bluuebunny/crossref_metadata_2025 huggingface dataset:
Concerns, quality of life, access to care and productivity of the general population during the first 8 weeks of the coronavirus lockdown in Belgium and the Netherlands
Authors: van Ballegooijen Hanne , Goossens Lucas , Bruin Ralph H. , Michels Renée , Krol Marieke
Published: July 2020

Background

The COVID-19 pandemic has a disruptive impact on our society. We therefore conducted a population survey to describe: 1) stress, concerns and quality of life 2) access to healthcare and cancelled/delayed healthcare and 3) productivity during the first 8 weeks of the coronavirus lockdown in the general population.

Methods

An online survey was conducted in a representative sample after 8 weeks of the coronavirus lockdown in Belgium and the Netherlands. The survey included questions about stress, concerns, quality of life delayed/cancelled medical care and productivity loss using validated questionnaires.

Results

In total, 2099 Belgian and 2058 Dutch respondents completed the survey with a mean age of 46.4 and 42.0 years, respectively. Half of the respondents were female in both countries. A small proportion tested positive for COVID-19, 1.4% vs 4.7%, respectively. The majority of respondents with a medical condition was worried about their current health state due to the pandemic (53%) vs (63%), respectively. Respondents experienced postponed/cancelled care (26%) and were concerned about the availability of medication (32%) for both countries. Productivity losses due to the COVID-19 restrictions were calculated in absenteeism (36%) and presenteeism (30%) for Belgium, and (19%) and (35%) for the Netherlands. Most concerns and productivity losses were reported by respondents with children <12 years, respondents aged 18-35 and respondents with an (expected) COVID-19 infection.

Conclusions

This study describes stress, quality of life, medical resource loss and productivity losses in Belgium and the Netherlands after 8 weeks of coronavirus lockdown. The results underline the burden on society.
The impact of COVID-19 on patients with asthma
Authors: Izquierdo José Luis , Almonacid Carlos , González Yolanda , Del Rio-Bermúdez Carlos , Ancochea Julio , Cárdenas Remedios , Soriano Joan B
Published: July 2020

Background

From the onset of the COVID-19 pandemic, an association between the severity of COVID-19 and the presence of certain medical chronic conditions has been suggested. However, unlike influenza and other viruses, the burden of the disease in patients with asthma has been less evident.

Objective

This study aims at a better understanding of the burden of COVID-19 in patients with asthma and the impact of asthma, its related comorbidities, and treatment on the prognosis of COVID-19.

Methods

We analyzed clinical data from patients with asthma from January 1st to May 10th, 2020 using big data analytics and artificial intelligence through the SAVANA Manager® clinical platform.

Results

Out of 71,192 patients with asthma, 1,006 (1.41%) suffered from COVID-19. Compared to asthmatic individuals without COVID-19, patients with asthma and COVID-19 were significantly older (55 vs. 42 years), predominantly female (66% vs. 59%), had higher prevalence of hypertension, dyslipidemias, diabetes, and obesity, and smoked more frequently. Contrarily, allergy-related factors such as rhinitis and eczema were less frequent in asthmatic patients with COVID-19 (P < .001). Higher prevalence of hypertension, dyslipidemia, diabetes, and obesity was also confirmed in those patients with asthma and COVID-19 who required hospital admission. The percentage of individuals using inhaled corticosteroids (ICS) was lower in patients who required hospitalization due to COVID-19, as compared to non-hospitalized patients (48.3% vs. 61.5%; OR: 0.58: 95% CI 0.44 - 0.77). During the study period, 865 (1.21%) patients with asthma were being treated with biologics. Although these patients showed increased severity and more comorbidities at the ear, nose, and throat (ENT) level, their hospital admission rates due to COVID-19 were relatively low (0.23%). COVID-19 increased inpatient mortality in asthmatic patients (2.29% vs 0.54%; OR 2.29: 95% CI 4.35 – 6.66).

Conclusion

Our results indicate that the number of COVID-19 cases in patients with asthma has been low, although higher than the observed in the general population. Patients with asthma and COVID-19 were older and were at increased risk due to comorbidity-related factors. ICS and biologics are generally safe and may be associated with a protective effect against severe COVID-19 infection.
Finding drug targeting mechanisms with genetic evidence for Parkinson’s disease
Authors: Storm Catherine S. , Kia Demis A. , Almramhi Mona , Bandres-Ciga Sara , Finan Chris , Hingorani Aroon D. ,   International Parkinson’s Disease Genomics Consortium (IPDGC), Wood Nicholas W.
Published: July 2020

