Rapid generation of incremental truncation libraries for protein engineering using α-phosphothioate nucleotides

Incremental truncation for the creation of hybrid enzymes (ITCHY) is a novel tool for the generation of combinatorial libraries of hybrid proteins independent of DNA sequence homology. We herein report a fundamentally different methodology for creating incremental truncation libraries using nucleotide triphosphate analogs. Central to the method is the polymerase catalyzed, low frequency, random incorporation of α-phosphothioate dNTPs into the region of DNA targeted for truncation. The resulting phosphothioate internucleotide linkages are resistant to 3′→5′ exonuclease hydrolysis, rendering the target DNA resistant to degradation in a subsequent exonuclease III treatment. From an experimental perspective the protocol reported here to create incremental truncation libraries is simpler and less time consuming than previous approaches by combining the two gene fragments in a single vector and eliminating additional purification steps. As proof of principle, an incremental truncation library of fusions between the N-terminal fragment of Escherichia coli glycinamide ribonucleotide formyltransferase (PurN) and the C-terminal fragment of human glycinamide ribonucleotide formyltransferase (hGART) was prepared and successfully tested for functional hybrids in an auxotrophic E.coli host strain. Multiple active hybrid enzymes were identified, including ones fused in regions of low sequence homology.

Stimulation of phosphatidylinositol 3-kinase by fibroblast growth factor receptors is mediated by coordinated recruitment of multiple docking proteins

The docking protein FRS2 is a major downstream effector that links fibroblast growth factor (FGF) and nerve growth factor receptors with the Ras/mitogen-activated protein kinase signaling cascade. In this report, we demonstrate that FRS2 also plays a pivotal role in FGF-induced recruitment and activation of phosphatidylinositol 3-kinase (PI3-kinase). We demonstrate that tyrosine phosphorylation of FRS2α leads to Grb2-mediated complex formation with the docking protein Gab1 and its tyrosine phosphorylation, resulting in the recruitment and activation of PI3-kinase. Furthermore, Grb2 bound to tyrosine-phosphorylated FRS2 through its SH2 domain interacts primarily via its carboxyl-terminal SH3 domain with a proline-rich region in Gab1 and via its amino-terminal SH3 domain with the nucleotide exchange factor Sos1. Assembly of FRS2α:Grb2:Gab1 complex induced by FGF stimulation results in activation of PI3-kinase and downstream effector proteins such as the S/T kinase Akt, whose cellular localization and activity are regulated by products of PI3-kinase. These experiments reveal a unique mechanism for generation of signal diversity by growth factor-induced coordinated assembly of a multidocking protein complex that can activate the Ras/mitogen-activated protein kinase cascade to induce cell proliferation and differentiation, and PI3-kinase to activate a mediator of a cell survival pathway.

The generation of oscillations in networks of electrically coupled cells

In several biological systems, the electrical coupling of nonoscillating cells generates synchronized membrane potential oscillations. Because the isolated cell is nonoscillating and electrical coupling tends to equalize the membrane potentials of the coupled cells, the mechanism underlying these oscillations is unclear. Here we present a dynamic mechanism by which the electrical coupling of identical nonoscillating cells can generate synchronous membrane potential oscillations. We demonstrate this mechanism by constructing a biologically feasible model of electrically coupled cells, characterized by an excitable membrane and calcium dynamics. We show that strong electrical coupling in this network generates multiple oscillatory states with different spatio-temporal patterns and discuss their possible role in the cooperative computations performed by the system.

Adaptive mutations in Escherichia coli as a model for the multiple mutational origins of tumors.

The cells in most tumors are found to carry multiple mutations; however, based upon mutation rates determined by fluctuation tests, the frequency of such multiple mutations should be so low that tumors are never detected within human populations. Fluctuation tests, which determine the cell-division-dependent mutation rate per cell generation in growing cells, may not be appropriate for estimating mutation rates in nondividing or very slowly dividing cells. Recent studies of time-dependent, "adaptive" mutations in nondividing populations of microorganisms suggest that similar measurements may be more appropriate to understanding the mutation origins of tumors. Here I use the ebgR and ebgA genes of Escherichia coli to measure adaptive mutation rates where multiple mutations are required for rapid growth. Mutations in either ebgA or ebgR allow very slow growth on lactulose (4-O-beta-D-galactosyl-D-fructose), with doubling times of 3.2 and 17.3 days, respectively. However, when both mutations are present, cells can grow rapidly with doubling times of 2.7 hr. I show that during prolonged (28-day) selection for growth on lactulose, the number of lactulose-utilizing mutants that accumulate is 40,000 times greater than can be accounted for on the basis of mutation rates measured by fluctuation tests, but is entirely consistent with the time-dependent adaptive mutation rates measured under the same conditions of prolonged selection.

