Molecular Machines that Facilitate Bacterial Outer Membrane Protein Biogenesis.

Almost all outer membrane proteins (OMPs) in Gram-negative bacteria contain a ß-barrel domain that spans the outer membrane (OM). To reach the OM, OMPs must be translocated across the inner membrane by the Sec machinery, transported across the crowded periplasmic space through the assistance of molecular chaperones, and finally assembled (folded and inserted into the OM) by the ß-barrel assembly machine. In this review, we discuss how considerable new insights into the contributions of these factors to OMP biogenesis have emerged in recent years through the development of novel experimental, computational, and predictive methods. In addition, we describe recent evidence that molecular machines that were thought to function independently might interact to form dynamic intermembrane supercomplexes. Finally, we discuss new results that suggest that OMPs are inserted primarily near the middle of the cell and packed into supramolecular structures (OMP islands) that are distributed throughout the OM.

Cryo-EM structures reveal multiple stages of bacterial outer membrane protein folding.

Transmembrane ß barrel proteins are folded into the outer membrane (OM) of Gram-negative bacteria by the ß barrel assembly machinery (BAM) via a poorly understood process that occurs without known external energy sources. Here, we used single-particle cryo-EM to visualize the folding dynamics of a model ß barrel protein (EspP) by BAM. We found that BAM binds the highly conserved "ß signal" motif of EspP to correctly orient ß strands in the OM during folding. We also found that the folding of EspP proceeds via "hybrid-barrel" intermediates in which membrane integrated ß sheets are attached to the essential BAM subunit, BamA. The structures show an unprecedented deflection of the membrane surrounding the EspP intermediates and suggest that ß sheets progressively fold toward BamA to form a ß barrel. Along with in vivo experiments that tracked ß barrel folding while the OM tension was modified, our results support a model in which BAM harnesses OM elasticity to accelerate ß barrel folding.

Measurement of the axial vector form factor from antineutrino-proton scattering.

Scattering of high energy particles from nucleons probes their structure, as was done in the experiments that established the non-zero size of the proton using electron beams1. The use of charged leptons as scattering probes enables measuring the distribution of electric charges, which is encoded in the vector form factors of the nucleon2. Scattering weakly interacting neutrinos gives the opportunity to measure both vector and axial vector form factors of the nucleon, providing an additional, complementary probe of their structure. The nucleon transition axial form factor, FA, can be measured from neutrino scattering from free nucleons, νµn → µ-p and [Formula: see text], as a function of the negative four-momentum transfer squared (Q2). Up to now, FA(Q2) has been extracted from the bound nucleons in neutrino-deuterium scattering3-9, which requires uncertain nuclear corrections10. Here we report the first high-statistics measurement, to our knowledge, of the [Formula: see text] cross-section from the hydrogen atom, using the plastic scintillator target of the MINERvA11 experiment, extracting FA from free proton targets and measuring the nucleon axial charge radius, rA, to be 0.73 ± 0.17 fm. The antineutrino-hydrogen scattering presented here can access the axial form factor without the need for nuclear theory corrections, and enables direct comparisons with the increasingly precise lattice quantum chromodynamics computations12-15. Finally, the tools developed for this analysis and the result presented are substantial advancements in our capabilities to understand the nucleon structure in the weak sector, and also help the current and future neutrino oscillation experiments16-20 to better constrain neutrino interaction models.

Function of the Omp85 Superfamily of Outer Membrane Protein Assembly Factors and Polypeptide Transporters.

The Omp85 protein superfamily is found in the outer membrane (OM) of all gram-negative bacteria and eukaryotic organelles of bacterial origin. Members of the family catalyze both the membrane insertion of ß-barrel proteins and the translocation of proteins across the OM. Although the mechanism(s) by which these proteins function is unclear, striking new insights have emerged from recent biochemical and structural studies. In this review we discuss the entire Omp85 superfamily but focus on the function of the best-studied member, BamA, which is an essential and highly conserved component of the bacterial barrel assembly machinery (BAM). Because BamA has multiple functions that overlap with those of other Omp85 proteins, it is likely the prototypical member of the Omp85 superfamily. Furthermore, BamA has become a protein of great interest because of the recent discovery of small-molecule inhibitors that potentially represent an important new class of antibiotics.

