Evaluation of GPROF V05 Precipitation Retrievals under Different Cloud Regimes

Precipitation retrievals from passive microwave satellite observations form the basis of many widely used precipitation products, but the performance of the retrievals depends on numerous factors such as surface type and precipitation variability. Previous evaluation efforts have identified bias dependence on precipitation regime, which may reflect the influence on retrievals of recurring factors. In this study, the concept of a regime-based evaluation of precipitation from the Goddard Profiling (GPROF) algorithm is extended to cloud regimes. Specifically, GPROF V05 precipitation retrievals under four different cloud regimes are evaluated against ground radars over the United States. GPROF is generally able to accurately retrieve the precipitation associated with both organized convection and less organized storms, which collectively produce a substantial fraction of global precipitation. However, precipitation from stratocumulus systems is underestimated over land and overestimated over water. Similarly, precipitation associated with trade cumulus environments is underestimated over land, while biases over water depend on the sensor’s channel configuration. By extending the evaluation to more sensors and suppressed environments, these results complement insights previously obtained from precipitation regimes, thus demonstrating the potential of cloud regimes in categorizing the global atmosphere into discrete systems.

Cy3-ATP labeling of unfixed, permeabilized mouse hair cells

ATP-utilizing enzymes play key roles in hair bundles, the mechanically sensitive organelles of sensory hair cells in the inner ear. We used a fluorescent ATP analog, EDA-ATP-Cy3 (Cy3-ATP), to label ATP-binding proteins in two different preparations of unfixed hair-cell stereocilia of the mouse. In the first preparation, we lightly permeabilized dissected cochleas, then labeled them with Cy3-ATP. Hair cells and their stereocilia remained intact, and stereocilia tips in rows 1 and 2 were labeled particularly strongly with Cy3-ATP. In many cases, vanadate (Vi) traps nucleotides at the active site of myosin isoforms and presents nucleotide dissociation. Co-application with Vi enhanced the tip labeling, which is consistent with myosin isoforms being responsible. By contrast, the actin polymerization inhibitors latrunculin A and cytochalasin D had no effect, suggesting that actin turnover at stereocilia tips was not involved. Cy3-ATP labeling was substantially reduced—but did not disappear altogether—in mutant cochleas lacking MYO15A; by contrast, labeling remained robust in cochleas lacking MYO7A. In the second preparation, used to quantify Cy3-ATP labeling, we labeled vestibular stereocilia that had been adsorbed to glass, which demonstrated that tip labeling was higher in longer stereocilia. We found that tip signal was reduced by ~ 50% in Myo15ash2/sh2 stereocilia as compared to Myo15ash2/+stereocilia. These results suggest that MYO15A accounts for a substantial fraction of the Cy3-ATP tip labeling in vestibular hair cells, and so this novel preparation could be utilized to examine the control of MYO15A ATPase activity in situ.

Vγ usage distinguishes pro- and anti-tumor intestinal γδ T cell subsets

γδ T cells physiologically scan the intestinal epithelium, representing a substantial fraction of infiltrating lymphocytes in colorectal cancer (CRC), albeit their role in CRC remains unclear. Using murine CRC models, we found that most γδ T cells in pre- or non-tumor colon express Vγ1+ or Vγ7+ and exhibit a cytotoxic profile. Targeting these γδ T cell subsets, as well as conditionally interfering with γδ T cell function at early stages of tumorigenesis led to heightened tumor development, suggesting anti-CRC functions for Vγ1+ and Vγ7+ subsets. In contrast, RORγt+ γδ T cell subsets, including Vg4+ and microbiota-dependent Vγ6+, accumulated during CRC progression. Conditional deletion of RORγt or Vγ chains revealed redundant roles for IL-17-producing Vγ4+ and Vγ6+ γδ T cells in promoting tumor growth. Our results uncover pro- and anti-tumor roles for γδ T cell subsets.

Impactor material records the ancient lunar magnetic field in antipodal anomalies

The Moon presently has no dynamo, but magnetic fields have been detected over numerous portions of its crust. Most of these regions are located antipodal to large basins, leading to the hypothesis that lunar rock ejected during basin-forming impacts accumulated at the basin antipode and recorded the ambient magnetic field. However, a major problem with this hypothesis is that lunar materials have low iron content and cannot become strongly magnetized. Here we simulate oblique impacts of 100-km-diameter impactors at high resolution and show that an ~700 m thick deposit of potentially iron-rich impactor material accumulates at the basin antipode. The material is shock-heated above the Curie temperature and therefore may efficiently record the ambient magnetic field after deposition. These results explain a substantial fraction of the Moon’s crustal magnetism, and are consistent with a dynamo field strength of at least several tens of microtesla during the basin-forming epoch.

Analytic approximations to photoabsorption cross sections of once-ionized helium in magnetar atmospheres

Magnetar atmospheres can contain a substantial fraction of once-ionized helium. At the magnetic fields about 1014 −1015 G, typical of magnetars, Landau quantization is important not only for the electrons, but also for the centre-of-mass (CM) motion of the He+ ion. The CM and internal motions are mutually dependent, which complicates theoretical studies of the He+ characteristics. We present asymptotic analytic expressions for the binding energies, oscillator strengths, and photoionization cross sections of the moving hydrogenlike ions in an ultra-strong magnetic field, which can be used to construct approximate models of magnetar atmospheres.

