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  1. Green plants play a fundamental role in ecosystems, human health, and agriculture. As de novo genomes are being generated for all known eukaryotic species as advocated by the Earth BioGenome Project, increasing genomic information on green land plants is essential. However, setting standards for the generation and storage of the complex set of genomes that characterize the green lineage of life is a major challenge for plant scientists. Such standards will need to accommodate the immense variation in green plant genome size, transposable element content, and structural complexity while enabling research into the molecular and evolutionary processes that have resultedmore »in this enormous genomic variation. Here we provide an overview and assessment of the current state of knowledge of green plant genomes. To date fewer than 300 complete chromosome-scale genome assemblies representing fewer than 900 species have been generated across the estimated 450,000 to 500,000 species in the green plant clade. These genomes range in size from 12 Mb to 27.6 Gb and are biased toward agricultural crops with large branches of the green tree of life untouched by genomic-scale sequencing. Locating suitable tissue samples of most species of plants, especially those taxa from extreme environments, remains one of the biggest hurdles to increasing our genomic inventory. Furthermore, the annotation of plant genomes is at present undergoing intensive improvement. It is our hope that this fresh overview will help in the development of genomic quality standards for a cohesive and meaningful synthesis of green plant genomes as we scale up for the future.« less
    Free, publicly-accessible full text available January 25, 2023
  2. ABSTRACT We study the optical gri photometric variability of a sample of 190 quasars within the SDSS Stripe 82 region that have long-term photometric coverage during ∼1998−2020 with SDSS, PanSTARRS-1, the Dark Energy Survey, and dedicated follow-up monitoring with Blanco 4m/DECam. With on average ∼200 nightly epochs per quasar per filter band, we improve the parameter constraints from a Damped Random Walk (DRW) model fit to the light curves over previous studies with 10–15 yr baselines and ≲ 100 epochs. We find that the average damping time-scale τDRW continues to rise with increased baseline, reaching a median value of ∼750 d (gmore »band) in the rest frame of these quasars using the 20-yr light curves. Some quasars may have gradual, long-term trends in their light curves, suggesting that either the DRW fit requires very long baselines to converge, or that the underlying variability is more complex than a single DRW process for these quasars. Using a subset of quasars with better-constrained τDRW (less than 20 per cent of the baseline), we confirm a weak wavelength dependence of τDRW∝λ0.51 ± 0.20. We further quantify optical variability of these quasars over days to decades time-scales using structure function (SF) and power spectrum density (PSD) analyses. The SF and PSD measurements qualitatively confirm the measured (hundreds of days) damping time-scales from the DRW fits. However, the ensemble PSD is steeper than that of a DRW on time-scales less than ∼ a month for these luminous quasars, and this second break point correlates with the longer DRW damping time-scale.« less
    Free, publicly-accessible full text available June 2, 2023
  3. Multiple gram-negative bacteria encode type III secretion systems (T3SS) that allow them to inject effector proteins directly into host cells to facilitate colonization. To be secreted, effector proteins must be at least partially unfolded to pass through the narrow needle-like channel (diameter <2 nm) of the T3SS. Fusion of effector proteins to tightly packed proteins—such as GFP, ubiquitin, or dihydrofolate reductase (DHFR)—impairs secretion and results in obstruction of the T3SS. Prior observation that unfolding can become rate-limiting for secretion has led to the model that T3SS effector proteins have low thermodynamic stability, facilitating their secretion. Here, we first show thatmore »the unfolding free energy ( Δ G unfold 0 ) of two Salmonella effector proteins, SptP and SopE2, are 6.9 and 6.0 kcal/mol, respectively, typical for globular proteins and similar to published Δ G unfold 0 for GFP, ubiquitin, and DHFR. Next, we mechanically unfolded individual SptP and SopE2 molecules by atomic force microscopy (AFM)-based force spectroscopy. SptP and SopE2 unfolded at low force ( F unfold ≤ 17 pN at 100 nm/s), making them among the most mechanically labile proteins studied to date by AFM. Moreover, their mechanical compliance is large, as measured by the distance to the transition state (Δ x ‡ = 1.6 and 1.5 nm for SptP and SopE2, respectively). In contrast, prior measurements of GFP, ubiquitin, and DHFR show them to be mechanically robust ( F unfold > 80 pN) and brittle (Δ x ‡ < 0.4 nm). These results suggest that effector protein unfolding by T3SS is a mechanical process and that mechanical lability facilitates efficient effector protein secretion.« less
