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Kress, W. John; Soltis, Douglas E.; Kersey, Paul J.; Wegrzyn, Jill L.; Leebens-Mack, James H.; Gostel, Morgan R.; Liu, Xin; Soltis, Pamela S.(
, Proceedings of the National Academy of Sciences)
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
LeBlanc, Marc-André; Fink, Morgan R.; Perkins, Thomas T.; Sousa, Marcelo C.(
, Proceedings of the National Academy of Sciences)
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
Stone, Zachary; Shen, Yue; Burke, Colin J; Chen, Yu-Ching; Yang, Qian; Liu, Xin; Gruendl, R A; Adamów, M; Andrade-Oliveira, F; Annis, J; et al(
, Monthly Notices of the Royal Astronomical Society)
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
Mau, S.; Nadler, E. O.; Wechsler, R. H.; Drlica-Wagner, A.; Bechtol, K.; Green, G.; Huterer, D.; Li, T. S.; Mao, Y.-Y.; Martínez-Vázquez, C. E.; et al(
, The Astrophysical Journal)
Abstract We use a recent census of the Milky Way (MW) satellite galaxy population to constrain the lifetime of particle dark matter (DM). We consider two-body decaying dark matter (DDM) in which a heavy DM particle decays with lifetime τ comparable to the age of the universe to a lighter DM particle (with mass splitting ϵ ) and to a dark radiation species. These decays impart a characteristic “kick velocity,” V kick = ϵ c , on the DM daughter particles, significantly depleting the DM content of low-mass subhalos and making them more susceptible to tidal disruption. We fit themore »suppression of the present-day DDM subhalo mass function (SHMF) as a function of τ and V kick using a suite of high-resolution zoom-in simulations of MW-mass halos, and we validate this model on new DDM simulations of systems specifically chosen to resemble the MW. We implement our DDM SHMF predictions in a forward model that incorporates inhomogeneities in the spatial distribution and detectability of MW satellites and uncertainties in the mapping between galaxies and DM halos, the properties of the MW system, and the disruption of subhalos by the MW disk using an empirical model for the galaxy–halo connection. By comparing to the observed MW satellite population, we conservatively exclude DDM models with τ < 18 Gyr (29 Gyr) for V kick = 20 kms −1 (40 kms −1 ) at 95% confidence. These constraints are among the most stringent and robust small-scale structure limits on the DM particle lifetime and strongly disfavor DDM models that have been proposed to alleviate the Hubble and S 8 tensions.« less
Free, publicly-accessible full text available June 1, 2023
Akhazhanov, A; More, A; Amini, A; Hazlett, C; Treu, T; Birrer, S; Shajib, A; Liao, K; Lemon, C; Agnello, A; et al(
, Monthly Notices of the Royal Astronomical Society)
ABSTRACT Strongly lensed quadruply imaged quasars (quads) are extraordinary objects. They are very rare in the sky and yet they provide unique information about a wide range of topics, including the expansion history and the composition of the Universe, the distribution of stars and dark matter in galaxies, the host galaxies of quasars, and the stellar initial mass function. Finding them in astronomical images is a classic ‘needle in a haystack’ problem, as they are outnumbered by other (contaminant) sources by many orders of magnitude. To solve this problem, we develop state-of-the-art deep learning methods and train them on realisticmore »simulated quads based on real images of galaxies taken from the Dark Energy Survey, with realistic source and deflector models, including the chromatic effects of microlensing. The performance of the best methods on a mixture of simulated and real objects is excellent, yielding area under the receiver operating curve in the range of 0.86–0.89. Recall is close to 100 per cent down to total magnitude i ∼ 21 indicating high completeness, while precision declines from 85 per cent to 70 per cent in the range i ∼ 17–21. The methods are extremely fast: training on 2 million samples takes 20 h on a GPU machine, and 108 multiband cut-outs can be evaluated per GPU-hour. The speed and performance of the method pave the way to apply it to large samples of astronomical sources, bypassing the need for photometric pre-selection that is likely to be a major cause of incompleteness in current samples of known quads.« less
Free, publicly-accessible full text available May 5, 2023
Drlica-Wagner, A.; Ferguson, P. S.; Adamów, M.; Aguena, M.; Allam, S.; Andrade-Oliveira, F.; Bacon, D.; Bechtol, K.; Bell, E. F.; Bertin, E.; et al(
, The Astrophysical Journal Supplement Series)
Abstract We present the second public data release (DR2) from the DECam Local Volume Exploration survey (DELVE). DELVE DR2 combines new DECam observations with archival DECam data from the Dark Energy Survey, the DECam Legacy Survey, and other DECam community programs. DELVE DR2 consists of ∼160,000 exposures that cover >21,000 deg 2 of the high-Galactic-latitude (∣ b ∣ > 10°) sky in four broadband optical/near-infrared filters ( g , r , i , z ). DELVE DR2 provides point-source and automatic aperture photometry for ∼2.5 billion astronomical sources with a median 5 σ point-source depth of g = 24.3, rmore »= 23.9, i = 23.5, and z = 22.8 mag. A region of ∼17,000 deg 2 has been imaged in all four filters, providing four-band photometric measurements for ∼618 million astronomical sources. DELVE DR2 covers more than 4 times the area of the previous DELVE data release and contains roughly 5 times as many astronomical objects. DELVE DR2 is publicly available via the NOIRLab Astro Data Lab science platform.« less
Free, publicly-accessible full text available August 1, 2023
Packer, Morgan R.; Parker, Jillian A.; Chung, Jean K.; Li, Zhenlu; Lee, Young Kwang; Cookis, Trinity; Guterres, Hugo; Alvarez, Steven; Hossain, Md Amin; Donnelly, Daniel P.; et al(
, Proceedings of the National Academy of Sciences)
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.
Somboonpanyakul, T.; McDonald, M.; Noble, A.; Aguena, M.; Allam, S.; Amon, A.; Andrade-Oliveira, F.; Bacon, D.; Bayliss, M. B.; Bertin, E.; et al(
, The Astronomical Journal)
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
