NOMAD: a versatile strategy for in vitro DNA manipulation applied to promoter analysis and vector design.

Molecular analysis of complex modular structures, such as promoter regions or multi-domain proteins, often requires the creation of families of experimental DNA constructs having altered composition, order, or spacing of individual modules. Generally, creation of every individual construct of such a family uses a specific combination of restriction sites. However, convenient sites are not always available and the alternatives, such as chemical resynthesis of the experimental constructs or engineering of different restriction sites onto the ends of DNA fragments, are costly and time consuming. A general cloning strategy (nucleic acid ordered assembly with directionality, NOMAD; WWW resource locator http:@Lmb1.bios.uic.edu/NOMAD/NOMAD.htm l) is proposed that overcomes these limitations. Use of NOMAD ensures that the production of experimental constructs is no longer the rate-limiting step in applications that require combinatorial rearrangement of DNA fragments. NOMAD manipulates DNA fragments in the form of "modules" having a standardized cohesive end structure. Specially designed "assembly vectors" allow for sequential and directional insertion of any number of modules in an arbitrary predetermined order, using the ability of type IIS restriction enzymes to cut DNA outside of their recognition sequences. Studies of regulatory regions in DNA, such as promoters, replication origins, and RNA processing signals, construction of chimeric proteins, and creation of new cloning vehicles, are among the applications that will benefit from using NOMAD.

Role of the C2A domain of synaptotagmin in transmitter release as determined by specific antibody injection into the squid giant synapse preterminal.

Squid synaptotagmin (Syt) cDNA, including its open reading frame, was cloned and polyclonal antibodies were obtained in rabbits immunized with glutathione S-transferase (GST)-Syt-C2A. Binding assays indicated that the antibody, anti-Syt-C2A, recognized squid Syt and inhibited the Ca(2+)-dependent phospholipid binding to the C2A domain. This antibody, when injected into the preterminal at the squid giant synapse, blocked transmitter release in a manner similar to that previously reported for the presynaptic injection of members of the inositol high-polyphosphate series. The block was not accompanied by any change in the presynaptic action potential or the amplitude or voltage dependence of the presynaptic Ca2+ current. The postsynaptic potential was rather insensitive to repetitive presynaptic stimulation, indicating a direct effect of the antibody on the transmitter release system. Following block of transmitter release, confocal microscopical analysis of the preterminal junction injected with rhodamine-conjugated anti-Syt-C2A demonstrated fluorescent spots at the inner surface of the presynaptic plasmalemma next to the active zones. Structural analysis of the same preparations demonstrated an accumulation of synaptic vesicles corresponding in size and distribution to the fluorescent spots demonstrated confocally. Together with the finding that such antibody prevents Ca2+ binding to a specific receptor in the C2A domain, these results indicate that Ca2+ triggers transmitter release by activating the C2A domain of Syt. We conclude that the C2A domain is directly related to the fusion of synaptic vesicles that results in transmitter release.

Mathematical analysis of activation thresholds in enzyme-catalyzed positive feedbacks: application to the feedbacks of blood coagulation.

A hierarchy of enzyme-catalyzed positive feedback loops is examined by mathematical and numerical analysis. Four systems are described, from the simplest, in which an enzyme catalyzes its own formation from an inactive precursor, to the most complex, in which two sequential feedback loops act in a cascade. In the latter we also examine the function of a long-range feedback, in which the final enzyme produced in the second loop activates the initial step in the first loop. When the enzymes generated are subject to inhibition or inactivation, all four systems exhibit threshold properties akin to excitable systems like neuron firing. For those that are amenable to mathematical analysis, expressions are derived that relate the excitation threshold to the kinetics of enzyme generation and inhibition and the initial conditions. For the most complex system, it was expedient to employ numerical simulation to demonstrate threshold behavior, and in this case long-range feedback was seen to have two distinct effects. At sufficiently high catalytic rates, this feedback is capable of exciting an otherwise subthreshold system. At lower catalytic rates, where the long-range feedback does not significantly affect the threshold, it nonetheless has a major effect in potentiating the response above the threshold. In particular, oscillatory behavior observed in simulations of sequential feedback loops is abolished when a long-range feedback is present.

