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Monocyte-derived alveolar macrophages drive lung injury and fibrosis in murine models and are associated with pulmonary fibrosis in humans. Monocyte-derived alveolar macrophages have been suggested to develop a phenotype that promotes lung repair as injury resolves. We compared single-cell and cytokine profiling of the alveolar space in a cohort of 35 patients with post-acute sequelae of COVID-19 who had persistent respiratory symptoms and abnormalities on a computed tomography scan of the chest that subsequently improved or progressed. The abundance of monocyte-derived alveolar macrophages, their gene expression programs, and the level of the monocyte chemokine CCL2 in bronchoalveolar lavage fluid positively associated with the severity of radiographic fibrosis. Monocyte-derived alveolar macrophages from patients with resolving or progressive fibrosis expressed the same set of profibrotic genes. Our findings argue against a distinct reparative phenotype in monocyte-derived alveolar macrophages, highlighting their utility as a biomarker of failed lung repair and a potential target for therapy., (© 2024. The Author(s).)

Statistical shape analysis, or morphometrics, is a technique commonly used in evolutionary biology to summarise a population of samples. Theoretical morphometrics extends the current population of samples into a theoretical space. Using the lawn tennis racket as an example, this paper showcases the potential of morphometrics as a tool for inspiring design concepts for novel sporting goods. It showcases how morphometrics can be applied to summarise the shape of a sample of rackets and applies theoretical morphometrics to systematically present new candidate designs that fall outside of the inputted existing, racket population. The input population was 514 tennis rackets dating back to the origins of the game. The shape analysis was performed on "front-on" silhouette images of the rackets using the R Package Momocs. The outline shape of each racket was reconstructed using the elliptical Fourier transform curve fitting technique. A principal component analysis performed on the reconstructed outlines showed that >90% of the variance in the shape of the rackets was captured by the first two principal components. An evenly spaced grid of theoretical racket shape outlines was then created in a principal component 2 vs. principal component 1 "morphospace". The limits of this space were then expanded to give a theoretical morphospace that extended beyond the range of the first two principal components for the 514 samples. We propose that the shapes located within such a theoretical morphospace could inspire designers and help them to systematically identify candidates for novel products. Specifically, we suggest that experimenting with wide-angled throats and heads with angled sides might be an interesting starting point for exploring future tennis racket design concepts. The novel technique presented here could be used by a sporting goods brand during the ideation phase of product development to schematically summarise current designs and identify candidates for new ones., Competing Interests: None, (Copyright: © 2024 Grant et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The evolution of T cell molecular signatures in the distal lung of patients with severe pneumonia is understudied. Here, we analyzed T cell subsets in longitudinal bronchoalveolar lavage fluid samples from 273 patients with severe pneumonia, including unvaccinated patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) or with respiratory failure not linked to pneumonia. In patients with SARS-CoV-2 pneumonia, activation of interferon signaling pathways, low activation of the NF-κB pathway and preferential targeting of spike and nucleocapsid proteins early after intubation were associated with favorable outcomes, whereas loss of interferon signaling, activation of NF-κB-driven programs and specificity for the ORF1ab complex late in disease were associated with mortality. These results suggest that in patients with severe SARS-CoV-2 pneumonia, alveolar T cell interferon responses targeting structural SARS-CoV-2 proteins characterize individuals who recover, whereas responses against nonstructural proteins and activation of NF-κB are associated with poor outcomes., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Microglia are necessary for central nervous system (CNS) function during development and play roles in ageing, Alzheimer's disease and the response to demyelinating injury 1-5 . The mitochondrial respiratory chain (RC) is necessary for conventional T cell proliferation 6 and macrophage-dependent immune responses 7-10 . However, whether mitochondrial RC is essential for microglia proliferation or function is not known. We conditionally deleted the mitochondrial complex III subunit Uqcrfs1 (Rieske iron-sulfur polypeptide 1) in the microglia of adult mice to assess the requirement of microglial RC for survival, proliferation and adult CNS function in vivo. Notably, mitochondrial RC function was not required for survival or proliferation of microglia in vivo. RNA sequencing analysis showed that loss of RC function in microglia caused changes in gene expression distinct from aged or disease-associated microglia. Microglia-specific loss of mitochondrial RC function is not sufficient to induce cognitive decline. Amyloid-β plaque coverage decreased and microglial interaction with amyloid-β plaques increased in the hippocampus of 5xFAD mice with mitochondrial RC-deficient microglia. Microglia-specific loss of mitochondrial RC function did impair remyelination following an acute, reversible demyelinating event. Thus, mitochondrial respiration in microglia is dispensable for proliferation but is essential to maintain a proper response to CNS demyelinating injury., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Reducing neuroinflammation, a key contributor to brain aging and neurodegenerative diseases, is a promising strategy for improving cognitive function in these settings. The FDA-approved nucleoside reverse transcriptase inhibitor 3TC (Lamivudine) has been reported to improve cognitive function in old wild-type mice and multiple mouse models of neurodegenerative disease, but its effects on the brain have not been comprehensively investigated. In the current study, we used transcriptomics to broadly characterize the effects of long-term supplementation with a human-equivalent therapeutic dose of 3TC on the hippocampal transcriptome in male and female rTg4510 mice (a commonly studied model of tauopathy-associated neurodegeneration). We found that tauopathy increased hippocampal transcriptomic signatures of neuroinflammation/immune activation, but 3TC treatment reversed some of these effects. We also found that 3TC mitigated tauopathy-associated activation of key transcription factors that contribute to neuroinflammation and immune activation, and these changes were related to improved recognition memory performance. Collectively, our findings suggest that 3TC exerts protective effects against tauopathy in the hippocampus by modulating inflammation and immune activation, and they may provide helpful insight for ongoing clinical efforts to determine if 3TC and/or related therapeutics hold promise for treating neurodegeneration., Competing Interests: Declaration of competing interest None to report., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The ability to sense and respond to proteotoxic insults declines with age, leaving cells vulnerable to chronic and acute stressors. Reproductive cues modulate this decline in cellular proteostasis to influence organismal stress resilience in Caenorhabditis elegans We previously uncovered a pathway that links the integrity of developing embryos to somatic health in reproductive adults. Here, we show that the nuclear receptor NHR-49, an ortholog of mammalian peroxisome proliferator-activated receptor α (PPARα), regulates stress resilience and proteostasis downstream from embryo integrity and other pathways that influence lipid homeostasis and upstream of HSF-1. Disruption of the vitelline layer of the embryo envelope, which activates a proteostasis-enhancing intertissue pathway in somatic cells, triggers changes in lipid catabolism gene expression that are accompanied by an increase in fat stores. NHR-49, together with its coactivator, MDT-15, contributes to this remodeling of lipid metabolism and is also important for the elevated stress resilience mediated by inhibition of the embryonic vitelline layer. Our findings indicate that NHR-49 also contributes to stress resilience in other pathways known to change lipid homeostasis, including reduced insulin-like signaling and fasting, and that increased NHR-49 activity is sufficient to improve proteostasis and stress resilience in an HSF-1-dependent manner. Together, our results establish NHR-49 as a key regulator that links lipid homeostasis and cellular resilience to proteotoxic stress., (© 2024 Sala et al.; Published by Cold Spring Harbor Laboratory Press.)

