Untangling causality in midlatitude aerosol–cloud adjustments

Aerosol–cloud interactions represent the leading uncertainty in our ability to infer climate sensitivity from the observational record. The forcing from changes in cloud albedo driven by increases in cloud droplet number (Nd) (the first indirect effect) is confidently negative and has narrowed its probable range in the last decade, but the sign and strength of forcing associated with changes in cloud macrophysics in response to aerosol (aerosol–cloud adjustments) remain uncertain. This uncertainty reflects our inability to accurately quantify variability not associated with a causal link flowing from the cloud microphysical state to the cloud macrophysical state. Once variability associated with meteorology has been removed, covariance between the liquid water path (LWP) averaged across cloudy and clear regions (here characterizing the macrophysical state) and Nd (characterizing the microphysical) is the sum of two causal pathways linking Nd to LWP: Nd altering LWP (adjustments) and precipitation scavenging aerosol and thus depleting Nd. Only the former term is relevant to constraining adjustments, but disentangling these terms in observations is challenging. We hypothesize that the diversity of constraints on aerosol–cloud adjustments in the literature may be partly due to not explicitly characterizing covariance flowing from cloud to aerosol and aerosol to cloud. Here, we restrict our analysis to the regime of extratropical clouds outside of low-pressure centers associated with cyclonic activity. Observations from MAC-LWP (Multisensor Advanced Climatology of Liquid Water Path) and MODIS are compared to simulations in the Met Office Unified Model (UM) GA7.1 (the atmosphere model of HadGEM3-GC3.1 and UKESM1). The meteorological predictors of LWP are found to be similar between the model and observations. There is also agreement with previous literature on cloud-controlling factors finding that increasing stability, moisture, and sensible heat flux enhance LWP, while increasing subsidence and sea surface temperature decrease it. A simulation where cloud microphysics are insensitive to changes in Nd is used to characterize covariance between Nd and LWP that is induced by factors other than aerosol–cloud adjustments. By removing variability associated with meteorology and scavenging, we infer the sensitivity of LWP to changes in Nd. Application of this technique to UM GA7.1 simulations reproduces the true model adjustment strength. Observational constraints developed using simulated covariability not induced by adjustments and observed covariability between Nd and LWP predict a 25 %–30 % overestimate by the UM GA7.1 in LWP change and a 30 %–35 % overestimate in associated radiative forcing

New material of Paleocene-eocene pellornis (aves: Gruiformes) clarifies the pattern and timing of the extant gruiform radiation

Pellornis mikkelseni is an early gruiform from the latest Paleocene-earliest Eocene Fur Formation of Denmark. At approximately 54 million years old, it is among the earliest clear records of the Gruiformes. The holotype specimen, and only material thus far recognised, was originally considered to comprise a partial postcranial skeleton. However, additional mechanical preparation of the nodule containing the holotype revealed that the skeleton is nearly complete and includes a well-preserved skull. In addition to extracting new information from the holotype, we identify and describe two additional specimens of P. mikkelseni which reveal further morphological details of the skeleton. Together, these specimens show that P. mikkelseni possessed a schizorhinal skull and shared many features with the well-known Paleogene Messelornithidae (“Messel rails”). To reassess the phylogenetic position of P. mikkelseni, we modified an existing morphological dataset by adding 20 characters, four extant gruiform taxa, six extinct gruiform taxa, and novel scorings based on the holotype and referred specimens. Phylogenetic analyses recover a clade containing P. mikkelseni, Messelornis, Songzia and crown Ralloidea, supporting P. mikkelseni as a crown gruiform. The phylogenetic position of P. mikkelseni illustrates that some recent divergence time analyses have underestimated the age of crown Gruiformes. Our results suggest a Paleocene origin for this important clade, bolstering evidence for a rapid early radiation of Neoaves following the end-Cretaceous mass extinction.</jats:p

A Regime-Oriented Approach to Observationally Constraining Extratropical Shortwave Cloud Feedbacks

