Rational modification of ligand-binding preference of avidin by circular permutation and mutagenesis

Chicken avidin is a key component used in a wide variety of biotechnological applications. Here we present a circularly permuted avidin (cpAvd4-->3) that lacks the loop between beta-strands 3 and 4. Importantly, the deletion of the loop has a positive effect on the binding of 4'-hydroxyazobenzene-2-carboxylic acid (HABA) to avidin. To increase the HABA affinity of cpAvd4-->3 even further, we mutated asparagine 118 on the bottom of the ligand-binding pocket to methionine, which simultaneously caused a significant drop in biotin-binding affinity. The X-ray structure of cpAvd4--> 3(N118M) allows an understanding of the effect of mutation to biotin-binding, whereas isothermal titration calorimetry revealed that the relative binding affinity of biotin and HABA had changed by over one billion-fold between wild-type avidin and cpAvd4-->3(N118M). To demonstrate the versatility of the cpAvd4-->3 construct, we have shown that it is possible to link cpAvd4-->3 and cpAvd5-->4 to form the dual-chain avidin called dcAvd2. These novel avidins might serve as a basis for the further development of self-organising nanoscale avidin building blocks.     

Detailed modeling of the kraft pulping chemistry: carbohydrate reactions

The article introduces a detailed model for carbohydrate chemistry in kraft pulping. This article is continuation to the modeling work carried out for hot water extraction and chemical pulp bleaching. The model includes galactoglucomannan, xylan, and cellulose acid–base equilibria, in addition to peeling, stopping, and alkaline hydrolysis reactions of the same carbohydrates, as well as hexenuronic acid formation and degradation reactions. The Arrhenius parameters were applied from the literature or regressed against experimental data in the present study. The model is very successful in predicting the experimental data of carbohydrate reactions during kraft pulping. Many features of the pulping-related model can be applied to specific fractionation chemistry considerations. The detailed knowledge on carbohydrates composition at any stage of pulping gives possibility for further development of biorefinery cases based on kraft pulping, such as biofuel and chemicals production.     

Application of an inclined-strip-yield crack tip plasticity model to predict constant amplitude fatigue crack growth

A mathematical model for fatigue crack growth under arbitrarily varying cyclic loads based on the inclined-strip-yield superdislocation representation of crack tip plasticity was initiated in previous work. The results showed promise, but also exhibited some deficiencies. Steps to improve the general model using a heuristic model (in which the superdislocation pairs representing the residual plasticity left behind by a crack growing under constant amplitude loading are lumped into one aggregate pair) are described in this paper. It is shown that this simple model matches the main features of experimental observations on fatigue crack growth. While pointing the way to developing a practical model to treat spectrum loading, the results also offer some potentially valuable insights into the analysis of plasticity-enhanced fatigue crack growth. Of most significance, the results suggest that the compressive stress acting at a crack tip due to residual plasticity may be inseparably linked with crack closure. The generality of the model is also demonstrated by applications to biaxial and crack line loading conditions.

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Résumé Dans un travail précédent, on a présenté un modèle mathématique décrivant la croissance d'une fissure de fatigue sous charges cycliques variant de façon arbitraire, en se basant sur une représentation de la plasticité à l'extrémité de la fissure en une superdislocation associée à des écoulements plastiques en bandes suivant une certaine inclinaison. Ces résultats semblaient prometteurs, encore que révélant certaines faiblesses. Le mémoire décrit les étapes parcourues pour améliorer le modèle général en recourant à un modèle heuristique. Dans ce dernier, les paires de superdislocations représentant la plasticité résiduelle qui demeure après croissance de la fissure sous amplitude de charge variable, sont réunies en une seule paire. On montre que ce modèle simplifié rend compte des caractéristiques principales de la croissance des fissures de fatigue, telles qu'elles ressortent des observations expérimentales. Les résultats indiquent la voie à suivre pour développer un modèle pratique décrivant le cas de la sollicitation suivant un spectre de charges. Ils ouvrent également des perspectives intéressantes dans l'analyse de la croissance d'une fissure de fatigue activée par l'entrée en plasticité. Mais, par dessus tout, ils suggèrent que la contrainte de compression due à la plasticité résiduelle et agissant à l'extrémité de la fissure peut être indissolublement liée à la fermeture de la fissure. Des applications à des conditions de mise en charge biaxiale, ou à une sollicitation concentrée sur la fissure elle même, démontrent les généralisations possibles du modèle étudié.

