Oligomeric State in the Crystal Structure of Modular FAD Synthetase Provides Insights into Its Sequential Catalysis in Prokaryotes

The crystal structure of the modular flavin adenine dinucleotide (FAD) synthetase from Corynebacterium ammoniagenes has been solved at 1.95 Å resolution. The structure of C. ammoniagenes FAD synthetase presents two catalytic modules—a C-terminus with ATP-riboflavin kinase activity and an N-terminus with ATP-flavin mononucleotide (FMN) adenylyltransferase activity—that are responsible for the synthesis of FAD from riboflavin in two sequential steps. In the monomeric structure, the active sites from both modules are placed 40 Å away, preventing the direct transfer of the product from the first reaction (FMN) to the second catalytic site, where it acts as substrate. Crystallographic and biophysical studies revealed a hexameric assembly formed by the interaction of two trimers. Each trimer presents a head-tail configuration, with FMN adenylyltransferase and riboflavin kinase modules from different protomers approaching the active sites and allowing the direct transfer of FMN. Experimental results provide molecular-level evidences of the mechanism of the synthesis of FMN and FAD in prokaryotes in which the oligomeric state could be involved in the regulation of the catalytic efficiency of the modular enzyme.     

An efficient approach to the travelling salesman problem using self-organizing maps

This paper presents an approach to the well-known Travelling Salesman Problem (TSP) using Self-Organizing Maps (SOM). The SOM algorithm has interesting topological information about its neurons configuration on cartesian space, which can be used to solve optimization problems. Aspects of initialization, parameters adaptation, and complexity analysis of the proposed SOM based algorithm are discussed. The results show an average deviation of 3.7% from the optimal tour length for a set of 12 TSP instances.     

Evolving specificity from variability for protein interaction domains

An important question in modular domain-peptide interactions, which play crucial roles in many biological processes, is how the diverse specificities exhibited by different members of a domain family are encoded in a common scaffold. Analysis of the Src homology (SH) 2 family has revealed that its specificity is determined, in large part, by the configuration of surface loops that regulate ligand access to binding pockets. In a distinct manner, SH3 domains employ loops for ligand recognition. The PDZ domain, in contrast, achieves specificity by co-evolution of binding-site residues. Thus, the conformational and sequence variability afforded by surface loops and binding sites provides a general mechanism by which to encode the wide spectrum of specificities observed for modular protein interaction domains.     

Cellular fate of a modular DNA delivery system mediated by silica nanoparticles

Development of efficient molecular medicines, including gene therapeutics, RNA therapeutics, and DNA vaccines, depends on efficient means of transfer of DNA or RNA into the cell. Potential problems, including toxicity and immunogenicity, surrounding viral methods of DNA delivery have necessitated the use of nonviral, synthetic carriers. To better design synthetic carriers, or transfection reagents, the modular design of viruses has inspired a modular approach to DNA and RNA delivery. Each modular component can be designed to circumvent each of the many barriers. The modular approach will allow modification of individual components for a specific application. By utilizing a dense silica nanoparticle to form a ternary complex, transfection efficiency of a DNA-transfection reagent complex was increased by a factor of approximately 10 by concentrating the DNA at the surface of cells. Surface modification of the silica nanoparticles allowed determination of the cellular uptake mechanism with only minor alteration of transfection efficiency. Nanoparticles are internalized by an endosome-lysosomal route followed by perinuclear accumulation. The modification mechanism confirms that surface modification of the modular system can allow specific moieties to be incorporated into the modular system without significant alteration of the transfection efficiency. By showing that the modular system based upon concentration of DNA at the level of the cell can be used to increase transfection efficiency, we have shown that further modification of the system may better target DNA delivery and overcome other barriers of DNA expression.     

A microcalorimetric vessel for monitoring cytotoxic reactions in the micro-submicrowatt region

A microcalorimetric vessel for monitoring the initial phases of cytotoxic reactions in the micro-submicrowatt region has been designed and tested. The vessel is intended to be used with a multichannel microcalorimetric system from Thermometric, J?rf?lla, Sweden and can be built up stepwise in a modular way. The different functions of perfusion, stirring and addition of small amounts of soluble immune reactants can be used separately but also in combination. This is accomplished by the use of a vertical stirring mechanism and a reaction vessel of low volume, 200 microliters. The simplicity of the vessel permits an identical vessel to be used on the reference side, handled in parallel with the measuring vessel. No gas phase is present.     