Parkinson’s disease (PD) is a neurodegenerative movement disorder that currently has no disease-modifying treatment, partly owing to inefficiencies in drug target identification and validation using human evidence. Here, we use Mendelian randomization to investigate more than 3000 genes that encode druggable proteins, seeking to predict their efficacy as drug targets for PD. We use expression and protein quantitative trait loci for druggable genes to mimic exposure to medications, and we examine the causal effect on PD risk (in two large case-control cohorts), PD age at onset and progression. We propose 23 potential drug targeting mechanisms for PD, of which four are repurposing opportunities of already-licensed or clinical-phase drugs. We identify two drugs which may increase PD risk. Importantly, there is remarkably little overlap between our MR-supported drug targeting mechanisms to prevent PD and those that reduce PD progression, suggesting that molecular mechanisms driving disease risk and progression differ. Drugs with genetic support are considerably more likely to be successful in clinical trials, and we provide compelling genetic evidence and an analysis pipeline that can be used to prioritise drug development efforts for PD.
Activation of pancreatic β-cell genes by multiplex epigenetic CRISPR-editing
Authors: Alejandra Gimenez Carla , Lucia Curti , Ho Hyon Sung , Luis Grosembacher , Juan Ross Pablo , Federico Pereyra-Bonnet
Published: July 2020

CRISPR-based systems for epigenetic editing are promising molecular tools that could be harnessed for directed differentiation of pluripotent stem cells. We used the CRISPR/dCas9-VP160, CRISPR/dCas9-TET1 and CRISPR/dCas9-P300 systems for multiplex epigenetic editing and activation of human beta pancreatic genes (PDX1, NEUROG3, PAX4andINS). The CRISPR/dCas9-P300 system was the most effective at activating genes with reduced number of sgRNA. Using small number of sgRNA per gene was important to induce multiplex gene activation. Combined activation of transcription factors (TFs) involved in beta cell development resulted inINSgene expression; in which sequential TFs activation was more effective than simultaneous activation. Full CRISPR RNA-based delivery system was able to activate all targeted genes. Overall, this study shows the utility of CRISPR tools for epigenetic editing and directed cellular differentiation.
Top-down engineering of complex communities by directed evolution
Authors: Chang Chang-Yu , Vila Jean C.C. , Bender Madeline , Li Richard , Mankowski Madeleine C. , Bassette Molly , Borden Julia , Golfier Stefan , Sanchez Paul G. , Waymack Rachel , Zhu Xinwen , Diaz-Colunga Juan , Estrela Sylvie , Rebolleda-Gomez Maria , Sanchez Alvaro
Published: July 2020

Directed evolution has been used for decades to engineer biological systems from the top-down. Generally, it has been applied at or below the organismal level, by iteratively sampling the mutational landscape in a guided search for genetic variants of higher function. Above the organismal level, a small number of studies have attempted to artificially select microbial communities and ecosystems, with uneven and generally modest success. Our theoretical understanding of artificial ecosystem selection is still limited, particularly for large assemblages of asexual organisms, and we know little about designing efficient methods to direct their evolution. To address this issue, we have developed a flexible modeling framework that allows us to systematically probe any arbitrary selection strategy on any arbitrary set of communities and selected functions, in a wide range of ecological conditions. By artificially selecting hundreds ofin-silicomicrobial metacommunities under identical conditions, we examine the fundamental limits of the two main breeding methods used so far, and prescribe modifications that significantly increase their power. We identify a range of directed evolution strategies that, particularly when applied in combination, are better suited for the top-down engineering of large, diverse, and stable microbial consortia. Our results emphasize that directed evolution allows an ecological structure-function landscape to be navigated in search for dynamically stable and ecologically and functionally resilient high-functioning communities.
TheParacaedibacter-like endosymbiont ofBodo saltans(Kinetoplastida) uses multiple putative toxin-antitoxin systems to maintain its host association
Authors: Midha Samriti , Rigden Daniel J. , Siozios Stefanos , Hurst Gregory D. D. , Jackson Andrew P.
Published: July 2020

Bacterial endosymbiosis has been instrumental in eukaryotic evolution, and includes both mutualistic, dependent and parasitic associations. Here we characterize an intracellular bacterium inhabiting the flagellated protistBodo saltans(Kinetoplastida). We present a complete bacterial genome comprising a 1.39 Mb circular chromosome with 40.6% GC content. Fluorescent in situ hybridisation confirms that the endosymbiont is located adjacent to the nuclear membrane, and a detailed model of its intracellular niche is generated using serial block-face scanning electron microscopy. Phylogenomic analysis shows that the endosymbiont belongs to the Holosporales, most closely related to other α-proteobacterial endosymbionts of ciliates and amoebae. Comparative genomics indicates that it has a limited metabolism and is nutritionally host-dependent. However, the endosymbiont genome does encode diverse symbiont-specific secretory proteins, including a type VI secretion system and three separate toxin-antitoxin systems. We show that these systems are actively transcribed and hypothesize they represent a mechanism by whichB. saltansbecomes addicted to its endosymbiont. Consistent with this idea, attempts to cureBodoof endosymbionts led to rapid and uniform cell death. This study adds kinetoplastid flagellates to ciliates and amoebae as hosts ofParacaedibacter-likebacteria, suggesting that these antagonistic endosymbioses became established very early in Eukaryotic evolution.
Identification, Mapping and Relative Quantitation of SARS-CoV-2 Spike Glycopeptides by Mass-Retention Time Fingerprinting
Authors: Chalk R. , Greenland W. , Moreira T. , Coker J. , Mukhopadhyay S.M.M , Williams E. , Manning C. , Bohstedt T. , McCrorie R. , Fernandez-Cid A. , Burgess-Brown N.A.
Published: July 2020