Nucleoprotein (NP) is a key structural protein of influenza ribonucleoprotein complexes and is central to viral RNA packing and trafficking. NP also determines the sensitivity of influenza to myxovirus resistance protein 1 (MxA), an innate immunity factor that restricts influenza replication. A few critical MxA-resistant mutations have been identified in NP, including the highly conserved proline-283 substitution. This essential proline-283 substitution impairs influenza growth, a fitness defect that becomes particularly prominent at febrile temperature (39°C) when host chaperones are depleted. Here, we biophysically characterize proline-283 NP and serine-283 NP to test whether the fitness defect is caused by the proline-283 substitution introducing folding defects. We show that the proline-283 substitution changes the folding pathway of NP, making NP more aggregation prone during folding, but does not alter the native structure of the protein. These findings suggest that influenza has evolved to hijack host chaperones to promote the folding of otherwise biophysically incompetent viral proteins that enable innate immune system escape.

BACKGROUNDSurvivors of pneumonia, including SARS-CoV-2 pneumonia, are at increased risk for cognitive dysfunction and dementia. In rodent models, cognitive dysfunction following pneumonia has been linked to the systemic release of lung-derived pro-inflammatory cytokines. Microglia are poised to respond to inflammatory signals from the circulation, and their dysfunction has been linked to cognitive impairment in murine models of dementia and in humans.METHODSWe measured levels of 55 cytokines and chemokines in bronchoalveolar lavage fluid and plasma from 341 patients with respiratory failure and 13 healthy controls, including 93 unvaccinated patients with COVID-19 and 203 patients with other causes of pneumonia. We used flow cytometry to sort neuroimmune cells from postmortem brain tissue from 5 patients who died from COVID-19 and 3 patients who died from other causes for single-cell RNA-sequencing.RESULTSMicroglia from patients with COVID-19 exhibited a transcriptomic signature suggestive of their activation by circulating pro-inflammatory cytokines. Peak levels of pro-inflammatory cytokines were similar in patients with pneumonia irrespective of etiology, but cumulative cytokine exposure was higher in patients with COVID-19. Treatment with corticosteroids reduced expression of COVID-19-specific cytokines.CONCLUSIONProlonged lung inflammation results in sustained elevations in circulating cytokines in patients with SARS-CoV-2 pneumonia compared with those with pneumonia secondary to other pathogens. Microglia from patients with COVID-19 exhibit transcriptional responses to inflammatory cytokines. These findings support data from rodent models causally linking systemic inflammation with cognitive dysfunction in pneumonia and support further investigation into the role of microglia in pneumonia-related cognitive dysfunction.FUNDINGSCRIPT U19AI135964, UL1TR001422, P01AG049665, P01HL154998, R01HL149883, R01LM013337, R01HL153122, R01HL147290, R01HL147575, R01HL158139, R01ES034350, R01ES027574, I01CX001777, U01TR003528, R21AG075423, T32AG020506, F31AG071225, T32HL076139.

Astrocytes contribute to brain inflammation in neurological disorders but the molecular mechanisms controlling astrocyte reactivity and their relationship to neuroinflammatory endpoints are complex and poorly understood. In this study, we assessed the role of the calcium channel, Orai1, for astrocyte reactivity and inflammation-evoked depression behaviors in mice. Transcriptomics and metabolomics analysis indicated that deletion of Orai1 in astrocytes downregulates genes in inflammation and immunity, metabolism, and cell cycle pathways, and reduces cellular metabolites and ATP production. Systemic inflammation by peripheral lipopolysaccharide (LPS) increases hippocampal inflammatory markers in WT but not in astrocyte Orai1 knockout mice. Loss of Orai1 also blunts inflammation-induced astrocyte Ca 2+ signaling and inhibitory neurotransmission in the hippocampus. In line with these cellular changes, Orai1 knockout mice showed amelioration of LPS-evoked depression-like behaviors including anhedonia and helplessness. These findings identify Orai1 as an important signaling hub controlling astrocyte reactivity and astrocyte-mediated brain inflammation that is commonly observed in many neurological disorders., (© 2023. Springer Nature Limited.)

One of the largest ecological transitions in carnivoran evolution was the shift from terrestrial to aquatic lifestyles, which has driven morphological diversity in skulls and other skeletal structures. In this paper, we investigate the association between those lifestyles and whisker morphology. However, comparing whisker morphology over a range of species is challenging since the number of whiskers and their positions on the mystacial pads vary between species. Also, each whisker will be at a different stage of growth and may have incurred damage due to wear and tear. Identifying a way to easily capture whisker morphology in a small number of whisker samples would be beneficial. Here, we describe individual and species variation in whisker morphology from two-dimensional scans in red fox, European otter and grey seal. A comparison of long, caudal whiskers shows inter-species differences most clearly. We go on to describe global whisker shape in 24 species of carnivorans, using linear approximations of curvature and taper, as well as traditional morphometric methods. We also qualitatively examine surface texture, or the presence of scales, using scanning electron micrographs. We show that gross whisker shape is highly conserved, with whisker curvature and taper obeying simple linear relationships with length. However, measures of whisker base radius, length, and maybe even curvature, can vary between species and substrate preferences. Specifically, the aquatic species in our sample have thicker, shorter whiskers that are smoother, with less scales present than those of terrestrial species. We suggest that these thicker whiskers may be stiffer and able to maintain their shape and position during underwater sensing, but being stiffer may also increase wear., (© 2023 The Authors. Journal of Morphology published by Wiley Periodicals LLC.)

BACKGROUNDDespite guidelines promoting the prevention and aggressive treatment of ventilator-associated pneumonia (VAP), the importance of VAP as a driver of outcomes in mechanically ventilated patients, including patients with severe COVID-19, remains unclear. We aimed to determine the contribution of unsuccessful treatment of VAP to mortality for patients with severe pneumonia.METHODSWe performed a single-center, prospective cohort study of 585 mechanically ventilated patients with severe pneumonia and respiratory failure, 190 of whom had COVID-19, who underwent at least 1 bronchoalveolar lavage. A panel of intensive care unit (ICU) physicians adjudicated the pneumonia episodes and endpoints on the basis of clinical and microbiological data. Given the relatively long ICU length of stay (LOS) among patients with COVID-19, we developed a machine-learning approach called CarpeDiem, which grouped similar ICU patient-days into clinical states based on electronic health record data.RESULTSCarpeDiem revealed that the long ICU LOS among patients with COVID-19 was attributable to long stays in clinical states characterized primarily by respiratory failure. While VAP was not associated with mortality overall, the mortality rate was higher for patients with 1 episode of unsuccessfully treated VAP compared with those with successfully treated VAP (76.4% versus 17.6%, P < 0.001). For all patients, including those with COVID-19, CarpeDiem demonstrated that unresolving VAP was associated with a transitions to clinical states associated with higher mortality.CONCLUSIONSUnsuccessful treatment of VAP is associated with higher mortality. The relatively long LOS for patients with COVID-19 was primarily due to prolonged respiratory failure, placing them at higher risk of VAP.FUNDINGNational Institute of Allergy and Infectious Diseases (NIAID), NIH grant U19AI135964; National Heart, Lung, and Blood Institute (NHLBI), NIH grants R01HL147575, R01HL149883, R01HL153122, R01HL153312, R01HL154686, R01HL158139, P01HL071643, and P01HL154998; National Heart, Lung, and Blood Institute (NHLBI), NIH training grants T32HL076139 and F32HL162377; National Institute on Aging (NIA), NIH grants K99AG068544, R21AG075423, and P01AG049665; National Library of Medicine (NLM), NIH grant R01LM013337; National Center for Advancing Translational Sciences (NCATS), NIH grant U01TR003528; Veterans Affairs grant I01CX001777; Chicago Biomedical Consortium grant; Northwestern University Dixon Translational Science Award; Simpson Querrey Lung Institute for Translational Science (SQLIFTS); Canning Thoracic Institute of Northwestern Medicine.