Switching effect of predation on competitive prey species

The fact that the predation pressure has a stabilizing effect on the community of competitive species is demonstrated by a mathematical model of two-preys and one-predator system which has the switching property of predation. By analyzing a dynamical system for these three species populations, it is shown that, in a wide range of parameter space, the system has stable coexisting equilibrium states and the manifold of stable stationary points exhibits a cusp catastrophe and there exist two stable stationary points in the cusp region in the parameter space. Thus, it has been shown that Cause's competitive exclusion is actually relaxed by the switching mechanism of predation.     

The expression and characterization of rat IgE produced by construction of the epsilon-heavy chain gene from exon modules.

A system of exon "modules" was produced from the functionally rearranged epsilon-heavy gene isolated from the rat IgE-secreting immunocytoma IR162. The five individual exons, encoding the variable and constant region domains, were isolated and subcloned into the multiple cloning site of a pair of plasmid vectors with opposed orientation multiple cloning sites. The use of opposed orientation multiple cloning sites and the flanking restriction enzyme sites contained therein allows for the modular manipulation of the gene. These exon modules were initially used to reconstruct the epsilon-heavy chain gene into the native configuration to demonstrate the efficacy of the modular system for synthesis of IgE. Upon transfection into the rat myeloma cell line Y3, the reconstructed gene produced a polypeptide that associated with the endogenous light chain polypeptide and was secreted from the cell as tetrameric IgE. All physical and functional characterizations indicate that the IgE molecule produced is indistinguishable from native IR162 IgE. This modular system of exons will facilitate the manipulation of IgE structure through the systematic assembly of different epsilon-heavy chain mutant constructions. The resulting novel IgE proteins will be very useful to study the molecular nature of the interaction of IgE with its Fc receptor.     

Isomap transform for segmenting human body shapes

Segmentation of the 3D human body is a very challenging problem in applications exploiting volume capture data. Direct clustering in the Euclidean space is usually complex or even unsolvable. This paper presents an original method based on the Isomap (isometric feature mapping) transform of the volume data-set. The 3D articulated posture is mapped by Isomap in the pose of Da Vinci's Vitruvian man. The limbs are unrolled from each other and separated from the trunk and pelvis, and the topology of the human body shape is recovered. In such a configuration, Hoshen-Kopelman clustering applied to concentric spherical shells is used to automatically group points into the labelled principal curves. Shepard interpolation is utilised to back-map points of the principal curves into the original volume space. The experimental results performed on many different postures have proved the validity of the proposed method. Reliability of less than 2?cm and 3° in the location of the joint centres and direction axes of rotations has been obtained, respectively, which qualifies this procedure as a potential tool for markerless motion analysis.     

A general method for determining the functional role of a muscle

This paper presents a general classification method for determining the functional role of any muscle, and a procedure for determining the sensitivity of that role to small changes in system parameters. The classification method is based on the premise that the system model, when acted upon solely by the muscle of interest, will depart from any initial rest configuration in such a way as to decrease the muscle's length. This method is particularly useful for multiple-joint muscles, and is illustrated by examining a slider-crank mechanism and straight line muscle model to determine the functional role of the hamstrings during a constrained leg flexion motion.     

Process Variety Modeling for Process Configuration in Mass Customization: An Approach Based on Object-Oriented Petri Nets with Changeable Structures

Mass customization strategies could be usefully deployed by companies whose products are characterized by a modular design. Typically, each module serves a specific aspect of the overall product function at varying performance levels. Each product variant (constructed through a unique combination of modular performance levels), therefore, serves to customize the overall performance of the product, thus serving the unique needs of each customer. The high demand for each module guarantees economies of scale and, eventually, low cost to customer. The rationale of configuring production processes for producing individual product variants originates from the fact that massive process data is commonly available in a firm and there exists a generic process structure underlying the production of similar products in a family. To design a decision support mechanism that constructs process configuration corresponding to a given product configuration, this paper develops a formal modeling of process variety using Petri nets. Object-oriented Petri nets (PNs) with changeable structures (OPNs-CS) are applied to deal with the issues of generic representation, constraints compliance, and operational sequence requirements. Object-oriented PN (OPN) models facilitate generic representation of product and process variety as well as their instantiations. The OPNs-CS model is tested with simulation. Based on simulation results, the optimal configuration of production processes can be determined for each individual product as well as the cohort of a product family. To illustrate the feasibility and potential of OPNs-CS based process variety modeling, a case study of process configuration for mass customized textile spindles is reported.     

