Background: Disparities in atrial fibrillation (AF) care are partially attributed to inadequate access to providers with specialized training in AF. Primary care providers (PCPs) are often the sole providers of AF care in under-resourced regions. Objective: To create a virtual education intervention for PCPs and evaluate its impact on use of stroke risk reduction strategies in AF patients. Methods: A multi-disciplinary team mentored PCPs on AF management over 6 months using a virtual case-based training format. Surveys of participant knowledge and confidence in AF care were compared pre- and post-intervention. Hierarchical logistic regression modeling was used to evaluate change in stroke risk reduction therapies among patients seen by participants before or after training. Results: Of 41 participants trained, 49% worked in family medicine, 41% internal medicine, and 10% general cardiology. Participants attended a mean of 14 one-hour sessions. Overall, appropriate use of oral anticoagulation (OAC) therapy (CHA2DS2-VASc score >/=1 men, >/=2 women) increased from 37% to 46% (p<.001) comparing patients seen pre- (n=1739) to post- (n=610) intervention. Factors independently associated with appropriate OAC use included participant training (OR 1.4, p=.002) and participant competence in AF management (by survey). Factors associated with decreased OAC use included patient age (OR 0.8 per 10 years, p=.008), nonwhite race (OR 0.7, p=.028). Provider knowledge and confidence in AF care both improved (p<.001). Conclusions: A virtual case-based PCP training intervention improved use of stroke risk reduction therapy in outpatients with AF. This widely scalable intervention could improve AF care in under-resourced communities. | Make paid
Objective: To create case definitions for confirmed COVID diagnoses, COVID vaccination status, and three separate definitions of high risk of severe COVID, as well as to assess whether the implementation of these definitions in a cohort reflected the sociodemographic and clinical characteristics of COVID epidemiology in England. Design: Retrospective cohort study Setting: Electronic healthcare records from primary care (Clinical Practice Research Datalink, or CPRD) linked to secondary care data (Hospital Episode Statistics, or HES) data covering 24% of the population in England Participants: 2,271,072 persons aged 1 year and older diagnosed with COVID in CPRD Aurum between August 1, 2020 through January 31, 2022. Main Outcome Measures: Age, sex, and regional distribution of COVID cases and COVID vaccine doses received prior to diagnosis were assessed separately for the cohorts of cases identified in primary care and those hospitalized for COVID (primary diagnosis code of ICD-10 U07.1 COVID-19). Smoking status, body mass index and Charlson Comorbidity Index were compared for the two cohorts, as well as for three separate definitions of high risk of severe disease used in the United Kingdom (NHS Highest Risk, PANORAMIC trial eligibility, UK Health Security Agency Clinical Risk prioritization for vaccination). Results: Compared to national estimates, CPRD case estimates underrepresented older adults in both the primary care (age 65-84: 6% in CPRD vs 9% nationally) and hospitalized (31% vs 40%) cohorts, and overrepresented people living in regions with the highest median wealth areas of England (20% primary care and 20% hospital admitted cases in South East, vs 15% nationally). The majority of non-hospitalized cases and all hospitalized cases had not completed primary series vaccination. In primary care, persons meeting high risk definitions were older, more often smokers, overweight or obese, and had higher Charlson Comorbidity Index score. Conclusions: CPRD primary care data is a robust real-world data source and can be used for some COVID research questions, however limitations of the data availability should be carefully considered. Included in this publication are supplemental files for a total of over 28,000 codes to define each of three definitions of high risk of severe disease. | Make paid
Background: Congenital anomalies of the kidney and urinary tract (CAKUT) are the predominant cause for chronic kidney disease below 30 years of age. Many monogenic forms have been discovered mainly due to comprehensive genetic testing like exome sequencing (ES). However, disease-causing variants in known disease-associated genes still only explain a proportion of cases. Aim of this study was to unravel the underlying molecular mechanism of syndromic CAKUT in a multiplex Arab and a Turkish family with presumed autosomal recessive inheritance. Methods and Results: ES in the index individuals revealed two different rare homozygous variants in FOXD2, a transcription factor not previously implicated in CAKUT in humans: a frameshift in the Arab and a missense variant in the Turkish family with family segregation patterns consistent with autosomal-recessive inheritance. CRISPR/Cas9-derived Foxd2 knock-out (KO) mice presented with bilateral dilated renal pelvis accompanied by renal papilla atrophy while extrarenal features included mandibular, ophthalmologic, and behavioral anomalies, recapitulating the phenotype of humans with FOXD2 dysfunction. To study the pathomechanism of FOXD2-dysfunction-mediated developmental renal defects, in a complementary approach, we generated CRISPR/Cas9-mediated KO of Foxd2 in ureteric-bud-induced mouse metanephric mesenchyme cells. Transcriptomic analyses revealed enrichment of numerous differentially expressed genes important in renal/urogenital development, including Pax2 and Wnt4 as well as gene expression changes indicating a cell identity shift towards a stromal cell identity. Histology of Foxd2 KO mouse kidneys confirmed increased fibrosis. Further, GWAS data (genome-wide association studies) suggests that FOXD2 could play a role for maintenance of podocyte integrity during adulthood. Conclusions: In summary, our data implicate that FOXD2 dysfunction is a very rare cause of autosomal recessive syndromic CAKUT and suggest disturbances of the PAX2-WNT4 cell signaling axis contribute to this phenotype. | Make paid
