Mbd1 is recruited to both methylated and nonmethylated CpGs via distinct DNA binding domains

MBD1 is a vertebrate methyl-CpG binding domain protein (MBD) that can bring about repression of methylated promoter DNA sequences. Like other MBD proteins, MBD1 localizes to nuclear foci that in mice are rich in methyl-CpG. In methyl-CpG-deficient mouse cells, however, Mbd1 remains localized to heterochromatic foci whereas other MBD proteins become dispersed in the nucleus. We find that Mbd1a, a major mouse isoform, contains a CXXC domain (CXXC-3) that binds specifically to nonmethylated CpG, suggesting an explanation for methylation-independent localization. Transfection studies demonstrate that the CXXC-3 domain indeed targets nonmethylated CpG sites in vivo. Repression of nonmethylated reporter genes depends on the CXXC-3 domain, whereas repression of methylated reporters requires the MBD. Our findings indicate that MBD1 can interpret the CpG dinucleotide as a repressive signal in vivo regardless of its methylation status

Warm water deuterium fractionation in IRAS 16293-2422 - The high-resolution ALMA and SMA view

Measuring the water deuterium fractionation in the inner warm regions of low-mass protostars has so far been hampered by poor angular resolution obtainable with single-dish ground- and space-based telescopes. Observations of water isotopologues using (sub)millimeter wavelength interferometers have the potential to shed light on this matter. Observations toward IRAS 16293-2422 of the 5(3,2)-4(4,1) transition of H2-18O at 692.07914 GHz from Atacama Large Millimeter/submillimeter Array (ALMA) as well as the 3(1,3)-2(2,0) of H2-18O at 203.40752 GHz and the 3(1,2)-2(2,1) transition of HDO at 225.89672 GHz from the Submillimeter Array (SMA) are presented. The 692 GHz H2-18O line is seen toward both components of the binary protostar. Toward one of the components, "source B", the line is seen in absorption toward the continuum, slightly red-shifted from the systemic velocity, whereas emission is seen off-source at the systemic velocity. Toward the other component, "source A", the two HDO and H2-18O lines are detected as well with the SMA. From the H2-18O transitions the excitation temperature is estimated at 124 +/- 12 K. The calculated HDO/H2O ratio is (9.2 +/- 2.6)*10^(-4) - significantly lower than previous estimates in the warm gas close to the source. It is also lower by a factor of ~5 than the ratio deduced in the outer envelope. Our observations reveal the physical and chemical structure of water vapor close to the protostars on solar-system scales. The red-shifted absorption detected toward source B is indicative of infall. The excitation temperature is consistent with the picture of water ice evaporation close to the protostar. The low HDO/H2O ratio deduced here suggests that the differences between the inner regions of the protostars and the Earth's oceans and comets are smaller than previously thought.Comment: Accepted for publication in Astronomy & Astrophysic

