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Abstract Proteins containing both intrinsically disordered regions (IDRs) and RNA binding domains (RBDs) can phase separate in vitro, forming bodies similar to cellular biomolecular condensates. However, how IDR and RBD domains contribute to in vivo recruitment of proteins to biomolecular condensates remains poorly understood. Here, we analyzed the roles of IDRs and RBDs in L-bodies, biomolecular condensates present in Xenopus oocytes. We show that a cytoplasmic isoform of hnRNPAB, which contains two RBDs and an IDR, is highly enriched in L-bodies. While both of these domains contribute to hnRNPAB self-association and phase separation in vitro and mediate enrichment into L-bodies in oocytes, neither the RBDs nor the IDR replicate the localization of full-length hnRNPAB. Our results suggest a model where the combined effects of the IDR and RBDs regulate hnRNPAB partitioning into L-bodies. This model likely has widespread applications as proteins containing RBD and IDR domains are common biomolecular condensate residents.

Abstract Targeting Anaplastic lymphoma kinase (ALK) is a promising therapeutic strategy for aberrant ALK-expressing malignancies including neuroblastoma, but resistance to ALK tyrosine kinase inhibitors (ALK TKI) is a distinct possibility necessitating drug combination therapeutic approaches. Using high-throughput, genome-wide CRISPR-Cas9 knockout screens, we identify miR-1304-5p loss as a desensitizer to ALK TKIs in aberrant ALK-expressing neuroblastoma; inhibition of miR-1304-5p decreases, while mimics of this miRNA increase the sensitivity of neuroblastoma cells to ALK TKIs. We show that miR-1304-5p targets NRAS, decreasing cell viability via induction of apoptosis. It follows that the farnesyltransferase inhibitor (FTI) lonafarnib in addition to ALK TKIs act synergistically in neuroblastoma, inducing apoptosis in vitro. In particular, on combined treatment of neuroblastoma patient derived xenografts with an FTI and an ALK TKI complete regression of tumour growth is observed although tumours rapidly regrow on cessation of therapy. Overall, our data suggests that combined use of ALK TKIs and FTIs, constitutes a therapeutic approach to treat high risk neuroblastoma although prolonged therapy is likely required to prevent relapse.

Objective To investigate the effect of the covid-19 pandemic on the number of patients with group A streptococcal infections and related antibiotic prescriptions.Design Retrospective cohort study in England using OpenSAFELY-TPP.Setting Primary care practices in England that used TPP SystmOne software, 1 January 2018 to 31 March 2023, with the approval of NHS England.Participants Patients registered at a TPP practice at the start of each month of the study period. Patients with missing data for sex or age were excluded, resulting in a population of 23 816 470 in January 2018, increasing to 25 541 940 by March 2023.Main outcome measures Monthly counts and crude rates of patients with group A streptococcal infections (sore throat or tonsillitis, scarlet fever, and invasive group A streptococcal infections), and recommended firstline, alternative, and reserved antibiotic prescriptions linked with a group A streptococcal infection before (pre-April 2020), during, and after (post-April 2021) covid-19 restrictions. Maximum and minimum count and rate for each infectious season (time from September to August), as well as the rate ratio of the 2022-23 season compared with the last comparably high season (2017-18).Results The number of patients with group A streptococcal infections, and antibiotic prescriptions linked to an indication of group A streptococcal infection, peaked in December 2022, higher than the peak in 2017-18. The rate ratios for monthly sore throat or tonsillitis (possible group A streptococcal throat infection), scarlet fever, and invasive group A streptococcal infection in 2022-23 relative to 2017-18 were 1.39 (95% confidence interval (CI) 1.38 to 1.40), 2.68 (2.59 to 2.77), and 4.37 (2.94 to 6.48), respectively. The rate ratio for prescriptions of first line, alternative, and reserved antibiotics to patients with group A streptococcal infections in 2022-23 relative to 2017-18 were 1.37 (95% CI 1.35 to 1.38), 2.30 (2.26 to 2.34), and 2.42 (2.24 to 2.61), respectively. For individual antibiotic prescriptions in 2022-23, azithromycin showed the greatest relative increase versus 2017-18, with a rate ratio of 7.37 (6.22 to 8.74). This finding followed a marked decrease in the recording of patients with group A streptococcal infections and associated prescriptions during the period of covid-19 restrictions where the maximum count and rates were lower than any minimum rates before the covid-19 pandemic.Conclusions Recording of rates of scarlet fever, sore throat or tonsillitis, and invasive group A streptococcal infections, and associated antibiotic prescribing, peaked in December 2022. Primary care data can supplement existing infectious disease surveillance through linkages with relevant prescribing data and detailed analysis of clinical and demographic subgroups.