Objective: To evaluate the effects of an interdisciplinary care team (ICT) model delivered by telemedicine on patients with low back pain (LBP)., Design: Retrospective analysis of deidentified pre-existing data., Setting: Retrospective observational study of patients presenting with LBP to a nationwide telemedicine practice using an ICT model., Participants: Over a 9-month period all patients with a diagnosis related to LBP and who had an ICT evaluation (medical doctor, advanced practice provider, health coach, and physical therapist) were included in the study (n=36). A minimum of 2 follow-up physical therapy visits were required for inclusion., Interventions: Patients were evaluated for LBP, received a diagnosis, and were offered a multidisciplinary treatment plan. Additional real-time audio visual medical, health coaching, registered dietician, and physical therapy services were received as deemed clinically appropriate., Main Outcome Measures: Baseline, 30 day, and final pain (mean 81 day) measurements via numerical pain rating scale (NPRS). Baseline and final Patient-Reported Outcomes Measurement Information System (PROMIS)-10 Global Mental/Physical domains., Secondary Outcome Measures: Use of prescription medication, referral for imaging, need for injections, or surgery., Results: 36 patients met criteria. Pain levels included mild (n=6, 16.7%), moderate (n=19, 52.8%), and severe (n=11, 30.6%). Clinically significant pain improvements were noted in 83.3% (n=25) of those with moderate or severe pain. PROMIS Mental and Physical Health categorization from Fair/Poor to Good/Excellent significantly improved over time. The initial 20% (n=7) in Fair/Poor Mental Health improved to 6.3% (n=2) at finish, while the 80% (n=28) in Good/Excellent Mental Health at start improved to 93.8% (n=30) at finish. Regarding Physical Health, 51.4% (n=18) rated Fair/Poor at start and 31.3% (n=10) at finish, while the 48.6% (n=17) rated Good/Excellent at start improved to 68.8% (n=22) at finish. The need for prescription medication was low (n=6, 16.7%) and spinal imaging orders were negligible (n=1, 2.8%). Injections were warranted in 11.4% (n=4) of patients and surgical referral with operative treatment in 2.8% (n=1)., Conclusion: Interdisciplinary care delivered through telemedicine can significantly improve pain and support improved health-related quality of life in patients with LBP, with low rates of imaging, prescription, and interventional use., (© 2023 The Authors.)

Aging is the primary risk factor for most neurodegenerative diseases, including Alzheimer's disease. Major hallmarks of brain aging include neuroinflammation/immune activation and reduced neuronal health/function. These processes contribute to cognitive dysfunction (a key risk factor for Alzheimer's disease), but their upstream causes are incompletely understood. Age-related increases in transposable element (TE) transcripts might contribute to reduced cognitive function with brain aging, as the reverse transcriptase inhibitor 3TC reduces inflammation in peripheral tissues and TE transcripts have been linked with tau pathology in Alzheimer's disease. However, the effects of 3TC on cognitive function with aging have not been investigated. Here, in support of a role for TE transcripts in brain aging/cognitive decline, we show that 3TC: (a) improves cognitive function and reduces neuroinflammation in old wild-type mice; (b) preserves neuronal health with aging in mice and Caenorhabditis elegans; and (c) enhances cognitive function in a mouse model of tauopathy. We also provide insight on potential underlying mechanisms, as well as evidence of translational relevance for these observations by showing that TE transcripts accumulate with brain aging in humans, and that these age-related increases intersect with those observed in Alzheimer's disease. Collectively, our results suggest that TE transcript accumulation during aging may contribute to cognitive decline and neurodegeneration, and that targeting these events with reverse transcriptase inhibitors like 3TC could be a viable therapeutic strategy., (© 2023 The Authors. Aging Cell published by Anatomical Society and John Wiley & Sons Ltd.)

Apoptosis is important for development and tissue homeostasis, and its dysregulation can lead to diseases, including cancer. As an apoptotic effector, BAK undergoes conformational changes that promote mitochondrial outer membrane disruption, leading to cell death. This is termed "activation" and can be induced by peptides from the human proteins BID, BIM, and PUMA. To identify additional peptides that can regulate BAK, we used computational protein design, yeast surface display screening, and structure-based energy scoring to identify 10 diverse new binders. We discovered peptides from the human proteins BNIP5 and PXT1 and three non-native peptides that activate BAK in liposome assays and induce cytochrome c release from mitochondria. Crystal structures and binding studies reveal a high degree of similarity among peptide activators and inhibitors, ruling out a simple function-determining property. Our results shed light on the vast peptide sequence space that can regulate BAK function and will guide the design of BAK-modulating tools and therapeutics., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2023 Elsevier Ltd. All rights reserved.)

Aim: Osteoarthritis (OA) prevalence is increased in ageing and obese populations. This prospective single-arm cohort study aimed to investigate the efficacy of autologous microfragmented adipose tissue treatment of severe knee or shoulder OA. Materials & methods: Participants received an intra-articular microfragmented adipose tissue injection to the affected joint(s). Multiple patient reported outcome measures (PROMS) were recorded from 0 to 52 weeks for 63 consecutive joints. Results: Compared with baseline, there were significant improvements in all PROMS from 2 to 12 weeks and maintained at 52 weeks. Regression analysis revealed an inverse correlation with BMI and change in PROMS for knee joints. Conclusion: Our observed findings suggest this approach represents a safe, effective treatment for moderate-to-severe knee and shoulder OA, although efficacy may be reduced with increasing obesity.

