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Ecologists are being challenged to predict how ecosystems will respond to climate changes. According to the Multi-Colored World (MCW) hypothesis, climate impacts may not manifest because consumers such as fire and herbivory can override the influence of climate on ecosystem state. One MCW interpretation is that climate determinism fails because alternative ecosystem states (AES) are possible at some locations in climate space. We evaluated theoretical and empirical evidence for the proposition that forest and savanna are AES in Africa. We found that maps which infer where AES zones are located were contradictory. Moreover, data from longitudinal and experimental studies provide inconclusive evidence for AES. That is, although the forest-savanna AES proposition is theoretically sound, the existing evidence is not yet convincing. We conclude by making the case that the AES proposition has such fundamental consequences for designing management actions to mitigate and adapt to climate change in the savanna-forest domain that it needs a more robust evidence base before it is used to prescribe management actions.

Agrobacterium tumefaciens causes crown gall disease in plants by the horizontal transfer of oncogenic DNA. The conjugation is mediated by the VirB/D4 type 4 secretion system (T4SS) that assembles an extracellular filament, the T-pilus, and is involved in mating pair formation between A. tumefaciens and the recipient plant cell. Here, we present a 3 Å cryoelectron microscopy (cryo-EM) structure of the T-pilus solved by helical reconstruction. Our structure reveals that the T-pilus is a stoichiometric assembly of the VirB2 major pilin and phosphatidylglycerol (PG) phospholipid with 5-start helical symmetry. We show that PG head groups and the positively charged Arg 91 residues of VirB2 protomers form extensive electrostatic interactions in the lumen of the T-pilus. Mutagenesis of Arg 91 abolished pilus formation. While our T-pilus structure is architecturally similar to previously published conjugative pili structures, the T-pilus lumen is narrower and positively charged, raising questions of whether the T-pilus is a conduit for ssDNA transfer.

The Legionella pneumophila Dot/Icm type IV secretion system (T4SS) delivers effector proteins into host cells during infection. Despite its significance as a potential drug target, our current understanding of its atomic structure is limited to isolated subcomplexes. In this study, we used subtomogram averaging and integrative modeling to construct a nearly-complete model of the Dot/Icm T4SS accounting for seventeen protein components. We locate and provide insights into the structure and function of six new components including DotI, DotJ, DotU, IcmF, IcmT, and IcmX. We find that the cytosolic N-terminal domain of IcmF, a key protein forming a central hollow cylinder, interacts with DotU, providing insight into previously uncharacterized density. Furthermore, our model, in combination with analyses of compositional heterogeneity, explains how the cytoplasmic ATPase DotO is connected to the periplasmic complex via interactions with membrane-bound DotI/DotJ proteins. Coupled with in situ infection data, our model offers new insights into the T4SS-mediated secretion mechanism.

In situ neutron powder diffraction experiments are applied to physical, kinetic, and microstructural characterization of uranium mononitride as a promising light water reactor fuel material. The temperaturevariable coefficient of thermal expansion and isotropic Debye Waller factors are obtained by sequential Rietveld refinement over 499-1873 K. Oxidation of a UN pellet (95.2% density) under flow of 11 mg/min D 2 O is observed to initiate above 623 K and the rate increases by a factor of approximately 10 from 673 to 773 K, with activation energy 50.6 +/- 1.3 kJ/mol; uranium oxide is the only solid corrosion product.Crown Copyright, QC 20230315

Climate change is affecting global weather patterns, but nowhere is this more apparent than in the Arctic. The Arctic is an extreme environment going through rapid climate change, resulting in the opening of new shipping lanes and leading to less multiyear ice formation. This increases the risk of collision with the sea ice making it difficult to make long term voyage plans based on sea ice predictions. The Automatic Identification System (AIS) provides important services for marine domain awareness. For safe and effective ship traffic management and the development of new artificial intelligence (AI) marine algorithms, precise AIS readings for hull size and type are typically required. In this paper, we provide a summary of ship activities as well as relevant ice information in Alaskan waters that may result in ice-ship interactions and discuss them. AIS ship data was used to determine the ship speed distribution in different areas in the Alaskan waters. Ship movement in ice infested regions was compared with sea ice data from the Copernicus Reanalysis Products and sea ice thickness was estimated using empirical equations to identify potential ship-sea ice interactions. Data from 2015 to 2020 was analyzed to determine if there is an increase in maritime activity that can be linked to a decline in sea ice extent in Alaskan waters. The AIS data was also sorted by ship hull types to see how the different sectors of the Alaskan maritime industry are changing over time in ice-covered areas., Offshore Engineering

We analyze the spectrum of gravitational waves generated by the induced spectrum of tensor fluctuation during warm natural inflation. In our previous work it has been demonstrated that an epoch of warm natural inflation can lead to cosmologically relevant dark matter production in the form of primordial black holes. Here we show that models which solve the dark-matter production also produce a contribution to the cosmic gravitational wave background that satisfies current constraints from pulsar timing and big bang nucleosynthesis. More importantly, this gravitational wave background may be observable in the next generation of space-based and ground-based gravitational wave interferometers., Comment: 8 pages, 2 figures

The partcle-induced hadronic de-excitation of the Hoyle state in $^{12}$C induced by inelastic scattering in a hot and dense plasma can enhance the triple-alpha reaction rate. This prevents the production of heavy nuclei within the neutrino-driven winds of core-collapse supernovae and raises a question as to the contribution of proton-rich neutrino-driven winds as the origin of $p$-nuclei in the solar system abundances. Here we study $\nu p$-process nucleosynthesis in proton-rich neutrino-driven winds relevant to the production of $^{92,94}\mathrm{Mo}$ and $^{96,98}\mathrm{Ru}$ by considering such particle-induced de-excitation. We show that the enhancement of the triple-alpha reaction rate induced by neutron inelastic scattering hardly affects the $\nu p$-process, while the proton scattering contributes to the nucleosynthesis in proton-rich neutrino-driven winds at low temperature. The associated enhanced triple-alpha reaction rate decreases the production of $^{92,94}\mathrm{Mo}$ and $^{96,98}\mathrm{Ru}$ in a wind model of ordinary core-collapse supernovae. On the other hand, the abundances of these $p$-nuclei increase in an energetic hypernova wind model. Hence, we calculate the galactic chemical evolution of $^{92,94}\mathrm{Mo}$ and $^{96,98}\mathrm{Ru}$ by taking account of both contributions from core-collapse supernovae and hypernovae. We show that the hypernova $\nu p$-process can enhance the calculated solar isotopic fractions of $^{92,94}\mathrm{Mo}$ and $^{96,98}\mathrm{Ru}$ and make a significant impact on the GCE of $p$-nuclei regardless of the particle-induced Hoyle state de-excitation., Comment: 16 pages, 7 figures

