@misc{Zuellich2011, type = {Master Thesis}, author = {Z{\"u}llich, Gunda}, title = {Migration and development in Senegal : a system dynamics analysis of the feedback relationships}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-57836}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {This thesis investigates the reciprocal relationship between migration and development in Senegal. Therewith, it contributes to the debate as to whether migration in developing countries enhances or rather impedes the development process. Even though extensive and controversial discussions can be found in the scientific literature regarding the impact of migration on development, research has scarcely examined the feedback relationships between migration and development. Science however agrees with both the fact that migration affects development as well as that the level of development in a country determines migration behaviour. Thus, both variables are neither dependent nor independent, but endogenous variables influencing each other and producing behavioural pattern that cannot be investigated using a static and unidirectional approach. On account of this, the thesis studies the feedback mechanisms existing between migration and development and the behavioural pattern generated by the high interdependence in order to be able to draw conclusions concerning the impact of changes in migration behaviour on the development process. To explore these research questions, the study applies the computer simulation method 'System Dynamics' and amplifies the simulation model for national development planning called 'Threshold 21' (T21), representing development processes endogenously and integrating economic, social and environmental aspects, using a structure that portrays the reasons and consequences of migration. The model has been customised to Senegal, being an appropriate representative of the theoretical interesting universe of cases. The comparison of the model generated scenarios - in which the intensity of emigration, the loss and gain of education, the remittances or the level of dependence changes - facilitates the analysis. The present study produces two important results. The first outcome is the development of an integrative framework representing migration and development in an endogenous way and incorporating several aspects of different theories. This model can be used as a starting point for further discussions and improvements and it is a fairly relevant and useful result against the background that migration is not integrated into most of the development planning tools despite its significant impact. The second outcome is the gained insights concerning the feedback relations between migration and development and the impact of changes in migration on development. To give two examples: It could be found that migration impacts development positively, indicated by HDI, but that the dominant behaviour of migration and development is a counteracting behaviour. That means that an increase in emigration leads to an improvement in development, while this in turn causes a decline in emigration, counterbalancing the initial increase. Another insight concerns the discovery that migration causes a decline in education in the short term, but leads to an increase in the long term, after approximately 25 years - a typical worse-before-better behaviour. From these and further observations, important policy implications can be derived for the sending and receiving countries. Hence, by overcoming the unidirectional perspective, this study contributes to an improved understanding of the highly complex relationship between migration and development and their feedback relations.}, language = {en} } @phdthesis{Zurell2011, author = {Zurell, Damaris}, title = {Integrating dynamic and statistical modelling approaches in order to improve predictions for scenarios of environmental change}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus-56845}, school = {Universit{\"a}t Potsdam}, year = {2011}, abstract = {Species respond to environmental change by dynamically adjusting their geographical ranges. Robust predictions of these changes are prerequisites to inform dynamic and sustainable conservation strategies. Correlative species distribution models (SDMs) relate species' occurrence records to prevailing environmental factors to describe the environmental niche. They have been widely applied in global change context as they have comparably low data requirements and allow for rapid assessments of potential future species' distributions. However, due to their static nature, transient responses to environmental change are essentially ignored in SDMs. Furthermore, neither dispersal nor demographic processes and biotic interactions are explicitly incorporated. Therefore, it has often been suggested to link statistical and mechanistic modelling approaches in order to make more realistic predictions of species' distributions for