Inositol hexakisphosphate (IP6) potently stimulates HIV-1 particle assembly in vitro and infectious particle production in vivo. However, knockout cells lacking inositol-pentakisphosphate 2-kinase ...(IPPK-KO), the enzyme that produces IP6 by phosphorylation of inositol pentakisphosphate (IP5), were still able to produce infectious HIV-1 particles at a greatly reduced rate. HIV-1 in vitro assembly can also be stimulated to a lesser extent with IP5, but until recently, it was not known if IP5 could also function in promoting assembly in vivo. Here we addressed whether there is an absolute requirement for IP6 or IP5 in the production of infectious HIV-1 particles. IPPK-KO cells expressed no detectable IP6 but elevated IP5 levels and displayed a 20-100-fold reduction in infectious particle production, correlating with lost virus release. Transient transfection of an IPPK expression vector stimulated infectious particle production and release in IPPK-KO but not wildtype cells. Several attempts to make IP6/IP5 deficient stable cells were not successful, but transient expression of the enzyme multiple inositol polyphosphate phosphatase-1 (MINPP1) into IPPK-KOs resulted in near ablation of IP6 and IP5. Under these conditions, we found that HIV-1 infectious particle production and virus release were essentially abolished (1000-fold reduction) demonstrating an IP6/IP5 requirement. However, other retroviruses including a Gammaretrovirus, a Betaretrovirus, and two non-primate Lentiviruses displayed only a modest (3-fold) reduction in infectious particle production from IPPK-KOs and were not significantly altered by expression of IPPK or MINPP1. The only other retrovirus found to show a clear IP6/IP5 dependence was the primate (macaque) Lentivirus Simian Immunodeficiency Virus, which displayed similar sensitivity as HIV-1. We were not able to determine if producer cell IP6/IP5 is required at additional steps beyond assembly because viral particles devoid of both molecules could not be generated. Finally, we found that loss of IP6/IP5 in viral target cells had no effect on permissivity to HIV-1 infection.
During retroviral replication, unspliced viral genomic RNA (gRNA) must escape the nucleus for translation into viral proteins and packaging into virions. "Complex" retroviruses, such as human ...immunodeficiency virus (HIV), use
-acting elements on the unspliced gRNA in conjunction with
-acting viral proteins to facilitate this escape. "Simple" retroviruses, such as Mason-Pfizer monkey virus (MPMV) and murine leukemia virus (MLV), exclusively use
-acting elements on the gRNA in conjunction with host nuclear export proteins for nuclear escape. Uniquely, the simple retrovirus Rous sarcoma virus (RSV) has a Gag structural protein that cycles through the nucleus prior to plasma membrane binding. This trafficking has been implicated in facilitating gRNA nuclear export and is thought to be a required mechanism. Previously described mutants that abolish nuclear cycling displayed enhanced plasma membrane binding, enhanced virion release, and a significant loss in genome incorporation resulting in loss of infectivity. Here, we describe a nuclear cycling-deficient RSV Gag mutant that has similar plasma membrane binding and genome incorporation to wild-type (WT) virus and surprisingly is replication competent, albeit with a slower rate of spread than observed in WT virus. This mutant suggests that RSV Gag nuclear cycling is not strictly required for RSV replication.
While mechanisms for retroviral Gag assembly at the plasma membrane are beginning to be characterized, characterization of intermediate trafficking locales remain elusive. This is in part due to the difficulty of tracking individual proteins from translation to plasma membrane binding. Rous sarcoma virus (RSV) Gag nuclear cycling is a unique phenotype that may provide comparative insight to viral trafficking evolution and may present a model intermediate to
- and
-acting mechanisms for gRNA export.
Abstract
Measurements of the star formation efficiency (SFE) of giant molecular clouds (GMCs) in the Milky Way generally show a large scatter, which could be intrinsic or observational. We use ...magnetohydrodynamic simulations of GMCs (including feedback) to forward-model the relationship between the true GMC SFE and observational proxies. We show that individual GMCs trace broad ranges of observed SFE throughout collapse, star formation, and disruption. Low measured SFEs (${\ll} 1\hbox{ per cent}$) are ‘real’ but correspond to early stages; the true ‘per-freefall’ SFE where most stars actually form can be much larger. Very high (${\gg} 10\hbox{ per cent}$) values are often artificially enhanced by rapid gas dispersal. Simulations including stellar feedback reproduce observed GMC-scale SFEs, but simulations without feedback produce 20× larger SFEs. Radiative feedback dominates among mechanisms simulated. An anticorrelation of SFE with cloud mass is shown to be an observational artefact. We also explore individual dense ‘clumps’ within GMCs and show that (with feedback) their bulk properties agree well with observations. Predicted SFEs within the dense clumps are ∼2× larger than observed, possibly indicating physics other than feedback from massive (main-sequence) stars is needed to regulate their collapse.
