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BACKGROUND Circadian rhythms are evident in basic immune processes, but it is unclear if rhythms exist in clinical endpoints like vaccine protection. Here, we examined associations between COVID-19 vaccination timing and effectiveness.METHODS We retrospectively analyzed a large Israeli cohort with timestamped COVID-19 vaccinations (n = 1,515,754 patients over 12 years old, 99.2% receiving BNT162b2). Endpoints included COVID-19 breakthrough infection and COVID-19–associated emergency department visits and hospitalizations. Our main comparison was among patients vaccinated during morning (800–1159 hours), afternoon (1200–1559 hours), or evening hours (1600–1959 hours). We employed Cox regression to adjust for differences in age, sex, and comorbidities.RESULTS Breakthrough infections differed based on vaccination time, with lowest the rates associated with late morning to early afternoon and highest rates associated with evening vaccination. Vaccination timing remained significant after adjustment for patient age, sex, and comorbidities. Results were consistent in patients who received the basic 2-dose series and who received booster doses. The relationship between COVID-19 immunization time and breakthrough infections was sinusoidal, consistent with a biological rhythm that modifies vaccine effectiveness by 8.6%–25%. The benefits of daytime vaccination were concentrated in younger (50 years old). COVID-19–related hospitalizations varied significantly with the timing of the second booster dose, an intervention reserved for older and immunosuppressed patients (HR = 0.64, morning vs. evening; 95% CI, 0.43–0.97; P = 0.038).CONCLUSION We report a significant association between the time of COVID-19 vaccination and its effectiveness. This has implications for mass vaccination programs.FUNDING NIH.

Metacognition, the ability to think about and regulate one's thinking, is an important factor in effective student learning. One intervention to promote student metacognition is the exam wrapper--a reflection students complete after an exam noting how their performance related to their preparation. Results are mixed on the effect of the exam wrapper use on student achievement in single STEM courses. In this study, we implemented exam wrappers in five large science and math courses and examined their impact on students' course outcomes, as well as students' self-reported behaviors on the Metacognitive Awareness Inventory (results for over 1,100 distinct individuals). Our data include a subset of students who completed exam wrappers in multiple courses simultaneously. We observed a modest but statistically significant positive relation between exam wrapper use and course grades in each course. The relation between exam wrapper use in multiple courses and cumulative grade point average was also statistically significant for male students. These results did not correlate with students' metacognitive awareness, however. These findings have important implications for how instructors construct and implement wrappers to maximize their potential usefulness.

The radiant energy budget and internal heat are fundamental properties of giant planets, but precise determination of these properties remains a challenge. Here, we report measurements of Jupiter's radiant energy budget and internal heat based on Cassini multi-instrument observations. Our findings reveal that Jupiter's Bond albedo and internal heat, 0.503 ± 0.012 and 7.485 ± 0.160 W m-2 respectively, are significantly larger than 0.343 ± 0.032 and 5.444 ± 0.425 Wm-2, the previous best estimates. The new results help constrain and improve the current evolutionary theories and models for Jupiter. Furthermore, the significant wavelength dependency of Jupiter's albedo implies that the radiant energy budgets and internal heat of the other giant planets in our solar system should be re-examined. Finally, the data sets of Jupiter's characteristics of reflective solar spectral irradiance provide an observational basis for the models of giant exoplanets.

