Mechanistic aspects of proton chain transfer: A computational study for the green fluorescent protein chromophore

We explore several models for the ground-state proton chain transfer pathway between the green fluorescent protein chromophore and its surrounding protein matrix, with a view to elucidating mechanistic aspects of this process. We have computed quantum chemically the minimum energy pathways (MEPs) in the ground electronic state for one-, two-, and three-proton models of the chain transfer. There are no stable intermediates for our models, indicating that the proton chain transfer is likely to be a single, concerted kinetic step. However, despite the concerted nature of the overall energy profile, a more detailed analysis of the MEPs reveals clear evidence of sequential movement of protons in the chain. The ground-state proton chain transfer does not appear to be driven by the movement of the phenolic proton off the chromophore onto the neutral water bridge. Rather, this proton is the last of the three protons in the chain to move. We find that the first proton movement is from the bridging Ser205 moiety to the accepting Glu222 group. This is followed by the second proton moving from the bridging water to the Ser205for our model this is where the barrier occurs. The phenolic proton on the chromophore is hence the last in the chain to move, transferring to a bridging “water” that already has substantial negative charge.

Searching for convergence in phylogenetic Markov chain Monte Carlo

Markov chain Monte Carlo (MCMC) is a methodology that is gaining widespread use in the phylogenetics community and is central to phylogenetic software packages such as MrBayes. An important issue for users of MCMC methods is how to select appropriate values for adjustable parameters such as the length of the Markov chain or chains, the sampling density, the proposal mechanism, and, if Metropolis-coupled MCMC is being used, the number of heated chains and their temperatures. Although some parameter settings have been examined in detail in the literature, others are frequently chosen with more regard to computational time or personal experience with other data sets. Such choices may lead to inadequate sampling of tree space or an inefficient use of computational resources. We performed a detailed study of convergence and mixing for 70 randomly selected, putatively orthologous protein sets with different sizes and taxonomic compositions. Replicated runs from multiple random starting points permit a more rigorous assessment of convergence, and we developed two novel statistics, delta and epsilon, for this purpose. Although likelihood values invariably stabilized quickly, adequate sampling of the posterior distribution of tree topologies took considerably longer. Our results suggest that multimodality is common for data sets with 30 or more taxa and that this results in slow convergence and mixing. However, we also found that the pragmatic approach of combining data from several short, replicated runs into a metachain to estimate bipartition posterior probabilities provided good approximations, and that such estimates were no worse in approximating a reference posterior distribution than those obtained using a single long run of the same length as the metachain. Precision appears to be best when heated Markov chains have low temperatures, whereas chains with high temperatures appear to sample trees with high posterior probabilities only rarely. [Bayesian phylogenetic inference; heating parameter; Markov chain Monte Carlo; replicated chains.]

The Function and Consequences of Alternative Fresh Produce Supply Chain Models

Around the world, consumers and retailers of fresh produce are becoming more and more discerning about factors such as food safety and traceability, health, convenience and the sustainability of production systems, and in doing so they are changing the way in which fresh produce supply chains are configured and managed. When consumers demand fresh, safe, convenient, value-for-money produce, retailers in an increasingly competitive environment are attracted to those business models most capable of meeting these demands profitably. Traditional models are proving less and less able to deliver competitive advantage in such an environment. As a result, opportunistic, adversarial, price-based approaches to doing business between chain members are being replaced by approaches that are more strategic, collaborative and value-based. The shaping force behind this change is the need for producers, wholesalers, category managers, retailers and consumers to have more certainty about the performance of the supply chains upon which they rely. Certainty is generated through the supply chain's ability to create, deliver and share value. How to build supply chains that create, deliver and share value is arguably the single biggest challenge to the competitiveness of fresh produce firms, and therefore to the industries to which they belong.