We describe a novel analytical method for rapid and robust identification, mapping and relative quantitation of glycopeptides from SARS-CoV-2 Spike protein. The method may be executed using any LC-TOF mass spectrometer, requires no specialised knowledge of glycan analysis and makes use of the differential resolving power of reversed phase HPLC. While this separation technique resolves peptides with high efficiency, glycans are resolved poorly, if at all. Consequently, glycopeptides consisting of the same peptide bearing different glycan structures will all possess very similar retention times and co-elute. While this has previously been viewed as a disadvantage, we show that shared retention time can be used to map multiple glycan species to the same peptide and location. In combination with MSMS and pseudo MS3, we have constructed a detailed mass-retention time database for Spike. This database allows any ESI-TOF equipped lab to reliably identify and quantify spike glycans from a single overnight elastase protein digest in less than 90 minutes.
Development of predictive QSAR models on the phosphopeptide binding affinity against 14-3-3 isoforms
Authors: Fan Ying , Wang Xiaojun , Wang Chao
Published: July 2020

Abstract

14-3-3s present in multiple isoforms in human cells and mediate signal transduction by binding to phosphoserine-containing proteins. Recent findings have demonstrated that 14-3-3s act as a key factor in promoting chemoresistance of cancer. Here, we aimed to develop the predictive models that can determine the binding affinity of phosphopeptide fragments against 14-3-3s. It is found that the hydrophobic property of residues in phosphopeptides has a significant contribution to the binding affinity for most of 14-3-3 isoforms. The conserved patterns of 14-3-3 biding motifs were verified by our predictions. A group of peptide sequences were predicted with high binding affinity and high sequence conservation, which had agreement with 14-3-3s ligands. Overall, our results demonstrate that how the residues are likely to function in 14-3-3s interaction and the computational methods we introduced may contribute to the further research.
DLX5/6GABAergic expression affects social vocalization: implications for human evolution
Authors: Levi Giovanni , de Lombares Camille , Giuliani Cristina , Iannuzzi Vincenzo , Aouci Rym , Garagnani Paolo , Franceschi Claudio , Grimaud-Hervé Dominique , Narboux-Nême Nicolas
Published: July 2020

DLX5 and DLX6 are two closely related transcription factors involved in brain development and in GABAergic differentiation. TheDLX5/6locus is regulated by FoxP2, a gene involved in language evolution and has been associated to neurodevelopmental disorders and mental retardation. Targeted inactivation ofDlx5/6in mouse GABAergic neurons (Dlx5/6VgatCremice) results in behavioural and metabolic phenotypes notably increasing lifespan by 33%.

Here, we show thatDlx5/6VgatCremice present a hyper-vocalization and hyper-socialization phenotype. While only 7% of control mice emitted more than 700 vocalizations/10min, 30% and 56% of heterozygous or homozygousDlx5/6VgatCremice emitted more than 700 and up to 1400 calls/10min with a higher proportion of complex and modulated calls. Hyper-vocalizing animals were more sociable: the time spent in dynamic interactions with an unknown visitor was more than doubled compared to low-vocalizing individuals.

The characters affected by Dlx5/6 in the mouse (sociability, vocalization, skull and brain shape…) overlap those affected in the “domestication syndrome”. We therefore explored the possibility that DLX5/6 played a role in human evolution and “self-domestication” comparingDLX5/6genomic regions from Neanderthal and modern humans. We identify an introgressed Neanderthal haplotype (DLX5/6-N-Haplotype) present in 12.6% of European individuals that coversDLX5/6coding and regulatory sequences. TheDLX5/6-N-Haplotype includes the binding site for GTF2I, a gene associated to Williams-Beuren syndrome, a hyper-sociability and hyper-vocalization neurodevelopmental disorder. TheDLX5/6-N-Haplotype is significantly underrepresented in semi-supercentenarians (>105y of age), a well-established human model of healthy ageing and longevity, suggesting their involvement in the co-evolution of longevity, sociability and speech.
In SilicoDriven Prediction of MAPK14 Off-Targets Reveals Unrelated Proteins with High Accuracy
Authors: Kaiser Florian , Plach Maximilian G. , Leberecht Christoph , Schubert Thomas , Haupt V. Joachim
Published: July 2020

