Bacteria synthesize inorganic polyphosphate (polyP) in response to a wide variety of stresses, and production of polyP is essential for stress response and survival in many important pathogens and ...bacteria used in biotechnological processes. However, surprisingly little is known about the molecular mechanisms that control polyP synthesis. We have therefore developed a novel genetic screen that specifically links growth of
to polyP synthesis, allowing us to isolate mutations leading to enhanced polyP production. Using this system, we have identified mutations in the polyP-synthesizing enzyme polyP kinase (PPK) that lead to dramatic increases in
polyP synthesis but do not substantially affect the rate of polyP synthesis by PPK
These mutations are distant from the PPK active site and found in interfaces between monomers of the PPK tetramer. We have also shown that high levels of polyP lead to intracellular magnesium starvation. Our results provide new insights into the control of bacterial polyP accumulation and suggest a simple, novel strategy for engineering bacteria with increased polyP contents.
PolyP is an ancient, universally conserved biomolecule and is important for stress response, energy metabolism, and virulence in a remarkably broad range of microorganisms. PolyP accumulation by bacteria is also important in biotechnology applications. For example, it is critical to enhanced biological phosphate removal (EBPR) from wastewater. Understanding how bacteria control polyP synthesis is therefore of broad importance in both the fields of bacterial pathogenesis and biological engineering. Using
as a model organism, we have identified the first known mutations in polyP kinase that lead to increases in cellular polyP content.
We consider a class of multi-qubit dephasing models that combine classical noise sources and linear coupling to a bosonic environment, and are controlled by arbitrary sequences of dynamical ...decoupling pulses. Building on a general transfer filter-function framework for open-loop control, we provide an exact representation of the controlled dynamics for arbitrary stationary non-Gaussian classical and quantum noise statistics, with analytical expressions emerging when all dephasing sources are Gaussian. This exact characterization is used to establish two main results. First, we construct multi-qubit sequences that ensure maximum high-order error suppression in both the time and frequency domain and that can be exponentially more efficient than existing ones in terms of total pulse number. Next, we show how long-time multi-qubit storage may be achieved by meeting appropriate conditions for the emergence of a fidelity plateau under sequence repetition, thereby generalizing recent results for single-qubit memory under Gaussian dephasing. In both scenarios, the key step is to endow multi-qubit sequences with a suitable displacement anti-symmetry property, which is of independent interest for applications ranging from environment-assisted entanglement generation to multi-qubit noise spectroscopy protocols.
IMPORTANCE: There are currently no approved treatments for peanut allergy. OBJECTIVE: To assess the efficacy and adverse events of epicutaneous immunotherapy with a peanut patch among peanut-allergic ...children. DESIGN, SETTING, AND PARTICIPANTS: Phase 3, randomized, double-blind, placebo-controlled trial conducted at 31 sites in 5 countries between January 8, 2016, and August 18, 2017. Participants included peanut-allergic children (aged 4-11 years n = 356 without a history of a severe anaphylactic reaction) developing objective symptoms during a double-blind, placebo-controlled food challenge at an eliciting dose of 300 mg or less of peanut protein. INTERVENTIONS: Daily treatment with peanut patch containing either 250 μg of peanut protein (n = 238) or placebo (n = 118) for 12 months. MAIN OUTCOMES AND MEASURES: The primary outcome was the percentage difference in responders between the peanut patch and placebo patch based on eliciting dose (highest dose at which objective signs/symptoms of an immediate hypersensitivity reaction developed) determined by food challenges at baseline and month 12. Participants with baseline eliciting dose of 10 mg or less were responders if the posttreatment eliciting dose was 300 mg or more; participants with baseline eliciting dose greater than 10 to 300 mg were responders if the posttreatment eliciting dose was 1000 mg or more. A threshold of 15% or more on the lower bound of a 95% CI around responder rate difference was prespecified to determine a positive trial result. Adverse event