Background: Studying natural, complex behaviours over a range of different species provides insights into the evolution of the brain and behaviour. Whisker movements reveal complex behaviours; however, there does not yet exist a protocol that is able to capture whisker movements and behaviours in a range of different species., New Method: We develop a new protocol and make recommendations for measuring comparative whisker movements and behaviours. Using two set-ups - an enclosure camera set-up and a high-speed video set-up - we capture and measure the whisker movements of sixteen different captive mammal species from four different animal collections., Results: We demonstrate the ability to describe whisker movements and behaviours across a wide range of mammalian species. We describe whisker movements in European hedgehog, Cape porcupine, domestic rabbit, domestic ferret, weasel, European otter and red fox for the first time. We observe whisker movements in all the species we tested, although movement, positions and behaviours vary in a species-specific way., Comparison With Existing Method(s): The high-speed video set-up is based on the protocols of previous studies. The addition of an enclosure video set-up is entirely new, and allows us to include more species, especially large and shy species that cannot be moved into a high-speed filming arena., Conclusions: We make recommendations for comparative whisker behaviour studies, particularly incorporating individual and species-specific considerations. We believe that flexible, comparative behavioural protocols have wide-ranging applications, specifically to better understand links between the brain and complex behaviours., Competing Interests: Declarations of interest None., (Copyright © 2022 The Authors. Published by Elsevier B.V. All rights reserved.)

The sporting goods sector can serve as a proving ground for new technologies. We propose that climbing shoes are an excellent case study for showcasing a systematic approach to bio-inspired design. Foot adaptations to climbing have been described before in some animals and have even been incorporated into bio-inspired products. However, there has not yet been a systematic description of climbing adaptations in mammals, and especially in rock climbing species. We present a description of foot morphology in mammals and compare rock climbing species to those with other locomotion types. Our results show that rock climbing species in our sample had fewer digits and larger anterior pads than arboreal species. Rock climbing species often had hooves or, if they had foot pads, these were relatively smooth. These examples look a bit like current climbing shoe designs, perhaps suggesting convergent evolution. However, there was also variation, with rock climbing species having pads varying in shape, placement and texture. Much of this variation is likely to be dependent on the relatedness of species, with those that are more related having more similar feet. We suggest that incorporation of novel textures and compliant pads might be an interesting focus for future climbing shoe designs.

Facial bristles are one of the least described feather types and have not yet been systematically studied across phylogenetically diverse avian species. Consequently, little is known about their form, function and evolutionary history. Here we address this knowledge gap by characterising the evolution of facial bristles for the first time. We especially focus on rictal bristle presence and their associations with foraging behaviour, diet and habitat preferences in 1022 avian species, representing 91 families in 29 orders. Results reveal that upper rictal, lower rictal and interramal bristles were likely to be present in the most recent common ancestor of this avian phylogeny, whereas narial bristles were likely to be absent. Rictal bristle presence, length and shape varied both within and between avian orders, families and genera. Rictal bristles were gained or lost multiple times throughout evolution, which suggest that the different morphologies observed within species might not be homologous. Phylogenetic relatedness is also not likely to be the only driver of rictal bristle presence and morphology. Rictal bristle presence and length were associated with species-specific ecological traits, especially nocturnality. Our findings suggest that species foraging in low-light conditions are likely to have longer rictal bristles, and that rictal bristles are likely to have evolved in early birds., (© 2022. The Author(s).)

Aging is among the most important risk factors for morbidity and mortality. To contribute toward a molecular understanding of aging, we analyzed age-resolved transcriptomic data from multiple studies. Here, we show that transcript length alone explains most transcriptional changes observed with aging in mice and humans. We present three lines of evidence supporting the biological importance of the uncovered transcriptome imbalance. First, in vertebrates the length association primarily displays a lower relative abundance of long transcripts in aging. Second, eight antiaging interventions of the Interventions Testing Program of the National Institute on Aging can counter this length association. Third, we find that in humans and mice the genes with the longest transcripts enrich for genes reported to extend lifespan, whereas those with the shortest transcripts enrich for genes reported to shorten lifespan. Our study opens fundamental questions on aging and the organization of transcriptomes., (© 2022. The Author(s).)

Alzheimer's disease is the most frequent form of dementia in elderly people. The triple transgenic (3xTg-AD) mouse model of Alzheimer's Disease is important in biomedical research as these mice develop both neuropathological and behavioural phenotypes. However, their behavioural phenotype is variable, with findings depending on the specific task, as well as the age and sex of the mice. Whisker movements show motor, sensory and cognitive deficits in mouse models of neurodegenerative disease. Therefore, we examined whisker movements in 3, 12.5 and 17-month-old female 3xTg-AD mice and their B6129S/F2 wildtype controls. Mice were filmed using a high-speed video camera (500 fps) in an open arena during a novel object exploration task. Genotype and age differences were found in mice exploring the arena prior to object contact. Prior to whisker contact, the 3-month-old 3xTg-AD mice had smaller whisker angles compared with the wildtype controls, suggesting an early motor phenotype in these mice. Pre-contact mean angular position at 3 months and whisking amplitude at 17 months of age differed between the 3xTg-AD and wildtype mice. During object contact 3xTg-AD mice did not reduce whisker spread as frequently as the wildtype mice at 12.5 and 17 months, which may suggest sensory or attentional deficits. We show that whisker movements are a powerful behavioural measurement tool for capturing behavioural deficits in mouse models that show complex phenotypes, such as the 3xTg-AD mouse model., (© 2022 The Authors. Genes, Brain and Behavior published by International Behavioural and Neural Genetics Society and John Wiley & Sons Ltd.)

Many nocturnal avian species, such as Strigiformes, Caprimulgiformes and Apterygiformes, have sensitive vibrotactile bristles on their upper bill, especially on their rictus. The anatomy of these bristles can vary, especially in terms of sensitivity (Herbst corpuscle number), bristle length and bristle number. This variation is thought to be associated with foraging - such that diurnal, open foragers have smaller and less-sensitive bristles. Here, we describe bristle morphology and follicle anatomy in the western barn owl (Tyto alba) for the first time, using both live and roadkill wild owls. We show that T. alba have both narial and rictal bristles that are likely to be vibrotactile, since they have Herbst corpuscles around their follicles. We observed more numerous (~8) and longer bristles (~16 mm) on the nares of T. alba, than on the rictal region (~4 and ~13 mm respectively). However, the narial bristle follicles contained fewer Herbst corpuscles in their surroundings (~5) than the rictal bristles (~7); indicating that bristle length is not indicative of sensitivity. As well as bristle length and number varying between different facial regions, they also varied between individuals, although the cause of this variation remains unclear. Despite this variation, the gross anatomy of facial bristle follicles appears to be conserved between nocturnal Strigiformes, Caprimulgiformes and Apterygiformes. Understanding more about how T. alba use their bristles would, therefore, give us greater insights into the function of avian bristles in general., (© 2022 The Authors. Journal of Anatomy published by John Wiley & Sons Ltd on behalf of Anatomical Society.)

Recent advances in non-invasive imaging methods have revitalised the field of comparative anatomy, and reproductive anatomy has been no exception. The reproductive systems of female amniotes present specific challenges, namely their often internal "hidden" anatomy. Quantifying female reproductive systems is crucial to recognising reproductive pathologies, monitoring menstrual cycles, and understanding copulatory mechanics. Here we conduct a review of the application of non-invasive imaging techniques to female amniote reproductive anatomy. We introduce the commonly used imaging modalities of computed tomography (CT) and magnetic resonance imaging (MRI), highlighting their advantages and limitations when applied to female reproductive tissues, and make suggestions for future advances. We also include a case study of micro CT and MRI, along with their associated staining protocols, applied to cadavers of female adult stoats (Mustela erminea). In doing so, we will progress the discussion surrounding the imaging of female reproductive anatomy, whilst also impacting the fields of sexual selection research and comparative anatomy more broadly., (© The Author(s) 2022. Published by Oxford University Press on behalf of the Society for Integrative and Comparative Biology.)