The first extrasolar planet discovered with a new-generation high-throughput Doppler instrument

We report the detection of the first extrasolar planet, ET-1 (HD 102195b), using the Exoplanet Tracker (ET), a new-generation Doppler instrument. The planet orbits HD 102195, a young star with solar metallicity that may be part of the local association. The planet imparts radial velocity variability to the star with a semiamplitude of 63.4 ± 2.0 m s^-1 and a period of 4.11 days. The planetary minimum mass (m sin i) is 0.488MJ ± 0.015M_J. The planet was initially detected in the spring of 2005 with the Kitt Peak National Observatory (KPNO) 0.9 m coudé feed telescope. The detection was confirmed by radial velocity observations with the ET at the KPNO 2.1 m telescope and also at the 9 m Hobby-Eberly Telescope (HET) with its High Resolution Spectrograph. This planetary discovery with a 0.9 m telescope around a V = 8.05 magnitude star was made possible by the high throughput of the instrument: 49% measured from the fiber output to the detector. The ET's interferometer-based approach is an effective method for planet detection. In addition, the ET concept is adaptable to multiple-object Doppler observations or very high precision observations with a cross-dispersed echelle spectrograph to separate stellar fringes over a broad wavelength band. In addition to spectroscopic observations of HD 102195, we obtained brightness measurements with one of the automated photometric telescopes at Fairborn Observatory. Those observations reveal that HD 102195 is a spotted variable star with an amplitude of ~0.015 mag and a 12.3 ± 0.3 day period. This is consistent with spectroscopically observed Ca II H and K emission levels and line-broadening measurements but inconsistent with rotational modulation of surface activity as the cause of the radial velocity variability. Our photometric observations rule out transits of the planetary companion.

Renewable Energy Generation at Copper Mountain Resort

Copper Mountain, a Colorado ski area, evaluated onsite renewable energy generation to save on energy costs and reduce carbon emissions. Multiple resort locations were analyzed to determine suitable sites for implementation of solar electricity generation, wind electricity generation and biomass heat production. Potential project sites were assessed based on four criteria: costs and financial returns, environmental impacts, implementation and maintenance, and public relations/marketing opportunities. Solar projects had the lowest capital cost of the three types of renewable energy, and wind projects had high capital costs and low financial returns. Biomass projects had high capital costs, solid financial projections and good marketing value compared to wind and solar technologies. Project implementation recommendations were given based upon the evaluation.

COMPENDIUM: a text summarisation tool for generating summaries of multiple purposes, domains, and genres

In this paper, we present a Text Summarisation tool, compendium, capable of generating the most common types of summaries. Regarding the input, single- and multi-document summaries can be produced; as the output, the summaries can be extractive or abstractive-oriented; and finally, concerning their purpose, the summaries can be generic, query-focused, or sentiment-based. The proposed architecture for compendium is divided in various stages, making a distinction between core and additional stages. The former constitute the backbone of the tool and are common for the generation of any type of summary, whereas the latter are used for enhancing the capabilities of the tool. The main contributions of compendium with respect to the state-of-the-art summarisation systems are that (i) it specifically deals with the problem of redundancy, by means of textual entailment; (ii) it combines statistical and cognitive-based techniques for determining relevant content; and (iii) it proposes an abstractive-oriented approach for facing the challenge of abstractive summarisation. The evaluation performed in different domains and textual genres, comprising traditional texts, as well as texts extracted from the Web 2.0, shows that compendium is very competitive and appropriate to be used as a tool for generating summaries.