evaluation included collection of treatment-emergent adverse events (TEAEs). RESULTS: Among 356 participants randomized (median age, 7 years; 61.2% male), 89.9% completed the trial; the mean treatment adherence was 98.5%. The responder rate was 35.3% with peanut-patch treatment vs 13.6% with placebo (difference, 21.7% 95% CI, 12.4%-29.8%; P < .001). The prespecified lower bound of the CI threshold was not met. TEAEs, primarily patch application site reactions, occurred in 95.4% and 89% of active and placebo groups, respectively. The all-causes rate of discontinuation was 10.5% in the peanut-patch group vs 9.3% in the placebo group. CONCLUSIONS AND RELEVANCE: Among peanut-allergic children aged 4 to 11 years, the percentage difference in responders at 12 months with the 250-μg peanut-patch therapy vs placebo was 21.7% and was statistically significant, but did not meet the prespecified lower bound of the confidence interval criterion for a positive trial result. The clinical relevance of not meeting this lower bound of the confidence interval with respect to the treatment of peanut-allergic children with epicutaneous immunotherapy remains to be determined. TRIAL REGISTRATION: ClinicalTrials.gov Identifier: NCT02636699
Cranial endocasts, or the internal molds of the braincase, are a crucial correlate for investigating the neuroanatomy of extinct vertebrates and tracking brain evolution through deep time. ...Nevertheless, the validity of such studies pivots on the reliability of endocasts as a proxy for brain morphology. Here, we employ micro‐computed tomography imaging, including diffusible iodine‐based contrast‐enhanced CT, and a three‐dimensional geometric morphometric framework to examine both size and shape differences between brains and endocasts of two exemplar archosaur taxa – the American alligator (Alligator mississippiensis) and the domestic chicken (Gallus gallus). With ontogenetic sampling, we quantitatively evaluate how endocasts differ from brains and whether this deviation changes during development. We find strong size and shape correlations between brains and endocasts, divergent ontogenetic trends in the brain‐to‐endocast correspondence between alligators and chickens, and a comparable magnitude between brain–endocast shape differences and intraspecific neuroanatomical variation. The results have important implications for paleoneurological studies in archosaurs. Notably, we demonstrate that the pattern of endocranial shape variation closely reflects brain shape variation. Therefore, analyses of endocranial morphology are unlikely to generate spurious conclusions about large‐scale trends in brain size and shape. To mitigate any artifacts, however, paleoneurological studies should consider the lower brain–endocast correspondence in the hindbrain relative to the forebrain; higher size and shape correspondences in chickens than alligators throughout postnatal ontogeny; artificially ‘pedomorphic’ shape of endocasts relative to their corresponding brains; and potential biases in both size and shape data due to the lack of control for ontogenetic stages in endocranial sampling.
Background
Epicutaneous immunotherapy with investigational Viaskin™ Peanut 250 μg (DBV712) has demonstrated statistically superior desensitization versus placebo in peanut‐allergic children in ...clinical trials. It is unclear whether serologic biomarkers predict response.
Methods
Serum‐specific IgG4 and IgE (whole peanut and components) from subjects enrolled in the phase 3 Efficacy and Safety of Viaskin Peanut in Children With IgE‐Mediated Peanut Allergy study were examined by exploratory univariate and multivariate analyses to determine trajectories and predictors of treatment response, based upon peanut protein eliciting dose (ED) at Month (M) 12 double‐blind placebo‐controlled food challenge.
Results
Among Viaskin Peanut‐treated subjects, peanut sIgG4 significantly increased from baseline through M12 and peanut sIgE peaked at M3 and fell below baseline by M12, with sIgG4 and sIgE peanut components mirroring these trajectories. Placebo subjects had no significant changes. By univariate analysis, M12 peanut sIgG4/sIgE was higher in treatment responders (p < 0.001) and had highest area under the curve (AUC) for predicting ED ≥300 mg and ≥1000 mg (AUC 69.5% and 69.9%, respectively). M12 peanut sIgG4/sIgE >20.1 predicted M12 ED ≥300 mg (80% positive predictive value). The best performing component was Ara h 1 sIgE <15.7 kUA/L (AUC 66.5%). A multivariate model combining Ara h 1 and peanut sIgG4/sIgE had an AUC of 68.2% (ED ≥300 mg) and 67.8% (ED ≥1000 mg).
