bluuebunny/crossref_metadata_2025 huggingface dataset:
Key questions for modelling COVID-19 exit strategies
Authors: Thompson Robin N. , Hollingsworth T. Déirdre , Isham Valerie , Arribas-Bel Daniel , Ashby Ben , Britton Tom , Challenor Peter , Chappell Lauren H. K. , Clapham Hannah , Cunniffe Nik J. , Dawid A. Philip , Donnelly Christl A. , Eggo Rosalind M. , Funk Sebastian , Gilbert Nigel , Glendinning Paul , Gog Julia R. , Hart William S. , Heesterbeek Hans , House Thomas , Keeling Matt , Kiss István Z. , Kretzschmar Mirjam E. , Lloyd Alun L. , McBryde Emma S. , McCaw James M. , McKinley Trevelyan J. , Miller Joel C. , Morris Martina , O'Neill Philip D. , Parag Kris V. , Pearson Carl A. B. , Pellis Lorenzo , Pulliam Juliet R. C. , Ross Joshua V. , Tomba Gianpaolo Scalia , Silverman Bernard W. , Struchiner Claudio J. , Tildesley Michael J. , Trapman Pieter , Webb Cerian R. , Mollison Denis , Restif Olivier
Published: August 2020

Combinations of intense non-pharmaceutical interventions (lockdowns) were introduced worldwide to reduce SARS-CoV-2 transmission. Many governments have begun to implement exit strategies that relax restrictions while attempting to control the risk of a surge in cases. Mathematical modelling has played a central role in guiding interventions, but the challenge of designing optimal exit strategies in the face of ongoing transmission is unprecedented. Here, we report discussions from the Isaac Newton Institute ‘Models for an exit strategy’ workshop (11–15 May 2020). A diverse community of modellers who are providing evidence to governments worldwide were asked to identify the main questions that, if answered, would allow for more accurate predictions of the effects of different exit strategies. Based on these questions, we propose a roadmap to facilitate the development of reliable models to guide exit strategies. This roadmap requires a global collaborative effort from the scientific community and policymakers, and has three parts: (i) improve estimation of key epidemiological parameters; (ii) understand sources of heterogeneity in populations; and (iii) focus on requirements for data collection, particularly in low-to-middle-income countries. This will provide important information for planning exit strategies that balance socio-economic benefits with public health.
Two new species of Leptographium associated with Tomicus spp. infesting Pinus spp. in Southwestern China
Authors: Pan Yue , Lu Jun , Zhou Xu-Dong , Yu Ze-fen , Chen Peng , Wang Juan , Ye Hui
Published: August 2020

Leptographium panxianense and L. puerense are proposed as new taxa based on sequence data and morphological characters. The phylogenetic analyses based on ITS2-partial LSU rDNA region, β-tubulin and elongation factor 1-α genes showed that L. panxianense and L. puerense formed well-supported clades and were closely related to L. yunnanense, L. wushanense and L. conjunctum, and then nested within the L. lundbergii complex. The two species differ in their conidial size and shape. The conidia of L. panxianense are larger than those of L. puerense while the conidial shape of L. puerense is more ovovoid. The optimal growth temperature of both L. panxianense and L. puerense is at 20 °C, which is different from those of L. yunnanense, L. wushanense and L. conjunctum. Comparison of sequence data and morphological characters confirmed the placement of the two undescribed taxa in the genus of Leptographium.
Use of a small DNA virus model to investigate mechanisms of CpG dinucleotide-induced attenuation of virus replication
Authors: Loew Lisa , Goonawardane Niluka , Ratcliff Jeremy , Nguyen Dung , Simmonds Peter
Published: August 2020

Suppression of the CpG dinucleotide is widespread in RNA viruses infecting vertebrates and plants, and in the genomes of retroviruses and small mammalian DNA viruses. The functional basis for CpG suppression in the latter was investigated through the construction of mutants of the parvovirus, minute virus of mice (MVM) with increased CpG or TpA dinucleotides in the VP gene. CpG-high mutants displayed extraordinary attenuation in A9 cells compared to wild-type MVM (>six logs), while TpA elevation showed no replication effect. Attenuation was independent of Toll-like receptor 9 and STING-mediated DNA recognition pathways and unrelated to effects on translation efficiency. While translation from codon-optimized VP RNA was enhanced in a cell-free assay, MVM containing this sequence was highly attenuated. Further mutational analysis indicated that this arose through its increased numbers of CpG dinucleotides (7→70) and separately from its increased G+C content (42.3→57.4 %), which independently attenuated replication. CpG-high viruses showed impaired NS mRNA expression by qPCR and reduced NS and particularly VP protein expression detected by immunofluorescence and replication in A549 cells, effects reversed in zinc antiviral protein (ZAP) knockout cells, even though nuclear relocalization of VP remained defective. The demonstrated functional basis for CpG suppression in MVM and potentially other small DNA viruses and the observed intolerance of CpGs in coding sequences, even after codon optimization, has implications for the use of small DNA virus vectors in gene therapy and immunization.
Love during lockdown: findings from an online survey examining the impact of COVID-19 on the sexual practices of people living in Australia
Authors: Coombe Jacqueline , Kong Fabian , Bittleston Helen , Williams Hennie , Tomnay Jane , Vaisey Alaina , Malta Sue , Goller Jane , Temple-Smith Meredith , Bourchier Louise , Lau Andrew , Chow Eric P.F. , Hocking Jane S
Published: August 2020

Introduction

Australia recorded its first case of COVID-19 in late January 2020. On 22ndMarch 2020, amid increasing daily case numbers, the Australian Government implemented lockdown restrictions to help ‘flatten the curve’. Our study aimed to understand the impact of lockdown restrictions on sexual and reproductive health. Here we focus on sexual practices.

