Optimizing information flow in small genetic networks. II: Feed forward interactions

Central to the functioning of a living cell is its ability to control the readout or expression of information encoded in the genome. In many cases, a single transcription factor protein activates or represses the expression of many genes. As the concentration of the transcription factor varies, the target genes thus undergo correlated changes, and this redundancy limits the ability of the cell to transmit information about input signals. We explore how interactions among the target genes can reduce this redundancy and optimize information transmission. Our discussion builds on recent work [Tkacik et al, Phys Rev E 80, 031920 (2009)], and there are connections to much earlier work on the role of lateral inhibition in enhancing the efficiency of information transmission in neural circuits; for simplicity we consider here the case where the interactions have a feed forward structure, with no loops. Even with this limitation, the networks that optimize information transmission have a structure reminiscent of the networks found in real biological systems

Temperature effects on the 15-85-micron spectra of olivines and pyroxenes

Far-infrared spectra of laboratory silicates are normally obtained at room temperature even though the grains responsible for astronomical silicate emission bands seen at wavelengths >20 micron are likely to be at temperatures below ~150 K. In order to investigate the effect of temperature on silicate spectra, we have obtained absorption spectra of powdered forsterite and olivine, along with two orthoenstatites and diopside clinopyroxene, at 3.5+-0.5 K and at room temperature (295+-2K). To determine the changes in the spectra the resolution must be increased from 1 to 0.25 cm^-1 at both temperatures since a reduction in temperature reduces the phonon density, thereby reducing the width of the infrared peaks. Several bands observed at 295 K split at 3.5 K. At 3.5 K the widths of isolated single bands in olivine, enstatites and diopside are ~ 90% of their 295 K-widths. However, in forsterite the 3.5-K-widths of the 31-, 49- and 69-micron bands are, respectively, 90%, 45% and 31% of their 295 K widths. Due to an increase in phonon energy as the lattice contracts, 3.5-K-singlet peaks occur at shorter wavelengths than do the corresponding 295-K peaks; the magnitude of the wavelength shift increases from \~ 0-0.2 micron at 25 micron to ~0.9 micron at 80 micron. Changes in the relative absorbances of spectral peaks are also observed. The temperature dependence of lambda_pk and bandwidth shows promise as a means to deduce characteristic temperatures of mineralogically distinct grain populations. In addition, the observed changes in band strength with temperature will affect estimates of grain masses and relative mineral abundances inferred using room-temperature laboratory data.Comment: 11 pages, 7 figures including figures 3a and 3b. includes latex and eps files. Accepted by MNRAS on 15th March 200

Variability Tests for Intrinsic Absorption Lines in Quasar Spectra

Quasar spectra have a variety of absorption lines whose origins range from energetic winds expelled from the central engines to unrelated, intergalactic clouds. We present multi-epoch, medium resolution spectra of eight quasars at z~2 that have narrow ``associated'' absorption lines (AALs, within $\pm$5000 km s^{-1} of the emission redshift). Two of these quasars were also known previously to have high-velocity mini-broad absorption lines (mini-BALs). We use these data, spanning ~17 years in the observed frame with two to four observations per object, to search for line strength variations as an identifier of absorption that occurs physically near (``intrinsic'' to) the central AGN. Our main results are the following: Two out of the eight quasars with narrow AALs exhibit variable AAL strengths. Two out of two quasars with high-velocity mini-BALs exhibit variable mini-BAL strengths. We also marginally detect variability in a high-velocity narrow absorption line (NAL) system, blueshifted \~32,900 km s^{-1}$ with respect to the emission lines. No other absorption lines in these quasars appeared to vary. The outflow velocities of the variable AALs are 3140 km s^{-1} and 1490 km s^{-1}. The two mini-BALs identify much higher velocity outflows of ~28,400 km s^{-1} and ~52,000 km s^{-1}. Our temporal sampling yields upper limits on the variation time scales from 0.28 to 6.1 years in the quasar rest frames. The corresponding minimum electron densities in the variable absorbers, based on the recombination time scale, are \~40,000 cm^{-3} to ~1900 cm^{-3}. The maximum distances of the absorbers from the continuum source, assuming photoionization with no spectral shielding, range from ~1.8 kpc to ~7 kpc.Comment: 16 pages, 4 figures, ApJ, accepte

Valuing sustainable change in the built environment : using SuROI to appraise built environment projects

