bluuebunny/crossref_metadata_2025 huggingface dataset:
Time is of the essence: containment of the SARS-CoV-2 epidemic in Switzerland from February to May 2020
Authors: Althaus Christian L. , Probst Daniel , Hauser Anthony , Riou Julien
Published: July 2020

AIM

In late February and early March 2020, Switzerland experienced rapid growth of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections with 30,243 confirmed cases and 1,860 deaths as of 10 May 2020. The sequential introduction of non-pharmaceutical interventions (NPIs) resulted in successful containment of the epidemic. A better understanding of how the timing of implementing NPIs influences the dynamics and outcome of SARS-CoV-2 epidemics will be crucial for the management of a potential resurgence in Switzerland.

METHODS

We developed a dynamic transmission model that describes infection, hospitalization, recovery and death due to SARS-CoV-2 in Switzerland. Using a maximum likelihood framework, we fitted the model to aggregated daily numbers of hospitalized patients, ICU occupancy and death from 25 February to 10 May 2020. We estimated critical parameters of SARS-CoV-2 transmission in Switzerland and explored counterfactual scenarios of an earlier and later implementation of NPIs.

RESULTS

We estimated the basic reproduction numberR0= 2.61 (95% compatibility interval, CI: 2.51–2.71) during the early exponential phase of the SARS-CoV-2 epidemic in Switzerland. After the implementation of NPIs, the effective reproduction number approachedRe= 0.64 (95% CI: 0.61–0.66). Based on the observed doubling times of the epidemic before and after the implementation of NPIs, we estimated that one week of early exponential spread required 3.1 weeks (95% CI: 2.8–3.3 weeks) of ‘lockdown’ to reduce the number of infections to the same level. Introducing the same sequence of NPIs one week earlier or later would have resulted in substantially lower (399, 95% prediction interval, PI: 347–458) and higher (8,683, 95% PI: 8,038–9,453) numbers of deaths, respectively.

CONCLUSIONS

The introduction of NPIs in March 2020 prevented thousands of SARS-CoV-2-related deaths in Switzerland. Early implementation of NPIs during SARS-CoV-2 outbreaks can reduce the number of deaths and the necessary duration of strict control measures considerably.
Development and external validation of machine learning algorithms for postnatal gestational age estimation using clinical data and metabolomic markers
Authors: Hawken Steven , Ducharme Robin , Murphy Malia S.Q. , Olibris Brieanne , Bota A. Brianne , Wilson Lindsay A. , Cheng Wei , Little Julian , Potter Beth K. , Denize Kathryn M. , Lamoureux Monica , Henderson Matthew , Rittenhouse Katelyn J. , Price Joan T. , Mwape Humphrey , Vwalika Bellington , Musonda Patrick , Pervin Jesmin , Chowdhury AK Azad , Rahman Anisur , Chakraborty Pranesh , Stringer Jeffrey S.A. , Wilson Kumanan
Published: July 2020

Accurate estimates of gestational age at birth are important for preterm birth surveillance but can be challenging to reliably acquire in low and middle income countries. Our objective was to develop machine learning models to accurately estimate gestational age shortly after birth using clinical and metabolic data. We derived and internally validated three models using ELASTIC NET multivariable linear regression in heel prick blood samples and clinical data from a retrospective cohort of newborns from Ontario, Canada. We conducted external model validation in heel prick and cord blood sample data collected from prospective birth cohorts in Lusaka, Zambia (N=311) and Matlab, Bangladesh (N=1176). The best-performing model accurately estimated gestational age within about 6 days of early pregnancy ultrasound estimates in both cohorts when applied to heel prick data (MAE (95% CI) = 0.79 weeks (0.69, 0.90) for Zambia; 0.81 weeks (0.75, 0.86) for Bangladesh), and within about 7 days when applied to cord blood data (1.02 weeks (0.90, 1.15) for Zambia; 0.95 weeks (0.90, 0.99) for Bangladesh). Algorithms developed in Canada provided accurate estimates of gestational age when applied to external cohorts from Zambia and Bangladesh. Model performance was superior in heel prick data as compared to cord blood data.
Endemic Chikungunya Fever in Kenyan Children
Authors: Nyamwaya Doris K. , Otiende Mark , Omuoyo Donwilliams O. , Githinji George , Karanja Henry K. , Gitonga John N. , de Laurent Zaydah , Otieno James R. , Sang Rosemary , Kamau Everlyn , Cheruiyot Stanley , Otieno Edward , Agoti Charles N. , Bejon Philip , Thumbi Samuel M. , Warimwe George M.
Published: July 2020

Background

Chikungunya virus (CHIKV) was first identified in Tanzania in 1952. Several epidemics including East Africa are described, but there are no descriptions of longitudinal surveillance of endemic disease. Here, we estimate the incidence of CHIKV and describe viral phylogeny in coastal Kenya.

Methods

Over a 5-year period (2014-2018), 11,708 febrile illnesses in 5,569 children visiting two primary healthcare facilities linked to a demographic surveillance system in coastal Kenya were recorded and blood samples obtained. Reverse-transcriptase PCR was used to identify CHIKF cases in 3,500 children randomly selected from the 5,569 children.

Results

We found CHIKF to be endemic in this setting, associated with 12.7% (95% CI 11.60, 13.80) of all febrile presentations to primary healthcare. The prevalence of CHIKV infections among asymptomatic children in a community survey was 0.7% (95% CI 0.22, 2.12). CHIKF incidence among children <1 year of age was 1703 cases/100,000-person years and 46 cases/100,000-person years among children aged ≥ 10 years. Recurrent CHIKF episodes, associated with fever and viraemia, were observed among 19 of 170 children with multiple febrile episodes during the study period and confirmed by genome sequencing. All sequenced viral genomes mapped to the ECSA genotype albeit distinct from CHIKV strains associated with the 2004 East African epidemic.

