Role of SNX16 in the Dynamics of Tubulo-Cisternal Membrane Domains of Late Endosomes

In this paper, we report that the PX domain-containing protein SNX16, a member of the sorting nexin family, is associated with late endosome membranes. We find that SNX16 is selectively enriched on tubulo-cisternal elements of this membrane system, whose highly dynamic properties and formation depend on intact microtubules. By contrast, SNX16 was not found on vacuolar elements that typically contain LBPA, and thus presumably correspond to multivesicular endosomes. We conclude that SNX16, together with its partner phosphoinositide, define a highly dynamic subset of late endosomal membranes, supporting the notion that late endosomes are organized in distinct morphological and functional regions. Our data also indicate that SNX16 is involved in tubule formation and cholesterol transport as well as trafficking of the tetraspanin CD81, suggesting that the protein plays a role in the regulation of late endosome membrane dynamics

7th Drug hypersensitivity meeting: part two

No abstract availabl

Symmetry in the Language of Gene Expression: A Survey of Gene Promoter Networks in Multiple Bacterial Species and Non-σ Regulons

The language of gene expression displays topological symmetry. An important step during gene expression is the binding of transcriptional proteins to DNA promoters adjacent to a gene. Some proteins bind to many promoters in a genome, defining a regulon of genes wherein each promoter might vary in DNA sequence relative to the average consensus. Here we examine the linguistic organization of gene promoter networks, wherein each node in the network represents a promoter and links between nodes represent the extent of base pair-sharing. Prior work revealed a fractal nucleus in several σ-factor regulons from Escherichia coli. We extend these findings to show fractal nuclei in gene promoter networks from three bacterial species, E. coli, Bacillus subtilis, and Pseudomonas aeruginosa. We surveyed several non-σ transcription factors from these species and found that many contain a nucleus that is both visually and numerically fractal. Promoter footprint size scaled as a negative power-law with both information entropy and fractal dimension, while the latter two parameters scaled positively and linearly. The fractal dimension of the diffuse networks (dB = ~1.7) was close to that expected of a diffusion limited aggregation process, confirming prior predictions as to a possible mechanism for development of this structure

Symmetry in the Language of Gene Expression: A Survey of Gene Promoter Networks in Multiple Bacterial Species and Non-σ Regulons

The language of gene expression displays topological symmetry. An important step during gene expression is the binding of transcriptional proteins to DNA promoters adjacent to a gene. Some proteins bind to many promoters in a genome, defining a regulon of genes wherein each promoter might vary in DNA sequence relative to the average consensus. Here we examine the linguistic organization of gene promoter networks, wherein each node in the network represents a promoter and links between nodes represent the extent of base pair-sharing. Prior work revealed a fractal nucleus in several σ-factor regulons from Escherichia coli. We extend these findings to show fractal nuclei in gene promoter networks from three bacterial species, E. coli, Bacillus subtilis, and Pseudomonas aeruginosa. We surveyed several non-σ transcription factors from these species and found that many contain a nucleus that is both visually and numerically fractal. Promoter footprint size scaled as a negative power-law with both information entropy and fractal dimension, while the latter two parameters scaled positively and linearly. The fractal dimension of the diffuse networks (dB = ~1.7) was close to that expected of a diffusion limited aggregation process, confirming prior predictions as to a possible mechanism for development of this structure

Hybridization network for the system of woody plant gene pools in the United States

<div><p></p><p>Hybridization generates similarities among gene pools. This structure can be visualized and analyzed at the systems level using networks. Here we construct a network of the 315 woody plant species native or naturalized in the United States using data compiled by the Forest Service of the US Department of Agriculture (USFS). Each species is represented by a node in the network whose size is proportional to a recent census for live stems in the continental United States. Each of the 416 links between node pairs represents evidence for hybridization compiled from the USFS manual <i>Silvics of North America</i>. The total network resolved into 100 separate connected components or clusters (mean size, 3.15 species), with 44% of species linked to at least one other. <i>Betula</i> had the largest component (18 species) following by the separate <i>Quercus</i> clusters (17 red oaks and 16 white oaks); <i>Q. velutina</i> was the most genetically connected woody plant in the continental US. The number of species held together per component (i.e. size) scaled as a power–law albeit a slightly truncated one. The truncation suggests there are fewer than expected hybridizing species within the large woody genera of plants in the US.</p> </div

The role of population pharmacokinetic analysis in rational antibiotic therapy in neonates

status: publishe