Two different classes of co-occurring motif pairs found by a novel visualization method in human promoter regions

<p>Abstract</p> <p>Background</p> <p>It is essential in modern biology to understand how transcriptional regulatory regions are composed of <it>cis</it>-elements, yet we have limited knowledge of, for example, the combinational uses of these elements and their positional distribution.</p> <p>Results</p> <p>We predicted the positions of 228 known binding motifs for transcription factors in phylogenetically conserved regions within -2000 and +1000 bp of transcriptional start sites (TSSs) of human genes and visualized their correlated non-overlapping occurrences. In the 8,454 significantly correlated motif pairs, two major classes were observed: 248 pairs in Class 1 were mainly found around TSSs, whereas 4,020 Class 2 pairs appear at rather arbitrary distances from TSSs. These classes are distinct in a number of aspects. First, the positional distribution of the Class 1 constituent motifs shows a single peak near the TSSs, whereas Class 2 motifs show a relatively broad distribution. Second, genes that harbor the Class 1 pairs are more likely to be CpG-rich and to be expressed ubiquitously than those that harbor Class 2 pairs. Third, the 'hub' motifs, which are used in many different motif pairs, are different between the two classes. In addition, many of the transcription factors that correspond to the Class 2 hub motifs contain domains rich in specific amino acids; these domains may form disordered regions important for protein-protein interaction.</p> <p>Conclusion</p> <p>There exist at least two classes of motif pairs with respect to TSSs in human promoters, possibly reflecting compositional differences between promoters and enhancers. We anticipate that our visualization method may be useful for the further characterisation of promoters.</p

ELUTION BEHAVIOR OF DEPHOSPHORAZATION SLAG TO VARIOUS ACIDS AND EFFECT OF ADDITION OF AQUEOUS ALKALI TO ACID ELUATE

We recently developed a method for efficiently recovering phosphoric acid from dephosphorization slag. The most important processes in this recovery technique involve elution of the dephosphorization slag into an acid solution (acid-elution process) and the addition of an alkali to the acid eluate to form a precipitate (alkali-precipitation process). Ultimately, we settled the use of an aqueous nitric acid solution for the acid-elution step, while an aqueous ammonia solution proved to be the optimal choice to accomplish alkali precipitation. Herein, we describe the procedures used to compare the utility of nitric acid with that of hydrochloric acid, sulfuric acid, and citric acid in the acid-elution process, and describe our comparison of an aqueous sodium hydroxide with that of an aqueous ammonia in the alkali-precipitation process. Finally, we summarize our findings on the acids and alkalis that proved to be suitable for this technology

Recovery of Phosphoric Acid and Calcium Phosphate from Dephosphorization Slag

We previously reported that by adding aqueous ammonia to the nitric acid extract of dephosphorization slag, a solid with enhanced concentrations of calcium and phosphorus, could be recovered. The present study shows that a considerable amount of manganese and iron also remains, however, which creates difficulties in directly reusing the recovered solid. The recovered material was again dissolved in nitric acid and the resultant filtrate was passed through a cation exchange resin that mostly removed various cations from the yield of an aqueous phosphoric acid solution. The recovery of phosphoric acid was confirmed via 31P NMR. Furthermore, when calcium nitrate was added to this aqueous solution, calcium hydroxyapatite, which was converted to calcium phosphate after the calcination at 1073 K. Phosphoric acid, calcium hydroxyapatite, and calcium phosphate are raw materials that are used to produce various industrial products containing phosphorus, and the suggested process greatly improves the technology for recovering phosphorus-containing materials that are mostly used as fertilizer

A NuSTAR and XMM-Newton Study of the Two Most Actively Star-forming Green Pea Galaxies (SDSS J0749+3337 and SDSS J0822+2241)