Conclusions

CHIKF may be a substantial public health burden in primary healthcare on the East African coast outside epidemic years, and recurrent infections are common.
Previous and active tuberculosis in COVID-19 patients increases risk of death and prolongs recovery
Authors: Sy Karla Therese L. , Haw Nel Jason L. , Uy Jhanna
Published: July 2020

Background

There is growing literature on the association of SARS-CoV-2 and other chronic respiratory conditions, such as COPD and asthma. However, little is known about the relationship between coinfection with tuberculosis (TB) and COVID-19. We aimed to compare the risk and survival time of death and recovery among COVID-19 patients with and without TB.

Methods

We created a 4:1 propensity score matched sample of COVID-19 patients without and with TB, using SARS-CoV-2 surveillance data in the Philippines. We conducted a longitudinal cohort analysis of matched COVID-19 patients as of May 17, 2020, following them until June 15, 2020. The primary analysis estimated the risk ratios of death and recovery comparing COVID-19 patients with and without TB. Kaplan-Meier curves described time-to-death and time-to-recovery stratified by TB status, and differences in survival were assessed using the Wilcoxon test. We also conducted the same analysis on a subsample of admitted COVID-19 patients only.

Results

The risk of death in COVID-19 patients with TB was 2.17 times greater compared to those without TB (95% CI: 1.40-3.37). The risk of recovery in TB patients was 25% less than the risk among those without TB (RR=0.75, 0.63-0.91). Similarly, time-to-death among COVID-19 patients with TB was significantly shorter (p=0.0031) and time-to-recovery in TB patients was significantly longer than patients without TB (p=0.0046).

Among those admitted, COVID-19 TB patients also had a similar significant increase in risk of death (RR=2.25, 95% CI: 1.35-3.75); however, the risk of recovery was not significantly less (RR=0.84, 95% CI: 0.68-1.06). Time-to-death among those with TB was also significantly longer (p=0.0031) than those without TB, but there was no difference in time-to-recovery (p=0.17).

Conclusions

Our findings show that coinfection with tuberculosis increases morbidity and mortality in COVID-19 patients. Our findings reiterate the need to prioritize routine and testing services for tuberculosis, even with increased disruptions to health systems during the SARS-CoV-2 pandemic. Additional research needs to focus on the interrelationship between TB and COVID-19 for appropriate planning and resource allocation, as SARS-CoV-2 continues to spread worldwide.
Hospital Trainees’ Worries, Perceived Sufficiency of Information and Reported Psychological Health During The COVID-19 Pandemic
Authors: Aziminia Nikoo , Khani Aria , Smith Colette , Bakhai Ameet , Lisk Clifford
Published: July 2020

Introduction

The COVID-19 pandemic has been unsurpassed in clinical severity or infectivity since the 1918 Spanish influenza pandemic and continues to impact the world. During the A/H1N1 influenza pandemic, healthcare workers presented frequent concerns regarding their ownand their families’ health, as well as high levels of psychological distress.

Objectives

To assess hospital trainees ‘concerns, perceived sufficiency of information, behaviour and reported psychological health during the COVID-19 pandemic in the NHS

Design

Cross-sectional 39-point questionnaire study conducted in May 2020

Setting

A large NHS foundation trust in London

Participants

204 hospital trainee doctors

Outcome measures

Quantitative analysis of trainees’ worries and concerns while working during the COVID-19 pandemic were assessed across 8 domains: trainee demographics; concerns and worries regarding COVID-19; perceived sufficiency of information about the COVID-19 pandemic; social distancing; use of personal protective equipment (PPE) and training in PPE; COVID-19 acquisition and risk; reported psychological health; and medical education.

Results

91.7% looked after COVID-19 patients. 91.6% were worried about COVID-19; the most frequent concern was that of family and friends dying from COVID-19 (74.6%). 22.2% reported being infected with COVID-19. 6.8% of trainees were so concerned about COVID-19 infection that they would avoid going to work. Perceived sufficiency of information about COVID-19 was moderately high. 25.9% reported that they were able to socially distance at work compared to 94.4% able to socially distance outside work. 98.2% reported using PPE and 24.7% were confident the provided PPE protected them against infection with COVID-19. 41.9% reported that their psychological health had been affected by their work with the commonest being anxiety (56.6%), emotional distress (50.9%) and burnout (37.7%). 95.6% felt it is important to have a service that provides psychological support during this pandemic and 62.5% reported they would consider using this at work.

Conclusions

A significant proportion of hospital trainees are worried about the COVID-19 pandemic with high levels of reported psychological distress. Given that almost a third would not use psychological support services at work, hospital leaders and liaison psychiatry need to explore the reasons for not wanting to use services at work and highlight the provision of psychological services provided outside work such that provided by the London deaneries professional support unit (PSU). Seeking solutions to support trainee wellbeing in addition to this, such as larger offices, adequate rest facilities and alternative methods of teaching, with their input would enable empowerment of trainees and improve their health and morale while working in a pandemic.
Anatomy of digital contact tracing: role of age, transmission setting, adoption and case detection
Authors: Moreno López Jesús A. , García Beatriz Arregui , Bentkowski Piotr , Bioglio Livio , Pinotti Francesco , Boëlle Pierre-Yves , Barrat Alain , Colizza Vittoria , Poletto Chiara
Published: July 2020

