Performance-based selection of likelihood models for phylogeny estimation

Phylogenetic estimation has largely come to rely on explicitly model-based methods. This approach requires that a model be chosen and that that choice be justified. To date, justification has largely been accomplished through use of likelihood-ratio tests (LRTs) to assess the relative fit of a nested series of reversible models. While this approach certainly represents an important advance over arbitrary model selection, the best fit of a series of models may not always provide the most reliable phylogenetic estimates for finite real data sets, where all available models are surely incorrect. Here, we develop a novel approach to model selection, which is based on the Bayesian information criterion, but incorporates relative branch-length error as a performance measure in a decision theory (DT) framework. This DT method includes a penalty for overfitting, is applicable prior to running extensive analyses, and simultaneously compares all models being considered and thus does not rely on a series of pairwise comparisons of models to traverse model space. We evaluate this method by examining four real data sets and by using those data sets to define simulation conditions. In the real data sets, the DT method selects the same or simpler models than conventional LRTs. In order to lend generality to the simulations, codon-based models (with parameters estimated from the real data sets) were used to generate simulated data sets, which are therefore more complex than any of the models we evaluate. On average, the DT method selects models that are simpler than those chosen by conventional LRTs. Nevertheless, these simpler models provide estimates of branch lengths that are more accurate both in terms of relative error and absolute error than those derived using the more complex (yet still wrong) models chosen by conventional LRTs. This method is available in a program called DT-ModSel.     

A widely applicable, high-throughput TR-FRET assay for the measurement of kinase autophosphorylation: VEGFR-2 as a prototype

Homogeneous time-resolved fluorescence resonance energy transfer (TR-FRET) assays represent a highly sensitive and robust high-throughput screening (HTS) method for the quantification of kinase activity. Traditional TR-FRET kinase assays detect the phosphorylation of an exogenous substrate. The authors describe the development and optimization of a TR-FRET technique that measures the autophosphorylation of vascular endothelial growth factor receptor 2 (VEGFR-2) kinase and extend its applicability to a variety of other kinases. The VEGFR-2 assay demonstrated dose-dependent inhibition by compounds known to modulate the catalytic activity of this receptor. In addition, kinetic analysis of a previously characterized VEGFR-2 inhibitor was performed using the method, and results were consistent with those obtained using a different assay format. Because of the known involvement of VEGFR-2 in angiogenesis, this assay should facilitate HTS for antiangiogenic agents. In addition, this general technique should have utility for the screening for inhibitors of kinases as potential therapeutic agents for many other disease indications.     

Visual motion retards alternations between conflicting perceptual interpretations

When the visual system is faced with conflicting or ambiguous stimulus information, visual perception fluctuates over time. We found that perceptual alternations are slowed when inducing stimuli move within the visual field, constantly engaging fresh, unadapted neural tissue. During binocular rivalry, dominance durations were longer when rival figures moved compared to when they were stationary, yielding lower alternation rates. Rate was not reduced, however, when observers tracked the moving targets, keeping the images on approximately the same retinal area. Alternations were reliably triggered when rival targets passed through a local region of the visual field preadapted to one of the rival targets. During viewing of a kinetic globe whose direction of rotation was ambiguous, observers experienced fewer alternations in perceived direction when the globe moved around the visual field or when the globe's axis of rotation changed continuously. Evidently, local neural adaptation is a key ingredient in the instability of perception.     

Pro-inflammatory effects of Burkholderia cepacia on cystic fibrosis respiratory epithelium

Burkholderia cepacia causes pulmonary infection with high mortality in cystic fibrosis (CF) patients which is likely to involve interaction with respiratory epithelium. In this study the pro-inflammatory properties of B. cepacia were examined using a range of respiratory epithelial cell lines. B. cepacia and cell-free culture supernatants were used to stimulate cell lines with (SigmaCFTE29o- and IB3) and without (A549) the CF transmembrane conductance regulator mutation (CFTR), together with corrected cell lines (C38 and S9). Interleukin (IL)-6 and IL-8, but not GM-CSF or IL-1beta, were released from all the cell lines whereas PGE(2) (prostaglandin E(2)) was released from the A549, IB3 and S9 cell lines only. Nuclear factor (NF)-kappaB activation preceded cytokine release and suppression of NF-kappaB activity diminished cytokine release. These studies indicated that B. cepacia secretory products are potent pro-inflammatory agents for respiratory epithelium and suggest functional CFTR is not required for cytokine or prostanoid responses.     

Specifying functional units and reference flows for comparable alternatives

Goal, Scope, and Background  

Despite documentation of product lifetime, performance, and system dependency issues, requirements for specifying functional units and reference flows in LCA have not been developed. The ISO standards simply note that selection between functions is dependent on the goals and scope of the study, that the functional unit must be clearly defined and measurable, and that the reference flows are the amount of product necessary per functional unit. The goal of this work is to suggest and demonstrate the use a set of requirements for specifying the functional unit and reference flows for comparative LCAs.     