Local translation in nuclear condensate amyloid bodies.

Biomolecular condensates concentrate molecules to facilitate basic biochemical processes, including transcription and DNA replication. While liquid-like condensates have been ascribed various functions, solid-like condensates are generally thought of as amorphous sites of protein storage. Here, we show that solid-like amyloid bodies coordinate local nuclear protein synthesis (LNPS) during stress. On stimulus, translationally active ribosomes accumulate along fiber-like assemblies that characterize amyloid bodies. Mass spectrometry analysis identified regulatory ribosomal proteins and translation factors that relocalize from the cytoplasm to amyloid bodies to sustain LNPS. These amyloidogenic compartments are enriched in newly transcribed messenger RNA by Heat Shock Factor 1 (HSF1). Depletion of stress-induced ribosomal intergenic spacer noncoding RNA (rIGSRNA) that constructs amyloid bodies prevents recruitment of the nuclear protein synthesis machinery, abolishes LNPS, and impairs the nuclear HSF1 response. We propose that amyloid bodies support local nuclear translation during stress and that solid-like condensates can facilitate complex biochemical reactions as their liquid counterparts can.

The Escherichia coli outer membrane protein OmpA acquires secondary structure prior to its integration into the membrane.

Almost all proteins that reside in the outer membrane (OM) of Gram-negative bacteria contain a membrane-spanning segment that folds into a unique ß barrel structure and inserts into the membrane by an unknown mechanism. To obtain further insight into outer membrane protein (OMP) biogenesis, we revisited the surprising observation reported over 20 years ago that the Escherichia coli OmpA ß barrel can be assembled into a native structure in vivo when it is expressed as two noncovalently linked fragments. Here, we show that disulfide bonds between ß strand 4 in the N-terminal fragment and ß strand 5 in the C-terminal fragment can form in the periplasmic space and greatly increase the efficiency of assembly of "split" OmpA, but only if the cysteine residues are engineered in perfect register (i.e., they are aligned in the fully folded ß barrel). In contrast, we observed only weak disulfide bonding between ß strand 1 in the N-terminal fragment and ß strand 8 in the C-terminal fragment that would form a closed or circularly permutated ß barrel. Our results not only demonstrate that ß barrels begin to fold into a ß-sheet-like structure before they are integrated into the OM but also help to discriminate among the different models of OMP biogenesis that have been proposed.

Simultaneous Measurement of Muon Neutrino ν_{µ} Charged-Current Single π

Neutrino-induced charged-current single π^{+} production in the Δ(1232) resonance region is of considerable interest to accelerator-based neutrino oscillation experiments. In this Letter, high statistic differential cross sections are reported for the semiexclusive reaction ν_{µ}A→µ^{-}π^{+}+ nucleon(s) on scintillator, carbon, water, iron, and lead targets recorded by MINERvA using a wideband ν_{µ} beam with ⟨E_{ν}⟩≈6 GeV. Suppression of the cross section at low Q^{2} and enhancement of low T_{π} are observed in both light and heavy nuclear targets compared with phenomenological models used in current neutrino interaction generators. The cross sections per nucleon for iron and lead compared with CH across the kinematic variables probed are 0.8 and 0.5 respectively, a scaling which is also not predicted by current generators.

Neutrino-Induced Coherent π

MINERvA has measured the ν_{µ}-induced coherent π^{+} cross section simultaneously in hydrocarbon (CH), graphite (C), iron (Fe), and lead (Pb) targets using neutrinos from 2 to 20 GeV. The measurements exceed the predictions of the Rein-Sehgal and Berger-Sehgal PCAC based models at multi-GeV ν_{µ} energies and at produced π^{+} energies and angles, E_{π}>1 GeV and θ_{π}<10°. Measurements of the cross-section ratios of Fe and Pb relative to CH reveal the effective A scaling to increase from an approximate A^{1/3} scaling at few GeV to an A^{2/3} scaling for E_{ν}>10 GeV.

Simultaneous Measurement of ν_{µ} Quasielasticlike Cross Sections on CH, C, H_{2}O, Fe, and Pb as a Function of Muon Kinematics at MINERvA.