Ionizing radiation-induced tissue damage recruits monocytes into the exposed area where they are differentiated to macrophages. These implement phagocytic removal of dying cells and elicit an acute ...inflammatory response, but can also facilitate tumorigenesis due to production of anti-inflammatory cytokines. Using primary human monocyte-derived macrophages (MDMs) and the THP1 monocytic cell line, we demonstrate that gamma radiation triggers monocyte differentiation toward the macrophage phenotype with increased expression of type I interferons (IFN-I) and both pro- and anti-inflammatory macrophage activation markers. We found that these changes correlate with significantly upregulated expression of 622 retroelements from various groups, particularly of several clades of human endogenous retroviruses (HERVs). Elevated transcription was detected in both sense and antisense directions in the HERV subgroups tested, including the most genetically homogeneous clade HML-2. The level of antisense transcription was three- to five-fold higher than of the sense strand levels. Using a proximity ligation assay and immunoprecipitation followed by RNA quantification, we identified an increased amount of the dsRNA receptors MDA-5 and TLR3 bound to an equivalent number of copies of sense and antisense chains of HERVK HML-2 RNA. This binding triggered MAVS-associated signaling pathways resulting in increased expression of IFN-I and inflammation related genes that enhanced the cumulative inflammatory effect of radiation-induced senescence. HML-2 knockdown was accompanied with reduced expression and secretion of IFNα, pro-inflammatory (IL-1β, IL-6, CCL2, CCL3, CCL8, and CCL20) and anti-inflammatory (IL10) modulators in irradiated monocytes and MDMs. Taken together, our data indicate that radiation stress-induced HERV expression enhances the IFN-I and cytokine response and results in increased levels of pro-inflammatory modulators along with expression of anti-inflammatory factors associated with the macrophage tumorigenic phenotype.
We measure the mass function for a sample of 840 young star clusters with ages between 10 and 300 Myr observed by the Panchromatic Hubble Andromeda Treasury (PHAT) survey in M31. The data show clear ...evidence of a high-mass truncation: only 15 clusters more massive than are observed, compared to the ∼100 expected for a canonical pure power-law mass function with the same total number of clusters above the catalog completeness limit. Adopting a Schechter function parameterization, we fit a characteristic truncation mass of M☉. Although previous studies have measured cluster mass function truncations, the characteristic truncation mass we measure is the lowest ever reported. Combining this M31 measurement with previous results, we find that the cluster mass function truncation correlates strongly with the characteristic star formation rate surface density of the host galaxy, where . We also find evidence that suggests the observed Mc- relation also applies to globular clusters, linking the two populations via a common formation pathway. If so, globular cluster mass functions could be useful tools for constraining the star formation properties of their progenitor host galaxies in the early universe.
We present a study of the three-dimensional (3D) structure of the Large Magellanic Cloud (LMC) using ∼2.2 million red clump (RC) stars selected from the Survey of the MAgellanic Stellar History. To ...correct for line-of-sight dust extinction, the intrinsic RC color and magnitude and their radial dependence are carefully measured by using internal nearly dust-free regions. These are then used to construct an accurate 2D reddening map (165 deg2 area with ∼10′ resolution) of the LMC disk and the 3D spatial distribution of RC stars. An inclined disk model is fit to the 2D distance map, yielding a best-fit inclination angle degrees with random errors of 0 19 and line-of-nodes position angle degrees with random errors of 0 49. These angles vary with galactic radius, indicating that the LMC disk is warped and twisted likely due to the repeated tidal interactions with the Small Magellanic Cloud (SMC). For the first time, our data reveal a significant warp in the southwestern part of the outer disk starting at ∼ 7° that departs from the defined LMC plane up to ∼4 kpc toward the SMC, suggesting that it originated from a strong interaction with the SMC. In addition, the inner disk encompassing the off-centered bar appears to be tilted up to 5°-15° relative to the rest of the LMC disk. These findings on the outer warp and the tilted bar are consistent with the predictions from the Besla et al. simulation of a recent direct collision with the SMC.