As neutron stars merge they can approach very high nuclear density. Here, we summarized recent results for the evolution and gravitational wave emission from binary neutron star mergers using a a variety of nuclear equations of state with and without a crossover transition to quark matter. We discuss how the late time gravitational wave emission from binary neutron star mergers may possibly reveal the existence of a crossover transition to quark matter., Comment: Proceedings of the XVth Quark Confinement and the Hadron Spectrum, Stvanger, Norway, August 1-6, 2022

The dynamics of the satellite systems of Milky-Way-like galaxies offer a useful means by which to study the galaxy formation process in the cosmological context. It has been suggested that the currently observed anisotropic distribution of the satellites in such galaxy systems is inconsistent with the concordance $\Lambda CDM$ cosmology model on the galactic scale if the observed satellites are random samples of the dark matter (DM) sub-halos that are nearly isotropically distributed around the central galaxy. In this study, we present original high-resolution zoom-in studies of central galaxies and satellite systems based upon initial conditions for the DM distribution from the Aquarius simulations but with substantial high-resolution baryon physics added. We find that the galaxy most like the Milky Way in this study does indeed contain a disk of satellites (DOS). Although one galaxy DOS system does not answer the question of how common such disks are, it does allow the opportunity to explore the properties and dynamics of the DOS system. Our investigation centers on the spatial arrangement (distances, angles, etc.) of satellites in this Milky-Way-like galaxy system with a specific emphasis on identifying and analyzing the disk-like structure along with its dynamical and morphological properties. Among the conclusions from this study, we find that the satellites and DM sub-halos in the galaxy simulations are anisotropically distributed. The dynamical properties of the satellites, however, indicate that the direction of the angular momentum vector of the whole satellite system is different from the normal direction of the fitted DOS and from the normal direction of the velocity dispersion of the system. Hence, the fitted DOS appears to be comprised of infalling sub-halos and is not a rotationally supported system., Comment: 22 pages, 14 figures

We herein describe the cell-specific release of alcohol-containing payloads via a sulfatase-sensitive linker in antibody-drug conjugates (ADCs). The linker shows efficient sulfatase-mediated release and high stability in human and mouse plasma. In vitro evaluation demonstrates potent antigen dependent toxicity towards breast cancer cell lines.

The process by which bacterial cells build their intricate flagellar motility apparatuses has long fascinated scientists. Our understanding of this process comes mainly from studies of purified flagella from two species, Escherichia coli and Salmonella enterica. Here, we used electron cryo-tomography (cryo-ET) to image the assembly of the flagellar motor in situ in diverse Proteobacteria: Hylemonella gracilis, Helicobacter pylori, Campylobacter jejuni, Pseudomonas aeruginosa, Pseudomonas fluorescens, and Shewanella oneidensis. Our results reveal the in situ structures of flagellar intermediates, beginning with the earliest flagellar type III secretion system core complex (fT3SScc) and MS-ring. In high-torque motors of Beta-, Gamma-, and Epsilon-proteobacteria, we discovered novel cytoplasmic rings that interact with the cytoplasmic torque ring formed by FliG. These rings, associated with the MS-ring, assemble very early and persist until the stators are recruited into their periplasmic ring; in their absence the stator ring does not assemble. By imaging mutants in Helicobacter pylori, we found that the fT3SScc proteins FliO and FliQ are required for the assembly of these novel cytoplasmic rings. Our results show that rather than a simple accretion of components, flagellar motor assembly is a dynamic process in which accessory components interact transiently to assist in building the complex nanomachine.

We investigate the neutrino flavor change effects due to neutrino self-interaction, shock wave propagation as well as matter effect on the neutrino process of the core-collapsing supernova. For the hydrodynamics, we use two models: a simple thermal bomb model and a specified hydrodynamic model for SN1987A. As a pre-supernova model, we take an updated model adjusted to explain the SN1987A employing recent development of the $(n,\gamma)$ reaction rates for nuclei near the stability line $(A \sim 100)$. As for the neutrino luminosity, we adopt two different models: equivalent neutrino luminosity and non-equivalent luminosity models. The latter is taken from the synthetic analyses of the CCSN simulation data which involved quantitatively the results obtained by various neutrino transport models. Relevant neutrino-induced reaction rates are calculated by a shell model for light nuclei and a quasi-particle random phase approximation model for heavy nuclei. For each model, we present abundances of the light nuclei ($^7$Li, $^7$Be, $^{11}$B and $^{11}$C) and heavy nuclei ($^{92}$Nb, $^{98}$Tc, $^{138}$La and $^{180}$Ta) produced by the neutrino-process. The light nuclei abundances turn out to be sensitive to the Mikheyev-Smirnov-Wolfenstein region around ONeMg region while the heavy nuclei are mainly produced prior to the MSW region. Through the detailed analyses of the numerical abundances, we find that neutrino self-interaction becomes a key ingredient in addition to the MSW effect for understanding the neutrino process and the relevant nuclear abundances. However, the whole results are shown to depend on the adopted neutrino luminosity scheme. Detailed evaluations of the nuclear abundances for the two possible neutrino mass hierarchies are performed with the comparison to the available meteorite analyses data. The normal mass hierarchy is shown to be more compatible with the meteoritic data.