Epithelial polyploidization after injury is a conserved phenomenon recently shown to improve barrier restoration during wound healing. Whether lung injury can induce alveolar epithelial polyploidy is not known. We show that bleomycin injury induces alveolar type 2 cell (AT2) hypertrophy and polyploidy. AT2 polyploidization is also seen in short term ex vivo cultures, where AT2-to-AT1 transdifferentiation is associated with substantial binucleation due to failed cytokinesis. Both hypertrophic and polyploid features of AT2 cells can be attenuated by inhibiting the integrated stress response using the small molecule ISRIB. These data suggest that AT2 hypertrophic growth and polyploidization may be a feature of alveolar epithelial injury. Because AT2 cells serve as facultative progenitors for the distal lung epithelium, a propensity for injury-induced binucleation has implications for AT2 self-renewal and regenerative potential upon reinjury, which may benefit from targeting the integrated stress response.

Of all mammalian vibrissae, those of certain species of pinnipeds are exceptional. Researchers believe that their curious undulating form evolved for hydrodynamic detection. Our understanding of how these whiskers work depends on a geometrical model that captures the crucial pertinent features of the natural vibrissae including its tapering and curvature. It should also account for the form of the whisker when it flexes under external loading. We introduce and study a normal skeleton of a two-dimensional projection of a harbour seal whisker. The normal skeleton is a complete shape descriptor that involves reduction to the centreline equipped with a thickness function of the orthogonal cross-section. The contours of the whisker shape are extracted from a 2D greyscale scan. Our analysis reveals correspondence between the undulations of the width and oscillations of the centreline curvature as functions of arc length. We discuss two possible explanations for that remarkable feature: one based on consideration of growth and the other of plastic deformation. For the latter we employ a mechanical model to demonstrate appearance of curvature oscillations caused by extensive deflection of the undulating whisker due to external loading., (© 2022 IOP Publishing Ltd.)

Most cetaceans are born with vibrissae but they can be lost or reduced in adulthood, especially in odontocetes. Despite this, some species of odontocetes have been found to have functioning vibrissal follicles (including the follicle itself and any remaining vibrissal hair shaft) that play a role in mechanoreception, proprioception and electroreception. This reveals a greater diversity of vibrissal function in odontocetes than in any other mammalian group. However, we know very little about vibrissal follicle form and function across the Cetacea. Here, we qualitatively describe the gross vibrissal follicle anatomy of fetuses of three species of cetaceans, including two odontocetes: Atlantic white-sided dolphin (Lagenorhynchus acutus), harbour porpoise (Phocoena phocoena), and one mysticete: minke whale (Balaenoptera acutorostrata), and compared our findings to previous anatomical descriptions. All three species had few, short vibrissae contained within a relatively simple, single-part follicle, lacking in muscles. However, we observed differences in vibrissal number, follicle size and shape, and innervation distribution between the species. While all three species had nerve fibers around the follicles, the vibrissal follicles of Balaenoptera acutorostrata were innervated by a deep vibrissal nerve, and the nerve fibers of the odontocetes studied were looser and more branched. For example, in Lagenorhynchus acutus, branches of nerve fibers travelled parallel to the follicle, and innervated more superficial areas, rather than just the base. Our anatomical descriptions lend support to the observation that vibrissal morphology is diverse in cetaceans, and is worth further investigation to fully explore links between form and function., (© 2021 The Authors. The Anatomical Record published by Wiley Periodicals LLC on behalf of American Association for Anatomy.)

Pinniped vibrissae are well-adapted to sensing in an aquatic environment, by being morphologically diverse and more sensitive than those of terrestrial species. However, it is both challenging and time-consuming to measure vibrissal sensitivity in many species. In terrestrial species, the infraorbital foramen (IOF) area is associated with vibrissal sensitivity and increases with vibrissal number. While pinnipeds are thought to have large IOF areas, this has not yet been systematically measured before. We investigated vibrissal morphology, IOF area, and skull size in 16 species of pinniped and 12 terrestrial Carnivora species. Pinnipeds had significantly larger skulls and IOF areas, longer vibrissae, and fewer vibrissae than the other Carnivora species. IOF area and vibrissal number were correlated in Pinnipeds, just as they are in terrestrial mammals. However, despite pinnipeds having significantly fewer vibrissae than other Carnivora species, their IOF area was not smaller, which might be due to pinnipeds having vibrissae that are innervated more. We propose that investigating normalized IOF area per vibrissa will offer an alternative way to approximate gross individual vibrissal sensitivity in pinnipeds and other mammalian species. Our data show that many species of pinniped, and some species of felids, are likely to have strongly innervated individual vibrissae, since they have high values of normalized IOF area per vibrissa. We suggest that species that hunt moving prey items in the dark will have more sensitive and specialized vibrissae, especially as they have to integrate between individual vibrissal signals to calculate the direction of moving prey during hunting., (© 2021 The Authors. The Anatomical Record published by Wiley Periodicals LLC on behalf of American Association for Anatomy.)

Tennis racket design has changed from its conception in 1874. While we know that modern tennis rackets are lighter and have larger heads than their wooden predecessors, it is unknown how their gross shape has changed specifically. It is also unknown how racket shape is related to factors that influence performance, like the Transverse and Polar moments of inertia. The aim of this study was to quantify how tennis racket shape has changed over time, with a view to furthering our understanding of how such developments have influenced the game. Two-dimensional morphometric analysis was applied to silhouettes extracted from photographs of 514 rackets dating from 1874 to 2017. A principal component analysis was conducted on silhouette outlines, to allow racket shape to be summarised. The rackets were grouped by age and material for further analysis. Principal Component 1 accounted for 87% of the variation in racket shape. A pairwise Pearson's correlation test indicated that head width and length were both strongly correlated to Principal Component 1 (r = 0.916 & r = 0.801, p-values<0.001). Principal Component 1 was also correlated to the Polar (r = 0.862, p<0.001) and Transverse (r = -0.506, p<0.001) moments of inertia. Racket age and material had a medium (p<0.001, η2p = 0.074) and small (p = 0.015, η2p = 0.017) effect on Principal Component 1, respectively. Mean racket shapes were also generated from the morphometric analyses for the material and age groupings, and we consider how these shape changes may have influenced performance and injury risk. These mean shape groupings could support the development of models, such as finite element analysis, for predicting how historical developments in tennis equipment have affected performance and injury risk., Competing Interests: The authors have declared that no competing interests exist.