Abstract Ubiquitination is a post-translational modification initiated by the E1 enzyme UBA1, which transfers ubiquitin to ~35 E2 ubiquitin-conjugating enzymes. While UBA1 loss is cell lethal, it remains unknown how partial reduction in UBA1 activity is endured. Here, we utilize deep-coverage mass spectrometry to define the E1-E2 interactome and to determine the proteins that are modulated by knockdown of UBA1 and of each E2 in human cells. These analyses define the UBA1/E2-sensitive proteome and the E2 specificity in protein modulation. Interestingly, profound adaptations in peroxisomes and other organelles are triggered by decreased ubiquitination. While the cargo receptor PEX5 depends on its mono-ubiquitination for binding to peroxisomal proteins and importing them into peroxisomes, we find that UBA1/E2 knockdown induces the compensatory upregulation of other PEX proteins necessary for PEX5 docking to the peroxisomal membrane. Altogether, this study defines a homeostatic mechanism that sustains peroxisomal protein import in cells with decreased ubiquitination capacity.

Myofiber atrophy occurs in many diseases but the mechanisms responsible for myofiber size determination are incompletely understood. Here, the authors show that the muscle-secreted factor Fibcd1 is necessary to maintain myofiber size and mitigates myofiber atrophy induced by cancer cachexia

The stress that the COVID-19 pandemic has placed on health systems internationally has forced difficult decisions concerning the rationing of medical care and has put the bioethical structures that inform those choices under scrutiny. Often, ethical approaches to pandemic circumstances center around utilitarianism, dehumanizing the treatment process and ignoring the plurality of other philosophical doctrines that inform non-Western bioethics, which could be of use in addressing the pandemic. This paper focuses on philosophical Taoism, as developed in the Tao Te Ching and Zhuangzi, in order to suggest an alternative approach to medical care when medical capacity is limited, grounded in the concept of wu-wei, or inaction.

Abstract Quantifying the extent to which animals detect and respond to human presence allows us to identify pressure (disturbance) and inform conservation management objectively; however, obtaining baselines against which to compare human impact is hindered in areas where human activities are already well established. For example, Zakynthos Island (Greece, Mediterranean) receives around 850,000 visitors each summer, while supporting an important loggerhead sea turtle rookery (~300 individuals/season). The coronavirus (COVID‐19)‐driven absence of tourism in May–June 2020 provided an opportunity to evaluate the distribution dynamics of this population in the absence (2020) vs. presence (2018 and 2019) of visitors using programmed unmanned aerial system (UAS) surveys. Ambient sea temperature transitioned from suboptimal for breeding in May to optimal in late June, with turtle distribution appearing to shift from shallow (to benefit from waters 3–5°C above ambient) to deeper waters in 2018 and 2019, but not 2020. The 2020 data set demonstrated that increased tourism pressure, not temperature, drives turtles offshore. Specifically, >50% of turtles remained within 100 m of shore at densities of 25–50 visitors/km, even when sea temperature rose, with 2018 and 2019 data supporting this trend. Reduced access to warmer, nearshore waters by tourism could delay the onset of nesting and increase the length of the egg maturation period between nesting events (internesting interval) at this site. A coastal refuge zone could be delimited in May–June where touristic infrastructure is minimal, but also where turtles frequently aggregate. In conclusion, sea turtles appear capable of perceiving changes in the level of human pressure at fine spatial and temporal scales and adjusting their distribution accordingly.

