@misc{ShapiroHofreiter2014, author = {Shapiro, B. and Hofreiter, Michael}, title = {A paleogenomic perspective on evolution and gene function: new insights from ancient DNA}, series = {Science}, volume = {343}, journal = {Science}, number = {6169}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {0036-8075}, doi = {10.1126/science.1236573}, pages = {7}, year = {2014}, abstract = {The publication of partial and complete paleogenomes within the last few years has reinvigorated research in ancient DNA. No longer limited to short fragments of mitochondrial DNA, inference of evolutionary processes through time can now be investigated from genome-wide data sampled as far back as 700,000 years. Tremendous insights have been made, in particular regarding the hominin lineage. With rare exception, however, a paleogenomic perspective has been mired by the quality and quantity of recoverable DNA. Though conceptually simple, extracting ancient DNA remains challenging, and sequencing ancient genomes to high coverage remains prohibitively expensive for most laboratories. Still, with improvements in DNA isolation and declining sequencing costs, the taxonomic and geographic purview of paleogenomics is expanding at a rapid pace. With improved capacity to screen large numbers of samples for those with high proportions of endogenous ancient DNA, paleogenomics is poised to become a key technology to better understand recent evolutionary events.}, language = {en} } @misc{LecourieuxKappelLecourieuxetal.2014, author = {Lecourieux, Fatma and Kappel, Christian and Lecourieux, David and Serrano, Alejandra and Torres, Elizabeth and Arce-Johnson, Patricio and Delrot, Serge}, title = {An update on sugar transport and signalling in grapevine}, series = {Journal of experimental botany}, volume = {65}, journal = {Journal of experimental botany}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/ert394}, pages = {821 -- 832}, year = {2014}, abstract = {In addition to their role as a source of reduced carbon, sugars may directly or indirectly control a wide range of activities in plant cells, through transcriptional and post-translational regulation. This control has been studied in detail using Arabidopsis thaliana, where genetic analysis offers many possibilities. Much less is known about perennial woody species. For several years, various aspects of sugar sensing and signalling have been investigated in the grape (Vitis vinifera L.) berry, an organ that accumulates high concentrations of hexoses in the vacuoles of flesh cells. Here we review various aspects of this topic: the molecular basis of sugar transport and its regulation by sugars in grapevine; the functional analysis of several sugar-induced genes; the effects of some biotic and abiotic stresses on the sugar content of the berry; and finally the effects of exogenous sugar supply on the ripening process in field conditions. A picture of complex feedback and multiprocess regulation emerges from these data.}, language = {en} } @misc{MillerSchwarz2014, author = {Miller, Jeff and Schwarz, Wolfgang}, title = {Brain signals do not demonstrate unconscious decision making: An interpretation based on graded conscious awareness}, series = {Consciousness and cognition}, volume = {24}, journal = {Consciousness and cognition}, publisher = {Elsevier}, address = {San Diego}, issn = {1053-8100}, doi = {10.1016/j.concog.2013.12.004}, pages = {12 -- 21}, year = {2014}, abstract = {Neuroscientific studies have shown that brain activity correlated with a decision to move can be observed before a person reports being consciously aware of having made that decision (e.g., Libet, Gleason, Wright, \& Pearl, 1983; Soon, Brass, Heinze, \& Haynes, 2008). Given that a later event (i.e., conscious awareness) cannot cause an earlier one (i.e., decision-related brain activity), such results have been interpreted as evidence that decisions are made unconsciously (e.g., Libet, 1985). We argue that this interpretation depends upon an all-or-none view of consciousness, and we offer an alternative interpretation of the early decision-related brain activity based on models in which conscious awareness of the decision to move develops gradually up to the level of a reporting criterion. Under this interpretation, the early brain activity reflects sub-criterion levels of awareness rather than complete absence of awareness and thus does not suggest that decisions are made unconsciously.}, language = {en} } @misc{MacaulaySobelMikolaichuketal.2014, author = {Macaulay, Euan A. and Sobel, Edward and Mikolaichuk, Alexander and Kohn, Barry and Stuart, Finlay M.