Background: Evidence on the long-term employment consequences of SARS-CoV-2 infection is lacking. We used data from a large, community-based sample in the UK to estimate associations between Long Covid and subsequent employment outcomes. Methods: This was an observational, longitudinal study using a pre-post design. We included UK COVID-19 Infection Survey participants who completed questionnaires on Long Covid from 3 February 2021 to 30 September 2022 when they were aged 16 to 64 years and not in full-time education. We used conditional logit modelling to explore the time-varying relationship between Long Covid status [≥]12 weeks after a first test-confirmed SARS-CoV-2 infection (reference: pre-infection) and labour market inactivity (neither working nor looking for work) or workplace absence lasting [≥]4 weeks. Results: Of 206,299 included participants (mean age 45 years, 54% female, 92% white), 15% were ever inactive in the labour market and 10% were ever long-term absent during follow-up. Compared with pre-infection, inactivity was higher in participants reporting Long Covid 30 to <40 weeks (adjusted odds ratio (aOR): 1.45; 95% CI: 1.17 to 1.81) or 40 to <52 weeks (1.34; 1.05 to 1.72) post-infection. Compared with pre-infection, reporting Long Covid was also associated with increased odds of long-term absence 18 to <24 weeks (1.40; 1.04 to 1.90) and 24 to <30 weeks (1.45; 1.03 to 2.04) post-infection, but not beyond 30 weeks. Combining with official statistics on Long Covid prevalence, our estimates translate to 27,000 (95% CI: 6,000 to 47,000) working-age adults in the UK being inactive because of their Long Covid symptoms in July 2022. Conclusions: Long Covid is likely to have contributed to reduced levels of participation in the UK labour market, though it is unlikely to be the sole driver. Further research is required to quantify the contribution of other factors, such as indirect health effects of the pandemic. | Make paid
Abstract
Background: Widespread human-to-human transmission of the severe acute respiratory syndrome coronavirus two (SARS-CoV-2) stems from a strong affinity for the cellular receptor angiotensin converting enzyme two (ACE2). We investigate the relationship between a patient's nasopharyngeal ACE2 transcription and secondary transmission within a series of concurrent hospital associated SARS-CoV-2 outbreaks in British Columbia, Canada. Methods: Epidemiological case data from the outbreak investigations was merged with public health laboratory records and viral lineage calls, from whole genome sequencing, to reconstruct the concurrent outbreaks using infection tracing transmission network analysis. ACE2 transcription and RNA viral load were measured by quantitative real-time polymerase chain reaction. The transmission network was resolved to calculate the number of potential secondary cases. Bivariate and multivariable analyses using Poisson and Negative Binomial regression models was performed to estimate the association between ACE2 transcription the number of SARS-CoV-2 secondary cases. Results: The infection tracing transmission network provided n = 76 potential transmission events across n = 103 cases. Bivariate comparisons found that on average ACE2 transcription did not differ between patients and healthcare workers (P = 0.86). High ACE2 transcription was observed in 98.6% of transmission events, either the primary or secondary case had above average ACE2. Multivariable analysis found that the association between ACE2 transcription and the number of secondary transmission events differs between patients and healthcare workers. In health care workers Negative Binomial regression estimated that a one unit change in ACE2 transcription decreases the number of secondary cases (B = -0.132 (95%CI: -0.255 to -0.0181) adjusting for RNA viral load. Conversely, in patients a one unit change in ACE2 transcription increases the number of secondary cases (B = 0.187 (95% CI: 0.0101 to 0.370) adjusting for RNA viral load. Sensitivity analysis found no significant relationship between ACE2 and secondary transmission in health care workers and confirmed the positive association among patients. Conclusion: Our study suggests that ACE2 transcription has a positive association with SARS-CoV-2 secondary transmission in admitted inpatients, but not health care workers in concurrent hospital associated outbreaks, and it should be further investigated as a risk-factor for viral transmission. | Make paid
Chronic pain is one of the most common reasons adults seek medical care in the US, with estimates of prevalence ranging from 11% to 40% and relatively higher rates in diverse populations. Mindfulness meditation has been associated with significant improvements in pain, depression, physical and mental health, sleep, and overall quality of life. Group medical visits are increasingly common and are effective at treating myriad illnesses including chronic pain. Integrative Medical Group Visits (IMGV) combine mindfulness techniques, evidence based integrative medicine, and medical group visits and can be used as adjuncts to medications, particularly in diverse underserved populations with limited access to non-pharmacological therapies. The objective of the present study was to assess the effects of race on the primary pain outcomes and evaluate potential relationships between race and additional patient characteristics in data from a randomized clinical trial of IMGV in socially diverse, marginalized patients suffering from chronic pain and depression. It was hypothesized that there would be racial differences in the effects of IMGV on pain outcomes. Our analyses identified significant racial differences in the response to IMGV. Black subjects had increased pain severity throughout the duration of the 21-week study but were less likely to respond to the pain intervention compared to White subjects. These results may be related to differential comorbidity rates, catastrophizing, and digital health literacy among these participant groups. To improve patient outcomes in similar studies, interactions between pain outcomes and these factors require further investigation to affect levels and trajectory of pain severity and enhance the response to complimentary interventions. | Make paid