Development of a novel pyrolysis-gas chromatography/mass spectrometry method for the analysis of poly(lactic acid) thermal degradation products

Thermal degradation of PLA is a complex process since it comprises many simultaneous reactions. The use of analytical techniques, such as differential scanning calorimetry (DSC) and thermogravimetry (TGA), yields useful information but a more sensitive analytical technique would be necessary to identify and quantify the PLA degradation products. In this work the thermal degradation of PLA at high temperatures was studied by using a pyrolyzer coupled to a gas chromatograph with mass spectrometry detection (Py-GC/MS). Pyrolysis conditions (temperature and time) were optimized in order to obtain an adequate chromatographic separation of the compounds formed during heating. The best resolution of chromatographic peaks was obtained by pyrolyzing the material from room temperature to 600 °C during 0.5 s. These conditions allowed identifying and quantifying the major compounds produced during the PLA thermal degradation in inert atmosphere. The strategy followed to select these operation parameters was by using sequential pyrolysis based on the adaptation of mathematical models. By application of this strategy it was demonstrated that PLA is degraded at high temperatures by following a non-linear behaviour. The application of logistic and Boltzmann models leads to good fittings to the experimental results, despite the Boltzmann model provided the best approach to calculate the time at which 50% of PLA was degraded. In conclusion, the Boltzmann method can be applied as a tool for simulating the PLA thermal degradation.

Social Network Analysis and Qualitative Comparative Analysis: Their mutual benefit for the explanation of policy network structures

By switching the level of analysis and aggregating data from the micro-level of individual cases to the macro-level, quantitative data can be analysed within a more case-based approach. This paper presents such an approach in two steps: In a first step, it discusses the combination of Social Network Analysis (SNA) and Qualitative Comparative Analysis (QCA) in a sequential mixed-methods research design. In such a design, quantitative social network data on individual cases and their relations at the micro-level are used to describe the structure of the network that these cases constitute at the macro-level. Different network structures can then be compared by QCA. This strategy allows adding an element of potential causal explanation to SNA, while SNA-indicators allow for a systematic description of the cases to be compared by QCA. Because mixing methods can be a promising, but also a risky endeavour, the methodological part also discusses the possibility that underlying assumptions of both methods could clash. In a second step, the research design presented beforehand is applied to an empirical study of policy network structures in Swiss politics. Through a comparison of 11 policy networks, causal paths that lead to a conflictual or consensual policy network structure are identified and discussed. The analysis reveals that different theoretical factors matter and that multiple conjunctural causation is at work. Based on both the methodological discussion and the empirical application, it appears that a combination of SNA and QCA can represent a helpful methodological design for social science research and a possibility of using quantitative data with a more case-based approach.

A test mode approach to fault detection in sequential circuits,

"C00-1469-0117."

Immunohistological analysis of Tannerella forsythia-induced lesions in a murine model

Tannerella forsythia has been implicated as a defined periodontal pathogen. In the present study a mouse model was used to determine the phenotype of leukocytes in the lesions induced by subcutaneous injections of either live (group A) or nonviable (group B) T. forsythia. Control mice (group C) received the vehicle only. Lesions were excised at days 1, 2, 4, and 7. An avidin-biotin immunoperoxidase method was used to stain infiltrating CD4(+) and CD8(+) T cells, CD14(+) macrophages, CD19(+) B cells, and neutrophils. Hematoxylin and eosin sections demonstrated lesions with central necrotic cores surrounded by neutrophils, macrophages and lymphocytes in both group A and group B mice. Lesions from control mice exhibited no or only occasional solitary leukocytes. In both groups A and B, neutrophils were the dominant leukocyte in the lesion 1 day after injection, the numbers decreasing over the 7-day experimental period. There was a relatively low mean percent of CD4(+) and CD8(+) T cells in the lesions and, whereas the percent of CD8(+) T cells remained constant, there was a significant increase in the percent of CD4(+) T cells at day 7. This increase was more evident in group A mice. The mean percent of CD14(+) macrophages and CD19(+) B cells remained low over the experimental period, although there was a significantly higher mean percent of CD19(+) B cells at day 1. In conclusion, the results showed that immunization of mice with live T. forsythia induced a stronger immune response than nonviable organisms. The inflammatory response presented as a nonspecific immune response with evidence of an adaptive (T-cell) response by day 7. Unlike Porphyromonas gingivalis, there was no inhibition of neutrophil migration.

An optimal sequential procedure for a buying-selling problem with independent observations

We consider a buying-selling problem when two stops of a sequence of independent random variables are required. An optimal stopping rule and the value of a game are obtained.

Quantitative analysis and characterization of biofunctionalized fluorescent silica particles

A strategy for the production and subsequent characterization of biofunctionalized silica particles is presented. The particles were engineered to produce a bifunctional material capable of both (a) the attachment of fluorescent dyes for particle encoding and (b) the sequential modification of the surface of the particles to couple oligonucleotide probes. A combination of microscopic and analytical methods is implemented to demonstrate that modification of the particles with 3-aminopropyl trimethoxysilane results in an even distribution of amine groups across the particle surface. Evidence is provided to indicate that there are negligible interactions between the bound fluorescent dyes and the attached biomolecules. A unique approach was adopted to provide direct quantification of the oligonucleotide probe loading on the particle surface through X-ray photoelectron spectroscopy, a technique which may have a major impact for current researchers and users of bead-based technologies. A simple hybridization assay showing high sequence specificity is included to demonstrate the applicability of these particles to DNA screening.

