Abstract: The genetic make-up of an individual contributes to the susceptibility and response to viral infection. Although environmental, clinical and social factors have a role in the chance of exposure to SARS-CoV-2 and the severity of COVID-19 1,2 , host genetics may also be important. Identifying host-specific genetic factors may reveal biological mechanisms of therapeutic relevance and clarify causal relationships of modifiable environmental risk factors for SARS-CoV-2 infection and outcomes. We formed a global network of researchers to investigate the role of human genetics in SARS-CoV-2 infection and COVID-19 severity. Here we describe the results of three genome-wide association meta-analyses that consist of up to 49,562 patients with COVID-19 from 46 studies across 19 countries. We report 13 genome-wide significant loci that are associated with SARS-CoV-2 infection or severe manifestations of COVID-19. Several of these loci correspond to previously documented associations to lung or autoimmune and inflammatory diseases 3–7 . They also represent potentially actionable mechanisms in response to infection. Mendelian randomization analyses support a causal role for smoking and body-mass index for severe COVID-19 although not for type II diabetes. The identification of novel host genetic factors associated with COVID-19 was made possible by the community of human genetics researchers coming together to prioritize the sharing of data, results, resources and analytical frameworks. This working model of international collaboration underscores what is possible for future genetic discoveries in emerging pandemics, or indeed for any complex human disease.

Abstract: We report an improved draft nucleotide sequence of the 2.3-gigabase genome of maize, an important crop plant and model for biological research. Over 32,000 genes were predicted, of which 99.8% were placed on reference chromosomes. Nearly 85% of the genome is composed of hundreds of families of transposable elements, dispersed nonuniformly across the genome. These were responsible for the capture and amplification of numerous gene fragments and affect the composition, sizes, and positions of centromeres. We also report on the correlation of methylation-poor regions with Mu transposon insertions and recombination, and copy number variants with insertions and/or deletions, as well as how uneven gene losses between duplicated regions were involved in returning an ancient allotetraploid to a genetically diploid state. These analyses inform and set the stage for further investigations to improve our understanding of the domestication and agricultural improvements of maize.

Abstract: We propose a new model for the alignment of fibrillin molecules within fibrillin microfibrils. Automated electron tomography was used to generate three-dimensional microfibril reconstructions to 18.6-Å resolution, which revealed many new organizational details of untensioned microfibrils, including heart-shaped beads from which two arms emerge, and interbead diameter variation. Antibody epitope mapping of untensioned microfibrils revealed the juxtaposition of epitopes at the COOH terminus and near the proline-rich region, and of two internal epitopes that would be 42-nm apart in unfolded molecules, which infers intramolecular folding. Colloidal gold binds microfibrils in the absence of antibody. Comparison of colloidal gold and antibody binding sites in untensioned microfibrils and those extended in vitro, and immunofluorescence studies of fibrillin deposition in cell layers, indicate conformation changes and intramolecular folding. Mass mapping shows that, in solution, microfibrils with periodicities of & lt;70 and & gt;140 nm are stable, but periodicities of ∼100 nm are rare. Microfibrils comprise two in-register filaments with a longitudinal symmetry axis, with eight fibrillin molecules in cross section. We present a model of fibrillin alignment that fits all the data and indicates that microfibril extensibility follows conformation-dependent maturation from an initial head-to-tail alignment to a stable approximately one-third staggered arrangement.