Long-range translational coupling in single-stranded RNA bacteriophages: an evolutionary analysis

In coliphage MS2 RNA a long-distance interaction (LDI) between an internal segment of the upstream coat gene and the start region of the replicase gene prevents initiation of replicase synthesis in the absence of coat gene translation. Elongating ribosomes break up the repressor LDI and thus activate the hidden initiation site. Expression studies on partial MS2 cDNA clones identified base pairing between 1427-1433 and 1738-1744, the so-called Min Jou (MJ) interaction, as the molecular basis for the long-range coupling mechanism. Here, we examine the biological significance of this interaction for the control of replicase gene translation. The LDI was disrupted by mutations in the 3'-side and the evolutionary adaptation was monitored upon phage passaging. Two categories of pseudorevertants emerged. The first type had restored the MJ interaction but not necessarily the native sequence. The pseudorevertants of the second type acquired a compensatory substitution some 80 nt downstream of the MJ interaction that stabilizes an adjacent LDI. In one examined case we confirmed that the second site mutations had restored coat-replicase translational coupling. Our results show the importance of translational control for fitness of the phage. They also reveal that the structure that buries the replicase start extends to structure elements bordering the MJ interaction.

Supply chain strategies for competitive manufacture

Few people would argue that there is one single solution to the design of a manufacturing supply chain. Relatively recent concepts such as strategic outsourcing and partnership sourcing are extremely valuable to some manufacturing organisations. This paper presents the findings of a comprehensive survey of manufacturing sourcing practices in the UK. This study has set out to understand current and intended practices that manufacturing companies have with their key suppliers, and also the decision processes and circumstances that have caused these relationships to occur.

A conceptual framework for supply chain collaboration:empirical evidence from the agri-food industry

Purpose - The purpose of this paper is to analyse the concept of supply chain collaboration and to provide an overall framework that can be used as a conceptual landmark for further empirical research. In addition, the concept is explored in the context of agri-food industry and particularities are identified. Finally, the paper submits empirical evidence from an exploratory case study in the agri-food industry, at the grower-processor interface, and information regarding the way the concept is actually applied in small medium-sized enterprises (SMEs) is presented. Design/methodology/approach - The paper employed case study research by conducting in-depth interviews in the two companies. Findings - Supply chain collaboration concept is of significant importance for the agri-food industry however, some constraints arise due to the nature of industry's products, and the specific structure of the sector. Subsequently, collaboration in the supply chain is often limited to operational issues and to logistics-related activities. Research limitations/implications - Research is limited to a single case study and further qualitative testing of the conceptual model is needed in order to adjust the model before large scale testing. Practical implications - Case study findings may be transferable to other similar dual relationships at the grower-processor interface. Weaker parts in asymmetric relationships have opportunities to improve their position, altering the dependence balance, by achieving product/process excellence. Originality/value - The paper provides evidence regarding the applicability of the supply chain collaboration concept in the agri-food industry. It takes into consideration not relationships between big multinational companies, but SMEs. © Emerald Group Publishing Limited.

Integrated logistics and supply chain management:the state of practice in Ireland

The Republic of Ireland and Northern Ireland were provided with aid to offset locational disadvantages in the run up to the Single European Market. Since then the Republic has emerged as the fastest growing member of the E.U. Success has not been underpinned by the transport system, suggesting that business has had to overcome locational disadvantages by strong performance elsewhere in the supply chain. The evidence indicates that there are Irish firms operating supply chain management techniques at a truly international standard. The problem is that there are so few in that category Meeting Ireland’s competitiveness challenge means closing the gap between the small group of large and foreign-owned firms, which display excellence in SCM, and the larger group of indigenous small and medium size businesses, which do not.

catena-[μ-tris(1,2-bis(tetrazol-1-yl)ethane-N4,N4')iron(II)] bis(tetrafluoroborate): Synthesis, structure, spectroscopic and magnetic characterisation of a chain-type coordination polymer spin-crossover compound.

