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Prion diseases or transmissible spongiform encephalopathies (TSEs) are rare neurological disorders that may be of genetic or infectious origin, but most frequently occur sporadically in humans. Their outcome is invariably fatal. The infectious agent has been defined as prion (from proteinaceous infectious only) in 1992 by Stanley B. Prusiner and represent mainly, if not solely, an abnormal, protease-resistant isoform (PrPSc) of a cellular protein, the prion protein or PrPC. According to the “protein only” hypothesis, the prion is devoid of informational nucleic acids and consists of an “infectious” protein that is capable of converting the normal host protein PrPC into a likeness of itself. TSEs can be distinguished from other neurodegenerative diseases because of their infectivity and transmission capability. The only organ system in which severe histopathological damage can be demonstrated as a consequence of infection with prions is the nervous system. The communal lesions are neuronal loss, spongiosis and astrogliosis, accompanied by an intra- and extracellular accumulation of PrPSc, occasionally in form of amyloid plaques. Even if a strong activation of microglia and astrocytes occurs, no immunological response is usually detectable as consequence of prion infection. Despite the considerable attention for its involvement in TSEs, the physiological role of the cellular, nonpathogenic isoform of PrPC, has not yet been determined. In the last years, several putative cellular functions have been attributed to PrPC: its localization in “lipid rafts” is consistent with a possible role in cell adhesion, transmembrane signalling or as a recognition molecule. Furthermore, PrPC has been implicated in protection against oxidative stress, copper metabolism, apoptosis, cell proliferation and in the regeneration of blood precursors stem cells in the adult. It has also been shown that PrPC interacts with the neuronal cell adhesion molecule NCAM, promoting neurite outgrowth. However, both the PrPC-mediated effects and the role of PrPC-dependent pathways on neuronal differentiation are still not elucidated. First objective of this Ph.D thesis was the establishment of a novel in vitro cellular model for the study of the role of PrPC in neuronal differentiation and neurite outgrowth. Furthermore, an additional goal of this project was the indentification of the PrPC domains responsible for the induction of neuronal differentiation. A novel PrPC-depleted cell line (PrP0/0 ML) was derived from murine primary PrP-knockout neuronal cells by SV40 large T antigen-mediated immortalization. A temperature sensitive form of this oncogenic protein was used, allowing a temperature-mediated regulation of its expression. This cell line was then characterised for its growth potential, for the expression of specific cellular markers and for its ability to differentiate. It was found that, under culture conditions promoting the expression of the temperature-sensitive SV40 large T antigen, the cells expressed nestin, a specific marker of neuronal precursor cells. Therefore, the PrP0/0 ML cell line was identified as a potential neuronal stem cell line. In fact, under nonpermissive culture conditions when the expression of the temperature-sensitive SV40 large T antigen is downregulated, the PrP0/0 ML cells differentiated into neurons. Noteworthy, maintenance of the cells in conditions that promote cell differentiation induced a progressive reduction in the expression levels of nestin, an event that strongly correlated with the appearance of the specific neuronal markers MAP-2b and NeuN. In order to investigate the role of PrPC in the process of neuronal differentiation, the PrP0/0 ML cells were then reconstituted for the expression of either the full-length PrP or a N-terminal truncated PrPC form (PrPdel32-134). The differentiation potential of both reconstituted cell lines under nonpermissive culture conditions was then compared with that of the parenteral PrP0/0 ML cells. This in vitro study clearly highlights that PrPC expression in the PrP0/0 ML cell line accelerates neuronal differentiation and that the N-terminal domain of the prion protein is not necessary for this PrP-mediated function. Prion diseases like BSE, vCJK, Kuru and the majority of iatrogenic cases of CJK are caused by a peripheral infection. Infectious prions accumulate in the central and peripheral nervous system as well as in extracerebral tissues, such as the secondary lymphoid organs and muscles. The prion pathogenesis is a dynamic process which can be defined temporary and spatially in different phases: i) infection and peripheral replication, ii) neuroinvasion, transport of prions from the periphery to the central nervous system (CNS), and iii) neurodegeneration. In the last years, progresses in the elucidation of the peripheral prion pathogenesis were achieved. The identification of the cell types involved in the lymphoreticular prion replication phase and the recognition of the role of the peripheral nervous system in the process of prion spread from the periphery to the CNS have elucidated some of the cellular mechanisms that are involved in prion uptake, replication and propagation. However, relatively little information is available about the mechanism(s) underlying intercellular prion transfer and tissue-to tissue prion spread. Microvesicles (MVs) are submicron vesicles (0,03-1 microm.) with a single membrane and are shed from most eukaryotic cells undergoing activation or apoptosis. The segregation of specific proteins is followed by blebbing of the membrane surface, leading to the formation of MVs and their release in the extracellular environment. MVs can be also secreted