Low-Cost Plasmonic Carbon Spacer for Surface Plasmon-Coupled Emission Enhancements and Ethanol Detection: a Smartphone Approach

Surface plasmon-coupled emission (SPCE) has led to significant advancements in analytical techniques on account of its unique characteristics that include highly polarized photon-sorting ability. In this study, we report the use of a low-cost activated carbon as a plasmonic spacer in the SPCE substrate for achieving 30-fold enhancement in fluorescence emission. We extend the use of this spacer in the presence of Rhodamine B Base, a lactone dye as the sensing material for smartphone-based ethanol detection on the SPCE platform. Ethanol detection from 1 to 6% concentration highlights the potential use of this technique in monitoring fermentation processes.     

Structure activity relationships of anthranilic acid-based compounds on cellular and in vivo mitogen activated protein kinase-5 signaling pathways

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A Screen for Candidate Targets of Lysine Polyphosphorylation Uncovers a Conserved Network Implicated in Ribosome Biogenesis

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Nitrate reductase activity and uptake of nitrate and oxygen as affected by nitrate supply to detached maize organs

Supply of 1, 2, 5, 10 or 20 mM nitrate to detached roots, scutella or shoots from 5- to 6-d-old Zea mays L. seedlings increased in vitro nitrate reductase (NR) activity in all the organs and NADPH specific NR (NADPH:NR) activity in roots and scutella but not in the shoots. Usually 2 to 5 mM nitrate supported maximum enzyme activity, the higher concentration did not increase it further. The protein content in the roots, scutella and shoots increased up to 5, 2 and 20 mM medium nitrate, respectively. Nitrate uptake also increased with increasing nitrate concentration in roots and shoots, but it increased only slightly in the scutella. In both roots and scutella, methionine sulfoximine had no effect, while cycloheximide and tungstate abolished nitrate induced NADH:NR activity completely and NADPH:NR partially. Methionine sulfoximine increased nitrate uptake by roots and scutella slightly, but other inhibitors had no effect. The depletion of dissolved oxygen from the medium was lower in the presence of nitrate than in its absence or in the presence of ammonium, especially in the scutella. This revised version was published online in July 2006 with corrections to the Cover Date.     

Molecular characterization and phylogenetic analysis of a novel glutenin gene (Dy10.1t) from Aegilops tauschii.

A novel y-type high molecular mass glutenin subunit (HMM-GS) possessing a mobility that is slightly slower than that of the subunit Dy10 obtained by SDS-PAGE, named Dy10.1t, in the wild wheat Aegilops tauschii was identified by 1- and 2-dimensional gel electrophoresis, capillary electrophoresis, and matrix-assisted laser desorption ionization time of flight mass spectrometry (MALDI-TOF-MS). The gene encoding the HMM subunit Dy10.1t was amplified with allele-specific PCR primers, and the amplified products were cloned and sequenced. The coding domain of the Dy10.1t subunit gene consisted of 1980 bp encoding a protein of 658 residues with an M rs of 68 611 Da, which was similar to the M rs determined by MALDI-TOF-MS. The deduced amino acid sequence indicated that Dy10.1t subunit displayed a greater similarity to the Dy12 subunit, differing by only 8 amino acid substitutions. Six coding region single-nucleotide polymorphisms were discovered in the Dy10.1t gene by multiple alignments (1 per 330 bp), 1 in the N-terminal domain and the others in the central repeats. Five of them resulted in residue substitutions, whereas 3 created enzyme site changes. The homology and neighbour-joining trees constructed from code domain sequences of 20 x- and y-type glutenin genes from different Triticum species separated into 2 halves, which corresponded to the x-type and y-type HMM glutenin alleles. Phylogenetic analysis revealed that the Glu-1 gene duplication event probably occurred at about 16.83 million years ago, whereas the divergence times of A, B, and D genomes within x-type and y-type halves were before 7.047 and 10.54 million years ago, respectively.     

Detecting conserved interaction patterns in biological networks.

Molecular interaction data plays an important role in understanding biological processes at a modular level by providing a framework for understanding cellular organization, functional hierarchy, and evolutionary conservation. As the quality and quantity of network and interaction data increases rapidly, the problem of effectively analyzing this data becomes significant. Graph theoretic formalisms, commonly used for these analysis tasks, often lead to computationally hard problems due to their relation to subgraph isomorphism. This paper presents an innovative new algorithm, MULE, for detecting frequently occurring patterns and modules in biological networks. Using an innovative graph simplification technique based on ortholog contraction, which is ideally suited to biological networks, our algorithm renders these problems computationally tractable and scalable to large numbers of networks. We show, experimentally, that our algorithm can extract frequently occurring patterns in metabolic pathways and protein interaction networks from the KEGG, DIP, and BIND databases within seconds. When compared to existing approaches, our graph simplification technique can be viewed either as a pruning heuristic, or a closely related, but computationally simpler task. When used as a pruning heuristic, we show that our technique reduces effective graph sizes significantly, accelerating existing techniques by several orders of magnitude! Indeed, for most of the test cases, existing techniques could not even be applied without our pruning step. When used as a stand-alone analysis technique, MULE is shown to convey significant biological insights at near-interactive rates. The software, sample input graphs, and detailed results for comprehensive analysis of nine eukaryotic PPI networks are available at www.cs.purdue.edu/homes/koyuturk/mule.