Introduction: Sedentary behaviours have been associated with increased risks of some common cancers in epidemiological studies; however, it is unclear if these associations are causal. Methods: We used univariable and multivariable two-sample Mendelian randomization (MR) to examine potential causal relationships between sedentary behaviours and risks of breast, colorectal, and prostate cancer. Genetic variants associated with self-reported leisure television watching and computer use were identified from a recent genome-wide association study (GWAS). Data related to cancer risk were obtained from cancer GWAS consortia. A series of sensitivity analyses were applied to examine the robustness of the results to the presence of confounding. Results: In the univariable models, a 1-standard deviation (SD:1.5 hours/day) increment in hours of television watching increased risk of breast cancer (OR per 1-SD: 1.15, 95% confidence interval [CI]: 1.05, 1.26) and colorectal cancer (OR per 1-SD: 1.32, 95%CI: 1.16, 1.49) while there was little evidence of an association for prostate cancer risk (OR per 1-SD: 0.94, 95%CI: 0.84, 1.06). In multivariable MR models adjusted for years of education, the effect estimates for television watching were attenuated towards the null (breast cancer, OR per 1-SD: 1.08, 95%CI: 0.92, 1.27; colorectal cancer, OR per 1-SD: 1.08, 95%CI: 0.90, 1.31). However, in post-hoc analyses we found evidence of years of education having a possible confounding and mediating role in the association between television watching with breast and colorectal cancer. Consistent results were observed for each cancer site according to sex (colorectal cancer), anatomical subsites, and cancer subtypes. There was little evidence of associations between genetically predicted computer use and risk of all three cancers. Conclusion: We found evidence of positive associations between hours of television watching and risks of breast and colorectal cancer. However, these findings should be interpreted cautiously given the complex confounding and mediating role we found for years of education on the television watching and cancer relationship. Future studies using objective measures of exposure (e.g., accelerometers) can provide new insights into the possible role of sedentary behaviour in cancer development. | Make paid
BackgroundDetermining the genetic architecture of Alzheimers disease (AD) pathologies can enhance mechanistic understanding and inform precision medicine strategies. A genome-wide association study (GWAS) of cortical tau quantified by positron emission tomography (PET) was performed. MethodParticipants included 3,136 non-Hispanic White older adults from 12 independent studies (n=1,449 discovery sample; n=1,687 replication sample) spanning preclinical and clinical stages of AD. Genetic variants associated with cortical tau measured using [18F]flortaucipir or [18F]MK-6240 PET were assessed including relevant covariates. Voxel-wise analysis was used to map the topographic distribution of identified associations. Supporting evidence for the identified SNP from gene expression, methylation quantitative trait loci (QTL), and AD mouse data were evaluated. FindingsTwo novel SNPs at the CYP1B1-RMDN2 (Cytochrome P450 Family 1 Subfamily B Member 1 and Regulator of Microtubule Dynamics 2) locus were associated with tau deposition. The most significant signal was at rs2113389 (p-value=1.37x10-8), which explained 4.3% of the variation in cortical tau, while APOE4 rs429358 accounted for 3.6%. The minor allele of rs2113389 (T; MAF=0.146) was associated with higher tau and faster cognitive decline. Additive effects, but no interactions, were observed between rs2113389 and diagnosis, APOE4, and A{beta} positivity. Voxel-wise analysis revealed higher tau in AD-related regions in rs2113389 T-allele carriers. CYP1B1 was upregulated in the temporal cortex in AD. The rs2113389 T-allele was associated with higher temporal cortex CYP1B1 expression and methylation levels. Mouse model studies provided additional functional evidence for a relationship between CYP1B1 and tau deposition but not A{beta}. InterpretationThe minor allele of rs2113389 may be a risk variant for tau and faster cognitive decline in AD. Further investigation of CYP1B1 and RMDN2 is warranted and may provide insight into the genetic basis of cerebral tau and novel pathways for therapeutic development in AD. Studies of multiethnic populations are also needed. | Make paid
The intergenerational transmission of educational attainment from parents to their children is one of the most important and studied relationships in social science. Longitudinal studies have found strong associations between parents' and their children's educational outcomes, which could be due to the effects of parents. Here we provide new evidence about whether parents' educational attainment affects their parenting behaviours and children's early educational outcomes using within-family Mendelian randomization and data from 40,907 genotyped parent-child trios from the Norwegian Mother, Father and Child Cohort (MoBa) study. We found evidence suggesting that parents' educational attainment affects their children's educational outcomes from age 5 to 14. More studies are needed to provide more samples of parent-child trios and assess the potential consequences of selection bias and grandparental effects. | Make paid