The human proteome is replete with short linear motifs (SLiMs) of four to six residues that are critical for protein-protein interactions, yet the importance of the sequence surrounding such motifs is underexplored. We devised a proteomic screen to examine the influence of SLiM sequence context on protein-protein interactions. Focusing on the EVH1 domain of human ENAH, an actin regulator that is highly expressed in invasive cancers, we screened 36-residue proteome-derived peptides and discovered new interaction partners of ENAH and diverse mechanisms by which context influences binding. A pocket on the ENAH EVH1 domain that has diverged from other Ena/VASP paralogs recognizes extended SLiMs and favors motif-flanking proline residues. Many high-affinity ENAH binders that contain two proline-rich SLiMs use a noncanonical site on the EVH1 domain for binding and display a thermodynamic signature consistent with the two-motif chain engaging a single domain. We also found that photoreceptor cilium actin regulator (PCARE) uses an extended 23-residue region to obtain a higher affinity than any known ENAH EVH1-binding motif. Our screen provides a way to uncover the effects of proteomic context on motif-mediated binding, revealing diverse mechanisms of control over EVH1 interactions and establishing that SLiMs can't be fully understood outside of their native context., Competing Interests: TH, SP, SH, RG, MI, VS, GM, AK No competing interests declared, (© 2022, Hwang et al.)

Metazoan proteomes contain many paralogous proteins that have evolved distinct functions. The Ena/VASP family of actin regulators consists of three members that share an EVH1 interaction domain with a 100 % conserved binding site. A proteome-wide screen revealed photoreceptor cilium actin regulator (PCARE) as a high-affinity ligand for ENAH EVH1. Here, we report the surprising observation that PCARE is ~100-fold specific for ENAH over paralogs VASP and EVL and can selectively bind ENAH and inhibit ENAH-dependent adhesion in cells. Specificity arises from a mechanism whereby PCARE stabilizes a conformation of the ENAH EVH1 domain that is inaccessible to family members VASP and EVL. Structure-based modeling rapidly identified seven residues distributed throughout EVL that are sufficient to differentiate binding by ENAH vs. EVL. By exploiting the ENAH-specific conformation, we rationally designed the tightest and most selective ENAH binder to date. Our work uncovers a conformational mechanism of interaction specificity that distinguishes highly similar paralogs and establishes tools for dissecting specific Ena/VASP functions in processes including cancer cell invasion., Competing Interests: TH, SP, SH, MI, RG, GM, AK No competing interests declared, (© 2021, Hwang et al.)

While the average human life span continues to increase, there is little evidence that this is leading to a contemporaneous increase in "healthy years" experienced by our aging population. Consequently, many scientists focus their research on understanding the process of aging and trialing interventions that can promote healthspan. The 2021 Midwest Aging Consortium consensus statement is to develop and further the understanding of aging and age-related disease using the wealth of expertise across universities in the Midwestern United States. This report summarizes the cutting-edge research covered in a virtual symposium held by a consortium of researchers in the Midwestern United States, spanning topics such as senescence biomarkers, serotonin-induced DNA protection, immune system development, multisystem impacts of aging, neural decline following severe infection, the unique transcriptional impact of calorie restriction of different fat depots, the pivotal role of fasting in calorie restriction, the impact of peroxisome dysfunction, and the influence of early life trauma on health. The symposium speakers presented data from studies conducted in a variety of common laboratory animals as well as less-common species, including Caenorhabditis elegans, Drosophila, mice, rhesus macaques, elephants, and humans. The consensus of the symposium speakers is that this consortium highlights the strength of aging research in the Midwestern United States as well as the benefits of a collaborative and diverse approach to geroscience., (© The Author(s) 2021. Published by Oxford University Press on behalf of The Gerontological Society of America. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Active sensing is the process of moving sensors to extract task-specific information. Whisker touch is often referred to as an active sensory system as whiskers are moved with purposeful control. Even though whisker movements are found in many species, it is unknown whether any animal can make task-specific movements with their whiskers. California sea lions (Zalophus californianus) make large, purposeful whisker movements and are capable of performing many whisker-related discrimination tasks. Therefore, California sea lions are an ideal species to explore the active nature of whisker touch sensing. Here, we show that California sea lions can make task-specific whisker movements. California sea lions move their whiskers with large amplitudes around object edges to judge size, make smaller, lateral stroking movements to judge texture and make very small whisker movements during a visual task. These findings, combined with the ease of training mammals and measuring whisker movements, makes whiskers an ideal system for studying mammalian perception, cognition and motor control., Competing Interests: Competing interests The authors declare no competing or financial interests., (© 2021. Published by The Company of Biologists Ltd.)

Rationale: Current guidelines recommend patients with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pneumonia receive empirical antibiotics for suspected bacterial superinfection on the basis of weak evidence. Rates of ventilator-associated pneumonia (VAP) in clinical trials of patients with SARS-CoV-2 pneumonia are unexpectedly low. Objectives: We conducted an observational single-center study to determine the prevalence and etiology of bacterial superinfection at the time of initial intubation and the incidence and etiology of subsequent bacterial VAP in patients with severe SARS-CoV-2 pneumonia. Methods: Bronchoscopic BAL fluid samples from all patients with SARS-CoV-2 pneumonia requiring mechanical ventilation were analyzed using quantitative cultures and a multiplex PCR panel. Actual antibiotic use was compared with guideline-recommended therapy. Measurements and Main Results: We analyzed 386 BAL samples from 179 patients with SARS-CoV-2 pneumonia requiring mechanical ventilation. Bacterial superinfection within 48 hours of intubation was detected in 21% of patients. Seventy-two patients (44.4%) developed at least one VAP episode (VAP incidence rate = 45.2/1,000 ventilator days); 15 (20.8%) initial VAPs were caused by difficult-to-treat pathogens. The clinical criteria did not distinguish between patients with or without bacterial superinfection. BAL-based management was associated with significantly reduced antibiotic use compared with guideline recommendations. Conclusions: In patients with SARS-CoV-2 pneumonia requiring mechanical ventilation, bacterial superinfection at the time of intubation occurs in <25% of patients. Guideline-based empirical antibiotic management at the time of intubation results in antibiotic overuse. Bacterial VAP developed in 44% of patients and could not be accurately identified in the absence of microbiologic analysis of BAL fluid.

Targeting protein - protein interactions (PPIs) has emerged as an important area of discovery for anticancer therapeutic development. In the case of phospho-dependent PPIs, such as the polo-like kinase 1 (Plk1) polo-box domain (PBD), a phosphorylated protein residue can provide high-affinity recognition and binding to target protein hot spots. Developing antagonists of the Plk1 PBD can be particularly challenging if one relies solely on interactions within and proximal to the phospho-binding pocket. Fortunately, the affinity of phospho-dependent PPI antagonists can be significantly enhanced by taking advantage of interactions in both the phospho-binding site and hidden "cryptic" pockets that may be revealed on ligand binding. In our current paper, we describe the design and synthesis of macrocyclic peptide mimetics directed against the Plk1 PBD, which are characterized by a new glutamic acid analog that simultaneously serves as a ring-closing junction that provides accesses to a cryptic binding pocket, while at the same time achieving proper orientation of a phosphothreonine (pT) residue for optimal interaction in the signature phospho-binding pocket. Macrocycles prepared with this new amino acid analog introduce additional hydrogen-bonding interactions not found in the open-chain linear parent peptide. It is noteworthy that this new glutamic acid-based amino acid analog represents the first example of extremely high affinity ligands where access to the cryptic pocket from the pT-2 position is made possible with a residue that is not based on histidine. The concepts employed in the design and synthesis of these new macrocyclic peptide mimetics should be useful for further studies directed against the Plk1 PBD and potentially for ligands directed against other PPI targets.