The efficacy of digital contact tracing against COVID-19 epidemic is debated: smartphone penetration is limited in many countries, non-uniform across age groups, with low coverage among elderly, the most vulnerable to SARS-CoV-2. We developed an agent-based model to precise the impact of digital contact tracing and household isolation on COVID-19 transmission. The model, calibrated on French population, integrates demographic, contact-survey and epidemiological information to describe the risk factors for exposure and transmission of COVID-19. We explored realistic levels of case detection, app adoption, population immunity and transmissibility. Assuming a reproductive ratio R = 2.6 and 50% detection of clinical cases, a ~20% app adoption reduces peak incidence by ~35%. With R = 1.7, >30% app adoption lowers the epidemic to manageable levels. Higher coverage among adults, playing a central role in COVID-19 transmission, yields an indirect benefit for elderly. These results may inform the inclusion of digital contact tracing within a COVID-19 response plan.
Theta and gamma connectivity is linked with affective and cognitive symptoms in Parkinson’s disease
Authors: Iyer Kartik K. , Au Tiffany R. , Angwin Anthony J. , Copland David A. , Dissanayaka Nadeeka N.
Published: July 2020

Background

The progression of Parkinson’s disease (PD) can often exacerbate symptoms of depression, anxiety, and/or cognitive impairment. In this study, we explore the possibility that multiple brain network responses are associated with symptoms of depression, anxiety and cognitive impairment in PD. This association is likely to provide insights into a single multivariate relationship, where common affective symptoms occurring in PD cohorts are related with alterations to electrophysiological response.

Methods

70 PD patients and 21 healthy age-matched controls (HC) participated in a high-density electroencephalography (EEG) study. Functional connectivity differences between PD and HC groups of oscillatory activity at rest and during completion of an emotion-cognition task were examined to identify key brain oscillatory activities. A canonical correlation analysis (CCA) was applied to identify a putative multivariate relationship between connectivity patterns and affective symptoms in PD groups.

Results

A CCA analysis identified a single mode of co-variation linking theta and gamma connectivity with affective symptoms in PD groups. Increases in frontotemporal gamma, frontal and parietal theta connectivity were related with increased anxiety and cognitive impairment. Decreases in temporal region theta and frontoparietal gamma connectivity were associated with higher depression ratings and PD patient age.

Limitations

This study only reports on optimal dosage of dopaminergic treatment (‘on’ state) in PD and didn’t investigate at “off” medication.

Conclusions

Theta and gamma connectivity during rest and task-states are linked to affective and cognitive symptoms within fronto-temporo-parietal networks, suggesting a potential assessment avenue for understanding brain-behavior associations in PD with electrophysiological task paradigms.
Potential impact of individual exposure histories to endemic human coronaviruses on age-dependence in severity of COVID-19
Authors: Pinotti Francesco , Wikramaratna Paul S , Obolski Uri , Paton Robert S , Damineli Daniel S C , Alcantara Luiz C J , Giovanetti Marta , Gupta Sunetra , Lourenço José
Published: July 2020

Cross-reactivity to SARS-CoV-2 from previous exposure to endemic coronaviruses (eHCoV) is gaining increasing attention as a possible driver of both protection against infection and severity of COVID-19 disease. Here, we use a stochastic individual-based model to show that heterogeneities in individual exposure histories to endemic coronaviruses are able to explain observed age patterns of hospitalisation due to COVID-19 in EU/EEA countries and the UK, provided there is (i) a decrease in cross-protection to SARS-CoV-2 with the number of eHCoV exposures and (ii) an increase in potential disease severity with number of eHCoV exposures or as a result of immune senescence. We also show that variation in health care capacity and testing efforts is compatible with country-specific differences in hospitalisation rates. Our findings call for further research on the role of cross-reactivity to endemic coronaviruses and highlight potential challenges arising from heterogeneous health care capacity and testing.
Effect of Cholesterol vs. Ergosterol on DPPC Bilayer Properties: Insights from Atomistic Simulations
Authors: Alavizargar Azadeh , Keller Fabian , Wedlich-Söldner Roland , Heuer Andreas
Published: July 2020

Sterols have been ascribed a major role in the organization of biological membranes, in particular for the formation of liquid ordered domains in complex lipid mixtures. Here, we employed molecular dynamics simulations to compare the effects of cholesterol and ergosterol as the major sterol of mammalian and fungal cells, respectively, on binary mixtures with 1,2-dipalmitoyl-sn-glycero-3-phosphocholine (DPPC) as a proxy for saturated lipids. In agreement with previous work, we observe that the addition of sterol molecules modifies the order of DPPC both in the gel phase and in the liquid phase. When disentangling the overall tilt angle and the structure of the tail imposed by trans/gauche configurations of torsion angles in the tail, respectively, a more detailed picture of the impact of sterols can be formulated, revealing, e.g., an approximate temperature-concentration superposition ranging from the liquid to the gel phase. Furthermore, a new quantitative measure to identify the presence of collective sterol effects is discussed. Moreover, when comparing both types of sterols, addition of cholesterol has a noticeably stronger impact on phospholipid properties than of ergosterol. The observed differences can be attributed to higher planarity of the cholesterol ring system. This planarity combined with an inherent asymmetry in its molecular interactions leads to better alignment and hence stronger interaction with saturated acyl chains. Our results suggest that the high order demonstrated for ergosterol in fungal plasma membranes must therefore be generated via additional mechanisms.
Spotting genome-wide pigmentation variation in a brown trout admixture context
Authors: Valette T. , Leitwein M. , Lascaux J.-M. , Desmarais E. , Berrebi P. , Guinand B.
Published: July 2020