Since the outset of the COVID-19 pandemic, substantial public attention has focused on the role of seasonality in suppressing transmission. Misconceptions have relied on seasonal mediation of respiratory diseases driven solely by environmental variables. However, seasonality is expected to be driven by host social behavior, particularly in highly susceptible populations. A key gap in understanding the role of social behavior in respiratory disease seasonality is our incomplete understanding of the seasonality of indoor human activity. We leverage a novel data stream on human mobility to characterize activity in indoor versus outdoor environments in the United States. We use an observational mobile app-based location dataset encompassing over 5 million locations nationally. We classify locations as primarily indoor (e.g. stores, offices) or outdoor (e.g. playgrounds, farmers markets), disentangling location-specific visitor counts into indoor and outdoor, to arrive at a fine-scale measure of indoor to outdoor human activity across time and space. We find the proportion of indoor to outdoor activity during a baseline year is seasonal, peaking in winter months. The measure displays a latitudinal gradient with stronger seasonality at northern latitudes and an additional summer peak in southern latitudes. We statistically fit this baseline indoor-outdoor activity measure to inform incorporation of this complex empirical pattern into infectious disease dynamic models. However, we find that the disruption of the COVID-19 pandemic caused these patterns to shift significantly from baseline, and the empirical patterns are necessary to predict spatio-temporal heterogeneity in disease dynamics. Our work empirically characterizes, for the first time, the seasonality of human social behavior at a large-scale with high spatio-temporal resolution, and provides a parsimonious parameterization of seasonal behavior that can be included in infectious disease dynamics models. We provide critical evidence and methods necessary to inform the public health of seasonal and pandemic respiratory pathogens and improve our understanding of the relationship between the physical environment and infection risk in the context of global ecological change. | Make paid
The authors have withdrawn their manuscript as they are reviewing the study and the manuscript. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author. | Make paid
BackgroundThe sustainability of school-based oral health programs depends on the utilization of effective, efficient treatments and the availability of a trained clinical workforce. The objective of this study was to determine whether registered nurses are non-inferior to dental hygienists in the application and effectiveness of silver diamine fluoride (SDF) for dental caries. MethodsCariedAway was a school-based cluster-randomized trial of SDF versus dental sealants and atraumatic restorations. Within the SDF arm, subjects were treated by either a licensed dental hygienist or a registered nurse, both under the supervision of a pediatric dentist. The proportion of children who remained caries free after two years was analyzed using two-group proportion tests, adjusting for the clustering effect of schools. Results417 children were analyzed including 298 treated by hygienists and 119 by nurses. The proportion of caries-free individuals was 0.812 and 0.798 for hygienists and nurses, respectively, for a difference of 0.014 (95% CI = -0.07, 0.098) and within the pre-determined non-inferiority margin. ConclusionsResults support silver diamine fluoride and fluoride varnish delivery by nurses in school-based oral health programs. | Make paid
BACKGROUND: Serious and severe harms of the COVID-19 vaccines have been downplayed or deliberately excluded by the study sponsors in high impact medical journals. METHODS: Systematic review of papers with data on serious adverse events (SAEs) associated with a COVID-19 vaccine. RESULTS: We included 18 systematic reviews, 14 randomised trials, and 34 other studies with a control group. Most studies were of poor quality. A systematic review of regulatory data on the two pivotal trials of the mRNA vaccines found significantly more SAEs of special interest with the vaccines compared to placebo, and the excess risk was considerably larger than the benefit, the risk of hospitalisation. The adenovirus vector vaccines increased the risk of venous thrombosis and thrombocytopenia, and the mRNA-based vaccines increased the risk of myocarditis, with a mortality of about 1-2 per 200 cases. We found evidence of serious neurological harms, including Bells palsy, Guillain-Barre syndrome, myasthenic disorder and stroke, which are likely due to an autoimmune reaction. Severe harms, i.e. those that prevent daily activities, were underreported in the randomised trials. These harms were very common in studies of booster doses after a full vaccination and in a study of vaccination of previously infected people. CONCLUSIONS: Further randomised trials are needed. Authorities have recommended population-wide COVID-19 vaccination and booster doses. They do not consider that the balance between benefits and harms becomes negative in low-risk groups such as children and people who have already recovered from COVID-19 infection. | Make paid
BackgroundThe purpose of this study was to evaluate whether a bivalent COVID-19 vaccine protects against COVID-19. MethodsEmployees of Cleveland Clinic in employment when the bivalent COVID-19 vaccine first became available, were included. Cumulative incidence of COVID-19 over the following 26 weeks was examined. Protection provided by vaccination (analyzed as a time-dependent covariate) was evaluated using Cox proportional hazards regression, with change in dominant circulating lineages over time accounted for by time-dependent coefficients. The analysis was adjusted for the pandemic phase when the last prior COVID-19 episode occurred, and the number of prior vaccine doses. ResultsAmong 51017 employees, COVID-19 occurred in 4424 (8.7%) during the study. In multivariable analysis, the bivalent vaccinated state was associated with lower risk of COVID-19 during the BA.4/5 dominant (HR, .71; 95% C.I., .63-.79) and the