Four Lessons in Versatility or How Query Languages Adapt to the Web

Exposing not only human-centered information, but machine-processable data on the Web is one of the commonalities of recent Web trends. It has enabled a new kind of applications and businesses where the data is used in ways not foreseen by the data providers. Yet this exposition has fractured the Web into islands of data, each in different Web formats: Some providers choose XML, others RDF, again others JSON or OWL, for their data, even in similar domains. This fracturing stifles innovation as application builders have to cope not only with one Web stack (e.g., XML technology) but with several ones, each of considerable complexity. With Xcerpt we have developed a rule- and pattern based query language that aims to give shield application builders from much of this complexity: In a single query language XML and RDF data can be accessed, processed, combined, and re-published. Though the need for combined access to XML and RDF data has been recognized in previous work (including the W3C’s GRDDL), our approach differs in four main aspects: (1) We provide a single language (rather than two separate or embedded languages), thus minimizing the conceptual overhead of dealing with disparate data formats. (2) Both the declarative (logic-based) and the operational semantics are unified in that they apply for querying XML and RDF in the same way. (3) We show that the resulting query language can be implemented reusing traditional database technology, if desirable. Nevertheless, we also give a unified evaluation approach based on interval labelings of graphs that is at least as fast as existing approaches for tree-shaped XML data, yet provides linear time and space querying also for many RDF graphs. We believe that Web query languages are the right tool for declarative data access in Web applications and that Xcerpt is a significant step towards a more convenient, yet highly efficient data access in a “Web of Data”

Are the trapping dynamics in Photosystem II sensitive to QA redox potential?

Original article can be found at: http://www.sciencedirect.com/science/journal/10106030 Copyright Elsevier B.V. DOI: 10.1016/S1010-6030(01)00506-8 [Full text of this article is not available in the UHRA]Removal of the manganese complex from photosystem II (PSII) causes a 145 meV shift in the redox potential of the plastoquinone QA [Biochim. Biophys. Acta 1229 (1995) 193; Photosynthetica 27 (1–2) (1992) 89; Biochim. Biophys. Acta 1229 (1995) 202]. Time resolved single photon counting has been used to monitor the time dependent concentrations of the singlet states in intact and manganese depleted BBY-type core particles studied with QA in a fully open state. Surprisingly, no difference is observed between the experimental results obtained from the intact and manganese depleted samples. We demonstrate that this could be indicative of a very deep primary radical pair trap formed in PSII core particles with QA in a fully open state. Alternatively, static inhomogeneity or a possible time-dependence of the QA redox potential via relaxations such as proton motions should be considered.Peer reviewe

Replacement of Tyrosine D with Phenylalanine Affects the Normal Proton Transfer Pathways for the Reduction of P680+ in Oxygen-Evolving Photosystem II Particles from Chlamydomonas

Original article can be found at: http://pubs.acs.org/journals/bichaw/index.html Copyright American Chemical Society DOI: 10.1021/bi020558e [Full text of this article is not available in the UHRA]Peer reviewe

Similarity between electron donor side reactions in the solubilized Photosystem II–LHC II supercomplex and Photosystem-II-containing membranes

“The original publication is available at www.springerlink.com”. Copyright Springer. [Full text of this article is not available in the UHRA]The PS II–LHC II supercomplex is a novel type of oxygen evolving Photosystem II (PS II) core particle that contains the light harvesting complex proteins Lhcb1/2/4/5 in addition to the PS II reaction centre, oxygen evolving complex (OEC) and inner antennae [Hankamer et al. (1997) Eur J Biochem 243: 422–429]. The 33 and 23 kDa extrinsic proteins in these particles have been localised by image analysis of electron micrographs and averaging techniques [Boekema et al. (1998) Eur J Biochem 252: 268–276]. To assay the functionality of the water splitting complex, we compared the single flash P680+ reduction kinetics in these supercomplexes with those of PS II-rich granal stack membranes (BBYs). We found that the P680+ reduction kinetics in PS II–LHC II supercomplexes were indistinguishable from those in BBYs. We also examined a number of PS II core particles lacking the Lhcb components. All of these had different P680+ reduction kinetics, which we attributed to partial loss of OEC function before and during the measurements.Peer reviewe