Viral Ejection Proteins: Mosaically Conserved, Conformational Gymnasts

Bacterial viruses (or bacteriophages) have developed formidable ways to deliver their genetic information inside bacteria, overcoming the complexity of the bacterial-cell envelope. In short-tailed phages of the Podoviridae superfamily, genome ejection is mediated by a set of mysterious internal virion proteins, also called ejection or pilot proteins, which are required for infectivity. The ejection proteins are challenging to study due to their plastic structures and transient assembly and have remained less characterized than classical components such as the phage coat protein or terminase subunit. However, a spate of recent cryo-EM structures has elucidated key features underscoring these proteins’ assembly and conformational gymnastics that accompany their expulsion from the virion head through the portal protein channel into the host. In this review, we will use a phage-T7-centric approach to critically review the status of the literature on ejection proteins, decipher the conformational changes of T7 ejection proteins in the pre- and post-ejection conformation, and predict the conservation of these proteins in other Podoviridae. The challenge is to relate the structure of the ejection proteins to the mechanisms of genome ejection, which are exceedingly complex and use the host’s machiner

Nesting Ecology of Greater Sage-Grouse Centrocercus urophasianus at the Eastern Edge of their Historic Distribution

Greater sage-grouse Centrocercus urophasianus populations in North Dakota declined approximately 67% between 1965 and 2003, and the species is listed as a Priority Level 1 Species of Special Concern by the North Dakota Game and Fish Department. The habitat and ecology of the species at the eastern edge of its historical range is largely unknown. We investigated nest site selection by greater sage-grouse and nest survival in North Dakota during 2005 - 2006. Sage-grouse selected nest sites in sagebrush Artemisia spp. with more total vegetative cover, greater sagebrush density, and greater 1-m visual obstruction from the nest than at random sites. Height of grass and shrub (sagebrush) at nest sites were shorter than at random sites, because areas where sagebrush was common were sites in low seral condition or dense clay or clay-pan soils with low productivity. Constant survival estimates of incubated nests were 33% in 2005 and 30% in 2006. Variables that described the resource selection function for nests were not those that modeled nest survival. Nest survival was positively influenced by percentage of shrub (sagebrush) cover and grass height. Daily nest survival decreased substantially when percentage of shrub cover declined below about 9% and when grass heights were less than about 16 cm. Daily nest survival rates decreased with increased daily precipitation

Pervasive remagnetization of detrital zircon host rocks in the Jack Hills, Western Australia and implications for records of the early geodynamo

It currently is unknown when Earth's dynamo magnetic field originated. Paleomagnetic studies indicate that a field with an intensity similar to that of the present day existed 3.5 billion years ago (Ga). Detrital zircon crystals found in the Jack Hills of Western Australia are some of the very few samples known to substantially predate this time. With crystallization ages ranging from 3.0–4.38 Ga, these zircons might preserve a record of the missing first billion years of Earth's magnetic field history. However, a key unknown is the age and origin of magnetization in the Jack Hills zircons. The identification of >3.9 Ga (i.e., Hadean) field records requires first establishing that the zircons have avoided remagnetization since being deposited in quartz-rich conglomerates at 2.65–3.05 Ga. To address this issue, we have conducted paleomagnetic conglomerate, baked contact, and fold tests in combination with U–Pb geochronology to establish the timing of the metamorphic and alteration events and the peak temperatures experienced by the zircon host rocks. These tests include the first conglomerate test directly on the Hadean-zircon bearing conglomerate at Erawandoo Hill. Although we observed little evidence for remagnetization by recent lightning strikes, we found that the Hadean zircon-bearing rocks and surrounding region have been pervasively remagnetized, with the final major overprinting likely due to thermal and/or aqueous effects from the emplacement of the Warakurna large igneous province at ∼1070 million years ago (Ma). Although localized regions of the Jack Hills might have escaped complete remagnetization, there currently is no robust evidence for pre-depositional (>3.0 Ga) magnetization in the Jack Hills detrital zircons

DSM-5 insomnia disorder in pregnancy: associations with depression, suicidal ideation, and cognitive and somatic arousal, and identifying clinical cutoffs for detection