This Letter presents the first simultaneous measurement of the quasielasticlike neutrino-nucleus cross sections on C, water, Fe, Pb, and scintillator (hydrocarbon or CH) as a function of longitudinal and transverse muon momentum. The ratio of cross sections per nucleon between Pb and CH is always above unity and has a characteristic shape as a function of transverse muon momentum that evolves slowly as a function of longitudinal muon momentum. The ratio is constant versus longitudinal momentum within uncertainties above a longitudinal momentum of 4.5 GeV/c. The cross section ratios to CH for C, water, and Fe remain roughly constant with increasing longitudinal momentum, and the ratios between water or C to CH do not have any significant deviation from unity. Both the overall cross section level and the shape for Pb and Fe as a function of transverse muon momentum are not reproduced by current neutrino event generators. These measurements provide a direct test of nuclear effects in quasielasticlike interactions, which are major contributors to long-baseline neutrino oscillation data samples.

Movement kinematic and postural control differences when performing a visuomotor skill in real and virtual environments.

Immersive technologies, like virtual and mixed reality, pose a novel challenge for our sensorimotor systems as they deliver simulated sensory inputs that may not match those of the natural environment. These include reduced fields of view, missing or inaccurate haptic information, and distortions of 3D space; differences that may impact the control of motor actions. For instance, reach-to-grasp movements without end-point haptic feedback are characterised by slower and more exaggerated movements. A general uncertainty about sensory input may also induce a more conscious form of movement control. We tested whether a more complex skill like golf putting was also characterized by more consciously controlled movement. In a repeated-measures design, kinematics of the putter swing and postural control were compared between (i) real-world putting, (ii) VR putting, and (iii) VR putting with haptic feedback from a real ball (i.e., mixed reality). Differences in putter swing were observed both between the real world and VR, and between VR conditions with and without haptic information. Further, clear differences in postural control emerged between real and virtual putting, with both VR conditions characterised by larger postural movements, which were more regular and less complex, suggesting a more conscious form of balance control. Conversely, participants actually reported less conscious awareness of their movements in VR. These findings highlight how fundamental movement differences may exist between virtual and natural environments, which may pose challenges for transfer of learning within applications to motor rehabilitation and sport.

A clostripain-like protease plays a major role in generating the secretome of enterotoxigenic Bacteroides fragilis.

Bacteroides fragilis toxin (BFT) is a protein secreted by enterotoxigenic (ETBF) strains of B. fragilis. BFT is synthesized as a proprotein (proBFT) that is predicted to be a lipoprotein and that is cleaved into two discrete fragments by a clostripain-like protease called fragipain (Fpn). In this study, we obtained evidence that Fpn cleaves proBFT following its transport across the outer membrane. Remarkably, we also found that the disruption of the fpn gene led to a strong reduction in the level of >100 other proteins, many of which are predicted to be lipoproteins, in the culture medium of an ETBF strain. Experiments performed with purified Fpn provided direct evidence that the protease releases at least some of these proteins from the cell surface. The observation that wild-type cells outcompeted an fpn- strain in co-cultivation assays also supported the notion that Fpn plays an important role in cell physiology and is not simply dedicated to toxin biogenesis. Finally, we found that purified Fpn altered the adhesive properties of HT29 intestinal epithelial cells. Our results suggest that Fpn is a broad-spectrum protease that not only catalyzes the protein secretion on a wide scale but that also potentially cleaves host cell proteins during colonization.

Simultaneous Measurement of Proton and Lepton Kinematics in Quasielasticlike ν_{µ}-Hydrocarbon Interactions from 2 to 20 GeV.

Neutrino charged-current quasielastic-like scattering, a reaction category extensively used in neutrino oscillation measurements, probes nuclear effects that govern neutrino-nucleus interactions. This Letter reports the first measurement of the triple-differential cross section for ν_{µ} quasielastic-like reactions using the hydrocarbon medium of the MINERvA detector exposed to a wideband beam spanning 2≤E_{ν}≤20 GeV. The measurement maps the correlations among transverse and longitudinal muon momenta and summed proton kinetic energies, and compares them to predictions from a state-of-art simulation. Discrepancies are observed that likely reflect shortfalls with modeling of pion and nucleon intranuclear scattering and/or spectator nucleon ejection from struck nuclei. The separate determination of leptonic and hadronic variables can inform experimental approaches to neutrino-energy estimation.

