Towards the Exact Minimization of BDDs—An Elitism-Based Distributed Evolutionary Algorithm

Binary Decision Diagrams (BDDs) are the state-of-the-art data structure for representation and manipulation of Boolean functions. In general, exact BDD minimization is NP-complete. For BDD-based technology, a small improvement in the number of nodes often simplifies the follow-up problem tremendously. This paper proposes an elitism-based evolutionary algorithm (EBEA) for BDD minimization. It can efficiently find the optimal orderings of variables for all LGSynth91 benchmark circuits with a known minimum size. Moreover, we develop a distributed model of EBEA, DEBEA, which obtains the best-ever variable orders for almost all benchmarks in the LGSynth91. Experimental results show that DEBEA is able to achieve super-linear performance compared to EBEA for some hard benchmarks.     

Reversible 5′-end biotinylation and affinity purification of synthetic RNA

A reversible biotinylation phosphoramidite was synthesized and incorporated onto the 5′-end of an oligoribonucleotide on a solid phase synthesizer. After cleavage and deprotection, the crude synthetic oligomer mixture was incubated with NeutrAvidin^® coated microspheres, and the failure sequences removed by washing with a buffer followed by treating the microspheres with tetrabutylammonium fluoride to give a high quality unmodified full-length oligoribonucleotide.     

Macroscopic non-equilibrium thermodynamics in dynamic calorimetry

What is really measured in dynamic calorimetric experiments is still an open question. This paper is devoted to this question, which can be usefully envisaged by means of macroscopic non-equilibrium thermodynamics. From the pioneer work of De Donder on chemical reactions and with other authors along the 20th century, the question is tackled under an historical point of view. A special attention is paid about the notions of frequency dependent complex heat capacity and entropy production due to irreversible processes occurring during an experiment. This phenomenological approach based on thermodynamics, not widely spread in the literature of calorimetry, could open significant perspectives on the study of macro-systems undergoing physico-chemical transformations probed by dynamic calorimetry.     

High resolution protein separations using affinity ultrafiltration with small charged ligands

Although the feasibility of affinity ultrafiltration was demonstrated more than 20 years ago, commercial applications have not developed due to the high cost and practical limitations of the large macroligands needed for highly selective separations. The objective of this study was to examine the use of small charged affinity ligands for protein purification by exploiting electrostatic interactions between the charged complex and an electrically-charged membrane. Experiments were performed using bovine serum albumin and ovalbumin with Cibacron Blue as the affinity ligand. Negatively charged versions of a composite regenerated cellulose membrane were generated by covalent attachment of a sulfonic acid functionality. Binding experiments were used to identify appropriate conditions for protein separations. The selectivity for the separation of BSA and ovalbumin was a function of the solution conditions, Cibacron Blue concentration, and membrane charge, with the addition of Cibacron Blue causing a 30-fold increase in selectivity. A diafiltration process was performed at the optimal conditions, giving a BSA product with a purification factor of more than 90-fold and a yield greater than 90%. These results clearly demonstrate the potential of using a small charged affinity ligand for high resolution protein separations.     

Affinity Chromatography of Insulin with a Heptapeptide Ligand Selected from Phage Display Library

A heptapeptide phage display library was screened with insulin to find its ligands for affinity chromatography. The peptide was synthesized and coupled to EAH Sepharose 4B (5.4 mol mL^–1 bed). Then, insulin chromatography was carried out with mobile phases of different pH values and by the addition of urea and ethylene glycol. It was found that electrostatic interactions were predominant for the affinity binding, and hydrogen bonding might also contribute somewhat to the affinity. Finally, frontal analysis was performed and the dynamic binding capacity of the affinity column for insulin at 50% breakthrough was estimated at 60.6 mg mL^–1 bed, which was about two times higher than the theoretical binding capacity of the monomeric insulin. The result suggests that insulin was bound in dimer state in a stoichiometric relationship with the coupled peptide, indicating the high binding efficiency of the peptide ligand for insulin.     

Self-assembled luminescent CdSe-ZnS quantum dot bioconjugates prepared using engineered poly-histidine terminated proteins

We report a simple and versatile approach for the conjugation of luminescent CdSe-ZnS core-shell quantum dots (QDs) to proteins through coordination of engineered C-terminal oligohistidine sequences. Several histidine tail containing proteins were self-assembled onto the QD surface using this method. A recombinant antibody specific for the high explosive 2,4,6-trinitrotoluene (TNT) was conjugated to QDs through a carboxy terminal histidine tail and the bioconjugate used to detect TNT by competitive immunoassay. TNT was detected over the range of 10 μg/ml down to 41 ng/ml using the scFv conjugated to QDs. These results open up the possibility to conjugate luminescent QDs to a whole range of proteins to form QD bioconjugates that can be effectively used in bio-oriented applications, such as sensing, imaging, immunoassay and other diagnostics.     