During the discovery and development of new drugs, candidates with undesired and potentially harmful side-effects can arise at all stages, which poses significant scientific and economic risks. Most of such phenotypic side-effects can be attributed to binding of the drug candidate to unintended proteins, so-called off-targets. The early identification of potential off-targets is therefore of utmost importance to mitigate any downstream risks. We showcase how the combination of knowledge-basedin silicooff-target screening and state-of-the-art biophysics can be applied to rapidly identify off-targets for a MAPK14 inhibitor. Out of 13 predicted off-targets, six proteins were confirmed to interact with the inhibitorin vitro, which translates to an exceptional hit rate of 46%. For two proteins, affinities in the lower micromolar range were obtained: The kinase IRE1 and the Hematopoietic Prostaglandin D Synthase, which is entirely unrelated to MAPK14 and is involved in different cell-regulatory processes. The whole off-target identification/validation pipeline can be completed as fast as within two months, excluding delivery times of proteins. These results emphasize how computational off-target screening in combination with MicroScale Thermophoresis can effectively reduce downstream development risks in a very competitive time frame and at low cost.
The Defensive Activation theory: dreaming as a mechanism to prevent takeover of the visual cortex
Authors: Eagleman David M. , Vaughn Don A.
Published: July 2020

Regions of the brain maintain their territory with continuous activity: if activity slows or stops (e.g., because of blindness), the territory tends to be taken over by its neighbors. A surprise in recent years has been the speed of takeover, which is measurable within an hour. These findings lead us to a new hypothesis on the origin of dream sleep. We hypothesize that the circuitry underlying dreaming serves to amplify the visual system’s activity periodically throughout the night, allowing it to defend its territory against takeover from other senses. We find that measures of plasticity across 25 species of primates correlate positively with the proportion of rapid eye movement (REM) sleep. We further find that plasticity and REM sleep increase in lockstep with evolutionary recency to humans. Finally, our hypothesis is consistent with the decrease in REM sleep and parallel decrease in neuroplasticity with aging.
PACIFIC: A lightweight deep-learning classifier of SARS-CoV-2 and co-infecting RNA viruses
Authors: Mateos Pablo Acera , Balboa Renzo F. , Easteal Simon , Eyras Eduardo , Patel Hardip R.
Published: July 2020

Viral co-infections occur in COVID-19 patients, potentially impacting disease progression and severity. However, there is currently no dedicated method to identify viral co-infections in patient RNA-seq data. We developed PACIFIC, a deep-learning algorithm that accurately detects SARS-CoV-2 and other common RNA respiratory viruses from RNA-seq data. Usingin silicodata, PACIFIC recovers the presence and relative concentrations of viruses with >99% precision and recall. PACIFIC accurately detects SARS-CoV-2 and other viral infections in 63 independentin vitrocell culture and patient datasets. PACIFIC is an end-to-end tool that enables the systematic monitoring of viral infections in the current global pandemic.
nPhase: An accurate and contiguous phasing method for polyploids
Authors: Abou Saada Omar , Tsouris Andreas , Friedrich Anne , Schacherer Joseph
Published: July 2020

While genome sequencing and assembly are now routine, we still do not have a full and precise picture of polyploid genomes. Phasing these genomes,i.e.deducing haplotypes from genomic data, remains a challenge. Despite numerous attempts, no existing polyploid phasing method provides accurate and contiguous haplotype predictions. To address this need, we developed nPhase, a ploidy agnostic pipeline and algorithm that leverage the accuracy of short reads and the length of long reads to solve reference alignment-based phasing for samples of unspecified ploidy (https://github.com/nPhasePipeline/nPhase). nPhase was validated on virtually constructed polyploid genomes of the model speciesSaccharomyces cerevisiae, generated by combining sequencing data of homozygous isolates. nPhase obtained on average >95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover >90% of each chromosome (heterozygosity rate ≥0.5%). This new phasing method opens the door to explore polyploid genomes through applications such as population genomics and hybrid studies.
Tissue-specific and interferon-inducible expression of non-functional ACE2 through endogenous retrovirus co-option
Authors: Ng Kevin , Attig Jan , Bolland William , Young George R. , Major Jack , Wack Andreas , Kassiotis George
Published: July 2020

Angiotensin-converting enzyme 2 (ACE2) is an entry receptor for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), as well as a regulator of several physiological processes.ACE2has recently been proposed to be interferon-inducible, suggesting that SARS-CoV-2 may exploit this phenomenon to enhance viral spread and questioning the efficacy of interferon treatment in Coronavirus disease 2019 (COVID-19). Using a recentde novotranscript assembly that captured previously unannotated transcripts, we describe a novel isoform ofACE2, generated by co-option of an intronic long terminal repeat (LTR) retroelement promoter. The novel transcript, termedLTR16A1-ACE2, exhibits specific expression patterns across the aerodigestive and gastrointestinal tracts and, importantly, is highly responsive to interferon stimulation. In stark contrast, expression of canonicalACE2is completely unresponsive to interferon stimulation. Moreover, theLTR16A1-ACE2translation product is a truncated, unstable ACE2 form, lacking domains required for SARS-CoV-2 binding and therefore unlikely to contribute to or enhance viral infection.
Maintenance of mitochondrial integrity in midbrain dopaminergic neurons governed by a conserved developmental transcription factor
Authors: Miozzo Federico , Stickley Luca , Valencia-Alarcón Eva P. , Dorcikova Michaela , Petrelli Francesco , Tas Damla , Loncle Nicolas , Nikonenko Irina , Dib Peter Bou , Nagoshi Emi
Published: July 2020