STUDY OBJECTIVES: The study had three primary goals. First, we estimated survey-assessed DSM-5 insomnia disorder rates in pregnancy, and described associated sociodemographics, and sleep-wake and mental health symptoms. Second, we derived cutoffs for detecting DSM-5 insomnia disorder using common self-report measures of sleep symptoms. Third, we identified clinically relevant cut-points on measures of nocturnal cognitive and somatic arousal. METHODS: Ninety-nine women (85.9% in the 2nd trimester) completed online surveys including DSM-5 insomnia disorder criteria, the Insomnia Severity Index (ISI), Pittsburgh Sleep Quality Index (PSQI), Presleep Arousal Scale’s Cognitive (PSASC) and Somatic (PSASS) factors, and Edinburgh Postnatal Depression Scale. RESULTS: DSM-5 insomnia disorder rate was 19.2%. Insomnia was associated with depression, suicidality, nocturnal cognitive and somatic arousal, and daytime sleepiness. An ISI scoring method that aligns with DSM-5 criteria yielded excellent metrics for detecting insomnia disorder and good sleep. Regarding quantitative cutoffs, ISI ≥ 10 and ISI ≥ 11 (but not ISI ≥ 15) were supported for detecting DSM-5 insomnia, whereas ISI ≤ 7 and ISI ≤ 9 performed well for detecting good sleep. PSQI cutoff of 5 was supported for detecting insomnia and good sleep. The optimal cutoff for nocturnal cognitive arousal was PSASC ≥ 18, whereas the optimal cutoff for somatic arousal was PSASS ≥ 13. CONCLUSIONS: Insomnia disorder affects a large segment of pregnant women. Empirically derived cutoffs for insomnia, good sleep, cognitive arousal, and somatic arousal may inform case identification and future perinatal sleep research methodology

Biophysical analysis of Pseudomonas-phage PaP3 small terminase suggests a mechanism for sequence-specific DNA-binding by lateral interdigitation.

The genome packaging motor of tailed bacteriophages and herpesviruses is a powerful nanomachine built by several copies of a large (TerL) and a small (TerS) terminase subunit. The motor assembles transiently at the portal vertex of an empty precursor capsid (or procapsid) to power genome encapsidation. Terminase subunits have been studied in-depth, especially in classical bacteriophages that infect Escherichia coli or Salmonella, yet, less is known about the packaging motor of Pseudomonas-phages that have increasing biomedical relevance. Here, we investigated the small terminase subunit from three Podoviridae phages that infect Pseudomonas aeruginosa. We found TerS is polymorphic in solution but assembles into a nonamer in its high-affinity heparin-binding conformation. The atomic structure of Pseudomonas phage PaP3 TerS, the first complete structure for a TerS from a cos phage, reveals nine helix-turn-helix (HTH) motifs asymmetrically arranged around a β-stranded channel, too narrow to accommodate DNA. PaP3 TerS binds DNA in a sequence-specific manner in vitro. X-ray scattering and molecular modeling suggest TerS adopts an open conformation in solution, characterized by dynamic HTHs that move around an oligomerization core, generating discrete binding crevices for DNA. We propose a model for sequence-specific recognition of packaging initiation sites by lateral interdigitation of DNA

A Consistently High‐Latitude South China From 820 to 780 Ma: implications for Exclusion From Rodinia and the Feasibility of Large‐Scale True Polar Wander

The Tonian supercontinent Rodinia is hypothesized to have included almost all Proterozoic continental blocks. Competing models variably place South China at the core or periphery of Rodinia or separated from it entirely. Tonian paleogeographic models also vary in whether they incorporate hypothesized large and rapid oscillatory true polar wander associated with the ca. 810–795 Ma Bitter Springs Stage. Here, we present paleomagnetic data paired with U-Pb chemical abrasion isotope dilution thermal ionization mass spectrometry zircon geochronology from the Tonian Xiajiang Group in South China to establish the craton's position and test the Bitter Springs Stage true polar wander hypothesis. Fine-grained siliciclastic sediments and ashes of the Xiajiang Group post-date the Jiangnan Orogeny, which united the Yangtze and Cathaysia blocks. A U-Pb zircon date of 815.73 ± 0.18 Ma from a tuff near the base of the Xiajiang Group constrains the Jiangnan Orogeny to have ended between ca. 830 and 816 Ma. The paleomagnetic and geochronologic data constrain South China to high latitudes ca. 813 Ma and indicate a relatively stable high-latitude position from ca. 821 to 805 Ma. These high-latitude constraints either connect the craton to Rodinia along its periphery or disconnect it from the supercontinent entirely. The difference in pole position between the pre-Bitter Springs Stage Xiajiang Group pole and the syn-Bitter Springs Stage Madiyi Formation pole is significantly less than that predicted for the Bitter Springs Stage true polar wander hypothesis. If this pole difference is interpreted as true polar wander superimposed upon differential plate motion, it requires South China to have been separate from Rodinia

