Monitoring Replication Protein A (RPA) Dynamics in Homologous Recombination Through Site-specific Incorporation of Non-canonical Amino Acids

An essential coordinator of all DNA metabolic processes is Replication Protein A (RPA). RPA orchestrates these processes by binding to single-stranded DNA (ssDNA) and interacting with several other DNA binding proteins. Determining the real-time kinetics of single players such as RPA in the presence of multiple DNA processors to better understand the associated mechanistic events is technically challenging. To overcome this hurdle, we utilized non-canonical amino acids and bio-orthogonal chemistry to site-specifically incorporate a chemical fluorophore onto a single subunit of heterotrimeric RPA. Upon binding to ssDNA, this fluorescent RPA (RPAf) generates a quantifiable change in fluorescence, thus serving as a reporter of its dynamics on DNA in the presence of multiple other DNA binding proteins. Using RPAf, we describe the kinetics of facilitated self-exchange and exchange by Rad51 and mediator proteins during various stages in homologous recombination. RPAf is widely applicable to investigate its mechanism of action in processes such as DNA replication, repair and telomere maintenance

Variable Hard X-ray Emission from the Candidate Accreting Black Hole in Dwarf Galaxy Henize 2-10

We present an analysis of the X-ray spectrum and long-term variability of the nearby dwarf starburst galaxy Henize 2-10. Recent observations suggest that this galaxy hosts an actively accreting black hole with mass ~10^6 M_sun. The presence of an AGN in a low-mass starburst galaxy marks a new environment for active galactic nuclei (AGNs), with implications for the processes by which "seed" black holes may form in the early Universe. In this paper, we analyze four epochs of X-ray observations of Henize 2-10, to characterize the long-term behavior of its hard nuclear emission. We analyze observations with Chandra from 2001 and XMM-Newton from 2004 and 2011, as well as an earlier, less sensitive observation with ASCA from 1997. Based on detailed analysis of the source and background, we find that the hard (2-10 keV) flux of the putative AGN has decreased by approximately an order of magnitude between the 2001 Chandra observation and exposures with XMM-Newton in 2004 and 2011. The observed variability confirms that the emission is due to a single source. It is unlikely that the variable flux is due to a supernova or ultraluminous X-ray source, based on the observed long-term behavior of the X-ray and radio emission, while the observed X-ray variability is consistent with the behavior of well-studied AGNs.Comment: 7 pages, 4 figures, 2 tables; accepted for publication in Ap

In vivo monitoring of fetoplacental Vegfr2 gene activity in a murine pregnancy model using a Vegfr2-luc reporter gene and bioluminescent imaging

<p>Abstract</p> <p>Background</p> <p>Vascular endothelial growth factor receptor-2 (VEGFR2) plays a pivotal role in angiogenesis by eliciting vascular endothelial cell growth when bound to VEGF, a powerful pro-angiogenic ligand. While Vegf and Vegfr2 are expressed throughout gestation, the latter third of gestation in mice is characterized by a marked increase in fetoplacental angiogenesis. Thus, the objective of this study was to determine the feasibility of monitoring fetoplacental Vegfr2 gene activity non-invasively using a Vegfr2-luc reporter transgenic mouse and bioluminescent imaging.</p> <p>Methods</p> <p>Imaging parameters were optimized using two wild-type (WT) females, bearing Vegfr2-luc fetuses. Then, seven WT females, bred to Vegfr2-luc males, were imaged from gestational day (GD) 12 to 18 to determine the usefulness of the Vegfr2-luc mouse as a model for studying fetoplacental Vegfr2 activity during pregnancy. Semi-quantitative RT-PCR of Vegfr2 was also performed on whole fetoplacental units during this time. Additionally, resultant neonates were imaged at postnatal day (PND) 7, 14 and 21 to monitor Vegfr2 activity during post-natal development.</p> <p>Results</p> <p>Fetoplacental Vegfr2 gene activity was detected as light emissions beginning on GD 12 of gestation and increased throughout the imaging period (P < 0.05), and this paralleled the Vegfr2 mRNA data obtained from RT-PCR analysis. A decline in fetoplacental light emissions was associated with a poor pregnancy outcome in one pregnancy, indicating that this approach has potential use for studies monitoring pregnancy well being. Additionally, neonatal Vegfr2 activity was detected at PND 7, 14 and 21 but declined with time (P < 0.0001).</p> <p>Conclusions</p> <p><it>In utero </it>fetoplacental Vegfr2 gene activity was monitored longitudinally in a quantitative manner using a luciferase reporter gene and bioluminescent imaging during the latter third of gestation. This study demonstrates the feasibility of using the Vegfr2-luc mouse to monitor late gestation fetoplacental angiogenic activity under normal and experimental conditions. Additionally, neonatal Vegfr2 gene activity was monitored for three weeks postpartum, allowing continuous monitoring of Vegfr2 activity during the latter third of gestation and postnatal development within the same animals.</p