Methods

An online survey was open from the 23rdApril 2020 to the 11thMay 2020. Participants were recruited online via social media and other networks and were asked to report on their sexual practices in 2019 and during lockdown. Logistic regression was used to calculate the difference (including 95% confidence intervals) in the proportion of sex practices between time periods.

Results

Of the 1187 who commenced the survey, 965 (81.3%) completed it. Overall 70% were female and 66.3% were aged 18 to 29 years. Most (53.5%) reported less sex during lockdown than in 2019. Compared with 2019, participants were more likely to report sex with a spouse (35.3% vs 41.7%; difference=6.4%; 95%CI: 3.6, 9.2) and less likely to report sex with a girl/boyfriend (45.1% vs 41.8%; diff=-3.3%; 95%CI: -7.0, -0.4) or with casual hook-up (31.4% vs 7.8%; 95%CI:-26.9, -19.8). Solo sex activities increased, 14.6% (123/840) reported using sex toys more often and 26.0% (218/838) reported masturbating more often. Dating app use decreased during lockdown compared with 2019 (42.1% vs 27.3%; difference= -14.8%; 95%CI: -17.6, -11.9). Using dating apps for chatting/texting (89.8% vs 94.5%; diff=4.7%; 95%CI:1.0, 8.5) and for setting up virtual dates (2.6% vs 17.2%; diff=14.6%; 95%CI:10.1, 19.2) increased during lockdown.

Conclusion

Although significant declines in sexual activity during lockdown were reported, people did not completely stop engaging in sexual activities during the pandemic, highlighting the importance of ensuring availability of normal sexual and reproductive health services during global emergencies.

KEY MESSAGES

Sexual activity declined among our participants during the COVID-19 lockdown restrictions in Australia, with more than half reporting having less sex than in 2019

Sexual practices also changed during lockdown, with more people reporting solo sex activities like masturbating alone or using a sex toy.

Use of dating apps also declined among our participants. Of those still using apps, we saw increased use for chatting/texting and setting up virtual dates.
Meta-analysis of the gut microbiome of Parkinson’s disease patients suggests alterations linked to intestinal inflammation
Authors: Romano Stefano , Savva George M. , Bedarf Janis R. , Charles Ian G. , Hildebrand Falk , Narbad Arjan
Published: August 2020

The gut microbiota is emerging as an important modulator of neurodegenerative diseases, and accumulating evidence has linked gut microbes to Parkinson’s disease (PD) symptomatology and pathophysiology. PD is often preceded by gastrointestinal symptoms and alterations of the enteric nervous system accompany the disease. Several studies have analyzed the gut microbiome in PD, but a consensus on the features of the PD-specific microbiota is missing. Here, we conduct a meta-analysis re-analyzing 10 currently available 16S microbiome datasets to investigate whether underlying alterations in the gut microbiota of PD patients exist. We found consistent alterations in PD-associated microbiome, which are significant and robust to confounders across studies, although differences in microbiome structure between PD and controls are limited. Enrichment of the generaLactobacillus, Akkermansia, andBifidobacteriumand depletion of bacteria belonging to the families Lachnospiraceae and Ruminococcaceae, which are important short-chain fatty acids producers, emerged as the most consistent PD gut microbiome alterations. This dysbiosis might result in a pro-inflammatory status which could explain the recurrent gastrointestinal symptoms affecting PD patients.
Hospital length of stay for severe COVID-19 patients: implications for Remdesivir’s value
Authors: Anderson Michaela R , Bach Peter B. , Baldwin Matthew R.
Published: August 2020

Remdesivir has been granted emergency use authorization for treatment of severe COVID-19. Remdesivir's pricing is based on a presumed reduction of hospital length of stay (LOS) by four days. But the Adaptive COVID-19 Treatment Trial (ACTT-1) that suggested this treatment benefit excluded patients who were expected to be discharged within 72 hours. Perhaps as a result, median time to recovery was unusually long in both arms of the study (15 days vs 11 days). Remdesivir requires a 5-day inpatient stay, so patients who would otherwise be discharged in fewer than 5 days may remain hospitalized to complete treatment while patients who would be discharged between 5 and 8 days, would only have potential reductions in their hospital LOS of 0-3 days. In a retrospective analysis of 1643 adults with severe COVID-19 admitted to Columbia University Medical Center and the Allen community hospital between March 9, 2020 and April 23, 2020, median hospital LOS was 7 (3-14) days. Five-hundred and eighty-six patients (36%) had a LOS of 1-4 days, 384 (23%) had a LOS of 5-8 days, and 673 (41%) were hospitalized for greater than or equal to 9 days. Remdesivir treatment may not provide the LOS reductions that the company relied on when pricing the therapy: 36% of the cohort would need to have LOS prolonged to receive a 5-day course, and only 41% of patients in our cohort had LOS of 9 days or more, meaning they could have their LOS shortened by 4 days and still receive a full Remdesivir course. Further investigation of shorter treatment courses and programs to facilitate outpatient intravenous Remdesivir administration are needed.
Underdetection of COVID-19 cases in France in the exit phase following lockdown
Authors: Pullano Giulia , Domenico Laura Di , Sabbatini Chiara E , Valdano Eugenio , Turbelin Clément , Debin Marion , Guerrisi Caroline , Kengne-Kuetche Charly , Souty Cécile , Hanslik Thomas , Blanchon Thierry , Boëlle Pierre-Yves , Figoni Julie , Vaux Sophie , Campèse Christine , Bernard-Stoecklin Sibylle , Colizza Vittoria
Published: August 2020