Sarcopenia is the age-associated functional decline and atrophy of muscle fibers, and it has been proposed that it might be counteracted by inducing myofiber hypertrophy. Here, the authors show that expression levels of the ubiquitin ligase UBR4 are increased with ageing, and that whilst its genetic ablation rescues muscle atrophy, it is also associated with reduced protein quality and impaired force production in Drosophila and mouse models.

Quantifying how animals use key habitats and resources for their survival allows managers to optimise conservation planning; however, obtaining representative sample sizes of wildlife distributions in both time and space is challenging, particularly in the marine environment. Here, we used unoccupied aircraft systems (UASs) to evaluate temporal and spatial variation in the distribution of loggerhead sea turtles (Caretta caretta) at two high-density breeding aggregations in the Mediterranean, and the effect of varying sample size and survey frequency. In May–June of 2017 to 2019, we conducted 69 surveys, assimilating 10,075 inwater turtle records at the two sites. Optimal time interval between surveys to capture the dynamics of aggregations over the breeding period was 500 turtles (from the combined surveys). This minimum threshold was attributed to the core-area use of female turtles shifting across surveys in relation to wind direction to access warmer nearshore waters and male presence. Males were more widely distributed within aggregations than females, particularly in May when mating encounters were high. Most males were recorded swimming and oriented parallel to shore, likely to enhance encounter rates with females. In contrast, most females were generally stationary (resting on the seabed or basking), likely to conserve energy for reproduction, with orientation appearing to shift in relation to male numbers at the breeding area. Thus, by identifying the main factors regulating the movement and distribution of animals, appropriate survey intervals can be selected for appropriate home range analyses. Our study demonstrates the versatility of UASs to capture the fine-scale dynamics of wildlife aggregations and associated factors, which is important for implementing effective conservation.

Peptide amphiphiles are a class of molecules that can self-assemble into a variety of supramolecular structures, including high-aspect-ratio nanofibers. It is challenging to model and predict the charges in these supramolecular nanofibers because the ionization state of the peptides are not fixed but liable to change due to the acid-base equilibrium that is coupled to the structural organization of the peptide amphiphile molecules. Here, we have developed a theoretical model to describe and predict the amount of charge found on self-assembled peptide amphiphiles as a function of pH and ion concentration. In particular, we computed the amount of charge of peptide amphiphiles nanofibers with the sequence C16 − V2A2E2. In our theoretical formulation, we consider charge regulation of the carboxylic acid groups, which involves the acid-base chemical equilibrium of the glutamic acid residues and the possibility of ion condensation. The charge regulation is coupled with the local dielectric environment by allowing for a varying dielectric constant that also includes a position-dependent electrostatic solvation energy for the charged species. We find that the charges on the glutamic acid residues of the peptide amphiphile nanofiber are much lower than the same functional group in aqueous solution. There is a strong coupling between the charging via the acid-base equilibrium and the local dielectric environment. Our model predicts a much lower degree of deprotonation for a position-dependent relative dielectric constant compared to a constant dielectric background. Furthermore, the shape and size of the electrostatic potential as well as the counterion distribution are quantitatively and qualitatively different. These results indicate that an accurate model of peptide amphiphile self-assembly must take into account charge regulation of acidic groups through acid–base equilibria and ion condensation, as well as coupling to the local dielectric environment.

Flare frequency distributions represent a key approach to addressing one of the largest problems in solar and stellar physics: determining the mechanism that counterintuitively heats coronae to temperatures that are orders of magnitude hotter than the corresponding photospheres. It is widely accepted that the magnetic field is responsible for the heating, but there are two competing mechanisms that could explain it: nanoflares or Alfvén waves. To date, neither can be directly observed. Nanoflares are, by definition, extremely small, but their aggregate energy release could represent a substantial heating mechanism, presuming they are sufficiently abundant. One way to test this presumption is via the flare frequency distribution, which describes how often flares of various energies occur. If the slope of the power law fitting the flare frequency distribution is above a critical threshold, α = 2 as established in prior literature, then there should be a sufficient abundance of nanoflares to explain coronal heating. We performed >600 case studies of solar flares, made possible by an unprecedented number of data analysts via three semesters of an undergraduate physics laboratory course. This allowed us to include two crucial, but nontrivial, analysis methods: preflare baseline subtraction and computation of the flare energy, which requires determining flare start and stop times. We aggregated the results of these analyses into a statistical study to determine that α = 1.63 ± 0.03. This is below the critical threshold, suggesting that Alfvén waves are an important driver of coronal heating.