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey: measuring structure growth using passive galaxies

We explore the benefits of using a passively evolving population of galaxies to measure the evolution of the rate of structure growth between z=0.25 and z=0.65 by combining data from the SDSS-I/II and SDSS-III surveys. The large-scale linear bias of a population of dynamically passive galaxies, which we select from both surveys, is easily modeled. Knowing the bias evolution breaks degeneracies inherent to other methodologies, and decreases the uncertainty in measurements of the rate of structure growth and the normalization of the galaxy power-spectrum by up to a factor of two. If we translate our measurements into a constraint on sigma_8(z=0) assuming a concordance cosmological model and General Relativity (GR), we find that using a bias model improves our uncertainty by a factor of nearly 1.5. Our results are consistent with a flat Lambda Cold Dark Matter model and with GR.Comment: Accepted for publication in MNRAS (clarifications added, results and conclusions unchanged

The role of CDC48 in the retro-translocation of non-ubiquitinated toxin substrates in plant cells

When the catalytic A subunits of the castor bean toxins ricin and Ricinus communis agglutinin (denoted as RTA and RCA A, respectively) are delivered into the endoplasmic reticulum (ER) of tobacco protoplasts, they become substrates for ER-associated protein degradation (ERAD). As such, these orphan polypeptides are retro-translocated to the cytosol, where a significant proportion of each protein is degraded by proteasomes. Here we begin to characterise the ERAD pathway in plant cells, showing that retro-translocation of these lysine-deficient glycoproteins requires the ATPase activity of cytosolic CDC48. Lysine polyubiquitination is not obligatory for this step. We also show that while RCA A is found in a mannose-untrimmed form prior to its retro-translocation, a significant proportion of newly synthesised RTA cycles via the Golgi and becomes modified by downstream glycosylation enzymes. Despite these differences, both proteins are similarly retro-translocated

The clustering of galaxies in the SDSS-III Baryon Oscillation Spectroscopic Survey : baryon acoustic oscillations in the Data Releases 10 and 11 Galaxy samples

We present a one per cent measurement of the cosmic distance scale from the detections of the baryon acoustic oscillations (BAO) in the clustering of galaxies from the Baryon Oscillation Spectroscopic Survey, which is part of the Sloan Digital Sky Survey III. Our results come from the Data Release 11 (DR11) sample, containing nearly one million galaxies and covering approximately 8500 square degrees and the redshift range 0.2 < z < 0.7. We also compare these results with those from the publicly released DR9 and DR10 samples. Assuming a concordance Λ cold dark matter (ΛCDM) cosmological model, the DR11 sample covers a volume of 13 Gpc3 and is the largest region of the Universe ever surveyed at this density. We measure the correlation function and power spectrum, including density-field reconstruction of the BAO feature. The acoustic features are detected at a significance of over 7σ in both the correlation function and power spectrum. Fitting for the position of the acoustic features measures the distance relative to the sound horizon at the drag epoch, rd, which has a value of rd,fid = 149.28 Mpc in our fiducial cosmology. We find DV = (1264 ± 25 Mpc)(rd/rd,fid) at z = 0.32 and DV = (2056 ± 20 Mpc)(rd/rd,fid) at z = 0.57. At 1.0 per cent, this latter measure is the most precise distance constraint ever obtained from a galaxy survey. Separating the clustering along and transverse to the line of sight yields measurements at z = 0.57 of DA = (1421 ± 20 Mpc)(rd/rd,fid) and H = (96.8 ± 3.4 km s−1 Mpc−1)(rd,fid/rd). Our measurements of the distance scale are in good agreement with previous BAO measurements and with the predictions from cosmic microwave background data for a spatially flat CDM model with a cosmological constant.Publisher PDFPeer reviewe