Metabolic engineering of Agrobacterium sp. strain ATCC 31749 for production of an α-Gal epitope

<p>Abstract</p> <p>Background</p> <p>Oligosaccharides containing a terminal Gal-α1,3-Gal moiety are collectively known as α-Gal epitopes. α-Gal epitopes are integral components of several medical treatments under development, including flu and HIV vaccines as well as cancer treatments. The difficulty associated with synthesizing the α-Gal epitope hinders the development and application of these treatments due to the limited availability and high cost of the α-Gal epitope. This work illustrates the development of a whole-cell biocatalyst for synthesizing the α-Gal epitope, Gal-α1,3-Lac.</p> <p>Results</p> <p><it>Agrobacterium </it>sp. ATCC 31749 was engineered to produce Gal-α1,3-Lac by the introduction of a UDP-galactose 4'-epimerase:α1,3-galactosyltransferase fusion enzyme. The engineered <it>Agrobacterium </it>synthesized 0.4 g/L of the α-Gal epitope. Additional metabolic engineering efforts addressed the factors limiting α-Gal epitope production, namely the availability of the two substrates, lactose and UDP-glucose. Through expression of a lactose permease, the intracellular lactose concentration increased by 60 to 110%, subsequently leading to an improvement in Gal-α1,3-Lac production. Knockout of the curdlan synthase gene increased UDP-glucose availability by eliminating the consumption of UDP-glucose for synthesis of the curdlan polysaccharide. With these additional engineering efforts, the final engineered strain synthesized approximately 1 g/L of Gal-α1,3-Lac.</p> <p>Conclusions</p> <p>The <it>Agrobacterium </it>biocatalyst developed in this work synthesizes gram-scale quantities of α-Gal epitope and does not require expensive cofactors or permeabilization, making it a useful biocatalyst for industrial production of the α-Gal epitope. Furthermore, the engineered <it>Agrobacterium</it>, with increased lactose uptake and improved UDP-glucose availability, is a promising host for the production of other medically-relevant oligosaccharides.</p

Celecoxib concentration predicts decrease in prostaglandin E\u3csub\u3e2\u3c/sub\u3e concentrations in nipple aspirate fluid from high risk women

BACKGROUND: Epidemiologic studies suggest that long term low dose celecoxib use significantly lowers breast cancer risk. We previously demonstrated that 400 mg celecoxib taken twice daily for 2 weeks lowered circulating plasma and breast nipple aspirate fluid (NAF) prostaglandin (PG)E2 concentrations in post- but not premenopausal high risk women. We hypothesized that circulating concentrations of celecoxib influenced PGE2 response, and that plasma levels of the drug are influenced by menopausal status. To address these hypotheses, the aims of the study were to determine: 1) if circulating plasma concentrations of celecoxib correlated with the change in plasma or NAF PGE2 concentrations from baseline to end of treatment, and 2) whether menopausal status influenced circulating levels of celecoxib. METHODS: Matched NAF and plasma were collected from 46 high risk women who were administered celecoxib twice daily for two weeks, 20 subjects receiving 200 mg and 26 subjects 400 mg of the agent. NAF and plasma samples were collected before and 2 weeks after taking celecoxib. RESULTS: In women taking 400 mg bid celecoxib, plasma concentrations of the agent correlated inversely with the change in NAF PGE2 levels from pre- to posttreatment. Nonsignificant trends toward higher celecoxib levels were observed in post- compared to premenopausal women. There was a significant decrease in NAF but not plasma PGE2 concentrations in postmenopausal women who took 400 mg celecoxib (p = 0.03). CONCLUSION: In high risk women taking 400 mg celecoxib twice daily, plasma concentrations of celecoxib correlated with downregulation of PGE2 production by breast tissue. Strategies synergistic with celecoxib to downregulate PGE2 are of interest, in order to minimize the celecoxib dose required to have an effect

Comparing Infrared Dirac-Born-Infeld Brane Inflation to Observations

We compare the Infrared Dirac-Born-Infeld (IR DBI) brane inflation model to observations using a Bayesian analysis. The current data cannot distinguish it from the \LambdaCDM model, but is able to give interesting constraints on various microscopic parameters including the mass of the brane moduli potential, the fundamental string scale, the charge or warp factor of throats, and the number of the mobile branes. We quantify some distinctive testable predictions with stringy signatures, such as the large non-Gaussianity, and the large, but regional, running of the spectral index. These results illustrate how we may be able to probe aspects of string theory using cosmological observations.Comment: 54 pages, 13 figures. v2: non-Gaussianity constraint has been applied to the model; parameter constraints have tightened significantly, conclusions unchanged. References added; v3, minor revision, PRD versio