On the origin of H_2CO abundance enhancements in low-mass protostars

High angular resolution H_2CO 218 GHz line observations have been carried out toward the low-mass protostars IRAS 16293-2422 and L1448-C using the Owens Valley Millimeter Array at ~2" resolution. Simultaneous 1.37 mm continuum data reveal extended emission which is compared with that predicted by model envelopes constrained from single-dish data. For L1448-C the model density structure works well down to the 400 AU scale to which the interferometer is sensitive. For IRAS 16293-2422 , a known proto-binary object, the interferometer observations indicate that the binary has cleared much of the material in the inner part of the envelope, out to the binary separation of ~800 AU. For both sources there is excess unresolved compact emission centered on the sources, most likely due to accretion disks ≾200 AU in size with masses of ≳0.02 M_☉ (L1448-C) and ≳0.1 M_☉ (IRAS 16293-2422). The H_2CO data for both sources are dominated by emission from gas close to the positions of the continuum peaks. The morphology and velocity structure of the H_2CO array data have been used to investigate whether the abundance enhancements inferred from single-dish modelling are due to thermal evaporation of ices or due to liberation of the ice mantles by shocks in the inner envelope. For IRAS 16293-2422 the H_2CO interferometer observations indicate the presence of rotation roughly perpendicular to the large scale CO outflow. The H_2CO distribution differs from that of C^(18)O, with C^(18)O emission peaking near MM1 and H_2CO stronger near MM2. For L1448-C, the region of enhanced H_2CO emission extends over a much larger scale >1" than the radius of 50-100 K (0."6-0".15) where thermal evaporation can occur. The red-blue asymmetry of the emission is consistent with the outflow; however the velocities are significantly lower. The H_2CO 3_(22)-2_(21)/3_(03)-2_(02) flux ratio derived from the interferometer data is significantly higher than that found from single-dish observations for both objects, suggesting that the compact emission arises from warmer gas. Detailed radiative transfer modeling shows, however, that the ratio is affected by abundance gradients and optical depth in the 3_(03)-2_(02) line. It is concluded that a constant H_2CO abundance throughout the envelope cannot fit the interferometer data of the two H_2CO lines simultaneously on the longest and shortest baselines. A scenario in which the H_2CO abundance drops in the cold dense part of the envelope where CO is frozen out but is undepleted in the outermost region provides good fits to the single-dish and interferometer data on short baselines for both sources. Emission on the longer baselines is best reproduced if the H_2CO abundance is increased by about an order of magnitude from ~ 10^(-10) to ~ 10^(-9) in the inner parts of the envelope due to thermal evaporation when the temperature exceeds ~50 K. The presence of additional H_2CO abundance jumps in the innermost hot core region or in the disk cannot be firmly established, however, with the present sensitivity and resolution. Other scenarios, including weak outflow-envelope interactions and photon heating of the envelope, are discussed and predictions for future generation interferometers are presented, illustrating their potential in distinguishing these competing scenarios

COMPARISON OF GROWTH PERFORMANCE OF BEEF CALVES FROM DIFFERENT GENETIC STRAINS REARED UNDER ORGANIC CONDITIONs (D. 3.2)

The objective of the present study was to compare growth performance of 15 Danish Holstein bull (DHB) calves, 15 Limousine x Danish Holstein crossbred bull (CB) calves and 15 Limousine x Danish Holstein crossbred heifer (CH) calves reared under organic conditions. Spring-born calves were puchased at private farms and arrived at approximately 20 days of age with an average initial body weight of 52.9, 58.5 and 56.1 kg, (SEM 2.6) for DHB, CB and CH, respectively. Calves were kept indoor until weaning at 3 months of age. Calves were gradually introduced to a grass-silage based ration from 3 to 4 months of age. From 4 to 7 months calves were kept on mix grass pasture of ryegrass and white clover. There were significant differences between treatment groups in terms of average daily gain (ADGP1) during the first summer pasture period, average daily gain (ADGI) during the indoor winter period, and average daily gain (ADGP2) during the second summer pasture period (first 7 weeks). Thus, CB had significantly greater ADG than CH for all three periods with DHB being in between. CB had greater values than DHB and CH in terms of LWP1 144, 140 and 135 (SEM 4) kg, ADGP1 1.15, 1.04 and 0.95 (SEM 0.05) kg/d, LW Indoor 222, 213, and 201 (SEM 5) kg and ADGI 1.06, 1.02 and 0.95 (SEM 0.02) kg/d, LWP2 462, 445 and 414 (SEM 9) kg and ADGP2 1.24, 0.98 and 0.68 (SEM 0.04) kg/d for CB, DHB and CH, respectively. The final live weight were not different between CB and DHB but was significantly lower for CH than DHB and CB (483, 539 and 582 (SEM 8) kg, for CH, DHB and CB, respectively). Overall growth performance across all periods was 13% higher for CB than CH

The effect of a strong external radiation field on protostellar envelopes in Orion

