Analyses of pyrimidine and purine bases by a combination of paper chromatography and time of flight mass spectrometry

Paper chromatography and mass spectrometry for analyses of pyrimidine and purine base

ALMA twenty-six arcmin2 survey of GOODS-S at one millimeter (ASAGAO): Millimeter properties of stellar mass selected galaxies

We make use of the ASAGAO, deep 1.2 mm continuum observations of a 26 arcmin$^2$ region in the GOODS-South field obtained with ALMA, to probe dust-enshrouded star formation in $K$-band selected (i.e., stellar mass selected) galaxies, which are drawn from the ZFOURGE catalog. Based on the ASAGAO combined map, which was created by combining ASAGAO and ALMA archival data in the GOODS-South field, we find that 24 ZFOURGE sources have 1.2 mm counterparts with a signal-to-noise ratio $>$ 4.5 (1$\sigma\simeq$ 30 - 70 $\mu$Jy beam$^{-1}$ at 1.2 mm). Their median redshift is estimated to be $z_\mathrm{median}=$ 2.38 $\pm$ 0.14. They generally follow the tight relationship of the stellar mass versus star formation rate (i.e., the main sequence of star-forming galaxies). ALMA-detected ZFOURGE sources exhibit systematically larger infrared (IR) excess (IRX $\equiv L_\mathrm{IR}/L_\mathrm{UV}$) compared to ZFOURGE galaxies without ALMA detections even though they have similar redshifts, stellar masses, and star formation rates. This implies the consensus stellar-mass versus IRX relation, which is known to be tight among rest-frame-UV-selected galaxies, can not fully predict the ALMA detectability of stellar-mass-selected galaxies. We find that ALMA-detected ZFOURGE sources are the main contributors to the cosmic IR star formation rate density at $z$ = 2 - 3.Comment: Accepted for publication in PASJ. A version with a high resolution figure and ALMA fits files are available from https://sites.google.com/view/asagao26

ALMA deep field in SSA22: Blindly detected CO emitters and [C ii] emitter candidates

We report the identification of four millimeter line-emitting galaxies with the Atacama Large Milli/submillimeter Array (ALMA) in SSA22 Field (ADF22). We analyze the ALMA 1.1-mm survey data, with an effective survey area of 5 arcmin2, frequency ranges of 253.1–256.8 and 269.1–272.8 GHz, angular resolution of 0 ′′. .′′ 7 and rms noise of 0.8 mJy beam−1 at 36 km s−1 velocity resolution. We detect four line-emitter candidates with significance levels above 6σ. We identify one of the four sources as a CO(9–8) emitter at z = 3.1 in a member of the proto-cluster known in this field. Another line emitter with an optical counterpart is likely a CO(4–3) emitter at z = 0.7. The other two sources without any millimeter continuum or optical/near-infrared counterpart are likely to be [C II] emitter candidates at z = 6.0 and 6.5. The equivalent widths of the [C II] candidates are consistent with those of confirmed high-redshift [C II] emitters and candidates, and are a factor of 10 times larger than that of the CO(9–8) emitter detected in this search. The [C II] luminosity of the candidates are 4–7 × 108 L⊙. The star formation rates (SFRs) of these sources are estimated to be 10–20 M⊙ yr−1 if we adopt an empirical [C II] luminosity–SFR relation. One of them has a relatively low S/N ratio, but shows features characteristic of emission lines. Assuming that at least one of the two candidates is a [C II] emitter, we derive a lower limit of [C II]-based star formation rate density (SFRD) at z ∼ 6. The resulting value of >10−2 M⊙ yr−1 Mpc−3 is consistent with the dust-uncorrected UV-based SFRD. Future millimeter/submillimeter surveys can be used to detect a number of high-redshift line emitters, with which to study the star formation history in the early universe

Metabolism of 2-Chloro-4-Nitrophenol in a Gram Negative Bacterium, Burkholderia sp. RKJ 800