BQ dominant (HR, .80; 95% C.I., .69-.94) phases, but decreased risk was not found during the XBB dominant phase (HR, .96; 95% C.I., .82-.1.12). Estimated vaccine effectiveness (VE) was 29% (95% C.I., 21%-37%), 20% (95% C.I., 6%-31%), and 4% (95% C.I., -12%-18%), during the BA.4/5, BQ, and XBB dominant phases, respectively. Risk of COVID-19 also increased with time since most recent prior COVID-19 episode and with the number of vaccine doses previously received. ConclusionsThe bivalent COVID-19 vaccine given to working-aged adults afforded modest protection overall against COVID-19 while the BA.4/5 lineages were the dominant circulating strains, afforded less protection when the BQ lineages were dominant, and effectiveness was not demonstrated when the XBB lineages were dominant. SummaryAmong 51017 working-aged Cleveland Clinic employees, the bivalent COVID-19 vaccine was 29% effective in preventing infection while the BA.4/5 lineages were dominant, and 20% effective while the BQ lineages were. Effectiveness was not demonstrated when the XBB lineages were dominant. | Make paid
Mounting evidence suggests considerable diversity in brain aging trajectories, primarily arising from the complex interplay between age, genetic and environmental risk factors, leading to distinct patterns of micro- and macro-cerebral aging. The underlying mechanisms of such effects still remain unclear. We conducted a comprehensive association analysis between cerebral structural measures and prevalent risk factors, using data from 35,035 UK Biobank subjects aged 44-82. Participants were assessed for brain volume, white matter diffusivity, Apolipoprotein E (APOE) genotypes, polygenic risk scores, lifestyles and socioeconomic status. We examined genetic and environmental effects and their interactions with age and sex, and identified 726 signals, with education, alcohol, and smoking affecting most brain regions. Our analysis revealed negative age-APOE-{varepsilon}4 and positive age-APOE-{varepsilon}2 interaction effects, respectively, especially in females on the volume of amygdala, positive age-sex-APOE-{varepsilon}4 interaction on the cerebellar volume, positive age-excessive-alcohol interaction effect on the mean diffusivity of the splenium of the corpus callosum, positive age-healthy-diet interaction effect on the paracentral volume, and negative APOE-{varepsilon}4-moderate-alcohol interaction effects on the axial diffusivity of the superior fronto-occipital fasciculus. These findings highlight the need of considering age, sex, genetic and environmental joint effects in elucidating normal or abnormal brain aging. | Make paid
Purpose: Globally, transgender women (TGW) experience wide ranging barriers to health and care, with disproportionately high risks of infectious and chronic diseases. Despite these vulnerabilities, research on access to care for transgender populations in low and middle income countries is extremely limited. Furthermore, existing studies have primarily focused on human immunodeficiency virus infection and acquired immune deficiency syndrome (HIV/AIDS), with less emphasis on the broader health needs of TGW. This study analyzed patterns of morbidity and health service uptake among TGW in Lima, Peru. The purpose was to better understand health outreach and service needs to inform targeting and design of future community level interventions. Methods: This cross sectional study surveyed a convenience sample of 301 TGW in metropolitan Lima, Peru. Data was collected between September to October 2020. This paper provides descriptive statistics and results of bivariate and multivariable regression models. Results: Health coverage and access to care were suboptimal. Less education and older age were positively associated with illness and HIV and tuberculosis (TB) testing. Gender identity sub-group (i.e., woman, trans or transgender, transsexual, 'transformista,' 'travesti,' and other) was associated with HIV testing and pre-exposure prophylaxis (PrEP) usage. Both awareness of and interest in PrEP were low, as was usage among those who were interested in taking PrEP. Conclusion: Future public health efforts should be tailored to meet the diverse needs of TGW, expand TB testing, bridge the gap between PrEP interest and use, and increase insurance coverage and access to trans friendly services to promote improved health outcomes. | Make paid
Assembling actin filaments work together with myosins to accomplish a wide array of biological processes. During clathrin-mediated endocytosis (CME), actin assembly and type I myosin cooperate to bend the plasma membrane into a pit that undergoes scission to internalize a cargo-bearing vesicle. How actin assembly and myosin work together in this process is a critical, unanswered question. Some type I myosins directly power motility, while others act as force-sensitive clamps. The Saccharomyces cerevisiae endocytic type I myosin Myo5 has been meticulously studied in vivo, yet whether this protein's essential CME function is to power membrane invagination or to bind to force-bearing actin filaments to collect and organize them for optimal force production has not been established. We report that Myo5 is a low-duty-ratio motor with a working stroke that is rapid and force-insensitive compared to related myosins that act as force-sensitive anchors. We therefore propose that Myo5 generates power to augment actin assembly-based forces during endocytosis. | Make paid