In analogy to a common synthesis of 1-substituted 5-H tetrazoles (Tetrahedron Lett. 36 (1995)1759; Beloruss. Gos. Univ., Minsk, USSR. Khim. Geterotsikl. Soedin. 11 (1985) 1521; Beloruss. Gos. Univ., Minsk, USSR. Khim. Geterotsikl. Soedin. 1 (1991) 66; BGU, Belarus. Vestsi Akad. Navuk Belarusi, Ser. Khim. Navuk 1 (1992) 73), the new bidentate ligand 1,2-bis(tetrazol-1-yl)ethane [endi] was synthesized and characterized by X-ray diffraction, NMR, IR and UV–Vis spectroscopy. By using iron(II) tetrafluoroborate hexahydrate the complexation with this ligand yields a 1-dimensional linear coordination polymer similar to the recently published chain compound (Inorg. Chem. 39 (2000) 1891) exhibiting a thermally induced spin-crossover phenomenon. Similar to the 1,2-bis(tetrazol-1-yl)propane-bridged compound, our 1,2-bis(tetrazol-1-yl)ethane-bridged compound shows a gradual spin transition, but the spin-crossover temperature T1/2≈140 K is found to be 10 K above the other T1/2. The T1/2 was determined by temperature-dependent 57Fe-Mössbauer, far FT-IR and UV–Vis spectroscopy as well as by temperature-dependent magnetic susceptibility measurements. Single crystals of the complex were grown in situ from a solution of the ligand and iron(II) tetrafluoroborate. The X-ray structure determinations of both the high spin as well as the low spin state of the compound revealed a solid state structure, which is comparable to that of catena-[Fe(1,2-bis(tetrazole-1-yl)propane)3](ClO4)2 (Inorg. Chem. 39 (2000) 1891; 2nd TMR-TOSS Meeting, 4th Spin Crossover Family Meeting, Lufthansa Training Center, Seeheim/Germany, April 30–May 2, 1999). Both the 1,2-bis(tetrazol-1-yl)propane-bridged and our compound do not show a thermal hysteresis effect (J. Am. Chem. Soc. 115 (1993) 9810; Inorg. Chim. Acta 37 (1979) 169; Chem. Phys. Lett. 93 (1982) 567). The synthesis of the complex described in the experimental section yielded a fine powdered product being poorly soluble in most common solvents. The single crystal measurements were done with crystals obtained by various diffusion methods. Most of them yielded either thin needles or small hexagonal prism crystals depending on the specific conditions.

Crystal structure and physical properties of the new linear chain compound [Cu(1,2-bis(tetrazol-1-yl)ethane)3](ClO4)2

The synthesis and crystal structure of a novel one-dimensional Cu(II) compound [Cu(1,2-bis(tetrazol-1-yl)ethane)3](ClO4)2 are described. The single-crystal X-ray structure determination was carried out at 298 K. The molecular structure consists of a linear chain in which the Cu(II) ions are linked by three N4,N4' coordinating bis(tetrazole) ligands in syn conformation. The Cu(II) ions are in a Jahn-Teller distorted octahedral environment (Cu(1)-N(11)=2.034(2) Å, Cu(1)-N(21)=2.041(2) Å and Cu(1)-N(31)=2.391(2) Å). The Cu⋯Cu separations are 7.420(3) Å.

Using the max-sum algorithm for supply chain emergence in dynamic multiunit environments

Supply chain formation (SCF) is the process of determining the set of participants and exchange relationships within a network with the goal of setting up a supply chain that meets some predefined social objective. Many proposed solutions for the SCF problem rely on centralized computation, which presents a single point of failure and can also lead to problems with scalability. Decentralized techniques that aid supply chain emergence offer a more robust and scalable approach by allowing participants to deliberate between themselves about the structure of the optimal supply chain. Current decentralized supply chain emergence mechanisms are only able to deal with simplistic scenarios in which goods are produced and traded in single units only and without taking into account production capacities or input-output ratios other than 1:1. In this paper, we demonstrate the performance of a graphical inference technique, max-sum loopy belief propagation (LBP), in a complex multiunit unit supply chain emergence scenario which models additional constraints such as production capacities and input-to-output ratios. We also provide results demonstrating the performance of LBP in dynamic environments, where the properties and composition of participants are altered as the algorithm is running. Our results suggest that max-sum LBP produces consistently strong solutions on a variety of network structures in a multiunit problem scenario, and that performance tends not to be affected by on-the-fly changes to the properties or composition of participants.

