@misc{ZhangLenhard2017,
  author    = {Zhang, Yunming and Lenhard, Michael},
  title     = {Exiting Already? Molecular Control of Cell-Proliferation Arrest in Leaves: Cutting Edge},
  series = {Molecular plant},
  volume    = {10},
  journal   = {Molecular plant},
  publisher = {Cell Press},
  address   = {Cambridge},
  issn      = {1674-2052},
  doi       = {10.1016/j.molp.2017.05.004},
  pages     = {909 -- 911},
  year      = {2017},
  language  = {en}
}
@phdthesis{Zhang2018,
  author    = {Zhang, Yunming},
  title     = {Understanding the functional specialization of poly(A) polymerases in Arabidopsis thaliana},
  school      = {Universit{\"a}t Potsdam},
  pages     = {131},
  year      = {2018},
  language  = {de}
}
@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}
}
@misc{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 = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {5},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-52425},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-524254},
  pages     = {14},
  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{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}
}
@phdthesis{Zhang2016,
  author    = {Zhang, Youjun},
  title     = {Investigation of the TCA cycle and glycolytic metabolons and their physiological impacts in plants},
  school      = {Universit{\"a}t Potsdam},
  pages     = {175},
  year      = {2016},
  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{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}
}
@phdthesis{Zhang2019,
  author    = {Zhang, Xiaorong},
  title     = {Electrosynthesis and characterization of molecularly imprinted polymers for peptides and proteins},
  school      = {Universit{\"a}t Potsdam},
  pages     = {116},
  year      = {2019},
  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{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{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{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{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}
}
@phdthesis{Zhang2020,
  author    = {Zhang, Jianrui},
  title     = {Completely water-based emulsions as compartmentalized systems via pickering stabilization},
  doi       = {10.25932/publishup-47654},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-476542},
  school      = {Universit{\"a}t Potsdam},
  pages     = {II, 119},
  year      = {2020},
  abstract  = {Completely water-based systems are of interest for the development of novel material for various reasons: On one hand, they provide benign environment for biological systems and on the other hand they facilitate effective molecular transport in a membrane-free environment. In order to investigate the general potential of aqueous two-phase systems (ATPSs) for biomaterials and compartmentalized systems, various solid particles were applied to stabilize all-aqueous emulsion droplets. The target ATPS to be investigated should be prepared via mixing of two aqueous solutions of water-soluble polymers, which turn biphasic when exceeding a critical polymer concentration. Hydrophilic polymers with a wide range of molar mass such as dextran/poly(ethylene glycol) (PEG) can therefore be applied. Solid particles adsorbed at the interfaces can be exceptionally efficient stabilizers forming so-called Pickering emulsions, and nanoparticles can bridge the correlation length of polymer solutions and are thereby the best option for water-in-water emulsions. The first approach towards the investigation of ATPS was conducted with all aqueous dextran-PEG emulsions in the presence of poly(dopamine) particles (PDP) in Chapter 4. The water-in-water emulsions were formed with a PEG/dextran system via utilizing PDP as stabilizers. Studies of the formed emulsions were performed via laser scanning confocal microscope (CLSM), optical microscope (OM), cryo-scanning electron microscope (SEM) and tensiometry. The stable emulsions (at least 16 weeks) were demulsified easily via dilution or surfactant addition. Furthermore, the solid PDP at the water-water interface were crosslinked in order to inhibit demulsification of the Pickering emulsion. Transmission electron microscope (TEM) and scanning electron microscope (SEM) were used to visualize the morphology of PDP before and after crosslinking. PDP stabilized water-in-water emulsions were utilized in the following Chapter 5 to form supramolecular compartmentalized hydrogels. Here, hydrogels were prepared in pre-formed water-in-water emulsions and gelled via α-cyclodextrin-PEG (α-CD-PEG) inclusion complex formation. Studies of the formed complexes were performed via X-ray powder diffraction (XRD) and the mechanical properties of the hydrogels were measured with oscillatory shear rheology. In order to verify the compartmentalized state and its triggered decomposition, hydrogels and emulsions were assessed via OM, SEM and CLSM. The last chapter broadens the investigations from the previous two systems by utilizing various carbon nitrides (CN) as different stabilizers in ATPS. CN introduces another way to trigger demulsification, namely irradiation with visible light. Therefore, emulsification and demulsification with various triggers were probed. The investigated all aqueous multi-phase systems will act as model for future fabrication of biocompatible materials, cell micropatterning as well as separation of compartmentalized systems.},
  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{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{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}
}
@misc{ZhangIgnatova2009,
  author    = {Zhang, Gong and Ignatova, Zoya},
  title     = {Generic algorithm to predict the speed of translational elongation : implications for protein biogenesis},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-45007},
  year      = {2009},
  abstract  = {Synonymous codon usage and variations in the level of isoaccepting tRNAs exert a powerful selective force on translation fidelity. We have developed an algorithm to evaluate the relative rate of translation which allows large-scale comparisons of the non-uniform translation rate on the protein biogenesis. Using the complete genomes of Escherichia coli and Bacillus subtilis we show that stretches of codons pairing to minor tRNAs form putative sites to locally attenuate translation; thereby the tendency is to cluster in near proximity whereas long contiguous stretches of slow-translating triplets are avoided. The presence of slow-translating segments positively correlates with the protein length irrespective of the protein abundance. The slow-translating clusters are predominantly located down-stream of the domain boundaries presumably to fine-tune translational accuracy with the folding fidelity of multidomain proteins. Translation attenuation patterns at highly structurally and functionally conserved domains are preserved across the species suggesting a concerted selective pressure on the codon selection and species-specific tRNA abundance in these regions.},
  language  = {en}
}
@misc{ZhangIgnatova2011,
  author    = {Zhang, Gong and Ignatova, Zoya},
  title     = {Folding at the birth of the nascent chain: coordinating translation with co-translational folding},
  series = {Current opinion in structural biology : review of all advances ; evaluation of key references ; comprehensive listing of papers},
  volume    = {21},
  journal   = {Current opinion in structural biology : review of all advances ; evaluation of key references ; comprehensive listing of papers},
  number    = {1},
  publisher = {Elsevier},
  address   = {London},
  issn      = {0959-440X},
  doi       = {10.1016/j.sbi.2010.10.008},
  pages     = {25 -- 31},
  year      = {2011},
  abstract  = {In the living cells, the folding of many proteins is largely believed to begin co-translationally, during their biosynthesis at the ribosomes. In the ribosomal tunnel, the nascent peptide may establish local interactions and stabilize alpha-helical structures. Long-range contacts are more likely outside the ribosomes after release of larger segments of the nascent chain. Examples suggest that domains can attain native-like structure on the ribosome with and without population of folding intermediates. The co-translational folding is limited by the speed of the gradual extrusion of the nascent peptide which imposes conformational restraints on its folding landscape. Recent experimental and in silico modeling studies indicate that translation kinetics fine-tunes co-translational folding by providing a time delay for sequential folding of distinct portions of the nascent chain.},
  language  = {en}
}