22 research outputs found
Light Spanners
A -spanner of a weighted undirected graph , is a subgraph
such that for all . The sparseness of
the spanner can be measured by its size (the number of edges) and weight (the
sum of all edge weights), both being important measures of the spanner's
quality -- in this work we focus on the latter.
Specifically, it is shown that for any parameters and ,
any weighted graph on vertices admits a
-stretch spanner of weight at most , where is the weight of a minimum
spanning tree of . Our result is obtained via a novel analysis of the
classic greedy algorithm, and improves previous work by a factor of .Comment: 10 pages, 1 figure, to appear in ICALP 201
Systematic Approach to Conformational Sampling for Assigning Absolute Configuration Using Vibrational Circular Dichroism
Systematic
methods that speed-up the assignment of absolute configuration
using vibrational circular dichrosim (VCD) and simplify its usage
will advance this technique into a robust platform technology. Applying
VCD to pharmaceutically relevant compounds has been handled in an
ad hoc fashion, relying on fragment analysis and technical shortcuts
to reduce the computational time required. We leverage a large computational
infrastructure to provide adequate conformational exploration which
enables an accurate assignment of absolute configuration. We describe
a systematic approach for rapid calculation of VCD/IR spectra and
comparison with corresponding measured spectra and apply this approach
to assign the correct stereochemistry of nine test cases. We suggest
moving away from the fragment approach when making VCD assignments.
In addition to enabling faster and more reliable VCD assignments of
absolute configuration, the ability to rapidly explore conformational
space and sample conformations of complex molecules will have applicability
in other areas of drug discovery
Recruitment of mRNA cleavage/polyadenylation machinery by the yeast chromatin protein Sin1p/Spt2p
The yeast chromatin protein Sin1p/Spt2p has long been studied, but the understanding of its function has remained elusive. The protein has sequence similarity to HMG1, specifically binds crossing DNA structures, and serves as a negative transcriptional regulator of a small family of genes that are activated by the SWI/SNF chromatin-remodeling complex. Recently, it has been implicated in maintaining the integrity of chromatin during transcription elongation. Here we present experiments whose results indicate that Sin1p/Spt2 is required for, and is directly involved in, the efficient recruitment of the mRNA cleavage/polyadenylation complex. This conclusion is based on the following findings: Sin1p/Spt2 frequently binds specifically downstream of many ORFs but almost always upstream of the first polyadenylation site. It directly interacts with Fir1p, a component of the cleavage/polyadenylation complex. Disruption of Sin1p/Spt2p results in foreshortened poly(A) tracts on mRNA. It is synthetically lethal with Cdc73p, which is involved in the recruitment of the complex. This report shows that a chromatin component is involved in 3âČ end processing of RNA