The extratropical shortwave (SW) cloud feedback is primarily due to increases in extratropical liquid cloud extent and optical depth. Here, we examine the response of extratropical (35°–75°) marine cloud liquid water path (LWP) to a uniform 4-K increase in sea surface temperature (SST) in global climate models (GCMs) from phase 5 of the Coupled Model Intercomparison Project (CMIP5) and variants of the HadGEM3-GC3.1 GCM. Compositing is used to partition data into periods inside and out of cyclones. The response of extratropical LWP to a uniform SST increase and associated atmospheric response varies substantially among GCMs, but the sensitivity of LWP to cloud controlling factors (CCFs) is qualitatively similar. When all other predictors are held constant, increasing moisture flux drives an increase in LWP. Increasing SST, holding all other predictors fixed, leads to a decrease in LWP. The combinations of these changes lead to LWP, and by extension reflected SW, increasing with warming in both hemispheres. Observations predict an increase in reflected SW over oceans of 0.8–1.6 W m−2 per kelvin SST increase (35°–75°N) and 1.2–1.9 W m−2 per kelvin SST increase (35°–75°S). This increase in reflected SW is mainly due to increased moisture convergence into cyclones because of increasing available moisture. The efficiency at which converging moisture is converted into precipitation determines the amount of liquid cloud. Thus, cyclone precipitation processes are critical to constraining extratropical cloud feedbacks

Immune-mediated competition in rodent malaria is most likely caused by induced changes in innate immune clearance of merozoites

Malarial infections are often genetically diverse, leading to competitive interactions between parasites. A quantitative understanding of the competition between strains is essential to understand a wide range of issues, including the evolution of virulence and drug resistance. In this study, we use dynamical-model based Bayesian inference to investigate the cause of competitive suppression of an avirulent clone of Plasmodium chabaudi (AS) by a virulent clone (AJ) in immuno-deficient and competent mice. We test whether competitive suppression is caused by clone-specific differences in one or more of the following processes: adaptive immune clearance of merozoites and parasitised red blood cells (RBCs), background loss of merozoites and parasitised RBCs, RBC age preference, RBC infection rate, burst size, and within-RBC interference. These processes were parameterised in dynamical mathematical models and fitted to experimental data. We found that just one parameter μ, the ratio of background loss rate of merozoites to invasion rate of mature RBCs, needed to be clone-specific to predict the data. Interestingly, μ was found to be the same for both clones in single-clone infections, but different between the clones in mixed infections. The size of this difference was largest in immuno-competent mice and smallest in immuno-deficient mice. This explains why competitive suppression was alleviated in immuno-deficient mice. We found that competitive suppression acts early in infection, even before the day of peak parasitaemia. These results lead us to argue that the innate immune response clearing merozoites is the most likely, but not necessarily the only, mediator of competitive interactions between virulent and avirulent clones. Moreover, in mixed infections we predict there to be an interaction between the clones and the innate immune response which induces changes in the strength of its clearance of merozoites. What this interaction is unknown, but future refinement of the model, challenged with other datasets, may lead to its discovery

Maternal effects on anogenital distance in a wild marmot population

Peer reviewedPublisher PD

The acute effects of cocoa flavanols on temporal and spatial attention

In this study, we investigated how the acute physiological effects of cocoa flavanols might result in specific cognitive changes, in particular in temporal and spatial attention. To this end, we pre-registered and implemented a randomized, double-blind, placebo- and baseline-controlled crossover design. A sample of 48 university students participated in the study and each of them completed the experimental tasks in four conditions (baseline, placebo, low dose, and high-dose flavanol), administered in separate sessions with a 1-week washout interval. A rapid serial visual presentation task was used to test flavanol effects on temporal attention and integration, and a visual search task was similarly employed to investigate spatial attention. Results indicated that cocoa flavanols improved visual search efficiency, reflected by reduced reaction time. However, cocoa flavanols did not facilitate temporal attention nor integration, suggesting Potential underlying mechanisms are discussed

In vitro evaluation of modified surface microhardness measurement, focus variation 3D microscopy and contact stylus profilometry to assess enamel surface loss after erosive-abrasive challenges