To help cells cope with protein misfolding and aggregation, Hsp70 molecular chaperones selectively bind a variety of sequences (“selective promiscuity”). Statistical analyses from substrate-derived peptide arrays reveal that DnaK, the E. coli Hsp70, binds to sequences containing three to five branched hydrophobic residues, although otherwise the specific amino acids can vary considerably. Several high-resolution structures of the substrate -binding domain (SBD) of DnaK bound to peptides reveal a highly conserved configuration of the bound substrate and further suggest that the substrate-binding cleft consists of five largely independent sites for interaction with five consecutive substrate residues. Importantly, both substrate backbone orientations (N- to C- and C- to N-) allow essentially the same backbone hydrogen-bonding and side-chain interactions with the chaperone. In order to rationalize these observations, we performed atomistic molecular dynamics simulations to sample the interactions of all 20 amino acid side chains in each of the five sites of the chaperone in the context of the conserved substrate backbone configurations. The resulting interaction energetics provide the basis set for deriving a predictive model that we call Paladin (Physics-based model of DnaK-Substrate Binding). Trained using available peptide array data, Paladin can distinguish binders and nonbinders of DnaK with accuracy comparable to existing predictors and further predicts the detailed configuration of the bound sequence. Tested using existing DnaK-peptide structures, Paladin correctly predicted the binding register in 10 out of 13 substrate sequences that bind in the N- to C- orientation, and the binding orientation in 16 out of 22 sequences. The physical basis of the Paladin model provides insight into the origins of how Hsp70s bind substrates with a balance of selectivity and promiscuity. The approach described here can be extended to other Hsp70s where extensive peptide array data is not available. Author summary Molecular chaperones are proteins that help prevent misfolding and aggregation of their substrates. This is a complex task, as the cell is very crowded, and the chaperone must efficiently bind to misfolded regions of the client protein while avoiding well-folded proteins. An additional confounding detail is that proteins can enter the binding cleft of some Hsp70s in two orientations, a fact often unaccounted for by existing sequence-based models. Here, we developed a model to describe how client proteins bind to DnaK, the E. coli Hsp70, using physics-based molecular dynamics simulations to quantify the interactions between a variety of peptide substrates and key sites on DnaK. The resulting model, which we call Paladin, provides a physical basis to understand how DnaK binds to specific peptides. Given a sequence, Paladin can predict the precise residues that bind at a specific site on DnaK and can further explain challenging features like the binding orientation, which are typically not predicted by sequence-only models. The Paladin model could be used to design ‘super-binder’ therapeutic peptides to inhibit chaperones like DnaK in E. coli.

This article examines the ways that a shared faculty experience across five partner institutions led to a deep awareness of the curriculum and pedagogy of general chemistry coursework, and ultimately, to a collaborative action plan for student success. The team identified key differences and similarities in course content and instructional experiences. The comparative analysis yielded many more similarities than differences, and therefore, the team shifted its focus from "gap analysis" to an exploration of common curricular challenges. To address these challenges, the team developed content for targeted instructional resources that promoted the success of all STEM students across institutions. This article contextualizes the interinstitutional collaboration and closely examines the interactive components (awareness, analysis, and action), critical tools, and productive attitudes that undergirded the curricular alignment process of the STEM Transfer Student Success Initiative (t-STEM).

Clickers are often used as an active learning tool in face-to-face classes to enhance student engagement and assess student learning. In this article we share the variety of ways that we use clicker questions to promote deliberate practice in large science courses. Deliberate practice is the use of specifically structured exercises that develop the skills and habits of mind essential to improve performance. We use clickers across five different courses in biology, chemistry, and physics at a midsize public research university to develop students' abilities in scientific reasoning and problem solving. We gathered students' views of our practices using the Classroom Response System Perceptions (CRiSP) Questionnaire. Even given the differences in our approaches, the majority of the 1,614 students who responded reported that our clicker questions enhanced their motivation, attention, engagement, and participation in class. Students recognized that we used clickers to provide practice and feedback, addressing their learning needs in real time. Students were less positive about clicker questions making class more enjoyable, and a third of students reported answering without really understanding. These responses may reflect that clickers require students to test themselves before the exam--a critical, though sometimes discomfiting, step to learning.

Radiant energy budgets and internal heat play a key role in the evolution of planets. Here, the authors analyze data from the Cassini mission to show that Jupiter’s radiant energy and internal heat budgets are significantly larger than previous estimates.

The folding fate of a protein in vivo is determined by the interplay between a protein’s folding energy landscape and the actions of the proteostasis network, including molecular chaperones and degradation enzymes. The mechanisms of individual components of the E. coli proteostasis network have been studied extensively, but much less is known about how they function as a system. We used an integrated experimental and computational approach to quantitatively analyze the folding outcomes (native folding versus aggregation versus degradation) of three test proteins biosynthesized in E. coli under a variety of conditions. Overexpression of the entire proteostasis network benefited all three test proteins, but the effect of upregulating individual chaperones or the major degradation enzyme, Lon, varied for proteins with different biophysical properties. In sum, the impact of the E. coli proteostasis network is a consequence of concerted action by the Hsp70 system (DnaK/DnaJ/GrpE), the Hsp60 system (GroEL/GroES), and Lon.