The dust-to-metals ratio describes the fraction of heavy elements contained in dust grains, and its variation provides key insights into the life cycle of dust. We measure the dust-to-metals ratio in ...M101, a nearby galaxy with a radial metallicity (Z) gradient spanning ∼1 dex. We fit the spectral energy distribution of dust from 100 to 500 m with five variants of the modified blackbody dust emission model in which we vary the temperature distribution and how emissivity depends on wavelength. Among them, the model with a single-temperature blackbody modified by a broken power-law emissivity gives the statistically best fit and physically most plausible results. Using these results, we show that the dust-to-gas ratio is proportional to . This implies that the dust-to-metals ratio is not constant in M101, but decreases as a function of radius, which is equivalent to a lower fraction of metals trapped in dust at low metallicity (large radius). The dust-to-metals ratio in M101 remains at or above what would be predicted by the minimum depletion level of metals observed in the Milky Way. Our current knowledge of the metallicity-dependent CO-to-H2 conversion factor suggests that variations in the conversion factor cannot be responsible for the trends in dust-to-metals ratio we observe. This change of dust-to-metals ratio is significantly correlated with the mass fraction of molecular hydrogen, which suggests that the accretion of gas-phase metals onto existing dust grains could contribute to a variable dust-to-metals ratio.
Retrovirus assembly is driven by the multidomain structural protein Gag. Interactions between the capsid domains (CA) of Gag result in Gag multimerization, leading to an immature virus particle that ...is formed by a protein lattice based on dimeric, trimeric, and hexameric protein contacts. Among retroviruses the inter- and intra-hexamer contacts differ, especially in the N-terminal sub-domain of CA (CANTD). For HIV-1 the cellular molecule inositol hexakisphosphate (IP6) interacts with and stabilizes the immature hexamer, and is required for production of infectious virus particles. We have used in vitro assembly, cryo-electron tomography and subtomogram averaging, atomistic molecular dynamics simulations and mutational analyses to study the HIV-related lentivirus equine infectious anemia virus (EIAV). In particular, we sought to understand the structural conservation of the immature lentivirus lattice and the role of IP6 in EIAV assembly. Similar to HIV-1, IP6 strongly promoted in vitro assembly of EIAV Gag proteins into virus-like particles (VLPs), which took three morphologically highly distinct forms: narrow tubes, wide tubes, and spheres. Structural characterization of these VLPs to sub-4Å resolution unexpectedly showed that all three morphologies are based on an immature lattice with preserved key structural components, highlighting the structural versatility of CA to form immature assemblies. A direct comparison between EIAV and HIV revealed that both lentiviruses maintain similar immature interfaces, which are established by both conserved and non-conserved residues. In both EIAV and HIV-1, IP6 regulates immature assembly via conserved lysine residues within the CACTD and SP. Lastly, we demonstrate that IP6 stimulates in vitro assembly of immature particles of several other retroviruses in the lentivirus genus, suggesting a conserved role for IP6 in lentiviral assembly.
Abstract
We present analysis using a citizen science campaign to improve the cosmological measures from the Hobby–Eberly Telescope Dark Energy Experiment (HETDEX). The goal of HETDEX is to measure ...the Hubble expansion rate,
H
(
z
), and angular diameter distance,
D
A
(
z
), at
z
= 2.4, each to percent-level accuracy. This accuracy is determined primarily from the total number of detected Ly
α
emitters (LAEs), the false positive rate due to noise, and the contamination due to O
ii
emitting galaxies. This paper presents the citizen science project, Dark Energy Explorers (
https://www.zooniverse.org/projects/erinmc/dark-energy-explorers
), with the goal of increasing the number of LAEs and decreasing the number of false positives due to noise and the O
ii
galaxies. Initial analysis shows that citizen science is an efficient and effective tool for classification most accurately done by the human eye, especially in combination with unsupervised machine learning. Three aspects from the citizen science campaign that have the most impact are (1) identifying individual problems with detections, (2) providing a clean sample with 100% visual identification above a signal-to-noise cut, and (3) providing labels for machine-learning efforts. Since the end of 2022, Dark Energy Explorers has collected over three and a half million classifications by 11,000 volunteers in over 85 different countries around the world. By incorporating the results of the Dark Energy Explorers, we expect to improve the accuracy on the
D
A
(
z
) and
H
(
z
) parameters at
z
= 2.″4 by 10%–30%. While the primary goal is to improve on HETDEX, Dark Energy Explorers has already proven to be a uniquely powerful tool for science advancement and increasing accessibility to science worldwide.
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