A novel testing policy was implemented in May in France to systematically screen potential COVID-19 infections and suppress local outbreaks while lifting lockdown restrictions. 20,736 virologically-confirmed cases were reported in mainland France from May 13, 2020 (week 20, end of lockdown) to June 28 (week 26). Accounting for missing data and the delay from symptom onset to confirmation test, this corresponds to 7,258 [95% CI 7,160-7,336] cases with symptom onset during this period, a likely underestimation of the real number. Using age-stratified transmission models parameterized to behavioral data and calibrated to regional hospital admissions, we estimated that 69,115 [58,072-77,449] COVID-19 symptomatic cases occurred, suggesting that 9 out of 10 cases with symptoms were not ascertained. Median detection rate increased from 7% [6-9]% to 31% [28-35]% over time, with regional estimates varying from 11% (Grand Est) to 78% (Normandy) by the end of June. Healthcare-seeking behavior in COVID-19 suspect cases remained low (31%) throughout the period. Model projections for the incidence of symptomatic cases (4.5 [3.9-5.0] per 100,000) were compatible with estimates integrating participatory and virological surveillance data, assuming all suspect cases consulted. Encouraging healthcare-seeking behavior and awareness in suspect cases is critical to improve detection. Substantially more aggressive and efficient testing with easier access is required to act as a pandemic-fighting tool. These elements should be considered in light of the currently observed resurgence of cases in France and other European countries.
At-level allodynia after mid-thoracic contusion in the rat
Authors: Blumenthal G. H. , Nandakumar B. , Schnider A. K. , Detloff M. R. , Ricard J. , Bethea J. R. , Moxon K. A.
Published: August 2020

The rat mid-thoracic contusion model has been used to study at-level tactile allodynia after spinal cord injury (SCI), one of the more common types of allodynia. An important advantage of this model is that not all animals develop allodynia and, therefore, it could be used to more clearly examine mechanisms that are strictly related to pain development separately from mechanisms related to the injury itself. However, how to separate those that develop allodynia from those that do not is unclear. The aims of the current study were to identify where allodynia and spasticity develop and use this information to identify metrics that separate animals that develop allodynia from those that do not in order study difference in their behavior. To accomplish these aims, a standardized grid was used to localize pain on the dorsal trunk and map it to thoracic dermatomes, providing for the development of a pain score that relied on supraspinal responses and separated subgroups of animals. Similar to human studies, the development of allodynia often occurred with the development of spasticity or hyperreflexia. Moreover, the time course and prevalence of pain phenotypes (at-, above-, or below level) produced by this model were similar to that observed in humans who have sustained an SCI. However, the amount of spared spinal matter in the injured cord did not explain the development of allodynia, as was previously reported. This approach can be used to study the mechanism underlying the development of allodynia separately from mechanisms related to the injury alone.
The conserved Arabidopsis PM19L1 protein functions as an osmosensor and regulator of dormancy and germination
Authors: Alexander Ross D. , Castillejo-Pons Pablo , Melzer Nina , Alsaif Omar , Strotmann Vivien I. , Stahl Yvonne , Seale Madeleine , Morris Peter C.
Published: August 2020

How plants perceive water, especially during the critical stages of seed formation and germination, is key to their survival. During development and germination, seeds undergo large changes in water content, down to around 10% during maturation and up to 90% again within 24 hours of germination. We find the evolutionary conserved Arabidopsis plasma membrane protein PM19L1 to be an osmosensor, regulating dormancy and germination under osmotic stress. The PM19L1 protein structurally resembles the yeast osmosensor Sho1, with four transmembrane domains, andPM19L1complements the osmosensitivesho1mutant. Arabidopsispm19l1mutants have enhanced dormancy and reduced germination under salt and osmotic stress, and enhanced ABA levels. In a striking parallel to osmosensing in yeast, signalling downstream of PM19L1 involves a MAP kinase signal transduction pathway.PM19L1is a positive regulator ofABI3, which promotes the late maturation of the seed, and negatively regulates theABI4andABI5dormancy- regulating transcription factors. These results have implications for the study of dormancy, drought, and salinity tolerance in crops, and may provide an insight into evolutionary adaptation of plants to a terrestrial environment.
The selection of reference genome and the search for the origin of SARS-CoV-2
Authors: Liu Yuan , Yan Changhui
Published: August 2020