Influenza A virus (IAV) infection relies on the action of the hemagglutinin (HA) and neuraminidase (NA) membrane proteins. The HA ligands anchor the IAV virion to the cell's surface by binding the sialic acid (SA) present on the host's receptors while NA is an enzyme capable of cleaving the SA from the extracellular environment. It is believed that the activity of NA ligands increases the motility of the virions favoring the propagation of the infection. In this work, we develop a numerical framework to study the dynamics of a virion moving across the cell surface for timescales much bigger than the typical ligand-receptor reaction times. We find that the rates controlling the ligand-receptor reactions and the maximal distance at which a pair of ligand-receptor molecules can interact greatly affect the motility of the virions. We also report on how different ways of organizing the two types of ligands on the virions' surface result in different types of motion that we rationalize using general principles. In particular, we show how the emerging motility of the virion is less sensitive to the rate controlling the enzymatic activity when NA ligands are clustered. These results help to assess how variations in the biochemical properties of the ligand-receptor interactions (as observed across different IAV subtypes) affect the dynamics of the virions at the cell surface. | Make paid
Despite medical interventions and several approved vaccines, the COVID-19 pandemic is continuing into its third year. Recent publications have explored single-dose intranasal (i.n.) adenovirus-based vaccines as an effective strategy for curbing SARS-CoV-2 in naive animal models. However, the effects of prior immunizations and infections have yet to be considered within these models. Here, we investigate the immunomodulatory effects of Mycobacterium bovis BCG pre-immunization on a subsequent S-protein expressing i.n. Ad vaccination, termed Ad(Spike). We found that Ad(Spike) alone conferred long-term protection from severe SARS-CoV-2 pathology within a mouse model, yet it was unable to limit initial infection 6 months post-vaccination. While i.n. Ad(Spike) retains some protective effect after 6 months, a single administration of BCG-Danish prior to Ad(Spike) vaccination potentiates its ability to control viral replication of the B.1.351 SARS-CoV-2 variant within the respiratory tract. Though BCG-Danish had no effect on the ability of Ad(Spike) to generate and maintain humoral immunity, it promoted the generation of cytotoxic and Th1 responses over suppressive FoxP3+ TREG cells in the lungs of infected mice. These data demonstrate a novel vaccination strategy that may prove useful in limiting future viral pandemics by potentiating the long-term efficacy of next generation mucosal vaccines within the context of the safe and widely distributed BCG vaccine. | Make paid
Factors of the innate immune response to SARS-CoV-2 in the lungs are pivotal for the ability of the host to deal with the infection. In humans, excessive macrophage infiltration is associated with disease severity. Using 3D spatiotemporal analysis of optically cleared hamster lung slices in combination with virological, immunohistochemical and RNA sequence analyses, we visualized the spread of SARS-CoV-2 through the lungs and the rapid anti-viral response in infected lung epithelial cells, followed by a wave of monocyte-derived macrophage (MDM) infiltration and virus elimination from the tissue. These SARS-CoV-2 induced innate immune processes are closely related to the onset of necrotizing inflammatory and consecutive remodelling responses in the lungs, which manifests as extensive cell death, vascular damage, thrombosis, and cell proliferation. Here we show that MDM are directly linked to virus clearance, and appear in connection with tissue injury and blood vessel damage. Rapid initiation of prothrombotic factor upregulation, tissue repair and alveolar cell proliferation results in tissue remodelling, which is followed by fibrosis development despite a decrease in inflammatory and anti-viral activities. Thus, although the hamsters are able to resolve the infection following the MDM influx and repair lung tissue integrity, longer-term alterations of the lung tissues arise as a result of concurrent tissue damage and regeneration processes. | Make paid
Cells harness multiple pathways to maintain lysosome integrity, a central homeostatic process. Damaged lysosomes can be repaired, or targeted for degradation by lysophagy, a selective autophagy process involving ATG8/LC3. Here, we describe a parallel ATG8/LC3 response to lysosome damage, mechanistically distinct from lysophagy. Using a comprehensive series of biochemical, pharmacological and genetic approaches, we show that lysosome damage induces rapid Conjugation of ATG8s to Single Membranes (CASM). ATG8 proteins are recruited directly onto damaged membranes, independently of ATG13/WIPI2, and conjugated to PS, as well as PE, a molecular hallmark of CASM. Lysosome damage drives V-ATPase V0-V1 association, and direct recruitment of ATG16L1, dependent on K490 (WD40-domain), and sensitive to Salmonella SopF. Lysosome damage-induced CASM is associated with the formation of dynamic LC3A-positive tubules, and promotes robust LC3A engagement with ATG2, a lipid transfer protein central to lysosome repair. Together, our data identify direct ATG8 conjugation as a rapid response to lysosome damage, with important links to lipid transfer and dynamics. | Make paid
The propagation of the membrane tension perturbations is a, potentially, essential mechanism of the mechanical signal transduction along surfaces of live cells. The efficiency of this process is determined by the propagation speed, which turned to be a hot and a controversial topic of the Cell Biophysics. In a stark contrast to the earlier results and expectations, the recent studies in several cell types revealed a wide range of the tension propagation speeds beginning from the strikingly low ones challenging the significance of the process and up to relatively high biologically relevant rates. The previously suggested models of the tension propagation have been based on assuming an unrealistic softness of the membranes for the stretching-compression deformations, which challenges the model ability to account for the observations. Here, we consider a different physics of the generation and the propagation of tension perturbations in cell membranes. We propose the tension to be controlled by an intra-cellular pressure and the propagation of the tension perturbations to be mediated by a membrane area redistribution between compartments, to which cell membranes are divided by the proteinic barriers, according to the picket-fence model. Using the established elastic features of cell membranes including their effective non-stretchability, this mechanism quantitatively accounts for the slowness of the propagation process and gives a natural explanation of the wide range of the observed propagation speeds. The model predictions are amenable to a direct experimental verification by controlled osmotic pressure variations. | Make paid
