Selection of optimal oligonucleotide probes for microarrays using multiple criteria, global alignment and parameter estimation

The oligonucleotide specificity for microarray hybridization can be predicted by its sequence identity to non-targets, continuous stretch to non-targets, and/or binding free energy to non-targets. Most currently available programs only use one or two of these criteria, which may choose ‘false’ specific oligonucleotides or miss ‘true’ optimal probes in a considerable proportion. We have developed a software tool, called CommOligo using new algorithms and all three criteria for selection of optimal oligonucleotide probes. A series of filters, including sequence identity, free energy, continuous stretch, GC content, self-annealing, distance to the 3′-untranslated region (3′-UTR) and melting temperature (T(m)), are used to check each possible oligonucleotide. A sequence identity is calculated based on gapped global alignments. A traversal algorithm is used to generate alignments for free energy calculation. The optimal T(m) interval is determined based on probe candidates that have passed all other filters. Final probes are picked using a combination of user-configurable piece-wise linear functions and an iterative process. The thresholds for identity, stretch and free energy filters are automatically determined from experimental data by an accessory software tool, CommOligo_PE (CommOligo Parameter Estimator). The program was used to design probes for both whole-genome and highly homologous sequence data. CommOligo and CommOligo_PE are freely available to academic users upon request

PS-TRUST: Provably Secure Solution for Truthful Double Spectrum Auctions

Truthful spectrum auctions have been extensively studied in recent years. Truthfulness makes bidders bid their true valuations, simplifying greatly the analysis of auctions. However, revealing one's true valuation causes severe privacy disclosure to the auctioneer and other bidders. To make things worse, previous work on secure spectrum auctions does not provide adequate security. In this paper, based on TRUST, we propose PS-TRUST, a provably secure solution for truthful double spectrum auctions. Besides maintaining the properties of truthfulness and special spectrum reuse of TRUST, PS-TRUST achieves provable security against semi-honest adversaries in the sense of cryptography. Specifically, PS-TRUST reveals nothing about the bids to anyone in the auction, except the auction result. To the best of our knowledge, PS-TRUST is the first provably secure solution for spectrum auctions. Furthermore, experimental results show that the computation and communication overhead of PS-TRUST is modest, and its practical applications are feasible.Comment: 9 pages, 4 figures, submitted to Infocom 201

Dilute magnetic semiconductor and half metal behaviors in 3d transition-metal doped black and blue phosphorenes: a first-principles study

We present first-principles density-functional calculations for the structural, electronic, and magnetic properties of substitutional 3d transition metal (TM) impurities in two-dimensional black and blue phosphorenes. We find that the magnetic properties of such substitutional impurities can be understood in terms of a simple model based on the Hund's rule. The TM-doped black phosphorenes with Ti, V, Cr, Mn, Fe and Ni impurities show dilute magnetic semiconductor (DMS) properties while those with Sc and Co impurities show nonmagnetic properties. On the other hand, the TM-doped blue phosphorenes with V, Cr, Mn and Fe impurities show DMS properties, those with Ti and Ni impurities show half-metal properties, whereas Sc and Co doped systems show nonmagnetic properties. We identify two different regimes depending on the occupation of the hybridized electronic states of TM and phosphorous atoms: (i) bonding states are completely empty or filled for Sc- and Co-doped black and blue phosphorenes, leading to non-magnetic; (ii) non-bonding d states are partially occupied for Ti-, V-, Cr-, Mn-, Fe- and Ni-doped black and blue phosphorenes, giving rise to large and localized spin moments. These results provide a new route for the potential applications of dilute magnetic semiconductor and half-metal in spintronic devices by employing black and blue phosphorenes.Comment: 9 pages, 7 figure

Far-Field Plasmonic Resonance Enhanced Nano-Particle Image Velocimetry within a Micro Channel

In this paper, a novel far-field plasmonic resonance enhanced nanoparticle-seeded Particle Image Velocimetry (nPIV) has been demonstrated to measure the velocity profile in a micro channel. Chemically synthesized silver nanoparticles have been used to seed the flow in the micro channel. By using Discrete Dipole Approximation (DDA), plasmonic resonance enhanced light scattering has been calculated for spherical silver nanoparticles with diameters ranging from 15nm to 200nm. Optimum scattering wavelength is specified for the nanoparticles in two media: water and air. The diffraction-limited plasmonic resonance enhanced images of silver nanoparticles at different diameters have been recorded and analyzed. By using standard PIV techniques, the velocity profile within the micro channel has been determined from the images.Comment: submitted to Review of Scientific Instrument

Predicting taxonomic and functional structure of microbial communities in acid mine drainage.

Predicting the dynamics of community composition and functional attributes responding to environmental changes is an essential goal in community ecology but remains a major challenge, particularly in microbial ecology. Here, by targeting a model system with low species richness, we explore the spatial distribution of taxonomic and functional structure of 40 acid mine drainage (AMD) microbial communities across Southeast China profiled by 16S ribosomal RNA pyrosequencing and a comprehensive microarray (GeoChip). Similar environmentally dependent patterns of dominant microbial lineages and key functional genes were observed regardless of the large-scale geographical isolation. Functional and phylogenetic β-diversities were significantly correlated, whereas functional metabolic potentials were strongly influenced by environmental conditions and community taxonomic structure. Using advanced modeling approaches based on artificial neural networks, we successfully predicted the taxonomic and functional dynamics with significantly higher prediction accuracies of metabolic potentials (average Bray-Curtis similarity 87.8) as compared with relative microbial abundances (similarity 66.8), implying that natural AMD microbial assemblages may be better predicted at the functional genes level rather than at taxonomic level. Furthermore, relative metabolic potentials of genes involved in many key ecological functions (for example, nitrogen and phosphate utilization, metals resistance and stress response) were extrapolated to increase under more acidic and metal-rich conditions, indicating a critical strategy of stress adaptation in these extraordinary communities. Collectively, our findings indicate that natural selection rather than geographic distance has a more crucial role in shaping the taxonomic and functional patterns of AMD microbial community that readily predicted by modeling methods and suggest that the model-based approach is essential to better understand natural acidophilic microbial communities

Separation and Identification of HSP-Associated Protein Complexes from Pancreatic Cancer Cell Lines Using 2D CN/SDS-PAGE Coupled with Mass Spectrometry

Protein complexes are a cornerstone of many biological processes and together they form various types of molecular machinery. A broad understanding of these protein complexes is crucial for revealing and building models of protein function and regulation. Pancreatic cancer is a highly lethal disease which is difficult to diagnose at early stage and even more difficult to cure. In this study, we applied a gradient clear native gel system combined with subsequent second-dimensional SDS-PAGE to separate protein complexes from cell lysates of SW1990 and PANC-1 pancreatic cancer cell lines with different degrees of differentiation. Ten heat-shock-protein- (HSP-) associated protein complexes were separated and identified, and the differentially expressed proteins related to cancers were also found, such as HSP60, protein disulfide-isomerase A4 (ERp72), and transitional endoplasmic reticulum ATPase (TER ATPase)