upon fusion of multivesicular endosomes with the plasma membrane (exosomes). The secretion of MVs is the result of a complex cellular process involving changes in the metabolism of lipids and proteins. The functional role of MVs is still largely unknown. However, there is evidence showing that they are important modulators of cell-to-cell communication, participate in a variety of intracellular adhesion processes and are able to induce cellular response(s). The release of PrPC and infectious PrPSc by prion infected epithelial, neuroglial and neuronal cells in association with exosomes has recently been highlighted. Furthermore, it has been shown that exosomes can propagate prion infectivity both in vitro and in vivo, suggesting that PrPSc-bearing exosomes may provide a mechanism for intercellular transmission of infectious prions in addition to cell-to-cell contact. Second objective of this Ph.D thesis was to determine the possible role of plasma membrane-derived microvesicles in the propagation and transmission of prions. The release of MVs was first studied in different murine neuronal cell lines. Here it is shown for the first time that neurons also shed plasma membrane derived MVs, in addition to exosomes. Immunoelectron microscopy and immunoblot analyses clearly demonstrated the presence of PrPC on the membrane of MVs released from PrPC-expressing cells. Characterization of lipid rafts components in MVs highlighted the presence of the ganglioside GM2, the tyrosine kinase p59Fyn, flotillin-2 and the neuronal protein GAP-43. In order to investigate whether MVs are involved in the intercellular transmission of prions, MVs were first isolated from two prion infected murine neuronal cell lines, namely the Neuro-2a PK1 and the N2a58 cells, and then used for in vitro and in vivo infection assays. Immunoblot analyses after proteinase K treatment demonstrated the association of PrPSc with the secreted MVs. The PrPSc-bearing MVs were then used to perform infection experiments on noninfected cells. By the use of cell blot assay, a method that allows the detection of PrPSc-amplification and -accumulation in cultured cells, the kinetic of prion infection in the de novo infected cells was followed. Noteworthy, it was found that PrPSc-bearing MVs were capable to transmit prions in vitro and to stably infect the recipient cells. In order to investigate the role of MVs in the transmission of infectivity in vivo, PrPSc-bearing MVs as well as MVs isolated from noninfected cells (as negative control) were injected intracerebrally in PrPC-overexpressing indicator mice (tga20). The development of clinical disease was followed in a time-dependent manner. Clinical symptoms could be observed only in the group of indicator mice inoculated with the PrPSc-bearing MVs, which then succumbed to desease. These findings clearly demonstrated that MVs are biological carriers of both PrPSc and prion infectivity. MVs could therefore participate in vivo in the processes of intercellular prion transmission and propagation.
Dan Janzen proposed in a paper in 1977 (loc. cit.), that a clone of aphids and for that matter dandelions consists, respectively, of one large ‘super-organism’. In effect a single evolutionary individual able to exploit resources over an expanded geographical range, and sometimes with aphids also, a wider range of resources (different kinds of host plants), much more than if the organism concerned were a single individual. Such a view is of course based on the notion that an asexual lineage (clone) has strict genetic fidelity, that is to say, is genetically identical over its entire genome between clone mates. This seems a highly unlikely scenario and indeed, modern molecular markers have revealed a plethora of mutational events within such so-called clones. Here in this talk I provide evidence from aphids that they are not ‘perfect forms’ but rather show a range of variations, including evidence of hybridization events, and that they can and do adapt to environmental circumstances, sometimes swiftly. Hence that even as asexual lineages, aphids are able to exploit new ecological circumstances and flourish, e.g. host adapted forms, whilst some species, notably the highly polyphagous peach-potato aphid (Myzus persicae), have also evolved resistance to a range of pesticides, and by so doing, have managed to survive in the face of these poisons. However, there are fitness costs associated with such adaptation, more especially in the highly resistant aphids. Because of the variation and adaptation shown by particular aphid species and asexual lineages, they cannot be described as a single evolutionary unit in a ‘Janzenian’ sense. What they show is ecological plasticity and an ability to adapt quickly, in large part enhanced by their incredible rate of reproduction and population expansion. Some migrating winged aphids are constrained in their exploitation of new habitats by environmental factors – geographical, climatic and ecological, especially lack of suitable hosts. In contrast, some other aphid species have seemingly colonized large areas of the world (probably aided by human agency) so that deciding what a population is exactly is a difficult task. It may even be that certain ‘super clones’ detected using molecular markers have indeed spread far and wide, clones which appear to fit the description of being ‘general purpose genotypes’ in that they can feed on a range of plant hosts under a range of different geographical-climatic conditions. As such, they are nearest to Dan Janzen’s views, although here again, strict genetic fidelity is not necessarily proven, only accepted from the application of a limited number of markers, e.g. multilocus genotypes in the case of microsatellite markers.