scenarios of environmental change. In this thesis, I present two different ways of such linkage. (i) Mechanistic modelling can act as virtual playground for testing statistical models and allows extensive exploration of specific questions. I promote this 'virtual ecologist' approach as a powerful evaluation framework for testing sampling protocols, analyses and modelling tools. Also, I employ such an approach to systematically assess the effects of transient dynamics and ecological properties and processes on the prediction accuracy of SDMs for climate change projections. That way, relevant mechanisms are identified that shape the species' response to altered environmental conditions and which should hence be considered when trying to project species' distribution through time. (ii) I supplement SDM projections of potential future habitat for black grouse in Switzerland with an individual-based population model. By explicitly considering complex interactions between habitat availability and demographic processes, this allows for a more direct assessment of expected population response to environmental change and associated extinction risks. However, predictions were highly variable across simulations emphasising the need for principal evaluation tools like sensitivity analysis to assess uncertainty and robustness in dynamic range predictions. Furthermore, I identify data coverage of the environmental niche as a likely cause for contrasted range predictions between SDM algorithms. SDMs may fail to make reliable predictions for truncated and edge niches, meaning that portions of the niche are not represented in the data or niche edges coincide with data limits. Overall, my thesis contributes to an improved understanding of uncertainty factors in predictions of range dynamics and presents ways how to deal with these. Finally I provide preliminary guidelines for predictive modelling of dynamic species' response to environmental change, identify key challenges for future research and discuss emerging developments.}, language = {en} } @article{ZuppingerDingleySchmidChenetal.2011, author = {Zuppinger-Dingley, D. and Schmid, Bernhard and Chen, Y. and Brandl, H. and van der Heijden, M. G. A. and Joshi, Jasmin Radha}, title = {In their native range, invasive plants are held in check by negative soil-feedbacks}, series = {Ecosphere : the magazine of the International Ecology University}, volume = {2}, journal = {Ecosphere : the magazine of the International Ecology University}, number = {5}, publisher = {Wiley}, address = {Washington}, issn = {2150-8925}, doi = {10.1890/ES11-00061.1}, pages = {12}, year = {2011}, abstract = {The ability of some plant species to dominate communities in new biogeographical ranges has been attributed to an innate higher competitive ability and release from co-evolved specialist enemies. Specifically, invasive success in the new range might be explained by release from biotic negative soil-feedbacks, which control potentially dominant species in their native range. To test this hypothesis, we grew individuals from sixteen phylogenetically paired European grassland species that became either invasive or naturalized in new ranges, in either sterilized soil or in sterilized soil with unsterilized soil inoculum from their native home range. We found that although the native members of invasive species generally performed better than those of naturalized species, these native members of invasive species also responded more negatively to native soil inoculum than did the native members of naturalized species. This supports our hypothesis that potentially invasive species in their native range are held in check by negative soil-feedbacks. However, contrary to expectation, negative soil-feedbacks in potentially invasive species were not much increased by interspecific competition. There was no significant variation among families between invasive and naturalized species regarding their feedback response (negative vs. neutral). Therefore, we conclude that the observed negative soil feedbacks in potentially invasive species may be quite widespread in European families of typical grassland species.}, language = {en} } @article{ZudePflanzSpinellietal.2011, author = {Zude, Manuela and Pflanz, Michael and Spinelli, Lorenzo and Dosche, Carsten and Torricelli, Alessandro}, title = {Non-destructive analysis of anthocyanins in cherries by means of Lambert-Beer and multivariate regression based on spectroscopy and scatter correction using time-resolved analysis}, series = {Journal of food engineering}, volume = {103}, journal = {Journal of food engineering}, number = {1}, publisher = {Elsevier}, address = {Oxford}, issn = {0260-8774}, doi = {10.1016/j.jfoodeng.2010.09.021}, pages = {68 -- 75}, year = {2011}, abstract = {In high-value sweet cherry (Prunus avium), the red coloration - determined by the anthocyanins content - is correlated with the fruit ripeness stage and market value. Non-destructive spectroscopy