the Mo center are transferred to an external electron acceptor via a heme domain, which can adopt two conformations: a "closed" conformation, suitable for internal electron transfer, and an "open" conformation suitable for intermolecular electron transfer. This conformational change is an integral part of the catalytic cycle. Sulfite oxidases have been wired to electrode surfaces, but their immobilization leads to a significant decrease in their catalytic activity, raising the question of the occurrence of the conformational change when the enzyme is on an electrode. We recorded and quantitatively modeled for the first time the transient response of the catalytic cycle of human sulfite oxidase immobilized on an electrode. We show that conformational changes still occur on the electrode, but at a lower rate than in solution, which is the reason for the decrease in activity of sulfite oxidases upon immobilization.},
  language  = {en}
}
@article{ZengPankratovFalketal.2015,
  author    = {Zeng, Ting and Pankratov, Dmitry and Falk, Magnus and Leimk{\"u}hler, Silke and Shleev, Sergey and Wollenberger, Ursula},
  title     = {Miniature direct electron transfer based sulphite/oxygen enzymatic fuel cells},
  series = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics},
  volume    = {66},
  journal   = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0956-5663},
  doi       = {10.1016/j.bios.2014.10.080},
  pages     = {39 -- 42},
  year      = {2015},
  abstract  = {A direct electron transfer (DET) based sulphite/oxygen biofuel cell is reported that utilises human sulphite oxidase (hSOx) and Myrothecium verrucaria bilirubin oxidase (MvBOx) and nanostructured gold electrodes. For bioanode construction, the nanostructured gold microelectrodes were further modified with 3,3'-dithiodipropionic acid di(N-hydroxysuccinimide ester) to which polyethylene imine was covalently attached. hSOx was adsorbed onto this chemically modified nanostructured electrode with high surface loading of electroactive enzyme and in presence of sulphite high anodic bioelectrocatalytic currents were generated with an onset potential of 0.05 V vs. NHE. The biocathode contained MyBOx directly adsorbed to the deposited gold nanoparticles for cathodic oxygen reduction starting at 0.71 V vs. NHE. Both enzyme electrodes were integrated to a DET-type biofuel cell. Power densities of 8 and 1 mu W cm(-2) were achieved at 0.15 V and 0.45 V of cell voltages, respectively, with the membrane based biodevices under aerobic conditions. (C) 2014 Elsevier B.V. All rights reserved.},
  language  = {en}
}
@article{ZhangTimmArndtetal.2010,
  author    = {Zhang, Fuzhong Z. and Timm, Katharina A. and Arndt, Katja Maren and Woolley, G. Andrew},
  title     = {Photocontrol of Coiled-Coil Proteins in Living Cells},
  issn      = {1433-7851},
  doi       = {10.1002/anie.201000909},
  year      = {2010},
  abstract  = {Light switching of the activity of a coiled-coil protein, the AP-1 transcription factor, in living cells was made possible by the introduction of a designed azobenzene-cross-linked dominant negative peptide, XAFosW (red and yellow in the picture). In the dark, XAFosW showed decreased helical content and decreased affinity for target Jun proteins (green); irradiation at 365 nm enhanced helicity and target affinity.},
  language  = {en}
}
@article{ZhangFedyuninKirchneretal.2012,
  author    = {Zhang, Gong and Fedyunin, Ivan and Kirchner, Sebastian and Xiao, Chuanle and Valleriani, Angelo and Ignatova, Zoya},
  title     = {FANSe: an accurate algorithm for quantitative mapping of large scale sequencing reads},
  series = {Nucleic acids research},
  volume    = {40},
  journal   = {Nucleic acids research},
  number    = {11},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0305-1048},
  doi       = {10.1093/nar/gks196},
  pages     = {11},
  year      = {2012},
  abstract  = {The most crucial step in data processing from high-throughput sequencing applications is the accurate and sensitive alignment of the sequencing reads to reference genomes or transcriptomes. The accurate detection of insertions and deletions (indels) and errors introduced by the sequencing platform or by misreading of modified nucleotides is essential for the quantitative processing of the RNA-based sequencing (RNA-Seq) datasets and for the identification of genetic variations and modification patterns. We developed a new, fast and accurate algorithm for nucleic acid sequence analysis, FANSe, with adjustable mismatch allowance settings and ability to handle indels to accurately and quantitatively map millions of reads to small or large reference genomes. It is a seed-based algorithm which uses the whole read information for mapping and high sensitivity and low ambiguity are achieved by using short and non-overlapping reads. Furthermore, FANSe uses hotspot score to prioritize the processing of highly possible matches and implements modified Smith-Watermann refinement with reduced scoring matrix to accelerate the calculation without compromising its sensitivity. The FANSe algorithm stably processes datasets from various sequencing platforms, masked or unmasked and small or large genomes. It shows a remarkable coverage of low-abundance mRNAs which is important for quantitative processing of RNA-Seq datasets.},
  language  = {en}
}
@article{ZhangFedyuninMiekleyetal.2010,
  author    = {Zhang, Gong and Fedyunin, Ivan and Miekley, Oskar and Valleriani, Angelo and Moura, Alessandro and Ignatova, Zoya},
  title     = {Global and local depletion of ternary complex limits translational elongation},
  issn      = {0305-1048},
  doi       = {10.1093/Nar/Gkq196},
  year      = {2010},