The bacterial flagellar type III secretion system (fT3SS) is a suite of membrane-embedded and cytoplasmic proteins responsible for building the flagellar motility machinery. Homologous nonflagellar (NF-T3SS) proteins form the injectisome machinery that bacteria use to deliver effector proteins into eukaryotic cells, and other family members were recently reported to be involved in the formation of membrane nanotubes. Here, we describe a novel, evolutionarily widespread, hat-shaped structure embedded in the inner membranes of bacteria, of yet-unidentified function, that is present in species containing fT3SS. Mutant analysis suggests a relationship between this novel structure and the fT3SS, but not the NF-T3SS. While the function of this novel structure remains unknown, we hypothesize that either some of the fT3SS proteins assemble within the hat-like structure, perhaps including the fT3SS core complex, or that fT3SS components regulate other proteins that form part of this novel structure.

We investigate the neutrino flavor change effects due to neutrino self-interaction, shock wave propagation as well as matter effect on the neutrino process of the core-collapsing supernova. For the hydrodynamics, we use two models: a simple thermal bomb model and a specified hydrodynamic model for SN1987A. As a pre-supernova model, we take an updated model adjusted to explain the SN1987A employing recent development of the $(n,\gamma)$ reaction rates for nuclei near the stability line $(A \sim 100)$. As for the neutrino luminosity, we adopt two different models: equivalent neutrino luminosity and non-equivalent luminosity models. The latter is taken from the synthetic analyses of the CCSN simulation data which involved quantitatively the results obtained by various neutrino transport models. Relevant neutrino-induced reaction rates are calculated by a shell model for light nuclei and a quasi-particle random phase approximation model for heavy nuclei. For each model, we present abundances of the light nuclei ($^7$Li, $^7$Be, $^{11}$B and $^{11}$C) and heavy nuclei ($^{92}$Nb, $^{98}$Tc, $^{138}$La and $^{180}$Ta) produced by the neutrino-process. The light nuclei abundances turn out to be sensitive to the Mikheyev-Smirnov-Wolfenstein region around ONeMg region while the heavy nuclei are mainly produced prior to the MSW region. Through the detailed analyses of the numerical abundances, we find that neutrino self-interaction becomes a key ingredient in addition to the MSW effect for understanding the neutrino process and the relevant nuclear abundances. However, the whole results are shown to depend on the adopted neutrino luminosity scheme. Detailed evaluations of the nuclear abundances for the two possible neutrino mass hierarchies are performed with the comparison to the available meteorite analyses data. The normal mass hierarchy is shown to be more compatible with the meteoritic data.

Background Most people have strong left-brain lateralisation for language, with a minority showing right- or bilateral language representation. On some receptive language tasks, however, lateralisation appears to be reduced or absent. This contrasting pattern raises the question of whether and how language laterality may fractionate within individuals. Building on our prior work, we postulated (a) that there can be dissociations in lateralisation of different components of language, and (b) these would be more common in left-handers. A subsidiary hypothesis was that laterality indices will cluster according to two underlying factors corresponding to whether they involve generation of words or sentences, vs. receptive language. Methods We tested these predictions in two stages: At Step 1 an online laterality battery (Dichotic listening, Rhyme Decision and Word Comprehension) was given to 621 individuals (56% left-handers); At Step 2, functional transcranial Doppler ultrasound (fTCD) was used with 230 of these individuals (51% left-handers). 108 left-handers and 101 right-handers gave usable data on a battery of three language generation and three receptive language tasks. Results Neither the online nor fTCD measures supported the notion of a single language laterality factor. In general, for both online and fTCD measures, tests of language generation were left-lateralised. In contrast, the receptive tasks were at best weakly left-lateralised or, in the case of Word Comprehension, slightly right-lateralised. The online measures were only weakly correlated, if at all, with fTCD measures. Most of the fTCD measures had split-half reliabilities of at least .7, and showed a distinctive pattern of intercorrelation, supporting a modified two-factor model in which Phonological Decision (generation) and Sentence Decision (reception) loaded on both factors. The same factor structure fitted data from left- and right-handers, but mean scores on the two factors were lower (less le

Many autotrophic bacteria rely on Rubisco for carbon dioxide fixation. Here the authors report the position, orientation, and structure of Rubisco within alpha-carboxysomes; showing how it polymerizes and can form a lattice inside this compartment. Despite the importance of microcompartments in prokaryotic biology and bioengineering, structural heterogeneity has prevented a complete understanding of their architecture, ultrastructure, and spatial organization. Here, we employ cryo-electron tomography to image alpha-carboxysomes, a pseudo-icosahedral microcompartment responsible for carbon fixation. We have solved a high-resolution subtomogram average of the Rubisco cargo inside the carboxysome, and determined the arrangement of the enzyme. We find that the H. neapolitanus Rubisco polymerizes in vivo, mediated by the small Rubisco subunit. These fibrils can further pack to form a lattice with six-fold pseudo-symmetry. This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 mu M. This characterization of Rubisco cargo inside the alpha-carboxysome provides insight into the balance between order and disorder in microcompartment organization.

Many autotrophic bacteria rely on Rubisco for carbon dioxide fixation. Here the authors report the position, orientation, and structure of Rubisco within alpha-carboxysomes; showing how it polymerizes and can form a lattice inside this compartment. Despite the importance of microcompartments in prokaryotic biology and bioengineering, structural heterogeneity has prevented a complete understanding of their architecture, ultrastructure, and spatial organization. Here, we employ cryo-electron tomography to image alpha-carboxysomes, a pseudo-icosahedral microcompartment responsible for carbon fixation. We have solved a high-resolution subtomogram average of the Rubisco cargo inside the carboxysome, and determined the arrangement of the enzyme. We find that the H. neapolitanus Rubisco polymerizes in vivo, mediated by the small Rubisco subunit. These fibrils can further pack to form a lattice with six-fold pseudo-symmetry. This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 mu M. This characterization of Rubisco cargo inside the alpha-carboxysome provides insight into the balance between order and disorder in microcompartment organization.