Quality of internet information to aid patient decision making in locally advanced and recurrent rectal cancer.

BACKGROUND: To review whether online decision aids are available for patients contemplating pelvic exenteration (PE) for locally advanced and recurrent rectal cancer (LARC and LRRC). METHODS: A grey literature review was carried out using the Google Search™ engine undertaken using a predefined search strategy (PROSPERO database CRD42019122933). Written health information was assessed using the DISCERN criteria and International Patient Decision Aids Standards (IPDAS) with readability content assessed using the Flesch-Kincaid reading ease test and Flesch-Kincaid grade level score. RESULTS: Google search yielded 27, 782, 200 results for the predefined search criteria. 131 sources were screened resulting in the analysis of 6 sources. No sources were identified as a decision aid according to the IPDAS criteria. All sources provided an acceptable quality of written health information, scoring a global score of 3 for the DISCERN written assessment. The median Flesch-Kincaid reading ease was 50.85 (32.5-80.8) equating to a reading age of 15-18 years and the median Flesch-Kincaid grade level score was 7.65 (range 3-9.7), which equates to a reading age of 13-14. CONCLUSIONS: This study has found that there is a paucity of online information for patients contemplating PE. Sources that are available are aimed at a high health literate patient. Given the considerable morbidity associated with PE surgery there is a need for high quality relevant information in this area. A PDA should be developed to improve decision making and ultimately improve patient experience.

Blood parasite diversity (Apicomplexa: Haemogregarinidae) within the western populations of the European pond turtle Emys orbicularis.

Molecular tools have revolutionized assessments of blood parasites in freshwater turtles. In the Iberian Peninsula and North Africa, two native species of terrapins occur, Emys orbicularis (Linnaeus) and Mauremys leprosa (Schweigger). Both have been identified as hosts for the blood parasite Haemogregarina stepanowi Danilewsky, 1885, which has also been found in related species. However, recent assessments of M. leprosa have identified several distinct genetic lineages of these parasites in this host, while only three haemogregarine lineages were identified in E. orbicularis in Tunisia. Here, we screened 215 individuals of E. orbicularis from the Iberian Peninsula, Menorca Island and Morocco for haemogregarine parasites using partial 18S rRNA gene sequences to estimate relationships. Three unrelated lineages of parasites were detected, one presumed H. stepanowi and two lineages previously known from M. leprosa. A considerable undescribed diversity of parasites exists within these vertebrate host species, while mixed infection and host-sharing is also widespread. Considering that E. orbicularis is near threatened in this region, it is of great importance to identify the parasites infecting it, and to further assess the potential deleterious impact of these diverse parasites on their hosts.

A Phylogenetic Assessment of Nematodes (Oxyuroidea: Pharyngodonidae) Infecting Moroccan Lizards.

Molecular tools can be used to estimate the phylogeny of species and to identify cryptic diversity, but their use for parasites has lagged behind that of free-ranging organisms. As an example, in North Africa there is minimal molecular data available for helminth parasites of lizards. In this work we used two molecular markers (the nuclear 18S rRNA and the mitochondrial Cytochrome c Oxidase subunit 1) to investigate the diversity of nematodes of the family Pharyngodonidae parasitizing three genera of lizards from Morocco (Chalcides, Quedenfeldtia and Tarentola) and to explore their co-evolutionary history. Morphological assessments indicated that members of three genera were present: Spauligodon, Thelandros, and Parapharyngodon. Phylogenetic analysis of 18S rRNA sequences indicated the monophyly of the genus Spauligodon, and that some lineages could be distinguished, including Spauligodon auziensis from the host species Tarentola mauritanica, and another unnamed lineage from hosts of the genus Chalcides. However, with this slow-evolving marker some species could not be distinguished. The genus Thelandros was not monophyletic, although relationships were not strongly supported. Analysis of the faster evolving mitochondrial marker clearly separated various species of Spauligodon, as well as distinct unnamed lineages identified in the host genus Chalcides and the host Quedenfeldtia moerens.

Development of an intervention to manage knee osteoarthritis risk and symptoms following anterior cruciate ligament injury.