  abstract  = {The translation of genetic information according to the sequence of the mRNA template occurs with high accuracy and fidelity. Critical events in each single step of translation are selection of transfer RNA (tRNA), codon reading and tRNA-regeneration for a new cycle. We developed a model that accurately describes the dynamics of single elongation steps, thus providing a systematic insight into the sensitivity of the mRNA translation rate to dynamic environmental conditions. Alterations in the concentration of the aminoacylated tRNA can transiently stall the ribosomes during translation which results, as suggested by the model, in two outcomes: either stress-induced change in the tRNA availability triggers the premature termination of the translation and ribosomal dissociation, or extensive demand for one tRNA species results in a competition between frameshift to an aberrant open-reading frame and ribosomal drop-off. Using the bacterial Escherichia coli system, we experimentally draw parallels between these two possible mechanisms.},
  language  = {en}
}
@article{ZhangHubalewskaIgnatova2009,
  author    = {Zhang, Gong and Hubalewska, Magdalena and Ignatova, Zoya},
  title     = {Transient ribosomal attenuation coordinates protein synthesis and co-translational folding},
  issn      = {1545-9985},
  doi       = {10.1038/Nsmb.1554},
  year      = {2009},
  abstract  = {Clustered codons that pair to low-abundance tRNA isoacceptors can form slow-translating regions in the mRNA and cause transient ribosomal arrest. We report that folding efficiency of the Escherichia coli multidomain protein Sufl can be severely perturbed by alterations in ribosome-mediated translational attenuation. Such alterations were achieved by global acceleration of the translation rate with tRNA excess in vitro or by synonymous substitutions to codons with highly abundant tRNAs both in vitro and in vivo. Conversely, the global slow-down of the translation rate modulated by low temperature suppresses the deleterious effect of the altered translational attenuation pattern. We propose that local discontinuous translation temporally separates the translation of segments of the peptide chain and actively coordinates their co-translational folding.},
  language  = {en}
}
@article{ZhangLukoszekMuellerRoeberetal.2011,
  author    = {Zhang, Gong and Lukoszek, Radoslaw and M{\"u}ller-R{\"o}ber, Bernd and Ignatova, Zoya},
  title     = {Different sequence signatures in the upstream regions of plant and animal tRNA genes shape distinct modes of regulation},
  series = {Nucleic acids research},
  volume    = {39},
  journal   = {Nucleic acids research},
  number    = {8},
  publisher = {Oxford Univ. Press},
  address   = {Oxford},
  issn      = {0305-1048},
  doi       = {10.1093/nar/gkq1257},
  pages     = {3331 -- 3339},
  year      = {2011},
  abstract  = {In eukaryotes, the transcription of tRNA genes is initiated by the concerted action of transcription factors IIIC (TFIIIC) and IIIB (TFIIIB) which direct the recruitment of polymerase III. While TFIIIC recognizes highly conserved, intragenic promoter elements, TFIIIB binds to the non-coding 5'-upstream regions of the tRNA genes. Using a systematic bioinformatic analysis of 11 multicellular eukaryotic genomes we identified a highly conserved TATA motif followed by a CAA-motif in the tRNA upstream regions of all plant genomes. Strikingly, the 5'-flanking tRNA regions of the animal genomes are highly heterogeneous and lack a common conserved sequence signature. Interestingly, in the animal genomes the tRNA species that read the same codon share conserved motifs in their upstream regions. Deep-sequencing analysis of 16 human tissues revealed multiple splicing variants of two of the TFIIIB subunits, Bdp1 and Brf1, with tissue-specific expression patterns. These multiple forms most likely modulate the TFIIIB-DNA interactions and explain the lack of a uniform signature motif in the tRNA upstream regions of animal genomes. The anticodon-dependent 5'-flanking motifs provide a possible mechanism for independent regulation of the tRNA transcription in various human tissues.},
  language  = {en}
}
@article{ZhangHankeGogokhiaJiangetal.2015,
  author    = {Zhang, Houbin and Hanke-Gogokhia, Christin and Jiang, Li and Li, Xiaobo and Wang, Pu and Gerstner, Cecilia D. and Frederick, Jeanne M. and Yang, Zhenglin and Baehr, Wolfgang},
  title     = {Mistrafficking of prenylated proteins causes retinitis pigmentosa 2},
  series = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology},
  volume    = {29},
  journal   = {The FASEB journal : the official journal of the Federation of American Societies for Experimental Biology},
  number    = {3},
  publisher = {Federation of American Societies for Experimental Biology},
  address   = {Bethesda},
  issn      = {0892-6638},
  doi       = {10.1096/fj.14-257915},
  pages     = {932 -- 942},
  year      = {2015},
  abstract  = {The retinitis pigmentosa 2 polypeptide (RP2) functions as a GTPase-activating protein (GAP) for ARL3 (Arf-like protein 3), a small GTPase. ARL3 is an effector of phosphodiesterase 6 Delta (PDE6D), a prenyl-binding protein and chaperone of prenylated protein in photoreceptors. Mutations in the human RP2 gene cause X-linked retinitis pigmentosa (XLRP) and cone-rod dystrophy (XL-CORD). To study mechanisms causing XLRP, we generated an RP2 knockout mouse. The RP2h(-/-) mice exhibited a slowly progressing rod-cone dystrophy simulating the human disease. RP2h(-/-) scotopic a-wave and photopic b-wave amplitudes declined at 1 mo of age and continued to decline over the next 6 mo. Prenylated PDE6 subunits and G-protein coupled receptor kinase 1 (GRK1) were unable to traffic effectively to the RP2h(-/-) outer segments. Mechanistically, absence of RP2 GAP activity increases ARL3-GTP levels, forcing PDE6D to assume a predominantly "closed" conformation that impedes binding of lipids. Lack of interaction disrupts trafficking of PDE6 and GRK1 to their destination, the photoreceptor outer segments. We propose that hyperactivity of ARL3-GTP in RP2 knockout mice and human patients with RP2 null alleles leads to XLRP resembling recessive rod-cone dystrophy.},
  language  = {en}
}
@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}
}
@article{ZhangHuYangetal.2022,
  author    = {Zhang, Kai and Hu, Jiege and Yang, Shuai and Xu, Wei and Wang, Zhichao and Zhuang, Peiwen and Grossart, Hans-Peter and Luo, Zhuhua},
  title     = {Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1},
  series = {Journal of hazardous materials},
  volume    = {437},