}, title = {Cenozoic deformation and exhumation history of the Central Kyrgyz Tien Shan}, series = {Tectonics}, volume = {33}, journal = {Tectonics}, number = {2}, publisher = {American Geophysical Union}, address = {Washington}, issn = {0278-7407}, doi = {10.1002/2013TC003376}, pages = {135 -- 165}, year = {2014}, abstract = {New low-temperature thermochronological data from 80 samples in eastern Kyrgyzstan are combined with previously published data from 61 samples to constrain exhumation in a number of mountain ranges in the Central Kyrgyz Tien Shan. All sampled ranges are found to have a broadly consistent Cenozoic exhumation history, characterized by initially low cooling rates (<1 degrees C/Myr) followed by a series of increases in exhumation that occurred diachronously across the region in the late Cenozoic that are interpreted to record the onset of deformation in different mountain ranges. Combined with geological estimates for the onset of proximal deformation, our data suggest that the Central Kyrgyz Tien Shan started deforming in the late Oligocene-early Miocene, leading to the development of several, widely spaced mountain ranges separated by large intermontane basins. Subsequently, more ranges have been constructed in response to significant shortening increases across the Central Kyrgyz Tien Shan, notably in the late Miocene. The order of range construction is interpreted to reflect variations in the susceptibility of inherited structures to reactivation. Reactivated structures are also shown to have significance along strike variations in fault vergence and displacement, which have influenced the development and growth of individual mountain ranges. Moreover, the timing of deformation allows the former extent of many intermontane basins that have since been partitioned to be inferred; this can be linked to the highly time-transgressive onset of late Cenozoic coarse clastic sedimentation.}, language = {en} } @misc{TroppmannBalfanzKrachetal.2014, author = {Troppmann, Britta and Balfanz, Sabine and Krach, Christian and Baumann, Arnd and Blenau, Wolfgang}, title = {Characterization of an Invertebrate-Type Dopamine Receptor of the American Cockroach, Periplaneta americana}, series = {International journal of molecular sciences}, volume = {15}, journal = {International journal of molecular sciences}, number = {1}, publisher = {MDPI}, address = {Basel}, issn = {1422-0067}, doi = {10.3390/ijms15010629}, pages = {629 -- 653}, year = {2014}, abstract = {We have isolated a cDNA coding for a putative invertebrate-type dopamine receptor (Peadop2) from P. americana brain by using a PCR-based strategy. The mRNA is present in samples from brain and salivary glands. We analyzed the distribution of the PeaDOP2 receptor protein with specific affinity-purified polyclonal antibodies. On Western blots, PeaDOP2 was detected in protein samples from brain, subesophageal ganglion, thoracic ganglia, and salivary glands. In immunocytochemical experiments, we detected PeaDOP2 in neurons with their somata being located at the anterior edge of the medulla bilaterally innervating the optic lobes and projecting to the ventro-lateral protocerebrum. In order to determine the functional and pharmacological properties of the cloned receptor, we generated a cell line constitutively expressing PeaDOP2. Activation of PeaDOP2-expressing cells with dopamine induced an increase in intracellular cAMP. In contrast, a C-terminally truncated splice variant of this receptor did not exhibit any functional property by itself. The molecular and pharmacological characterization of the first dopamine receptor from P. americana provides the basis for forthcoming studies focusing on the significance of the dopaminergic system in cockroach behavior and physiology.}, language = {en} } @misc{UnuabonahTaubert2014, author = {Unuabonah, Emmanuel Iyayi and Taubert, Andreas}, title = {Clay-polymer nanocomposites (CPNs): Adsorbents of the future for water treatment}, series = {Applied clay science : an international journal on the application and technology of clays and clay minerals}, volume = {99}, journal = {Applied clay science : an international journal on the application and technology of clays and clay minerals}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0169-1317}, doi = {10.1016/j.clay.2014.06.016}, pages = {83 -- 92}, year = {2014}, abstract = {A class of adsorbents currently receiving growing attention is the clay-polymer nanocomposite (CPN) adsorbents. CPNs effectively treat water by adsorption and flocculation of both inorganic and organic