Integrated fluid handling system for biomolecular interaction analysis.

An integrated fluid handling system used for multichannel biomolecular interaction analysis is described. Reactions between biological molecules are monitored in real time by measuring changes in the angular position where surface plasmon resonance occurs at a biospecific active surface. The adsorption efficiency of the analyte onto the biospecific active surface is up to approximately 3%, due to the low channel height, 50 microns, in the flow cell. When a large part of the total biospecific active surface for surface plasmon resonance probing (approximately 0.15 mm2) is used, the sensitivity is high. Sample sizes in the order of 1-50 microL can be injected. The sample zone dispersion is minimized by the low dead volume in the system (approximately 0.4 microL) accomplished by using integrated sample loops and thin conduits. An asset of this integration is the low reagent consumption. The sensor chip with the biospecific active surface is reusable and easily exchanged. Experimental results obtained with a theophylline monoclonal antibody as the analyte are compared with a theoretical model. The standard deviation for the repeatability is approximately 5% typically with 50 microL of 250 pM analyte, and the assay time is 10 min. The detection limit is approximately 10 pg of the analyte on the probed spot of the surface. Possible improvements of the sensitivity and detection limit are discussed.     

Interfering with the inhibitory mechanism of serpins: crystal structure of a complex formed between cleaved plasminogen activator inhibitor type 1 and a reactive-centre loop peptide

BACKGROUND: Plasminogen activator inhibitor type 1 (PAI-1) is an important endogenous regulator of the fibrinolytic system. Reduction of PAI-1 activity has been shown to enhance dissolution of blood clots. Like other serpins, PAI-1 binds covalently to a target serine protease, thereby irreversibly inactivating the enzyme. During this process the exposed reactive-centre loop of PAI-1 is believed to undergo a conformational change becoming inserted into beta sheet A of the serpin. Incubation with peptides from the reactive-centre loop transform serpins into a substrate for their target protease. It has been hypothesised that these peptides bind to beta sheet A, thereby hindering the conformational rearrangement leading to loop insertion and formation of the stable serpin-protease complex. RESULTS: We report here the 1.95 A X-ray crystal structure of a complex of a glycosylated mutant of PAI-1, PAI-1-ala335Glu, with two molecules of the inhibitory reactive-centre loop peptide N-Ac-TVASS-NH2. Both bound peptide molecules are located between beta strands 3A and 5A of the serpin. The binding kinetics of the peptide inhibitor to immobilised PAI-1-Ala335Glu, as monitored by surface plasmon resonance, is consistent with there being two different binding sites. CONCLUSIONS: This is the first reported crystal structure of a complex formed between a serpin and a serpin inhibitor. The localisation of the inhibitory peptide in the complex strongly supports the theory that molecules binding in the space between beta strands 3A and 5A of a serpin are able to prevent insertion of the reactive-centre loop into beta sheet A, thereby abolishing the ability of the serpin to irreversibly inactivate its target enzyme. The characterisation of the two binding sites for the peptide inhibitor provides a solid foundation for computer-aided design of novel, low molecular weight PAI-1 inhibitors.     

Service life planning and performance requirements

Service life planning comprises a model for the determination of a reasonable expected service life for buildings and components, and it establishes a routine for the assessment of design alternatives. A design option is considered reasonable when it meets or exceeds performance requirements over time that have been drawn up specifically for the specific project. Due to this assessment reference, there is a very evident link to the concept of performance-based building. Any stakeholder involved in the value chain or in the design process of the building, as well as regulators and building users, can express performance requirements. Identified requirements, both in relevance and in quality, will vary with the stakeholder and his/her perspective of interest. As building sector manufacturers develop most products with reference to standards rather than with reference to specific requirements, there is no direct link from user requirements to the product design. Instead, the building designer has the responsibility to ensure performance requirements are met by the performance of products integrated into the design. As these design decisions also have to be made at the material and component level, a performance-based building would benefit from an established rationale that enables the communication of performance requirements across the relevant system levels in the relevant design processes. A path for the connection of the established concepts of service life planning and performance-based building is presented. The aim is to identify key elements that need to be developed for the successful linkage of performance-based building with service life planning.     