Variation in body pigmentation attracted fish biologists for a while, but high-throughput genomic studies investigating its molecular basis remain limited to few species and associated conservation issues ignored. Using 75,684 SNPs, we explored the genomic basis of pigmentation pattern variation among individuals of the Atlantic and Mediterranean clades of the brown trout (Salmo trutta), a polytypic species in which Atlantic hatchery individuals are commonly used to supplement local wild populations. Using redundancy analyses and genome-wide association studies, a set of 337 independent “colour patterning loci” (CPLs) significantly associated with pigmentation traits such as the number of red and black spots on flanks, or the presence of a black spot on the pre-opercular bone was identified. CPLs map onto 35 out of 40 brown trout linkage groups indicating a polygenic basis to pigmentation patterns. They are mostly located in coding regions (43.4%) of 223 candidate genes, and correspond to GO-terms known to be involved in pigmentation (e.g. calcium and ion-binding, cell adhesion). Annotated candidates include genes with known pigmentation effects (e.g. SOX10, PEML, SLC45A2), but also the Gap-junction ⊗2 (GJD2) gene already shown differentially expressed in trout skin. Patterns of admixture were found significantly distinct when using either the full SNP data set or the set of CPLs, indicating that pigmentation patterns accessible to practitioners are not a reliable proxy of genome-wide admixture. Consequences for management are discussed.
No endospore formation confirmed in members of the phylum Proteobacteria
Authors: Beskrovnaya Polina , Fakih Doaa , Sexton Danielle L. , Xing Shipei , Golmohammadzadeh Mona , Morneau Isabelle , Bello Dainelys Guadarrama , Nanci Antonio , Huan Tao , Tocheva Elitza I.
Published: July 2020

Endospore formation is used by members of the phylum Firmicutes to withstand extreme environmental conditions. Several recent studies have documented endospore formation in species outside of Firmicutes, particularly inRhodobacter johriiandSerratia marcescens, members of the phylum Proteobacteria. Here, we aimed to investigate endospore formation in these two species by using advanced imaging and analytical approaches. Examination of the phase-bright structures observed inR. johriiandS. marcescensusing cryo-electron tomography failed to identify endospores or stages of endospore formation. We determined that the phase-bright objects inR. johriicells were triacylglycerol storage granules and those inS. marcescenswere aggregates of cellular debris. In addition,R. johriiandS. marcescenscontaining phase-bright objects do not possess phenotypic and genetic features of endospores, including enhanced resistance to heat, presence of dipicolinic acid, or the presence of many of the genes associated with endospore formation. Our results support the hypothesis that endospore formation is restricted to the phylum Firmicutes.

Importance

Endospore formation is a mechanism that allows bacteria to generate resilient dormant spores under harsh environmental conditions. Although this process has been traditionally restricted to the largely Gram-positive bacteria of the phylum Firmicutes, recent studies have also described endospores in some Proteobacteria. High complexity of endosporulation, reflected in extensive morphological transformations governed by hundreds of conserved genes, hinders its facile acquisition via horizontal gene transfer. Therefore, ability of distantly related bacteria to produce endospores would imply an ancient nature of this mechanism and potentially a pivotal role in species diversification and outer membrane biogenesis.
Dynamics of SARS-CoV-2 with Waning Immunity in the UK Population
Authors: Crellen Thomas , Pi Li , Davis Emma L. , Pollington Timothy M. , Lucas Tim C. D. , Ayabina Diepreye , Borlase Anna , Toor Jaspreet , Prem Kiesha , Medley Graham F. , Klepac Petra , Hollingsworth T. Déirdre
Published: July 2020

The dynamics of immunity are crucial to understanding the long-term patterns of the SARS-CoV-2 pandemic. Several cases of reinfection with SARS-CoV-2 have been documented 48–142 days after the initial infection and immunity to seasonal circulating coronaviruses is estimated to be shorter than one year. Using an age-structured, deterministic model, we explore potential immunity dynamics using contact data from the UK population. In the scenario where immunity to SARS-CoV-2 lasts an average of three months for non-hospitalised individuals, a year for hospitalised individuals, and the effective reproduction number after lockdown ends is 1.2 (our worst case scenario), we find that the secondary peak occurs in winter 2020 with a daily maximum of 387,000 infectious individuals and 125,000 daily new cases; three-fold greater than in a scenario with permanent immunity. Our models suggests that longitudinal serological surveys to determine if immunity in the population is waning will be most informative when sampling takes place from the end of the lockdown in June until autumn 2020. After this period, the proportion of the population with antibodies to SARS-CoV-2 is expected to increase due to the secondary wave. Overall, our analysis presents considerations for policy makers on the longer term dynamics of SARS-CoV-2 in the UK and suggests that strategies designed to achieve herd immunity may lead to repeated waves of infection as immunity to reinfection is not permanent.
Genes influencing phage host range in Staphylococcus aureus on a species-wide scale
Authors: Moller Abraham G , Winston Kyle , Ji Shiyu , Wang Junting , Hargita Davis Michelle N , Solis-Lemus Claudia R , Read Timothy
Published: July 2020