The anion-exchange substrate shuttle process: A new approach to two-stage biomethanation of organic and toxic wastes

A novel biomethanation process configuration is described which uses improved biocatalysts to enhance the productivity and stability of waste biomethanation systems. The design facilitates the maintenance of acetogenic and methanogenic bacteria under optimum substrate concentrations far above their K(s) values in a two-stage biomethanation system with closed loop reactors. Volatile fatty acid anions (VFA anions) are provided as substrates for the methanogenic stage by using an anion exchange unit coupled to the acidogenic stage. The slow growing and sensitive acetogenic and methanogenic bacteria are protected from oxygen, cationic pollutants, toxins, and microbial contamination by use of the substrate shuttle process. Due to the closed loop process configuration, washout of the ecoengineered biocatalysts is excluded. The modular system configuration allows industrial mass production of the system components. The new biomethanation process enhances both the BTU content of the gas and the methane production over state-of-the-art anaerobic digestor bioreactor concepts.     

Isomap transform for segmenting human body shapes

Segmentation of the 3D human body is a very challenging problem in applications exploiting volume capture data. Direct clustering in the Euclidean space is usually complex or even unsolvable. This paper presents an original method based on the Isomap (isometric feature mapping) transform of the volume data-set. The 3D articulated posture is mapped by Isomap in the pose of Da Vinci's Vitruvian man. The limbs are unrolled from each other and separated from the trunk and pelvis, and the topology of the human body shape is recovered. In such a configuration, Hoshen–Kopelman clustering applied to concentric spherical shells is used to automatically group points into the labelled principal curves. Shepard interpolation is utilised to back-map points of the principal curves into the original volume space. The experimental results performed on many different postures have proved the validity of the proposed method. Reliability of less than 2 cm and 3° in the location of the joint centres and direction axes of rotations has been obtained, respectively, which qualifies this procedure as a potential tool for markerless motion analysis.     

Pressure wave propagation in fluid-filled co-axial elastic tubes. Part 2: Mechanisms for the pathogenesis of syringomyelia

Our aim in this paper is to use a simple theoretical model of the intraspinal cerebrospinal-fluid system to investigate mechanisms proposed for the pathogenesis of syringomyelia. The model is based on an inviscid theory for the propagation of pressure waves in co-axial, fluid-filled, elastic tubes. According to this model, the leading edge of a pressure pulse tends to steepen and form an elastic jump, as it propagates up the intraspinal cerebrospinal-fluid system. We show that when an elastic jump is incident on a stenosis of the spinal subarachnoid space, it reflects to form a transient, localized region of high pressure within the spinal cord that for a cough-induced pulse is estimated to be 50 to 70 mm Hg or more above the normal level in the spinal subarachnoid space. We propose this as a new mechanism whereby pressure pulses created by coughing or sneezing can generate syrinxes. We also use the same analysis to investigate Williams' suck mechanism. Our results do not support his concept, nor, in cases where the stenosis is severe, the differential-pressure-propagation mechanism recently proposed by Greitz et al. Our analysis does provide some support for the piston mechanism recently proposed by Oldfield et al. and Heiss et al. For instance, it shows clearly how the spinal cord is compressed by the formation of elastic jumps over part of the cardiac cycle. What appears to be absent for this piston mechanism is any means whereby the elastic jumps can be focused (e.g., by reflecting from a stenosis) to form a transient, localized region of high pressure within the spinal cord. Thus it would seem to offer a mechanism for syrinx progression, but not for its formation.     

Experimental verification of facet load transmission by direct measurement of facet lamina contact pressure

This paper presents results of a new measuring technique by means of which facet tip contact pressure data were obtained. The aim of the paper is to demonstrate by direct measurement the existence of a load transmission mechanism through the facet joint. Six lumbar spine motion segments were used in 21 tests. Simulated extensor muscle action was provided to overcome moments due to eccentric loads which represented body weight and an external hand-held load acting 340 mm anterior to the center of the disc. Facet pressure was measured in all cases when muscle load was applied to counteract body weight. This pressure increased when more muscle force was applied to balance the externally applied flexion moment. When the anterior load was released suddenly, there was a large increase in facet pressure with a concomitant decrease in disc pressure.     

The purification and characterization of a beta-glucosidase from Alcaligenes faecalis

The beta-glucosidase from Alcaligenes faecalis has been purified to homogeneity (880-fold purification, 11% yield) using a combination of classical techniques and medium pressure ion-exchange chromatography. It is a dimeric enzyme of monomer molecular weight 50,000 and has no specific requirement for divalent metal ions. It has a high specificity for beta-glucosides and hydrolyses a wide variety of different chemical types wit retention of configuration at the anomeric centre. It has no exo-beta-1,4-glucanase activity. It is reversibly inhibited by a variety of sugars which have been shown previously to be very active against glucosidases, suggesting a normal mechanism of action. Measured Km values for cellobiose and p-nitrophenyl beta-D-glucopyranoside are quite low (0.70 and 0.08 mM, respectively), making this a good choice for cocloning into a cellulase system optimized for glucose production.     