Abstract: Food chain efficiency ( FCE ), the proportion of primary production converted to production of the top trophic level, can influence several ecosystem services as well as the biodiversity and productivity of each trophic level. Aquatic FCE is affected by light and nutrient supply, largely via effects on primary producer stoichiometry that propagate to herbivores and then carnivores. Here, we test the hypothesis that the identity of the top carnivore mediates FCE responses to changes in light and nutrient supply. We conducted a large‐scale, 6‐week mesocosm experiment in which we manipulated light and nutrient (nitrogen and phosphorus) supply and the identity of the carnivore in a 2 × 2 × 2 factorial design. We quantified the response of FCE and the biomass and productivity of each trophic level (phytoplankton, zooplankton, and carnivore). We used an invertebrate, Chaoborus americanus , and a vertebrate, bluegill sunfish ( Lepomis macrochirus ), as the two carnivores in this study because of the large difference in phosphorus requirements between these taxa. We predicted that bluegill would be more likely to experience P‐limitation due to higher P requirements, and hence that FCE would be lower in the bluegill treatments than in the Chaoborus treatments. We also expected the interactive effect of light and nutrients to be stronger in the bluegill treatments. Within a carnivore treatment, we predicted highest FCE under low light and high nutrient supply, as these conditions would produce high‐quality (low C:nutrient) algal resources. In contrast, if food quantity had a stronger effect on carnivore production than food quality, carnivore production would increase proportionally with primary production, thus FCE would be similar across light and nutrient treatments. Carnivore identity mediated the effects of light and nutrients on FCE , and as predicted FCE was higher in food chains with Chaoborus than with bluegill. Also as predicted, FCE in Chaoborus treatments was higher under low light. However, FCE in bluegill treatments was higher at high light supply, opposite to our predictions. In addition, bluegill production increased proportionally with primary production, while Chaoborus production was not correlated with primary production, suggesting that bluegill responded more strongly to food quantity than to food quality. These carnivore taxa differ in traits other than body stoichiometry, for example, feeding selectivity, which may have contributed to the observed differences in FCE between carnivores. Comparison of our results with those from previous experiments showed that FCE responds similarly to light and nutrients in food chains with Chaoborus and larval fish (gizzard shad: Clupeidae), but very differently in food chains with bluegill. These findings warrant further investigation into the mechanisms related to carnivore identity (e.g., developmental stage, feeding selectivity) underlying these responses, and highlight the importance of considering both top‐down and bottom‐up effects when evaluating food chain responses to changing light and nutrient conditions.

Abstract: Fibrillin is the principal structural component of the 10-12 nm diameter elastic microfibrils of the extracellular matrix. We have previously shown that both fibrillin molecules and assembled microfibrils are susceptible to degradation by serine proteases. In this study, we have investigated the potential catabolic effects of six matrix metalloproteinases (MMP-2, MMP-3, MMP-9, MMP-12, MMP-13 and MMP-14) on fibrillin molecules and on intact fibrillin-rich microfibrils isolated from ciliary zonules. Using newly synthesized recombinant fibrillin molecules, major cleavage sites within fibrillin-1 were identified. In particular, the six different MMPs generated a major degradation product of ~ 45 kDa from the N-terminal region of the molecule, whereas treatment of truncated, unprocessed and furin-processed C-termini also generated large degradation products. Introduction of a single ectopia lentis-causing amino acid substitution (E2447K; one-letter symbols for amino acids) in a calcium-binding epidermal growth factor-like domain, predicted to disrupt calcium binding, markedly altered the pattern of C-terminal fibrillin-1 degradation. However, the fragmentation pattern of a mutant fibrillin-1 with a comparable E → K substitution in an upstream calcium-binding epidermal growth factor-like domain was indistinguishable from wild-type molecules. Ultrastructural examination highlighted that fibrillin-rich microfibrils isolated from ciliary zonules were grossly disrupted by MMPs. This is the first demonstration that fibrillin molecules and fibrillin-rich microfibrils are degraded by MMPs and that certain amino acid substitutions change the fragmentation patterns. These studies have important implications for physiological and pathological fibrillin catabolism and for loss of connective tissue elasticity in ageing and disease.