CRISPR-Cas9 genome editing has enabled advanced T cell therapies, but occasional loss of the targeted chromosome remains a safety concern. To investigate whether Cas9-induced chromosome loss is a universal phenomenon and evaluate its clinical significance, we conducted a systematic analysis in primary human T cells. Arrayed and pooled CRISPR screens revealed that chromosome loss was generalizable across the genome and resulted in partial and entire loss of the chromosome, including in pre-clinical chimeric antigen receptor T cells. T cells with chromosome loss persisted for weeks in culture, implying the potential to interfere with clinical use. A modified cell manufacturing process, employed in our first-in-human clinical trial of Cas9-engineered T cells,1 dramatically reduced chromosome loss while largely preserving genome editing efficacy. Expression of p53 correlated with protection from chromosome loss observed in this protocol, suggesting both a mechanism and strategy for T cell engineering that mitigates this genotoxicity in the clinic. | Make paid
Food webs trace the flow of organic matter and energy among producers and consumers; for pelagic marine food webs, network complexity directly influences the amount and form of carbon exported to the deep ocean via the biological pump. Here we present a synoptic view of mixed layer food web dynamics observed during the late summer 2018 EXport Processes in the Ocean from Remote Sensing (EXPORTS) field campaign in the subarctic Northeast Pacific at the long-running time-series site, Ocean Station Papa. Carbon biomass reservoirs of phytoplankton, microzooplankton, and bacterioplankton, were approximately equal while mesozooplankton biomass was 70% lower. Live organisms composed ~40% of the total particulate organic carbon within the mixed layer: the remainder was attributed to detritus. Rates of carbon transfer among reservoirs indicated production and assimilation rates were well balanced by losses, leaving little organic carbon available for export. The slight positive net community production rate generated organic carbon that was exported from the system in the form of food web byproducts, such as large fecal pellets generated by mesozooplankton. This characteristically regenerative food web had relatively slow turnover times with small-magnitude transfers of carbon relative to standing stocks that occurred amidst a high background concentration of detrital particles and dissolved organic matter. The concurrent estimation of food web components and rates revealed that separated processes dominated the transfer of carbon within the food web compared to those that contributed to export. | Make paid
The evolutionary and functional studies suggested that the emergence of the Omicron variants can be determined by multiple fitness trade-offs including the immune escape, binding affinity for ACE2, conformational plasticity, protein stability and allosteric modulation. In this study, we systematically characterize conformational dynamics, protein stability and binding affinities of the SARS-CoV-2 Spike Omicron complexes with the host receptor ACE2 for BA.2 , BA.2.75, XBB.1 and XBB.1.5 variants. We combined multiscale molecular simulations and dynamic analysis of allosteric interactions together with the ensemble-based mutational scanning of the protein residues and network modeling of epistatic interactions. This multifaceted computational study characterized molecular mechanisms and identified energetic hotspots that can mediate the predicted increased stability and the enhanced binding affinity of the BA.2.75 and XBB.1.5 complexes. The results suggested a mechanism driven by the stability hotspots and a spatially localized group of the Omicron binding affinity centers, while allowing for functionally beneficial neutral Omicron mutations in other binding interface positions. A network-based community model for the analysis of non-additive epistatic contributions in the Omicron complexes is proposed revealing the key role of the binding hotspots R498 and Y501 in mediating community-based epistatic couplings with other Omicron sites and allowing for compensatory dynamics and binding energetic changes. The results also showed that mutations in the convergent evolutionary hotspot F486 can modulate not only local interactions but also rewire the global network of local communities in this region allowing the F486P mutation to restore both the stability and binding affinity of the XBB.1.5 variant which may explain the growth advantages over the XBB.1 variant. The results of this study are consistent with a broad range of functional studies rationalizing functional roles of the Omicron mutation sites that form a coordinated network of hotspots enabling balance of multiple fitness tradeoffs and shaping up a complex functional landscape of virus transmissibility. | Make paid
