Analysis of chimeric receptors shows that multiple distinct functional activities of scavenger receptor, class B, type I (SR-BI), are localized to the extracellular receptor domain

Scavenger receptor BI (SR-BI) mediates the selective uptake of high-density lipoprotein (HDL) cholesteryl ester (CE), a process by which HDL CE is taken into the cell without degradation of the HDL particle. In addition, SR-BI stimulates the bi-directional flux of free cholesterol (FC) between cells and lipoproteins, an activity that may be responsible for net cholesterol efflux from peripheral cells as well as the rapid hepatic clearance of FC from plasma HDL. SR-BI also increases cellular cholesterol mass and alters cholesterol distribution in plasma membrane domains as judged by the enhanced sensitivity of membrane cholesterol to extracellular cholesterol oxidase. In contrast, CD36, a closely related class B scavenger receptor, has none of these activities despite binding HDL with high affinity. In the present study, analyses of chimeric SR-BI/CD36 receptors and domain-deleted SR-BI have been used to test the various domains of SR-BI for functional activities related to HDL CE selective uptake, bi-directional FC flux, and the alteration of membrane cholesterol mass and distribution. The results show that each of these activities localizes to the extracellular domain of SR-BI. The N-terminal cytoplasmic tail and transmembrane domains appear to play no role in these activities other than targeting the receptor to the plasma membrane. The C-terminal tail of SR-BI is dispensable for activity as well for targeting to the plasma membrane. Thus, multiple distinct functional activities are localized to the SR-BI extracellular domain.     

SubcloneSeeker: a computational framework for reconstructing tumor clone structure for cancer variant interpretation and prioritization

Many tumors are composed of genetically divergent cell subpopulations. We report SubcloneSeeker, a package capable of exhaustive identification of subclone structures and evolutionary histories with bulk somatic variant allele frequency measurements from tumor biopsies. We present a statistical framework to elucidate whether specific sets of mutations are present within the same subclones, and the order in which they occur. We demonstrate how subclone reconstruction provides crucial information about tumorigenesis and relapse mechanisms; guides functional study by variant prioritization, and has the potential as a rational basis for informed therapeutic strategies for the patient. SubcloneSeeker is available at: https://github.com/yiq/SubcloneSeeker.

Electronic supplementary material

The online version of this article (doi:10.1186/s13059-014-0443-x) contains supplementary material, which is available to authorized users.     

HeatMapper: powerful combined visualization of gene expression profile correlations, genotypes, phenotypes and sample characteristics

Background  

Accurate interpretation of data obtained by unsupervised analysis of large scale expression profiling studies is currently frequently performed by visually combining sample-gene heatmaps and sample characteristics. This method is not optimal for comparing individual samples or groups of samples. Here, we describe an approach to visually integrate the results of unsupervised and supervised cluster analysis using a correlation plot and additional sample metadata.     

ESR spectroscopic evidence for hydration- and temperature-dependent spatial perturbations of a higher plant cell wall paramagnetic ion lattice

To study the influence of cell wall polyuronide structure on bound paramagnetic ion interactions, spin-spin coupling measurements were made on intact cell walls exchanged with a wide range fo Mn²⁺ and Cu²⁺ concentrations. These experiments were performed so that dimer-only intercationic nearest neighbor distances (d) and lattice constants (κ) could be calculated from the linewidth-concentration dependency. d values were estimated to be 12 and 14 Å for Cu²⁺ and Mn²⁺, respectively. At the maximal bound ion concentration, κ was 2.3–2.6, indicating that about 5–7 paramagnetic ion nearest neighbor spin-spin interactions occur per dipole in the nearly filled lattice. This latter observation strongly argues for the egg-box model of the cell wall-polyuronide lattice structure. Mn²⁺ linewidths of hydrated cell wall-bound paramagnetic ions displayed an unusual temperature dependency, whereby linewidths increased between 20°C and the temperature at which maximal linewidths were observed (T_max). T_max was inversely proportional to the degree of lattice hydration, indicating that the temperature dependency was not associated with the freezing of bound water. The relative change in Mn²⁺ linewidths, between 20°C and T_max, was affected by binding site-associated ¹H spin-lattice relaxation times, indicating that the temperature dependency is at least partially controlled by cell wall polyuronide structure.