Controlled synthesis of poly(neopentyl p-styrene sulfonate) via reversible addition-fragmentation chain transfer polymerisation

The controlled synthesis of poly(neopentyl p-styrene sulfonate) (PNSS) using RAFT polymerisation has been studied. Selected experimental conditions led to the production of PNSS with variable molecular weights and low dispersities (D{stroke}≤1.50). The controlled synthesis of poly(neopentyl p-styrene sulfonate) (PNSS) using reversible addition-fragmentation chain transfer polymerisation has been studied under a wide range of experimental conditions. PNSS can be used as an organic-soluble, thermally labile precursor for industrially valuable poly(p-styrene sulfonate), widely employed in technologies such as ionic exchange membranes and organic electronics. The suitability of two different chain transfer agents, three solvents, three different monomer concentrations and two different temperatures for the polymerisation of neopentyl p-styrene sulfonate is discussed in terms of the kinetics of the process and characteristics of the final polymer. Production of PNSS with systematically variable molecular weights and low dispersities (D{stroke} ≤1.50 in all cases) has been achieved using 2-azidoethyl 2-(dodecylthiocarbonothioylthio)-2-methylpropionate in anisole at 75°C, with an initial monomer concentration of 4.0molL-1. Finally, a poly(neopentyl p-styrene sulfonate)-b-polybutadiene-b-poly(neopentyl p-styrene sulfonate) (PNSS-b-PBD-b-PNSS) triblock copolymer has been synthesised via azide-alkyne click chemistry. Moreover, subsequent thermolysis of the PNSS moieties generated poly(p-styrene sulfonate) end blocks. This strategy allows the fabrication of amphiphilic copolymer films from single organic solvents without the need for post-deposition chemical treatment.

Single-Server Queueing System with Markov-Modulated Arrivals and Service Times

Key words: Markov-modulated queues, waiting time, heavy traffic.

Reach extension of high-capacity LR-PONs in chain configuration of distributed amplifier structure

We show 100-Gb/s single-channel transmission in LR-PONs with at least 512 way split and up to 160 km total distance is feasible by means of "chained" cable with amplifier solutions, and appropriate FIR filter designs. © 2015 OSA.

A Suite of Prey Traits Determine Predator and Nutrient Enrichment Effects in a Tri-Trophic Food Chain

Predation, predation risk, and resource quality affect suites of prey traits that collectively impact individual fitness, population dynamics, and community structure. However, studies of multi-trophic level effects generally focus on a single prey trait, failing to capture trade-offs among suites of covarying traits that govern population responses and emergent community patterns. We used structural equation models (SEM) to summarize the non-lethal and lethal effects of crayfish, Procambarus fallax, and phosphorus (P) addition, which affected prey food quality (periphyton), on the interactive effects of behavioral, morphological, developmental, and reproductive traits of snails, Planorbella duryi. Univariate and multivariate analyses suggested trade-offs between production (growth, reproduction) and defense (foraging behavior, shell shape) traits of snails in response to non-lethal crayfish and P addition, but few lethal effects. SEM revealed that non-lethal crayfish effects indirectly limited per capita offspring standing stock by increasing refuge use, slowing individual growth, and inducing snails to produce thicker, compressed shells. The negative effects of non-lethal crayfish on snails were strongest with P addition; snails increased allocation to shell defense rather than growth or reproduction. However, compared to ambient conditions, P addition with non-lethal crayfish still yielded greater per capita offspring standing stock by speeding individual snail growth enabling them to produce more offspring that also grew faster. Increased refuge use in response to non-lethal crayfish led to a non-lethal trophic cascade that altered the spatial distribution of periphyton. Independent of crayfish effects, snails stimulated periphyton growth through nutrient regeneration. These findings illustrate the importance of studying suites of traits that reveal costs associated with inducing different traits and how expressing those traits impacts population and community level processes.

The use of quantitative polymerase chain reaction amplification method to determine sex ratio of human spermatozoa in semen and to determine maternal contamination of amniotic fluid samples

We have modified a technique which uses a single pair of primer sets directed against homologous but distinct genes on the X and Y chromosomes, all of which are coamplified in the same reaction tube with trace amounts of radioactivity. The resulting bands are equal in length, yet distinguishable by restriction enzyme sites generating two independent bands, a 364 bp X-specific band and a 280 bp Y-specific band. A standard curve was generated to show the linear relationship between X/Y ratio average vs. %Y or %X chromosomal content. Of the 51 purified amniocyte DNA samples analyzed, 16 samples showed evidence of high % X contamination while 2 samples demonstrated higher % Y than the expected 50% X and 50% Y chromosomal content. With regards to the 25 processed sperm samples analyzed, X-sperm enrichment was evident when compared to the primary sex ratio whereas Y-sperm was enriched when we compared before and after selection samples.