micropollutants from aqueous solutions. Some of these CPNs - when modified with biocides - also have the ability to efficiently remove microorganisms such as Escherichia coli, Pseudomonas aeruginosa, Staphylococcus aureus and Candida albicans from water. CPNs are far more easily recovered from aqueous media than neat clay. They also exhibit far better treatment times than either polymer or clay adsorbents. They have higher adsorption capacity and better life cycles compared with clay alone. CPNs therefore show an excellent potential as highly efficient water and waste treatment agents. This article reviews the various CPNs that have been prepared recently and used as adsorbents in the removal of micropollutants (inorganic, organic and biological) from aqueous solutions. A special focus is placed on CPNs that are not only interesting from an academic point of view but also effectively reduce the concentration of micropollutants in water to safe limits and also on new developments bordering on CPN use as water treatment agent that have not yet realized their full potential. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @misc{PedojaHussonJohnsonetal.2014, author = {Pedoja, Kevin and Husson, Laurent and Johnson, Markes E. and Melnick, Daniel and Witt, Cesar and Pochat, Stephane and Nexer, Maelle and Delcaillau, Bernard and Pinegina, Tatiana and Poprawski, Yohann and Authemayou, Christine and Elliot, Mary and Regard, Vincent and Garestier, Franck}, title = {Coastal staircase sequences reflecting sea-level oscillations and tectonic uplift during the Quaternary and Neogene}, series = {Earth science reviews : the international geological journal bridging the gap between research articles and textbooks}, volume = {132}, journal = {Earth science reviews : the international geological journal bridging the gap between research articles and textbooks}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0012-8252}, doi = {10.1016/j.earscirev.2014.01.007}, pages = {13 -- 38}, year = {2014}, abstract = {Many coasts feature sequences of Quaternary and Neogene shorelines that are shaped by a combination of sea-level oscillations and tectonics. We compiled a global synthesis of sea-level changes for the following highstands: MIS 1, MIS 3, MIS 5e and MIS 11. Also, we date the apparent onset of sequences of paleoshorelines either from published data or tentatively extrapolating an age for the uppermost, purported oldest shoreline in each sequence. Including the most documented MIS 5e benchmark, we identify 926 sequences out of which 185 also feature Holocene shorelines. Six areas are identified where elevations of the MIS 3 shorelines are known, and 31 feature elevation data for MIS 11 shorelines. Genetic relationships to regional geodynamics are further explored based on the elevations of the MIS 5e benchmark. Mean apparent uplift rates range from 0.01 0.01 mm/yr (hotspots) to 1.47 0.08 mm/yr (continental collision). Passive margins appear as ubiquitously uplifting, while tectonic segmentation is more important on active margins. From the literature and our extrapolations, we infer ages for the onset of formation for -180 coastal sequences. Sea level fingerprinting on coastal sequences started at least during mid Miocene and locally as early as Eocene. Whether due to the changes in the bulk volume of seawater or to the temporal variations in the shape of ocean basins, estimates of eustasy fail to explain the magnitude of the apparent sea level drop. Thus, vertical ground motion is invoked, and we interpret the longlasting development of those paleoshore sequences as the imprint of glacial cycles on globally uplifted margins in response to continental compression. The geomorphological expression of the sequences matches the amplitude and frequency of glacial cyclicity. From middle Pleistocene to present-day, moderately fast (100,000 yrs) oscillating sea levels favor the development of well identified strandlines that are distinct from one another. Pliocene and Lower Pleistocene strandlines associated with faster cyclicity (40,000 yrs) are more compact and easily merge into rasas, whereas older Cenozoic low-frequency eustatic changes generally led to widespread flat-lying coastal plains.