Before the turn of the millenium the investigation of phylogenetic relationships was revolutionized by two major inputs, the use of molecular sequence data for phylogenetic reconstruction, paralleled by the sophistication of computer aided reconstruction methods. The ever growing number of data however did not only result in clarifications of open questions, but brought forth a number of new conflicting phylogenetic hypotheses. Sometimes they are wrongly referred to as conflicts between morphological and molecular approaches, which sporadically even culminated in the rejection of the usefulness of one of the two approaches (e.g. Scotland et al 2003). These scientists overlook the great advantage of having two a priori largely independent data sets (Wägele 2001) which in a synthetic way enable the greatest progress in phylogenetic research. However, solely putting data together will not suffice to choose among conflicting hypotheses. The increasing number of conflicts necessitates approaches that go beyond mere data congruence, but searching for the possible reasons of conflicts. In the present paper, problems in the reconstruction of the phylogenetic origin of Hexapoda, as well as of the early branchings within the Hexapoda, will exemplify approaches of critical re-evaluation and testing of data used in morphological data matrices for phylogenetic analyses. The early cladogenetic events of hexapods are especially suited for such a discussion for several reasons. The hexapods, as the most species-rich group of organisms, look back at a long and multi-faceted history of taxonomic and phylogenetic studies, culminating in a number of conflicting hypotheses. Triggered by incongruences with morphological analyses the reconstruction of the hexapodan roots likewise became a hot-spot of molecular research activities during^the last two decades. Furthermore the phylogenetic positions of the oldest lineages branching off within the hexapodan clade, the Diplura, Protura and Collembola, are in particular very difficult to reconstruct. While at least the latter two are well defined by morphological autapomorphies their phylogenetic position could not be reconstructed unambiguously, since their morphology seems highly derived with respect to the hexapodan ground pattern.
Hymenopteran endoparasitoids that develop inside their lepidopteran host may exert a multitude of interactions with their host until they are able to emerge successfully from a developmentally arrested host that finally dies. Parasitoid interferences comprise physiological and biochemical modifications in the host endocrine and immune system which in turn affect host growth and development (reviewed in Edwards & Weaver, 2001). We use the gypsy moth, Lymantria dispar (Lep., Lymantriidae) and the endoparasitic, polydnavirus (PDV)-carrying braconid wasp Glyptapanteles liparidis (Hym., Braconidae) as a model system to study the endocrine changes associated with parasitism. Following wasp oviposition into young gypsy moth larvae, the parasitoids develop through two endoparasitic instars, and then emerge as newly molted third instars from a host that dies in the larval stage. In previous studies we have already described the endocrine changes in parasitized gypsy moth larvae which show an increase in juvenile hormone (JH) titers, a shift from JH II to JH III as the dominant homologue, and a prominent decrease in the JH degrading enzymes (Schopf & al., 1996; Schafellner & al., 2004). Here, we investigated the possible mechanisms that account for the JH elevating effects such as (i) stimulated host corpora allata activity, (ii) reduced activity of the JH metabolic enzymes such as JH esterase, and (iii) synthesis and release of JH by the parasitoid larvae.
