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  • 2003  (13)
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  • 2003  (13)
  • 1
    Language: English
    In: Nucleic acids research, 15 November 2003, Vol.31(22), pp.6435-43
    Description: Recent bioinformatics-aided searches have identified many new small RNAs (sRNAs) in the intergenic regions of the bacterium Escherichia coli. Here, a shot-gun cloning approach (RNomics) was used to generate cDNA libraries of small sized RNAs. Besides many of the known sRNAs, we found new species that were not predicted previously. The present work brings the number of sRNAs in E.coli to 62. Experimental transcription start site mapping showed that some sRNAs were encoded from independent genes, while others were processed from mRNA leaders or trailers, indicative of a parallel transcriptional output generating sRNAs co-expressed with mRNAs. Two of these RNAs (SroA and SroG) consist of known (THI and RFN) riboswitch elements. We also show that two recently identified sRNAs (RyeB and SraC/RyeA) interact, resulting in RNase III-dependent cleavage. To the best of our knowledge, this represents the first case of two non-coding RNAs interacting by a putative antisense mechanism. In addition, intracellular metabolic stabilities of sRNAs were determined, including ones from previous screens. The wide range of half-lives (32 min) indicates that sRNAs cannot generally be assumed to be metabolically stable. The experimental characterization of sRNAs analyzed here suggests that the definition of an sRNA is more complex than previously assumed.
    Keywords: Escherichia Coli -- Genetics ; RNA, Bacterial -- Genetics ; RNA, Untranslated -- Genetics ; Transcription, Genetic -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 2
    Language: English
    In: Theory of Computing Systems, 2003, Vol.36(4), pp.375-386
    Description: In 1977 Young proposed a voting scheme that extends the Condorcet Principle based on the fewest possible number of voters whose removal yields a Condorcet winner. We prove that both the winner and the ranking problem for Young elections is complete for \p || NP , the class of problems solvable in polynomial time by parallel access to NP. Analogous results for Lewis Carroll's 1876 voting scheme were recently established by Hemaspaandra et al. In contrast, we prove that the winner and ranking problems in Fishburn's homogeneous variant of Carroll's voting scheme can be solved efficiently by linear programming.
    Keywords: Computation ; Elections ; Complexity ; Polynomials ; Linear Programming ; Ranking ; Voters ; Voting ; Computing Milieux (General) (Ci);
    ISSN: 1432-4350
    E-ISSN: 1433-0490
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  • 3
    Language: English
    In: Nucleic acids research, 01 June 2003, Vol.31(11), pp.2890-9
    Description: In contrast to certain model eubacteria, little is known as to where transcription is initiated in the genomes of cyanobacteria, which are largely distinct from other prokaryotes. In this work, 25 transcription start sites (TSS) of 21 different genes of Prochlorococcus sp. MED4 were determined experimentally. The data suggest more than one TSS for the genes ftsZ, petH, psbD and ntcA. In contrast, the rbcL-rbcS operon encoding ribulose 1,5-bisphosphate carboxylase/oxygenase lacks a detectable promoter and is co-transcribed with the upstream located gene ccmK. The entire set of experimental data was used in a genome-wide scan for putative TSS in Prochlorococcus. A -10 element could be defined, whereas at the -35 position there was no element common to all investigated sequences. However, splitting the data set into sub-classes revealed different types of putative -35 boxes. Only one of them resembled the consensus sequence TTGACA recognized by the vegetative sigma factor (sigma70) of enterobacteria. Using a scoring matrix of the -10 element, more than 3000 TSS were predicted, about 40% of which were estimated to be functional. This is the first systematic study of transcription initiation sites in a cyanobacterium.
    Keywords: Genes, Bacterial ; Transcription Initiation Site ; Cyanobacteria -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 4
    In: Synthesis, 2003, Issue 5, pp.0699-0706
    Description: β-Galactosidase from Bacillus circulans (EC 3.2.1.23) catalyses the transfer of galactose units to various glucose and galactose derivatives, forming β1→4 linkages. The synthesis of several biologically relevant tri- and tetrasaccharides {β- d -Gal p -(1→4)-β- d -Gal p -(1→4)-α,β- d -Glc p ( 2 ), β- d -Gal p -(1→4)-α- d -Glc p -(1→4)- d -Glc p -ol/Man p -ol ( 4 ), β- d -Gal p -(1→4)-α- d -Glc p -(1→6)-β- d -Fru f ( 6 ), β- d -Gal p -(1→4)-α- d -Glc p -(1↔2)-β- d -Fru f ( 8 ), β- d -Gal p -(1→4)-α- d -Glc p -(1↔2)-β- d -Fru f -(1↔2)-β- d -Fru f ( 10 ), β- d -Gal p -(1→4)-α- d -Glc p -(1→6)-[α- d -Glc p -(1↔2)]-β- d -Fru f ( 12a ), β- d -Gal p -(1→4)-α- d -Glc p -(1↔2)-[α- d -Glc p -(1→6)]-β- d -Fru f ( 12b ), α- d -Gal p -(1→6)-[β- d -Gal p -(1→4)]-α- d -Glc p -(1↔2)-β- d -Fru f ( 14a ), β- d -Gal p -(1→4)-α- d -Gal p -(1→6)-α- d -Glc p -(1↔2)-β- d -Fru f ( 14b )} has been achieved in 11-59% yields by application of this enzyme.