  journal   = {Journal of hazardous materials},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0304-3894},
  doi       = {10.1016/j.jhazmat.2022.129406},
  pages     = {10},
  year      = {2022},
  abstract  = {Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80\% of Impranil PU after 3 days of incubation at 28 celcius by breaking the carbonyl groups (1732 cm(-1)) and C-N-H bonds (1532 cm(-1) and 1247 cm(-1)) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation " was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.},
  language  = {en}
}
@article{ZhangCaoXuetal.2022,
  author    = {Zhang, Naimeng and Cao, Xianyong and Xu, Qinghai and Huang, Xiaozhong and Herzschuh, Ulrike and Shen, Zhongwei and Peng, Wei and Liu, Sisi and Wu, Duo and Wang, Jian and Xia, Huan and Zhang, Dongju and Chen, Fahu},
  title     = {Vegetation change and human-environment interactions in the Qinghai Lake Basin, northeastern Tibetan Plateau, since the last deglaciation},
  series = {Catena},
  volume    = {210},
  journal   = {Catena},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0341-8162},
  doi       = {10.1016/j.catena.2021.105892},
  pages     = {14},
  year      = {2022},
  abstract  = {The nature of the interaction between prehistoric humans and their environment, especially the vegetation, has long been of interest. The Qinghai Lake Basin in North China is well-suited to exploring the interactions between prehistoric humans and vegetation in the Tibetan Plateau, because of the comparatively dense distribution of archaeological sites and the ecologically fragile environment. Previous pollen studies of Qinghai Lake have enabled a detailed reconstruction of the regional vegetation, but they have provided relatively little information on vegetation change within the Qinghai Lake watershed. To address the issue we conducted a pollen-based vegetation reconstruction for an archaeological site (YWY), located on the southern shore of Qinghai Lake. We used high temporal-resolution pollen records from the YWY site and from Qinghai Lake, spanning the interval since the last deglaciation (15.3 kyr BP to the present) to quantitatively reconstruct changes in the local and regional vegetation using Landscape Reconstruction Algorithm models. The results show that, since the late glacial, spruce forest grew at high altitudes in the surrounding mountains, while the lakeshore environment was occupied mainly by shrub-steppe. From the lateglacial to the middle Holocene, coniferous woodland began to expand downslope and reached the YWY site at 7.1 kyr BP. The living environment of the local small groups of Paleolithic-Epipaleolithic humans (during 15.3-13.1 kyr BP and 9-6.4 kyr BP) changed from shrub-steppe to coniferous forest-steppe. The pollen record shows no evidence of pronounced changes in the vegetation community corresponding to human activity. However, based on a comparison of the local and regional vegetation reconstructions, low values of biodiversity and a significant increase in two indicators of vegetation degradation, Chenopodiaceae and Rosaceae, suggest that prehistoric hunters-gatherers likely disturbed the local vegetation during 9.0-6.4 kyr BP. Our findings are a preliminary attempt to study human-environment interactions at Paleolithic-Epipaleolithic sites in the region, and they contribute to ongoing environmental archaeology research in the Tibetan Plateau.},
  language  = {en}
}
@article{ZhangLiuMachatscheketal.2022,
  author    = {Zhang, Shanshan and Liu, Yue and Machatschek, Rainhard Gabriel and Lendlein, Andreas},
  title     = {Ultrathin collagen type I films formed at the air-water interface},
  series = {MRS advances : a journal of the Materials Research Society (MRS)},
  volume    = {7},
  journal   = {MRS advances : a journal of the Materials Research Society (MRS)},
  number    = {4},
  publisher = {Springer Nature Switzerland AG},
  address   = {Cham},
  issn      = {2059-8521},
  doi       = {10.1557/s43580-021-00160-8},
  pages     = {56 -- 62},
  year      = {2022},
  abstract  = {Collagen-based biomaterials with oriented fibrils have shown great application potential in medicine. However, it is still challenging to control the type I collagen fibrillogenesis in ultrathin films. Here, we report an approach to produce cohesive and well-organized type I collagen ultrathin films of about 10 nm thickness using the Langmuir-Blodgett technique. Ellipsometry, rheology, and Brewster angle microscopy are applied to investigate in situ how the molecules behave at the air-water interface, both at room temperature and 37 degrees C. The interfacial storage modulus observed at room temperature vanishes upon heating, indicating the existence and disappearance of the network structure in the protein nanosheet. The films were spanning over holes as large as 1 mm diameter when transferred at room temperature, proving the strong cohesive interactions. A highly aligned and fibrillar structure was observed by atomic force microscopy (AFM) and optical microscopy.},
  language  = {en}
}
@article{ZhangBramskiTutusetal.2019,
  author    = {Zhang, Shuhao and Bramski, Julia and Tutus, Murat and Pietruszka, J{\"o}rg and B{\"o}ker, Alexander and Reinicke, Stefan},
  title     = {A Biocatalytically Active Membrane Obtained from Immobilization of 2-Deoxy-D-ribose-5-phosphate Aldolase on a Porous Support},
  series = {ACS applied materials \& interfaces},
  volume    = {11},
  journal   = {ACS applied materials \& interfaces},
  number    = {37},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1944-8244},
  doi       = {10.1021/acsami.9b12029},
  pages     = {34441 -- 34453},
  year      = {2019},
