12,130 research outputs found
Colloidal Particles at Chiral Liquid Crystal Interfaces
Colloidal particles trapped at an interface between two fluids can form a
wide range of different structures. Replacing one of the fluid with a liquid
crystal increases the complexity of interactions and results in a greater range
of possible structures. New behaviour emerges when colloidal particles interact
with defects in the liquid crystal phases. Here we discuss the templating of
colloids at a cholesteric isotropic interface.Comment: 7 pages, 5 figure
GenomeFingerprinter and universal genome fingerprint analysis for systematic comparative genomics
How to compare whole genome sequences at large scale has not been achieved
via conventional methods based on pair-wisely base-to-base comparison;
nevertheless, no attention was paid to handle in-one-sitting a number of
genomes crossing genetic category (chromosome, plasmid, and phage) with farther
divergences (much less or no homologous) over large size ranges (from Kbp to
Mbp). We created a new method, GenomeFingerprinter, to unambiguously produce
three-dimensional coordinates from a sequence, followed by one
three-dimensional plot and six two-dimensional trajectory projections to
illustrate whole genome fingerprints. We further developed a set of concepts
and tools and thereby established a new method, universal genome fingerprint
analysis. We demonstrated their applications through case studies on over a
hundred of genome sequences. Particularly, we defined the total genetic
component configuration (TGCC) (i.e., chromosome, plasmid, and phage) for
describing a strain as a system, and the universal genome fingerprint map
(UGFM) of TGCC for differentiating a strain as a universal system, as well as
the systematic comparative genomics (SCG) for comparing in-one-sitting a number
of genomes crossing genetic category in diverse strains. By using UGFM,
UGFM-TGCC, and UGFM-TGCC-SCG, we compared a number of genome sequences with
farther divergences (chromosome, plasmid, and phage; bacterium, archaeal
bacterium, and virus) over large size ranges (6Kbp~5Mbp), giving new insights
into critical problematic issues in microbial genomics in the post-genomic era.
This paper provided a new method for rapidly computing, geometrically
visualizing, and intuitively comparing genome sequences at fingerprint level,
and hence established a new method of universal genome fingerprint analysis for
systematic comparative genomics.Comment: 63 pages, 15 figures, 5 table
Detection of the TCDD binding-fingerprint within the Ah receptor ligand binding domain by structurally driven mutagenesis and functional analysis
The aryl hydrocarbon receptor (AhR) is a ligand-dependent, basic helix-loop-helix Per-Arnt-Sim (PAS)-containing transcription factor that can bind and be activated by structurally diverse chemicals, including the toxic environmental contaminant 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD). Our previous three-dimensional homology model of the mouse AhR (mAhR) PAS B ligand binding domain allowed identification of the binding site and its experimental validation. We have extended this analysis by conducting comparative structural modeling studies of the ligand binding domains of six additional highaffinity mammalian AhRs. These results, coupled with site-directed mutagenesis and AhR functional analysis, have allowed detection of the "TCDD binding-fingerprint" of conserved residues within the ligand binding cavity necessary for high-affinity TCDD binding and TCDD-dependent AhR transformation DNA binding. The essential role of selected residues was further evaluated using molecular docking simulations of TCDD with both wild-type and mutant mAhRs. Taken together, our results dramatically improve our understanding of the molecular determinants of TCDD binding and provide a basis for future studies directed toward rationalizing the observed species differences in AhR sensitivity to TCDD and understanding the mechanistic basis for the dramatic diversity in AhR ligand structure. © 2009 American Chemical Society
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