Star Formation in Quasar Hosts and the Origin of Radio Emission in Radio-Quiet Quasars

Radio emission from radio-quiet quasars may be due to star formation in the quasar host galaxy, to a jet launched by the supermassive black hole, or to relativistic particles accelerated in a wide-angle radiatively-driven outflow. In this paper we examine whether radio emission from radio-quiet quasars is a byproduct of star formation in their hosts. To this end we use infrared spectroscopy and photometry from Spitzer and Herschel to estimate or place upper limits on star formation rates in hosts of ~300 obscured and unobscured quasars at z\u3c1. We find that low-ionization forbidden emission lines such as [NeII] and [NeIII] are likely dominated by quasar ionization and do not provide reliable star formation diagnostics in quasar hosts, while PAH emission features may be suppressed due to the destruction of PAH molecules by the quasar radiation field. While the bolometric luminosities of our sources are dominated by the quasars, the 160 micron fluxes are likely dominated by star formation, but they too should be used with caution. We estimate median star formation rates to be 6-29 Msun/year, with obscured quasars at the high end of this range. This star formation rate is insufficient to explain the observed radio emission from quasars by an order of magnitude, with log(L_radio, observed/L_radio, SF)=0.6-1.3 depending on quasar type and star formation estimator. Although radio-quiet quasars in our sample lie close to the 8-1000 micron infrared / radio correlation characteristic of the star-forming galaxies, both their infrared emission and their radio emission are dominated by the quasar activity, not by the host galaxy

An Open-Publishing Response to the COVID-19 Infodemic

The COVID-19 pandemic catalyzed the rapid dissemination of papers and preprints investigating the disease and its associated virus, SARS-CoV-2. The multifaceted nature of COVID-19 demands a multidisciplinary approach, but the urgency of the crisis combined with the need for social distancing measures present unique challenges to collaborative science. We applied a massive online open publishing approach to this problem using Manubot. Through GitHub, collaborators summarized and critiqued COVID-19 literature, creating a review manuscript. Manubot automatically compiled citation information for referenced preprints, journal publications, websites, and clinical trials. Continuous integration workflows retrieved up-to-date data from online sources nightly, regenerating some of the manuscript\u27s figures and statistics. Manubot rendered the manuscript into PDF, HTML, LaTeX, and DOCX outputs, immediately updating the version available online upon the integration of new content. Through this effort, we organized over 50 scientists from a range of backgrounds who evaluated over 1,500 sources and developed seven literature reviews. While many efforts from the computational community have focused on mining COVID-19 literature, our project illustrates the power of open publishing to organize both technical and non-technical scientists to aggregate and disseminate information in response to an evolving crisis

Deep Chandra Observations of the Compact Starburst Galaxy Henize 2–10: X-Rays from the Massive Black Hole