Many autotrophic bacteria rely on Rubisco for carbon dioxide fixation. Here the authors report the position, orientation, and structure of Rubisco within alpha-carboxysomes; showing how it polymerizes and can form a lattice inside this compartment. Despite the importance of microcompartments in prokaryotic biology and bioengineering, structural heterogeneity has prevented a complete understanding of their architecture, ultrastructure, and spatial organization. Here, we employ cryo-electron tomography to image alpha-carboxysomes, a pseudo-icosahedral microcompartment responsible for carbon fixation. We have solved a high-resolution subtomogram average of the Rubisco cargo inside the carboxysome, and determined the arrangement of the enzyme. We find that the H. neapolitanus Rubisco polymerizes in vivo, mediated by the small Rubisco subunit. These fibrils can further pack to form a lattice with six-fold pseudo-symmetry. This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 mu M. This characterization of Rubisco cargo inside the alpha-carboxysome provides insight into the balance between order and disorder in microcompartment organization.

The nuclear equation of state (EOS) is an important component in the evolution of core-collapse supernovae. In this paper we make a survey of various EOSs in the literature and analyze their effect on spherical core-collapse models in which the effects of three-dimensional turbulence is modeled by a general relativistic formulation of Supernova Turbulence In Reduced-dimensionality (STIR). We show that the viability of the explosion is quite EOS dependent and that it best correlates with the early-time interior entropy density of the proto–neutron star. We check that this result is not progenitor dependent, although the lowest-mass progenitors show different explosion properties, due to the different pre-collapse nuclear composition. Larger central entropies also induce more vigorous proto–neutron star convection in our one-dimensional turbulence model, as well as a wider convective layer.

Acoustic reporter genes based on gas vesicles (GVs) have enabled the use of ultrasound to noninvasively visualize cellular function in vivo. The specific detection of GV signals relative to background acoustic scattering in tissues is facilitated by nonlinear ultrasound imaging techniques taking advantage of the sonomechanical buckling of GVs. However, the effect of geometry on the buckling behavior of GVs under exposure to ultrasound has not been studied. To understand such geometric effects, we developed computational models of GVs of various lengths and diameters and used finite element simulations to predict their threshold buckling pressures and post-buckling deformations. We demonstrated that the GV diameter has an inverse cubic relation to the threshold buckling pressure, whereas length has no substantial effect. To complement these simulations, we experimentally probed the effect of geometry on the mechanical properties of GVs and the corresponding nonlinear ultrasound signals. The results of these experiments corroborate our computational predictions. This study provides fundamental insights into how geometry affects the sonomechanical properties of GVs, which, in turn, can inform further engineering of these nanostructures for high-contrast, nonlinear ultrasound imaging.STATEMENT OF SIGNIFICANCEGas vesicles (GVs) are an emerging class of genetically encodable and engineerable imaging agents for ultrasound whose sonomechanical buckling generates nonlinear contrast to enable sensitive and specific imaging in highly scattering biological systems. Though the effect of protein composition on GV buckling has been studied, the effect of geometry has not previously been addressed. This study reveals that geometry, especially GV diameter, significantly alters the threshold acoustic pressures required to induce GV buckling. Our computational predictions and experimental results provide fundamental understanding of the relationship between GV geometry and buckling pr

Staphylococcus aureus bloodstream (SAB) infection is a common and severe infectious disease, with a 90-day mortality of 15%–30%. Despite this, <3000 people have been randomized into clinical trials of treatments for SAB infection. The limited evidence base partly results from clinical trials for SAB infections being difficult to complete at scale using traditional clinical trial methods. Here we provide the rationale and framework for an adaptive platform trial applied to SAB infections. We detail the design features of the Staphylococcus aureus Network Adaptive Platform (SNAP) trial that will enable multiple questions to be answered as efficiently as possible. The SNAP trial commenced enrolling patients across multiple countries in 2022 with an estimated target sample size of 7000 participants. This approach may serve as an exemplar to increase efficiency of clinical trials for other infectious disease syndromes.

Faithful segregation of chromosomes during mitosis relies on a carefully coordinated and intricate interplay between the centromere, kinetochore, and spindle microtubules. Despite its importance, the architecture of this interface remains elusive. Here we used in situ cryo-electron tomography to visualize the native architecture of the kinetochore-microtubule interface in human U2OS cells at different stages of mitosis. We find that the centromere forms a pocket-like structure around kinetochore microtubules. Two morphologically distinct fibrillar densities form end-on and side-on connections to the plus-ends of microtubules within this centromeric pocket. Our data suggest a dynamic kinetochore-microtubule interface with multiple interactions between outer kinetochore components and spindle microtubules.

Cryogenic electron tomography (cryo-ET) combined with sub-tomogram averaging, allows in-situ visualisation and structure determination of macromolecular complexes at sub-nanometre resolution. Cryogenic focused ion beam (cryo-FIB) micromachining is used to prepare a thin lamella-shaped sample out of a frozen-hydrated cell for cryo-ET imaging, but standard cryo-FIB fabrication is blind to the precise location of the structure or proteins of interest. Fluorescence-guided focused ion beam (FIB) milling at target locations requires multiple sample transfers prone to contamination, and relocation and registration accuracy is often insufficient for 3D targeting. Here, we present in-situ fluoresence microscopy-guided FIB fabrication of a frozen-hydrated lamella to solve this problem: we built a coincident 3-beam cryogenic correlative microscope by retrofitting a compact cryogenic microcooler, custom positioning stage, and an inverted widefield fluorescence microscope (FM) on an existing focused ion-beam scanning electron microscope (FIB-SEM). We show FM controlled targeting at every milling step in the lamella fabrication process, validated with transmission electron microscope (TEM) tomogram reconstructions of the target regions. The ability to check the lamella during and after the milling process results in a higher success rate in the fabrication process and will increase the throughput of fabrication for lamellae suitable for high-resolution imaging.

Agrobacterium tumefaciens is a plant pathogen that causes crown gall disease by the horizontal transfer of oncogenic DNA that is integrated into the host’s genome. The conjugation is mediated by the conjugative VirB/D4 type 4 secretion system (T4SS). A. tumefaciens T4SS assembles an extracellular filament, the T-pilus, that is involved in the formation of a mating pair between A. tumefaciens and the recipient plant cell by a not fully understood mechanism. Here, we present a 3 Å cryo-EM structure of the T-pilus, solved by helical reconstruction. Our structure reveals that the T-pilus comprises the major pilin protein VirB2 and phosphatidylglycerol (PG) phospholipid at a 1:1 stoichiometric ratio with 5-start helical symmetry. We further show that PG-headgroups and the positively charged Arg 91 residues of VirB2 protomers form extensive electrostatic interactions in the lumen of the T-pilus. Mutagenesis of Arg 91 destabilized the VirB2 protein and completely abolished pilus formation. While our T-pilus structure shows architectural similarity with previously published conjugative pili structures, positively charged sidechains protrude into the lumen and the lumen is narrower, raising questions whether the T-pilus is a conduit for ssDNA transfer. We also show that the VirB2 subunits in T-pilus filament are not cyclic, as previously thought.