(Table 1) Chemical composition of interstitial waters from the area of gas hydrate generation, Sea of Okhotsk

Distributions of halogens (Cl, Br and I) in interstitial waters from sediments containing methane hydrate and in water of the hydrate itself are presented. High concentrations of halogens do not occur in interstitial waters from sediments that contain gas hydrates. The main reason for their low concentrations is the poverty of organic matter in sediments.

Stickleback F2 generation transgenerational plasticity experiment: egg and body size data

Nongenetic inheritance mechanisms such as transgenerational plasticity (TGP) can buffer populations against rapid environmental change such as ocean warming. Yet, little is known about how long these effects persist and whether they are cumulative over generations. Here, we tested for adaptive TGP in response to simulated ocean warming across parental and grandparental generations of marine sticklebacks. Grandparents were acclimated for two months during reproductive conditioning, whereas parents experienced developmental acclimation, allowing us to compare the fitness consequences of short-term vs. prolonged exposure to elevated temperature across multiple generations. We found that reproductive output of F1 adults was primarily determined by maternal developmental temperature, but carry-over effects from grandparental acclimation environments resulted in cumulative negative effects of elevated temperature on hatching success. In very early stages of growth, F2 offspring reached larger sizes in their respective paternal and grandparental environment down the paternal line, suggesting that other factors than just the paternal genome may be transferred between generations. In later growth stages, maternal and maternal granddam environments strongly influenced offspring body size, but in opposing directions, indicating that the mechanism(s) underlying the transfer of environmental information may have differed between acute and developmental acclimation experienced by the two generations. Taken together, our results suggest that the fitness consequences of parental and grandparental TGP are highly context dependent, but will play an important role in mediating some of the impacts of rapid climate change in this system.

Effects of leukapheresis protocol, cell processing and cryopreservation on the generation of monocyte-derived DC for immune therapy

Background Many clinical trials of DC-based immunotherapy involve administration of monocyte-derived DCs (Mo-DC) on multiple occasions. We aimed to determine the optimal cell processing procedures and timing (leukapheresis, RBC depletion and cryopreservation) for generation of Mo-DC for clinical purposes. Methods Leukapheresis was undertaken using a COBE Spectra. Two instrument settings were compared - the standard semi-automated software (Version 4.7) (n = 10) and the fully automated software (Version 6.0) (n = 40). Density gradient centrifugation using Ficoll, Percoll, a combination of these methods or neither for RBC depletion were compared. Outcomes (including cell yield and purity) were compared for cryopreserved unmanipulated monocytes and cryopreserved Mo-DC. Results Software Version 6.0 provided significantly better enrichment for monocytes (P

Physical and MAC layer techniques for next generation satellite communications

In this thesis, we consider four different scenarios of interest in modern satellite communications. For each scenario, we will propose the use of advanced solutions aimed at increasing the spectral efficiency of the communication links. First, we will investigate the optimization of the current standard for digital video broadcasting. We will increase the symbol rate of the signal and determine the optimal signal bandwidth. We will apply the time packing technique and propose a specifically design constellation. We will then compare some receiver architectures with different performance and complexity. The second scenario still addresses broadcast transmissions, but in a network composed of two satellites. We will compare three alternative transceiver strategies, namely, signals completely overlapped in frequency, frequency division multiplexing, and the Alamouti space-time block code, and, for each technique, we will derive theoretical results on the achievable rates. We will also evaluate the performance of said techniques in three different channel models. The third scenario deals with the application of multiuser detection in multibeam satellite systems. We will analyze a case in which the users are near the edge of the coverage area and, hence, they experience a high level of interference from adjacent cells. Also in this case, three different approaches will be compared. A classical approach in which each beam carries information for a user, a cooperative solution based on time division multiplexing, and the Alamouti scheme. The information theoretical analysis will be followed by the study of practical coded schemes. We will show that the theoretical bounds can be approached by a properly designed code or bit mapping. Finally, we will consider an Earth observation scenario, in which data is generated on the satellite and then transmitted to the ground. We will study two channel models, taking into account one or two transmit antennas, and apply techniques such as time and frequency packing, signal predistortion, multiuser detection and the Alamouti scheme.