We present follow-up X-ray observations of the candidate massive black hole (BH) in the nucleus of the low-mass, compact starburst galaxy Henize 2–10. Using new high-resolution observations from the Chandra X-ray Observatory totaling 200 ks in duration, as well as archival Chandraobservations from 2001, we demonstrate the presence of a previously unidentified X-ray point source that is spatially coincident with the known nuclear radio source in Henize 2–10 (i.e., the massive BH). We show that the hard X-ray emission previously identified in the 2001 observation is dominated by a source that is distinct from the nucleus, with the properties expected for a high-mass X-ray binary. The X-ray luminosity of the nuclear source suggests the massive BH is radiating significantly below its Eddington limit (∼10−6 LEdd), and the soft spectrum resembles other weakly accreting massive BHs including Sagittarius A*. Analysis of the X-ray light curve of the nucleus reveals the tentative detection of a ~9 hr periodicity, although additional observations are required to confirm this result. Our study highlights the need for sensitive high-resolution X-ray observations to probe low-level accretion, which is the dominant mode of BH activity throughout the universe

Multi-Epoch Spectroscopy of Dwarf Galaxies with AGN Signatures: Identifying Sources with Persistent Broad H Α Emission

We use time-domain optical spectroscopy to distinguish between broad emission lines powered by accreting black holes (BHs) or stellar processes (i.e., supernovae) for 16 galaxies identified as AGN candidates by Reines \etal (2013). Our study is primarily focused on those objects with narrow emission-line ratios dominated by star formation. Based on follow-up spectra taken with the Magellan Echellette Spectrograph (MagE), the Dual Imaging Spectrograph, and the Ohio State Multi-Object Spectrograph, we find that the broad Hα emission has faded or was ambiguous for all of the star-forming objects (14/16) over baselines ranging from 5 to 14 years. For the two objects in our follow-up sample with narrow-line AGN signatures (RGG 9 and RGG 119), we find persistent broad Hα emission consistent with an AGN origin. Additionally, we use our MagE observations to measure stellar velocity dispersions for 15 objects in the Reines et al. (2013) sample, all with narrow-line ratios indicating the presence of an AGN. Stellar masses range from ∼5×108 to 3×109~\msun, and we measure σ∗ ranging from 28−71 km s−1. These σ∗ correspond to some of the lowest-mass galaxies with optical signatures of AGN activity. We show that RGG 119, the one object which has both a measured σ∗ and persistent broad Hα emission, falls near the extrapolation of the MBH−σ⋆ relation to the low-mass end

Multi-Epoch Spectroscopy of Dwarf Galaxies with AGN Signatures: Identifying Sources with Persistent Broad H Α Emission

We use time-domain optical spectroscopy to distinguish between broad emission lines powered by accreting black holes (BHs) or stellar processes (i.e., supernovae) for 16 galaxies identified as AGN candidates by Reines \etal (2013). Our study is primarily focused on those objects with narrow emission-line ratios dominated by star formation. Based on follow-up spectra taken with the Magellan Echellette Spectrograph (MagE), the Dual Imaging Spectrograph, and the Ohio State Multi-Object Spectrograph, we find that the broad Hα emission has faded or was ambiguous for all of the star-forming objects (14/16) over baselines ranging from 5 to 14 years. For the two objects in our follow-up sample with narrow-line AGN signatures (RGG 9 and RGG 119), we find persistent broad Hα emission consistent with an AGN origin. Additionally, we use our MagE observations to measure stellar velocity dispersions for 15 objects in the Reines et al. (2013) sample, all with narrow-line ratios indicating the presence of an AGN. Stellar masses range from ∼5×108 to 3×109~\msun, and we measure σ∗ ranging from 28−71 km s−1. These σ∗ correspond to some of the lowest-mass galaxies with optical signatures of AGN activity. We show that RGG 119, the one object which has both a measured σ∗ and persistent broad Hα emission, falls near the extrapolation of the MBH−σ⋆ relation to the low-mass end