Myofiber atrophy occurs with aging and in many diseases but the underlying mechanisms are incompletely understood. Here, we have used >1,100 muscle-targeted RNAi interventions to comprehensively assess the function of 447 transcription factors in the developmental growth of body wall skeletal muscles in Drosophila. This screen identifies new regulators of myofiber atrophy and hypertrophy, including the transcription factor Deaf1. Deaf1 RNAi increases myofiber size whereas Deaf1 overexpression induces atrophy. Consistent with its annotation as a Gsk3 phosphorylation substrate, Deaf1 and Gsk3 induce largely overlapping transcriptional changes that are opposed by Deaf1 RNAi. The top category of Deaf1-regulated genes consists of glycolytic enzymes, which are suppressed by Deaf1 and Gsk3 but are upregulated by Deaf1 RNAi. Similar to Deaf1 and Gsk3 overexpression, RNAi for glycolytic enzymes reduces myofiber growth. Altogether, this study defines the repertoire of transcription factors that regulate developmental myofiber growth and the role of Gsk3/Deaf1/glycolysis in this process.

Summary: Defects in protein quality control are the underlying cause of age-related diseases. The western blot analysis of detergent-soluble and insoluble protein fractions has proven useful in identifying interventions that regulate proteostasis. Here, we describe the protocol for such analyses in Drosophila tissues, mouse skeletal muscle, human organoids, and HEK293 cells. We describe key adaptations of this protocol and provide key information that will help modify this protocol for future studies in other tissues and disease models.For complete details on the use and execution of this protocol, please refer to Rai et al. (2021) and Hunt el al. (2021).

Quantifying the capacity of protected area networks to shield multiple marine megafauna with diverse life histories is complicated, as many species are wide-ranging, requiring varied monitoring approaches. Yet, such information is needed to identify and assess the potential use of umbrella species and to plan how best to enhance conservation strategies. Here, we evaluated the effectiveness of part of the European Natura 2000 protected area network (western Greece) for marine megafauna and whether loggerhead sea turtles are viable umbrella species in this coastal region. We systematically surveyed inside and outside coastal marine protected areas (MPAs) at a regional scale using aerial drones (18,505 animal records) and combined them with distribution data from published datasets (tracking, sightings, strandings) of sea turtles, elasmobranchs, cetaceans and pinnipeds. MPAs covered 56% of the surveyed coastline (~1500 km). There was just a 22% overlap in the distributions of the four groups from aerial drone and other datasets, demonstrating the value of combining different approaches to improve records of coastal area use for effective management. All four taxonomic groups were more likely to be detected inside coastal MPAs than outside, confirming sufficient habitat diversity despite varied life history traits. Coastal habitats frequented by loggerhead turtles during breeding/non-breeding periods combined overlapped with 76% of areas used by the other three groups, supporting their potential use as an umbrella species. In conclusion, this study showed that aerial drones can be readily combined with other monitoring approaches in coastal areas to enhance the management of marine megafauna in protected area networks and to identify the efficacy of umbrella species.

Anaplastic lymphoma kinase (ALK) inhibitors are currently being considered in neuroblastoma (NB), but its acquired resistance is reported in non-small cell lung cancers. Here, the authors have found PIM1 overexpression decreases sensitivity to ALK inhibitors in NB and combined ALK and PIM1 inhibition enhances anti-tumour efficacy in vitro and in PDX models.

Abstract The GeneSwitch (GS) is a modified Gal4/UAS system, whereby transgene expression is induced in Drosophila by adding the drug RU486 to food. The GS system is routinely used in Drosophila aging and behavioral studies to avoid confounding effects related to genetic background mutations. Here, we report transcriptional and functional defects that are induced by RU486 in a stock- and tissue-dependent manner, such as defects in flight and mitochondrial gene expression. In addition to including proper controls, our findings suggest that context-specific side effects induced by RU486 should be considered in the experimental design and when interpreting the observed phenotypes.

