Predicting the dynamics and heterogeneity of genomic DNA content within bacterial populations across variable growth regimes

For many applications in microbial synthetic biology, optimizing a desired function requires careful tuning of the degree to which various genes are expressed. One challenge for predicting such effects or interpreting typical characterization experiments is that in bacteria such as E. coli, genome copy number varies widely across different phases and rates of growth, which also impacts how and when genes are expressed from different loci. While such phenomena are relatively well-understood at a mechanistic level, our quantitative understanding of such processes is essentially limited to ideal exponential growth. In contrast, common experimental phenomena such as growth on heterogeneous media, metabolic adaptation, and oxygen restriction all cause substantial deviations from ideal exponential growth, particularly as cultures approach the higher densities at which industrial biomanufacturing and even routine screening experiments are conducted. To meet the need for predicting and explaining how gene dosage impacts cellular functions outside of exponential growth, we here report a novel modeling strategy that leverages agent-based simulation and high performance computing to robustly predict the dynamics and heterogeneity of genomic DNA content within bacterial populations across variable growth regimes. We show that by feeding routine experimental data, such as optical density time series, into our heterogeneous multiphasic growth simulator, we can predict genomic DNA distributions over a range of nonexponential growth conditions. This modeling strategy provides an important advance in the ability of synthetic biologists to evaluate the role of genomic DNA content and heterogeneity in affecting the performance of existing or engineered microbial functions

A CO emission line from the optical and near-IR undetected submillimeter galaxy GN10

We report the detection of a CO emission line from the submillimiter galaxy (SMG) GN10 in the GOODS-N field. GN10 lacks any counterpart in extremely deep optical and near-IR imaging obtained with the Hubble Space Telescope and ground-based facilities. This is a prototypical case of a source that is extremely obscured by dust, for which it is practically impossible to derive a spectroscopic redshift in the optical/near-IR. Under the hypothesis that GN10 is part of a proto-cluster structure previously identified at z~4.05 in the same field, we searched for CO[4-3] at 91.4 GHz with the IRAM Plateau de Bure Interferometer, and successfully detected a line. We find that the most likely redshift identification is z=4.0424+-0.0013, based on: 1) the very low chance that the CO line is actually serendipitous from a different redshift; 2) a radio-IR photometric redshift analysis; 3) the identical radio-IR SED, within a scaling factor, of two other SMGs at the same redshift. The faintness at optical/near-IR wavelengths requires an attenuation of A_V~5-7.5 mag. This result supports the case that a substantial population of very high-z SMGs exists that had been missed by previous spectroscopic surveys. This is the first time that a CO emission line has been detected for a galaxy that is invisible in the optical and near-IR. Our work demonstrates the power of existing and planned facilities for completing the census of star formation and stellar mass in the distant Universe by measuring redshifts of the most obscured galaxies through millimeter spectroscopy.Comment: 5 pages, 4 figures. ApJ Letters in pres

Making Sense of a New Transport System: An Ethnographic Study of the Cambridgeshire Guided Busway

An increase in public transport use has the potential to contribute to improving population health, and there is growing interest in innovative public transport systems. Yet how new public transport infrastructure is experienced and integrated (or not) into daily practice is little understood. We investigated how the Cambridgeshire Guided Busway, UK, was used and experienced in the weeks following its opening, using the method of participant observation (travelling on the busway and observing and talking to passengers) and drawing on Normalization Process Theory to interpret our data. Using excerpts of field notes to support our interpretations, we describe how the ease with which the new transport system could be integrated into existing daily routines was important in determining whether individuals would continue to use it. It emerged that there were two groups of passengers with different experiences and attitudes. Passengers who had previously travelled frequently on regular bus services did not perceive the new system to be an improvement; consequently, they were frustrated that it was differentiated from and not coherent with the regular system. In contrast, passengers who had previously travelled almost exclusively by car appraised the busway positively and perceived it to be a novel and superior form of travel. Our rich qualitative account highlights the varied and creative ways in which people learn to use new public transport and integrate it into their everyday lives. This has consequences for the introduction and promotion of future transport innovations. It is important to emphasise the novelty of new public transport, but also the ways in which its use can become ordinary and routine. Addressing these issues could help to promote uptake of other public transport interventions, which may contribute to increasing physical activity and improving population health. © 2013 Jones et al

Electron impact excitation cross sections for allowed transitions in atoms

We present a semiempirical Gaunt factor for widely used Van Regemorter formula [Astrophys. J. 136, 906 (1962)] for the case of allowed transitions in atoms with the LS coupling scheme. Cross sections calculated using this Gaunt factor agree with measured cross sections to within the experimental error.Comment: RevTeX, 3 pages, 10 PS figures, 2 PS tables, submitted to Phys. Rev.