A 2-Chloro-4-nitrophenol (2C4NP) degrading bacterial strain designated as RKJ 800 was isolated from a pesticide contaminated site of India by enrichment method and utilized 2C4NP as sole source of carbon and energy. The stoichiometric amounts of nitrite and chloride ions were detected during the degradation of 2C4NP. On the basis of thin layer chromatography, high performance liquid chromatography and gas chromatography-mass spectrometry, chlorohydroquinone (CHQ) and hydroquinone (HQ) were identified as major metabolites of the degradation pathway of 2C4NP. Manganese dependent HQ dioxygenase activity was observed in the crude extract of 2C4NP induced cells of the strain RKJ 800 that suggested the cleavage of the HQ to γ-hydroxymuconic semialdehyde. On the basis of the 16S rRNA gene sequencing, strain RKJ 800 was identified as a member of genus Burkholderia. Our studies clearly showed that Burkholderia sp. RKJ 800 degraded 2-chloro-4-nitrophenol via hydroquinone pathway. The pathway identified in a gram negative bacterium, Burkholderia sp. strain RKJ 800 was differed from previously reported 2C4NP degradation pathway in another gram-negative Burkholderia sp. SJ98. This is the first report of the formation of CHQ and HQ in the degradation of 2C4NP by any gram-negative bacteria. Laboratory-scale soil microcosm studies showed that strain RKJ 800 is a suitable candidate for bioremediation of 2C4NP contaminated sites

Overexpression of podocalyxin-like protein is an independent factor of poor prognosis in colorectal cancer

Background:Podocalyxin-like 1 (PODXL) is a cell-adhesion glycoprotein and stem cell marker that has been associated with an aggressive tumour phenotype and poor prognosis in several forms of cancer. In this study, we investigated the prognostic impact of PODXL expression in colorectal cancer (CRC).Methods:Using tissue microarrays and immunohistochemistry, PODXL expression was evaluated in 536 incident CRC cases from a prospective, population-based cohort study. Kaplan-Meier analysis and Cox proportional hazards modelling were used to assess the impact of PODXL expression on cancer-specific survival (CSS) and overall survival (OS).Results:High PODXL expression was significantly associated with unfavourable clinicopathological characteristics, a shorter CSS (hazard ratio (HR)=1.98; 95% confidence interval (CI) 1.38-2.84, P<0.001) and 5-year OS (HR=1.85; 95% CI 1.29-2.64, P=0.001); the latter remaining significant in multivariate analysis (HR=1.52; 95% CI 1.03-2.25, P=0.036). In addition, in curatively resected stage III (T1-4, N1-2, M0) patients (n=122) with tumours with high PODXL expression, a significant benefit from adjuvant chemotherapy was demonstrated (p(interaction) =0.004 for CSS and 0.015 for 5-year OS in multivariate analysis).Conclusion:Podocalyxin-like 1 expression is an independent factor of poor prognosis in CRC. Our results also suggest that PODXL may be a useful marker to stratify patients for adjuvant chemotherapy

Lineage-specific distribution of high levels of genomic 5-hydroxymethylcytosine in mammalian development

Methylation of cytosine is a DNA modification associated with gene repression. Recently, a novel cytosine modification, 5-hydroxymethylcytosine (5-hmC) has been discovered. Here we examine 5-hmC distribution during mammalian development and in cellular systems, and show that the developmental dynamics of 5-hmC are different from those of 5-methylcytosine (5-mC); in particular 5-hmC is enriched in embryonic contexts compared to adult tissues. A detectable 5-hmC signal appears in pre-implantation development starting at the zygote stage, where the paternal genome is subjected to a genome-wide hydroxylation of 5-mC, which precisely coincides with the loss of the 5-mC signal in the paternal pronucleus. Levels of 5-hmC are high in cells of the inner cell mass in blastocysts, and the modification colocalises with nestin-expressing cell populations in mouse post-implantation embryos. Compared to other adult mammalian organs, 5-hmC is strongly enriched in bone marrow and brain, wherein high 5-hmC content is a feature of both neuronal progenitors and post-mitotic neurons. We show that high levels of 5-hmC are not only present in mouse and human embryonic stem cells (ESCs) and lost during differentiation, as has been reported previously, but also reappear during the generation of induced pluripotent stem cells; thus 5-hmC enrichment correlates with a pluripotent cell state. Our findings suggest that apart from the cells of neuronal lineages, high levels of genomic 5-hmC are an epigenetic feature of embryonic cell populations and cellular pluri- and multi-lineage potency. To our knowledge, 5-hmC represents the first epigenetic modification of DNA discovered whose enrichment is so cell-type specific

