14,871 research outputs found
Keyword-aware Optimal Route Search
Identifying a preferable route is an important problem that finds
applications in map services. When a user plans a trip within a city, the user
may want to find "a most popular route such that it passes by shopping mall,
restaurant, and pub, and the travel time to and from his hotel is within 4
hours." However, none of the algorithms in the existing work on route planning
can be used to answer such queries. Motivated by this, we define the problem of
keyword-aware optimal route query, denoted by KOR, which is to find an optimal
route such that it covers a set of user-specified keywords, a specified budget
constraint is satisfied, and an objective score of the route is optimal. The
problem of answering KOR queries is NP-hard. We devise an approximation
algorithm OSScaling with provable approximation bounds. Based on this
algorithm, another more efficient approximation algorithm BucketBound is
proposed. We also design a greedy approximation algorithm. Results of empirical
studies show that all the proposed algorithms are capable of answering KOR
queries efficiently, while the BucketBound and Greedy algorithms run faster.
The empirical studies also offer insight into the accuracy of the proposed
algorithms.Comment: VLDB201
A functional RNase P protein subunit of bacterial origin in some eukaryotes
RNase P catalyzes 5′-maturation of tRNAs. While bacterial RNase P comprises an RNA catalyst and a protein cofactor, the eukaryotic (nuclear) variant contains an RNA and up to ten proteins, all unrelated to the bacterial protein. Unexpectedly, a nuclear-encoded bacterial RNase P protein (RPP) homolog is found in several prasinophyte algae including Ostreococcus tauri. We demonstrate that recombinant O. tauri RPP can functionally reconstitute with bacterial RNase P RNAs (RPRs) but not with O. tauri organellar RPRs, despite the latter’s presumed bacterial origins. We also show that O. tauri PRORP, a homolog of Arabidopsis PRORP-1, displays tRNA 5′-processing activity in vitro. We discuss the implications of the striking diversity of RNase P in O. tauri, the smallest known free-living eukaryote.Ministerio de Ciencia e Innovación European Regional Fund BFU2007-60651Junta de AndalucÃa P06-CVI-01692National Science Foundation MCB-0238233 MCB-0843543European Union ASSEMBLE 22779
An Adaptation To Life In Acid Through A Novel Mevalonate Pathway.
Extreme acidophiles are capable of growth at pH values near zero. Sustaining life in acidic environments requires extensive adaptations of membranes, proton pumps, and DNA repair mechanisms. Here we describe an adaptation of a core biochemical pathway, the mevalonate pathway, in extreme acidophiles. Two previously known mevalonate pathways involve ATP dependent decarboxylation of either mevalonate 5-phosphate or mevalonate 5-pyrophosphate, in which a single enzyme carries out two essential steps: (1) phosphorylation of the mevalonate moiety at the 3-OH position and (2) subsequent decarboxylation. We now demonstrate that in extreme acidophiles, decarboxylation is carried out by two separate steps: previously identified enzymes generate mevalonate 3,5-bisphosphate and a new decarboxylase we describe here, mevalonate 3,5-bisphosphate decarboxylase, produces isopentenyl phosphate. Why use two enzymes in acidophiles when one enzyme provides both functionalities in all other organisms examined to date? We find that at low pH, the dual function enzyme, mevalonate 5-phosphate decarboxylase is unable to carry out the first phosphorylation step, yet retains its ability to perform decarboxylation. We therefore propose that extreme acidophiles had to replace the dual-purpose enzyme with two specialized enzymes to efficiently produce isoprenoids in extremely acidic environments
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