Algorithms for Fast Aggregated Convergecast in Sensor Networks

Fast and periodic collection of aggregated data is of considerable interest for mission-critical and continuous monitoring applications in sensor networks. In the many-to-one communication paradigm, referred to as convergecast, we focus on applications wherein data packets are aggregated at each hop en-route to the sink along a tree-based routing topology, and address the problem of minimizing the convergecast schedule length by utilizing multiple frequency channels. The primary hindrance in minimizing the schedule length is the presence of interfering links. We prove that it is NP-complete to determine whether all the interfering links in an arbitrary network can be removed using at most a constant number of frequencies. We give a sufficient condition on the number of frequencies for which all the interfering links can be removed, and propose a polynomial time algorithm that minimizes the schedule length in this case. We also prove that minimizing the schedule length for a given number of frequencies on an arbitrary network is NP-complete, and describe a greedy scheme that gives a constant factor approximation on unit disk graphs. When the routing tree is not given as an input to the problem, we prove that a constant factor approximation is still achievable for degree-bounded trees. Finally, we evaluate our algorithms through simulations and compare their performance under different network parameters

Amino acid sequence and side chain specific synthetic receptors targeting protein phosphorylation

Antibodies have become a critical component of many diagnostic assays and are used for therapeutic purposes. Nevertheless they often fail to meet the strict performance demands raised in industry and in the clinic (e.g. stability, reproducibility, selectivity, affinity). These issues are especially notable for assays targeting post translational modifications (PTM) of proteins (phosphorylation, glycosylation, sulfation etc.). Antibody-based technologies suffer from problems of a more general nature associated with the analytical use of biological receptors i.e.: i) limited stability requiring cold chain logistics, ii) high production costs, iii) batch to batch variability. The above emphasizes the need for alternative robust, reproducible and low cost “binders” and assays. The aim in this thesis is to design, develop and test molecularly imprinted polymers (MIPs) which were synthesized epitope and stoichiometric imprinting approaches targeting phosphorylation as a PTM. Protein phosphorylationis one of the most common PTM, which is based on covalent attachment of phosphate group to particular amino acids. Misregulation of phosphorylation process is found related with diseases such as cancer, diabetes, and neurodegeneration. MIPs are synthesized through copolymerization of functional monomers and crosslinkers in the presence of N- and C- terminal protected templates. The key recognition element employed in developed synthetic receptors was 1,3-diaryl urea functionalmonomer 1. This monomer is a potent hydrogen bond donor forming strong cyclichydrogen bonds with oxyanions. Amino acid sequence specific and side chain imprinted binders were prepared targeting phosphorylation on tyrosine (pTyr) and on histidine (pHis). pHis MIP-based approach is proposed as a solution to enrich pHis peptides in the presence of other phosphoesters such as phosphoserine (pSer) in complex mixture without pre-treatment like β-elimination. In pTyr, ZAP-70 (zeta associated 70 kDa protein), which is prognosticator for chronic lymphocytic leukemia (CLL), and pTyr-sequence specific motif Src-SH2 domain were chosen as targets to evaluate regio- or stoichiometric selectivity performance of imprinted polymers. The synthesized polymers are used as effective enrichment tools for target phosphorylated peptides from complex mixture prior to mass spectrometry. Overall, the results demonstrate unique proteomics enrichment tools that link with personalized medicine relying on diagnostic coupled cancer treatment strategies based on kinase inhibitors

Triboluminescent composite microspheres consisting of alginate and EuD(4)TEA crystals

Alginate is utilized to obtain luminescent composite microspheres containing europium tetrakis (dibenzoylmethide) triethylammonium (EuD4TEA) triboluminescent (TL) crystals. Na alginate is initially treated with Ca(II) and then Eu (III) so that physically-crosslinked alginate microspheres were obtained. EuD4TEA crystals are precipitated in situ on the surface of the spheres upon treatment with dibenzoylmethane (DBM) and triethylamine (TEA). The EuD4TEA/alginate composite spheres are swollen in aqueous system, the diameter of the microspheres increases from 180 up to 405 pm in 48 h. TL intensity of the spheres swollen in 1 h decreases 4 folds compared to dry spheres; however, it systematically increases as the swelling time is extended step-wise to 48 h. Swelling may develop structural homogenity in the microsphere that supresses the optical scattering and may lead to better transmittance of the TL signal. (C) 2017 Elsevier B.V. All rights reserved

Towards molecularly imprinted polymers that respond to and capture phosphorylated tyrosine epitopes using fluorescent bis-urea and bis-imidazolium receptors.