The degeneration of dopaminergic (DA) neurons in the substantia nigra is a hallmark of Parkinson’s disease (PD). Dysregulation of developmental transcription factors is implicated in dopaminergic neurodegeneration, but the underlying molecular mechanisms remain largely unknown.Drosophila Fer2is a prime example of a developmental transcription factor required for the birth and maintenance of midbrain DA neurons. Using an approach combining ChIP-seq, RNA-seq, and genetic epistasis experiments with PD-linked genes, here we demonstrate thatFer2controls a transcriptional network to maintain mitochondrial structure and function, and thus confers dopaminergic neuroprotection against genetic and oxidative insults. We further show that conditional ablation ofNato3,a mouse homolog ofFer2, in differentiated DA neurons results in locomotor impairments and mitochondrial abnormality in aged mice. Our results reveal the essential and conserved role ofFer2 homologs in the mitochondrial maintenance of midbrain DA neurons, opening new perspectives for modelling and treating PD.
How predictability affects habituation to novelty?
Authors: Ueda Kazutaka , Sekoguchi Takahiro , Yanagisawa Hideyoshi
Published: July 2020

One becomes accustomed to repeated exposures, even for a novel event. In the present study, we investigated how predictability affects habituation to novelty by applying a mathematical model of arousal that we previously developed, and conducted a psychophysiological experiment to test the model prediction. We formalized habituation to novelty as a decrement in Kullback-Leibler divergence from Bayesian prior to posterior (i.e., information gain) representing arousal evoked from a novel event through Bayesian update. The model predicted an interaction effect between initial uncertainty and initial prediction error (i.e., predictability) on habituation to novelty: The greater the initial uncertainty, the faster the information gain decreases (i.e., the sooner one is habituated). Experimental results using subjective reports of surprise and event-related potential (P300) evoked by visual-auditory incongruity supported the model prediction. Our findings suggest that in highly uncertain situations, repeated exposure to stimuli may enhance habituation to novel stimuli.
Can combined compost and biochar application improve the quality of a highly weathered coastal savanna soil?
Authors: Frimpong Kwame Agyei , Abban-Baidoo Emmanuel , Marschner Bernd
Published: July 2020

Soil fertility decline represents a major constraint to crop productivity in sub-Saharan Africa. Many studies have shown that addition of biochar or compost can effectively improve soil quality. Biochar produced from crop residues are often N-poor but rich in stable C while poultry manure composts, which is often rich in nutrients including N decomposes rapidly under high rainfall and temperature conditions. Combined biochar and compost application can compensate for the shortcomings of each other such that their interactive effect is likely to improve soil quality. A 30-days incubation experiment was carried out on a Haplic acrisol amended with corn cob biochar, rice husk biochar, coconut husk biochar, poultry manure compost and composted rice husk or corn cob biochar to examine the effect of compost and biochar, applied singly, in combination or as co-compost on basal soil respiration, and soil quality indicators such as soil pH; soil microbial carbon; cation exchange capacity; total organic carbon, total nitrogen and available nitrogen concentration. The results showed that addition of the different amendments increased soil pH compared with the untreated control with the combined corn cob and rice biochar and compost treatments recording the highest pH values. Basal respiration following sole compost, composted biochar and combined biochar and compost application were significantly greater than the sole biochar and the control treatments. TOC increased by 37% in the sole compost treatment to 117.3% in the combined corn cob biochar and compost treatment, respectively. MBC increased by 132.2% in the combined rice husk biochar and compost treatment and by 247% in the sole compost treatment compared to the control. The study has demonstrated the potential of compost, biochar and especially composted biochar to enhance soil quality, C stabilization and reduce soil C loss through basal respiration.
Activating NK- receptors, homing selectins and inhibitory Siglecs recognize EBOLA-GP and HPV-L1NK
Authors: Jarahian Mostafa , Marstaller Katharina , Wurmbäck Heribert , Banna Nadine , Ahani Roshanak , Etemadzadeh Hossein , Boller Lea Katharina , Azadmanesh Kayhan , Cid-Arregui Angel , Berger Martin R , Momburg Frank , Watzl Carsten
Published: July 2020