}, language = {en} } @misc{KonradSchmolkeHalama2014, author = {Konrad-Schmolke, Matthias and Halama, Ralf}, title = {Combined thermodynamic-geochemical modeling in metamorphic geology: Boron as tracer of fluid-rock interaction}, series = {Lithos : an international journal of mineralogy, petrology, and geochemistry}, volume = {208}, journal = {Lithos : an international journal of mineralogy, petrology, and geochemistry}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0024-4937}, doi = {10.1016/j.lithos.2014.09.021}, pages = {393 -- 414}, year = {2014}, abstract = {Quantitative geochemical modeling is today applied in a variety of geological environments from the petrogenesis of igneous rocks to radioactive waste disposal. In addition, the development of thermodynamic databases and computer programs to calculate equilibrium phase diagrams has greatly advanced our ability to model geodynamic processes. Combined with experimental data on elemental partitioning and isotopic fractionation, thermodynamic forward modeling unfolds enormous capacities that are far from exhausted. In metamorphic petrology the combination of thermodynamic and trace element forward modeling can be used to study and to quantify processes at spatial scales from mu m to km. The thermodynamic forward models utilize Gibbs energy minimization to quantify mineralogical changes along a reaction path of a chemically open fluid/rock system. These results are combined with mass balanced trace element calculations to determine the trace element distribution between rock and melt/fluid during the metamorphic evolution. Thus, effects of mineral reactions, fluid-rock interaction and element transport in metamorphic rocks on the trace element and isotopic composition of minerals, rocks and percolating fluids or melts can be predicted. Here we illustrate the capacities of combined thermodynamic-geochemical modeling based on two examples relevant to mass transfer during metamorphism. The first example focuses on fluid-rock interaction in and around a blueschist-facies shear zone in felsic gneisses, where fluid-induced mineral reactions and their effects on boron (B) concentrations and isotopic compositions in white mica are modeled. In the second example, fluid release from a subducted slab, the associated transport of B as well as variations in B concentrations and isotopic compositions in liberated fluids and residual rocks are modeled. We compare the modeled results of both examples to geochemical data of natural minerals and rocks and demonstrate that the combination of thermodynamic and geochemical models enables quantification of metamorphic processes and insights into element cycling that would have been unattainable if only one model approach was chosen. (C) 2014 Elsevier B.V. All rights reserved.}, language = {en} } @misc{FayyazJaptokKleuser2014, author = {Fayyaz, Susann and Japtok, Lukasz and Kleuser, Burkhard}, title = {Divergent role of sphingosine 1-Phosphate on insulin resistance}, series = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology}, volume = {34}, journal = {Cellular physiology and biochemistry : international journal of experimental cellular physiology, biochemistry and pharmacology}, number = {1}, publisher = {Karger}, address = {Basel}, issn = {1015-8987}, doi = {10.1159/000362990}, pages = {134 -- 147}, year = {2014}, abstract = {Insulin resistance is a complex metabolic disorder in which insulin-sensitive tissues fail to respond to the physiological action of insulin. There is a strong correlation of insulin resistance and the development of type 2 diabetes both reaching epidemic proportions. Dysfunctional lipid metabolism is a hallmark of insulin resistance and a risk factor for several cardiovascular and metabolic disorders. Numerous studies in humans and rodents have shown that insulin resistance is associated with elevations of non-esterified fatty acids (NEFA) in the plasma. Moreover, bioactive lipid intermediates such as diacylglycerol (DAG) and ceramides appear to accumulate in response to NEFA, which may interact with insulin signaling. However, recent work has also indicated that sphingosine 1-phosphate (S1P), a breakdown product of ceramide, modulate insulin signaling in different cell types. In this review, we summarize the current state of knowledge about S1P and insulin signaling in insulin sensitive cells. A specific focus is put on the action of S1P on hepatocytes, pancreatic beta-cells and skeletal muscle cells. In particular, modulation of S1P-signaling can be considered as a potential therapeutic target for the treatment of insulin resistance and type 2 diabetes.}, language = {en} } @misc{MaslinBrierleyMilneretal.2014, author = {Maslin, Mark A. and Brierley, Chris M. and Milner, Alice M. and Shultz, Susanne and Trauth, Martin H. and Wilson, Katy E.