To gain insight into the interplay of processes and species that maintain a correctly folded, functional proteome, we have developed a computational model called FoldEco. FoldEco models the cellular proteostasis network of the E. coli cytoplasm, including protein synthesis, degradation, aggregation, chaperone systems, and the folding characteristics of protein clients. We focused on E. coli because much of the needed input information—including mechanisms, rate parameters, and equilibrium coefficients—is available, largely from in vitro experiments; however, FoldEco will shed light on proteostasis in other organisms. FoldEco can generate hypotheses to guide the design of new experiments. Hypothesis generation leads to system-wide questions and shows how to convert these questions to experimentally measurable quantities, such as changes in protein concentrations with chaperone or protease levels, which can then be used to improve our current understanding of proteostasis and refine the model. A web version of FoldEco is available at http://foldeco.scripps.edu.

Abstract Allosteric coupling between protein domains is fundamental to many cellular processes. For example, Hsp70 molecular chaperones use ATP binding by their actin‐like N‐terminal ATPase domain to control substrate interactions in their C‐terminal substrate‐binding domain, a reaction that is critical for protein folding in cells. Here, we generalize the statistical coupling analysis to simultaneously evaluate co‐evolution between protein residues and functional divergence between sequences in protein sub‐families. Applying this method in the Hsp70/110 protein family, we identify a sparse but structurally contiguous group of co‐evolving residues called a ‘sector’, which is an attribute of the allosteric Hsp70 sub‐family that links the functional sites of the two domains across a specific interdomain interface. Mutagenesis of Escherichia coli DnaK supports the conclusion that this interdomain sector underlies the allosteric coupling in this protein family. The identification of the Hsp70 sector provides a basis for further experiments to understand the mechanism of allostery and introduces the idea that cooperativity between interacting proteins or protein domains can be mediated by shared sectors.

The versatile functions of the heat shock protein 70 (Hsp70) family of molecular chaperones rely on allosteric interactions between their nucleotide-binding and substrate-binding domains, NBD and SBD. Understanding the mechanism of interdomain allostery is essential to rational design of Hsp70 modulators. Yet, despite significant progress in recent years, how the two Hsp70 domains regulate each other's activity remains elusive. Covariance data from experiments and computations emerged in recent years as valuable sources of information towards gaining insights into the molecular events that mediate allostery. In the present study, conservation and covariance properties derived from both sequence and structural dynamics data are integrated with results from Perturbation Response Scanning and in vivo functional assays, so as to establish the dynamical basis of interdomain signal transduction in Hsp70s. Our study highlights the critical roles of SBD residues D481 and T417 in mediating the coupled motions of the two domains, as well as that of G506 in enabling the movements of the α-helical lid with respect to the β-sandwich. It also draws attention to the distinctive role of the NBD subdomains: Subdomain IA acts as a key mediator of signal transduction between the ATP- and substrate-binding sites, this function being achieved by a cascade of interactions predominantly involving conserved residues such as V139, D148, R167 and K155. Subdomain IIA, on the other hand, is distinguished by strong coevolutionary signals (with the SBD) exhibited by a series of residues (D211, E217, L219, T383) implicated in DnaJ recognition. The occurrence of coevolving residues at the DnaJ recognition region parallels the behavior recently observed at the nucleotide-exchange-factor recognition region of subdomain IIB. These findings suggest that Hsp70 tends to adapt to co-chaperone recognition and activity via coevolving residues, whereas interdomain allostery, critical to chaperoning, is robustly enabled by conserved interactions.

Fibroblast growth factors (FGFs) and their receptors are highly conserved signaling molecules that have been implicated in postnatal cardiac remodeling. However, it is not known whether cardiomyocyte-expressed FGF receptors are necessary or sufficient for ventricular remodeling in the adult heart. To determine whether cardiomyocytes were competent to respond to an activated FGF receptor, and to determine if this signal would result in the development of hypertrophy, we engineered a doxycycline (DOX)-inducible, cardiomyocyte-specific, constitutively active FGF receptor mouse model (αMHC-rtTA, TRE-caFgfr1-myc). Echocardiographic and hemodynamic analysis indicated that acute expression of caFGFR1 rapidly and directly increased cardiac contractility, while chronic expression resulted in significant hypertrophy with preservation of systolic function. Subsequent histologic analysis showed increased cardiomyocyte cross-sectional area and regions of myocyte disarray and fibrosis, classic features of hypertrophic cardiomyopathy (HCM). Analysis of downstream pathways revealed a lack of clear activation of classical FGF-mediated signaling pathways, but did demonstrate a reduction in Serca2 expression and troponin I phosphorylation. Isolated ventricular myocytes showed enhanced contractility and reduced relaxation, an effect that was partially reversed by inhibition of actin-myosin interactions. We conclude that adult cardiomyocytes are competent to transduce FGF signaling and that FGF signaling is sufficient to promote increased cardiomyocyte contractility in vitro and in vivo through enhanced intrinsic actin-myosin interactions. Long-term, FGFR overexpression results in HCM with a dynamic outflow tract obstruction, and may serve as a unique model of HCM.