Coxiella burnetii is an obligate zoonotic bacterium that targets macrophages to cause a disease known as Q fever. It has a biphasic developmental lifecycle where the extracellular and metabolically inactive small cell variant (SCV) transforms, under host acidic environment, into the vegetative large cell variant (LCV). However, the details about the morphological and structural changes that accompany this biphasic cycle are still lacking. Here, we used cryo-electron tomography to image the different cell variants of C. burnetii grown either under axenic conditions in different pH or purified directly from host cells revealing the major developmental, morphological and structural transitions. We show that SCVs are characterized by equidistant stacks of inner membrane that presumably allow a smooth transition to LCV, a transition coupled with the expression of the Dot/Icm type IVB secretion system (T4BSS). A class of T4BSS particles were associated with extracellular densities including a tubular structure possibly involved in host interaction or effector delivery. Also, SCVs and cells in the transition state contained spherical multilayered membrane structures of different sizes and locations suggesting that they are not related to a sporulation process as once assumed.

Many autotrophic bacteria rely on Rubisco for carbon dioxide fixation. Here the authors report the position, orientation, and structure of Rubisco within alpha-carboxysomes; showing how it polymerizes and can form a lattice inside this compartment. Despite the importance of microcompartments in prokaryotic biology and bioengineering, structural heterogeneity has prevented a complete understanding of their architecture, ultrastructure, and spatial organization. Here, we employ cryo-electron tomography to image alpha-carboxysomes, a pseudo-icosahedral microcompartment responsible for carbon fixation. We have solved a high-resolution subtomogram average of the Rubisco cargo inside the carboxysome, and determined the arrangement of the enzyme. We find that the H. neapolitanus Rubisco polymerizes in vivo, mediated by the small Rubisco subunit. These fibrils can further pack to form a lattice with six-fold pseudo-symmetry. This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 mu M. This characterization of Rubisco cargo inside the alpha-carboxysome provides insight into the balance between order and disorder in microcompartment organization.

Health assessment of individuals is an important aspect of monitoring endangered wildlife populations. Haematological and biochemical values are a common health assessment tool, and whilst reference values are well established for domestic species, they are often not available for wild animal species. This study established 31 haematological and biochemical reference intervals for golden eagle (Aquila chrysaetos) nestlings in Scotland, in order to improve the understanding of the species’ health and support conservation efforts. Reference intervals were created from 47 nestlings (ages 2–7.5 weeks old) across 37 nests, to date, the largest sample of wild individuals of this species and age cohort sampled for these purposes. Upper reference intervals for concentrations of lymphocytes, total protein, cholesterol, triglycerides, uric acid, and monocytes, calculated in this study, are higher than those found for adult raptors and the interval span is higher than that observed in adult raptors for concentrations of AST, albumin, eosinophil, LDH, and monocyte count. Statistically significant positive correlations were found with age and concentrations of haemoglobin, lymphocytes, serum pH, and creatine kinase, and significant negative correlations with age for concentrations of thrombocytes, heterophils, total protein, globulin, and lactate dehydrogenase. Packed cell volume was significantly higher for females than males, and concentration of calcium and eosinophils were higher for individuals in good body condition than those in moderate body condition. The reference intervals produced by this study will be of important use to the veterinary and conservation management communities and will aid the long-term monitoring of the Scottish golden eagle population health.

We report on a study of the natural warm inflationary paradigm (WNI). We show two important new results arise in this model. One is that the observational constraints on the primordial power spectrum from the cosmic microwave background (CMB) can be satisfied without going beyond the Planck scale of the effective field theory. The second is that WNI can inevitably provide perfect conditions for the production of primordial black holes (PBHs) in the golden window of black-hole mass range ($10^{-16} -10^{-11}M_{\odot}$) where it can account for all of the the dark matter content of the universe while satisfying observational constraints., Comment: 6 pages, 2 figures, Minor corrections added. Figure is modified to incorporate cold inflationary power spectrum. Published in PLB

BACKGROUND: Quality and safety in Australian healthcare is inequitably distributed, highlighted by gaps in the provision of quality care for Aboriginal and Torres Strait Islander children. Burns have potential for long-term adverse outcomes, and quality care, including culturally safe care, is critical to recovery. This study aimed to develop and apply an Aboriginal Patient Journey Mapping (APJM) tool to investigate the quality of healthcare systems for burn care with Aboriginal and Torres Strait Islander children. STUDY DESIGN: Interface research methodology, using biomedical and cultural evidence, informed the modification of an existing APJM tool. The tool was then applied to the journey of one family accessing a paediatric tertiary burn care site. Data were collected through yarning with the family, case note review and clinician interviews. Data were analysed using Emden's core story and thematic analysis methods. Reflexivity informed consideration of the implications of the APJM tool, including its effectiveness and efficiency in eliciting information about quality and cultural safety. RESULTS: Through application of a modified APJM tool, gaps in quality care for Aboriginal and Torres Strait Islander children and families were identified at the individual, service and system levels. Engagement in innovative methodology incorporating more than biomedical standards of care, uncovered critical information about the experiences of culturally safe care in complex patient journeys. CONCLUSION: Based on our application of the tool, APJM can identify and evaluate specific aspects of culturally safe care as experienced by Aboriginal and Torres Strait Islander peoples and be used for quality improvement.