Abstracts

The pandemic caused by SARS-CoV-2 has a great impact on the whole world. In a theory of the origin of SARS-CoV-2, pangolins were considered a potential intermediate host. To assemble the coronavirus found in pangolins, SARS-CoV-2 were used a reference genome in most of studies, assuming that pangolins CoV and SARS-CoV-2 are the closest neighbors in the evolution. However, this assumption may not be true. We investigated how the selection of reference genome affect the resulting CoV genome assembly. We explored various representative CoV as reference genome, and found significant differences in the resulting assemblies. The assembly obtained using RaTG13 as reference showed better statistics in total length and N50 than the assembly guided by SARS-CoV-2, indicating that RaTG13 maybe a better reference for assembling CoV in pangolin or other potential intermediate hosts.
The Ebola virus interferon antagonist VP24 undergoes active nucleocytoplasmic trafficking
Authors: Harrison Angela R. , Moseley Gregory W.
Published: August 2020

Viral interferon (IFN) antagonist proteins mediate evasion of IFN-mediated innate immunity and are often multifunctional, having distinct roles in viral replication processes. Functions of the Ebola virus (EBOV) IFN antagonist VP24 include nucleocapsid assembly during cytoplasmic replication and inhibition of IFN-activated signalling by STAT1. For the latter, VP24 prevents STAT1 nuclear importviacompetitive binding to nuclear import receptors (karyopherins). Many viral proteins, including proteins from viruses with cytoplasmic replication cycles, interact with the trafficking machinery to undergo nucleocytoplasmic transport, with key roles in pathogenesis. Despite established karyopherin interaction, the nuclear trafficking profile of VP24 has not been investigated. We find that VP24 becomes strongly nuclear following overexpression of karyopherin or inhibition of nuclear export pathways. Molecular mapping indicates that cytoplasmic localisation of VP24 depends on a CRM1-dependent nuclear export sequence at the VP24 C-terminus. Nuclear export is not required for STAT1 antagonism, consistent with competitive karyopherin binding being the principal antagonistic mechanism while export mediates return of nuclear VP24 to the cytoplasm for replication functions. Thus, nuclear export of VP24 might provide novel targets for antiviral approaches.

Importance

Ebola virus (EBOV) is the causative agent of ongoing outbreaks of severe haemorrhagic fever with case-fatality rates between 40 and 60%. Proteins of many viruses with cytoplasmic replication cycles similar to EBOV interact with the nuclear trafficking machinery, resulting in active nucleocytoplasmic shuttling important to immune evasion and other intranuclear functions. However, exploitation of host trafficking machinery for nucleocytoplasmic transport by EBOV has not been directly examined. We find that the EBOV protein VP24 is actively trafficked between the nucleus and cytoplasm, and identify the specific pathways and sequences involved. The data indicate that nucleocytoplasmic trafficking is important for the multifunctional nature of VP24, which has critical roles in immune evasion and viral replication, identifying a new mechanism in infection by this highly lethal pathogen, and potential target for antivirals.
Using serum metabolomics analysis to predict sub-clinical atherosclerosis in patients with SLE
Authors: Coelewij Leda , Waddington Kirsty E , Robinson George A , Chocano Elvira , McDonnell Thomas , Farinha Filipa , Peng Junjie , Dönnes Pierre , Smith Edward , Croca Sara , Griffin Maura , Nicolaides Andrew , Rahman Anisur , Jury Elizabeth C , Pineda-Torra Ines
Published: August 2020

Background

Patients with systemic lupus erythematosus (SLE) have an increased risk of developing cardiovascular disease (CVD) and 30-40% have sub-clinical atherosclerosis on vascular ultrasound scanning. Standard measurements of serum lipids in clinical practice do not predict CVD risk in patients with SLE. We hypothesise that more detailed analysis of lipoprotein taxonomy could identify better predictors of CVD risk in SLE.

Methods

Eighty patients with SLE and no history of CVD underwent carotid and femoral ultrasound scans; 30 had atherosclerosis plaques (SLE-P) and 50 had no plaques (SLE-NP). Serum samples obtained at the time of the scan were analysed using a lipoprotein-focused metabolomics platform assessing 228 metabolites by nuclear magnetic resonance spectroscopy. Data was analysed using logistic regression and five binary classification models with 10-fold cross validation; decision tree, random forest, support vector machine and lasso (Least Absolute Shrinkage and Selection Operator) logistic regression with and without interactions.

Results

Univariate logistic regression identified four metabolites associated with the presence of sub-clinical plaque; three subclasses of very low density lipoprotein (VLDL) (percentage of free cholesterol in medium and large VLDL particles and percentage of phospholipids in chylomicrons and extremely large VLDL particles) and Leucine. Together with age, these metabolites were also within the top features identified by the lasso logistic regression (with and without interactions) and random forest machine learning models. Logistic regression with interactions differentiated between SLE-P and SLE-NP with greatest accuracy (0.800). Notably, percentage of free cholesterol in large VLDL particles and age were identified by all models as being important to differentiate between SLE-P and SLE-NP patients.