The Ebola virus glycoprotein (EBOV)-GP is extensively glycosylated. Its expression induces a physical alteration of surface adhesion molecules, which causes cell rounding and detachment of the infected cells. This phenomenon likely plays a crucial role in viral pathogenicity. In this study, we show that such morphological changes are cell line-dependent as well as dependent on the surface proteins that interact with EBOV-GP incisandtrans. We have generated data showing that natural killer (NK) cell receptors (NCRs: NKp44 and NKp46), selectins (CD62E/P/L) and inhibitory Siglecs function as receptors for Ebola-GP and human papilloma virus (HPV-L1). We used HEK293 cells transfected with Ebola-GP and recombinant fusion proteins containing the extracellular domain of each of these receptors linked to the Fc of human IgG1, which showed significant differences in their virus-binding behavior compared to HEK293 cells transfected with empty vector. Further, to demonstrate that EBOV-GP is a ligand for NKp44 and other NK-receptors, and to investigate their role in immune escape, we also used human HEK-293, HeLa- and hamster CHO-GP-transfectants. Our data show that the NK receptors NKp44 and NKp46 play a key role in recognizing EBOV (Ebolavirus) and strongly suggest that other inhibitory (Siglec-7, Siglec-5) and non-inhibitory homing receptors (P-Selectin, L-Selectin, E-Selectin, and DC-SIGNR/DC-SIGN) take part in the interaction with virus particles. In addition, we show that NKp44, and NKp46, Siglec-7, and -5, and P-, L-, E-selectins as well as of and DC-SIGNR/DC-SIGN bind to the artificial viral envelope of a lentiviral vector that contains EBOV-GP. Altogether we prove that NCRs and a range of other inhibitory and activating receptors can interact with viral envelope/capsid proteins and that such interaction could play an important role in the elimination of virus infected cells. Our findings could be used to develop new strategies for prevention and treatment of infections by these viruses.

Author summary

The innate immune system is able to recognize specifically certain virus components. Here we show that activating NK-cell receptors (NKp44, and NKp46) are involved in such interaction by using HEK293 and CHOK1 cells transfected with the Ebola virus glycoprotein (EBOV-GP) and by binding studies with purified EBOV-GP. In detail, we have found moderate to strong affinity of Siglecs (Siglec-7, and -5), selectins (P-, L-, E-Selectin) and DC-SIGNR/DC-SIGN to purified EBOV-GP, and to cells transfected with EBOV-GP as well as to the envelope of a lentiviral vector carrying the EBOV-GP. Our findings show that NKp44, and NKp46, Siglec-7, and -5, as well as P-and L-selectins have a strong affinity to EBOV-G.
The BMP antagonistGremlin1contributes to the development of cortical excitatory neurons, motor balance and fear responses
Authors: Ichinose Mari , Suzuki Nobumi , Wang Tongtong , Kobayashi Hiroki , Vrbanac Laura , Ng Jia Q , Wright Josephine A , Lannagan Tamsin R M , Gieniec Krystyna A , Lewis Martin , Ando Ryota , Enomoto Atsushi , Koblar Simon , Thomas Paul , Worthley Daniel L , Woods Susan L
Published: July 2020

Bone morphogenetic protein (BMP) signaling is required for early forebrain development and cortical formation. How the endogenous modulators of BMP signaling regulate the structural and functional maturation of the developing brain remains unclear. Here we show that expression of the BMP antagonist,Grem1, marks a neuroprogenitor that gives rise to layer V and VI glutamatergic neurons in the embryonic mouse brain. Lineage tracing ofGrem1-expressing cells in the embryonic brain was examined by administration of tamoxifen to pregnantGrem1creERT Rosa26LSLTdtomatomice at 13.5 days post coitum (dpc), followed by collection of embryos later in gestation. In addition, at 14.5 dpc, bulk mRNA seq analysis of differentially expressed transcripts between FACS sortedGrem1positive and negative cells was performed. We also generatedEmx1-cremediatedGrem1conditional knockout mice (Emx1-Cre;Grem1flox/flox) in which theGrem1gene was deleted specifically in the dorsal telencephalon.Grem1Emx1cKOanimals had reduced cortical thickness, especially layers V and VI and impaired motor balance and fear sensitivity compared to littermate controls. This study has revealed new roles for Grem1 in the structural and functional maturation of the developing cortex.

Summary statement

The BMP antagonist,Grem1, marks neuroprogenitors that give rise to deep layer glutamatergic neurons in the embryonic mouse brain.Grem1conditional knockout mice display cortical and behavioural abnormalities.
Left hemispheric deficit in the sustained neuromagnetic response to periodic click trains in children with ASD
Authors: Stroganova T.A. , Komarov K.S , Goiaeva D.E. , Obukhova T.S. , Ovsiannikova T.M. , Prokofyev A.O. , Orekhova E.V.
Published: July 2020