Conclusions
Peanut sIgG4 rise most clearly differentiated Viaskin Peanut versus placebo subjects. sIgG4/sIgE ratios >20.1 and the combination of Ara h 1 and peanut sIgG4/sIgE had moderate ability to predict treatment response and could potentially be useful for clinical monitoring. Additional data are needed to confirm these relationships.
This phase 3 double‐blind placebo‐controlled food challenge examined serum‐specific IgG4 and IgE (whole peanut and components) in the subjects enrolled in Efficacy and Safety of Viaskin Peanut in Children With IgE‐Mediated Peanut Allergy study. Among 4‐ to 11‐year‐old participants, peanut‐specific IgG4 levels could distinguish DBV712‐treated subjects from placebo‐treated subjects. Month 12 peanut‐specific IgG4/IgE ratio as well as month 12 peanut‐specific Ara h 2 levels had moderate predictability for an eliciting dose ≥300 mg peanut protein.Abbreviations: AUC, area under the curve; DBPCFC, double‐blind placebo‐controlled food challenge; DBV712, investigational peanut EPIT; EPIT, epicutaneous immunotherapy; Ig, immunoglobulin; M, month; PEPITES, Efficacy and Safety of Viaskin Peanut in Children With IgE‐Mediated Peanut Allergy
One of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virulence factors is the ability to interact with high affinity to the ACE2 receptor, which mediates viral entry into cells. ...The results of our study demonstrate that within a few passages in cell culture, both the natural isolate of SARS-CoV-2 and the recombinant cDNA-derived variant acquire an additional ability to bind to heparan sulfate (HS). This promotes a primary attachment of viral particles to cells before their further interactions with the ACE2. Interaction with HS is acquired through multiple mechanisms. These include (i) accumulation of point mutations in the N-terminal domain (NTD) of the S protein, which increases the positive charge of the surface of this domain, (ii) insertions into the NTD of heterologous peptides containing positively charged amino acids, and (iii) mutation of the first amino acid downstream of the furin cleavage site. This last mutation affects S protein processing, transforms the unprocessed furin cleavage site into the heparin-binding peptide, and makes viruses less capable of syncytium formation. These viral adaptations result in higher affinity of viral particles to heparin, dramatic increase in plaque sizes, more efficient viral spread, higher infectious titers, and 2 orders of magnitude higher infectivity. The detected adaptations also suggest an active role of NTD in virus attachment and entry. As in the case of other RNA-positive (RNA+) viruses, evolution to HS binding may result in virus attenuation in vivo. IMPORTANCE The spike protein of SARS-CoV-2 is a major determinant of viral pathogenesis. It mediates binding to the ACE2 receptor and, later, fusion of viral envelope and cellular membranes. The results of our study demonstrate that SARS-CoV-2 rapidly evolves during propagation in cultured cells. Its spike protein acquires mutations in the NTD and in the P1′ position of the furin cleavage site (FCS). The amino acid substitutions or insertions of short peptides in NTD are closely located on the protein surface and increase its positive charge. They strongly increase affinity of the virus to heparan sulfate, make it dramatically more infectious for the cultured cells, and decrease the genome equivalent to PFU (GE/PFU) ratio by orders of magnitude. The S686G mutation also transforms the FCS into the heparin-binding peptide. Thus, the evolved SARS-CoV-2 variants efficiently use glycosaminoglycans on the cell surface for primary attachment before the high-affinity interaction of the spikes with the ACE2 receptor.