We explore X-ray evidence for the presence of active galactic nuclei (AGNs) in the two most actively star-forming Green Pea galaxies (GPs), SDSS J0749+3337 and SDSS J0822+2241, which have star-formation rates (SFRs) of $123~M_\odot$ yr$^{-1}$ and $78~M_\odot$ yr$^{-1}$, respectively. The GPs have red mid-infrared (MIR) spectral energy distributions and higher 22 $\mu$m luminosities than expected from a proxy of the SFR (H$\alpha$ luminosity), consistent with hosting AGNs with 2-10 keV luminosities of $\sim10^{44}$ erg s$^{-1}$. We thus obtain and analyze the first hard ($>$ 10 keV) X-ray data observed with NuSTAR and archival XMM-Newton data below 10 keV. From the NuSTAR $\approx$20 ksec data, however, we find no significant hard X-ray emission. By contrast, soft X-ray emission with 0.5--8 keV luminosities of $\approx10^{42}$ erg s$^{-1}$ is significantly detected in both targets, which can be explained only by star formation (SF). A possible reason for the lack of clear evidence is that a putative AGN torus absorbs most of the X-ray emission. Applying a smooth-density AGN torus model, we determine minimum hydrogen column densities along the equatorial plane ($N_{\rm H}^{\rm eq}$) consistent with the non-detection. The results indicate $N_{\rm H}^{\rm eq} \gtrsim 2\times10^{24}$ cm$^{-2}$ for SDSS J0749+3337 and $N_{\rm H}^{\rm eq} \gtrsim 5\times10^{24}$ cm$^{-2}$ for SDSS J0822+2241. Therefore, the GPs may host such heavily obscured AGNs. Otherwise, no AGN exists and the MIR emission is ascribed to SF. Active SF in low-mass galaxies is indeed suggested to reproduce red MIR colors. This would imply that diagnostics based on MIR photometry data alone may misidentify such galaxies as AGNs.Comment: 12 pages, 3 tables, 5 figures, accepted for publication in Ap

Phosphorus Species Recovery Dependence on Acid Type during Dissolution-Precipitation Treatment of the Incineration Ash of Chicken Manure

In order to utilize chicken manure as a source of phosphorus, we used dissolution-precipitation treatment to recover phosphorus from the incineration ash of chicken manure (IACM), which was used as fuel to power a boiler. In order to recover useful phosphorus-containing solids from IACM, it was dissolved into aqueous solutions of either nitric acid, hydrochloric acid, or sulfuric acid to elute phosphorus together with various component elements, followed by the use of aqueous NH3 to form a precipitate containing phosphorus. In using nitric acid and hydrochloric acid, calcium phosphate species such as calcium hydroxyapatite (Ca10(PO4)6(OH)2) and monetite (CaHPO4) were obtained following the precipitation treatment. By contrast, the use of sulfuric acid resulted in the precipitation of magnesium ammonium phosphate (MAP) species such as struvite (MgNH4PO4∙6H2O) and dittmarite (MgNH4PO4∙H2O). Both the calcium phosphate and MAP species can be used as a slow-acting fertilizer containing phosphorus, while the MAP species could be simultaneously used as a slow-acting fertilizer containing nitrogen. It is noteworthy that the calcium phosphate species obtained in the present study was equivalent to phosphate rock, which is widely used as a raw material in phosphorous-based industries, and the natural sources of this material could be depleted in the near future. Though IACM has not been used effectively until now, this new resource shows promise as s viable alternative to the dwindling supply of the natural sources of phosphorus

Recovery of Phosphate Rock Equivalents from Incineration Ash of Chicken Manure by Elution-Precipitation Treatment

