Linking microarray reporters with protein functions

Background  

The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualization tools are used to connect gene expression data with existing biological pathways by using specific database identifiers that link reporters with elements in the pathways.     

Discovery of XL888: A novel tropane-derived small molecule inhibitor of HSP90

With structural guidance, tropane-derived HTS hits were modified to optimize for HSP90 inhibition and a desirable in vivo profile. Through an iterative SAR development process 12i (XL888) was discovered and shown to reduce HSP90 client protein content in PD studies. Furthermore, efficacy experiments performed in a NCI-N87 mouse xenograft model demonstrated tumor regression in some dosing regimens.     

Vertebrate exploitation of pulsed marine prey: a review and the example of spawning herring

Short-term bursts of prey availability occur in many ecosystems and have potential important consequences for both predator biology and ecosystem function. Examples of prey ‘pulses’ in marine ecosystems include spawning runs of several anadromous and marine fishes, horseshoe crab spawning, and salmonid juvenile outmigrations, which are exploited by numerous species of vertebrate predators. In a few cases, the fitness or demographic consequences of such predator–prey interactions are known or inferred, but too often that information remains unknown. We explored the extent of temporal and spatial variation in one example of a pulsed marine resource: the spawning of Pacific herring (Clupea pallasii). Spawning herring provide a rich, aggregated resource to which dozens of species of vertebrate predators often exhibit strong numerical responses. However, the spawning events are often variable in both time (annual differences of several to many weeks) and space (both regional and more local differences in size and timing of events). Such variability must affect more mobile predators less than area-restricted predators, and thus its effect would vary not only among species but also within species, depending on constraints of the predator life history. Unpredictability of the prey concentrations, whatever their proximate causes, may contribute to maintenance of metapopulations of prey such as herring, if unpredictability lessens the impact of predation.     

Changes in Symptoms of Depression With Weight Loss: Results of a Randomized Trial

Recent studies of rimonabant have re‐awakened interest in the possible adverse psychiatric effects of weight loss, as well as of weight loss medications. This study examined changes in symptoms of depression in 194 obese participants (age = 43.7 ± 10.2 years; BMI = 37.6 ± 4.1 kg/m²) in a 1‐year randomized trial of lifestyle modification and medication. Participants were assigned to (i) sibutramine alone; (ii) lifestyle modification alone; (iii) sibutramine plus lifestyle modification (i.e., combined therapy); or (iv) sibutramine plus brief therapy. Participants completed the Beck Depression Inventory‐II (BDI‐II) at baseline and weeks 6, 10, 18, 26, 40, and 52. At 1 year, participants in combined therapy lost the most weight and those in sibutramine alone the least (12.1 ± 8.8% vs. 5.5 ± 6.5%; P < 0.01). Mean BDI‐II scores across all participants declined from 8.1 ± 6.9 to 6.2 ± 7.7 at 1 year (P < 0.001), with no significant differences among groups. Despite this favorable change, 13.9% of participants (across the four groups) reported potentially discernible increases (≥ 5 points on the BDI‐II) in symptoms of depression at week 52. They lost significantly less weight than participants in the rest of the sample (5.4 ± 7.8% vs. 9.0 ± 7.8%, respectively; P < 0.03). The baseline prevalence of suicidal ideation was 3.6%. Seven new cases of suicidal ideation were observed during the year, with three in lifestyle modification alone. Further research is needed to identify characteristics of obese patients at risk of negative mood changes (and suicidal ideation) in response to behavioral and pharmacologic therapies.     

Method for obtaining more-accurate covalently closed circular plasmid-to-chromosome ratios from bacterial lysates by dye-buoyant density centrifugation.

A method that gives high recovery of deoxyribonucleic acid (DNA) from crude bacterial lysates using ethidium bromide-cesium chloride density gradient centrifugation is presented. After Pronase digestion and shearing of the lysate, essentially 100% recovery of chromosomal DNA and a reproducible recovery of covalently closed circular (CCC) plasmid DNA is obtained for a specific plasmid in a given strain. This method should be useful for comparing the CCC plasmid/chromosome ratio of various plasmid-host combinations.     

Supramolecular structures of peptide assemblies in membranes by neutron off-plane scattering: method of analysis

In a previous paper (Yang et al., Biophys. J. 75:641-645, 1998), we showed a simple, efficient method of recording the diffraction patterns of supramolecular peptide assemblies in membranes where the samples were prepared in the form of oriented multilayers. Here we develop a method of analysis based on the diffraction theory of two-dimensional liquids. Gramicidin was used as a prototype model because its pore structure in membrane in known. At full hydration, the diffraction patterns of alamethicin and magainin are similar to gramicidin except in the scale of q (the momentum transfer of scattering), clearly indicating that both alamethicin and magainin form pores in membranes but of different sizes. When the hydration of the multilayer samples was decreased while the bilayers were still fluid, the in-plane positions of the membrane pores became correlated from one bilayer to the next. We believe that this is a new manifestation of the hydration force. The effect is most prominent in magainin patterns, which are used to demonstrate the method of analysis. When magainin samples were further dehydrated or cooled, the liquid-like diffraction turned into crystal-like patterns. This discovery points to the possibility of investigating the supramolecular structures with high-order diffraction.