Performance of a scramjet combustor with combined normal and tangential fuel injection

The performance of a scramjet combustor with combined normal and tangential injection was experimentally investigated. Experiments were performed on a 500-mm cylindrical scramjet combustor at a freestream Mach number of 4.5, a nozzle supply pressure of 35.8 MPa, and a nozzle supply enthalpy of 5.8 MJ/kg. Hydrogen fuel was injected normally through portholes to promote combustion and tangentially through a slot to reduce viscous drag. A series of fuel injectors were used to vary the proportion of tangential to normal fuel between 45 and 100%. Reductions in the viscous drag of up to 25% were observed with the greatest reductions occurring at the lowest total equivalence ratio tested for each injector. However, the average pressure produced by combustion with combined normal and tangential injection was approximately 50% less than that produced by normal injection alone. An analysis of the change in specific impulse of the scramjet combustor indicated that the best overall performance was produced by 100% normal injection.

Programs as paths: An approach to timing constraint analysis

A program can be decomposed into a set of possible execution paths. These can be described in terms of primitives such as assignments, assumptions and coercions, and composition operators such as sequential composition and nondeterministic choice as well as finitely or infinitely iterated sequential composition. Some of these paths cannot possibly be followed (they are dead or infeasible), and they may or may not terminate. Decomposing programs into paths provides a foundation for analyzing properties of programs. Our motivation is timing constraint analysis of real-time programs, but the same techniques can be applied in other areas such as program testing. In general the set of execution paths for a program is infinite. For timing analysis we would like to decompose a program into a finite set of subpaths that covers all possible execution paths, in the sense that we only have to analyze the subpaths in order to determine suitable timing constraints that cover all execution paths.

Sequential pyrolysis of willow SRC at low and high heating rates:implications for selective pyrolysis

The main aim of the work is to investigate sequential pyrolysis of willow SRC using two different heating rates (25 and 1500 °C/min) between 320 and 520 °C. Thermogravimetric analysis (TGA) and pyrolysis - gas chromatography - mass spectroscopy (Py-GC-MS) have been used for this analysis. In addition, laboratory scale processing has been undertaken to compare product distribution from fast and slow pyrolysis at 500 °C. Fast pyrolysis was carried out using a 1 kg/h continuous bubbling fluidized bed reactor, and slow pyrolysis using a 100 g batch reactor. Findings from this study show that heating rate and pyrolysis temperatures have a significant influence on the chemical content of decomposition products. From the analytical sequential pyrolysis, an inverse relationship was seen between the total yield of furfural (at high heating rates) and 2-furanmethanol (at low heating rates). The total yield of 1,2-dihydroxybenzene (catechol) was found to be significant higher at low heating rates. The intermediates of catechol, 2-methoxy-4-(2-propenyl)phenol (eugenol); 2-methoxyphenol (guaiacol); 4-Hydroxy-3,5-dimethoxybenzaldehyde (syringaldehyde) and 4-hydroxy-3-methoxybenzaldehyde (vanillin), were found to be highest at high heating rates. It was also found that laboratory scale processing alters the pyrolysis bio-oil chemical composition, and the proportions of pyrolysis product yields. The GC-MS/FID analysis of fast and slow pyrolysis bio-oils reveals significant differences. © 2011 Elsevier Ltd. All rights reserved.

Flow field analysis of some mixing and conveying screw element regions, within a closely intermeshing, co-rotating twin-screw extruder.

Grafting of antioxidants and other modifiers onto polymers by reactive extrusion, has been performed successfully by the Polymer Processing and Performance Group at Aston University. Traditionally the optimum conditions for the grafting process have been established within a Brabender internal mixer. Transfer of this batch process to a continuous processor, such as an extruder, has, typically, been empirical. To have more confidence in the success of direct transfer of the process requires knowledge of, and comparison between, residence times, mixing intensities, shear rates and flow regimes in the internal mixer and in the continuous processor.The continuous processor chosen for the current work in the closely intermeshing, co-rotating twin-screw extruder (CICo-TSE). CICo-TSEs contain screw elements that convey material with a self-wiping action and are widely used for polymer compounding and blending. Of the different mixing modules contained within the CICo-TSE, the trilobal elements, which impose intensive mixing, and the mixing discs, which impose extensive mixing, are of importance when establishing the intensity of mixing. In this thesis, the flow patterns within the various regions of the single-flighted conveying screw elements and within both the trilobal element and mixing disc zones of a Betol BTS40 CICo-TSE, have been modelled using the computational fluid dynamics package Polyflow. A major obstacle encountered when solving the flow problem within all of these sets of elements, arises from both the complex geometry and the time-dependent flow boundaries as the elements rotate about their fixed axes. Simulation of the time dependent boundaries was overcome by selecting a number of sequential 2D and 3D geometries, used to represent partial mixing cycles. The flow fields were simulated using the ideal rheological properties of polypropylene and characterised in terms of velocity vectors, shear stresses generated and a parameter known as the mixing efficiency. The majority of the large 3D simulations were performed on the Cray J90 supercomputer situated at the Rutherford-Appleton laboratories, with pre- and postprocessing operations achieved via a Silicon Graphics Indy workstation. A mechanical model was constructed consisting of various CICo-TSE elements rotating within a transparent outer barrel. A technique has been developed using coloured viscous clays whereby the flow patterns and mixing characteristics within the CICo-TSE may be visualised. In order to test and verify the simulated predictions, the patterns observed within the mechanical model were compared with the flow patterns predicted by the computational model. The flow patterns within the single-flighted conveying screw elements in particular, showed good agreement between the experimental and simulated results.