Staphylococcus aureus is a human pathogen that causes serious diseases ranging from skin infections to septic shock. Bacteriophages ("phages") are both natural killers of S. aureus, offering therapeutic possibilities, as well as important vectors of horizontal gene transfer in the species. Here, we used high-throughput approaches to understand the genetic basis of strain-to-strain variation in sensitivity to phages, which defines the host range. We screened 259 diverse S. aureus strains covering more than 40 sequence types for sensitivity to eight phages, which were representatives of the three phage classes that infect the species. The phages were variable in host range, each infecting between 73 and 257 strains. Using genome-wide association approaches, we identified putative loci that affect host range and validated their function using USA300 transposon knockouts. In addition to rediscovering known host range determinants, we found several previously unreported genes affecting bacterial growth during phage infection, including trpA, phoR, isdB, sodM, fmtC, and relA. We used the data from our host range matrix to develop predictive models that achieved between 40 and 95% accuracy. This work illustrates the complexity of the genetic basis for phage susceptibility in S. aureus but also shows that with more data, we may be able to understand much of the variation. With a knowledge of host range determination, we can rationally design phage therapy cocktails that target the broadest host range of S. aureus strains and address basic questions regarding phage-host interactions, such as the impact of phage on S. aureus evolution.
Data-independent acquisition method for ubiquitinome analysis reveals regulation of circadian biology
Authors: Hansen Fynn M. , Tanzer Maria C. , Brüning Franziska , Bludau Isabell , Schulman Brenda A. , Robles Maria S. , Karayel Ozge , Mann Matthias
Published: July 2020

Protein ubiquitination is involved in virtually all cellular processes. Enrichment strategies employing antibodies targeting ubiquitin-derived diGly remnants combined with mass spectrometry (MS) have enabled investigations of ubiquitin signaling at a large scale. However, so far the power of data independent acquisition (DIA) with regards to sensitivity in single run analysis and data completeness have not yet been explored. We developed a sensitive workflow combining diGly antibody-based enrichment and optimized Orbitrap-based DIA with comprehensive spectral libraries together containing more than 90,000 diGly peptides. This approach identified 35,000 diGly peptides in single measurements of proteasome inhibitor-treated cells – double the number and quantitative accuracy of data dependent acquisition. Applied to TNF-alpha signaling, the workflow comprehensively captured known sites while adding many novel ones. A first systems-wide investigation of ubiquitination of the circadian cycle uncovered hundreds of cycling ubiquitination sites and dozens of cycling ubiquitin clusters within individual membrane protein receptors and transporters, highlighting novel connections between metabolism and circadian regulation.
Neurodegeneration induces a developmental RNA processing program by calpain-mediated MBNL2 degradation
Authors: Wang Lee-Hsin , Lin Yu-Mei , Lin Chien-Yu , Chern Yijuang , Wang Guey-Shin
Published: July 2020

The Muscleblind-like (MBNL) protein family plays an important role in regulating developmental RNA processing transition. Loss of MBNL2 function has been implicated in the neurodegeneration of myotonic dystrophy type 1 (DM1). However, the causal mechanism of neurodegeneration-induced MBNL2 loss of function remains elusive. Here, we show that neurodegenerative conditions including NMDAR-mediated excitotoxicity and dysregulated calcium homeostasis triggered nuclear translocation of calpain-2 resulting in MBNL2 degradation and reversion of MBNL2-regulated RNA processing to developmental patterns. The developmental stage featured nucleus-enriched distribution of calpain-2 and low expression of MBNL2. Increased MBNL2 expression during development is required for promoting developmental RNA processing transition and neuronal maturation. Knockdown of calpain-2 expression inhibited neurodegeneration-induced MBNL2 reduction and dysregulated RNA processing. Neurodegenerative disease mouse models including DM1 and Alzheimer’s disease showed nuclear translocation of calpain-2 associated with MBNL2 degradation and reversion of MBNL2-regulated RNA processing to the developmental pattern. Our results identify a novel regulatory mechanism for MBNL2 downregulation and suggest that reduced MBNL2 expression accompanied by the re-induction of a developmental RNA processing program may be a common feature of neurodegeneration.
Gradual centriole maturation associates with the mitotic surveillance pathway in mouse development
Authors: Xiao Cally , Grzonka Marta , Gerards Charlotte , Mack Miriam , Figge Rebecca , Bazzi Hisham
Published: July 2020

Centrosomes, composed of two centrioles and pericentriolar material, organize mitotic spindles during cell division and template cilia during interphase. The first few divisions during mouse development occur without centrioles, which form around embryonic day (E) 3. However, disruption of centriole biogenesis inSas-4null mice leads to embryonic arrest around E9. Centriole loss inSas-4−/−embryos causes prolonged mitosis and p53-dependent cell death. Studiesin vitrodiscovered a similar USP28-, 53BP1-, and p53-dependent mitotic surveillance pathway that leads to cell cycle arrest. In this study, we show that an analogous pathway is conservedin vivowhere 53BP1 and USP28 are upstream of p53 inSas-4−/−embryos. The data indicates that the pathway is established around E7 of development, four days after the centrioles appear. Our data suggest that the newly formed centrioles gradually mature to participate in mitosis and cilia formation around the beginning of gastrulation, coinciding with the activation of mitotic surveillance pathway upon centriole loss.
Interplay between medial nuclear stalling and lateral cellular flow underlies cochlear duct spiral morphogenesis
Authors: Ishii Mamoru , Tateya Tomoko , Matsuda Michiyuki , Hirashima Tsuyoshi
Published: July 2020