     

Towards gadget-free internet services: A roadmap of the Naked world

This paper presents a roadmap for the transition from current gadget-centric digital services towards a gadget-free services environment called the Naked world. The main idea of the Naked world is that all the services which are currently provided by gadgets will be provided by the infrastructure, thus no gadgets will be needed to use any kind of digital services. When a user in the Naked world intends to use a service, the infrastructure senses the user, the nearby intelligent surrounding launches an interactive user interface, performs identification through biometric identities, provides the service, and then closes the session when the user finishes the job. Therefore, the Naked world comprises highly intelligent and context-aware interactive environments. The vision of the Naked world is an evolution towards a user-friendly and ubiquitously available digital services, which is naturally bounded by the technological advancement. Henceforth, this paper presents the essential technologies and functional requirements along with the current and forthcoming novel technological concepts and challenges for the realization of the Naked world.     

Effect of Ultrafiltration on Anthocyanin and Flavonol Content of Black Currant Juice (Ribes nigrum L.)

This paper evaluates the efficiency of ultrafiltration and the effects of processing on the total anthocyanin and flavonol contents of black currant juice at chosen operational conditions. Ultrafiltration of black currant juices was carried out using Biomax 100?kDa polyethersulfone membrane. Ultrafiltration was used to process the juice prior concentration by reverse osmosis; with the aim to enhance the efficiency of the concentration process in terms of permeate flux. To avoid the fouling of the membrane, the juices were depectinized with Panzym Super E liquid enzyme preparation. The ultrafiltration was carried out at a transmembrane pressure of 2?bars and the operating temperature of 25?°C. The effect of processing on the valuable anthocyanin and flavonol content of the juices was evaluated based on the results of high-performance liquid chromatography analyses. The article includes detailed analyses of anthocyanin and flavonol compounds of the enzyme treated and ultrafiltered juice as compared with the original juice. The results indicate that, due to the enzymatic treatment, the valuable compound content of the juice increases. However, the ultrafiltration process resulted in a significant loss of a valuable content; 54% of total flavonol and 50% of total anthocyanins maintained in ultrafiltered juice when compared to the feed samples.     

HIBI Communication Network for System-on-Chip

This paper presents a communication network targeted for complex system-on-chip (SoC) and network-on-chip (NoC) designs. The Heterogeneous IP Block Interconnection (HIBI) aims at maximum efficiency and minimum energy per transmitted bit combined with quality-of-service (QoS) in transfers. Other features include support for hierarchical topologies with several clock domains, flexible scalability, and runtime reconfiguration of network parameters. HIBI is intended for integrating coarse-grain components such as intellectual property (IP) blocks that have size of thousands of gates.HIBI has been implemented in VHDL and SystemC and synthesized on several CMOS technologies and on FPGA. A 32-bit wrapper requires 5400 gates and runs with 315 MHz on 0.18 μ m technology which shows that only minimal area overhead is paid for the advanced features. The area and frequency results are well comparable to other NoC proposals.Furthermore, data transfers are shown to approach the maximum theoretical performance for protocol efficiency. HIBI network is accompanied with a design framework with tools for optimizing the system through automated design space exploration. Erno Salminen Tampere University of Technology (TUT), Finland.Currently he is working towards his PhD degree in the Institute of Digital and Computer Systems (DCS) at TUT. His main research interests are digital systems design and communication issues in SoCs. Tero KangasTampere University of Technology (TUT), Finland.Since 1999 he has been working as a research scientist in the Institute of Digital and Computer Systems (DCS) at TUT. Currently he is working towards his PhD degree and his main research topics are system architectures and SoC design methodologies in multimedia applications. Timo D. H?m?al?ainen Tampere University of Technology (TUT), Finland. He was nominated to full professor at TUT/Institute of Digital and Computer Systems in 2001. He heads the DACI research group that focuses on three main research areas: wireless sensor networks, high-performance multi-DSP and hardware based video encoding, and design flow tools for heterogeneous MP-SoC platforms. Jouni Riihi?mki Tampere University of Technology (TUT), Finland. Currently he is working as a senior design engineer at Nokia Technlogy Platforms. He is also working towards his PhD degree. His research interests include SoC design and verification methodologies. Vesa Lahtinen received his M.Sc. and Ph.D. from TUT in 1998 and 2004, respectively. In TUT, his main research areas were system-on-chips and their interconnects. Currently, Dr. Lahtinen is a Senior Research Engineer in the Computing Architectures Laboratory of Nokia Research Center (NRC) concentrating on architecture modeling and, specifically, memory architectures. Kimmo Kuusilinna Tampere University of Technology (TUT), Finland. His main research interests include system-level design and verification, on-chip interconnections, and parallel memories. Currently he is working as a senior research engineer at the Nokia Research Center.     