Deficits in perception and production of vocal pitch are often observed in people with autism spectrum disorders (ASD), but the neural basis of these abnormalities is unknown. In magnetoencephalogram (MEG), spectrally complex periodic sounds trigger two continuous neural responses – the Auditory Steady State Response (ASSR) and the Sustained Field (SF). It has been shown that the SF in neuro-typical individuals is associated with low-level analysis of pitch in the ‘pitch processing center’ of the Heschl’s gyrus. Therefore, this auditory response may reflect vocal pitch processing abnormalities in ASD. The SF, however, has never been studied in people with these disorders. We used MEG and individual brain models to investigate the ASSR and SF evoked by monaural 40 Hz click trains in 7-13-year-old boys with ASD (N=35) and neuro-typical (NT) boys (N=35). In agreement with the previous research in adults, the cortical sources of the SF in children were located in the left and the right Heschl’s gyri, anterolateral to those of the ASSR. In both groups, the SF and ASSR dominated in the right hemisphere and were higher contralaterally to the stimulated ear. The ASSR increased with age in both NT and ASD children and did not differ between the groups. The SF was moderately decreased in both hemispheres and was markedly delayed and displaced in the left hemisphere in boys with ASD. The SF delay in participants with ASD was present irrespective of their intelligence level and severity of autism symptoms. We suggest that the selective left-hemispheric SF abnormalities in children with ASD reflect a low-level deficiency in pitch processing that may contribute to their difficulties with perception and production of linguistic prosody.
The ecogenomics of dsDNA bacteriophages in feces of stabled and feral horses
Authors: Babenko V. V. , Millard A. , Kulikov E. E. , Spasskaya N.N. , Letarova M. A. , Konanov D. N. , Belalov I. Sh. , Letarov A.V.
Published: July 2020

The viromes of the mammalian lower gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing two groups of stabled horses, and a further group of feral horses that were isolated on an island. Our results indicate that the dsDNA viromes of the horse feces feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes, such as CrAssphage-related viruses found in humans, were identified. Additionally, many bacteriophage genus-level clusters were found to be present in all three geographically isolated populations. The diversity of the horse intestinal bacteriophages is severely undersampled, and so consequently only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways. Therefore, the diversity and structure of the intestinal virome in different animal species needs to be experimentally studied.

Short abstract (needed in some journals as eLife)

The viromes of the mammalian gut were shown to be heavily dominated by bacteriophages; however, only for humans were the composition and intervariability of the bacteriophage communities studied in depth. Here we present an ecogenomics survey of dsDNA bacteriophage diversity in the feces of horses (Equus caballus), comparing stabled horses, and feral horses that were isolated on an island. The viromes equine fecal viromes feature higher richness than in human viromes, with more even distribution of genotypes. No over-represented phage genotypes were identified. Additionally, many bacteriophage genus-level clusters were found to be present in geographically isolated populations. Only a minor fraction of the phage contigs could be linked with the bacteriophage genomes. Our study indicates that bacteriophage ecological parameters in the intestinal ecosystems in horses and humans differ significantly, leading them to shape their corresponding viromes in different ways.

Importance. (needed for mBio)

The study presents the first in depth analysis of the composition and variability of the gut dsDNA bacteriophage community in the mammalian species, other than humans. The study demonstrates that the bacteriophage ecology in the gut is substantially different in different animal species. The results also indicate that the genetic diversity of the equine intestinal bacteriophages is immense and almost totally unexplored by the moment.
A two-phase model of skin epidermal stratification: lessons from centrosomes
Authors: Damen Mareike , Wirtz Lisa , Soroka Ekaterina , Khatif Houda , Kukat Christian , Simons Benjamin D. , Bazzi Hisham
Published: July 2020

The development of complex stratified epithelial barriers in mammals is initiated from single-layered epithelia. How stratification is initiated and fueled are still open questions. Previous studies on skin epidermal stratification suggested a central role for perpendicular/asymmetric cell division orientation of the basal keratinocyte progenitors. Here, we use centrosomes, that organize the mitotic spindle, to test whether cell division orientation and stratification are linked. Genetically ablating centrosomes from the developing epidermis led to the activation of the p53-, 53BP1- and USP28-dependent mitotic surveillance pathway causing a thinner epidermis and hair follicle arrest. The centrosome/p53-double mutant keratinocyte progenitors significantly altered their division orientation in the later stages without majorly affecting epidermal differentiation. Together with time-lapse imaging and tissue growth dynamics measurements, the data suggested that the first and major phase of epidermal stratification is boosted by high proliferation rates of the basal and suprabasal transit-amplifying cells as well as cell delamination, whereas the second phase maybe uncoupled from the division orientation of the basal progenitors. The data provide insights for tissue homeostasis and hyperproliferative diseases that may recapitulate developmental programs.
Inhibition of the neuromuscular acetylcholine receptor with atracurium activates FOXO/DAF-16-induced longevity
Authors: McIntyre Rebecca L. , Denis Simone W. , Kamble Rashmi , Petr Michael , Schomakers Bauke V. , Jongejan Aldo , Scheibye-Knudsen Morten , Houtkooper Riekelt H. , Janssens Georges E.
Published: July 2020