Purpose – The paper aims to assess the strengths and weaknesses SuROI to determine it suitability as a means through which social value can be predicted in line with public procurement directives and the Social Value Act, whilst at the same time as fitting the developer’s business model and CSR commitments. Design/methodology/approach – Using a multi case design, findings from a comprehensive evaluation of three major housing-led mixed use regeneration developments are presented. The tree case study locations were selected on the basis of the developer’s strong commitment to place-making and social sustainability. Together with a strong strategic desire to reposition their organisation away from the traditional business as usual profit led model. Findings - Whilst the Social Return on Investment methodology is applicable to the charity sector, its use in the built environment is highly questionable. When applying the model to the mixed use housing projects the authors identified a number of technical limitations to the model, inter alia a lack of suitable proxies and especially proxies relating to the built environment for the valuation of identified outcomes, the use of monetisation as a evaluating measure which did not support some of the more abstract or softer benefits identified, problems collecting, identifying and evaluating data to inform the model given the complexity and scale of the project, the significant time and expense associated with the valuation and finally the inability to benchmark the report on completion. These findings have implications for the social housing providers and local authorities looking to use SuROI to evaluate potential built environment projects. Originality/value – The paper offers unique insights into the viability of using existing social value measurement methodologies. The paper identifies the significant limitations associated with the SuROI methodology

Early Dust Formation and a Massive Progenitor for SN 2011ja?

SN 2011ja was a bright (I = -18.3) Type II supernova occurring in the nearby edge on spiral galaxy NGC 4945. Flat-topped and multi-peaked H-alpha and H-beta spectral emission lines appear between 64 - 84 days post-explosion, indicating interaction with a disc-like circumstellar medium inclined 30-45 degrees from edge-on. After day 84 an increase in the H- and K-band flux along with heavy attenuation of the red wing of the emission lines are strong indications of early dust formation, likely located in the cool dense shell created between the forward shock of the SN ejecta and the reverse shock created as the ejecta plows into the existing CSM. Radiative transfer modeling reveals both ~1.5 x 10^-4 Msun of pre-existing dust located ~ 10^16.7 cm away and ~ 5 x 10^-5 Msun of newly formed dust. Spectral observations after 1.5 years reveal the possibility that the fading SN is located within a young (3-6 Myr) massive stellar cluster, which when combined with tentative 56Ni mass estimates of 0.2 Msun may indicate a massive (> 25 Msun) progenitor for SN 2011ja.Comment: 13 pages, 8 figures, submitted to MNRAS awaiting final referee repor

Thirty years of SN 1980K: Evidence for light echoes

We report optical and mid-infrared photometry of SN 1980K between 2004 and 2010, which show slow monotonic fading consistent with previous spectroscopic and photometric observations made 8 to 17 years after outburst. The slow rate-of-change over two decades suggests that this evolution may result from scattered and thermal light echoes off of extended circumstellar material. We present a semi- analytic dust radiative-transfer model that uses an empirically corrected effective optical depth to provide a fast and robust alternative to full Monte-Carlo radiative transfer modeling for homogenous dust at low to intermediate optical depths. We find that unresolved echoes from a thin circumstellar shell 14-15 lt-yr from the progenitor, and containing about 0.02 Msun of carbon-rich dust, can explain the broadband spectral and temporal evolution. The size, mass and dust composition are in good agreement with the contact discontinuity observed in scattered echoes around SN 1987A. The origin of slowly-changing high-velocity [O I] and Halpha lines is also considered. We propose an origin in shocked high-velocity metal-rich clumps of ejecta, rather than arising in the impact of ejecta on slowly-moving circumstellar material, as is the case with hot spots in SN 1987A.Comment: Accepted 2/14/12 to be published in ApJ. 15 pages, 10 figure

Elemental boron doping behavior in silicon molecular beam epitaxy

Boron-doped Si epilayers were grown by molecular beam epitaxy (MBE) using an elemental boron source, at levels up to 2×1020 cm−3, to elucidate profile control and electrical activation over the growth temperature range 450–900 °C. Precipitation and surface segregation effects were observed at doping levels of 2×1020 cm−3 for growth temperatures above 600 °C. At growth temperatures below 600 °C, excellent profile control was achieved with complete electrical activation at concentrations of 2×1020 cm−3, corresponding to the optimal MBE growth conditions for a range of Si/SixGe1−x heterostructures

