08081 Abstracts Collection -- Data Structures

From February 17th to 22nd 2008, the Dagstuhl Seminar 08081 ``Data Structures\u27\u27 was held in the International Conference and Research Center (IBFI), Schloss Dagstuhl. It brought together 49 researchers from four continents to discuss recent developments concerning data structures in terms of research but also in terms of new technologies that impact how data can be stored, updated, and retrieved. During the seminar a fair number of participants presented their current research. There was discussion of ongoing work, and in addition an open problem session was held. This paper first describes the seminar topics and goals in general, then gives the minutes of the open problem session, and concludes with abstracts of the presentations given during the seminar. Where appropriate and available, links to extended abstracts or full papers are provided

Binary Space Partitions for Fat Rectangles

This is the published version. Copyright © 2000 Society for Industrial and Applied Mathematic

An analysis of two-component regulatory systems in Myxococcus xanthus

Proteins of two-component regulatory systems (TCS) have essential functions in the sensing of external and self-generated signals in bacteria as well as in the generation of appropriate output responses. Accordingly, in Myxococcus xanthus TCS are important for fruiting body formation and sporulation as well as normal motility. In this study, I analyzed the M. xanthus genome for the presence and genetic organization of genes encoding TCS. 272 genes that encode TCS proteins were identified including 21 genes in eight loci, which encode TCS proteins that are part of chemotaxis-like systems. Sebsequent analyses focused on 251 TCS proteins (non chemotaxis-like) consisting of 118 histidine protein kinases (HPKs), 119 response regulators (RRs) and 14 HPK-like genes. 71% of the TCS genes are organized in unusual manners as orphan genes or in complex gene clusters whereas the remaining 29% display the standard paired gene organization. Bioinformatics analyses suggest that TCS proteins encoded by orphan genes and complex gene clusters are functionally distinct from TCS proteins encoded by paired genes. Experimentally, microarray data and quantitative real-time PCR suggest that orphan TCS genes are overrepresented among TCS genes that display altered transcription during fruiting body formation. The genetic analysis of 25 orphan HPKs, which are transcriptionally up-regulated during development, led to the identification of two HPKs that are likely essential for viability and seven HPKs including four novel HPKs that have important function in fruiting body formation or spore germination. As an attempt to identify functional partners of orphan TCS proteins in M. xanthus, I focused on the RR FruA, which has a key role in the C-signal transduction pathway. To identify the FruA kinase, two candidate approaches were used. The first candidate approach is based on the hypothesis that a FruA kinase gene shares characteristics with the fruA gene, i.e. it is orphan, developmentally up-regulated at the transcriptional level and a null mutant is deficient in development. Yeast two-hybrid analysis was used to investigate potential interactions between FruA and developmentally regulated orphan HPKs. Three best FruA kinase candidates (SdeK, Hpk8 and Hpk12) and four potentially redundant candidates (Hpk9, Hpk11, Hpk13 and Hpk29) were identified. In vivo analyses of the three best FruA kinase candidates support a model in which SdeK is the main FruA kinase, Hpk12 is a minor FruA kinase and Hpk8 is a phosphatase of FruA~P. Furthermore, SdeK may have other downstream targets in addition to FruA and there may be other HPKs that phosphorylate or cross talk to FruA. To obtain direct evidence for an interaction between FruA and the FruA kinase candidates in vitro, the relevant proteins have been purified. To date, the Hpk8 and Hpk12 proteins have been shown to autophosphorylate in vitro. Intriguingly, Hpk8 does not appear to be phosphorylated on the conserved His residue but is likely phosphorylated on a Tyr residue. Preliminary phosphotransfer assay suggests that Hpk8 engages in phosphotransfer to or phosphorylation of FruA. A possible interaction in vitro between SdeK and Hpk12 with FruA still remains to be shown. Hpk37 belongs to the group of orphan HPKs that are transcriptionally up-regulated during development and essential for development. However, the yeast two-hybrid analyses to determine a possible direct interaction with FruA were inconclusive. In vivo analyses demonstrated that Hpk37 is likely involved in the production or response to (p)ppGpp or the A-signal suggesting that Hpk37 is not a FruA kinase. Domain analyses of Hpk37 and analyses of the genetic organization of the hpk37 locus suggest that regulation of Hpk37 activity could involve a unique methylation/demethylation mechanism similar to that resulting in adaptation in chemosensory pathways. In a second candidate approach to identify a FruA kinase, candidates were predicted using an in silico method (White et al., 2007). In vivo analyses of mutants carrying mutations in the genes encoding the six best candidates strongly suggest that these HPK are not FruA kinases