Siliceous materials with the surface polymer layer composed of dextran-polyimine mixture as column packings for liquid chromatography

Summary Forming a polymer layer on the surface of siliceous materials is one of the methods for protecting the silica skeleton from dissolution in alkaline mobile phases as well as eliminating the negative influence of silanol groups on separated molecules e.g. proteins. Polysaccharides, especially their derivatives bearing amine groups, can play the role of the surface layer. This paper discusses the possibilities of preparing such a layer by cross-linking a dextran-polyimine mixture (rather than the traditionally used DEAE-dextran) deposited on the surface of the solid material. The results presented prove the utility of synthesized materials as supports for affinity ligands in high performance affinity chromatography or as supports for complexed metal ions in ligand-exchange chromatography. The properties of the sorbents with a polymer layer can be changed both by the composition of the cross-linked mixture and by chemical modification.     

Label-Free Impedance Biosensors: Opportunities and Challenges

Impedance biosensors are a class of electrical biosensors that show promise for point-of-care and other applications due to low cost, ease of miniaturization, and label-free operation. Unlabeled DNA and protein targets can be detected by monitoring changes in surface impedance when a target molecule binds to an immobilized probe. The affinity capture step leads to challenges shared by all label-free affinity biosensors; these challenges are discussed along with others unique to impedance readout. Various possible mechanisms for impedance change upon target binding are discussed. We critically summarize accomplishments of past label-free impedance biosensors and identify areas for future research.     

Adsorption isotherms of a molecular imprinted polymer prepared in the presence of a polymerisable template: Indirect evidence of the formation of template clusters in the binding site

The current opinion about molecular imprinted polymers (MIPs) is that their molecular recognition properties are due to the presence of nanocavities formed during a polymerization process developed in the presence of a template molecule. According to this principle, the shape of these nanocavities is complementary to that of the template and non-covalent interactions are established between the binding site and a single template molecule. Nevertheless, there are some experimental indications that the real molecular recognition mechanism involves clusters of template molecules being packed into the binding site. Recently, it has been proposed that template molecules covalently linked to the binding site can act as nucleation points, enhancing the formation of these molecular clusters.We have tested this hypothesis by studying the adsorption isotherms of polymers prepared by imprinting them with 2,4,5-trichlorophenoxyacetic acid (2,4,5-T). Three different polymers were considered: P0, prepared without the template, P1, whose template was represented by 2,4,5-T molecules, and P2, whose template was 1/3 constituted by the polymerisable 2-(2,4,5-trichlorophenoxyacetoxy)-ethylmethacrylate (2,4,5-TEMA) and 2/3 by 2,4,5-T. The polymers were prepared by thermoinduced polymerization of template mixtures, 4-vinylpyridine and ethylene dimethacrylate. The crushed polymers were packed into HPLC columns and frontal chromatographic runs were performed by eluting the columns with a mobile phase containing variable amounts of 2,4,5-T.The experimental adsorption isotherms were fitted by using several isotherm models, and the Freundlich-Langmuir model was found to give the best fitting in terms of F-test. All the models considered showed a significant difference between the affinity constant values measured for the polymer P1 and P2, with a higher value for the polymer P2 (for Freundlich-Langmuir model: polymer P1, k=(2.00±0.43)×10⁴ M⁻¹; polymer P2, k=(1.93±0.0535)×10⁵ M⁻¹; ratio P2/P1, 9.65±2.09). Such experimental results support the hypothesis that a polymer prepared with a limited amount of template covalently attached to the binding site shows an increased affinity for the template itself.     

Immobilized betulinic acid column and its interactions with phospholipase A2 and snake venom proteins

Betulinic acid (BA) is a plant-derived pentacyclic triterpenoid. Although BA has been found to have diverse pharmacological effects, including anti-tumor and anti-inflammatory actions and potential as inhibitor of phospholipase A2 (PLA2), its cellular targets remain unclear. In this study, BA was immobilized onto an acrylamide matrix. The immobilized-BA column could retain the purified PLA2 of bovine pancreas or the PLA2 of snake venom from Naja nigricollis. The bound PLA2 were not eluted by high salt concentrations but were eluted by either acid or calcium free buffer. Besides the PLA2, a group of basic proteins of snake venom with molecular weights of about 7 kDa were also strongly bound by immobilized BA. One of these proteins was identified as gamma-cardiotoxin. The usefulness of immobilized BA for exploring the cellular targets of BA is discussed.