Abstract: In conclusion, our studies address two important topics in lung biology: the lineage relationships of epithelial cells in the distal gas exchange region of the lung and the cellular origins of pulmonary fibrosis. A deeper understanding of epithelial progenitors will help to identify therapies to reverse the cell loss that occurs in a number of lung diseases and not just fibrosis. For fibrosis, defining the relative contributions of each of the different stromal cell types, including pericytes, to the fibrotic process will be important in future studies. In particular, we need to understand whether contributions are direct (through synthesis of ECM) or indirect (through production of growth factors and cytokines). This knowledge has the potential to lead to novel therapeutic strategies for the treatment of pulmonary fibrosis. It has been suggested that 30–50% of the myofibroblasts in the bleomycin model originate from epithelial cells, including type 2 alveolar epithelial cells (AEC2), through a process known as epithelial to mesenchymal transition. According to this model, epithelial cells lose their polarity and assume a fibroblast phenotype, including the expression of stromal markers and secretion of ECM. We addressed this popular hypothesis by generating a knock-in allele to induce the heritable expression of a fluorescent lineage tag in AEC2 cells. In the distal lung, these cells are a source of surfactant proteins, which are critical for proper lung function, and they may also act as a population of stem cells capable of differentiating into type 1 alveolar epithelial cells (AEC1s) ( 4 ). The lineage tag also enabled us to purify AEC2s and their descendants to confirm the morphological findings by examining the expression of different marker genes. Using confocal microscopy and our panel of stromal markers, we saw no evidence that lineage-labeled AEC2 gave rise to any kind of stromal cell. Rather, they differentiate into AEC1 cells, supporting classical models for the lineage relationship of these two cell types. Significantly, the slow conversion of AEC2 to AEC1 cells seen in control lungs is greatly enhanced in response to bleomycin-induced lung injury. Currently, we do not understand the mechanism underlying this change in behavior, but additional analysis of gene expression in AEC2 cells will address this question. We also used our Secretoglobin1a1-CreER knock-in allele to follow the response of epithelial cells of the airways (bronchioles) and a subset of alveolar epithelial cells to bleomycin. Unlike our previous findings with other injury models ( 5 ), we found striking changes in the proliferation and differentiation of these cells after bleomycin injury. However, again, we found no evidence that this labeled population generates fibroblasts. With this foundation in place, we used genetic lineage tracing in the mouse to determine the origin of the fibroblasts within the bleomycin-induced lesions. First, we tested the hypothesis that pericytes are a source of myofibroblasts. We used two different mouse strains carrying transgenes, Ng2-CreER and FoxJ1-CreER, to induce the expression of a fluorescent protein that is heritable and specifically expressed in pericyte-like cells within the alveolar wall. This florescent marker allowed us to follow the fate of this cell type in response to bleomycin. We found that these cells proliferated and expanded within fibroblast foci. Surprisingly, most of the lineage-labeled cells did not express high levels of aSMA. We began by staining tissue sections with antibodies against a panel of commonly used markers for stromal cells and viewing them by confocal microscopy to characterize these cell populations before bleomycin treatment and at different times after it. The markers included α-smooth muscle actin (aSMA and Acta2), which is generally considered a hallmark of myofibroblasts. We also examined other markers including S100a4 (Fsp1), desmin, vimentin, Pdgfra, Pdgfrb, and the surface glycoprotein Ng2 (Cspg4). Some of these markers mark pericytes, a population of cells implicated as a source of myofibroblasts in other fibrotic processes ( 2 , 3 ). These studies revealed a surprising diversity of cells in the fibrotic lesions, with aSMA-positive cells showing the greatest abundance relatively early after the administration of bleomycin. A survey of fresh biopsy samples from patients with IPF suggested that a similar diversity exists in human fibrotic lesions. One factor complicating the study of IPF is that surprisingly little is known about the identities, behaviors, and lineage relationships of the different cell types that make up the gas exchange region of the lung where the disease occurs. This region has a complex 3D structure in which a vast network of capillaries and nonepithelial stromal cells surrounds the millions of thin-walled, air-filled epithelial sacs known as alveoli ( Fig. P1 ; ref. 1 ). To fully understand the process of fibrosis, we focused on high-resolution microscopy of intact normal and fibrotic lung tissue rather than study of cells grown in culture. Idiopathic pulmonary fibrosis (IPF) is a debilitating disease in which the delicate gas exchange region of the lung is gradually replaced by accumulations of ECM and myofibroblasts. These cells are commonly thought to produce components of the ECM, including collagen. Conflicting ideas about the cellular origin of the fibrotic lesions may slow progress to the development of effective therapies for IPF. To address this problem, we combined the power of cell lineage tracing in mice with a model of pulmonary fibrosis induced by bleomycin, an anticancer agent that often results in pulmonary fibrosis as a side effect. We provide evidence that the behaviors of pericytes, a cell type associated with blood vessels, and epithelial cells are modulated in response to bleomycin-induced lung injury. However, neither cell type is a major source of myofibroblasts. These findings should help to focus future efforts at developing therapies for the treatment of IPF.