An interactive multi-objective approach to heat exchanger network synthesis

In this work we present a multi-objective approach to heat exchanger network synthesis. The approach solves a modified version of the Synheat model using an interactive multi-objective optimisation method, NIMBUS, which is implemented in GAMS. The results obtained demonstrate the potential of interactive multi-objective optimisation.     

Performance analysis of the RandomPOD wear test system

The type of relative motion between the bearing surfaces of prosthetic joints is known to strongly influence their wear behaviour. The previously validated 16-station wear simulator of the pin-on-disc type, called RandomPOD, was used to study the wear of a conventional, gamma-sterilized ultra-high molecular weight polyethylene (UHMWPE). The counterface was polished CoCr and the lubricant was diluted calf serum. Two test conditions were compared, random motion/random load and circular translation/static load. With random motion, the accumulated change of the direction of sliding was 2.8 times higher than that with circular translation. The test duration with both test conditions was 880 h. Random motion/random load resulted in a mean wear factor 23% higher than that produced with circular translation/static load. The difference was statistically significant. The wear mechanisms however were similar and in agreement with clinical observations. As earlier studies have shown that the type of load is of secondary importance, the present study confirms the earlier findings that the type of relative motion is tribologically of fundamental importance. In particular, the complex, yet biomechanically realistic non-cyclic motion, represented by the random track, resulted in a wear factor significantly higher than that produced by a fixed slide track shape.     

Chemical composition of ripe fruits of Rubus chamaemorus L. grown in different habitats

BACKGROUND: Cloudberry (Rubus chamaemorus L.) is one of the most valuable berry‐producing plants because of its nutritional properties. The chemical composition and crop yield of ripe fruits of cloudberry grown wild in 10 habitats in northern Finland was analysed over two consecutive summers. For comparison, two clones of cultivated cloudberries were studied as well. RESULTS: The concentrations of citric and malic acids, α‐tocopherol, anthocyanins and β‐carotene had notable variations between habitats. In particularly, cloudberries grown on open habitats had higher content of citric acid and less α‐tocopherol compared to those grown on shaded sites. In a colder and rainy summer the content of anthocyanins and the unsaturation level of fatty acids were significantly higher than in a warmer and drier summer. Crop yields were higher in the warmer summer, except in open sites where yields were quite equal. CONCLUSION: Cloudberries grown in open habitats showed notable differences in chemical composition when compared to those grown on shaded sites. Results suggest that the amount of sunlight and temperature levels could be the main factors affecting crop yield and chemical composition of cloudberry. In addition, the amount of rainfall may have an effect on anthocyanin concentrations. Copyright © 2011 Society of Chemical Industry     

Molecular characterization of spoilage bacteria as a means to observe the microbiological quality of carrot

This study characterized the bacteria causing decay of carrots during storage and marketing. Spoilage strains were identified by 16S-amplified rDNA restriction analysis and intergenic transcribed spacer-PCR-restriction fragment length polymorphism (ITS-PCR-RFLP). Genotypic fingerprinting by RFLP-pulsed-field gel electrophoresis was used to assess the genetic diversity of the isolates. A total of 252 Pseudomonas isolates from carrots were identified and classified into eight separate groups. Most strains belonged to group A (Pseudomonas fluorescens, Pseudomonas marginalis, and Pseudomonas veronii) and group B (Pseudomonas putida). The strains identified as Pectobacterium carotovorum subsp. carotovorum, Pectobacterium atrosepticum, Dickeya chrysanthemi, and Erwinia rhapontici were distinguished by ITS-PCR-RFLP. All isolates belonging to the genera Pectobacterium and Erwinia were responsible for carrot spoilage. This work has led to the development of new strategies for the identification and genotyping of vegetable-spoiling strains of Pseudomonas, Pectobacterium, and Erwinia. This is also the first report describing the occurrence of carrot-spoiling E. rhapontici. Early recognition of spoilage bacteria in vegetables is important for the implementation of effective handling strategies. Pectolytic bacteria may cause considerable financial losses because they account for a large proportion of bacterial rot of fruits and vegetables during storage, transit, and marketing.