A notable example of spiral architecture in organs is the mammalian cochlear duct, where the duct morphology is critical for hearing function. Molecular genetics has revealed the necessary signaling molecules for the formation of spirals in organs, but it remains unclear how cellular dynamics generate bending and coiling of the cochlear duct during development. Here we show two modes of multicellular dynamics underlying the morphogenetic process by combining deep tissue live-cell imaging, Förster resonance energy transfer (FRET)-based quantitation, and mathematical modeling. First, surgical separation of the cochlear duct revealed that bending forces reside primarily in the medial side of the duct. In the medial pseudostratified epithelium, we found that nuclei stall at the luminal side during interkinetic nuclear migration, which would cause the extension of the luminal side, thereby bending the duct. Second, long-term organ-scale FRET imaging of extracellular signal-regulated kinase (ERK) activity showed that helical ERK activation waves propagate from the duct tip concomitant with the reverse multicellular flow in the lateral side of the duct, resulting in advection-based duct elongation. We propose an interplay of distinct multicellular behaviors underpinning spiral morphogenesis in the developing cochlear duct.
Adaptive divergence of meiotic recombination rate in ecological speciation
Authors: Neupane Swatantra , Xu Sen
Published: July 2020

Theories predict that directional selection during adaptation to a novel habitat results in elevated meiotic recombination rate. Yet the lack of population-level recombination rate data leaves this hypothesis untested in natural populations. Here we examine the population-level recombination rate variation in two incipient ecological species, the microcrustaceanDaphnia pulex(an ephemeral-pond species) andD. pulicaria(a permanent-lake species). The divergence ofD. pulicariafromD. pulexinvolved habitat shifts from pond to lake habitats as well as strong local adaptation due to directional selection. Using a novel single-sperm genotyping approach, we estimated the male-specific recombination rate of two linkage groups in multiple populations of each species in common garden experiments and identified a significantly elevated recombination rate inD. pulicaria. Most importantly, population genetic analyses show that the divergence in recombination rate between these two species is most likely due to divergent selection in distinct ecological habitats rather than neutral evolution.

Significance statement

Whether directional selection during adaptation to a novel habitat results in elevated meiotic recombination remains largely untested in natural populations. This work examines the population-level recombination rate in two closely related microcructacean speciesDaphnia pulexandD. pulicariausing single-sperm genotyping approach. Recombination rate data from two linkage groups show elevated recombination rates inD. pulicariawhose divergence fromD. pulexis accompanied by a habitat shift. Importantly, population genetic analysis suggests that this divergence of recombination is likely adaptive rather than neutral.
A nutrient-responsive hormonal circuit controls energy and water homeostasis inDrosophila
Authors: Koyama Takashi , Terhzaz Selim , Naseem Muhammad T. , Nagy Stanislav , Rewitz Kim , Dow Julian A. T. , Davies Shireen A. , Halberg Kenneth A.
Published: July 2020

The regulation of systemic energy balance involves the coordinated activity of specialized organs, which control nutrient uptake, utilization and storage to promote metabolic homeostasis during environmental challenges. The humoral signals that drive such homeostatic programs are largely unidentified. Here we show that three pairs of central neurons in adultDrosophilarespond to internal water and nutrient availability by releasing Capa-1 and -2 hormones that signal through the Capa receptor (CapaR) to exert systemic metabolic control. Loss of Capa/CapaR signaling leads to intestinal hypomotility and impaired nutrient absorption, which gradually deplete internal nutrient stores and reduce organismal lifespan. Conversely, hyperactivation of the Capa circuitry stimulates fluid and waste excretion. Furthermore, we demonstrate that Capa/CapaR regulates energy metabolism by modulating the release of the glucagon-like adipokinetic hormone, which governs lipolysis in adipose tissue to stabilize circulating energy levels. Altogether, our results uncover a novel inter-tissue program that plays a central role in coordinating post-prandial responses that are essential to maintain adult viability.
A twofold strategy for the protection of therapeutic peptides by attachment to the protease-resistant and fusogenic protein, saposin C
Authors: Sandin Suzanne I. , Randolph Christopher J. , de Alba Eva
Published: July 2020

A great challenge of therapeutic peptides (biologics) is their short half-life. However, biologics can be protected by encapsulation in liposomes used as drug-delivery platforms. Liposomes are typically incorporated into cells by endocytic pathways, which eventually expose therapeutics to favorable proteolytic conditions. To enhance biologics protection, we report the design and characterization of a liposome-protein chimera combining the liposome fusogenic properties of peripheral-membrane protein saposin C, covalently linked to a proapoptotic peptide (the active domain of Bcl-2 protein PUMA). We show by NMR that the saposin C component of the chimera is capable of binding liposomes and that the peptide binds prosurvival Bcl-xL, thus following known PUMA’s mechanism to induce cell death. These results indicate that the function of the individual components is preserved in the chimera. Our results point to a promising twofold strategy for drug delivery to; 1) avoid endocytosis by promoting liposome-membrane fusion, 2) provide additional protection by attachment to a stable, protease-resistant protein, which is a well-known method commonly used to prolong biologics half-life.
The lysosomal V-ATPase B1 subunit in renal proximal tubule is linked to nephropathic cystinosis
Authors: Jamalpoor Amer , van Eerde Albertien M , Lilien Marc R , van Gelder Charlotte AGH , Zaal Esther A , Valentijn Floris A , Broekhuizen Roel , Zielhuis Eva , Egido Julia E , Altelaar Maarten , Berkers Celia R , Masereeuw Rosalinde , Janssen Manoe J
Published: July 2020