Conclusion

Serum metabolites are a promising biomarker for prediction of sub-clinical atherosclerosis development in SLE patients and could provide novel insight into mechanisms of early atherosclerosis development.
A Comprehensive Classification of Coronaviruses and Inferred Cross-Host Transmissions
Authors: Fu Yiran , Pistolozzi Marco , Yang Xiaofeng , Lin Zhanglin
Published: August 2020

In this work, we present a unified and robust classification scheme for coronaviruses based on concatenated protein clusters. This subsequently allowed us to infer the apparent “horizontal gene transfer” events via reconciliation with the corresponding gene trees, which we argue can serve as a marker for cross-host transmissions. The cases of SARS-CoV, MERS-CoV, and SARS-CoV-2 are discussed. Our study provides a possible technical route to understand how coronaviruses evolve and are transmitted to humans.
AT-527 is a potentin vitroreplication inhibitor of SARS-CoV-2, the virus responsible for the COVID-19 pandemic
Authors: Good Steven S. , Westover Jonna , Jung Kie Hoon , La Colla Paolo , Collu Gabriella , Moussa Adel , Canard Bruno , Sommadossi Jean-Pierre
Published: August 2020

AT-527, an orally administered double prodrug of a guanosine nucleotide analog, has been shown previously to be highly efficacious and well tolerated in HCV-infected subjects. Herein we report the potentin vitroactivity of AT-511, the free base form of AT-527, against several coronaviruses, including SARS-CoV-2, the causative agent of COVID-19. In normal human airway epithelial (HAE) cell preparations, the average concentration of AT-511 required to inhibit replication of SARS-CoV-2 by 90% (EC90) was 0.5 µM, very similar to the EC90for AT-511 against HCoV-229E, HCoV-OC43 and SARS-CoV in Huh-7 cells. No cytotoxicity was observed for AT-511 in any of the antiviral assays up to the highest concentration tested (100 µM). Surprisingly, AT-511 was 30-fold less active against MERS-CoV. This differential activity may provide a clue to the apparent unique mechanism of action of the guanosine triphosphate analog formed from AT-527.
Ana1 recruits PLK1 to mother centrioles to promote mitotic PCM assembly and centriole elongation
Authors: Alvarez-Rodrigo Ines , Wainman Alan , Raff Jordan W.
Published: August 2020

Polo kinase (PLK1) is a master cell cycle regulator that is recruited to various subcellular structures by its Polo-Box domain (PBD), which binds to phosphorylated S-pS/pT motifs. Polo has multiple functions at centrioles and centrosomes, and we previously showed that phosphorylated Sas-4 initiates Polo recruitment to newly formed centrioles, while phosphorylated Spd-2 recruits Polo to the mitotic Pericentriolar Material (PCM) that assembles around mother centrioles. Here, we investigate whether additional proteins recruit Polo to centrioles and/or centrosomes, and find that Ana1 (Cep295 in mammals) helps recruit Polo to mother centrioles. If this function is impaired, mother centrioles can still duplicate and disengage from their daughters, but they can no longer efficiently assemble a mitotic PCM or elongate their centrioles in G2. Thus, Ana1 is part of a sequential phosphorylation cascade that recruits Polo to centrioles to drive mitotic centrosome assembly and centriole elongation in G2, but not centriole duplication or disengagement.
Model-based prediction of bacterial population dynamics in gastrointestinal infection
Authors: Geißert Janina K. , Bohn Erwin , Mostolizadeh Reihaneh , Dräger Andreas , Autenrieth Ingo B. , Beier Sina , Deusch Oliver , Eichner Martin , Schütz Monika S.
Published: August 2020

The complex interplay of a pathogen with the host immune response and the endogenous microbiome determines the course and outcome of gastrointestinal infection (GI). Expansion of a pathogen within the gastrointestinal tract implies an increased risk to develop systemic infection. Through computational modeling, we aimed to calculate bacterial population dynamics in GI in order to predict infection course and outcome. For the implementation and parameterization of the model, oral mouse infection experiments withYersinia enterocoliticawere used. Our model takes into account pathogen specific characteristics, such as virulence, as well as host properties, such as microbial colonization resistance or immune responses. We were able to confirm the model calculations in these scenarios by experimental mouse infections and show that it is possible to computationally predict the infection course. Far future clinical application of computational modeling of infections may pave the way for personalized treatment and prevention strategies of GI.
Lactoferrin as potential supplementary nutraceutical agent in COVID-19 patients:in vitroandin vivopreliminary evidences
Authors: Campione Elena , Lanna Caterina , Cosio Terenzio , Rosa Luigi , Conte Maria Pia , Iacovelli Federico , Romeo Alice , Falconi Mattia , Del Vecchio Claudia , Franchin Elisa , Lia Maria Stella , Minieri Marilena , Chiaramonte Carlo , Ciotti Marco , Nuccetelli Marzia , Terrinoni Alessandro , Magrini Andrea , Bernardini Sergio , Andreoni Massimo , Sarmati Loredana , Miani Alessandro , Piscitelli Prisco , Valenti Piera , Bianchi Luca
Published: August 2020

Lactoferrin, a multifunctional cationic glycoprotein, secreted by exocrine glands and neutrophils, possesses an antiviral activity extendable to SARS-CoV-2.

We performedin vitroassays proving lactoferrin antiviral activity through direct attachment to both virus and cell surface components. This activity varied according to concentration (100/500μg/ml), multiplicity of infection (0.1/0.01) and cell type (Vero E6/Caco-2 cells).

Interestingly, thein silicoresults strongly supported the hypothesis of a direct recognition between the lactoferrin and the Spike S glycoprotein, thus hindering the viral entry into the cells.

Hence, we conducted a clinical trial to investigate effect and tolerability of a liposomal lactoferrin formulation as a supplementary nutraceutical agent in mild-to-moderate and asymptomatic COVID-19 patients.