Aphids annually infest winter wheat, Triticum aestivum L., in late spring and early summer in Central Europe, but densities leading to strong yield losses are reached only occasionally (Basedow et al., 1994). Three aphid species, Sitobion avenae Fabr., Metopolophium dirhodum Walk. and R. padi L., usually occur in cereal crops with increasing densities from late spring onwards (Basedow et al., 1994). Modelling population levels of cereal aphids is a key tool in integrated pest management for winter wheat. Over the last 30 years, considerable efforts have been made to investigate the population dynamics of aphids (DeWit and Rabbinge, 1979; Entwistle and Dixon, 1987). In Central Europe to date, two models have attained greater importance in late spring: LAUS (Friesland, 1986) and GETLAUS01 (Gosselke et al., 2001). The first one estimates the population level of S. avenae in spring in winter wheat fields and has obtained regional significance in practical plant protection. In contrast, the model GETLAUS01 is a scientific model, not designed for practical plant protection. It describes in great detail the population dynamics of S. avenae, R. padi and M. dirhodum. Both models have been improved over time and extended with several factors, e.g. by including the effects of antagonists, fertilisation, crop density, plant protection agents and meteorological parameters on population development. The objective of this study was to analyse the following three factors in terms of their impact on population and migration characteristics: cultivar, proximity between winter and summer hosts and migration (according to meteorological parameters).
Both, G. mellonella and S. exigua, are most important pests in tropical countries. G. mellonella has five to six generations per year (Abid et al. 1997; Ali 1996), there, and feeding in bee combs they find, besides wax, residues of honey, insect skin and pollen (Hachiro & Knox 2000). Li et al. (1987) have shown the efficacy of Bacillus thuringiensis aizawai against G. mellonella. It is registered in the EU as Mellonex for its control, but NeemAzal T/S may also be active, and will have some advantages (Leymann et al. 2000, Melathopoulos et al. 2000). Therefore we conducted new studies here, on the results we shall report. S. exigua is an important polyphagous pest of crops in tropical areas (Brown & Dewhurst 1975). By repeated control with synthetic insecticides, especially by illiterate farmers (Armes et al. 1992; Aggarwal et al. 2006a) resistance to a lot of those insecticides has been built up, making plant protection very difficult. Therefore the need is pronounced for microbial and botanical pesticides (Nagarkatti 1982; Rao et al. 1990), which have different modes of action than synthetic insecticides. Aggarwal et al. (2006b) have started to test such ingredients, but the time of observation was too short (3 days), since the effects of Neem products occur later than those of synthetic insecticides (Basedow et al. 2002). So we conducted new, longer lasting experiments (with 5 to 30 days), on which we give a report here. The experiments were conducted during guest stays of the three co-authors (from Mymensingh, Bangladesh, from Nazreth, Ethiopia, and from Khartoum, Sudan) at the Experimental Station of the Institute of Phytopathology and Applied Zoology at Giessen Univerity.
Reggie-1 (flotillin-2) and reggie-2 (flotillin-1) are membrane microdomain proteins which are associated with the membrane by means of acylation. They influence different cellular signaling processes, such as neuronal, T-cell and insulin signaling. Upon stimulation of the EGF receptor, reggie-1 becomes phosphorylated and undergoes tyrosine 163 dependent translocation from the plasma membrane to endosomal compartments. In addition, reggie-1 was shown to influence actindependent processes. Reggie-2 has been demonstrated to affect caveolin- and clathrin-independent endocytosis. Both proteins form homo- and hetero-oligomers, but the function of these oligomers has remained elusive. Moreover, it has not been clarified if functions of reggie-1 are also influenced by reggie-2 and vice versa. The first aim of the study was to further investigate the interplay and the heterooligomerization of reggie proteins and their functional effects. Both reggie proteins were individually depleted by means of siRNA. In different siRNA systems and various cell lines, reggie-1 depleted cells showed reduced protein amounts of reggie-1 and reggie-2, but reggie-2 knock down cells still expressed reggie-1 protein. The decrease of reggie-2 in reggie-1 depleted cells was only detected at protein but not at mRNA level. Furthermore, reggie-2 expression could be rescued by expression of siRNA resistant wild type reggie-1-EGFP constructs, but not by the soluble myristoylation mutant G2A. This mutant was also not able to associate with endogenous reggie-1 or reggie-2, which demonstrates that membrane association of reggie-1 is necessary for