A methodology for the generation and evaluation of biorefinery process chains, in order to identify the most promising biorefineries for the EU

The topic of bioenergy, biofuels and bioproducts remains at the top of the current political and research agenda. Identification of the optimum processing routes for biomass, in terms of efficiency, cost, environment and socio-economics is vital as concern grows over the remaining fossil fuel resources, climate change and energy security. It is known that the only renewable way of producing conventional hydrocarbon fuels and organic chemicals is from biomass, but the problem remains of identifying the best product mix and the most efficient way of processing biomass to products. The aim is to move Europe towards a biobased economy and it is widely accepted that biorefineries are key to this development. A methodology was required for the generation and evaluation of biorefinery process chains for converting biomass into one or more valuable products that properly considers performance, cost, environment, socio-economics and other factors that influence the commercial viability of a process. In this thesis a methodology to achieve this objective is described. The completed methodology includes process chain generation, process modelling and subsequent analysis and comparison of results in order to evaluate alternative process routes. A modular structure was chosen to allow greater flexibility and allowing the user to generate a large number of different biorefinery configurations The significance of the approach is that the methodology is defined and is thus rigorous and consistent and may be readily re-examined if circumstances change. There was the requirement for consistency in structure and use, particularly for multiple analyses. It was important that analyses could be quickly and easily carried out to consider, for example, different scales, configurations and product portfolios and so that previous outcomes could be readily reconsidered. The result of the completed methodology is the identification of the most promising biorefinery chains from those considered as part of the European Biosynergy Project.

Switching and generation of ultrashort pulses using all-fibre devices

Serial and parallel interconnection of photonic devices is integral to the construction of any all-optical data processing system. This thesis presents results from a series of experiments centering on the use of the nonlinear-optical loop mirror (NOLM) switch in architectures for the manipulation and generation of ultrashort pulses. Detailed analysis of soliton switching in a single NOLM and cascade of two NOLM's is performed, centering on primary limitations to device operation, effect of cascading on amplitude response, and impact of switching on the characteristics of incident pulses. By using relatively long input pulses, device failure due to stimulated Raman generation is postponed to demonstrate multiple-peaked switching for the first time. It is found that while cascading leads to a sharpening of the overall switching characteristic, pulse spectral and temporal integrity is not significantly degraded, and emerging pulses retain their essential soliton character. In addition, by including an asymmetrically placed in-fibre Bragg reflector as a wavelength selective loss element in the basic NOLM configuration, both soliton self-switching and dual-wavelength control-pulse switching are spectrally quantised. Results are presented from a novel dual-wavelength laser configuration generating pulse trains with an ultra-low rms inter-pulse-stream timing jitter level of 630fs enabling application in ultrafast switching environments at data rates as high as 130GBits/s. In addition, the fibre NOLM is included in architectures for all-optical memory, demonstrating storage and logical inversion of a 0.5kByte random data sequence; and ultrafast phase-locking of a gain-switched distributed feedback laser at 1.062GHz, the fourteenth harmonic of the system baseband frequency. The stringent requirements for environmental robustness of these architectures highlight the primary weaknesses of the NOLM in its fibre form and recommendations to overcome its inherent drawbacks are presented.

A simple, sensitive and selective quantum-dot-based western blot method for the simultaneous detection of multiple targets from cell lysates

Quantum dots (Qdots) are fluorescent nanoparticles that have great potential as detection agents in biological applications. Their optical properties, including photostability and narrow, symmetrical emission bands with large Stokes shifts, and the potential for multiplexing of many different colours, give them significant advantages over traditionally used fluorescent dyes. Here, we report the straightforward generation of stable, covalent quantum dot-protein A/G bioconjugates that will be able to bind to almost any IgG antibody, and therefore can be used in many applications. An additional advantage is that the requirement for a secondary antibody is removed, simplifying experimental design. To demonstrate their use, we show their application in multiplexed western blotting. The sensitivity of Qdot conjugates is found to be superior to fluorescent dyes, and comparable to, or potentially better than, enhanced chemiluminescence. We show a true biological validation using a four-colour multiplexed western blot against a complex cell lysate background, and have significantly improved previously reported non-specific binding of the Qdots to cellular proteins.