A total of 92 mild-to-moderate (67/92) and asymptomatic (25/92) COVID-19 patients were recruited and divided in 3 groups according to the administered regimen. Thirty-two patients, 14 hospitalised and 18 in home-based insolation received oral and intranasal liposomal bovine lactoferrin (bLf), 32 hospitalised patients were treated with standard of care treatment (hydroxychloroquine, azitromicin and lopinavir/darunavir), and 28, in home-based isolation, did not take any medication. Furthermore, 32 COVID-19 negative, not-treated, healthy subjects were added as a control group for ancillary analysis.

bLf-supplemented COVID-19 patients obtained an earlier and significant (p < 0,0001.) median rRT-PCR SARS-COV-2 RNA negative conversion than standard of care-treated and non-treated COVID-19 patients (14.25 vs 27.13 vs 32.61 days, respectively).

In addition, bLf-supplemented COVID-19 patients showed significant fast clinical symptoms recovery than standard of care-treated and non-treated COVID-19 patients. Moreover, in bLf-supplemented patients, a significant decrease of either serum ferritin or IL-6 levels or host iron overload, all parameters characterizing inflammatory processes, were observed. Serum D-dimers was also found significantly decreased following bLf supplement. No adverse events were reported.

Thesein vitroandin vivoobservations led us to speculate a potential and safe supplementary role of Blf in the management of mild-to-moderate and asymptomatic COVID-19 patients.
Structural and molecular basis for Cardiovirus 2A protein as a viral gene expression switch
Authors: Hill Chris H. , Napthine Sawsan , Pekarek Lukas , Kibe Anuja , Firth Andrew E. , Graham Stephen C. , Caliskan Neva , Brierley Ian
Published: August 2020

Programmed −1 ribosomal frameshifting (PRF) in cardioviruses is activated by the 2A protein: a multi-functional virulence factor that also inhibits cap-dependent translational initiation. Here we present the X-ray crystal structure of 2A and show that it selectively binds to and stabilises the PRF stimulatory RNA element in the viral genome. Using optical tweezers, we define the conformational repertoire of this element and measure changes in unfolding pathways arising from mutation and 2A binding. Next, we demonstrate a strong interaction between 2A and the small ribosomal subunit and present a cryo-EM structure of 2A bound to initiated 70S ribosomes. Multiple copies of 2A bind to the 16S rRNA where they may compete for binding with initiation and elongation factors. Together, these results define the structural basis for RNA recognition by 2A, expand our understanding of the 2A-dependent gene expression switch and reveal how 2A accumulation may shut down translation during virus infection.
Ambroxol and Ciprofloxacin Show Activity Against SARS-CoV2 in Vero E6 Cells at Clinically-Relevant Concentrations
Authors: Bradfute Steven B , Ye Chunyan , Clarke Elizabeth C , Kumar Suresh , Timmins Graham S , Deretic Vojo
Published: August 2020

We studied the activity of a range of weakly basic and moderately lipophilic drugs against SARS CoV2 in Vero E6 cells, using Vero E6 survival, qPCR of viral genome and plaque forming assays. No clear relationship between their weakly basic and hydrophobic nature upon their activity was observed. However, the approved drugs ambroxol and ciprofloxacin showed potent activity at concentrations that are clinically relevant and within their known safety profiles, and so may provide potentially useful agents for preclinical and clinical studies in COVID-19.
A 3.4-Å cryo-EM structure of the human coronavirus spike trimer computationally derived from vitrified NL63 virus particles
Authors: Zhang Kaiming , Li Shanshan , Pintilie Grigore , Chmielewski David , Schmid Michael F. , Simmons Graham , Jin Jing , Chiu Wah
Published: August 2020

Human coronavirus NL63 (HCoV-NL63) is an enveloped pathogen of the family Coronaviridae that spreads worldwide and causes up to 10% of all annual respiratory diseases. HCoV-NL63 is typically associated with mild upper respiratory symptoms in children, elderly and immunocompromised individuals. It has also been shown to cause severe lower respiratory illness. NL63 shares ACE2 as a receptor for viral entry with SARS-CoV and SARS-CoV-2. Here we present the in situ structure of HCoV-NL63 spike (S) trimer at 3.4-Å resolution by single-particle cryo-EM imaging of vitrified virions without chemical fixative. It is structurally homologous to that obtained previously from the biochemically purified ectodomain of HCoV-NL63 S trimer, which displays a 3-fold symmetric trimer in a single conformation. In addition to previously proposed and observed glycosylation sites, our map shows density at other amino acid positions as well as differences in glycan structures. The domain arrangement within a protomer is strikingly different from that of the SARS-CoV-2 S and may explain their different requirements for activating binding to the receptor. This structure provides the basis for future studies of spike proteins with receptors, antibodies, or drugs, in the native state of the coronavirus particles.
Jasmonic Acid coordinates with Light, Glucose and Auxin signalling in Regulating Branching Angle ofArabidopsisLateral Roots
Authors: Sharma Manvi , Sharma Mohan , Muhammed Jamsheer K , Laxmi Ashverya
Published: August 2020