Skeletal muscles are impressive as they can achieve reversible, macroscopic, anisotropic motion in soft materials. Here the authors show a bottom-up design of macroscopic hydrogel tubes containing supramolecular nanofibers that can undergo anisotropic actuation by thermal stimuli.

Temperature is often used to infer how climate influences wildlife distributions; yet, other parameters also contribute, separately and combined, with effects varying across geographical scales. Here, we used an unoccupied aircraft system to explore how environmental parameters affect the regional distribution of the terrestrial and marine breeding habitats of threatened loggerhead sea turtles (Caretta caretta). Surveys spanned four years and ~620 km coastline of western Greece, encompassing low (

Summary: Skeletal muscle cell (myofiber) atrophy is a detrimental component of aging and cancer that primarily results from muscle protein degradation via the proteasome and ubiquitin ligases. Transcriptional upregulation of some ubiquitin ligases contributes to myofiber atrophy, but little is known about the role that most other ubiquitin ligases play in this process. To address this question, we have used RNAi screening in Drosophila to identify the function of > 320 evolutionarily conserved ubiquitin ligases in myofiber size regulation in vivo. We find that whereas RNAi for some ubiquitin ligases induces myofiber atrophy, loss of others (including the N-end rule ubiquitin ligase UBR4) promotes hypertrophy. In Drosophila and mouse myofibers, loss of UBR4 induces hypertrophy via decreased ubiquitination and degradation of a core set of target proteins, including the HAT1/RBBP4/RBBP7 histone-binding complex. Together, this study defines the repertoire of ubiquitin ligases that regulate myofiber size and the role of UBR4 in myofiber hypertrophy. : Hunt et al. use the fruit fly Drosophila to identify ubiquitin-related enzymes that regulate skeletal muscle cell (myofiber) size, including the ubiquitin ligase UBR4. Loss of UBR4 promotes myofiber hypertrophy in Drosophila and mice via decreased ubiquitination and degradation of a core set of target proteins. Keywords: ubiquitin ligase, skeletal muscle growth, myofiber hypertrophy, muscle wasting, cancer cachexia, UBR4, Drosophila, myofiber size, HAT1, proteolysis

Purpose: The purpose of this study is to examine the impact of a mixed format, experiential course on changes in Honors students’ attitudes about various issues of inequality. Methodology: Students enrolled in the course (N = 75), taught during the 2016 Presidential election, were asked about their opinions on a variety of inequality topics using a pre-test and post-test survey, with the post-test survey including questions on how perceptions of inequality had changed over the course of the semester. Findings and implications: Results indicate that some students became more self-aware of their position in society and were less sure that people in general, and they themselves in particular, would be responsible for their own hard work. Importantly, students were less likely to believe that people faced fair and equal opportunities in the labor market and their overall level of support for unions increased during the semester. Most students agreed that the outside speakers, a key component of the course, provided new information on various aspects of inequality and impacted their overall perceptions of inequality. However, students were much less agreed on how they felt both about the future of the country and the future of inequality.

Given the depth of research on negative advertising in campaigns, scholars have wondered why candidates continue to attack their opponents. We build on this research by considering real-world campaign contexts in which candidates are working in competition with each other and have to react to the decisions of the opposing campaign. Our results suggest that it is never efficacious for candidates to run attack ads, but running positive ads can increase a candidate’s margin of victory. These results are conditioned by two factors: candidates must both stay positive and out-advertise their opponent. Second, the effects of positive advertising are strongest in areas where the candidate is losing or winning by a large margin—areas where they might be tempted to not advertise at all.