Early detection of cancer is essential for successful treatment and improvement in patient prognosis. Deregulation of post-translational modifications (PTMs) of proteins, especially phosphorylation, is present in many types of cancer. Therefore, the development of materials for the rapid sensing of low abundant phosphorylated peptides in biological samples can be of great therapeutic value. In this work, we have synthesised fluorescent molecularly imprinted polymers (fMIPs) for the detection of the phosphorylated tyrosine epitope of ZAP70, a cancer biomarker. The polymers were grafted as nanometer-thin shells from functionalised submicron-sized silica particles using a reversible addition-fragmentation chain-transfer (RAFT) polymerisation. Employing the combination of fluorescent urea and intrinsically cationic bis-imidazolium receptor cross-linkers, we have developed fluorescent sensory particles, showing an imprinting factor (IF) of 5.0. The imprinted polymer can successfully distinguish between phosphorylated and non-phosphorylated tripeptides, reaching lower micromolar sensitivity in organic solvents and specifically capture unprotected peptide complements in a neutral buffer. Additionally, we have shown the importance of assessing the influence of counterions present in the MIP system on the imprinting process and final material performance. The potential drawbacks of using epitopes with protective groups, which can co-imprint with targeted functionality, are also discussed

High salt compatible oxyanion receptors by dual ion imprinting

The design of hosts for either cations or anions is complicated due to the competition for binding by the host or guest counterions. Imprinting relying on self-assembly offers the possibility to stabilize the guest and its counterion in a favorable geometry. We here report on a comprehensive supramolecular approach to anion receptor design relying on concurrent recognition of both anion and cation. This was achieved by high order complex imprinting of the disodium salt of phenyl-phosphonic acid in combination with neutral urea and sodium ion selective 18-crown-6 monomers. The polymers displayed enhanced affinity for the template or inorganic phosphate or sulfate in competitive aqueous buffers, with affinity and selectivity increasing with increasing ionic strength. The presence of engineered sites for both ionic species dramatically increases the salt uptake in strongly competitive media such as brine

Mesoporous polymeric microspheres with high affinity for phosphorylated biomolecules

Bis-imidazolium functionalized mesoporous microspheres selectively extract phosphorylated peptides/lipids from biofluids.</p

Oxoanion Imprinting Combining Cationic and Urea Binding Groups : A Potent Glyphosate Adsorber

The use of polymerizable hosts in anion imprinting has led to powerful receptors with high oxyanion affinity and specificity in both aqueous and non-aqueous environments. As demonstrated in previous reports, a carefully tuned combination of orthogonally interacting binding groups, for example, positively charged and neutral hydrogen bonding monomers, allows receptors to be constructed for use in either organic or aqueous environments, in spite of the polymer being prepared in non-competitive solvent systems. We here report on a detailed experimental design of phenylphosphonic and benzoic acid-imprinted polymer libraries prepared using either urea-or thiourea-based host monomers in the presence or absence of cationic comonomers for charge-assisted anion recognition. A comparison of hydrophobic and hydrophilic crosslinking monomers allowed optimum conditions to be identified for oxyanion binding in non-aqueous, fully aqueous, or high-salt media. This showed that recognition improved with the water content for thiourea-based molecularly imprinted polymers (MIPs) based on hydrophobic EGDMA with an opposite behavior shown by the polymers prepared using the more hydrophilic crosslinker PETA. While the affinity of thiourea-based MIPs increased with the water content, the opposite was observed for the oxourea counterparts. Binding to the latter could however be enhanced by raising the pH or by the introduction of cationic amine-or Na+-complexing crown ether-based comonomers. Use of high-salt media as expected suppressed the amine-based charge assistance, whereas it enhanced the effect of the crown ether function. Use of the optimized receptors for removing the ubiquitous pesticide glyphosate from urine finally demonstrated their practical utility