Duality Cascade in Brane Inflation

We show that brane inflation is very sensitive to tiny sharp features in extra dimensions, including those in the potential and in the warp factor. This can show up as observational signatures in the power spectrum and/or non-Gaussianities of the cosmic microwave background radiation (CMBR). One general example of such sharp features is a succession of small steps in a warped throat, caused by Seiberg duality cascade using gauge/gravity duality. We study the cosmological observational consequences of these steps in brane inflation. Since the steps come in a series, the prediction of other steps and their properties can be tested by future data and analysis. It is also possible that the steps are too close to be resolved in the power spectrum, in which case they may show up only in the non-Gaussianity of the CMB temperature fluctuations and/or EE polarization. We study two cases. In the slow-roll scenario where steps appear in the inflaton potential, the sensitivity of brane inflation to the height and width of the steps is increased by several orders of magnitude comparing to that in previously studied large field models. In the IR DBI scenario where steps appear in the warp factor, we find that the glitches in the power spectrum caused by these sharp features are generally small or even unobservable, but associated distinctive non-Gaussianity can be large. Together with its large negative running of the power spectrum index, this scenario clearly illustrates how rich and different a brane inflationary scenario can be when compared to generic slow-roll inflation. Such distinctive stringy features may provide a powerful probe of superstring theory.Comment: Corrections in Eq.(5.47), Eq (5.48), Eq(5.49) and Fig

The highly variable time evolution of star-forming cores identified with dendrograms

We investigate the time evolution of dense cores identified in molecular cloud simulations using dendrograms, which are a common tool to identify hierarchical structure in simulations and observations of star formation. We develop an algorithm to link dendrogram structures through time using the three-dimensional density field from magnetohydrodynamical simulations, thus creating histories for all dense cores in the domain. We find that the population-wide distributions of core properties are relatively invariant in time, and quantities like the core mass function match with observations. Despite this consistency, an individual core may undergo large (>40%), stochastic variations due to the redefinition of the dendrogram structure between timesteps. This variation occurs independent of environment and stellar content. We identify a population of short-lived (<200 kyr) overdensities masquerading as dense cores that may comprise ~20% of any time snapshot. Finally, we note the importance of considering the full history of cores when interpreting the origin of the initial mass function; we find that, especially for systems containing multiple stars, the core mass defined by a dendrogram leaf in a snapshot is typically less than the final system stellar mass. This work reinforces that there is no time-stable density contour that defines a star-forming core. The dendrogram itself can induce significant structure variation between timesteps due to small changes in the density field. Thus, one must use caution when comparing dendrograms of regions with different ages or environment properties because differences in dendrogram structure may not come solely from the physical evolution of dense cores.Comment: 20 pages, 17 figures. Submitted to MNRA

Universality in D-brane Inflation

We study the six-field dynamics of D3-brane inflation for a general scalar potential on the conifold, finding simple, universal behavior. We numerically evolve the equations of motion for an ensemble of more than 7 \times 10^7 realizations, drawing the coefficients in the scalar potential from statistical distributions whose detailed properties have demonstrably small effects on our results. When prolonged inflation occurs, it has a characteristic form: the D3-brane initially moves rapidly in the angular directions, spirals down to an inflection point in the potential, and settles into single-field inflation. The probability of N_{e} e-folds of inflation is a power law, P(N_{e}) \propto N_{e}^{-3}, and we derive the same exponent from a simple analytical model. The success of inflation is relatively insensitive to the initial conditions: we find attractor behavior in the angular directions, and the D3-brane can begin far above the inflection point without overshooting. In favorable regions of the parameter space, models yielding 60 e-folds of expansion arise approximately once in 10^3 trials. Realizations that are effectively single-field and give rise to a primordial spectrum of fluctuations consistent with WMAP, for which at least 120 e-folds are required, arise approximately once in 10^5 trials. The emergence of robust predictions from a six-field potential with hundreds of terms invites an analytic approach to multifield inflation.Comment: 28 pages, 9 figure