  abstract  = {Aldol reactions play an important role in organic synthesis, as they belong to the class of highly beneficial C-C-linking reactions. Aldol-type reactions can be efficiently and stereoselectively catalyzed by the enzyme 2-deoxy-D-ribose-5-phosphate aldolase (DERA) to gain key intermediates for pharmaceuticals such as atorvastatin. The immobilization of DERA would open the opportunity for a continuous operation mode which gives access to an efficient, large-scale production of respective organic intermediates. In this contribution, we synthesize and utilize DERA/polymer conjugates for the generation and fixation of a DERA bearing thin film on a polymeric membrane support. The conjugation strongly increases the tolerance of the enzyme toward the industrial relevant substrate acetaldehyde while UV-cross-linkable groups along the conjugated polymer chains provide the opportunity for covalent binding to the support. First, we provide a thorough characterization of the conjugates followed by immobilization tests on representative, nonporous cycloolefinic copolymer supports. Finally, immobilization on the target supports constituted of polyacrylonitrile (PAN) membranes is performed, and the resulting enzymatically active membranes are implemented in a simple membrane module setup for the first assessment of biocatalytic performance in the continuous operation mode using the combination hexanal/acetaldehyde as the substrate.},
  language  = {en}
}
@article{ZhangUrbanMiharaetal.2010,
  author    = {Zhang, Wanjiao and Urban, Alexander and Mihara, Hisaaki and Leimk{\"u}hler, Silke and Kurihara, Tatsuo and Esaki, Nobuyoshi},
  title     = {IscS functions as a primary sulfur-donating enzyme by interacting specifically with MoeB and MoaD in the biosynthesis of molybdopterin in escherichia coli},
  issn      = {0021-9258},
  doi       = {10.1074/jbc.M109.082172},
  year      = {2010},
  abstract  = {The persulfide sulfur formed on an active site cysteine residue of pyridoxal 5'-phosphate-dependent cysteine desulfurases is subsequently incorporated into the biosynthetic pathways of a variety of sulfur-containing cofactors and thionucleosides. In molybdenum cofactor biosynthesis, MoeB activates the C terminus of the MoaD subunit of molybdopterin (MPT) synthase to form MoaD-adenylate, which is subsequently converted to a thiocarboxylate for the generation of the dithiolene group of MPT. It has been shown that three cysteine desulfurases (CsdA, SufS, and IscS) of Escherichia coli can transfer sulfur from L-cysteine to the thiocarboxylate of MoaD in vitro. Here, we demonstrate by surface plasmon resonance analyses that IscS, but not CsdA or SufS, interacts with MoeB and MoaD. MoeB and MoaD can stimulate the IscS activity up to 1.6-fold. Analysis of the sulfuration level of MoaD isolated from strains defective in cysteine desulfurases shows a largely decreased sulfuration level of the protein in an iscS deletion strain but not in a csdA/sufS deletion strain. We also show that another iscS deletion strain of E. coli accumulates compound Z, a direct oxidation product of the immediate precursor of MPT, to the same extent as an MPT synthase-deficient strain. In contrast, analysis of the content of compound Z in Delta csdA and Delta sufS strains revealed no such accumulation. These findings indicate that IscS is the primary physiological sulfur-donating enzyme for the generation of the thiocarboxylate of MPT synthase in MPT biosynthesis.},
  language  = {en}
}
@article{ZhangCasertaYarmanetal.2021,
  author    = {Zhang, Xiaorong and Caserta, Giorgio and Yarman, Aysu and Supala, Eszter and Tadjoung Waffo, Armel Franklin and Wollenberger, Ulla and Gyurcsanyi, Robert E. and Zebger, Ingo and Scheller, Frieder W.},
  title     = {"Out of Pocket" protein binding},
  series = {Chemosensors},
  volume    = {9},
  journal   = {Chemosensors},
  number    = {6},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2227-9040},
  doi       = {10.3390/chemosensors9060128},
  pages     = {13},
  year      = {2021},
  abstract  = {The epitope imprinting approach applies exposed peptides as templates to synthesize Molecularly Imprinted Polymers (MIPs) for the recognition of the parent protein. While generally the template protein binding to such MIPs is considered to occur via the epitope-shaped cavities, unspecific interactions of the analyte with non-imprinted polymer as well as the detection method used may add to the complexity and interpretation of the target rebinding. To get new insights on the effects governing the rebinding of analytes, we electrosynthesized two epitope-imprinted polymers using the N-terminal pentapeptide VHLTP-amide of human hemoglobin (HbA) as the template. MIPs were prepared either by single-step electrosynthesis of scopoletin/pentapeptide mixtures or electropolymerization was performed after chemisorption of the cysteine extended VHLTP peptide. Rebinding of the target peptide and the parent HbA protein to the MIP nanofilms was quantified by square wave voltammetry using a redox probe gating, surface enhanced infrared absorption spectroscopy, and atomic force microscopy. While binding of the pentapeptide shows large influence of the amino acid sequence, all three methods revealed strong non-specific binding of HbA to both polyscopoletin-based MIPs with even higher affinities than the target peptides.},
  language  = {en}
}
@article{ZhangYarmanErdossyetal.2018,
  author    = {Zhang, Xiaorong and Yarman, Aysu and Erdossy, Julia and Katz, Sagie and Zebger, Ingo and Jetzschmann, Katharina J. and Altintas, Zeynep and Wollenberger, Ulla and Gyurcsanyi, Robert E. and Scheller, Frieder W.},
  title     = {Electrosynthesized MIPs for transferrin},
  series = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics},
  volume    = {105},
  journal   = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics},
  publisher = {Elsevier},
  address   = {Oxford},
  issn      = {0956-5663},
  doi       = {10.1016/j.bios.2018.01.011},
  pages     = {29 -- 35},
  year      = {2018},