Embryonic development involves diffusion and proliferation of cells, as well as diffusion and reaction of molecules, within growing tissues. Mathematical models of these processes often involve reaction-diffusion equations on growing domains that have been primarily studied using approximate numerical solutions. Recently, we have shown how to obtain an exact solution to a single, uncoupled, linear reaction-diffusion equation on a growing domain, 0 < x < L(t), where L(t) is the domain length. The present work is an extension of our previous study, and we illustrate how to solve a system of coupled reaction-diffusion equations on a growing domain. This system of equations can be used to study the spatial and temporal distributions of different generations of cells within a population that diffuses and proliferates within a growing tissue. The exact solution is obtained by applying an uncoupling transformation, and the uncoupled equations are solved separately before applying the inverse uncoupling transformation to give the coupled solution. We present several example calculations to illustrate different types of behaviour. The first example calculation corresponds to a situation where the initially-confined population diffuses sufficiently slowly that it is unable to reach the moving boundary at x = L(t). In contrast, the second example calculation corresponds to a situation where the initially-confined population is able to overcome the domain growth and reach the moving boundary at x = L(t). In its basic format, the uncoupling transformation at first appears to be restricted to deal only with the case where each generation of cells has a distinct proliferation rate. However, we also demonstrate how the uncoupling transformation can be used when each generation has the same proliferation rate by evaluating the exact solutions as an appropriate limit.

Analytical solutions of partial differential equation (PDE) models describing reactive transport phenomena in saturated porous media are often used as screening tools to provide insight into contaminant fate and transport processes. While many practical modelling scenarios involve spatially variable coefficients, such as spatially variable flow velocity, v(x), or spatially variable decay rate, k(x), most analytical models deal with constant coefficients. Here we present a framework for constructing exact solutions of PDE models of reactive transport. Our approach is relevant for advection-dominant problems, and is based on a regular perturbation technique. We present a description of the solution technique for a range of one-dimensional scenarios involving constant and variable coefficients, and we show that the solutions compare well with numerical approximations. Our general approach applies to a range of initial conditions and various forms of v(x) and k(x). Instead of simply documenting specific solutions for particular cases, we present a symbolic worksheet, as supplementary material, which enables the solution to be evaluated for different choices of the initial condition, v(x) and k(x). We also discuss how the technique generalizes to apply to models of coupled multispecies reactive transport as well as higher dimensional problems.

Purpose: The purpose of this study is to examine the impact of a mixed format, experiential course on changes in Honors students' attitudes about various issues of inequality. Methodology: Students enrolled in the course (N = 75), taught during the 2016 Presidential election, were asked about their opinions on a variety of inequality topics using a pre- and post-test survey, with the post-test survey including questions on how perceptions of inequality had changed over the course of the semester. Findings and implications: Results indicate that some students became more self-aware of their position in society and were less sure that people in general, and they themselves in particular, would be responsible for their own success. Importantly, students were less likely to believe that people faced fair and equal opportunities in the labor market and their overall level of support for unions increased during the semester. Most students agreed that the outside speakers, a key component of the course, provided new information on various aspects of inequality and impacted their overall perceptions of inequality. However, students were much less agreed on how they felt both about the future of the country and the future of inequality.

BackgroundThe purpose of this study was to compare outcomes after hip fracture surgery between DNR/DNI and full code cohorts to determine whether DNR/DNI status is an independent predictor of complications and mortality within one year. A significant number of geriatric hip fracture patients carry a code status designation of DNR/DNI (Do-Not-Resuscitate/Do-Not-Intubate). There is limited data addressing how this designation may influence prognosis.MethodsA retrospective chart review of all geriatric hip fractures treated between 2002 and 2017 at a single level-I academic trauma center was performed. 434 patients were eligible for this study with 209 in the DNR/DNI cohort and 225 in the full code cohort. The independent variable was code-status and dependent variables included patient demographics, surgery performed, American Society of Anesthesiologists, score, Charlson Comorbidity Index, significant medical and surgical complications within one year of surgery, duration of follow-up by an orthopaedic surgeon, duration of follow-up by any physician, and mortality within 1 year of surgery. One-year complication rates were compared, and multiple logistic regression analyses were performed to analyze the relationship between independent and dependent variables.ResultsThe DNR/DNI cohort experienced significantly more surgical complications compared to the full code cohort (14.8% vs 7.6%, p = 0.024). There was a significantly higher rate of medical complications and mortality in the DNR/DNI cohort (57.9% vs 36%, p