Unveiling the Nature of Submillimeter Galaxy SXDF850.6

We present an 880 micron Submillimeter Array (SMA) detection of the submillimeter galaxy SXDF850.6. SXDF850.6 is a bright source (S(850 micron) = 8 mJy) detected in the SCUBA Half Degree Extragalactic Survey (SHADES), and has multiple possible radio counterparts in its deep radio image obtained at the VLA. Our new SMA detection finds that the submm emission coincides with the brightest radio emission that is found ~8" north of the coordinates determined from SCUBA. Despite the lack of detectable counterparts in deep UV/optical images, we find a source at the SMA position in near-infrared and longer wavelength images. We perform SED model fits to UV-optical-IR photometry (u, B, V, R, i', z', J, H, K, 3.6 micron, 4.5 micron, 5.8 micron, and 8.0 micron) and to submm-radio photometry (850 micron, 880 micron, 1100 micron, and 21 cm) independently, and we find both are well described by starburst templates at a redshift of z ~= 2.2 (+/- 0.3). The best-fit parameters from the UV-optical-IR SED fit are a redshift of z = 1.87 (+0.15/-0.07), a stellar mass of M_star = 2.5 +2.2/-0.3 x 10^11 M_sun, an extinction of A_V = 3.0 (+0.3/-1.0) mag, and an age of 720 (+1880/-210) Myr. The submm-radio SED fit provides a consistent redshift of z ~ 1.8-2.5, an IR luminosity of L_IR = (7-26) x 10^12 L_sun, and a star formation rate of 1300-4500 M_sun/yr. These results suggest that SXDF850.6 is a mature system already having a massive amount of old stellar population constructed before its submm bright phase and is experiencing a dusty starburst, possibly induced by major mergers.Comment: 7 pages, 5 figures, Accepted for publication in Astrophysical Journa

The Self-Regulated Growth of Supermassive Black Holes

We present a series of simulations of the self--regulated growth of supermassive black holes (SMBHs) in galaxies via three different fueling mechanisms: major mergers, minor mergers, and disk instabilities. The SMBHs in all three scenarios follow the same black hole fundamental plane (BHFP) and correlation with bulge binding energy seen in simulations of major mergers, and observed locally. Furthermore, provided that the total gas supply is significantly larger than the mass of the SMBH, its limiting mass is not influenced by the amount of gas available or the efficiency of black hole growth. This supports the assertion that SMBHs accrete until they reach a critical mass at which feedback is sufficient to unbind the gas locally, terminating the inflow and stalling further growth. At the same time, while minor and major mergers follow the same projected correlations (e.g., the $M_{BH}-\sigma$ and Magorrian relations), SMBHs grown via disk instabilities do not, owing to structural differences between the host bulges. This finding is supported by recent observations of SMBHs in pseudobulges and bulges in barred systems, as compared to those hosted by classical bulges. Taken together, this provides support for the BHFP and binding energy correlations as being more "fundamental" than other proposed correlations in that they reflect the physical mechanism driving the co-evolution of SMBHs and spheroids.Comment: 15 pages, 16 figures, accepted for publication in Ap

Electron Impact Excitation Cross Sections for Hydrogen-Like Ions

We present cross sections for electron-impact-induced transitions n --> n' in hydrogen-like ions C 5+, Ne 9+, Al 12+, and Ar 17+. The cross sections are computed by Coulomb-Born with exchange and normalization (CBE) method for all transitions with n < n' < 7 and by convergent close-coupling (CCC) method for transitions with n 2s and 1s --> 2p are presented as well. The CCC and CBE cross sections agree to better than 10% with each other and with earlier close-coupling results (available for transition 1 --> 2 only). Analytical expression for n --> n' cross sections and semiempirical formulae are discussed.Comment: RevTeX, 5 pages, 13 PostScript figures, submitted to Phys. Rev.

AzTEC Millimetre Survey of the COSMOS Field - II. Source Count Overdensity and Correlations with Large-Scale Structure

We report an over-density of bright sub-millimetre galaxies (SMGs) in the 0.15 sq. deg. AzTEC/COSMOS survey and a spatial correlation between the SMGs and the optical-IR galaxy density at z <~ 1.1. This portion of the COSMOS field shows a ~ 3-sigma over-density of robust SMG detections when compared to a background, or "blankfield", population model that is consistent with SMG surveys of fields with no extragalactic bias. The SMG over-density is most significant in the number of very bright detections (14 sources with measured fluxes S(1.1mm) > 6 mJy), which is entirely incompatible with sample variance within our adopted blank-field number densities and infers an over-density significance of >> 4. We find that the over-density and spatial correlation to optical-IR galaxy density are most consistent with lensing of a background SMG population by foreground mass structures along the line of sight, rather than physical association of the SMGs with the z <~ 1.1 galaxies/clusters. The SMG positions are only weakly correlated with weak-lensing maps, suggesting that the dominant sources of correlation are individual galaxies and the more tenuous structures in the region and not the massive and compact clusters. These results highlight the important roles cosmic variance and large-scale structure can play in the study of SMGs.Comment: 12 pages, 11 figures, 2 tables, accepted for publication in MNRA

Stark Broadening of the B III 2s-2p Lines

We present a quantum-mechanical calculation of Stark line widths from electron-ion collisions for the $2s_{1/2}-2p_{1/2,3/2}$, lambda = 2066 and 2067 A, resonance transitions in B III. The results confirm the previous quantum-mechanical R-matrix calculations but contradict recent measurements and semi-classical and some semi-empirical calculations. The differences between the calculations can be attributed to the dominance of small L partial waves in the electron-atom scattering, while the large Stark widths inferred from the measurements would be substantially reduced if allowance is made for hydrodynamic turbulence from high Reynolds number flows and the associated Doppler broadening.Comment: 21 pages, 4 figures; to be published in Phys. Rev.