    Keywords: Transglycosylations ; Β-galactosidase ; Bacillus Circulans ; Enzymes ; Tri- And Tetrasaccharides
    ISSN: 0039-7881
    E-ISSN: 1437-210X
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  • 5
    Description: In this paper, we propose a novel multicast routing algorithm that is based on application-level priorities and network characteristics: The application may specify an individual priority for each packet-receiver pair. The multicast distribution tree is then constructed such that the higher the priority, the more direct the path from the sender to the packet's destination and the lower the resulting end-to-end delay. This algorithm can be used to realize application-level multicast for delay-sensitive applications such as networked computer games. However, optimizing the multicast tree with respect to the end-to-end delay comes at the cost of an increase in link stress -- the more direct a path, the less likely it is that it can be integrated efficiently into an overlay distribution tree. Our algorithm takes this tradeoff into account and constructs efficient priority-based multicast trees. We demonstrate the performance and characteristics of the algorithm through simulation.
    Keywords: 004 Informatik
    Source: Mannheim University Library
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  • 6
    Language: English
    In: Atmospheric Environment, 2003, Vol.37(21), pp.2957-2966
    Description: Numerical simulations with a comprehensive mesoscale- γ model system were carried out to study the relative importance of individual sources for nitrous acid (HONO) on the daily cycle of the HONO concentration during the course of the day. The sources are the gas phase production, direct emissions of HONO, and heterogeneous reactions at aerosol surfaces and at the ground. The results of the simulations were compared to observations made during 18–19 October 2001 at the 200 m research tower at the Forschungszentrum Karlsruhe, Germany. We found that currently used chemical transport models are using a rate constant for the gas-phase reaction of NO with OH which is a factor of two lower than the recently published IUPAC data. The old rate constant gives 50% lower daytime HONO concentrations than the new one. The simulations showed that the direct emissions and the heterogeneous reactions at the ground are the most important sources of HONO during the night. While the observed nocturnal HONO concentrations close to the surface are reproduced by the simulations the daytime HONO concentrations are underestimated by 30–50%. We introduced an artificial photolytic HONO source which is proportional to the photolysis rate constant of NO 2 . This leads to a much better agreement between observed and simulated HONO concentrations during the day. In addition, we compared the production of the hydroxyl radical by the photolysis of HONO with its production via the photolysis of ozone. During 18 October 2001 when the ozone concentrations were low the photolysis of HONO is the dominant source of the OH radical while during a typical summer day the photolysis of HONO contributes only 20% of the photolysis of ozone.
    Keywords: Nitrous Acid ; Heterogeneous Chemistry ; Photolytic Source ; Modelling ; Hydroxyl Radical
    ISSN: 1352-2310
    E-ISSN: 18732844
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  • 7
    Language: English
    In: Atmospheric Environment, 2003, Vol.37(21), pp.2949-2955
    Description: Simultaneous nighttime HONO, NO, NO 2 and particle surface area density gradients in the altitude range 10–190 m were measured for the first time on the meteorological tower at the Forschungszentrum Karlsruhe/Germany using a new, very sensitive HONO instrument, a commercial NO x monitor and a SMPS system. For all gradient measurements during the campaign it was observed that the [HONO]/[NO 2 ] ratio decreased with increasing altitude below 100 m. In contrast, the particle surface area density was found to be more or less constant. Accordingly, no correlation between the [HONO]/[NO 2 ] ratio and the particle surface area density was observed showing that HONO formation was dominated by processes on ground surfaces and that significant HONO formation on particle surfaces could be excluded for the measurement site. Besides the nighttime gradient measurements, high daytime HONO concentrations were observed at constant altitude, which point to a significant and yet unknown daytime source of HONO. In addition, a HONO/NO x ratio from direct emissions of 0.8% was estimated from the field campaign.
    Keywords: No ; Hono ; Heterogeneous Chemistry ; Gradient Measurements ; Lopap
    ISSN: 1352-2310
    E-ISSN: 18732844
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  • 8
    Language: English
    In: BMJ, 10 July 2003, Vol.327(7406), p.75
    Description: To determine the effectiveness of extracorporeal shock wave therapy compared with placebo in the treatment of chronic plantar fasciitis.
    Keywords: Pain (Neurology) ; Physiotherapy ; Musculoskeletal Syndromes ; Sports and Exercise Medicine
    ISSN: 0959-8138
    ISSN: 09598138
    E-ISSN: 1468-5833
    E-ISSN: 14685833
    E-ISSN: 17561833
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  • 9
    Language: English
    In: Gastroenterology, 2003, Vol.124(4), pp.A550-A550
    ISSN: 0016-5085
    Source: ScienceDirect (Elsevier B.V.)
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  • 10
    Language: English
    In: ChemInform, 08 July 2003, Vol.34(27), pp.no-no
    Keywords: Carbohydrates ; Biochemical Syntheses ; Microbiological Syntheses
    ISSN: 0931-7597
    E-ISSN: 1522-2667
    Source: John Wiley & Sons, Inc.
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