has been introduced in practice and may be utilized as a tool to assess the fruit pigments in the supply chain processes. From the fruit spectrum in the visible (Vis) wavelength range, the pigment contents are analyzed separately at their specific absorbance wavelengths. A drawback of the method is the need for re-calibration due to varying optical properties of the fruit tissue. In order to correct for the scattering differences, most often the spectral intensity in the visible spectrum is normalized by wavelengths in the near infrared (NIR) range, or pre-processing methods are applied in multivariate calibrations. In the present study, the influence of the fruit scattering properties on the Vis/NIR fruit spectrum were corrected by the effective pathlength in the fruit tissue obtained from time-resolved readings of the distribution of time-of-flight (DTOF). Pigment analysis was carried out according to Lambert-Beer law, considering fruit spectral intensities, effective pathlength, and refractive index. Results were compared to commonly applied linear color and multivariate partial least squares (PLS) regression analysis. The approaches were validated on fruits at different ripeness stages, providing variation in the scattering coefficient and refractive index exceeding the calibration sample set. In the validation, the measuring uncertainty of non-destructively analyzing fruits with Vis/NIR spectra by means of PLS or Lambert-Beer in comparison with combined application of Vis/NIR spectroscopy and DTOF measurements showed a dramatic bias reduction as well as enhanced coefficients of determination when using both, the spectral intensities and apparent information on the scattering influence by means of DTOF readings. Corrections for the refractive index did not render improved results.}, language = {en} } @article{ZolotovProkhorovNamgaladzeetal.2011, author = {Zolotov, O. V. and Prokhorov, Boris E. and Namgaladze, Alexander A. and Martynenko, O. V.}, title = {Variations in the total electron content of the ionosphere during preparation of earthquakes}, series = {Russian journal of physical chemistry : B, Focus on physics}, volume = {5}, journal = {Russian journal of physical chemistry : B, Focus on physics}, number = {3}, publisher = {Pleiades Publ.}, address = {New York}, issn = {1990-7931}, doi = {10.1134/S1990793111030146}, pages = {435 -- 438}, year = {2011}, abstract = {The morphological features in the deviations of the total electron content (TEC) of the ionosphere from the background undisturbed state as possible precursors of the earthquake of January 12, 2010 (21:53 UT (16:53 LT), 18.46A degrees N, 72.5A degrees W, 7.0 M) in Haiti are analyzed. To identify these features, global and regional differential TEC maps based on global 2-h TEC maps provided by NASA in the IONEX format were plotted. For the considered earthquake, long-lived disturbances, presumably of seismic origin, were localized in the near-epicenter area and were accompanied by similar effects in the magnetoconjugate region. Both decreases and increases in the local TEC over the period from 22 UT of January 10 to 08 UT of January 12, 2010 were observed. The horizontal dimensions of the anomalies were similar to 40A degrees in longitude and similar to 20A degrees in latitude, with the magnitude of TEC disturbances reaching similar to 40\% relative to the background near the epicenter and more than 50\% in the magnetoconjugate area. No significant geomagnetic disturbances within January 1-12, 2010 were observed, i.e., the detected TEC anomalies were manifestations of interplay between processes in the lithosphere-atmosphere-ionosphere system.}, language = {en} } @article{ZimmermannOnea2011, author = {Zimmermann, Malte and Onea, Edgar}, title = {Focus marking and focus interpretation}, series = {LINGUA}, volume = {121}, journal = {LINGUA}, number = {11}, publisher = {ELSEVIER SCIENCE BV}, address = {AMSTERDAM}, issn = {0024-3841}, doi = {10.1016/j.lingua.2011.06.002}, pages = {1651 -- 1670}, year = {2011}, abstract = {The languages of the world exhibit a range of formal phenomena (e.g. accenting, syntactic reordering and morphological marking) that are commonly linked to the information-structural notion of focus. Crucially, there does not seem to be a one-to-one mapping between particular formal features (focus marking devices) and focus, neither from a cross-linguistic perspective, nor within individual languages. This raises the question of what is actually being expressed if we say that a constituent is focused in a particular language, and whether, or to what extent, the same semantic or pragmatic content is formally expressed by focus-marking across languages. This special issue addresses the question of focus and its grammatical realization from a number of theoretical and empirical perspectives. In this introductory article we elaborate on this question by making an explicit proposal about what we take to be the correct way of thinking about the information-structural category of focus and its formal realization. In the first part, we introduce a unified semantico-pragmatic perspective on focus in terms of alternatives and possible worlds. In the second part, we present a cursory cross-linguistic overview of focus marking strategies as found in the languages of the world. Finally, in the third part, we discuss the connection between the notion of focus, different pragmatic uses of focus and different focus marking strategies employed in the grammars of natural languages. (C) 2011 Elsevier B.V. All rights reserved.