Evolutionarily Divergent, Unstable Filamentous Actin Is Essential for Gliding Motility in Apicomplexan Parasites

Apicomplexan parasites rely on a novel form of actin-based motility called gliding, which depends on parasite actin polymerization, to migrate through their hosts and invade cells. However, parasite actins are divergent both in sequence and function and only form short, unstable filaments in contrast to the stability of conventional actin filaments. The molecular basis for parasite actin filament instability and its relationship to gliding motility remain unresolved. We demonstrate that recombinant Toxoplasma (TgACTI) and Plasmodium (PfACTI and PfACTII) actins polymerized into very short filaments in vitro but were induced to form long, stable filaments by addition of equimolar levels of phalloidin. Parasite actins contain a conserved phalloidin-binding site as determined by molecular modeling and computational docking, yet vary in several residues that are predicted to impact filament stability. In particular, two residues were identified that form intermolecular contacts between different protomers in conventional actin filaments and these residues showed non-conservative differences in apicomplexan parasites. Substitution of divergent residues found in TgACTI with those from mammalian actin resulted in formation of longer, more stable filaments in vitro. Expression of these stabilized actins in T. gondii increased sensitivity to the actin-stabilizing compound jasplakinolide and disrupted normal gliding motility in the absence of treatment. These results identify the molecular basis for short, dynamic filaments in apicomplexan parasites and demonstrate that inherent instability of parasite actin filaments is a critical adaptation for gliding motility

Conjugate heat transfer coupling relying on large eddy simulation with complex geometries in massively parallel environments

Progress in scientific computing has led to major advances in simulation and understanding of the different physical phenomena that exist in industrial gas turbines. However' most of these advances have focused on solving one problem at a time. Indeed' the combustion problem is solved independently from the thermal or radiation problems' etc... In reality all these problems interact: one speaks of coupled problems. Thus performing coupled computations can improve the quality of simulations and provide gas turbines engineers with new design tools. Recently' solutions have been developed to handle multiple physics simultaneously using generic solvers. However' due to their genericity these solutions reveal to be ineffective on expensive problems such as Large Eddy Simulation (LES). Another solution is to perform code coupling: specialized codes are connected together' one for each problem and they exchange data periodically. In this thesis a conjugate heat transfer problem is considered. A fluid domain solved by a combustion LES solver is coupled with a solid domain in which the conduction problem is solved. Implementing this coupled problem raises multiple issues which are addressed in this thesis. Firstly' the specific problem of coupling an LES solver to a conduction solver is considered: the impact of the inter-solver exchange frequency on convergence' possible temporal aliasing' and stability of the coupled system is studied. Then interpolation and geometrical issues are addressed: a conservative interpolation method is developed and compared to other methods. These methods are then applied to an industrial configuration' highlighting the problems and solutions specific to complex geometry. Finally' high performance computing (HPC) is considered: an efficient method to perform data exchange and interpolation between parallel codes is developed. This work has been applied to an aeronautical combustion chamber configuration

Synthesis, Characterizations And Release Study Of Ibuprofen-Encapsulated Magnetic Nanocellulose Alginate Hydrogel Beads

Nanokristal selulosa magnetik (m-CNC) telah disintesis daripada nanokristal selulosa (CNC) yang telah diasingkan daripada sekam padi. m-CNC tersebut telah digabungkan kedalam manik hidrogel alginat untuk aplikasi pelepasan dadah ibuprofen Magnetic cellulose nanocrystals (m-CNC) were synthesized from cellulose nanocrystals (CNC) that were isolated from rice husk. m-CNC were incorporated into alginate hydrogel beads for ibuprofen release applicatio