Inflammatory bowel diseases (IBD) are characterized by chronic inflammation of the gastrointestinal tract and profound alterations to the gut microbiome. Adherent-invasive Escherichia coli (AIEC) is a mucosa-associated pathobiont that colonizes the gut of patients with Crohn's disease, a form of IBD. Because AIEC exacerbates gut inflammation, strategies to reduce the AIEC bloom during colitis are highly desirable. To thrive in the inflamed gut, Enterobacteriaceae acquire the essential metal nutrient iron by producing and releasing siderophores. Here, we implemented an immunization-based strategy to target the siderophores enterobactin and its glucosylated derivative salmochelin to reduce the AIEC bloom in the inflamed gut. Using chemical (dextran sulfate sodium) and genetic (Il10-/- mice) IBD mouse models, we showed that immunization with enterobactin conjugated to the mucosal adjuvant cholera toxin subunit B potently elicited mucosal and serum antibodies against these siderophores. Siderophore-immunized mice exhibited lower AIEC gut colonization, diminished AIEC association with the gut mucosa, and reduced colitis severity. Moreover, Peyer's patches and the colonic lamina propria harbored enterobactin-specific B cells that could be identified by flow cytometry. The beneficial effect of siderophore immunization was primarily B cell-dependent because immunized muMT-/- mice, which lack mature B lymphocytes, were not protected during AIEC infection. Collectively, our study identified siderophores as a potential therapeutic target to reduce AIEC colonization and its association with the gut mucosa, which ultimately may reduce colitis exacerbation. Moreover, this work provides the foundation for developing monoclonal antibodies against siderophores, which could provide a narrow-spectrum strategy to target the AIEC bloom in Crohn's disease patients. IMPORTANCE Adherent-invasive Escherichia coli (AIEC) is abnormally prevalent in patients with ileal Crohn's disease and exac

Background Most people have strong left-brain lateralisation for language, with a minority showing right- or bilateral language representation. On some receptive language tasks, however, lateralisation appears to be reduced or absent. This contrasting pattern raises the question of whether and how language laterality may fractionate within individuals. Building on our prior work, we postulated (a) that there can be dissociations in lateralisation of different components of language, and (b) these would be more common in left-handers. A subsidiary hypothesis was that laterality indices will cluster according to two underlying factors corresponding to whether they involve generation of words or sentences, vs. receptive language. Methods We tested these predictions in two stages: At Step 1 an online laterality battery (Dichotic listening, Rhyme Decision and Word Comprehension) was given to 621 individuals (56% left-handers); At Step 2, functional transcranial Doppler ultrasound (fTCD) was used with 230 of these individuals (51% left-handers). 108 left-handers and 101 right-handers gave usable data on a battery of three language generation and three receptive language tasks. Results Neither the online nor fTCD measures supported the notion of a single language laterality factor. In general, for both online and fTCD measures, tests of language generation were left-lateralised. In contrast, the receptive tasks were at best weakly left-lateralised or, in the case of Word Comprehension, slightly right-lateralised. The online measures were only weakly correlated, if at all, with fTCD measures. Most of the fTCD measures had split-half reliabilities of at least .7, and showed a distinctive pattern of intercorrelation, supporting a modified two-factor model in which Phonological Decision (generation) and Sentence Decision (reception) loaded on both factors. The same factor structure fitted data from left- and right-handers, but mean scores on the two factors were lower (less le

Cryogenic electron tomography (cryo-ET) combined with sub-tomogram averaging, allows in-situ visualization and structure determination of macromolecular complexes at sub-nanometre resolution. Cryogenic focused ion beam (cryo-FIB) micromachining is used to prepare a thin lamella-shaped sample out of a frozen-hydrated cell for cryo-ET imaging, but standard cryo-FIB fabrication is blind to the precise location of the structure or proteins of interest. Fluorescence-guided focused ion beam (FIB) milling at target locations requires multiple sample transfers prone to contamination, and relocation and registration accuracy is often insufficient for 3D targeting. Here, we present in-situ fluorescence microscopy-guided FIB fabrication of a frozen-hydrated lamella to address this problem: we built a coincident 3-beam cryogenic correlative microscope by retrofitting a compact cryogenic microcooler, custom positioning stage, and an inverted widefield fluorescence microscope (FM) on an existing focused ion-beam scanning electron microscope (FIB-SEM). We show FM controlled targeting at every milling step in the lamella fabrication process, validated with transmission electron microscope (TEM) tomogram reconstructions of the target regions. The ability to check the lamella during and after the milling process results in a higher success rate in the fabrication process and will increase the throughput of fabrication for lamellae suitable for high-resolution imaging., ImPhys/Microscopy Instrumentation & Techniques, BN/Arjen Jakobi Lab

[Background]: ‘Megafire’ is an emerging concept commonly used to describe fires that are extreme in terms of size, behaviour, and/or impacts, but the term’s meaning remains ambiguous. [Approach]: We sought to resolve ambiguity surrounding the meaning of ‘megafire’ by conducting a structured review of the use and definition of the term in several languages in the peer-reviewed scientific literature. We collated definitions and descriptions of megafire and identified criteria frequently invoked to define megafire. We recorded the size and location of megafires and mapped them to reveal global variation in the size of fires described as megafires. [Results]: We identified 109 studies that define the term ‘megafire’ or identify a megafire, with the term first appearing in the peer-reviewed literature in 2005. Seventy-one (~65%) of these studies attempted to describe or define the term. There was considerable variability in the criteria used to define megafire, although definitions of megafire based on fire size were most common. Megafire size thresholds varied geographically from > 100–100,000 ha, with fires > 10,000 ha the most common size threshold (41%, 18/44 studies). Definitions of megafire were most common from studies led by authors from North America (52%, 37/71). We recorded 137 instances from 84 studies where fires were reported as megafires, the vast majority (94%, 129/137) of which exceed 10,000 ha in size. Megafires occurred in a range of biomes, but were most frequently described in forested biomes (112/137, 82%), and usually described single ignition fires (59% 81/137). [Conclusion]: As Earth’s climate and ecosystems change, it is important that scientists can communicate trends in the occurrence of larger and more extreme fires with clarity. To overcome ambiguity, we suggest a definition of megafire as fires > 10,000 ha arising from single or multiple related ignition events. We introduce two additional terms – gigafire (> 100,000 ha) and terafire (> 1,0