}, language = {en} } @article{Zimmermann2011, author = {Zimmermann, Malte}, title = {On the functional architecture of DP and the feature content of pronominal quantifiers in Low German}, series = {The journal of comparative Germanic linguistics}, volume = {14}, journal = {The journal of comparative Germanic linguistics}, number = {3}, publisher = {Springer}, address = {New York}, issn = {1383-4924}, doi = {10.1007/s10828-011-9046-z}, pages = {203 -- 240}, year = {2011}, abstract = {The article investigates the functional architecture of complex pronominal quantifying expressions (PQEs) in Low German, such as jeder-een 'everyone' and keen-een 'no-one', which provide overt evidence for a Num-projection, situated between the NP- and DP-layer. The feature specification of Num as [+lattice] or [-lattice] is responsible for whether the DP denotes into the domain of atomic or mass/plural entities, respectively. In the case of complex PQEs, the syntactic Num-head hosts the overt element een 'a, one', which carries a [-lattice] feature, thus ensuring that the PQE ranges exclusively over the domain of atomic entities, but not mass or plural entities. The Num-head een differs from its simplex counterpart wat 'something', which is analyzed as an NP-proform with an underspecified [lattice]-feature. As a result, wat can range over atomic and mass domains alike. In the final part of the article, it is argued that wat is also underspecified for the operator feature [rel/wh], for which reason it can also function as an interrogative expression (what) and as a relative pronoun (which), respectively, depending on the syntactic context. Throughout the article, the Low German data are compared with relevant data from other German dialects and Germanic and Romance languages, pointing out similarities and differences in the syntactic structure and feature content of PQEs across these languages and dialects.}, language = {en} } @article{Zimmermann2011, author = {Zimmermann, Malte}, title = {The grammatical expression of focus in West Chadic variation and uniformity in and across languages}, series = {Linguistics : an interdisciplinary journal of the language sciences}, volume = {49}, journal = {Linguistics : an interdisciplinary journal of the language sciences}, number = {5}, publisher = {De Gruyter Mouton}, address = {Berlin}, issn = {0024-3949}, doi = {10.1515/LING.2011.032}, pages = {1163 -- 1213}, year = {2011}, abstract = {The article provides an overview of the grammatical realization of focus in four West Chadic languages (Chadic, Afro-Asiatic). The languages discussed exhibit an intriguing crosslinguistic variation in the realization of focus, both among themselves as well as compared to European intonation languages. They also display language-internal variation in the formal realization of focus. The West Chadic languages differ widely in their ways of expressing focus, which range from syntactic over prosodic to morphological devices. In contrast to European intonation languages, the focus marking systems of the West Chadic languages are inconsistent in that focus is often not grammatically expressed, but these inconsistencies are shown to be systematic. Subject foci (contrastive or not) and contrastive nonsubject foci are always grammatically marked, whereas information focus on nonsubjects need not be marked as such. The absence of formal focus marking supports pragmatic theories of focus in terms of contextual resolution. The special status of focused subjects and contrastive foci is derived from the Contrastive Focus Hypothesis, which requires unexpected foci and unexpected focus contents to be marked as such, together with the assumption that canonical subjects in West Chadic receive a default interpretation as topics. Finally, I discuss certain focus ambiguities which are not attested in intonation languages, nor do they follow on standard accounts of focus marking, but which can be accounted for in terms of constraint interaction in the formal expression of focus.