  abstract  = {Molecularly imprinted polymer (MP) nanofilrns for transferrin (Trf) have been synthesized on gold surfaces by electro-polymerizing the functional monomer scopoletin in the presence of the protein target or around pre-adsorbed Trf. As determined by atomic force microscopy (AFM) the film thickness was comparable with the molecular dimension of the target. The target (re)binding properties of the electro-synthesized MIP films was evaluated by cyclic voltammetry (CV) and square wave voltammetry (SWV) through the target-binding induced permeability changes of the MIP nanofilms to the ferricyanide redox marker, as well as by surface plasmon resonance (SPR) and surface enhanced infrared absorption spectroscopy (SEIRAS) of the immobilized protein molecules. For Trf a linear concentration dependence in the lower micromolar range and an imprinting factor of similar to 5 was obtained by SWV and SPR. Furthermore, non-target proteins including the iron-free apo-Trf were discriminated by pronounced size and shape specificity. Whilst it is generally assumed that the rebinding of the target or of cross-reacting proteins exclusively takes place at the polymer here we considered also the interaction of the protein molecules with the underlying gold transducers. We demonstrate by SWV that adsorption of proteins suppresses the signal of the redox marker even at the bare gold surface and by SEIRAS that the treatment of the MIP with proteinase K or NaOH only partially removes the target protein. Therefore, we conclude that when interpreting binding of proteins to directly MIP-covered gold electrodes the interactions between the protein and the gold surface should also be considered.},
  language  = {en}
}
@article{ZhangChenSiemiatkowskaetal.2020,
  author    = {Zhang, Youjun and Chen, Moxian and Siemiatkowska, Beata and Toleco, Mitchell Rey and Jing, Yue and Strotmann, Vivien and Zhang, Jianghua and Stahl, Yvonne and Fernie, Alisdair R.},
  title     = {A highly efficient agrobacterium-mediated method for transient gene expression and functional studies in multiple plant species},
  series = {Plant Communications},
  volume    = {1},
  journal   = {Plant Communications},
  number    = {5},
  publisher = {Science Direct},
  address   = {New York},
  issn      = {2590-3462},
  pages     = {12},
  year      = {2020},
  abstract  = {Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.},
  language  = {en}
}
@article{ZhangSunFettkeetal.2014,
  author    = {Zhang, Youjun and Sun, Feng and Fettke, J{\"o}rg and Schoettler, Mark Aurel and Ramsden, Lawrence and Fernie, Alisdair R. and Lim, Boon Leong},
  title     = {Heterologous expression of AtPAP2 in transgenic potato influences carbon metabolism and tuber development},
  series = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences},
  volume    = {588},
  journal   = {FEBS letters : the journal for rapid publication of short reports in molecular biosciences},
  number    = {20},
  publisher = {Elsevier},
  address   = {Amsterdam},
  issn      = {0014-5793},
  doi       = {10.1016/j.febslet.2014.08.019},
  pages     = {3726 -- 3731},
  year      = {2014},
  abstract  = {Changes in carbon flow and sink/source activities can affect floral, architectural, and reproductive traits of plants. In potato, overexpression (OE) of the purple acid phosphatase 2 of Arabidopsis (AtPAP2) resulted in earlier flowering, faster growth rate, increased tubers and tuber starch content, and higher photosynthesis rate. There was a significant change in sucrose, glucose and fructose levels in leaves, phloem and sink biomass of the OE lines, consistent with an increased expression of sucrose transporter 1 (StSUT1). Furthermore, the expression levels and enzyme activity of sucrose-phosphate synthase (SPS) were also significantly increased in the OE lines. These findings strongly suggest that higher carbon supply from the source and improved sink strength can improve potato tuber yield. (C) 2014 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.},
  language  = {en}
}
@article{ZhangRammingHeinkeetal.2019,
  author    = {Zhang, Yunming and Ramming, Anna and Heinke, Lisa and Altschmied, Lothar and Slotkin, R. Keith and Becker, J{\"o}rg D. and Kappel, Christian and Lenhard, Michael},
  title     = {The poly(A) polymerase PAPS1 interacts with the RNA-directed DNA-methylation pathway in sporophyte and pollen development},
  series = {The plant journal},
  volume    = {99},
  journal   = {The plant journal},
  number    = {4},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0960-7412},
  doi       = {10.1111/tpj.14348},
  pages     = {655 -- 672},
  year      = {2019},
  abstract  = {RNA-based processes play key roles in the regulation of eukaryotic gene expression. This includes both the processing of pre-mRNAs into mature mRNAs ready for translation and RNA-based silencing processes, such as RNA-directed DNA methylation (RdDM). Polyadenylation of pre-mRNAs is one important step in their processing and is carried out by three functionally specialized canonical nuclear poly(A) polymerases in Arabidopsis thaliana. Null mutations in one of these, termed PAPS1, result in a male gametophytic defect. Using a fluorescence-labelling strategy, we have characterized this defect in more detail using RNA and small-RNA sequencing. In addition to global defects in the expression of pollen-differentiation genes, paps1 null-mutant pollen shows a strong overaccumulation of transposable element (TE) transcripts, yet a depletion of 21- and particularly 24-nucleotide-long short interfering RNAs (siRNAs) and microRNAs (miRNAs) targeting the corresponding TEs. Double-mutant analyses support a specific functional interaction between PAPS1 and components of the RdDM pathway, as evident from strong synergistic phenotypes in mutant combinations involving paps1, but not paps2 paps4, mutations. In particular, the double-mutant of paps1 and rna-dependent rna polymerase 6 (rdr6) shows a synergistic developmental phenotype disrupting the formation of the transmitting tract in the female gynoecium. Thus, our findings in A. thaliana uncover a potentially general link between canonical poly(A) polymerases as components of mRNA processing and RdDM, reflecting an analogous interaction in fission yeast.},
  language  = {en}
}
@article{ZhaoXiaWuetal.2018,
  author    = {Zhao, Liming and Xia, Yan and Wu, Xiao-Yuan and Schippers, Jos H. M. and Jing, Hai-Chun},
  title     = {Phenotypic analysis and molecular markers of leaf senescence},
  series = {Plant Senescence: Methods and Protocols},
  volume    = {1744},
  journal   = {Plant Senescence: Methods and Protocols},
  publisher = {Humana Press Inc.},
  address   = {Totowa},
  isbn      = {978-1-4939-7672-0},
  issn      = {1064-3745},