Many autotrophic bacteria rely on Rubisco for carbon dioxide fixation. Here the authors report the position, orientation, and structure of Rubisco within alpha-carboxysomes; showing how it polymerizes and can form a lattice inside this compartment. Despite the importance of microcompartments in prokaryotic biology and bioengineering, structural heterogeneity has prevented a complete understanding of their architecture, ultrastructure, and spatial organization. Here, we employ cryo-electron tomography to image alpha-carboxysomes, a pseudo-icosahedral microcompartment responsible for carbon fixation. We have solved a high-resolution subtomogram average of the Rubisco cargo inside the carboxysome, and determined the arrangement of the enzyme. We find that the H. neapolitanus Rubisco polymerizes in vivo, mediated by the small Rubisco subunit. These fibrils can further pack to form a lattice with six-fold pseudo-symmetry. This arrangement preserves freedom of motion and accessibility around the Rubisco active site and the binding sites for two other carboxysome proteins, CsoSCA (a carbonic anhydrase) and the disordered CsoS2, even at Rubisco concentrations exceeding 800 mu M. This characterization of Rubisco cargo inside the alpha-carboxysome provides insight into the balance between order and disorder in microcompartment organization.

We report on a study of the natural warm inflationary paradigm (WNI). We show two important new results arise in this model. One is that the observational constraints on the primordial power spectrum from the cosmic microwave background (CMB) can be satisfied without going beyond the Planck scale of the effective field theory. The second is that WNI can inevitably provide perfect conditions for the production of primordial black holes (PBHs) in the golden window of black-hole mass range ($10^{-16} -10^{-11}M_{\odot}$) where it can account for all of the the dark matter content of the universe while satisfying observational constraints., Comment: 6 pages, 2 figures, Minor corrections added. Figure is modified to incorporate cold inflationary power spectrum. Published in PLB

We present a simple criterion to predict the explodability of massive stars based on the density and entropy profiles before collapse. If a pronounced density jump is present near the Si/Si-O interface, the star will likely explode. We develop a quantitative criterion by using $\sim 1300$ 1D simulations where $\nu$-driven turbulence is included via time-dependent mixing-length theory. This criterion correctly identifies the outcome of the supernova more than $90 \%$ of the time. We also find no difference in how this criterion performs on two different sets of progenitors, evolved using two different stellar evolution codes: FRANEC and KEPLER. The explodability as a function of mass of the two sets of progenitors is very different, showing: (i) that uncertainties in the stellar evolution prescriptions influence the predictions of supernova explosions; (ii) the most important properties of the pre-collapse progenitor that influence the explodability are its density and entropy profiles. We highlight the importance that $\nu$-driven turbulence plays in the explosion by comparing our results to previous works., Comment: 20 pages, 12 figures, submitted to ApJ

We investigate the neutrino flavor change effects due to neutrino self-interaction, shock wave propagation as well as matter effect on the neutrino-process of the core-collapsing supernova (CCSN). For the hydrodynamics, we use two models: a simple thermal bomb model and a specified hydrodynamic model for SN1987A. As a pre-supernova model, we take an updated model adjusted to explain the SN1987A employing recent development of the $(n,\gamma)$ reaction rates for nuclei near the stability line $(A \sim 100)$. As for the neutrino luminosity, we adopt two different models: equivalent neutrino luminosity and non-equivalent luminosity models. The latter is taken from the synthetic analyses of the CCSN simulation data which involved quantitatively the results obtained by various neutrino transport models. Relevant neutrino-induced reaction rates are calculated by a shell model for light nuclei and a quasi-particle random phase approximation model for heavy nuclei. For each model, we present abundances of the light nuclei ($^7$Li, $^7$Be, $^{11}$B and $^{11}$C) and heavy nuclei ($^{92}$Nb, $^{98}$Tc, $^{138}$La and $^{180}$Ta) produced by the neutrino-process. The light nuclei abundances turn out to be sensitive to the Mikheyev-Smirnov-Wolfenstein (MSW) region around O-Ne-Mg region while the heavy nuclei are mainly produced prior to the MSW region. Through the detailed analyses, we find that neutrino self-interaction becomes a key ingredient in addition to the MSW effect for understanding the neutrino-process and the relevant nuclear abundances. The normal mass hierarchy is shown to be more compatible with the meteorite data. Main nuclear reactions for each nucleus are also investigated in detail.

The InSight lander rests on a regolith-covered, Hesperian to Early Amazonian lava plain in Elysium Planitia within a ∼27-m-diameter, degraded impact crater called Homestead hollow. The km to cm-scale stratigraphy beneath the lander is relevant to the mission's geophysical investigations. Geologic mapping and crater statistics indicate that ∼170 m of mostly Hesperian to Early Amazonian basaltic lavas are underlain by Noachian to Early Hesperian (∼3.6 Ga) materials of possible sedimentary origin. Up to ∼140 m of this volcanic resurfacing occurred in the Early Amazonian at 1.7 Ga, accounting for removal of craters ≤700 m in diameter. Seismic data however, suggest a clastic horizon that interrupts the volcanic sequence between depths of ∼30 and ∼75 m. Meter-scale stratigraphy beneath the lander is constrained by local and regional regolith thickness estimates that indicate up to 10–30 m of coarse-grained, brecciated regolith that fines upwards to a ∼3 m thick loosely-consolidated, sand-dominated unit. The maximum depth of Homestead hollow, at ∼3 m, indicates that the crater is entirely embedded in regolith. The hollow is filled by sand-size eolian sediments, with contributions from sand to cobble-size slope debris, and sand to cobble-size ejecta. Lander-based observations indicate that the fill at Homestead hollow contains a cohesive layer down to ∼10–20 cm depth that is visible in lander rocket-excavated pits and the HP3 mole hole. The surface of the landing site is capped by a ∼1 to 2 cm-thick loosely granular, sand-sized layer with a microns-thick surficial dust horizon.