Study Design: A case-control genome-wide association study (GWAS) on spondylosis., Objective: Leveraging Geisinger's MyCode initiative's multimodal dataset, we aimed to identify genetic associations with degenerative spine disease., Summary of Background Data: Degenerative spine conditions are a leading cause of global disability; however, the genetic underpinnings of these conditions remain under-investigated. Previous studies using candidate-gene approach suggest a genetic risk for degenerative spine conditions, but large-scale GWASs are lacking., Methods: We identified 4434 patients with a diagnosis of spondylosis using ICD diagnosis codes with genotype data available. We identified a population-based control of 12,522 patients who did not have any diagnosis for osteoarthritis. A linear-mix, additive genetic model was employed to perform the genetic association tests adjusting for age, sex, and genetic principal components to account for the population structure and relatedness. Gene-based association tests were performed and heritability and genetic correlations with other traits were investigated., Results: We identified a genome-wide significant locus at rs12190551 (odds ratio = 1.034, 95% confidence interval 1.022-1.046, P = 8.5 × 10-9, minor allele frequency = 36.9%) located in the intron of BMP6. Additionally, NIPAL1 and CNGA1 achieved Bonferroni significance in the gene-based association tests. The estimated heritability was 7.19%. Furthermore, significant genetic correlations with pain, depression, lumbar spine bone mineral density, and osteoarthritis were identified., Conclusion: We demonstrated the use of a massive database of genotypes combined with electronic health record data to identify a novel and significant association spondylosis. We also identified significant genetic correlations with pain, depression, bone mineral density, and osteoarthritis, suggesting shared genetic etiology and molecular pathways with these phenotypes.Level of Evidence: N/A., (Copyright © 2021 Wolters Kluwer Health, Inc. All rights reserved.)

Caseinolytic proteases (Clp) are central to bacterial proteolysis and control cellular physiology and stress responses. They are composed of a double-ring compartmentalized peptidase (ClpP) and a AAA+ unfoldase (ClpX or ClpA/ClpC). Unlike many bacteria, the opportunistic pathogen Pseudomonas aeruginosa contains two ClpP homologs: ClpP1 and ClpP2. The specific functions of these homologs, however, are largely elusive. Here, we report that the active form of PaClpP2 is a part of a heteromeric PaClpP1 7 P2 7 tetradecamer that is required for proper biofilm development. PaClpP1 14 and PaClpP1 7 P2 7 complexes exhibit distinct peptide cleavage specificities and interact differentially with P. aeruginosa ClpX and ClpA. Crystal structures reveal that PaClpP2 has non-canonical features in its N- and C-terminal regions that explain its poor interaction with unfoldases. However, experiments in vivo indicate that the PaClpP2 peptidase active site uniquely contributes to biofilm development. These data strongly suggest that the specificity of different classes of ClpP peptidase subunits contributes to the biological outcome of proteolysis. This specialized role of PaClpP2 highlights it as an attractive target for developing antimicrobial agents that interfere specifically with late-stage P. aeruginosa development., (© 2020 John Wiley & Sons Ltd.)

Pulmonary fibrosis is a relentlessly progressive and often fatal disease with a paucity of available therapies. Genetic evidence implicates disordered epithelial repair, which is normally achieved by the differentiation of small cuboidal alveolar type 2 (AT2) cells into large, flattened alveolar type 1 (AT1) cells as an initiating event in pulmonary fibrosis pathogenesis. Using models of pulmonary fibrosis in young adult and old mice and a model of adult alveologenesis after pneumonectomy, we show that administration of ISRIB, a small molecule that restores protein translation by EIF2B during activation of the integrated stress response (ISR), accelerated the differentiation of AT2 into AT1 cells. Accelerated epithelial repair reduced the recruitment of profibrotic monocyte-derived alveolar macrophages and ameliorated lung fibrosis. These findings suggest a dysfunctional role for the ISR in regeneration of the alveolar epithelium after injury with implications for therapy., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Encoding information into memory is sensitive to distraction while retrieving that memory may be compromised by proactive interference from pre-existing memories. These two debilitating effects are common in neuropsychiatric conditions, but modelling them preclinically to date is slow as it requires prolonged operant training. A step change would be the validation of functionally equivalent but fast, simple, high-throughput tasks based on spontaneous behaviour. Here, we show that spontaneous object preference testing meets these requirements in the subchronic phencyclidine rat model for cognitive impairments associated with schizophrenia. Subchronic phencyclidine rats show clear memory sensitivity to distraction in the standard novel object recognition task. However, due to this, standard novel object recognition task cannot assess proactive interference. Therefore, we compared subchronic phencyclidine performance in standard novel object recognition task to that using the continuous novel object recognition task, which offers minimal distraction, allowing disease-relevant memory deficits to be assessed directly. We first determined that subchronic phencyclidine treatment did not affect whisker movements during object exploration. Subchronic phencyclidine rats exhibited the expected distraction standard novel object recognition task effect but had intact performance on the first continuous novel object recognition task trial, effectively dissociating distraction using two novel object recognition task variants. In remaining continuous novel object recognition task trials, the cumulative discrimination index for subchronic phencyclidine rats was above chance throughout, but, importantly, their detection of object novelty was increasingly impaired relative to controls. We attribute this effect to the accumulation of proactive interference. This is the first demonstration that increased sensitivity to distraction and proactive interference, both key cognitive impairments in schizophrenia, can be dissociated in the subchronic phencyclidine rat using two variants of the same fast, simple, spontaneous object memory paradigm., Competing Interests: Declaration of conflicting interests: The author(s) declared no potential conflicts of interest with respect to the research, authorship and/or publication of this article., (© The Author(s) 2021.)

The huntingtin (HTT) protein transports various organelles, including vesicles containing neurotrophic factors, from embryonic development throughout life. To better understand how HTT mediates axonal transport and why this function is disrupted in Huntington's disease (HD), we study vesicle-associated HTT and find that it is dimethylated at a highly conserved arginine residue (R118) by the protein arginine methyltransferase 6 (PRMT6). Without R118 methylation, HTT associates less with vesicles, anterograde trafficking is diminished, and neuronal death ensues-very similar to what occurs in HD. Inhibiting PRMT6 in HD cells and neurons exacerbates mutant HTT (mHTT) toxicity and impairs axonal trafficking, whereas overexpressing PRMT6 restores axonal transport and neuronal viability, except in the presence of a methylation-defective variant of mHTT. In HD flies, overexpressing PRMT6 rescues axonal defects and eclosion. Arginine methylation thus regulates HTT-mediated vesicular transport along the axon, and increasing HTT methylation could be of therapeutic interest for HD., Competing Interests: Declaration of interests The authors declare no competing interests., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Some patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) develop severe pneumonia and acute respiratory distress syndrome 1 (ARDS). Distinct clinical features in these patients have led to speculation that the immune response to virus in the SARS-CoV-2-infected alveolus differs from that in other types of pneumonia 2 . Here we investigate SARS-CoV-2 pathobiology by characterizing the immune response in the alveoli of patients infected with the virus. We collected bronchoalveolar lavage fluid samples from 88 patients with SARS-CoV-2-induced respiratory failure and 211 patients with known or suspected pneumonia from other pathogens, and analysed them using flow cytometry and bulk transcriptomic profiling. We performed single-cell RNA sequencing on 10 bronchoalveolar lavage fluid samples collected from patients with severe coronavirus disease 2019 (COVID-19) within 48 h of intubation. In the majority of patients with SARS-CoV-2 infection, the alveolar space was persistently enriched in T cells and monocytes. Bulk and single-cell transcriptomic profiling suggested that SARS-CoV-2 infects alveolar macrophages, which in turn respond by producing T cell chemoattractants. These T cells produce interferon-γ to induce inflammatory cytokine release from alveolar macrophages and further promote T cell activation. Collectively, our results suggest that SARS-CoV-2 causes a slowly unfolding, spatially limited alveolitis in which alveolar macrophages containing SARS-CoV-2 and T cells form a positive feedback loop that drives persistent alveolar inflammation.