The role of jasmonates (JAs) in primary root growth and development and in plant response to external stimuli is already known. However, its role in lateral root (LR) development remains to be explored. Our work identified methyl jasmonate (MeJA) as a key phytohormone in determining the branching angle ofArabidopsisLRs. MeJA inclines the LRs to a more vertical orientation, which was dependent on the canonicalJAR1-COI1-MYC2, 3, 4signalling. Our work also highlights the dual roles of light in governing LR angle. Light signalling enhances JA biosynthesis, leading to erect root architecture; whereas, glucose (Glc) induces wider branching angles. Combining physiological and molecular assays, we revealed that Glc antagonizes the MeJA response via TARGET OF RAPAMYCIN (TOR) signalling. Moreover, physiological assays using auxin mutants, MYC2-mediated transcriptional activation ofLAZY2, LAZY4and auxin biosynthetic geneCYP79B2, and asymmetric distribution ofDR5::GFPandPIN2::GFPpinpointed the role of an intact auxin mechanism required by MeJA for vertical growth of LRs. We also demonstrated that light perception and signalling are indispensable for inducing vertical angles by MeJA. Thus, our investigation highlights antagonism between light and Glc signalling and how they interact with JA-auxin signals to optimize the branching angle of LRs.
Highly efficient genome modification of cultured primordial germ cells with lentiviral vectors to generate transgenic songbirds
Authors: Gessara Ivana , Dittrich Falk , Hertel Moritz , Hildebrand Staffan , Pfeifer Alexander , Frankl-Vilches Carolina , McGrew Mike , Gahr Manfred
Published: August 2020

SUMARY

The ability to genetically manipulate organisms has led to significant insights in functional genomics in many species. In birds, manipulation of the genome is hindered by the inaccessibility of the one-cell embryo. During embryonic development, avian primordial germ cells (PGCs) migrate through the blood stream and reach the gonadalanlage; where they develop into mature germ cells. Here, we explored the use of PGCs to produce transgenic offspring in the zebra finch, which is a major animal model for sexual brain differentiation, vocal learning and vocal communication. Zebra finch PGCs (zfPGCs) obtained from embryonic blood significantly proliferated when cultured in an optimized culture medium and conserved the expression of germ and stem cell markers. Transduction of cultured zfPGCs with lentiviral vectors was highly efficient leading to strong expression of the enhanced green fluorescent protein (eGFP). Transduced zfPGCs were injected into the host embryo and transgenic songbirds were successfully generated.
The effect of stimulus intensity on neural envelope tracking
Authors: Verschueren Eline , Vanthornhout Jonas , Francart Tom
Published: August 2020

Objectives

The last years there has been significant interest in attempting to recover the temporal envelope of a speech signal from the neural response to investigate neural speech processing. The research focus is now broadening from neural speech processing in normal-hearing listeners towards hearing-impaired listeners. When testing hearing-impaired listeners speech has to be amplified to resemble the effect of a hearing aid and compensate peripheral hearing loss. Until today, it is not known with certainty how or if neural speech tracking is influenced by sound amplification. As these higher intensities could influence the outcome, we investigated the influence of stimulus intensity on neural speech tracking.

Design

We recorded the electroencephalogram (EEG) of 20 normal-hearing participants while they listened to a narrated story. The story was presented at intensities from 10 to 80 dB A. To investigate the brain responses, we analyzed neural tracking of the speech envelope by reconstructing the envelope from EEG using a linear decoder and by correlating the reconstructed with the actual envelope. We investigated the delta (0.5-4 Hz) and the theta (4-8 Hz) band for each intensity. We also investigated the latencies and amplitudes of the responses in more detail using temporal response functions which are the estimated linear response functions between the stimulus envelope and the EEG.

Results

Neural envelope tracking is dependent on stimulus intensity in both the TRF and envelope reconstruction analysis. However, provided that the decoder is applied on data of the same stimulus intensity as it was trained on, envelope reconstruction is robust to stimulus intensity. In addition, neural envelope tracking in the delta (but not theta) band seems to relate to speech intelligibility. Similar to the linear decoder analysis, TRF amplitudes and latencies are dependent on stimulus intensity: The amplitude of peak 1 (30-50 ms) increases and the latency of peak 2 (140-160 ms) decreases with increasing stimulus intensity.

Conclusion

Although brain responses are influenced by stimulus intensity, neural envelope tracking is robust to stimulus intensity when using the same intensity to test and train the decoder. Therefore we can assume that intensity is not a confound when testing hearing-impaired participants with amplified speech using the linear decoder approach. In addition, neural envelope tracking in the delta band appears to be correlated with speech intelligibility, showing the potential of neural envelope tracking as an objective measure of speech intelligibility.
DIAPH3 deficiency links microtubules to mitotic errors, defective neurogenesis, and brain dysfunction
Authors: Lau Eva On-Chai , Damiani Devid , Jossin Yves , Chehade Georges , Schakman Olivier , Tajeddine Nicolas , Gailly Philippe , Tissir Fadel
Published: August 2020

Diaphanous (DIAPH) 3 is a member of the formin proteins that have the capacity to nucleate and elongate actin filaments and therefore, to remodel the cytoskeleton. DIAPH3 is essential for cytokinesis as its dysfunction impairs the contractile ring and produces multinucleated cells. Here, we report that DIAPH3 localizes at the centrosome during mitosis and regulates the assembly and polarity of the mitotic spindle. DIAPH3-deficient cells display disorganized cytoskeleton, multipolar spindles, and supernumerary centrosomes. DIAPH3-deficiency disrupts the expression and/or stability of microtubule-associated proteins SPAG5 and KNSTRN. SPAG5 and DIAPH3 have similar expression patterns in the developing brain and overlapping subcellular localization during mitosis. Knockdown of SPAG5 phenocopies the DIAPH3 deficiency, whereas its overexpression rescues the DIAH3 phenotype. Conditional inactivation ofDiaph3in the cerebral cortex profoundly disrupts neurogenesis depleting cortical progenitors and neurons; and leading to cortical malformation and autistic-like behavior. Our data uncover uncharacterized functions of DIAPH3 and provide evidence that this protein belongs to a molecular toolbox that links microtubule dynamics during mitosis to aneuploidy, cell death, fate determination defects, and cortical malformation.
The historical range and drivers of decline of the Tapanuli orangutan
Authors: Meijaard Erik , Ni’matullah Safwanah , Dennis Rona , Sherman Julie , Onrizal  , Wich Serge A.
Published: August 2020