The chemical modification of polymer blends by reactive processing

The primary objective of this research was to examine the concepts of the chemical modification of polymer blends by reactive processing using interlinking agents (multi-functional, activated vinyl compounds; trimethylolpropane triacrylates {TRIS} and divinylbenzene {DVD}) to target in-situ interpolymer formation between immiscible polymers in PS/EPDM blends via peroxide-initiated free radical reactions during melt mixing. From a comprehensive survey of previous studies of compatibility enhancement in polystyrene blends, it was recognised that reactive processing offers opportunities for technological success that have not yet been fully realised; learning from this study is expected to assist in the development and application of this potential. In an experimental-scale operation for the simultaneous melt blending and reactive processing of both polymers, involving manual injection of precise reactive agent/free radical initiator mixtures directly into molten polymer within an internal mixer, torque changes were distinct, quantifiable and rationalised by ongoing physical and chemical effects. EPDM content of PS/EPDM blends was the prime determinant of torque increases on addition of TRIS, itself liable to self-polymerisation at high additions, with little indication of PS reaction in initial reactively processed blends with TRIS, though blend compatibility, from visual assessment of morphology by SEM, was nevertheless improved. Suitable operating windows were defined for the optimisation of reactive blending, for use once routes to encourage PS reaction could be identified. The effectiveness of PS modification by reactive processing with interlinking agents was increased by the selection of process conditions to target specific reaction routes, assessed by spectroscopy (FT-IR and NMR) and thermal analysis (DSC) coupled dichloromethane extraction and fractionation of PS. Initiator concentration was crucial in balancing desired PS modification and interlinking agent self-polymerisation, most particularly with TRIS. Pre-addition of initiator to PS was beneficial in the enhancement of TRIS binding to PS and minimisation of modifier polymerisation; believed to arise from direct formation of polystyryl radicals for addition to active unsaturation in TRIS. DVB was found to be a "compatible" modifier for PS, but its efficacy was not quantified. Application of routes for PS reaction in PS/EPDM blends was successful for in-situ formation of interpolymer (shown by sequential solvent extraction combined with FT-IR and DSC analysis); the predominant outcome depending on the degree of reaction of each component, with optimum "between-phase" interpolymer formed under conditions selected for equalisation of differing component reactivities and avoidance of competitive processes. This was achieved for combined addition of TRIS+DVB at optimum initiator concentrations with initiator pre-addition to PS. Improvements in blend compatibility (by tensiles, SEM and thermal analysis) were shown in all cases with significant interpolymer formation, though physical benefits were not; morphology and other reactive effects were also important factors. Interpolymer from specific "between-phase" reaction of blend components and interlinking agent was vital for the realisation of positive performance on compatibilisation by the chemical modification of polymer blends by reactive processing.

Sequential, Bayesian geostatistics:a principled method for large data sets

The principled statistical application of Gaussian random field models used in geostatistics has historically been limited to data sets of a small size. This limitation is imposed by the requirement to store and invert the covariance matrix of all the samples to obtain a predictive distribution at unsampled locations, or to use likelihood-based covariance estimation. Various ad hoc approaches to solve this problem have been adopted, such as selecting a neighborhood region and/or a small number of observations to use in the kriging process, but these have no sound theoretical basis and it is unclear what information is being lost. In this article, we present a Bayesian method for estimating the posterior mean and covariance structures of a Gaussian random field using a sequential estimation algorithm. By imposing sparsity in a well-defined framework, the algorithm retains a subset of “basis vectors” that best represent the “true” posterior Gaussian random field model in the relative entropy sense. This allows a principled treatment of Gaussian random field models on very large data sets. The method is particularly appropriate when the Gaussian random field model is regarded as a latent variable model, which may be nonlinearly related to the observations. We show the application of the sequential, sparse Bayesian estimation in Gaussian random field models and discuss its merits and drawbacks.