  doi       = {10.1007/978-1-4939-7672-0_3},
  pages     = {35 -- 48},
  year      = {2018},
  abstract  = {The process of leaf senescence consists of the final stage of leaf development. It has evolved as a mechanism to degrade macromolecules and micronutrients and remobilize them to other developing parts of the plant; hence it plays a central role for the survival of plants and crop production. During senescence, a range of physiological, morphological, cellular, and molecular events occur, which are generally referred to as the senescence syndrome that includes several hallmarks such as visible yellowing, loss of chlorophyll and water content, increase of ion leakage and cell death, deformation of chloroplast and cell structure, as well as the upregulation of thousands of so-called senescence-associated genes (SAGs) and downregulation of photosynthesis-associated genes (PAGs). This chapter is devoted to methods characterizing the onset and progression of leaf senescence at the morphological, physiological, cellular, and molecular levels. Leaf senescence normally progresses in an age-dependent manner but is also induced prematurely by a variety of environmental stresses in plants. Focused on the hallmarks of the senescence syndrome, a series of protocols is described to asses quantitatively the senescence process caused by developmental cues or environmental perturbations. We first briefly describe the senescence process, the events associated with the senescence syndrome, and the theories and methods to phenotype senescence. Detailed protocols for monitoring senescence in planta and in vitro, using the whole plant and the detached leaf, respectively, are presented. For convenience, most of the protocols use the model plant species Arabidopsis and rice, but they can be easily extended to other plants.},
  language  = {en}
}
@article{ZhivkovaKieckerLangeretal.2018,
  author    = {Zhivkova, Veselina and Kiecker, Felix and Langer, Peter and Eberle, J{\"u}rgen},
  title     = {Crucial role of reactive oxygen species (ROS) for the proapoptotic effects of indirubin derivative DKP-073 in melanoma cells},
  series = {Molecular carcinogenesis},
  volume    = {58},
  journal   = {Molecular carcinogenesis},
  number    = {2},
  publisher = {Wiley},
  address   = {Hoboken},
  issn      = {0899-1987},
  doi       = {10.1002/mc.22924},
  pages     = {258 -- 269},
  year      = {2018},
  abstract  = {Melanoma represents a prime example demonstrating the success of targeted therapy in cancer. Nevertheless, it remained a deadly disease until now, and the identification of new, independent strategies as well as the understanding of their molecular mechanisms may help to finally overcome the high mortality. Both indirubins and TNF-related apoptosis-inducing ligand (TRAIL) represent promising candidates. Here, the indirubin derivative DKP-073 is shown to trigger apoptosis in melanoma cells, which is enhanced by the combination with TRAIL and is accompanied by complete loss of cell viability. Addressing the signaling cascade, characteristic molecular steps were identified as caspase-3 activation, downregulation of XIAP, upregulation of p53 and TRAIL receptor 2, loss of mitochondrial membrane potential, and STAT-3 dephosphorylation. The decisive step, however, turned out to be the early production of ROS already at 1 h. This was proven by antioxidant pretreatment, which completely abolished apoptosis induction and loss of cell viability as well as abrogated all signaling effects listed above. Thus, ROS appeared as upstream of all proapoptotic signaling. The data indicate a dominant role of ROS in apoptosis regulation, and the new pathway may expose a possible Achilles heel of melanoma.},
  language  = {en}
}
@article{ZhuSchluppTiedemann2017,
  author    = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph},
  title     = {Allele-specific expression at the androgen receptor alpha gene in a hybrid unisexual fish, the Amazon molly (Poecilia formosa)},
  series = {PLoS one},
  volume    = {12},
  journal   = {PLoS one},
  number    = {10},
  publisher = {PLoS},
  address   = {Lawrence, Kan.},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0186411},
  pages     = {1 -- 14},
  year      = {2017},
  abstract  = {The all-female Amazon molly (Poecilia formosa) is the result of a hybridization of the Atlantic molly (P. mexicana) and the sailfin molly (P. latipinna) approximately 120,000 years ago. As a gynogenetic species, P. formosa needs to copulate with heterospecific males including males from one of its bisexual ancestral species. However, the sperm only triggers embryogenesis of the diploid eggs. The genetic information of the sperm donor typically will not contribute to the next generation of P. formosa. Hence, P. formosa possesses generally one allele from each of its ancestral species at any genetic locus. This raises the question whether both ancestral alleles are equally expressed in P. formosa. Allele-specific expression (ASE) has been previously assessed in various organisms, e.g., human and fish, and ASE was found to be important in the context of phenotypic variability and disease. In this study, we utilized Real-Time PCR techniques to estimate ASE of the androgen receptor alpha (arα) gene in several distinct tissues of Amazon mollies. We found an allelic bias favoring the maternal ancestor (P. mexicana) allele in ovarian tissue. This allelic bias was not observed in the gill or the brain tissue. Sequencing of the promoter regions of both alleles revealed an association between an Indel in a known CpG island and differential expression. Future studies may reveal whether our observed cis-regulatory divergence is caused by an ovary-specific trans-regulatory element, preferentially activating the allele of the maternal ancestor.},
  language  = {en}
}
@article{ZhuSchluppTiedemann2016,
  author    = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph},
  title     = {Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors},
  series = {PLoS one},
  volume    = {11},
  journal   = {PLoS one},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1932-6203},
  doi       = {10.1371/journal.pone.0156209},