Comparison of central administration of corticotropin-releasing hormone and urocortin on food intake, conditioned taste aversion, and c-Fos expression

Corticotropin-releasing hormone (CRH) is a potent regulator of the hypothalamic-pituitary-adrenal axis, and reduces food intake when administered into the third cerebral ventricle (i3vt). However, CRH also promotes conditioned taste aversion (CTA) learning which indicates that its anorectic effects are accompanied by aversive consequences that would reduce food intake independently of energy regulation. Urocortin (Ucn) is a closely related mammalian peptide that binds to both identified CRH receptor subtypes and also reduces food intake when administered i3vt. The present experiments compared the aversive consequences of i3vt administration of CRH and Ucn at doses that produced comparable decrements in food intake. Experiment 1 found that 1.0 microg Ucn and 2.0 microg CRH produced similar reductions in food intake. Experiment 2 demonstrated that, at these doses, CRH but not Ucn promoted robust and reliable CTA learning. A third experiment showed comparable increased c-Fos-like immunoreactivity after Ucn and CRH in forebrain and hindbrain structures associated with food intake. It is concluded that Ucn, at doses that reduce food intake to levels like that observed after administration of CRH, do not produce similarly aversive consequences.     

Chemoinformatics - predicting the physicochemical properties of 'drug-like' molecules

A few major advances have occurred in the area of physicochemical modeling of organic compounds during the past several years, spurred on by changes in the pharmaceutical industry. Recent advances include the ability to categorize and screen the overall physicochemical properties of potential drug candidates based entirely on their molecular structures and the ability to model the components that contribute to the oral absorption characteristics of potential drug candidates.     

Molecular structure of a fibrillar Alzheimer's A beta fragment

Amyloid-beta (Abeta) peptide deposition as fibrillar senile plaques is a key element in the pathology of Alzheimer's disease. Here we present a high-resolution structure of an Abeta amyloid fibril using magnetically aligned preparations of a central Abeta domain which forms representative amyloid fibrils. Diffraction analysis of these samples revealed Bragg reflections on layer lines consistent with a preferred orientation, as opposed to the typical symmetry associated with fibers. These crystalline properties permitted a molecular replacement approach based upon a beta-hairpin motif resulting in a structure of the fibrillar Abeta peptide. This detailed molecular structure of Abeta in its fibrous state provides clues as to the mechanism of amyloid assembly and identifies potential targets for controlling the aggregation process.     

American Association of Tissue Banks: A Historical Reflection Upon Entering the 21st Century

The American Association of Tissue Banks (AATB) is a scientific, not-for-profit, peer-group organization founded in 1976 to facilitate the provision of transplantable tissues of uniform high quality in quantities sufficient to meet national needs. The Association was created well before there was governmental oversight of tissue banking. The organization consists of individuals involved in tissue banking, medical users, and scientists in the field. Current structure consists of a 13-member Board of Governors with specific subgroups including Musculoskeletal, Reproductive, Skin, Tissue Bank Councils and Council of Accredited Tissue Banks. A historical review shows the evolution from development of guidelines to publication of standards, and from an inspection conducted by peers to one conducted by an independent, trained professional inspector. Association growth and historical accomplishments are highlighted.     

SU6656, a selective src family kinase inhibitor, used to probe growth factor signaling

The use of small-molecule inhibitors to study molecular components of cellular signal transduction pathways provides a means of analysis complementary to currently used techniques, such as antisense, dominant-negative (interfering) mutants and constitutively activated mutants. We have identified and characterized a small-molecule inhibitor, SU6656, which exhibits selectivity for Src and other members of the Src family. A related inhibitor, SU6657, inhibits many kinases, including Src and the platelet-derived growth factor (PDGF) receptor. The use of SU6656 confirmed our previous findings that Src family kinases are required for both Myc induction and DNA synthesis in response to PDGF stimulation of NIH 3T3 fibroblasts. By comparing PDGF-stimulated tyrosine phosphorylation events in untreated and SU6656-treated cells, we found that some substrates (for example, c-Cbl, and protein kinase C delta) were Src family substrates whereas others (for example, phospholipase C-gamma) were not. One protein, the adaptor Shc, was a substrate for both Src family kinases (on tyrosines 239 and 240) and a distinct tyrosine kinase (on tyrosine 317, which is perhaps phosphorylated by the PDGF receptor itself). Microinjection experiments demonstrated that a Shc molecule carrying mutations of tyrosines 239 and 240, in conjunction with an SH2 domain mutation, interfered with PDGF-stimulated DNA synthesis. Deletion of the phosphotyrosine-binding domain also inhibited synthesis. These inhibitions were overcome by heterologous expression of Myc, supporting the hypothesis that Shc functions in the Src pathway. SU6656 should prove a useful additional tool for further dissecting the role of Src kinases in this and other signal transduction pathways.