In order to obtain calcium phosphates - a phosphate rock equivalent - from the incineration ash of chicken manure, which is obtained from power generation systems that use the manure for fuel, incineration ash was treated with an aqueous solution of nitric acid to elute phosphorus. By using 0.3 M of HNO3, most of the phosphorus could be eluted from 1.0 g of ash within 0.1 h. Compared with the composted chicken manure that was previously examined in our laboratory, the concentration of HNO3 was increased for this session of elution. Using the incineration ash of chicken manure made it possible to remove inorganic species at a lower boiling or sublimation temperature, and organic species by calcination in the power generation system. Compared with composted chicken manure, the concentrations of phosphorus contained in the incineration ash and the nitric acid extract were higher in the incineration ash. XRD analysis showed that the obtained nitric acid extract could be treated with aqueous NH3 to form a precipitation of poorly-crystallized calcium hydroxyapatite (Ca10(PO4)6(OH)2), which is one of main components in phosphate rock. In order to confirm the formation and purity of calcium phosphate species, the precipitation calcination was conducted at 1,078 K for 5 h. XRD revealed that the calcined solid was tricalcium phosphate, and no contamination was evident. These results reveal that a phosphate rock equivalent could be easily obtained from the incineration ash of chicken manure, which means that approximately 14% of the phosphate rock that is currently being imported into Japan could be replaced by this product

Ratio of black hole to galaxy mass of an extremely red dust-obscured galaxy at z = 2.52

We present a near-infrared (NIR) spectrum of WISE J1042+1641, an extremely red dust-obscured galaxy (DOG), which has been observed with the LIRIS on the 4.2m William Hershel Telescope. This object was selected as a hyper-luminous DOG candidate at z ~ 2 by combining the optical and IR photometric data based on the SDSS and WISE, although its redshift had not yet been confirmed. Based on the LIRIS observation, we confirmed its redshift of 2.521 and total IR luminosity of log(L_IR/L_sun) = 14.57, which satisfies the criterion for an extremely luminous IR galaxy (ELIRG). Moreover, we indicate that this object seems to have an extremely massive black hole with M_BH = 10^10.92 M_sun based on the broad Halpha line: the host stellar mass is derived as M_star = 10^13.55 M_sun by a fit of the spectral energy distribution. Very recently, it has been reported that this object is an anomalous gravitationally lensed quasar based on near-IR high-resolution imaging data obtained with the Hubble Space Telescope. Its magnification factor has also been estimated with some uncertainty (i.e., mu = 53-122). We investigate the ratio of the black hole to galaxy mass, which is less strongly affected by a lensing magnification factor, instead of the absolute values of the luminosities and masses. We find that the M_BH/M_star ratio (i.e., 0.0140-0.0204) is significantly higher than the local relation, following a sequence of unobscured quasars instead of obscured objects (e.g., submillimeter galaxies) at the same redshift. Moreover, the LIRIS spectrum shows strongly blueshifted oxygen lines with an outflowing velocity of ~ 1100 km/s, and our Swift X-ray observation also supports that this source is an absorbed AGN with an intrinsic column density of N_H = 4.9 x 10^23 cm^-2. These results imply that WISE J1042+1641 is in a blow-out phase at the end of the buried rapid black hole growth.Comment: 6 pages, 4 figures, accepted for publication in A&

Intrinsic Promoter Activities of Primary DNA Sequences in the Human Genome

In order to understand an overview of promoter activities intrinsic to primary DNA sequences in the human genome within a particular cell type, we carried out systematic quantitative luciferase assays of DNA fragments corresponding to putative promoters for 472 human genes which are expressed in HEK (human embryonic kidney epithelial) 293 cells. We observed the promoter activities of them were distributed in a bimodal manner; putative promoters belonging to the first group (with strong promoter activities) were designated as P1 and the latter (with weak promoter activities) as P2. The frequencies of the TATA-boxes, the CpG islands, and the overall G + C-contents were significantly different between these two populations, indicating there are two separate groups of promoters. Interestingly, similar analysis using 251 randomly isolated genomic DNA fragments showed that P2-type promoter occasionally occurs within the human genome. Furthermore, 35 DNA fragments corresponding to putative promoters of non-protein-coding transcripts (ncRNAs) shared similar features with the P2 in both promoter activities and sequence compositions. At least, a part of ncRNAs, which have been massively identified by full-length cDNA projects with no functional relevance inferred, may have originated from those sporadic promoter activities of primary DNA sequences inherent to the human genome