Pseudofinder: detection of pseudogenes in prokaryotic genomes

Prokaryotic genomes are generally gene dense and encode relatively few pseudogenes, or nonfunctional/inactivated remnants of genes. However, in certain contexts, such as recent ecological shifts or extreme population bottlenecks (such as those experienced by symbionts and pathogens), pseudogenes can quickly accumulate and form a substantial fraction of the genome. Identification of pseudogenes is, thus, a critical step for understanding the evolutionary forces acting upon, and the functional potential encoded within, prokaryotic genomes. Here, we present Pseudofinder, an open-source software dedicated to pseudogene identification and analysis. With Pseudofinder's multi-pronged, reference-based approach, we demonstrate its capacity to detect a wide variety of pseudogenes, including those that are highly degraded and typically missed by gene-calling pipelines, as well newly formed pseudogenes, which can have only one or a few inactivating mutations. Additionally, Pseudofinder can detect intact genes undergoing relaxed selection, which may indicate incipient pseudogene formation. Implementation of Pseudofinder in annotation pipelines will not only clarify the functional potential of sequenced microbes, but will also generate novel insights and hypotheses regarding the evolutionary dynamics of bacterial and archaeal genomes.

The effect of using local mean versus constant reference salinity to estimate Arctic Ocean freshwater content changes

Changes of high-latitude freshwater content (FWC) play an important role in shaping the variability of polar oceans. FWC is defined as depth-integrated departure of salinity from a reference salinity Sref divided by this Sref . A constant Sref is often used for high-latitude FWC estimates. Here it is argued that for analyzing FWC spatiotemporal changes the use of local mean Sref is a better choice. Analysis of 2007 FWC anomalies in the 25–75 m layer demonstrated, for example, that the choice of Sref = 34.8 (which is often used in climate studies) leads to FWC spatial anomalies exaggerated, on average, by ~0.6 m, which is a substantial fraction of total spatial FWC changes. The problem is aggravated in areas where the difference between the local Sref and Sref = 34.8 is greater. Thus, it is concluded that using climatological mean salinities as Sref provides superior estimates of spatiotemporal Arctic Ocean FWC changes.

Proteome-wide landscape of solubility limits in a bacterial cell

Proteins are prone to aggregate when they are expressed above their solubility limits, a phenomenon termed supersaturation. Aggregation may occur as proteins emerge from the ribosome or after they fold and accumulate in the cell, but the relative importance of these two routes remain poorly known. Here, we systematically probed the solubility limits of each Escherichia coli protein upon overexpression using an image-based screen coupled with machine learning. The analysis suggests that competition between folding and aggregation from the unfolded state governs the two aggregation routes. Remarkably, the majority (70%) of insoluble proteins have low supersaturation risks in their unfolded states and rather aggregate after folding. Furthermore, a substantial fraction (~35%) of the proteome remain soluble at concentrations much higher than those found naturally, indicating a large margin of safety to tolerate gene expression changes. We show that high disorder content and low surface stickiness are major determinants of high solubility and are favored in abundant bacterial proteins. Overall, our proteome-wide study provides empirical insights into the molecular determinants of protein aggregation routes in a bacterial cell.

Online tools to easily build augmented reality models of biomolecules that run right on the web

Several groups developed in the last years augmented and virtual reality (AR/VR) programs and apps to visualize 3D molecules, most rather static, limited in content, and requiring software installs, some even requiring specialized hardware. During the Covid-19 pandemic, our team launched moleculARweb (https://molecularweb.epfl.ch), a website that offers interactive content for chemistry and structural biology education through web-based AR that works on consumer devices like smartphones, tablets and laptops. The website quickly got thousands of student and teacher users, a substantial fraction of them accessing from their homes given the pandemic. Teachers have been increasingly requesting more biological macromolecules to be available in AR, a demand that we cannot satisfy individually. Therefore, to allow them to build their own material, and also to help us expedite development of activities, we built a web interface where any user can build any online AR experience in few steps starting from a PDB structure or from virtual objects/scenes exported from VMD. We here briefly describe the tool, that is accessible at https://molecularweb.epfl.ch/pages/pdb2ar.html.

A virus-specific monocyte inflammatory phenotype is induced by SARS-CoV2 at the immune-epithelial interface

Infection by SARS-CoV2 provokes a potentially fatal pneumonia with multiorgan failure, and high systemic inflammation. To gain mechanistic insight and ferret out the root of this immune dysregulation, we modeled by in vitro co-culture the interactions between infected epithelial cells and immunocytes. A strong response was induced in monocytes and B cells, with a SARS-CoV2-specific inflammatory gene cluster distinct from that seen in influenza-A or Ebola virus-infected co-cultures, and which reproduced deviations reported in blood or lung myeloid cells from COVID-19 patients. A substantial fraction of the effect could be reproduced after individual transfection of several SARS-CoV2 proteins (Spike and some non-structural proteins), mediated by soluble factors, but not via transcriptional induction. This response was greatly muted in monocytes from healthy children, perhaps a clue to the age-dependency of COVID-19. These results suggest that the inflammatory malfunction in COVID-19 is rooted in the earliest perturbations that SARS-CoV2 induces in epithelia.