The inclusion of microexons by alternative splicing is frequent in neuronal proteins. The roles of these sequences are in most cases unknown, but changes in their degree of inclusion are associated with neurodevelopmental diseases. We recently found that the decreased inclusion of a 24-nucleotide neuron-specific microexon in CPEB4, an RNA-binding protein that regulates translation through cytoplasmic changes in poly(A) tail length, is linked to idiopathic autism spectrum disorder (ASD). Why this microexon is required and how small changes in its degree of inclusion generate a dominant-negative effect on the expression of ASD-linked genes is not clear. Here we show that neuronal CPEB4 forms condensates that dissolve upon depolarization, a phase transition associated with a switch from translational repression to activation. Heterotypic intermolecular interactions between the microexon and a cluster of histidine residues kinetically stabilize the condensates by competing with homotypic interactions between clusters, that otherwise lead to the irreversible aggregation of CPEB4. We conclude that microexon 4 in neuronal CPEB4 is required to preserve the reversible regulation of CPEB4-mediated gene expression in response to neuronal stimulation. | Make paid
The single celled baker's yeast, Saccharomyces cerevisiae, can sustain a number of amyloid-based prions, with the three most prominent examples being [URE3] formed from the Ure2 protein (a regulator of nitrogen catabolism), [PSI+] formed from the Sup35 protein (a yeast translation termination release factor) and [PIN+] formed from the Rnq1 protein (of as yet unknown function). In a laboratory environment, haploid S. cerevisiae cells of a single mating type can acquire an amyloid prion in one of two ways (i.) Spontaneous nucleation of the prion within the yeast cell, and (ii.) Receipt via mother-to-daughter transmission during the cell division cycle. Similarly, prions can be lost from a yeast due to (i) Dissolution of the prion amyloid by its breakage into non-amyloid monomeric units, or (ii) Preferential donation/retention of prions between the mother and daughter during cell division. Here we present a computational tool, called MIL-CELL, for modelling these four general processes using a multiscale approach that is able to describe both spatial and kinetic aspects of the yeast life cycle and the amyloid-prion behavior. The yeast growth cycle is considered in two stages, a mature yeast that is competent to bud (M), and a daughter yeast (D) defined as a fully grown and detached bud. In the virtual plate experiment each transition in yeast growth is stochastically regulated, according to temporal and spatial characteristics, in a manner able to incorporate concepts of confluent growth. Between the relatively coarse time-points used for the particle level description, a set of differential equations, describing the nucleation, growth, fragmentation and clumping of amyloid fibrils, is solved numerically, for each individual yeast cell. Distribution of amyloid between the mother and the daughter is carried out by solving a set of kinetic partition equations between mother and the newly forming (and still attached) daughter during the yeast budding stage. In this paper we describe the workings of the model, the assumptions upon which it is based and some interesting simulation results that pertain to wave-like spread of the epigenetic prion elements through the yeast population. MIL-CELL (Monitoring Induction and Loss of prions in Cells) is provided as a stand-alone graphical user interface-based executable program for free download with the paper (supplementary section). | Make paid
Primary cilia are essential sensory organelles that develop when an inhibitory cap consisting of CP110 and other proteins is eliminated. Degradation of CP110 by the ubiquitin-dependent proteasome pathway mediated by NEURL4 and HYLS1 removes the inhibitory cap. Here, we investigated the suitability of rapamycin-mediated dimerization for centriolar recruitment and asked whether the induced recruitment of NEURL4 or HYLS1 to the centriole promotes primary cilia development and CP110 degradation. We used rapamycin-mediated dimerization with ODF2 to induce their targeted recruitment to the centriole. We found decreased CP110 levels in transfected cells, but independent of rapamycin-mediated dimerization. By knocking down ODF2, we show that ODF2 controls CP110 levels. Overexpression of ODF2 is not sufficient to promote the formation of primary cilia, but overexpression of NEURL4 or HYLS1 is. Co-expression of ODF2 and HYLS1 resulted in the formation of tube-like structures, indicating an interaction. Thus, ODF2 controls primary cilia formation by negatively regulating the concentration of CP110 levels. Our data suggest that ODF2 most likely acts as a scaffold for the binding of proteins such as NEURL4 or HYLS1 to mediate CP110 degradation. | Make paid
Biomolecular condensates form via phase transitions of condensate-specific biomacromolecules. Intrinsically disordered regions (IDRs) featuring the appropriate sequence grammar can contribute homotypic and heterotypic interactions to the driving forces for phase separation of multivalent proteins. At this juncture, experiments and computations have matured to the point where the concentrations of coexisting dense and dilute phases can be quantified for individual IDRs in complex milieus both in vitro and in vivo. For a macromolecule such as a disordered protein in a solvent, the locus of points that connects concentrations of the two coexisting phases defines a phase boundary or binodal. Often, only a few points along the binodal, especially in the dense phase, are accessible for measurement. In such cases and for quantitative and comparative analysis of parameters that describe the driving forces for phase separation, it is useful to fit measured or computed binodals to well-known mean-field free energies for polymer solutions. Unfortunately, the non-linearity of the underlying free energy functions makes it challenging to put mean-field theories into practice. Here, we present FIREBALL, a suite of computational tools designed to enable efficient construction, analysis, and fitting to experimental or computed data of binodals. We show that depending on the theory being used, one can also extract information regarding coil-to-globule transitions of individual macromolecules. Here, we emphasize the ease-of-use and utility of FIREBALL using examples based on data for two different IDRs. | Make paid