At low temperatures, protein degradation by the AAA+ HslUV protease is very slow. New crystal structures reveal that residues in the intermediate domain of the HslU 6 unfoldase can plug its axial channel, blocking productive substrate binding and subsequent unfolding, translocation, and degradation by the HslV 12 peptidase. Biochemical experiments with wild-type and mutant enzymes support a model in which heat-induced melting of this autoinhibitory plug activates HslUV proteolysis., Competing Interests: Declaration of interests We, the authors and our immediate family members, have no competing financial interests to declare., (Copyright © 2020 The Author(s). Published by Elsevier Inc. All rights reserved.)

Protein-protein interaction specificity is often encoded at the primary sequence level. However, the contributions of individual residues to specificity are usually poorly understood and often obscured by mutational robustness, sequence degeneracy, and epistasis. Using bacterial toxin-antitoxin systems as a model, we screened a combinatorially complete library of antitoxin variants at three key positions against two toxins. This library enabled us to measure the effect of individual substitutions on specificity in hundreds of genetic backgrounds. These distributions allow inferences about the general nature of interface residues in promoting specificity. We find that positive and negative contributions to specificity are neither inherently coupled nor mutually exclusive. Further, a wild-type antitoxin appears optimized for specificity as no substitutions improve discrimination between cognate and non-cognate partners. By comparing crystal structures of paralogous complexes, we provide a rationale for our observations. Collectively, this work provides a generalizable approach to understanding the logic of molecular recognition., Competing Interests: TL, RG, IN, ML, MG No competing interests declared, ML Reviewing editor, eLife, (© 2020, Lite et al.)

(p)ppGpp is a nucleotide messenger universally produced in bacteria following nutrient starvation. In E. coli, ppGpp inhibits purine nucleotide synthesis by targeting several different enzymes, but the physiological significance of their inhibition is unknown. Here, we report the structural basis of inhibition for one target, Gsk, the inosine-guanosine kinase. Gsk creates an unprecedented, allosteric binding pocket for ppGpp by restructuring terminal sequences, which restrains conformational dynamics necessary for catalysis. Guided by this structure, we generated a chromosomal mutation that abolishes Gsk regulation by ppGpp. This mutant strain accumulates abnormally high levels of purine nucleotides following amino-acid starvation, compromising cellular fitness. We demonstrate that this unrestricted increase in purine nucleotides is detrimental because it severely depletes pRpp and essential, pRpp-derived metabolites, including UTP, histidine, and tryptophan. Thus, our results reveal the significance of ppGpp's regulation of purine nucleotide synthesis and a critical mechanism by which E. coli coordinates biosynthetic processes during starvation., Competing Interests: Declaration of Interests The authors declare no competing interests., (Copyright © 2020 Elsevier Inc. All rights reserved.)

Whiskers are present in many species of mammals. They are specialised vibrotactile sensors that sit within strongly innervated follicles. Whisker size and shape will affect the mechanical signals that reach the follicle, and hence the information that reaches the brain. However, whisker size and shape have not been quantified across mammals before. Using a novel method for describing whisker curvature, this study quantifies whisker size and shape across 19 mammalian species. We find that gross two-dimensional whisker shape is relatively conserved across mammals. Indeed, whiskers are all curved, tapered rods that can be summarised by Euler spiral models of curvature and linear models of taper, which has implications for whisker growth and function. We also observe that aquatic and semi-aquatic mammals have relatively thicker, stiffer, and more highly tapered whiskers than arboreal and terrestrial species. In addition, smaller mammals tend to have relatively long, slender, flexible whiskers compared to larger species. Therefore, we propose that whisker morphology varies between larger aquatic species, and smaller scansorial species. These two whisker morphotypes are likely to induce quite different mechanical signals in the follicle, which has implications for follicle anatomy as well as whisker function., (© 2020 The Authors. Journal of Morphology published by Wiley Periodicals LLC.)

Avian rictal bristles are present in many species of birds, especially in nocturnal species. Rictal bristles occur along the upper beak and are morphologically similar to mammalian whiskers. Mammalian whiskers are important tactile sensors, guiding locomotion, foraging and social interactions, and have a well-characterised anatomy. However, it is not yet known whether avian rictal bristles have a sensory function, and their morphology, anatomy and function have also not been described in many species. Our study compares bristle morphology, follicle anatomy and their association with foraging traits, across 12 Caprimulgiform species. Rictal bristle morphology and follicle anatomy were diverse across the 12 species. Nine of the 12 species had mechanoreceptors around their bristle follicles; however, there was large variation in their musculature, mechanoreceptor numbers and bristle morphology. Overall, species with short, thin, branching bristles that lacked mechanoreceptors tended to forage pre-dusk in open habitats, whereas species with mechanoreceptors around their bristle follicle tended to forage at night and in more closed habitats. We suggest that rictal bristles are likely to be tactile in many species and may aid in navigation, foraging and collision avoidance; however, identifying rictal bristle function is challenging and demands further investigation in many species., (2020 The Authors. Journal of Anatomy published by John Wiley & Sons Ltd on behalf of Anatomical Society.)

Cat predation upon bat species has been reported to have significant effects on bat populations in both rural and urban areas. The majority of research in this area has focussed on observational data from bat rehabilitators documenting injuries, and cat owners, when domestic cats present prey. However, this has the potential to underestimate the number of bats killed or injured by cats. Here, we use forensic DNA analysis techniques to analyze swabs taken from injured bats in the United Kingdom, mainly including Pipistrellus pipistrellus (40 out of 72 specimens). Using quantitative PCR, cat DNA was found in two-thirds of samples submitted by bat rehabilitators. Of these samples, short tandem repeat analysis produced partial DNA profiles for approximately one-third of samples, which could be used to link predation events to individual cats. The use of genetic analysis can complement observational data and potentially provide additional information to give a more accurate estimation of cat predation., Competing Interests: The authors declare that they have no conflicts of interest to report., (© 2020 The Authors. Ecology and Evolution published by John Wiley & Sons Ltd.)