  pages     = {19},
  year      = {2016},
  abstract  = {The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., ar\&\#945;/ar\&\#946;, er\&\#945;/er\&\#946;1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, er\&\#946;1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of er\&\#945; in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.},
  language  = {en}
}
@article{ZhuSchluppTiedemann2016,
  author    = {Zhu, Fangjun and Schlupp, Ingo and Tiedemann, Ralph},
  title     = {Sequence Evolution and Expression of the Androgen Receptor and Other Pathway-Related Genes in a Unisexual Fish, the Amazon Molly, Poecilia formosa, and Its Bisexual Ancestors},
  series = {PLoS one},
  volume    = {11},
  journal   = {PLoS one},
  number    = {6},
  publisher = {PLoS},
  address   = {Lawrence, Kan.},
  issn      = {1932-6203},
  doi       = {10.1371/JOURNAL.PONE.0156209},
  pages     = {19},
  year      = {2016},
  abstract  = {The all-female Amazon molly (Poecilia formosa) originated from a single hybridization of two bisexual ancestors, Atlantic molly (Poecilia mexicana) and sailfin molly (Poecilia latipinna). As a gynogenetic species, the Amazon molly needs to copulate with a heterospecific male, but the genetic information of the sperm-donor does not contribute to the next generation, as the sperm only acts as the trigger for the diploid eggs' embryogenesis. Here, we study the sequence evolution and gene expression of the duplicated genes coding for androgen receptors (ars) and other pathway-related genes, i.e., the estrogen receptors (ers) and cytochrome P450, family19, subfamily A, aromatase genes (cyp19as), in the Amazon molly, in comparison to its bisexual ancestors. Mollies possess-as most other teleost fish—two copies of the ar, er, and cyp19a genes, i.e., arα/arβ, erα/erβ1, and cyp19a1 (also referred as cyp19a1a)/cyp19a2 (also referred to as cyp19a1b), respectively. Non-synonymous single nucleotide polymorphisms (SNPs) among the ancestral bisexual species were generally predicted not to alter protein function. Some derived substitutions in the P. mexicana and one in P. formosa are predicted to impact protein function. We also describe the gene expression pattern of the ars and pathway-related genes in various tissues (i.e., brain, gill, and ovary) and provide SNP markers for allele specific expression research. As a general tendency, the levels of gene expression were lowest in gill and highest in ovarian tissues, while expression levels in the brain were intermediate in most cases. Expression levels in P. formosa were conserved where expression did not differ between the two bisexual ancestors. In those cases where gene expression levels significantly differed between the bisexual species, P. formosa expression was always comparable to the higher expression level among the two ancestors. Interestingly, erβ1 was expressed neither in brain nor in gill in the analyzed three molly species, which implies a more important role of erα in the estradiol synthesis pathway in these tissues. Furthermore, our data suggest that interactions of steroid-signaling pathway genes differ across tissues, in particular the interactions of ars and cyp19as.},
  language  = {en}
}
@article{ZibulskiWesenerWilkesetal.2017,
  author    = {Zibulski, Romy and Wesener, Felix and Wilkes, Heinz and Plessen, Birgit and Pestryakova, Luidmila Agafyevna and Herzschuh, Ulrike},
  title     = {C / N ratio, stable isotope (delta C-13, delta N-15), and n-alkane patterns of brown mosses along hydrological gradients of low-centred polygons of the Siberian Arctic},
  series = {Biogeosciences},
  volume    = {14},
  journal   = {Biogeosciences},
  publisher = {Copernicus},
  address   = {G{\"o}ttingen},
  issn      = {1726-4170},
  doi       = {10.5194/bg-14-1617-2017},
  pages     = {1617 -- 1630},
  year      = {2017},
  abstract  = {Mosses are a major component of the arctic vegetation, particularly in wetlands. We present C / N atomic ratio, delta C-13 and delta N-15 data of 400 brown-moss samples belonging to 10 species that were collected along hydrological gradients within polygonal mires located on the southern Taymyr Peninsula and the Lena River delta in northern Siberia. Additionally, n-alkane patterns of six of these species (16 samples) were investigated. The aim of the study is to see whether the inter-and intraspecific differences in C / N, isotopic compositions and n-alkanes are indicative of habitat, particularly with respect to water level. Overall, we find high variability in all investigated parameters for two different moisture-related groups of moss species. The C / N ratios range between 11 and 53 (median: 32) and show large variations at the intraspecific level. However, species preferring a dry habitat (xero-mesophilic mosses) show higher C / N ratios than those preferring a wet habitat (meso-hygrophilic mosses). The delta C-13 values range between 37.0 and 22.5\% (median D 27.8 \%). The delta N-15 values range between 6.6 and C 1.7\%(median D 2.2 \%). We find differences in delta C-13 and delta N-15 compositions between both habitat types. For some species of the meso-hygrophilic group, we suggest that a relationship between the individ-ual habitat water level and isotopic composition can be inferred as a function of microbial symbiosis. The n-alkane distribution also shows differences primarily between xeromesophilic and meso-hygrophilic mosses, i. e. having a dominance of n-alkanes with long (n-C29, n-C31 /and intermediate (n-C25 /chain lengths, respectively. Overall, our results reveal that C / N ratios, isotopic signals and n-alkanes of studied brown-moss taxa from polygonal wetlands are characteristic of their habitat.},
  language  = {en}
}
@article{ZiegeHennigeSchulzMueckschetal.2012,
  author    = {Ziege, Madlen and Hennige-Schulz, Carmen and Muecksch, Frauke and Bierbach, David and Tiedemann, Ralph and Streit, Bruno and Plath, Martin},
  title     = {A comparison of two methods to assess audience-induced changes in male mate choice},
  series = {Current zoology},
  volume    = {58},
  journal   = {Current zoology},
  number    = {1},
  publisher = {Current Zoology},