}, language = {en} } @misc{Zimmermann2011, author = {Zimmermann, Malte}, title = {The grammatical expression of focus in West Chadic}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-93617}, pages = {1163 -- 1213}, year = {2011}, abstract = {The article provides an overview of the grammatical realization of focus in four West Chadic languages (Chadic, Afro-Asiatic). The languages discussed exhibit an intriguing crosslinguistic variation in the realization of focus, both among themselves as well as compared to European intonation languages. They also display language-internal variation in the formal realization of focus. The West Chadic languages differ widely in their ways of expressing focus, which range from syntactic over prosodic to morphological devices. In contrast to European intonation languages, the focus marking systems of the West Chadic languages are inconsistent in that focus is often not grammatically expressed, but these inconsistencies are shown to be systematic. Subject foci (contrastive or not) and contrastive nonsubject foci are always grammatically marked, whereas information focus on nonsubjects need not be marked as such. The absence of formal focus marking supports pragmatic theories of focus in terms of contextual resolution. The special status of focused subjects and contrastive foci is derived from the Contrastive Focus Hypothesis, which requires unexpected foci and unexpected focus contents to be marked as such, together with the assumption that canonical subjects in West Chadic receive a default interpretation as topics. Finally, I discuss certain focus ambiguities which are not attested in intonation languages, nor do they follow on standard accounts of focus marking, but which can be accounted for in terms of constraint interaction in the formal expression of focus.}, language = {en} } @article{ZimmermannDorschner2011, author = {Zimmermann, Andreas and Dorschner, Jonas}, title = {Article 22}, isbn = {978-0-19-954251-2}, year = {2011}, language = {en} } @article{Zimmermann2011, author = {Zimmermann, Andreas}, title = {Article 33, para. 2}, isbn = {978-0-19-954251-2}, year = {2011}, language = {en} } @article{Zimmermann2011, author = {Zimmermann, Andreas}, title = {Article 1 F}, isbn = {978-0-19-954251-2}, year = {2011}, language = {en} } @article{Zimmermann2011, author = {Zimmermann, Andreas}, title = {The obligation to prevent genocide: towards a general responsibility to protect?}, isbn = {978-0-19-958881-7}, year = {2011}, language = {en} } @article{ZilligesKehrMeissneretal.2011, author = {Zilliges, Yvonne and Kehr, Jan-Christoph and Meissner, Sven and Ishida, Keishi and Mikkat, Stefan and Hagemann, Martin and Kaplan, Aaron and B{\"o}rner, Thomas and Dittmann-Th{\"u}nemann, Elke}, title = {The cyanobacterial hepatotoxin microcystin binds to proteins and increases the fitness of microcystis under oxidative stress conditions}, series = {PLoS one}, volume = {6}, journal = {PLoS one}, number = {3}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0017615}, pages = {11}, year = {2011}, abstract = {Microcystins are cyanobacterial toxins that represent a serious threat to drinking water and recreational lakes worldwide. Here, we show that microcystin fulfils an important function within cells of its natural producer Microcystis. The microcystin deficient mutant Delta mcyB showed significant changes in the accumulation of proteins, including several enzymes of the Calvin cycle, phycobiliproteins and two NADPH-dependent reductases. We have discovered that microcystin binds to a number of these proteins in vivo and that the binding is strongly enhanced under high light and oxidative stress conditions. The nature of this binding was studied using extracts of a microcystin-deficient mutant in vitro. The data obtained provided clear evidence for a covalent interaction of the toxin with cysteine residues of proteins. A detailed investigation of one of the binding partners, the large subunit of RubisCO showed a lower susceptibility to proteases in the presence of microcystin in the wild type. Finally, the mutant defective in microcystin production exhibited a clearly increased sensitivity under high light conditions and after hydrogen peroxide treatment. Taken together, our data suggest a protein-modulating role for microcystin within the producing cell, which represents a new addition to the catalogue of functions that have been discussed for microbial secondary metabolites.}, language = {en} } @article{ZhongWangAdelsbergeretal.2011, author = {Zhong, Qi and Wang, Weinan and Adelsberger, Joseph and Golosova, Anastasia and Koumba, Achille M. Bivigou and Laschewsky, Andr{\´e} and Funari, Sergio S. and Perlich, Jan and Roth, Stephan V. and Papadakis, Christine M. and M{\"u}ller-Buschbaum, Peter}, title = {Collapse transition in thin films of poly(methoxydiethylenglycol acrylate)}, series = {Colloid and polymer science : official journal of the Kolloid-Gesellschaft}, volume = {289}, journal = {Colloid and polymer science : official journal of the Kolloid-Gesellschaft}, number = {5-6}, publisher = {Springer}, address = {New York}, issn = {0303-402X}, doi = {10.1007/s00396-011-2384-1}, pages = {569 -- 581}, year = {2011}, abstract = {The thermal behavior of poly(methoxydiethylenglycol acrylate) (PMDEGA) is studied in thin hydrogel films