}, title = {East African climate pulses and early human evolution}, series = {Quaternary science reviews : the international multidisciplinary research and review journal}, volume = {101}, journal = {Quaternary science reviews : the international multidisciplinary research and review journal}, publisher = {Elsevier}, address = {Oxford}, issn = {0277-3791}, doi = {10.1016/j.quascirev.2014.06.012}, pages = {1 -- 17}, year = {2014}, abstract = {Current evidence suggests that all of the major events in hominin evolution have occurred in East Africa. Over the last two decades, there has been intensive work undertaken to understand African palaeoclimate and tectonics in order to put together a coherent picture of how the environment of East Africa has varied in the past. The landscape of East Africa has altered dramatically over the last 10 million years. It has changed from a relatively flat, homogenous region covered with mixed tropical forest, to a varied and heterogeneous environment, with mountains over 4 km high and vegetation ranging from desert to cloud forest. The progressive rifting of East Africa has also generated numerous lake basins, which are highly sensitive to changes in the local precipitation-evaporation regime. There is now evidence that the presence of precession-driven, ephemeral deep-water lakes in East Africa were concurrent with major events in hominin evolution. It seems the unusual geology and climate of East Africa created periods of highly variable local climate, which, it has been suggested could have driven hominin speciation, encephalisation and dispersal out of Africa. One example is the significant hominin speciation and brain expansion event at -1.8 Ma that seems to have been coeval with the occurrence of highly variable, extensive, deep-water lakes. This complex, climatically very variable setting inspired first the variability selection hypothesis, which was then the basis for the pulsed climate variability hypothesis. The newer of the two suggests that the long-term drying trend in East Africa was punctuated by episodes of short, alternating periods of extreme humidity and aridity. Both hypotheses, together with other key theories of climate-evolution linkages, are discussed in this paper. Though useful the actual evolution mechanisms, which led to early hominins are still unclear and continue to be debated. However, it is clear that an understanding of East African lakes and their palaeoclimate history is required to understand the context within which humans evolved and eventually left East Africa. (C) 2014 The Authors. Published by Elsevier Ltd.}, language = {en} } @misc{LangerCarlsohn2014, author = {Langer, Henning and Carlsohn, Anja}, title = {Effects of different dietary proteins and amino acids on skeletal muscle hypertrophy in young adults after resistance exercise: A systematic review}, series = {Strength and conditioning journal}, volume = {36}, journal = {Strength and conditioning journal}, number = {3}, publisher = {Lippincott Williams \& Wilkins}, address = {Philadelphia}, issn = {1524-1602}, pages = {33 -- 42}, year = {2014}, abstract = {THIS ARTICLE REVIEWS THE AVAILABLE LITERATURE ON WHICH PROTEINS, AMINO ACIDS, OR COMBINATION OF BOTH SEEM TO BE OPTIMAL TO ENHANCE HYPERTROPHY AFTER RESISTANCE EXERCISE IN YOUNG ADULTS. DEPENDING ON THE CONTENT OF ESSENTIAL AMINO ACIDS AND PARTICULARLY LEUCINE, EITHER AN IMMEDIATE INGESTION OF similar to 20 G MILK PROTEIN FOLLOWED BY A SIMILAR AMOUNT similar to 1 HOUR LATER, OR A SINGLE BOLUS OF similar to 40 G SEEMS TO BE SUITABLE. GREATER AMOUNTS MIGHT BE NECESSARY IF A PROTEIN OF LOWER QUALITY IS CHOSEN ( I. E., PLANT-BASED PROTEINS) TO MATCH THE REQUIRED AMINO ACID QUANTITIES AND FACILITATE MUSCLE GROWTH.}, language = {en} } @misc{ReichetzederTsuprykovHocher2014, author = {Reichetzeder, Christoph and Tsuprykov, Oleg and Hocher, Berthold}, title = {Endothelin receptor antagonists in clinical research - Lessons learned from preclinical and clinical kidney studies}, series = {Life sciences : molecular, cellular and functional basis of therapy}, volume = {118}, journal = {Life sciences : molecular, cellular and functional basis of therapy}, number = {2}, publisher = {Elsevier}, address = {Oxford}, issn = {0024-3205}, doi = {10.1016/j.lfs.2014.02.025}, pages = {141 -- 148}, year = {2014}, abstract = {Endothelin receptor antagonists (ETRAs) are approved for the treatment of pulmonary hypertension and scleroderma-related digital ulcers. The efforts to approve this class of drugs for renal indications, however, failed so far. Preclinical studies were promising. Transgenic overexpression of ET-1 or ET-2 in rodents causes chronic renal failure. Blocking the ET system was effective in the