High-Resolution Keck Spectra of the Associated Absorption Lines in 3C 191

Associated absorption lines (AALs) are valuable probes of the gaseous environments near quasars. Here we discuss high-resolution (6.7 km/s) spectra of the AALs in the radio-loud quasar 3C 191 (redshift z=1.956). The measured AALs have ionizations ranging from Mg I to N V, and multi-component profiles that are blueshifted by ~400 to ~1400 km/s relative to the quasar's broad emission lines. These data yield the following new results. 1) The density based on Si II*/Si II lines is ~300 cm-3, implying a distance of ~28 kpc from the quasar if the gas is photoionized. 2) The characteristic flow time is thus \~3 x 10^7 yr. 3) Strong Mg I AALs identify neutral gas with very low ionization parameter and high density. We estimate n_H > 5 x 10^4 cm-3 in this region, compared to ~15 cm-3 where the N V lines form. 4) The total column density is N_H < 4 x 10^18 cm-2 in the neutral gas and N_H ~ 2 x 10^20 cm-2 in the moderately ionized regions. 5) The total mass in the AAL outflow is M ~ 2 x 10^9 Mo, assuming a global covering factor (as viewed from the quasar) of ~10% >. 6) The absorbing gas only partially covers the background light source(s) along our line(s) of sight, requiring absorption in small clouds or filaments <0.01 pc across. The ratio N_H/n_H implies that the clouds have radial (line- of-sight) thicknesses <0.2 pc. These properties might characterize a sub-class of AALs that are physically related to quasars but form at large distances. We propose a model for the absorber in which pockets of dense neutral gas are surrounded by larger clouds of generally lower density and higher ionization. This outflowing material might be leftover from a blowout associated with a nuclear starburst, the onset of quasar activity or a past broad absorption line (BAL) wind phase.Comment: 15 pages text plus 6 figures, in press with Ap

Broad P V Absorption in the BALQSO, PG 1254+047: Column Densities, Ionizations and Metal Abundances in BAL Winds

This paper discusses the detection of P V 1118,1128 and other broad absorption lines (BALs) in archival HST spectra of the low-redshift BALQSO, PG 1254+047. The P V identification is secured by excellent redshift and profile coincidences with the other BALs, such as C IV 1548,1550 and Si IV 1393,1403, and by photoionization calculations showing that other lines near this wavelength, e.g. Fe III 1123, should be much weaker than P V. The observed BAL strengths imply that either 1) there are extreme abundance ratios such as [C/H] >~ +1.0, [Si/H] >~ +1.8 and [P/C] >~ +2.2, or 2) at least some of the lines are much more optically thick than they appear. I argue that the significant presence of P V absorption indicates severe line saturation, which is disguised in the observed (moderate-strength) BALs because the absorber does not fully cover the continuum source(s) along our line(s) of sight. Computed optical depths for all UV resonance lines show that the observed BALs are consistent with solar abundances if 1) the ionization parameter is at least moderately high, log U >~ -0.6, 2) the total hydrogen column density is log N_H(cm-2) >~ 22.0, and 3) the optical depths in strong lines like C IV and O VI 1032,1038 are >~25 and >~80, respectively. These optical depths and column densities are at least an order of magnitude larger than expected from the residual intensities in the BAL troughs, but they are consistent with the large absorbing columns derived from X-ray observations of BALQSOs. The outflowing BALR, at velocities from -15,000 to -27,000 km/s in PG 1254+047, is therefore a strong candidate for the X-ray absorber in BALQSOs.Comment: 16 pages (LaTeX) plus 8 pages of figures in one file (pg1254_figs.ps.gz), in press with Ap

Information capacity of genetic regulatory elements

Changes in a cell's external or internal conditions are usually reflected in the concentrations of the relevant transcription factors. These proteins in turn modulate the expression levels of the genes under their control and sometimes need to perform non-trivial computations that integrate several inputs and affect multiple genes. At the same time, the activities of the regulated genes would fluctuate even if the inputs were held fixed, as a consequence of the intrinsic noise in the system, and such noise must fundamentally limit the reliability of any genetic computation. Here we use information theory to formalize the notion of information transmission in simple genetic regulatory elements in the presence of physically realistic noise sources. The dependence of this "channel capacity" on noise parameters, cooperativity and cost of making signaling molecules is explored systematically. We find that, at least in principle, capacities higher than one bit should be achievable and that consequently genetic regulation is not limited the use of binary, or "on-off", components.Comment: 17 pages, 9 figure