on solid supports and is compared with the behavior in aqueous solution. The PMDEGA hydrogel film thickness is varied from 2 to 422 nm. Initially, these films are homogenous, as measured with optical microscopy, atomic force microscopy, X-ray reflectivity, and grazing-incidence small-angle X-ray scattering (GISAXS). However, they tend to de-wet when stored under ambient conditions. Along the surface normal, no long-ranged correlations between substrate and film surface are detected with GISAXS, due to the high mobility of the polymer at room temperature. The swelling of the hydrogel films as a function of the water vapor pressure and the temperature are probed for saturated water vapor pressures between 2,380 and 3,170 Pa. While the swelling capability is found to increase with water vapor pressure, swelling in dependence on the temperature revealed a collapse phase transition of a lower critical solution temperature type. The transition temperature decreases from 40.6 A degrees C to 36.6 A degrees C with increasing film thickness, but is independent of the thickness for very thin films below a thickness of 40 nm. The observed transition temperature range compares well with the cloud points observed in dilute (0.1 wt.\%) and semi-dilute (5 wt.\%) solution which decrease from 45 A degrees C to 39 A degrees C with increasing concentration.}, language = {en} } @article{ZhirovPikovskijShepelyansky2011, author = {Zhirov, O. V. and Pikovskij, Arkadij and Shepelyansky, Dima L.}, title = {Quantum vacuum of strongly nonlinear lattices}, series = {Physical review : E, Statistical, nonlinear and soft matter physics}, volume = {83}, journal = {Physical review : E, Statistical, nonlinear and soft matter physics}, number = {1}, publisher = {American Physical Society}, address = {College Park}, issn = {1539-3755}, doi = {10.1103/PhysRevE.83.016202}, pages = {7}, year = {2011}, abstract = {We study the properties of classical and quantum strongly nonlinear chains by means of extensive numerical simulations. Due to strong nonlinearity, the classical dynamics of such chains remains chaotic at arbitrarily low energies. We show that the collective excitations of classical chains are described by sound waves whose decay rate scales algebraically with the wave number with a generic exponent value. The properties of the quantum chains are studied by the quantum Monte Carlo method and it is found that the low-energy excitations are well described by effective phonon modes with the sound velocity dependent on an effective Planck constant. Our results show that at low energies the quantum effects lead to a suppression of chaos and drive the system to a quasi-integrable regime of effective phonon modes.}, language = {en} } @article{ZhangWielandReicheetal.2011, author = {Zhang, Zhuodong and Wieland, Ralf and Reiche, Matthias and Funk, Roger and Hoffmann, Carsten and Li, Yong and Sommer, Michael}, title = {Wind modelling for wind erosion research by open source computational fluid dynamics}, series = {Ecological informatics : an international journal on ecoinformatics and computational ecolog}, volume = {6}, journal = {Ecological informatics : an international journal on ecoinformatics and computational ecolog}, number = {5}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1574-9541}, doi = {10.1016/j.ecoinf.2011.02.001}, pages = {316 -- 324}, year = {2011}, abstract = {The open source computational fluid dynamics (CFD) wind model (CFD-WEM) for wind erosion research in the Xilingele grassland in Inner Mongolia (autonomous region, China) is compared with two open source CFD models Gerris and OpenFOAM. The evaluation of these models was made according to software technology, implemented methods, handling, accuracy and calculation speed. All models were applied to the same wind tunnel data set. Results show that the simplest CFD-WEM has the highest calculation speed with acceptable accuracy, and the most powerful OpenFOAM produces the simulation with highest accuracy and the lowest calculation speed. Gerris is between CFD-WEM and OpenFOAM. It calculates faster than OpenFOAM, and it is capable to solve different CFD problems. CFD-WEM is the optimal model to be further developed for wind erosion research in Inner Mongolia grassland considering its efficiency and the uncertainties of other input data. However, for other applications using CFD technology, Gerris and OpenFOAM can be good choices. This paper shows the powerful capability of open source CFD software in wind erosion study, and advocates more involvement of open source technology in wind erosion and related ecological researches.}, language = {en} } @phdthesis{Zhang2011, author = {Zhang, Zhuodong}, title = {A regional scale study of wind erosion in the Xilingele grassland based on computational fluid dynamics}, address = {Potsdam}, pages = {143 S.}, year = {2011}, 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{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} }