We discuss the effects of an enhanced interstellar radiation field (ISRF) on the observables of protostellar cores in the Orion cloud region. Dust radiative transfer is used to constrain the envelope physical structure by reproducing SCUBA 850 micron emission. Previously reported 13CO, C17O and H2CO line observations are reproduced through detailed Monte Carlo line radiative transfer models. It is found that the 13CO line emission is marginally optically thick and sensitive to the physical conditions in the outer envelope. An increased temperature in this region is needed in order to reproduce the 13CO line strengths and it is suggested to be caused by a strong heating from the exterior, corresponding to an ISRF in Orion 10^3 times stronger than the "standard" ISRF. The typical temperatures in the outer envelope are higher than the desorption temperature for CO. The C17O emission is less sensitive to this increased temperature but rather traces the bulk envelope material. The data are only fit by a model where CO is depleted, except in the inner and outermost regions where the temperature increases above 30-40 K. The fact that the temperatures do not drop below approximately 25 K in any of the envelopes whereas a significant fraction of CO is frozen-out suggest that the interstellar radiation field has changed through the evolution of the cores. The H2CO lines are successfully reproduced in the model of an increased ISRF with constant abundances of 3-5x10^{-10}.Comment: 11 pages, 10 figures. Accepted for publication in A&

Subarcsecond resolution observations of warm water towards three deeply embedded low-mass protostars

Water is present during all stages of star formation: as ice in the cold outer parts of protostellar envelopes and dense inner regions of circumstellar disks, and as gas in the envelopes close to the protostars, in the upper layers of circumstellar disks and in regions of powerful outflows and shocks. In this paper we probe the mechanism regulating the warm gas-phase water abundance in the innermost hundred AU of deeply embedded (Class~0) low-mass protostars, and investigate its chemical relationship to other molecular species during these stages. Millimeter wavelength thermal emission from the para-H2-18O 3(1,3)-2(2,0) (Eu=203.7 K) line is imaged at high angular resolution (0.75"; 190 AU) with the IRAM Plateau de Bure Interferometer towards the deeply embedded low-mass protostars NGC 1333-IRAS2A and NGC 1333-IRAS4A. Compact H2-18O emission is detected towards IRAS2A and one of the components in the IRAS4A binary; in addition CH3OCH3, C2H5CN, and SO2 are detected. Extended water emission is seen towards IRAS2A, possibly associated with the outflow. The detections in all systems suggests that the presence of water on <100 AU scales is a common phenomenon in embedded protostars. We present a scenario in which the origin of the emission from warm water is in a flattened disk-like structure dominated by inward motions rather than rotation. The gas-phase water abundance varies between the sources, but is generally much lower than a canonical abundance of 10^-4, suggesting that most water (>96 %) is frozen out on dust grains at these scales. The derived abundances of CH3OCH3 and SO2 relative to H2-18O are comparable for all sources pointing towards similar chemical processes at work. In contrast, the C2H5CN abundance relative to H2-18O is significantly lower in IRAS2A, which could be due to different chemistry in the sources.Comment: 12 pages, 9 figure

The deuterium fractionation of water on solar-system scales in deeply-embedded low-mass protostars

(Abridged) The water deuterium fractionation (HDO/H$_2$O abundance ratio) has traditionally been used to infer the amount of water brought to Earth by comets. Measuring this ratio in deeply-embedded low-mass protostars makes it possible to probe the critical stage when water is transported from clouds to disks in which icy bodies are formed. We present sub-arcsecond resolution observations of HDO in combination with H$_2^{18}$O from the PdBI toward the three low-mass protostars NGC 1333-IRAS 2A, IRAS 4A-NW, and IRAS 4B. The resulting HDO/H$_2$O ratio is $7.4\pm2.1\times10^{-4}$ for IRAS 2A, $19.1\pm5.4\times10^{-4}$ for IRAS 4A-NW, and $5.9\pm1.7\times10^{-4}$ for IRAS 4B. Derived ratios agree with radiative transfer models within a factor of 2-4 depending on the source. Our HDO/H$_2$O ratios for the inner regions (where $T>100$ K) of four young protostars are only a factor of 2 higher than those found for pristine, solar system comets. These small differences suggest that little processing of water occurs between the deeply embedded stage and the formation of planetesimals and comets.Comment: 10 pages, 6 figures, accepted for publication in Astronomy and Astrophysic

Transport and reduction of nitrate in clayey till underneath forest and arable land.