  address   = {Beijing},
  issn      = {1674-5507},
  pages     = {84 -- 94},
  year      = {2012},
  abstract  = {Multidirectional communicative interactions in social networks can have a profound effect on mate choice behavior. Male Atlantic molly Poecilia mexicana exhibit weaker mating preferences when an audience male is presented. This could be a male strategy to reduce sperm competition risk: interacting more equally with different females may be advantageous because rivals might copy mate choice decisions. In line with this hypothesis, a previous study found males to show a strong audience effect when being observed while exercising mate choice, but not when the rival was presented only before the choice tests. Audience effects on mate choice decisions have been quantified in poeciliid fishes using association preference designs, but it remains unknown if patterns found from measuring association times translate into actual mating behavior. Thus, we created five audience treatments simulating different forms of perceived sperm competition risk and determined focal males' mating preferences by scoring pre-mating (nipping) and mating behavior (gonopodial thrusting). Nipping did not reflect the pattern that was found when association preferences were measured, while a very similar pattern was uncovered in thrusting behavior. The strongest response was observed when the audience could eavesdrop on the focal male's behavior. A reduction in the strength of focal males' preferences was also seen after the rival male had an opportunity to mate with the focal male's preferred mate. In comparison, the reduction of mating preferences in response to an audience was greater when measuring association times than actual mating behavior. While measuring direct sexual interactions between the focal male and both stimulus females not only the male's motivational state is reflected but also females' behavior such as avoidance of male sexual harassment.},
  language  = {en}
}
@article{ZiegeHermannKriestenetal.2020,
  author    = {Ziege, Madlen and Hermann, Bernd Timo and Kriesten, Stefanie and Merker, Stefan and Ullmann, Wiebke and Streit, Bruno and Wenninger, Sandra and Plath, Martin},
  title     = {Ranging behavior of European rabbits (Oryctolagus cuniculus) in urban and suburban landscapes},
  series = {Mammal research / Mammal Research Institute, Polish Academy of Sciences},
  volume    = {65},
  journal   = {Mammal research / Mammal Research Institute, Polish Academy of Sciences},
  number    = {3},
  publisher = {Springer},
  address   = {Heidelberg},
  issn      = {2199-2401},
  doi       = {10.1007/s13364-020-00490-2},
  pages     = {607 -- 614},
  year      = {2020},
  abstract  = {Various mammals, particularly carnivores, reportedly establish smaller home ranges in urban compared with rural areas. This may be because urban environments provide optimal resources within a small area, negating the requirement to range further, or because habitat fragmentation constrains ranging behavior. Comparable information on urban populations of herbivorous mammalian species (such as European rabbits) is scarce. To fill this knowledge gap, we radio-tracked 13 individuals (seven females and six males) equipped with radio collars in a suburban and an urban study site in the city of Frankfurt am Main in Germany during the reproductive season (March to September) of 2012. The study sites differed in levels of habitat fragmentation. We report the smallest home ranges ever described for this species, with mean 95\% minimum convex polygons (MCPs) covering 0.50 ha, while no consistent differences between sites were uncovered. We occasionally tracked individuals crossing streets underground (in burrows), suggesting that streets may restrict the ranging behavior of rabbits-and possibly other burrowing species-to a much lesser extent than previously thought. We conclude that heterogeneous landscape structures, made up of a diverse mosaic of buildings, parks, and gardens, provide sufficient food and shelter in close proximity to burrows at both study sites. Therefore, our data support the hypothesis that optimal resources constrain ranges in this case rather than habitat fragmentation.},
  language  = {en}
}
@article{ZielhoferSchmidtReicheetal.2022,
  author    = {Zielhofer, Christoph and Schmidt, Johannes and Reiche, Niklas and Tautenhahn, Marie and Ballasus, Helen and Burkart, Michael and Linst{\"a}dter, Anja and Dietze, Elisabeth and Kaiser, Knut and Mehler, Natascha},
  title     = {The lower Havel River Region (Brandenburg, Germany)},
  series = {Water},
  volume    = {14},
  journal   = {Water},
  number    = {3},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2073-4441},
  doi       = {10.3390/w14030480},
  pages     = {23},
  year      = {2022},
  abstract  = {Instrumental data show that the groundwater and lake levels in Northeast Germany have decreased over the past decades, and this process has accelerated over the past few years. In addition to global warming, the direct influence of humans on the local water balance is suspected to be the cause. Since the instrumental data usually go back only a few decades, little is known about the multidecadal to centennial-scale trend, which also takes long-term climate variation and the long-term influence by humans on the water balance into account. This study aims to quantitatively reconstruct the surface water areas in the Lower Havel Inner Delta and of adjacent Lake Gulpe in Brandenburg. The analysis includes the calculation of surface water areas from historical and modern maps from 1797 to 2020. The major finding is that surface water areas have decreased by approximately 30\% since the pre-industrial period, with the decline being continuous. Our data show that the comprehensive measures in Lower Havel hydro-engineering correspond with groundwater lowering that started before recent global warming. Further, large-scale melioration measures with increasing water demands in the upstream wetlands beginning from the 1960s to the 1980s may have amplified the decline in downstream surface water areas.},
  language  = {en}
}