treatment of renal failure in rodent models. However, various animal studies indicate that blocking the renal tubular ETAR and ETBR causes water and salt retention partially mediated via the epithelial sodium transporter in tubular cells. ETRAs were successfully tested clinically in renal indications in phase 2 trials for the treatment of diabetic nephropathy. They showed efficacy in terms of reducing albumin excretion on top of guideline based background therapy (RAS blockade). However, these promising results could not be translated to successful phase Ill trials so far. The spectrum of serious adverse events was similar to other phase III trials using ETRAs. Potential underlying reasons for these failures and options to solve these issues are discussed. In addition preclinical and clinical studies suggest caution when addressing renal patient populations such as patients with hepatorenal syndrome, patients with any type of cystic kidney disease and patients at risk of contrast media induced nephropathy. The lessons learned in renal indications are also important for other potential promising indications of ETRAs like cancer and heart failure. (C) 2014 The Authors. Published by Elsevier Inc. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).}, language = {en} } @misc{BandraukParamonov2014, author = {Bandrauk, Andre D. and Paramonov, Guennaddi K.}, title = {Excitation of muonic molecules dd mu and dt mu by super-intense attosecond soft X-ray laser pulses: Shaped post-laser-pulse muonic oscillations and enhancement of nuclear fusion}, series = {International journal of modern physics : E, Nuclear physics}, volume = {23}, journal = {International journal of modern physics : E, Nuclear physics}, number = {9}, publisher = {World Scientific}, address = {Singapore}, issn = {0218-3013}, doi = {10.1142/S0218301314300148}, pages = {34}, year = {2014}, abstract = {The quantum dynamics of muonic molecular ions dd mu and dt mu excited by linearly polarized along the molecular (z)-axis super-intense laser pulses is studied beyond the Born-Oppenheimer approximation by the numerical solution of the time-dependent Schrodinger equation within a three-dimensional model, including the internuclear distance R and muon coordinates z and rho. The peak-intensity of the super-intense laser pulses used in our simulations is I-0 = 3.51 x 10(22) W/cm(2) and the wavelength is lambda(l) = 5nm. In both dd mu and dt mu, expectation values < z > and of muon demonstrate "post-laser-pulse" oscillations after the ends of the laser pulses. In dd mu post-laser-pulse z-oscillations appear as shaped nonoverlapping "echo-pulses". In dt mu post-laser-pulse muonic z-oscillations appear as comparatively slow large-amplitude oscillations modulated with small-amplitude pulsations. The post-laser-pulse rho-oscillations in both dd mu and dt mu appear, for the most part, as overlapping "echo-pulses". The post-laser-pulse oscillations do not occur if the Born-Oppenheimer approximation is employed. Power spectra generated due to muonic motion along both optically active z and optically passive rho degrees of freedom are calculated. The fusion probability in dt mu can be increased by more than 11 times by making use of three sequential super-intense laser pulses. The energy released from the dt fusion in dt mu can by more than 20 GeV exceed the energy required to produce a usable muon and the energy of the laser pulses used to enhance the fusion. The possibility of power production from the laser-enhanced muon-catalyzed fusion is discussed.}, language = {en} } @misc{Wiemann2014, author = {Wiemann, Dirk}, title = {George, Rosemary Marangoly, Indian English and the Fiction of National Literature / [rezensiert von] Dirk Wiemann}, series = {Zeitschrift f{\"u}r Anglistik und Amerikanistik : ZAA ; a quarterly of language, literature and culture}, volume = {62}, journal = {Zeitschrift f{\"u}r Anglistik und Amerikanistik : ZAA ; a quarterly of language, literature and culture}, number = {4}, publisher = {DeGruyter}, address = {T{\"u}bingen}, issn = {0044-2305}, doi = {10.1515/zaa-2014-0039}, pages = {385 -- 388}, year = {2014}, abstract = {Rezensiertes Werk George, Rosemary Marangoly, Indian English and the Fiction of National Literature - Cambridge: Cambridge University Press, 2013. - Hb. viii, 285 pp. - (Zeitschrift f{\"u}r Anglistik und Amerikanistik ; 62(4)) ISBN 978-1-107-04000-7.