Variants in ATP6V1B1, the gene encoding the B1 subunit of the vacuolar H+-ATPase lead to distal renal tubular acidosis and hearing loss of variable degree. Apart from metabolic acidosis, a 23-month-old girl with pathogenic ATP6V1B1 variants presented with increased granulocyte cystine levels, and symptoms of renal Fanconi syndrome, indicating an unknown link to proximal tubulopathy and cystinosis, a disorder of the proximal tubule caused by variants in the CTNS gene. Here, we demonstrated that ATP6V1B1 is expressed in proximal tubules of human kidney tissue, though to a lesser extent than in distal tubules. Further, we used CRISPR/Cas9 technology to selectively knockout ATP6V1B1 or CTNS in human renal proximal tubule cells and performed a full metabolomic and proteomic analysis to compare their phenotype to isogenic control cells. In line with the clinical data, the loss of ATP6V1B1 disrupted the chemiosmotic coupling between the lysosomal V ATPase B1 subunit and cystinosin and resulted in intralysosomal accumulation of cystine and autophagy activation in renal proximal tubule cells. In conclusion, we identified ATP6V1B1 as a central player in renal proximal tubule cells, regulating lysosomal cystine transport and autophagy, and its absence can lead to proximal tubule dysfunction.
Kinetochore individualization in meiosis I is required for centromeric cohesin removal in meiosis II
Authors: Gryaznova Yulia , Keating Leonor , Touati Sandra A. , Cladière Damien , Yakoubi Warif El , Buffin Eulalie , Wassmann Katja
Published: July 2020

Partitioning of the genome in meiosis occurs through two highly specialized cell divisions, named meiosis I and II. Step-wise cohesin removal is required for chromosome segregation in meiosis I, and sister chromatid segregation in meiosis II. In meiosis I, mono-oriented sister kinetochores appear as fused together when examined by high resolution confocal microscopy, whereas they are clearly separated in meiosis II, when attachments are bipolar. It has been proposed that bipolar tension applied by the spindle is responsible for the physical separation of sister kinetochores, removal of cohesin protection and chromatid separation in meiosis II. We show here that this is not the case, and initial separation of sister kinetochores occurs already in anaphase I, when attachments are still monopolar, and independently of pericentromeric Sgo2 removal. This kinetochore individualization occurs also independently of spindle forces applied on sister kinetochores, but importantly, depends on cleavage activity of Separase. Crucially, without kinetochore individualization by Separase in meiosis I, oocytes separate bivalents into chromosomes and not sister chromatids in meiosis II, showing that whether centromeric cohesin is removed or not is determined by the kinetochore structure prior to meiosis II.
Myeloid lncRNALOUPMediates Opposing Regulatory Effects of RUNX1 and RUNX1-ETO in t(8;21) AML
Authors: Trinh Bon Q. , Ummarino Simone , Ebralidze Alexander K. , van der Kouwe Emiel , Bassal Mahmoud A. , Nguyen Tuan M. , Coffey Rory , Tenen Danielle E. , Fabiani Emiliano , Gurnari Carmelo , Wu Chan-Shuo , Angarica Vladimir Espinosa , Zhang Yanzhou , Ying Li , Yang Henry , Heller Gerwin , Chen Sisi , Zhang Hong , Thurm Abby R. , Marchi Francisco , Levantini Elena , Staber Philipp B. , Zhang Pu , Voso Maria Teresa , Pandolfi Pier Paolo , Ruscio Annalisa Di , Tenen Daniel G.
Published: July 2020

The mechanism underlying cell type-specific gene induction conferred by ubiquitous transcription factors as well as disruptions caused by their chimeric derivatives in leukemia is not well understood. Here we investigate whether RNAs coordinate with transcription factors to drive myeloid gene transcription. In an integrated genome-wide approach surveying for gene loci exhibiting concurrent RNA- and DNA-interactions with the broadly expressed transcription factor RUNX1, we identified the long noncoding RNALOUP. This myeloid-specific and polyadenylated lncRNA induces myeloid differentiation and inhibits cell growth, acting as a transcriptional inducer of the myeloid master regulatorPU.1. Mechanistically,LOUPrecruits RUNX1 to both thePU.1enhancer and the promoter, leading to the formation of an active chromatin loop. In t(8;21) acute myeloid leukemia, wherein RUNX1 is fused to ETO, the resulting oncogenic fusion protein RUNX1-ETO limits chromatin accessibility at theLOUPlocus, causing inhibition ofLOUPandPU.1expression. These findings highlight the important role of the interplay between cell type-specific RNAs and transcription factors as well as their oncogenic derivatives in modulating lineage-gene activation and raise the possibility that RNA regulators of transcription factors represent alternative targets for therapeutic development.

KEY POINTS

lncRNALOUPcoordinates with RUNX1 to inducesPU.1long-range transcription, conferring myeloid differentiation and inhibiting cell growth.

RUNX1-ETO limits chromatin accessibility at theLOUPlocus, causing inhibition ofLOUPandPU.1expression in t(8;21) AML.
The Ran GTPase Gradient Protects the Nucleolus from Aging-Associated Morphological Changes
Authors: Remlein Bartlomiej , Paschal Bryce M.
Published: July 2020