INTRODUCTION: Anterior cruciate ligament (ACL) injury is a risk factor for developing knee osteoarthritis (OA). We developed an intervention to support people manage risk factors for OA. METHODS: We conducted one-on-one interviews with 20 individuals with OA symptoms 6-15 years post ACL injury and used a nominal group process during a workshop with 40 patients and healthcare professionals (HCPs) to elicit information on the intervention content and delivery characteristics (timing, HCPs, and methods). Interview data were analyzed using content analysis. Nominal group ideas with importance ratings ≥5 of 7 met criteria for inclusion. Results were integrated, considering similarities and differences. RESULTS: Eight content categories were identified: 1. understanding knee injury and expectations about recovery; 2. understanding OA risk; 3. understanding OA signs and symptoms; 4. managing OA risk; 5. managing knee OA symptoms; 6. information for influencers; 7. credible sources; and, 8. updates on new evidence and treatments. Delivery timing reflected a lifespan approach from time of injury through symptomatic knee OA management. Although multiple media for delivery were identified, introductory face-to-face discussions and opportunity for re-accessing HCPs were critical. All HCPs who treat people with ACL should be familiar with and able to deliver the intervention. CONCLUSIONS: This co-development approach identified that an intervention to support people with ACL injury to limit and manage knee OA requires content embedded within an easily accessible, multi-media delivery model with capacity for check-back with HCPs that is appealing to different age groups and personal preferences over the lifespan post injury.

Fossil-calibrated time tree of Podarcis wall lizards provides limited support for biogeographic calibration models.

Podarcis wall lizards are endemic to the Mediterranean Basin where they represent the predominant reptile group. Despite being extensively used as model organisms in evolutionary and ecological studies their phylogeny and historical biogeography are still incompletely resolved. Moreover, molecular clock calibrations used in wall lizard phylogeography are based on the assumption of vicariant speciation triggered by the abrupt Mediterranean Sea level rise at the end of the Messinian salinity crisis (MSC). However, the validity of this biogeographic calibration remains untested. In this study we inferred a robust time tree based on multilocus data and fossil calibrations using both gene concatenation and species-tree approaches and including models with gene-flow. We found five deeply divergent, geographically coherent, and well-supported clades comprising species from i) Iberian Peninsula and North Africa; ii) Western Mediterranean islands, iii) Sicilian and Maltese islands; and iv-v) Balkan region and Aegean islands. The mitochondrial tree shows some inconsistencies with the species tree that warrant future investigation. Diversification of main clades is estimated in a short time frame during the Middle Miocene and might have been associated with a period of global climate cooling with the establishment of a marked climatic zonation in Europe. Cladogenetic events within the main clades are scattered throughout the time tree, from the Late Miocene to the Early Pleistocene, suggesting that speciation events in wall lizards reflect a complex interplay between regional topography, climate and geological history rather than a shared major climatic or paleogeographic event. Our absolute time estimates, as well as a relative dating approach, demonstrate that the assumption of a causal link between sea-level rise at the end of the MSC and the diversification of many island endemics is not justified. This study reinforces the notion that multiple dispersal and vicariant events, at different time frames, are required to explain current allopatric distributions and to account for the historical assembly of Mediterranean biota, and cautions against the use of biogeographic calibrations based on the assumption of vicariance.

Systematics, biogeography and evolution of the Saharo-Arabian naked-toed geckos genus Tropiocolotes.