Decision making with a fuzzy ontology

Knowledge mobilisation is a transition from the prevailing knowledge management technology that has been widely used in industry for the last 20?years to a new methodology and some innovative methods for knowledge representation, formation and development and for knowledge retrieval and distribution. Knowledge mobilisation aims at coming to terms with some of the problems of knowledge management and at the same time to introduce new theory, new methods and new technology. More precisely, this paper presents an outline of a fuzzy ontology as an enhanced version of classical ontology and demonstrates some advantages for practical decision making. We show that a number of soft computing techniques, e.g. aggregation functions and interval valued fuzzy numbers, will support effective and practical decision making on the basis of the fuzzy ontology. We demonstrate the knowledge mobilisation methods with the construction of a support system for finding the best available wine for a number of wine drinking occasions using a fuzzy wine ontology and fuzzy reasoning methods; the support system has been implemented for a Nokia N900 smart phone.     

A method for predicting the probability of business network profitability

In the design phase of business collaboration, it is desirable to be able to predict the profitability of the business-to-be. Therefore, techniques to assess qualities such as costs, revenues, risks, and profitability have been previously proposed. However, they do not allow the modeler to properly manage uncertainty with respect to the design of the considered business collaboration. In many real collaboration projects today, uncertainty regarding the business’ present or future characteristics is so significant that ignoring it becomes problematic. In this paper, we propose an approach based on the predictive, probabilistic architecture modeling framework (P²AMF), capable of advanced and probabilistically sound reasoning about profitability risks. The P²AMF-based approach for profitability risk prediction is also based on the e³-value modeling language and on the object constraint language. The paper introduces the prediction and modeling approach, and a supporting software tool. The use of the approach is illustrated by means of a case study originated from the Stockholm Royal Seaport smart city project.     

Pheromone specificity inEriocrania semipurpurella (Stephens) andE. sangii (Wood) (Lepidoptera: Eriocraniidae) based on chirality of semiochemicals

The fifth abdominal segment of femaleEriocrania semipurpurella (Stephens) andE. sangii (Wood) contains a pair of exocrine glands. Hexane extracts of this segment were prepared from both species and analyzed by gas chromatography with simultaneous flame ionization and electroantennographic detection (EAD). For both species, the EAD active peaks were identified as nonan-2-one, (Z)-6-nonen-2-one, and (Z)-6-nonen-2-ol by means of mass spectrometry and comparison of retention indices with those of synthetic standards. Enantiomeric separation of chiral alcohols from the female extracts was achieved by gas chromatographic analysis on a cyclodextrin column. InE. semipurpurella, a mixture of (2S,6Z)-nonen-2-ol and (2R,6Z)-nonen-2-ol (2: I) was found, whereas inE. sangii (2S,6Z)-nonen-2-ol was the predominant enantiomer and only traces of theR enantiomer were indicated by the antennal response. In field tests, a blend of the three compounds was not attractive to conspecific males. A subtractive assay showed that the alcohol in various enantiomeric mixtures was the only attractive compound, whereas addition of (Z)-6-nonen-2-one to the alcohol completely inhibited the attraction of both species. A trapping experiment including a wide range of ratios between theR andS enantiomers showed that baits containing 95–100% of theS enantiomer were attractive to maleE. sangii, whereas males ofE. semipurpurella were attracted to all tested ratios of the enantiomers. However, the response profiles of maleE. semipurpurella differed between populations from southern Sweden, south Finland, and the Kola Peninsula in Russia. In south Sweden males were maximally attracted to a racemic mixture of the alcohols. At the Kola PeninsulaE. semipurpurella was attracted to baits containing 95–100% of theR enantiomer. In south Finland all tested ratios between 0 and 100%R enantiomer trappedE. semipurpurella, but the trap catches appeared to be bimodally distributed with peaks around 15 and 70%R enantiomer. The trapping results suggest the existence of pheromone races or sibling species among the specimens identified asE. semipurpurella.Dedicated to Prof. H. J. Bestmann on the occasion of his 70th birthday.     

Conceptual aspects of geometric quantum computation

Geometric quantum computation is the idea that geometric phases can be used to implement quantum gates, i.e., the basic elements of the Boolean network that forms a quantum computer. Although originally thought to be limited to adiabatic evolution, controlled by slowly changing parameters, this form of quantum computation can as well be realized at high speed by using nonadiabatic schemes. Recent advances in quantum gate technology have allowed for experimental demonstrations of different types of geometric gates in adiabatic and nonadiabatic evolution. Here, we address some conceptual issues that arise in the realizations of geometric gates. We examine the appearance of dynamical phases in quantum evolution and point out that not all dynamical phases need to be compensated for in geometric quantum computation. We delineate the relation between Abelian and non-Abelian geometric gates and find an explicit physical example where the two types of gates coincide. We identify differences and similarities between adiabatic and nonadiabatic realizations of quantum computation based on non-Abelian geometric phases.