The Tapanuli Orangutan (Pongo tapanuliensis) is the most threatened great ape species in the world. It is restricted to an area of about 1,000 km2of upland forest where fewer than 800 animals survive in three declining subpopulations. Through a historical ecology approach involving analysis of newspaper, journals, books and museum records from the early 1800s to 2009, we demonstrate that historicallyPongo tapanuliensisinhabited a much larger area, and across a much wider range of habitat types than now. Its current Extent of Occurrence is between 2.5% and 5.0% of the historical range in the 1890s and 1940s respectively. A combination of historical fragmentation of forest habitats, mostly for small-scale agriculture, and unsustainable hunting likely drove various populations to the south, east and west of the current population to extinction. This happened prior to the industrial-scale forest conversion that started in the 1970s. Our findings indicate how sensitiveP. tapanuliensisis to the combined effects of habitat fragmentation and unsustainable take-off rates. Saving this species will require prevention of any further fragmentation and killings or other removal of animals from the remaining population. Without concerted action to achieve this, the remaining populations ofP. tapanuliensisare doomed to become extinct within several orangutan generations.
Sonlicromanol improves neuronal network dysfunction and transcriptome changes linked to m.3243A>G heteroplasmy in iPSC-derived neurons
Authors: Gunnewiek T.M. Klein , Verboven A. H. A. , Hogeweg M. , Schoenmaker C. , Renkema H. , Beyrath J. , Smeitink J. , de Vries B. B. A. , ’t Hoen P.A.C. , Kozicz T. , Kasri N. Nadif
Published: August 2020

Mitochondrial encephalomyopathy, lactic acidosis and stroke-like episodes (MELAS) is often caused by an adenine to guanine mutation at m.3243 (m.3243A>G) of theMT-TL1gene (tRNAleu(UUR)). To understand how this mutation affects the nervous system, we differentiated human induced-pluripotent stem cells (iPSCs) into excitatory neurons with normal (low heteroplasmy) and impaired (high heteroplasmy) mitochondrial function from MELAS patients with the m.3243A>G mutation. We combined micro-electrode array (MEA) measurements with RNA sequencing (MEA-seq) and found that the m.3243A>G mutation affects expression of genes involved in mitochondrial respiration- and presynaptic function, as well as non-cell autonomous processes in co-cultured astrocytes. Finally, we show that the clinical II stage drug sonlicromanol (KH176) improved neuronal network activity in a patient-specific manner when treatment is initiated early in development. This was intricately linked with changes in the neural transcriptome. Overall, MEA-seq is a powerful approach to identify mechanisms underlying the m.3243A>G mutation and to study the effect of pharmacological interventions in iPSC-derived neurons.

Highlights

- High m.3243A>G heteroplasmy leads to lower neuronal network activity and synchronicity

- High heteroplasmy affects expression of genes involved in mitochondrial ATP production and the synaptic function / the presynaptic vesicle cycle

- High neuronal heteroplasmy non cell autonomously affects gene expression in healthy co-cultured astrocytes

- Sonlicromanol partially rescues neuronal network activity and transcriptome changes induced by high heteroplasmy

eTOC Blurb

Using human inducible pluripotent stem cell-derived neurons with high levels of m.3243A>G heteroplasmy, Klein Gunnewiek et al. show transcriptome changes underlying the functional neuronal network phenotype, and how sonlicromanol can partially improve both this neuronal network phenotype, and the transcriptome changes, in a patient-specific manner.
Dissociating harmonic and non-harmonic phase-amplitude coupling in the human brain
Authors: Giehl Janet , Noury Nima , Siegel Markus
Published: August 2020

Phase-amplitude coupling (PAC) has been hypothesized to coordinate cross-frequency interactions of neuronal activity in the brain. However, little is known about the distribution of PAC across the human brain and the frequencies involved. Furthermore, it remains unclear to what extend PAC may reflect spurious cross-frequency coupling induced by physiological artifacts or rhythmic non-sinusoidal signals with higher harmonics. Here, we combined MEG, source-reconstruction and different measures of cross-frequency coupling to systematically characterize PAC across the resting human brain. We show that cross-frequency measures of phase-amplitude, phase-phase, and amplitude-amplitude coupling are all sensitive to signals with higher harmonics. In conjunction, these measures allow to distinguish harmonic and non-harmonic PAC. Based on these insights, we found no evidence for non-harmonic PAC in resting-state MEG. Instead, we found cortically and spectrally wide-spread PAC driven by harmonic signals. Furthermore, we show how physiological artifacts and spectral leakage cause spurious PAC across wide frequency ranges. Our result clarify how different measures of cross-frequency interactions can be combined to characterize PAC and cast doubt on the presence of prominent non-harmonic phase-amplitude coupling in human resting-state MEG.