hetero-oligomerization. In addition, fluorescence microscopy studies and membrane fractionations showed that correct localization of overexpressed reggie-2 was dependent on co-overexpressed reggie-1. Thus, hetero-oligomerization is crucial for membrane association of reggie-2 and for its protein stability or protein expression. Moreover, the binding of reggie-2 to reggie-1 required tyrosine 163 of reggie-1 which was previously shown to be important for endosomal translocation of reggie-1. Since reggie-2 was implicated to function in clathrin- and caveolin-independent endocytosis pathways, the effect of reggie-2 depletion on reggie-1 endocytosis was investigated. Indeed, reggie-1 was dependent on reggie-2 for endosomal localization and EGF-induced endocytosis. By FRET-FLIM analysis it could be shown that reggie heterooligomers are dynamic in size or conformation upon EGF stimulation. Thus, it can be concluded that reggie proteins are interdependent in different aspects, such as protein stability or expression, membrane association and subcellular localization. In addition, these results demonstrate that the hetero-oligomers are dynamic and reggie proteins influence each other in terms of function. A further aim was the characterization of reggie-1 and reggie-2 function in actindependent processes, where so far only reggie-1 was known to play a role. Depletion of either of the proteins reduced cell migration, cell spreading and the number of focal adhesions in steady state cells. Thus, also reggie-2 affects actin-dependent processes. Further investigation of the focal adhesions during cell spreading revealed that depletion of reggie-1 displayed different effects as compared to reggie-2 knock down. Reggie-1 depleted cells had elongated cell-matrix-adhesions and showed reduced activation of FAK and ERK2. On the other hand, depletion of reggie-2 resulted in a restricted localization of focal adhesion at the periphery of the cell and decreased ERK2 phosphorylation, but it did not affect FAK autophosphorylation. Hence, reggie proteins influence the regulation of cell-matrix-adhesions differently. A link between reggie proteins and focal adhesions is the actin cross-linking protein -actinin. The interaction of -actinin with reggie-1 could be verified by means of co-immunoprecipitations and FRET-FLIM analysis. Reggie-1 binds -actinin especially in membrane ruffles and in other locations where actin remodeling takes place. Moreover, -actinin showed a different localization pattern during cell spreading in reggie-1 depleted cells, as compared to the control cells. These results provide further insights into the function of both reggie proteins. Their interplay and hetero-oligomerization was shown to be crucial for their role in endocytosis. In addition, both reggie proteins influence actin-dependent processes and differentially affect focal adhesion regulation.
A data set of annual values of area equipped for irrigation for all 236 countries in the world during the time period 1900 - 2003 was generated. The basis for this data product was information available through various online data bases and from other published materials. The complete time series were then constructed around the reported data applying six statistical methods. The methods are discussed in terms of reliability and data uncertainties. The total area equipped for irrigation in the world in 1900 was 53.2 million hectares. Irrigation was mainly practiced in all the arid regions of the globe and in paddy rice areas of South and East Asia. In some temperate countries in Western Europe irrigation was practiced widely on pastures and meadows. The time series suggest a modest rate of increase of irrigated areas in the first half of the 20th century followed by a more dynamic development in the second half. The turn of the century is characterized by an overall consolidating trend resulting at a total of 285.8 million hectares in 2003. The major contributing countries have changed little throughout the century. This data product is regarded as a preliminary result toward an ongoing effort to develop a detailed data set and map of areas equipped for irrigation in the world over the 20th century using sub-national statistics and historical irrigation maps.
The problem of vocalization, or diacritization, is essential to many tasks in Arabic NLP. Arabic is generally written without the short vowels, which leads to one written form having several pronunciations with each pronunciation carrying its own meaning(s). In the experiments reported here, we define vocalization as a classification problem in which we decide for each character in the unvocalized word whether it is followed by a short vowel. We investigate the importance of different types of context. Our results show that the combination of using memory-based learning with only a word internal context leads to a word error rate of 6.64%. If a lexical context is added, the results deteriorate slowly.