Optimizing the application of entomopathogenic nematodes: experimental set-up

The complex issue concerning the spray application of Entomopathogenic Nematodes (EPNs) with a hydraulic sprayer is still not solved. This research project focuses on the effect of spray application technique on the viability and deposition of EPNs. In this paper the experimental set-up used for this evaluation is described. A modular spray application system has been developed and is currently used to evaluate the effect of different parts of a sprayer on the viability of the EPNs. Based on the results of experiments using this modular spray application system, recommendations regarding pump type, mixing system, nozzle type and filter size will be formulated. Because of the large number of experiments in this research project, an image analysis system for the determination of the viability of the nematodes is developed. This paper describes two experiments comparing the new developed image processing technique with the standard microscopic counting technique.     

A controllable artificial afterload for isolated heart studies

This paper presents an artificial afterload, based on the Westerhof model, for use in isolated heart preparations. The system has adjustable elements representing peripheral resistance and total arterial compliance, together with a fixed element representing aortic impedance. It is controlled by a computer in a manner which incorporates feed forward and feedback techniques. The system maintains constant ‘arteria’ pressure in the face of large excursions of the flow through it. It can be programmed to change this pressure in a dynamic fashion. The time taken to recover from large changes in flow and to reset the pressure is at most 3 s. Absolute values of peripheral resistance are easily obtained without any knowledge of the actual flow being required. Tests of the system demonstrate its stability and rapid transient characteristics.     

An alternative method to the osmotic stressing polymers: the osmomanometer

Although stressing polymers have been widely and successfully used to determine the osmotic properties of solutes in aqueous media, the osmotic stress method presents some limitations. To overcome these drawbacks, an alternative and more direct method, which has been named the osmomanometer, is described in this letter. The osmotic pressure accessible by this method ranges typically from 1 to 30 kPa using a simple hydrostatic effect and can be extended to higher pressures by using pressurized gas. This method needs neither a pressure sensor nor calibration.     

Experimental analysis of pulsatile flow through elastic collapsible tubes: application to cardiac assist device

This study presents a simulated analysis of Phased Compression Cardiac Assist Device (PCCAD) and evaluation of its applicability as a non-invasive temporary assist for a failing heart. The new technique is based on the chest pump mechanism for blood flow augmentation during external massage by phased compression of the abdominal and thoracic cavities. A semi-closed hydraulic system to simulate the systemic circulation was constructed; the system includes a left ventricle which functions according to the Starling principle and a pneumatic system which controls the pressures applied to the thoracic and abdominal cavities, in complete synchronization with the beating normal or failing heart. The possibility of manipulating the three pumps in series (venous, heart, and arterial) has been checked, and the principal parameters which effect the efficiency of the PCCAD were evaluated. This in vitro analysis shows the high potential of a non-invasive temporary cardiac assist device. It points to the necessary measures one has to take in order to achieve good synchronization and to interfere externally with the augmentation of cardiac output or with the augmentation of root aortic pressure.     

How MAP kinase modules function as robust,yet adaptable,circuits

Genetic and biochemical studies have revealed that the diversity of cell types and developmental patterns evident within the animal kingdom is generated by a handful of conserved, core modules. Core biological modules must be robust, able to maintain functionality despite perturbations, and yet sufficiently adaptable for random mutations to generate phenotypic variation during evolution. Understanding how robust, adaptable modules have influenced the evolution of eukaryotes will inform both evolutionary and synthetic biology. One such system is the MAP kinase module, which consists of a 3-tiered kinase circuit configuration that has been evolutionarily conserved from yeast to man. MAP kinase signal transduction pathways are used across eukaryotic phyla to drive biological functions that are crucial for life. Here we ask the fundamental question, why do MAPK modules follow a conserved 3-tiered topology rather than some other number? Using computational simulations, we identify a fundamental 2-tiered circuit topology that can be readily reconfigured by feedback loops and scaffolds to generate diverse signal outputs. When this 2-kinase circuit is connected to proximal input kinases, a 3-tiered modular configuration is created that is both robust and adaptable, providing a biological circuit that can regulate multiple phenotypes and maintain functionality in an uncertain world. We propose that the 3-tiered signal transduction module has been conserved through positive selection, because it facilitated the generation of phenotypic variation during eukaryotic evolution.