Investigation of the oxidative degradation mechanisms and melt stabilisation of a new generation metallocene polytehylene

The two main objectives of the research work conducted were firstly, to investigate the processing and rheological characteristics of a new generation metallocene catalysed linear low density polyethylene (m-LLDPE), in order to establish the thermal oxidative degradation mechanism, and secondly, to examine the role of selected commercial stabilisers on the melt stability of the polymers. The unstabilised m-LLDPE polymer was extruded (pass I) using a twin screw extruder, at different temperatures (210-285°C) and screw speeds (50-20rpm) and was subjected to multiple extrusions (passes, 2-5) carried out under the same processing conditions used in the first pass. A traditional Ziegler/Natta catalysed linear low density polyethylene (z-LLDPE) produced by the same manufacturer was also subjected to a similar processing regime in order to compare the processability and the oxidative degradation mechanism (s) of the new m-LLDPE with that of the more traditional z-LLDPE. The effect of some of the main extrusion characteristics of the polymers (m-LLDPE and z-LLDPE) on their melt rheological behaviour was investigated by examining their melt flow performance monitored at two fixed low shear rate values, and their rheological behaviour investigated over the entire shear rates experienced during extrusion using a twin-bore capillary rheometer. Capillary rheometric measurements, which determine the viscous and elastic properties of polymers, have shown that both polymers are shear thinning but the m-LLDPE has a higher viscosity than z-LLDPE and the extent of reduction in viscosity of the former when the extrusion temperature was increased from 210°C to 285°C was much higher than in the case of the z-LLDPE polymer. This was supplied by the findings that the m-LLDPE polymer required higher power consumption under all extrusion conditions examined. It was fUliher revealed that the m-LLDPE undergoes a higher extent of melt fracture, the onset of which occurs under much lower shear rates than the Ziegler-based polymer and this was attributed to its higher shear viscosity and narrower molecular weight distribution (MWD). Melt flow measurements and GPC have shown that after the first extrusion pass, the initial narrower MWD of m-LLDPE is retained (compared to z-LLDPE), but upon further multiple extrusion passes it undergoes much faster broadening of its MWD which shifts to higher Mw polymer fractions, paliicularly at the high screw speeds. The MWD of z-LLDPE polymer on the other hand shifts towards the lower Mw end. All the evidence suggest therefore the m-LLDPE undergoes predominantly cross-linking reactions under all processing conditions whereas z-LLDPE undergoes both cross-linking and chain scission reactions with the latter occurring predominantly under more severe processing conditions (higher temperatures and screw speeds, 285°CI200rpm). The stabilisation of both polymers with synergistic combinations of a hindered phenol (Irganox 1076) and a phosphite (Weston 399) at low concentrations has shown a high extent of melt stabilisation in both polymers (extrusion temperatures 210-285°C and screw speeds 50-200rpm). The best Irganox 1076/Weston 399 system was found to be at an optimum 1:4 w/w ratio, respectively and was found to be most effective in the z-LLDPE polymer. The melt stabilising effectiveness of a Vitamin E/Ultranox 626 system used at a fraction of the total concentration of Irganox 1076/Weston 399 system was found to be higher in both polymers (under all extrusion conditions). It was found that AOs which operate primarily as alkyl (Re) radical scavengers are the most effective in inhibiting the thermal oxidative degradation of m-LLDPE in the melt; this polymer was shown to degrade in the melt primarily via alky radicals resulting in crosslinking. Metallocene polymers stabilised with single antioxidants of Irganox HP 136 (a lactone) and Irganox E201 (vitamin E) produced the highest extent of melt stability and the least discolouration during processing (260°C/1 OOrpm). Furthermore, synergistic combinations of Irganox HP I 36/Ultranox 626 (XP-60) system produced very high levels of melt and colour stability (comparable to the Vitamin E based systems) in the mLLDPE polymer. The addition of Irganox 1076 to an Irganox HP 136/Ultranox 626 system was found not to result in increasing melt stability but gave rise to increasing discolouration of the m-LLDPE polymer. The blending of a hydroxylamine (lrgastab FS042) with a lactone and Vitamin E (in combination with a phosphite) did not increase melt stability but induced severe discolouration of resultant polymer samples.