How to compare treebanks
(2008)
Recent years have seen an increasing interest in developing standards for linguistic annotation, with a focus on the interoperability of the resources. This effort, however, requires a profound knowledge of the advantages and disadvantages of linguistic annotation schemes in order to avoid importing the flaws and weaknesses of existing encoding schemes into the new standards. This paper addresses the question how to compare syntactically annotated corpora and gain insights into the usefulness of specific design decisions. We present an exhaustive evaluation of two German treebanks with crucially different encoding schemes. We evaluate three different parsers trained on the two treebanks and compare results using EVALB, the Leaf-Ancestor metric, and a dependency-based evaluation. Furthermore, we present TePaCoC, a new testsuite for the evaluation of parsers on complex German grammatical constructions. The testsuite provides a well thought-out error classification, which enables us to compare parser output for parsers trained on treebanks with different encoding schemes and provides interesting insights into the impact of treebank annotation schemes on specific constructions like PP attachment or non-constituent coordination.
We argue for incorporating the financial economics of market microstructure into the financial econometrics of asset return volatility estimation. In particular, we use market microstructure theory to derive the cross-correlation function between latent returns and market microstructure noise, which feature prominently in the recent volatility literature. The cross-correlation at zero displacement is typically negative, and cross-correlations at nonzero displacements are positive and decay geometrically. If market makers are sufficiently risk averse, however, the cross-correlation pattern is inverted. Our results are useful for assessing the validity of the frequently-assumed independence of latent price and microstructure noise, for explaining observed cross-correlation patterns, for predicting as-yet undiscovered patterns, and for making informed conjectures as to improved volatility estimation methods.
The future of securitization
(2008)
Securitization is a financial innovation that experiences a boom-bust cycle, as many other innovations before. This paper analyzes possible reasons for the breakdown of primary and secondary securitization markets, and argues that misaligned incentives along the value chain are the primary cause of the problems. The illiquidity of asset and interbank markets, in this view, is a market failure derived from ill-designed mechanisms of coordinating financial intermediaries and investors. Thus, illiquidity is closely related to the design of the financial chains. Our policy conclusions emphasize crisis prevention rather than crisis management, and the objective is to restore a “comprehensive incentive alignment”. The toe-hold for strengthening regulation is surprisingly small. First, we emphasize the importance of equity piece retention for the long-term quality of the underlying asset pool. As a consequence, equity piece allocation needs to be publicly known, alleviating market pricing. Second, on a micro level, accountability of managers can be improved by compensation packages aiming at long term incentives, and penalizing policies with destabilizing effects on financial markets. Third, on a macro level, increased transparency relating to effective risk transfer, risk-related management compensation, and credible measurement of rating performance stabilizes the valuation of financial assets and, hence, improves the solvency of financial intermediaries. Fourth, financial intermediaries, whose risk is opaque, may be subjected to higher capital requirements.
Proteorhodopsin (PR) originally isolated from uncultivated γ-Proteobacterium as a result of biodiversity screens, is highly abundant ocean wide. PR, a Type I retinal binding protein with 26% sequence identity, is a bacterial homologue of Bacteriorhodopsin (BR). The members within this family share about 78% of sequence identity and display a 40 nm difference in the absorption spectra. This property of the PR family members provides an excellent model system for understanding the mechanism of spectral tuning. Functionally PR is a photoactive proton pump and is suggested to exhibit a pH dependent vectorality of proton transfer. This raises questions about its potential role as pH dependent regulator. The abundance of PR in huge numbers within the cell, its widespread distribution ocean wide at different depths hints towards the involvement of PR in utilization of solar energy, energy metabolism and carbon recycling in the Sea. Contrary to BR, which is known to be a natural 2D crystal, no such information is available for PR til date. Neither its functional mechanism nor its 3D structure has been resolved so far. This PhD project is an attempt to gain a deeper insight so as to understand structural and functional characterization of PR. The approach combines the potentials of 2D crystallography, Atomic Force Microscopy and Solid State NMR techniques for characterization of this protein. Wide range of crystalline conditions was obtained as a result of 2D crystallization screens. This hints towards dominant protein protein interactions. Considering the high number of PR molecules reported per cell, it is likely that driven by such interactions, the protein has a native dense packing in the environment. The projection map represented low resolution of these crystals but