}, language = {en} } @misc{ZouharSauer2014, author = {Zouhar, Jan and Sauer, Michael}, title = {Helping hands for budding prospects: ENTH/ANTH/VHS accessory proteins in endocytosis, vacuolar transport, and secretion}, series = {The plant cell}, volume = {26}, journal = {The plant cell}, number = {11}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {1040-4651}, doi = {10.1105/tpc.114.131680}, pages = {4232 -- 4244}, year = {2014}, abstract = {Coated vesicles provide a major mechanism for the transport of proteins through the endomembrane system of plants. Transport between the endoplasmic reticulum and the Golgi involves vesicles with COPI and COPII coats, whereas clathrin is the predominant coat in endocytosis and post-Golgi trafficking. Sorting of cargo, coat assembly, budding, and fission are all complex and tightly regulated processes that involve many proteins. The mechanisms and responsible factors are largely conserved in eukaryotes, and increasing organismal complexity tends to be associated with a greater numbers of individual family members. Among the key factors is the class of ENTH/ANTH/VHS domain-containing proteins, which link membrane subdomains, clathrin, and other adapter proteins involved in early steps of clathrin coated vesicle formation. More than 30 Arabidopsis thaliana proteins contain this domain, but their generally low sequence conservation has made functional classification difficult. Reports from the last two years have greatly expanded our knowledge of these proteins and suggest that ENTH/ANTH/VHS domain proteins are involved in various instances of clathrin-related endomembrane trafficking in plants. This review aims to summarize these new findings and discuss the broader context of clathrin-dependent plant vesicular transport.}, language = {en} } @misc{TrukenbrodEngbert2014, author = {Trukenbrod, Hans Arne and Engbert, Ralf}, title = {ICAT: a computational model for the adaptive control of fixation durations}, series = {Psychonomic bulletin \& review : a journal of the Psychonomic Society}, volume = {21}, journal = {Psychonomic bulletin \& review : a journal of the Psychonomic Society}, number = {4}, publisher = {Springer}, address = {New York}, issn = {1069-9384}, doi = {10.3758/s13423-013-0575-0}, pages = {907 -- 934}, year = {2014}, abstract = {Eye movements depend on cognitive processes related to visual information processing. Much has been learned about the spatial selection of fixation locations, while the principles governing the temporal control (fixation durations) are less clear. Here, we review current theories for the control of fixation durations in tasks like visual search, scanning, scene perception, and reading and propose a new model for the control of fixation durations. We distinguish two local principles from one global principle of control. First, an autonomous saccade timer initiates saccades after random time intervals (local-I). Second, foveal inhibition permits immediate prolongation of fixation durations by ongoing processing (local-II). Third, saccade timing is adaptive, so that the mean timer value depends on task requirements and fixation history (Global). We demonstrate by numerical simulations that our model qualitatively reproduces patterns of mean fixation durations and fixation duration distributions observed in typical experiments. When combined with assumptions of saccade target selection and oculomotor control, the model accounts for both temporal and spatial aspects of eye movement control in two versions of a visual search task. We conclude that the model provides a promising framework for the control of fixation durations in saccadic tasks.}, language = {en} } @misc{UestuenBoernke2014, author = {Uestuen, Suayib and B{\"o}rnke, Frederik}, title = {Interactions of Xanthomonas type-III effector proteins with the plant ubiquitin and ubiquitin-like pathways}, series = {Frontiers in plant science}, volume = {5}, journal = {Frontiers in plant science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2014.00736}, pages = {6}, year = {2014}, abstract = {In eukaryotes, regulated protein turnover is required during many cellular processes, including defense against pathogens. Ubiquitination and degradation of ubiquitinated proteins via the ubiquitin proteasome system (UPS) is the main pathway for the turnover of intracellular proteins in eukaryotes. The extensive utilization of the UPS in host cells makes it an ideal pivot for the manipulation of cellular processes by pathogens. Like many other Gram-negative bacteria, Xanthomonas species secrete a suite of type-III effector proteins (T3Es) into their host cells to promote virulence. Some of these T3Es exploit the plant UPS to interfere with immunity. This review summarizes T3E examples from the genus Xanthomonas with a proven or suggested interaction with the host UPS or UPS-like systems and also discusses the apparent paradox that arises from the presence of T3Es that inhibit the UPS in general while others rely on its activity for their function.