Many vertebrates (e.g., chameleons, bovids, hornbills) possess cranial elaborations; however, studies investigating the morphological variation of these structures are rare. For example, the ...conspicuous cranial casques of modern cassowaries have long been hypothesized to perform a number of functions (e.g., physical ramming, vocalization, thermoregulation, visual display) despite an absence of quantitative methodologies to determine whether ornament shape variation within the group aligns with proposed biological roles. In order to fill this data gap, we compared casque shape between sexes and native geographic regions in a large sample of adult southern cassowaries (Casuarius casuarius; n = 103). We quantified casque shape in lateral and rostral views using elliptical Fourier analysis, ordinated the shape data, and used multivariate analysis of variance to address specific comparisons. We hypothesized that casques would be sexually dimorphic and regionally specific, consistent with proposed display functions. However, we found no significant differences in casque shape between female and male C. casuariusand few significant shape differences between individuals from specific geographical areas. Much of the intraspecific casque shape variation, particularly from the rostral aspect, is due to asymmetries across the midline. In our sample, casques were 77.5% rightward deviating, 20.7% leftward deviating, and 1.8% non‐deviating. Although it is unclear if this directional casque asymmetry provides a functional advantage, future studies may elucidate this feature. Altogether, two‐dimensional shape analysis does not support a role for the casque as a de factodiscriminator between sexes nor regional sub‐populations in C. casuarius. These findings stand in contrast to those of other ornamented birds (e.g., Numida meleagris) and potentially point towards alternative biological functions.
Extant cassowaries (Casuarius) are unique flightless birds found in the tropics of Indo‐Australia. They have garnered substantial attention from anatomists with focus centered on the bony makeup and ...function of their conspicuous cranial casques, located dorsally above the orbits and neurocranium. The osteological patterning of the casque has been formally described previously; however, there are differing interpretations between authors. These variable descriptions suggest that an anatomical understanding of casque anatomy and its constituent elements may be enhanced by developmental studies aimed at further elucidating this bizarre structure. In the present study, we clarify casque osteology of the southern cassowary (C. casuarius) by detailing casque anatomy across an extensive growth series for the first time. We used micro‐computed tomography (μCT) imaging to visualize embryonic development and post‐hatching ontogeny through adulthood. We also sampled closely related emus (Dromaius novaehollandiae) and ostriches (Struthio camelus) to provide valuable comparative context. We found that southern cassowary casques are comprised of three paired (i.e., nasals, lacrimals, frontals) and two unpaired elements (i.e., mesethmoid, median casque element). Although lacrimals have rarely been considered as casque elements, the contribution to the casque structure was evident in μCT images. The median casque element has often been cited as a portion of the mesethmoid. However, through comparisons between immature C. casuarius and D. novaehollandiae, we document the median casque element as a distinct unit from the mesethmoid.
Immunoglobulin A nephropathy (IgAN) is the most common primary glomerulonephritis worldwide and a frequent cause of kidney failure. Currently, the diagnosis necessitates a kidney biopsy, with routine ...immunofluorescence microscopy revealing IgA as the dominant or co-dominant immunoglobulin in the glomerular immuno-deposits, often with IgG and sometimes IgM or both. Complement protein C3 is observed in most cases. IgAN leads to kidney failure in 20-40% of patients within 20 years of diagnosis and reduces average life expectancy by about 10 years. There is increasing clinical, biochemical, and genetic evidence that the complement system plays a paramount role in the pathogenesis of IgAN. The presence of C3 in the kidney immuno-deposits differentiates the diagnosis of IgAN from subclinical glomerular mesangial IgA deposition. Markers of complement activation via the lectin and alternative pathways in kidney-biopsy specimens are associated with disease activity and are predictive of poor outcome. Levels of select complement proteins in the circulation have also been assessed in patients with IgAN and found to be of prognostic value. Ongoing genetic studies have identified at least 30 loci associated with IgAN. Genes within some of these loci encode complement-system regulating proteins that can interact with immune complexes. The growing appreciation for the central role of complement components in IgAN pathogenesis highlighted these pathways as potential treatment targets and sparked great interest in pharmacological agents targeting the complement cascade for the treatment of IgAN, as evidenced by the plethora of ongoing clinical trials.
Vesicular stomatitis virus is a negative-stranded RNA virus. Its nucleoprotein (N) binds the viral genomic RNA and is involved in multiple functions including transcription, replication, and ...assembly. We have determined a 2.9 angstrom structure of a complex containing 10 molecules of the N protein and 90 bases of RNA. The RNA is tightly sequestered in a cavity at the interface between two lobes of the N protein. This serves to protect the RNA in the absence of polynucleotide synthesis. For the RNA to be accessed, some conformational change in the N protein should be necessary.
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