Plate tectonics constitute one of the main mechanisms of biological diversification on Earth, often being associated with cladogenetic events at different phylogenetic levels, as well as with exchange of faunas and floras across previously isolated biogeographic regions. North Africa and Arabia share a complex geological history that dates back to the break-up of the Arabian plate from the African plate ~30-25 Mya, followed by various geological events, such as the formation of the Red Sea or the connection between the African, Arabian and Eurasian plates. Species with Saharo-Arabian distributions have shown a close association between their evolutionary history and these geological events. In this study, we investigate the systematics, biogeography and evolution of the genus Tropiocolotes, a group of small ground-dwelling geckos, comprised by 12 species distributed from the Atlantic coast of North Africa to southwestern Iran. Species delimitation analyses uncovered the existence of high levels of undescribed diversity, with forms here considered at the species level including Tropiocolotes tripolitanus (Mauritania and southern Morocco), T. nattereri (southern Israel) and T. scorteccii (Yemen and Oman). Phylogenetic and biogeographic analyses recovered two main clades, an exclusively African clade and a Saharo-Arabian clade, that split ~25 Mya following the vicariant event mediated by the separation of the Arabian and African plates. The complex geological activity around the Red Sea is associated with the diversification within the Saharo-Arabian clade, including the colonization of North Africa from a second Tropiocolotes group. Results also provide new insights into the geographic distribution of Tropiocolotes nubicus, previously considered as exclusively associated to the Nile River valley, extending its known distribution further west, up to the Central Mountains of the Sahara. Accordingly, the Nile River seems to act as a major biogeographic barrier, separating Tropiocolotes nubicus and T. steudneri in their western and eastern margins, respectively.

Molecular phylogenetics of sub-Saharan African natricine snakes, and the biogeographic origins of the Seychelles endemic Lycognathophis seychellensis.

Phylogenetic relationships of sub-Saharan African natricine snakes are understudied and poorly understood, which in turn has precluded analyses of the historical biogeography of the Seychelles endemic Lycognathophis seychellensis. We inferred the phylogenetic relationships of Seychelles and mainland sub-Saharan natricines by analysing a multilocus DNA sequence dataset for three mitochondrial (mt) and four nuclear (nu) genes. The mainland sub-Saharan natricines and L. seychellensis comprise a well-supported clade. Two maximally supported sets of relationships within this clade are (Limnophis,Natriciteres) and (Afronatrix,(Hydraethiops,Helophis)). The relationships of L. seychellensis with respect to these two lineages are not clearly resolved by analysing concatenated mt and nu data. Analysed separately, nu data best support a sister relationship of L. seychellensis with (Afronatrix,(Hydraethiops,Helophis)) and mt data best support a sister relationship with all mainland sub-Saharan natricines. Methods designed to cope with incomplete lineage sorting strongly favour the former hypothesis. Genetic variation among up to 33 L. seychellensis from five Seychelles islands is low. Fossil calibrated divergence time estimates support an overseas dispersal of the L. seychellensis lineage to the Seychelles from mainland Africa ca. 43-25 million years before present (Ma), rather than this taxon being a Gondwanan relic.

Long-term cancer surveillance: results from the Forteo Patient Registry Surveillance Study.

The Forteo Patient Registry estimated the incidence of osteosarcoma in US patients treated with teriparatide and enrolled in the study between 2009 and 2019. No incident cases of osteosarcoma were identified among patients registered, and the crude incidence rate was 0 (95% confidence interval [CI], 0-10.2) cases per million person-years. PURPOSE: The prospective, voluntary Forteo Patient Registry was established to estimate the incidence of osteosarcoma in patients who have received treatment with teriparatide (Forteo). METHODS: Information on US adults prescribed teriparatide and enrolled in the Forteo Patient Registry 2009-2019 was linked with data from participating state cancer registries annually (2010-2019) to identify incident osteosarcoma cases using a standardized linkage algorithm. Teriparatide exposure was ascertained from self-reported data that included teriparatide initiation and demographics necessary to complete linkage. Osteosarcoma cases diagnosed on or after January 1, 2009, were identified by participating state cancer registries. The crude incidence rate (IR) and standardized incidence ratio (SIR) of observed cases to the expected number of cases adjusted to the background rate (3 per million person-years) and corresponding 95% CIs for the occurrence of osteosarcoma were calculated whereby the cumulative amount of person-time observed was adjusted for mortality. RESULTS: Data for 75,247 enrolled patients (representing 361,763 cumulative person-years) were linked to each of 42 participating state cancer registries (covering 93% of the US population), which included information on 6180 cases of osteosarcoma. No matches with incident cases of osteosarcoma following registry enrollment were found. The crude IR was 0 (95% CI, 0-10.2) cases per million person-years and the SIR was 0 (95% CI, 0-3.0). CONCLUSIONS: The ability to draw conclusions about the incidence of osteosarcoma among patients participating in the registry was limited due to the smaller than expected amount of patient follow-up time and the fact that no cases were identified.