Signaling network prediction by the Ontology Fingerprint enhanced Bayesian network

Abstract Background Despite large amounts of available genomic and proteomic data, predicting the structure and response of signaling networks is still a significant challenge. While statistical method such as Bayesian network has been explored to meet this challenge, employing existing biological knowledge for network prediction is difficult. The objective of this study is to develop a novel approach that integrates prior biological knowledge in the form of the Ontology Fingerprint to infer cell-type-specific signaling networks via data-driven Bayesian network learning; and to further use the trained model to predict cellular responses. Results We applied our novel approach to address the Predictive Signaling Network Modeling challenge of the fourth (2009) Dialog for Reverse Engineering Assessment's and Methods (DREAM4) competition. The challenge results showed that our method accurately captured signal transduction of a network of protein kinases and phosphoproteins in that the predicted protein phosphorylation levels under all experimental conditions were highly correlated (R2 = 0.93) with the observed results. Based on the evaluation of the DREAM4 organizer, our team was ranked as one of the top five best performers in predicting network structure and protein phosphorylation activity under test conditions. Conclusions Bayesian network can be used to simulate the propagation of signals in cellular systems. Incorporating the Ontology Fingerprint as prior biological knowledge allows us to efficiently infer concise signaling network structure and to accurately predict cellular responses.http://deepblue.lib.umich.edu/bitstream/2027.42/109490/1/12918_2012_Article_989.pd

Metal-slotted polymer optical waveguide device

Metal-slotted optical waveguides (MSOWs) using an electro-optic polymer material have been experimentally demonstrated. The device consists of a three-layered slab waveguide in that the thin metal (gold) film strips are embedded on top of the lower cladding. The optical mode shapes and effective index of the propagation modes of the proposed waveguide structure were calculated using a simplified effective index method and a simulation tool. The fabrication and the device characteristics of a variable optical attenuator and an optical phase modulator based on MSOWs are discussed.open5

Spatially-resolved electronic and vibronic properties of single diamondoid molecules

Diamondoids are a unique form of carbon nanostructure best described as hydrogen-terminated diamond molecules. Their diamond-cage structures and tetrahedral sp3 hybrid bonding create new possibilities for tuning electronic band gaps, optical properties, thermal transport, and mechanical strength at the nanoscale. The recently-discovered higher diamondoids (each containing more than three diamond cells) have thus generated much excitement in regards to their potential versatility as nanoscale devices. Despite this excitement, however, very little is known about the properties of isolated diamondoids on metal surfaces, a very relevant system for molecular electronics. Here we report the first molecular scale study of individual tetramantane diamondoids on Au(111) using scanning tunneling microscopy and spectroscopy. We find that both the diamondoid electronic structure and electron-vibrational coupling exhibit unique spatial distributions characterized by pronounced line nodes across the molecular surfaces. Ab-initio pseudopotential density functional calculations reveal that the observed dominant electronic and vibronic properties of diamondoids are determined by surface hydrogen terminations, a feature having important implications for designing diamondoid-based molecular devices.Comment: 16 pages, 4 figures. to appear in Nature Material

The Synthesis of Certain Phomentrioloxin A Analogues and Their Evaluation as Herbicidal Agents

A series of 28 analogues of the phytotoxic geranylcyclohexentriol (−)-phomentrioloxin A (1) has been synthesized through cross-couplings of various enantiomerically pure haloconduritols or certain deoxygenated derivatives with either terminal alkynes or borylated alkenes. Some of these analogues display modest herbicidal activities, and physiological profiling studies suggest that analogue 4 inhibits photosystem II in isolated thylakoids in vitro

Extensive Genetic Diversity and Substructuring Among Zebrafish Strains Revealed through Copy Number Variant Analysis

Copy number variants (CNVs) represent a substantial source of genomic variation in vertebrates and have been associated with numerous human diseases. Despite this, the extent of CNVs in the zebrafish, an important model for human disease, remains unknown. Using 80 zebrafish genomes, representing three commonly used laboratory strains and one native population, we constructed a genome-wide, high-resolution CNV map for the zebrafish comprising 6,080 CNV elements and encompassing 14.6% of the zebrafish reference genome. This amount of copy number variation is four times that previously observed in other vertebrates, including humans. Moreover, 69% of the CNV elements exhibited strain specificity, with the highest number observed for Tubingen. This variation likely arose, in part, from Tubingen's large founding size and composite population origin. Additional population genetic studies also provided important insight into the origins and substructure of these commonly used laboratory strains. This extensive variation among and within zebrafish strains may have functional effects that impact phenotype and, if not properly addressed, such extensive levels of germ-line variation and population substructure in this commonly used model organism can potentially confound studies intended for translation to human diseases.Stem Cell and Regenerative Biolog

Species responses to changing precipitation depend on trait plasticity rather than trait means and intraspecific variation

Trait-based approaches are key to develop mechanistic understanding of differences in plant species performance under environmental change. While mean trait values have been widely used to link functional traits to species performance, the contribution of intraspecific trait variation and trait plasticity remains unclear. Moreover, environmentally induced changes in species biomass are caused by changes in the number of individuals and individual growth rate, both of which should be influenced by trait differences and plasticity. Our goal in this study is to use trait-based information to explain species performance via changes in species abundance and individual weight. We measured the mean, intraspecific variation and plasticity of nine above-ground plant traits, and a further three mean root traits from 10 common species in a precipitation manipulation experiment in semi-arid grassland. We used this trait information to explain differences in the responses of species biomass, abundance and mean individual weight to changing precipitation. Species responses were calculated as the normalised slopes of the regressions between species biomass, abundance and individual weight with the manipulated precipitation amount. We found strong differences in species responses to changing precipitation for species biomass, abundance and mean individual weight. Reduced precipitation decreased biomass, abundance and mean individual weight for some species, but increased them for others. Biomass and mean individual weight of species with resource-acquisitive traits, such as shallow rooted species, showed stronger positive responses to changing precipitation compared to resource-conservative traits, like those with deep roots. For above-ground traits, trait plasticity was the strongest predictor of species responses compared to mean traits and intraspecific trait variation. In addition, trait plasticity regulated changes in species biomass more via changes in species abundance than mean individual weight. These results indicate that trait plasticity is a key driver for determining species-specific responses to changing precipitation and needs more consideration for understanding and predicting ecosystem structure and functioning in future climate scenarios. A free Plain Language Summary can be found within the Supporting Information of this article