Catalysis of ADP-ATP exchange by nucleotide exchange factors (NEFs) is central to the activity of Hsp70 molecular chaperones. Yet, the mechanism of interaction of this family of chaperones with NEFs is not well understood in the context of the sequence evolution and structural dynamics of Hsp70 ATPase domains. We studied the interactions of Hsp70 ATPase domains with four different NEFs on the basis of the evolutionary trace and co-evolution of the ATPase domain sequence, combined with elastic network modeling of the collective dynamics of the complexes. Our study reveals a subtle balance between the intrinsic (to the ATPase domain) and specific (to interactions with NEFs) mechanisms shared by the four complexes. Two classes of key residues are distinguished in the Hsp70 ATPase domain: (i) highly conserved residues, involved in nucleotide binding, which mediate, via a global hinge-bending, the ATPase domain opening irrespective of NEF binding, and (ii) not-conserved but co-evolved and highly mobile residues, engaged in specific interactions with NEFs (e.g., N57, R258, R262, E283, D285). The observed interplay between these respective intrinsic (pre-existing, structure-encoded) and specific (co-evolved, sequence-dependent) interactions provides us with insights into the allosteric dynamics and functional evolution of the modular Hsp70 ATPase domain.

The south residual polar cap of Mars, rich in C[O.sub.2] ice, is compositionally distinct from the north residual cap which is dominantly [H.sub.2]O ice. The south cap is also morphologically distinct, displaying a bewildering variety of depressions formed in thin layered deposits, which have been observed to change by scarp retreat over an interval of one Mars year (Malin et al., 2001, Science 294, 2146-2148). The climatically sensitive locale of the residual caps suggests that their behavior may help in the interpretation of recent fluctuations or repeatability of the Mars climate. We have used Mars Global Surveyor Mars Orbiter Camera (MOC) images obtained in three southern summers to map the variety of features in the south residual cap and to evaluate changes over two Mars years (Mars y). The images show that there are two distinct layered units which were deposited at different times separated by a period of degradation. The older unit, ~10 m thick, has layers approximately 2 m thick. The younger unit has variable numbers of layers, each ~1 m thick. The older unit is eroding by scarp retreat averaging 3.6 m/Mars y, a rate greater than the retreat of 2.2 m/Mars y observed for the younger unit. The rates of scarp retreat and sizes of the different types of depressions indicate that the history of the residual cap has been short periods of deposition interspersed with longer erosional periods. Erosion of the older unit probably occupied ~100-150 Mars y. One layer may have been deposited after the Mariner 9 observations in 1972. Residual cap layers appear to differ from normal annual winter deposits by having a higher albedo and perhaps by having higher porosities. These properties might be produced by differences in the depositional meteorology that affect the fraction of high porosity snow included in the winter deposition. Keywords: Mars; Poles; Atmosphere; Climate

Author(s): F. M. Flasar (corresponding author) [1]; V. G. Kunde [2]; R. K. Achterberg [3]; B. J. Conrath [4]; A. A. Simon-Miller [1]; C. A. Nixon [2]; P. J. Gierasch [...]

Variable surface albedo features on Mars are likely caused by the entrainment and deposition of dust by the wind. Most discrete markings are associated with topographic forms or with regional slopes that serve to alter the effective wind shear stress on the surface. Some of the largest variable features, here termed mesoscale linear streaks, are up to 400 km in length and repeatedly occur in one of the smoothest regions of Mars: Amazonis Planitia. Their orientations and apparent season of variability as observed by Viking and Mars Orbiter cameras indicate linear streak formation by enhanced surface wind stresses during regional or local dust storms and during the initial stages of global dust storms. They provide an example of the ability of large-scale winds, without significant local enhancement, to initiate dust motion on Mars. The sizes and spacing of the linear streaks may be controlled by boundary layer rolls. The repetitive formation of these streaks, over a span of more than 11 Mars years, gives one measure of the stability of Mars' eolian processes. Keywords: Mars; Eolian; Geology; Atmosphere