ALMA 26 arcmin² Survey of GOODS-S at One-millimeter (ASAGAO):X-Ray AGN Properties of Millimeter-selected Galaxies

We investigate the X-ray active galactic nucleus (AGN) properties of millimeter galaxies in the Great Observatories Origins Deep Survey South (GOODS-S) field detected with the Atacama Large Millimeter/submillimeter Array (ALMA), by utilizing the Chandra 7-Ms data, the deepest X-ray survey to date. Our millimeter galaxy sample comes from the ASAGAO survey covering 26 arcmin$^2$ (12 sources at a 1.2-mm flux-density limit of $\approx$0.6 mJy), supplemented by the deeper but narrower 1.3-mm survey of a part of the ASAGAO field by Dunlop et al.\ (2017). Fourteen out of the total 25 millimeter galaxies have Chandra counterparts. The observed AGN fractions at $z=1.5-3$ is found to be 90$^{+8}_{-19}$\% and $57^{+23}_{-25}$\% for the ultra/luminous infrared galaxies with $\log L_{\rm IR}/L_{\odot} = 12-12.8$ and $\log L_{\rm IR}/L_{\odot} = 11.5-12$, respectively. The majority ($\sim$2/3) of the ALMA and/or Herschel detected X-ray AGNs at $z=1.5-3$ appear to be star-formation dominant populations, having $L_{\rm X}$/ $L_{\rm IR}$ ratios smaller than the "simultaneous evolution" value expected from the local black-hole mass to stellar mass ($M_{\rm BH}$-$M_*$) relation. On the basis of the $L_{\rm X}$ and stellar mass relation, we infer that a large fraction of star-forming galaxies at $z=1.5-3$ have black hole masses smaller than those expected from the local $M_{\rm BH}$-$M_*$ relation. This is opposite to previous reports on luminous AGN at same redshifts detected in wider and shallower surveys, which are subject to selection biases against lower luminosity AGN. Our results are consistent with an evolutionary scenario that star formation occurs first, and an AGN-dominant phase follows later, in objects finally evolving into galaxies with classical bulges.Comment: 14 pages including 5 figures and 1 table, accepted for publication in Ap

The E. coli Anti-Sigma Factor Rsd: Studies on the Specificity and Regulation of Its Expression

Background: Among the seven different sigma factors in E. coli s 70 has the highest concentration and affinity for the core RNA polymerase. The E. coli protein Rsd is regarded as an anti-sigma factor, inhibiting s 70-dependent transcription at the onset of stationary growth. Although binding of Rsd to s 70 has been shown and numerous structural studies on Rsd have been performed the detailed mechanism of action is still unknown. Methodology/Principal Findings: We have performed studies to unravel the function and regulation of Rsd expression in vitro and in vivo. Cross-linking and affinity binding revealed that Rsd is able to interact with s 70, with the core enzyme of RNA polymerase and is able to form dimers in solution. Unexpectedly, we find that Rsd does also interact with s 38, the stationary phase-specific sigma factor. This interaction was further corroborated by gel retardation and footprinting studies with different promoter fragments and s 38-ors 70-containing RNA polymerase in presence of Rsd. Under competitive in vitro transcription conditions, in presence of both sigma factors, a selective inhibition of s 70-dependent transcription was prevailing, however. Analysis of rsd expression revealed that the nucleoid-associated proteins H-NS and FIS, StpA and LRP bind to the regulatory region of the rsd promoters. Furthermore, the major promoter P2 was shown to be down-regulated in vivo by RpoS, the stationary phase-specific sigma factor and the transcription factor DksA, while induction of the stringent control enhanced rsd promoter activity. Most notably, the dam-dependent methylation of a cluster of GATC sites turned ou

The DNA Methylome of Human Peripheral Blood Mononuclear Cells

Analysis across the genome of patterns of DNA methylation reveals a rich landscape of allele-specific epigenetic modification and consequent effects on allele-specific gene expression