In the context of its regulatory function for nucleocytoplasmic transport, the Ran GTPase undergoes cycles of nuclear import, GTP loading, nuclear export, and GTP hydrolysis. These reactions give rise to a nuclear:cytoplasmic (N:C) Ran gradient. In Hutchinson-Gilford Progeria Syndrome, disruption of the Ran gradient suppresses nuclear import of high molecular mass complexes by reducing the nuclear concentration of Ran. Here, we report that cells undergoing senescence, as a consequence of passage number, chemical induction, and altered nuclear lamina structure, all display a Ran gradient disruption quantitatively similar to that observed in Progeria patient cells. We found that the Ran gradient is critical for maintenance of nucleolar structure, as its disruption increases the size and decreases the average number of nucleoli per cell. Nucleolar number and size are biomarkers of longevity in diverse organisms, thus the nuclear level of Ran may be important for the nucleolar morphology in aging. The contribution of the Ran gradient includes regulating import of nucleolin and nucleophosmin, nucleolar proteins that assemble into high molecular mass complexes. The steepness of the Ran gradient is highly dependent on nuclear heterochromatin, which is reduced by passage number and chemical induction of senescence in cultured cells, and is known to decline during normal aging. Our data suggest that the Ran gradient senses nuclear heterochromatin, and through its function as a transport regulator, helps maintain the protein composition and structure of the nucleolus.
Synapsin-caveolin-1 mitigates cognitive deficits and neurodegeneration in Alzheimer’s disease mice
Authors: Wang Shanshan , Leem Joseph S. , Podvin Sonia , Hook Vivian , Kleschevnikov Natalia , Savchenko Paul , Dhanani Mehul , Zhou Kimberly , Kelly Isabella C. , Zhang Tong , Miyanohara Atsushi , Kleschevnikov Alexander , Wagner Steve L. , Trojanowski John Q. , Roth David M. , Patel Hemal H. , Patel Piyush M. , Head Brian P.
Published: July 2020

AD presents with severe neurodegeneration which leads to cognitive deficits and dementia. Identifying the molecular signals that attenuate neurodegeneration in AD may be exploited as therapeutic targets. This study revealed that transgenic AD mice (PSAPP) exhibit decreased caveolin-1 (Cav-1), a membrane/lipid raft (MLR) scaffolding protein that organizes synaptic signaling components. Subcellularly, Cav-1 and full length (fl)-TrkB were significantly decreased in MLRs. We thus developed an in vivo gene therapy that re-expresses neuronal-targeted Cav-1 using the synapsin promoter (SynCav1). While AD mice showed significant learning and memory deficits at 9 and 11 months, AD mice that received hippocampalSynCav1(AD-SynCav1) maintained normal learning and memory at 9 and 11 months respectively. Furthermore, AD-SynCav1mice showed preserved hippocampal MLR-localized fl-TrkB, synaptic ultrastructure, dendritic arborization and axonal myelin content, all of which occurred independent of reducing amyloid deposit and astrogliosis. Thus,SynCav1demonstrates translational potential to treat AD by delaying neurodegeneration.

Transgenic PSAPP mice exhibit decreased hippocampal expression of the membrane lipid raft (MLR) scaffolding protein caveolin-1. Synapsin-promoted re-expression of Cav-1 (termedSynCav1) mitigated neuropathology and cognitive deficits.SynCav1gene therapy has the potential to treat AD and other forms of neurodegeneration.
Regulation of trehalase activity by multi-site phosphorylation and 14-3-3 interaction
Authors: Dengler Lisa , Örd Mihkel , Schwab Lucca M. , Loog Mart , Ewald Jennifer C.
Published: July 2020

Protein phosphorylation enables a rapid adjustment of cellular activities to diverse intracellular and environmental stimuli. Many phosphoproteins are targeted on more than one site, which allows the integration of multiple signals and the implementation of complex responses. However, the hierarchy and interplay between multiple phospho-sites are often unknown. Here, we study multi-site phosphorylation using the yeast trehalase Nth1 and its activator, the 14-3-3 protein Bmh1, as a model. Nth1 is known to be phosphorylated by the metabolic kinase PKA on four serine residues and by the cell cycle kinase CDK on one residue. However, how these five phospho-sites adjust Nth1 activity remains unclear. Using a novel reporter construct, we investigated the contribution of the individual sites for the regulation of the trehalase and its 14-3-3 interactor. In contrast to the constitutively phosphorylated S20 and S83, the weaker sites S21 and S60 are only phosphorylated by increased PKA activity. For binding Bmh1, S83 functions as the high-affinity “gatekeeper” site, but successful binding of the Bmh1 dimer and thus Nth1 activation requires S60 as a secondary site. Under nutrient-poor conditions with low PKA activity, S60 is not efficiently phosphorylated and the cell cycle dependent phosphorylation of S66 by Cdk1 contributes to Nth1 activity, likely by providing an alternative Bmh1 binding site. Additionally, the PKA sites S20 and S21 modulate the dephosphorylation of Nth1 on downstream Bmh1 sites. In summary, our results expand our molecular understanding of Nth1 regulation and provide a new aspect of the interaction of 14-3-3 proteins with their targets.
Separation and quantification of 2-Keto-3-deoxy-gluconate (KDG) a major metabolite in pectin and alginate degradation pathways
Authors: Martis B Shiny , Droux Michel , Deboudard Florelle , Nasser William , Meyer Sam , Reverchon Sylvie
Published: July 2020

A rapid and sensitive High Performance Liquid Chromatography (HPLC) method with photometric and fluorescence detection is developed for routine analysis of 2-Keto-3-deoxy-gluconate (KDG), a catabolite product of pectin and alginate. These polysaccharides are primary-based compounds for biofuel production and for generation of high-value-added products. HPLC is performed, after derivatization of the 2-oxo-acid groups of the metabolite with o-phenylenediamine (oPD), using a linear gradient of trifluoroacetic acid and acetonitrile. Quantification is accomplished with an internal standard method. The gradient is optimized to distinguish KDG from its close structural analogues such as 5-keto-4-deoxyuronate (DKI) and 2,5-diketo-3-deoxygluconate (DKII). The proposed method is simple, highly sensitive and accurate for time course analysis of pectin or alginate degradation.

Highlights

A fluorescent based-HPLC method report the quantification of KDG, a metabolite originating from alginate and from pectin degradation pathways, using derivatization with o-phenylenediamine (oPD)