Transport and reduction of nitrate in a typically macroporous clayey till were examined at variable flow rate and nitrate flux. The experiments were carried out using saturated, large diameter (0.5 m), undisturbed soil columns (LUC), from a forest and nearby agricultural sites. Transport of nitrate was controlled by flow along the macropores (fractures and biopores) in the columns. Nitrate reduction (denitrification) determined under active flow mainly followed first order reactions with half-lives (t1/2) increasing with depth (1.5–3.5 m) from 7 to 35 days at the forest site and 1–7 h at the agricultural site. Nitrate reduction was likely due to microbial degradation of accumulated organic matter coupled with successive consumption of O2 and NO3− in the macropore water followed by reductive dissolution of Fe and Mn from minerals along the macropores. Concentrations of total organic carbon measured in soil samples were near identical at the two study sites and consequently not useful as indicator for the observed differences in nitrate reduction. Instead the high reduction rates at the agricultural site were positively correlated with elevated concentration of water-soluble organic carbon and nitrate-removing bacteria relative to the forest site. After high concentrations of water-soluble organic carbon in the columns from the agricultural site were leached they lost their elevated reduction rates, which, however, was successfully re-established by infiltration of new reactive organics represented by pesticides. Simulations using a calibrated discrete fracture matrix diffusion (DFMD) model could reasonably reproduce the denitrification and resulting flux of nitrate observed during variable flow rate from the columns

Exploring the Origins of Earth's Nitrogen: Astronomical Observations of Nitrogen-bearing Organics in Protostellar Environments

It is not known whether the original carriers of Earth's nitrogen were molecular ices or refractory dust. To investigate this question, we have used data and results of Herschel observations towards two protostellar sources: the high-mass hot core of Orion KL, and the low-mass protostar IRAS 16293-2422. Towards Orion KL, our analysis of the molecular inventory of Crockett et al. (2014) indicates that HCN is the organic molecule that contains by far the most nitrogen, carrying $74_{-9}^{+5}\%$ of nitrogen-in-organics. Following this evidence, we explore HCN towards IRAS 16293-2422, which we consider a solar analog. Towards IRAS 16293-2422, we have reduced and analyzed Herschel spectra of HCN, and fit these observations against "jump" abundance models of IRAS 16293-2422's protostellar envelope. We find an inner-envelope HCN abundance $X_{\textrm{in}} = 5.9\pm0.7 \times 10^{-8}$ and an outer-envelope HCN abundance $X_{\textrm{out}} = 1.3 \pm 0.1 \times 10^{-9}$. We also find the sublimation temperature of HCN to be $T_{\textrm{jump}} = 71 \pm 3$~K; this measured $T_{\textrm{jump}}$ enables us to predict an HCN binding energy $E_{\textrm{B}}/k = 3840 \pm 140$~K. Based on a comparison of the HCN/H2O ratio in these protostars to N/H2O ratios in comets, we find that HCN (and, by extension, other organics) in these protostars is incapable of providing the total bulk N/H2O in comets. We suggest that refractory dust, not molecular ices, was the bulk provider of nitrogen to comets. However, interstellar dust is not known to have 15N enrichment, while high 15N enrichment is seen in both nitrogen-bearing ices and in cometary nitrogen. This may indicate that these 15N-enriched ices were an important contributor to the nitrogen in planetesimals and likely to the Earth.Comment: Accepted to ApJ; 21 pages, 4 figure