The aim of the study was to compare surface loss values after erosion-abrasion cycles obtained with modified surface microhardness measurement (mSMH), focus variation 3D microscopy (FVM) and contact stylus profilometry (CSP). We cut human molars into buccal and lingual halves, embedded them in resin and ground 200 μm of enamel away. The resulting surfaces were polished. To maintain a reference area, we applied Block-Out resin to partly cover the enamel surface. The samples were incubated in artificial saliva (37°C; 1 h), then rinsed in deionized water (10 s) and dried with oil-free air (5 s). We immersed the specimens individually in 30 mL citric acid (1%, pH 3.6) for 2 min (25°C, 70 rpm dynamic conditions) before brushing them (50 strokes, 200 g) in an automatic brushing machine with toothpaste-slurry. We calculated the surface loss as per mSMH, by re-measuring the length of the same six indentations made before the abrasive challenge. The experiment consisted of five experimental groups that received between 2 and 10 erosion-abrasion cycles. Each group contained 15 specimens and samples in groups 1, 2, 3, 4 and 5 underwent a total of 2, 4, 6, 8 and 10 cycles, respectively. The resin was removed from the reference area in one piece under 10× magnification and the FVM and CSP were performed. Agreement between the methods was calculated with the intraclass correlation coefficient (ICC) and depicted in Bland-Altman plots. All methods presented a linear pattern of surface loss measurements throughout the experiment, leading overall to a strong, statistically significant correlation between the methods (ICC = 0.85; p<0.001). So, despite the different surface loss values, all methods presented consistent results for surface loss measurement

A Phylogenomic Supertree of Birds

It has long been appreciated that analyses of genomic data (e.g., whole genome sequencing or sequence capture) have the potential to reveal the tree of life, but it remains challenging to move from sequence data to a clear understanding of evolutionary history, in part due to the computational challenges of phylogenetic estimation using genome-scale data. Supertree methods solve that challenge because they facilitate a divide-and-conquer approach for large-scale phylogeny inference by integrating smaller subtrees in a computationally efficient manner. Here, we combined information from sequence capture and whole-genome phylogenies using supertree methods. However, the available phylogenomic trees had limited overlap so we used taxon-rich (but not phylogenomic) megaphylogenies to weave them together. This allowed us to construct a phylogenomic supertree, with support values, that included 707 bird species (~7% of avian species diversity). We estimated branch lengths using mitochondrial sequence data and we used these branch lengths to estimate divergence times. Our time-calibrated supertree supports radiation of all three major avian clades (Palaeognathae, Galloanseres, and Neoaves) near the Cretaceous-Paleogene (K-Pg) boundary. The approach we used will permit the continued addition of taxa to this supertree as new phylogenomic data are published, and it could be applied to other taxa as well.This research was funded by the US National Science Foundation, grant numbers DEB-1655683, DEB-1655624, DEB-1655559, DEB-1655736

Lysine-91 of the tetraheme c-type cytochrome CymA is essential for quinone interaction and arsenate respiration in Shewanella sp. strain ANA-3

The tetraheme c-type cytochrome, CymA, is essential for arsenate respiratory reduction in Shewanella sp. ANA-3, a model arsenate reducer. CymA is predicted to mediate electron transfer from quinols to the arsenate respiratory reductase (ArrAB). Here, we present biochemical and physiological evidence that CymA interacts with menaquinol (MQH2) substrates. Fluorescence quench titration with the MQH2 analog, 2-n-heptyl-4-hydroxyquinoline-N-oxide (HOQNO), was used to demonstrate quinol binding of E. coli cytoplasmic membranes enriched with various forms of CymA. Wild-type CymA bound HOQNO with a Kd of 0.1–1 μM. It was also shown that the redox active MQH2 analog, 2,3-dimethoxy-1,4-naphthoquinone (DMNH2), could reduce CymA in cytoplasmic membrane preparations. Based on a CymA homology model made from the NrfH tetraheme cytochrome structure, it was predicted that Lys91 would be involved in CymA-quinol interactions. CymA with a K91Q substitution showed little interaction with HOQNO. In addition, DMNH2-dependent reduction of CymA-K91Q was diminished by 45% compared to wild-type CymA. A ΔcymA ANA-3 strain containing a plasmid copy of cymA-K91Q failed to grow with arsenate as an electron acceptor. These results suggest that Lys91 is physiologically important for arsenate respiration and support the hypothesis that CymA interacts with menaquinol resulting in the reduction of the cytochrome