suggested a donut shape oligomeric arrangement of protein in a hexagonal lattice with unit cell size of 87Å*87Å. Preliminary FTIR measurements indicated that the crystalline environment does not obstruct the photocycle of PR and K as well as M intermediate states could be identified. Single molecule force spectroscopy and atomic force microscopy on these 2D crystals was used to probe further information about the oligomeric state and nature of unfolding. The data revealed that protein predominantly exists as hexamers in crystalline as well as densely reconstituted regions but a small percentage of pentamers is also observed. The unfolding mechanism was similar to the other relatively well-characterized members of rhodopsin family. A good correlation of the atomic force microscopy and the electron microscopy data was achieved. Solid State NMR of the isotopically labeled 2D crystalline preparations using uniformly and selectively labeling schemes, allowed to obtain high quality SSNMR spectra with typical 15N line width in the range of 0.6-1.2 ppm. The measured 15N chemical shift value of the Schiff base in the 2D crystalline form was observed to be similar to the Schiff base chemical shift values for the functionally active reconstituted samples. This provides an indirect evidence for the active functionality of the protein and hence the folding. The first 15N assignment has been achieved for the Tryptophan with the help of Rotational Echo Double Resonance experiments. The 2D Cross Polarization Lee Goldberg measurements reflect the dynamic state of the protein inspite of restricted mobility in the crystalline state. The behavior of lipids as measured by 31P from the lipid head group showed that the lipids are not tightly bound to the protein but behave more like the lipid bilayer. The 13C-13C homonulear correlation experiments with optimized mixing time based on build up curve analysis, suggest that it is possible to observe individual resonances as seen in case of glutamic acid. The signal to noise was good enough to record a decent spectrum in a feasible period. The selective unlabeling is an efficient method for reduction in the spectral overlap. However, more efficient labeling schemes are required for further characterization. The present spectral resolution is good for individual amino acid investigation but for uniformly labeled samples, further improvement is required.
In this paper, we present an open-source parsing environment (Tübingen Linguistic Parsing Architecture, TuLiPA) which uses Range Concatenation Grammar (RCG) as a pivot formalism, thus opening the way to the parsing of several mildly context-sensitive formalisms. This environment currently supports tree-based grammars (namely Tree-Adjoining Grammars (TAG) and Multi-Component Tree-Adjoining Grammars with Tree Tuples (TT-MCTAG)) and allows computation not only of syntactic structures, but also of the corresponding semantic representations. It is used for the development of a tree-based grammar for German.
This paper investigates the relation between TT-MCTAG, a formalism used in computational linguistics, and RCG. RCGs are known to describe exactly the class PTIME; simple RCG even have been shown to be equivalent to linear context-free rewriting systems, i.e., to be mildly context-sensitive. TT-MCTAG has been proposed to model free word order languages. In general, it is NP-complete. In this paper, we will put an additional limitation on the derivations licensed in TT-MCTAG. We show that TT-MCTAG with this additional limitation can be transformed into equivalent simple RCGs. This result is interesting for theoretical reasons (since it shows that TT-MCTAG in this limited form is mildly context-sensitive) and, furthermore, even for practical reasons: We use the proposed transformation from TT-MCTAG to RCG in an actual parser that we have implemented.
TT-MCTAG lets one abstract away from the relative order of co-complements in the final derived tree, which is more appropriate than classic TAG when dealing with flexible word order in German. In this paper, we present the analyses for sentential complements, i.e., wh-extraction, thatcomplementation and bridging, and we work out the crucial differences between these and respective accounts in XTAG (for English) and V-TAG (for German).
Developing linguistic resources, in particular grammars, is known to be a complex task in itself, because of (amongst others) redundancy and consistency issues. Furthermore some languages can reveal themselves hard to describe because of specific characteristics, e.g. the free word order in German. In this context, we present (i) a framework allowing to describe tree-based grammars, and (ii) an actual fragment of a core multicomponent tree-adjoining grammar with tree tuples (TT-MCTAG) for German developed using this framework. This framework combines a metagrammar compiler and a parser based on range concatenation grammar (RCG) to respectively check the consistency and the correction of the grammar. The German grammar being developed within this framework already deals with a wide range of scrambling and extraction phenomena.
In this paper we present a parsing architecture that allows processing of different mildly context-sensitive formalisms, in particular Tree-Adjoining Grammar (TAG), Multi-Component Tree-Adjoining Grammar with Tree Tuples (TT-MCTAG) and simple Range Concatenation Grammar (RCG). Furthermore, for tree-based grammars, the parser computes not only syntactic analyses but also the corresponding semantic representations.
Women and Halakha Shiur
(2008)