Clinical and therapeutic implications of BRAF mutation heterogeneity in metastatic melanoma

Heterogeneity of BRAF mutation in melanoma has been a controversial subject. Quantitative data on BRAF allele frequency (AF) are sparse, and the potential relationship with response to BRAF inhibitors (BRAFi) in patients with metastatic melanoma is unknown. We quantitatively measured BRAF AF in a cohort of treatment naïve metastatic melanoma samples by pyrosequencing and correlated with survival data in patients treated with BRAFi as part of their clinical care. Fifty‐two samples from 50 patients were analysed. BRAF V600E mutations were detected in 71.1% of samples followed by V600K (25%) and V600R (3.9%). There was a wide range of AF from 3.9% to 80.3% (median 41.3%). In 33 patients treated with BRAFi, there was no difference in overall or progression‐free survival when the patients were categorized into high or low AF groups. There was no correlation between AF and degree of response, and no difference in survival based on genotype.     

Synthesis and biochemical evaluation of novel inhibitors of aromatase (AR) using an enhanced representation of the active site of AR derived from the consideration of the reaction mechanism

A novel molecular modeling study, involving inhibitors bound to the iron of cytochrome P450 heme, is described for nonsteroidal inhibitors of aromatase (AR). Study of compounds such as aminoglutethimide (AG) suggests that it utilizes hydrogen bonding group(s) at the active site which would usually H-bond to the steroid C(17) carbonyl group. Interaction between AG's carbonyl groups and the area of the active site corresponding to the substrate C(3)==O group is not possible due to steric interaction. Possible reasons for the difference in activity of enantiomers of alternative inhibitors is also suggested, as well as the mode of action of the new AR inhibitor, Arimidex-whose inhibitory activity previously has not been rationalized. The present study proposes that it is able to use hydrogen bonding groups at the active site corresponding to the steroid C(17)==O and C(3)==O area, contradicting a previous study where it is postulated that azole-type compounds only use polar groups at the active site corresponding to the steroid D ring. Using the hypotheses of the modeling study, we designed and synthesized a number of novel (enantiomerically pure) inhibitors, which upon biochemical evaluation were found to be good inhibitors; the N-nonyl derivative of the S-enantiomer was found to possess 39% inhibition at 100 microM inhibitor concentration (using androstenedione as the substrate), under similar conditions, and AG possessed 20% inhibition.     

Mechanisms driving the density–area relationship in a saproxylic beetle

Mechanisms underlying density–area relationships (correlations between population density and patch size) have rarely been tested experimentally. It is often assumed that higher density on large patches is evidence that large patches are high quality (i.e. have greater survival and reproduction), but the same pattern could result from disproportionate movement from small to large patches. Movement-based and within-patch processes must be experimentally separated to show that large patches are indeed of higher quality, but few studies have done so. We experimentally tested movement-based and within-patch hypotheses to explain the positive density–area relationship observed for a saproxylic (decayed wood-dependent) beetle, Odontotaenius disjunctus Illiger (Coleoptera: Passalidae). In separate experiments we quantified (1) immigration into and (2) finite growth rate within logs (=patches) that varied in size and density of conspecific beetles. A log was 11.7-fold [95 % confidence interval (CI) 3.4–40.8) and 10.5-fold (95 % CI 2.7–40.9) more likely to contain a new immigrant if it was large or contained a conspecific pair of beetles, respectively. Neither log size nor conspecific density was associated with changes in finite growth rate that would lead to higher density: decreased log size and increased conspecific density reduced finite growth rate in direct proportion to the loss in available resources per mating pair. We conclude that movement behavior rather than habitat quality is responsible for the positive density–area relationship for O. disjunctus. An important implication of our results is that population density is an imperfect indicator of habitat quality.     

Particle Diffusivity and Free-Energy Profiles in Hydrogels from Time-Resolved Penetration Data

A combined experimental and theoretical method to simultaneously determine diffusivity and free-energy profiles of particles that penetrate into inhomogeneous hydrogel systems is presented. As the only input, arbitrarily normalized concentration profiles from fluorescence intensity data of labeled tracer particles for different penetration times are needed. The method is applied to dextran molecules of varying size that penetrate into hydrogels of polyethylene-glycol chains with different lengths that are covalently cross-linked by hyperbranched polyglycerol hubs. Extracted dextran bulk diffusivities agree well with fluorescence correlation spectroscopy data obtained separately. Empirical scaling laws for dextran diffusivities and free energies inside the hydrogel are identified as a function of the dextran mass. An elastic free-volume model that includes dextran as well as polyethylene-glycol linker flexibility quantitively describes the repulsive dextran-hydrogel interaction free energy, which is of steric origin, and furthermore suggests that the hydrogel mesh-size distribution is rather broad and particle penetration is dominated by large hydrogel pores. Particle penetration into hydrogels for steric particle-hydrogel interactions is thus suggested to be governed by an elastic size-filtering mechanism that involves the tail of the hydrogel pore-size distribution.