The InSight lander rests on a regolith-covered, Hesperian to Early Amazonian lava plain in Elysium Planitia within a ∼27-m-diameter, degraded impact crater called Homestead hollow. The km to cm-scale stratigraphy beneath the lander is relevant to the mission's geophysical investigations. Geologic mapping and crater statistics indicate that ∼170 m of mostly Hesperian to Early Amazonian basaltic lavas are underlain by Noachian to Early Hesperian (∼3.6 Ga) materials of possible sedimentary origin. Up to ∼140 m of this volcanic resurfacing occurred in the Early Amazonian at 1.7 Ga, accounting for removal of craters ≤700 m in diameter. Seismic data however, suggest a clastic horizon that interrupts the volcanic sequence between depths of ∼30 and ∼75 m. Meter-scale stratigraphy beneath the lander is constrained by local and regional regolith thickness estimates that indicate up to 10–30 m of coarse-grained, brecciated regolith that fines upwards to a ∼3 m thick loosely-consolidated, sand-dominated unit. The maximum depth of Homestead hollow, at ∼3 m, indicates that the crater is entirely embedded in regolith. The hollow is filled by sand-size eolian sediments, with contributions from sand to cobble-size slope debris, and sand to cobble-size ejecta. Lander-based observations indicate that the fill at Homestead hollow contains a cohesive layer down to ∼10–20 cm depth that is visible in lander rocket-excavated pits and the HP3 mole hole. The surface of the landing site is capped by a ∼1 to 2 cm-thick loosely granular, sand-sized layer with a microns-thick surficial dust horizon.

It is anticipated that the gravitational radiation detected in future gravitational wave (GW) detectors from binary neutron star (NS) mergers can probe the high-density equation of state (EOS). We perform the first simulations of binary NS mergers which adopt various parametrizations of the quark-hadron crossover (QHC) EOS. These are constructed from combinations of a hadronic EOS ($n_{b} < 2~n_0$) and a quark-matter EOS ($n_{b} >~5~n_0$), where $n_{b}$ and $n_0$ are the baryon number density and the nuclear saturation density, respectively. At the crossover densities ($2~ n_0 < n_{b} < 5~ n_0$) the QHC EOSs continuously soften, while remaining stiffer than hadronic and first-order phase transition EOSs, achieving the stiffness of strongly correlated quark matter. This enhanced stiffness leads to significantly longer lifetimes of the postmerger NS than that for a pure hadronic EOS. We find a dual nature of these EOSs such that their maximum chirp GW frequencies $f_{max}$ fall into the category of a soft EOS while the dominant peak frequencies ($f_{peak}$) of the postmerger stage fall in between that of a soft and stiff hadronic EOS. An observation of this kind of dual nature in the characteristic GW frequencies will provide crucial evidence for the existence of strongly interacting quark matter at the crossover densities for QCD., Comment: 8 pages, 3 figures

Alcohol hangover (AH) has been associated with poor sleep due to the negative effects of alcohol intoxication on sleep quantity and sleep quality. The aim of the current study was to further explore the relationship between AH severity and sleep using a naturalistic study design. A further aim was to determine whether quantitative aspects of sleep were a mediating influence on the relationship between AH severity and cognitive performance. As part of the naturalistic study design, 99 drinkers were recruited following a night of drinking in an Australian state capital, with breath alcohol concentration (BrAC) measured as participants were leaving the entertainment district. The following morning at home, participants answered online questions regarding their drinking behaviour on the previous evening, current AH symptoms and sleep quality. Participants also completed an online version of the Trail-Making Test B (TMT-B) to assess cognitive performance. The findings reveal the duration of nightly awakenings to be negatively related to six individual AH symptoms as well as overall AH severity. The number of nightly awakenings, sleep quality and total sleep time correlated with four AH symptoms including overall AH severity. Total AH severity accounted for a moderate amount of variance (11%) in the time to complete the TMT-B. These findings confirm that alcohol consumption negatively affects sleep, which is related to higher next-day hangover severity ratings and poorer cognitive performance.

Structure-determination methods are needed to resolve the atomic details that underlie protein function. X-ray crystallography has provided most of our knowledge of protein structure, but is constrained by the need for large, well ordered crystals and the loss of phase information. The rapidly developing methods of serial femtosecond crystallography, micro-electron diffraction and single-particle reconstruction circumvent the first of these limitations by enabling data collection from nanocrystals or purified proteins. However, the first two methods also suffer from the phase problem, while many proteins fall below the molecular-weight threshold required for single-particle reconstruction. Cryo-electron tomography of protein nanocrystals has the potential to overcome these obstacles of mainstream structure-determination methods. Here, a data-processing scheme is presented that combines routines from X-ray crystallography and new algorithms that have been developed to solve structures from tomograms of nanocrystals. This pipeline handles image-processing challenges specific to tomographic sampling of periodic specimens and is validated using simulated crystals. The tolerance of this workflow to the effects of radiation damage is also assessed. The simulations indicate a trade-off between a wider tilt range to facilitate merging data from multiple tomograms and a smaller tilt increment to improve phase accuracy. Since phase errors, but not merging errors, can be overcome with additional data sets, these results recommend distributing the dose over a wide angular range rather than using a finer sampling interval to solve the protein structure.

Rocks around the InSight lander were measured in lander orthoimages of the near field (<10 m), in panoramas of the far field (<40 m), and in a high-resolution orbital image around the lander (1 km²). The cumulative fractional area versus diameter size-frequency distributions for four areas in the near field fall on exponential model curves used for estimating hazards for landing spacecraft. The rock abundance varies in the near field from 0.6% for the sand and pebble rich area to the east within Homestead hollow, to ~3-5% for the progressively rockier areas to the south, north and west. The rock abundance of the entire near field is just over 3%, which falls between that at the Phoenix (2%) and Spirit (5%) landing sites. Rocks in the far field (<40 m) that could be identified in both the surface panorama and a high-resolution orbital image fall on the same exponential model curve as the average near field rocks. Rocks measured in a high-resolution orbital image (27.5 cm/pixel) within ~500 m of the lander that includes several rocky ejecta craters fall on 4-5% exponential model curves, similar to the northern and western near field areas. As a result, the rock abundances observed from orbit falls on the same exponential model rock abundance curves as those viewed from the surface. These rock abundance measurements around the lander are consistent with thermal imaging estimates over larger pixel areas as well as expectations from fragmentation theory of an impacted Amazonian/Hesperian lava flow.