  4. Abstract We present the results of an analysis of Wide-field Infrared Survey Explorer (WISE) observations of the full 2500 deg 2 South Pole Telescope (SPT)-Sunyaev–Zel’dovich cluster sample. We describe a process for identifying active galactic nuclei (AGN) in brightest cluster galaxies (BCGs) based on WISE mid-IR color and redshift. Applying this technique to the BCGs of the SPT-SZ sample, we calculate the AGN-hosting BCG fraction, which is defined as the fraction of BCGs hosting bright central AGNs over all possible BCGs. Assuming an evolving single-burst stellar population model, we find statistically significant evidence (>99.9%) for a mid-IR excess at highmore »redshift compared to low redshift, suggesting that the fraction of AGN-hosting BCGs increases with redshift over the range of 0 < z < 1.3. The best-fit redshift trend of the AGN-hosting BCG fraction has the form (1 + z ) 4.1±1.0 . These results are consistent with previous studies in galaxy clusters as well as as in field galaxies. One way to explain this result is that member galaxies at high redshift tend to have more cold gas. While BCGs in nearby galaxy clusters grow mostly by dry mergers with cluster members, leading to no increase in AGN activity, BCGs at high redshift could primarily merge with gas-rich satellites, providing fuel for feeding AGNs. If this observed increase in AGN activity is linked to gas-rich mergers rather than ICM cooling, we would expect to see an increase in scatter in the P cav versus L cool relation at z > 1. Last, this work confirms that the runaway cooling phase, as predicted by the classical cooling-flow model, in the Phoenix cluster is extremely rare and most BCGs have low (relative to Eddington) black hole accretion rates.« less
    Free, publicly-accessible full text available March 3, 2023
  5. Ras dimerization is critical for Raf activation. Here we show that the Ras binding domain of Raf (Raf-RBD) induces robust Ras dimerization at low surface densities on supported lipid bilayers and, to a lesser extent, in solution as observed by size exclusion chromatography and confirmed by SAXS. Community network analysis based on molecular dynamics simulations shows robust allosteric connections linking the two Raf-RBD D113 residues located in the Galectin scaffold protein binding site of each Raf-RBD molecule and 85 Å apart on opposite ends of the dimer complex. Our results suggest that Raf-RBD binding and Ras dimerization are concerted eventsmore »that lead to a high-affinity signaling complex at the membrane that we propose is an essential unit in the macromolecular assembly of higher order Ras/Raf/Galectin complexes important for signaling through the Ras/Raf/MEK/ERK pathway.

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  6. Abstract On 2019 August 14 at 21:10:39 UTC, the LIGO/Virgo Collaboration (LVC) detected a possible neutron star–black hole merger (NSBH), the first ever identified. An extensive search for an optical counterpart of this event, designated GW190814, was undertaken using the Dark Energy Camera on the 4 m Victor M. Blanco Telescope at the Cerro Tololo Inter-American Observatory. Target of Opportunity interrupts were issued on eight separate nights to observe 11 candidates using the 4.1 m Southern Astrophysical Research (SOAR) telescope’s Goodman High Throughput Spectrograph in order to assess whether any of these transients was likely to be an optical counterpartmore »of the possible NSBH merger. Here, we describe the process of observing with SOAR, the analysis of our spectra, our spectroscopic typing methodology, and our resultant conclusion that none of the candidates corresponded to the gravitational wave merger event but were all instead other transients. Finally, we describe the lessons learned from this effort. Application of these lessons will be critical for a successful community spectroscopic follow-up program for LVC observing run 4 (O4) and beyond.« less
    Free, publicly-accessible full text available April 1, 2023
  7. Abstract We present morphological classifications of ∼27 million galaxies from the Dark Energy Survey (DES) Data Release 1 (DR1) using a supervised deep learning algorithm. The classification scheme separates: (a) early-type galaxies (ETGs) from late-types (LTGs), and (b) face-on galaxies from edge-on. Our Convolutional Neural Networks (CNNs) are trained on a small subset of DES objects with previously known classifications. These typically have mr ≲ 17.7mag; we model fainter objects to mr < 21.5 mag by simulating what the brighter objects with well determined classifications would look like if they were at higher redshifts. The CNNs reach 97% accuracy tomore »mr < 21.5 on their training sets, suggesting that they are able to recover features more accurately than the human eye. We then used the trained CNNs to classify the vast majority of the other DES images. The final catalog comprises five independent CNN predictions for each classification scheme, helping to determine if the CNN predictions are robust or not. We obtain secure classifications for ∼ 87% and 73% of the catalog for the ETG vs. LTG and edge-on vs. face-on models, respectively. Combining the two classifications (a) and (b) helps to increase the purity of the ETG sample and to identify edge-on lenticular galaxies (as ETGs with high ellipticity). Where a comparison is possible, our classifications correlate very well with Sérsic index (n), ellipticity (ε) and spectral type, even for the fainter galaxies. This is the largest multi-band catalog of automated galaxy morphologies to date.« less
  8. Free, publicly-accessible full text available August 16, 2022