}, language = {en} } @misc{LandHilbert2014, author = {Land-Hilbert, Stefanie}, title = {Massacre Street}, series = {British journal of Canadian studies}, volume = {27}, journal = {British journal of Canadian studies}, number = {2}, publisher = {Liverpool Univ. Press}, address = {Liverpool}, issn = {0269-9222}, pages = {256 -- 257}, year = {2014}, language = {en} } @misc{AugusiakVandenBrinkGrimm2014, author = {Augusiak, Jacqueline and Van den Brink, Paul J. and Grimm, Volker}, title = {Merging validation and evaluation of ecological models to 'evaludation': A review of terminology and a practical approach}, series = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, volume = {280}, journal = {Ecological modelling : international journal on ecological modelling and engineering and systems ecolog}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3800}, doi = {10.1016/j.ecolmodel.2013.11.009}, pages = {117 -- 128}, year = {2014}, abstract = {Confusion about model validation is one of the main challenges in using ecological models for decision support, such as the regulation of pesticides. Decision makers need to know whether a model is a sufficiently good representation of its real counterpart and what criteria can be used to answer this question. Unclear terminology is one of the main obstacles to a good understanding of what model validation is, how it works, and what it can deliver. Therefore, we performed a literature review and derived a standard set of terms. 'Validation' was identified as a catch-all term, which is thus useless for any practical purpose. We introduce the term 'evaludation', a fusion of 'evaluation' and 'validation', to describe the entire process of assessing a model's quality and reliability. Considering the iterative nature of model development, the modelling cycle, we identified six essential elements of evaludation: (i) 'data evaluation' for scrutinising the quality of numerical and qualitative data used for model development and testing; (ii) 'conceptual model evaluation' for examining the simplifying assumptions underlying a model's design; (iii) 'implementation verification' for testing the model's implementation in equations and as a computer programme; (iv) 'model output verification' for comparing model output to data and patterns that guided model design and were possibly used for calibration; (v) 'model analysis' for exploring the model's sensitivity to changes in parameters and process formulations to make sure that the mechanistic basis of main behaviours of the model has been well understood; and (vi) 'model output corroboration' for comparing model output to new data and patterns that were not used for model development and parameterisation. Currently, most decision makers require 'validating' a model by testing its predictions with new experiments or data. Despite being desirable, this is neither sufficient nor necessary for a model to be useful for decision support. We believe that the proposed set of terms and its relation to the modelling cycle can help to make quality assessments and reality checks of ecological models more comprehensive and transparent. (C) 2013 Elsevier B.V. All rights reserved.}, language = {en} } @misc{BaldKeller2014, author = {Bald, Ilko and Keller, Adrian}, title = {Molecular processes studied at a single-molecule level using DNA origami nanostructures and atomic force microscopy}, series = {Molecules}, volume = {19}, journal = {Molecules}, number = {9}, publisher = {MDPI}, address = {Basel}, issn = {1420-3049}, doi = {10.3390/molecules190913803}, pages = {13803 -- 13823}, year = {2014}, abstract = {DNA origami nanostructures allow for the arrangement of different functionalities such as proteins, specific DNA structures, nanoparticles, and various chemical modifications with unprecedented precision. The arranged functional entities can be visualized by atomic force microscopy (AFM) which enables the study of molecular processes at a single-molecular level. Examples comprise the investigation of chemical reactions, electron-induced bond breaking, enzymatic binding and cleavage events, and conformational transitions in DNA. In this paper, we provide an overview of the advances achieved in the field of single-molecule investigations by applying atomic force microscopy to functionalized DNA origami substrates.}, language = {en} }