Transcriptome-based drug screening is emerging as a powerful tool to identify geroprotective compounds to intervene in age-related disease. We hypothesized that, by mimicking the transcriptional signature of the highly conserved longevity intervention ofFOXO3(daf-16in worms) overexpression, we could identify and repurpose compounds with similar downstream effects to increase longevity. Ourin silicoscreen, utilizing the LINCS transcriptome database of genetic and compound interventions, identified several FDA-approved compounds that activate FOXO downstream targets in mammalian cells. These included the neuromuscular blocker atracurium, which also robustly extends both lifespan and healthspan inC. elegans. This longevity is dependent on bothdaf-16signaling and inhibition of the neuromuscular acetylcholine receptor. Other neuromuscular blockers tubocurarine and pancuronium caused similar healthspan benefits. We demonstrate nuclear localization of DAF-16 upon atracurium treatment, and, using RNAseq transcriptomics, identify activation of DAF-16 downstream effectors. Together, these data demonstrate the capacity to mimic genetic lifespan interventions with drugs, and in doing so, reveal that the neuromuscular acetylcholine receptor regulates the highly conserved FOXO/DAF-16 longevity pathway.
A quantitative analysis of the interplay of environment, neighborhood and cell state in 3D spheroids
Authors: Zanotelli Vito RT , Leutenegger Matthias , Lun Xiao-Kang , Georgi Fanny , de Souza Natalie , Bodenmiller Bernd
Published: July 2020

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Cells react to their microenvironment by integrating external stimuli into phenotypic decisions via an intracellular signaling network. Even cells with deregulated signaling can adapt to their environment. To analyze the interplay of environment, neighborhood, and cell state on phenotypic variability, we developed an experimental approach that enables multiplexed mass cytometric imaging to analyze up to 240 pooled spheroid microtissues. This system allowed us to quantify the contributions of environment, neighborhood, and intracellular state to phenotypic variability in spheroid cells. A linear model explained on average more than half of the variability of 34 markers across four cell lines and six growth conditions. We found that the contributions of cell-intrinsic and environmental factors are hierarchically interdependent. By overexpression of 51 signaling protein constructs in subsets of cells, we identified proteins that have cell-intrinsic and extrinsic effects, exemplifying how cell states depend on the cellular neighborhood in spheroid culture. Our study deconvolves factors influencing cellular phenotype in a 3D tissue and provides a scalable experimental system, analytical principles, and rich multiplexed imaging datasets for future studies.
Population Genomics Reveals Molecular Determinants of Specialization to Tomato in the Polyphagous Fungal PathogenBotrytis cinereain France
Authors: Mercier Alex , Simon Adeline , Lapalu Nicolas , Giraud Tatiana , Bardin Marc , Walker Anne-Sophie , Viaud Muriel , Gladieux Pierre
Published: July 2020

Many fungal plant pathogens encompass multiple populations specialized on different plant species. Understanding the factors underlying pathogen adaptation to their hosts is a major challenge of evolutionary microbiology, and it should help preventing the emergence of new specialized pathogens on novel hosts. Previous studies have shown that French populations of the grey mould pathogenBotrytis cinereaparasitizing tomato and grapevine are differentiated from each other, and have higher aggressiveness on their host-of-origin than on other hosts, indicating some degree of host specialization in this polyphagous pathogen. Here, we aimed at identifying the genomic features underlying the specialization ofB. cinereapopulations to tomato and grapevine. Based on whole genome sequences of 32 isolates, we confirmed the subdivision ofB. cinereapathogens into two genetic clusters on grapevine and another, single cluster on tomato. Levels of genetic variation in the different clusters were similar, suggesting that the tomato-specific cluster has not recently emerged following a bottleneck. Using genome scans for selective sweeps and divergent selection, tests of positive selection based on polymorphism and divergence at synonymous and non-synonymous sites and analyses of presence/absence variation, we identified several candidate genes that represent possible determinants of host specialization in the tomato-associated population. This work deepens our understanding of the genomic changes underlying the specialization of fungal pathogen populations.
Expression, subcellular localization, and phosphorylation of MK5 in adult cardiac ventricular fibroblasts
Authors: Sahadevan Pramod , Nawaito Sherin A. , Trépanier Joëlle , Benamar Sabrina , Sahmi Fatiha , Theberge-Julien Gabriel , Villeneuve Louis R. , Gaestel Matthias , Tardif Jean-Claude , Allen Bruce G.
Published: July 2020

MAP kinase-activated protein kinase-5 (MK5) plays an important role in cardiac fibroblast function. Although p38 MAPK and atypical MAPKs and ERK3 and ERK4 have been identified as activators of MK5, the kinases that activate MK5 remain controversial. Here we examined the expression, subcellular distribution, and regulation of MK5 in cardiac ventricular myofibroblasts and myocytes. The copy numbers for MK5 and ERK4 mRNA were comparable in myocytes and myofibroblasts, whereas that of ERK3 was much higher in myofibroblasts. Interestingly, MK5 and ERK3 immunoreactivity was detected in myofibroblasts but not myocytes whereas ERK4 immunoreactivity was detected in myocytes: treating in myocytes with a proteasome inhibitor or hypertrophic agonists failed to rescue MK5 immunoreactivity. In myofibroblasts, MK5 and ERK3 immunoreactivity was predominantly nuclear and cytosolic, respectively. In serum-starved cardiac myofibroblasts, phosphothreonine-182 MK5 (pT182-MK5) immunoreactivity was predominantly nuclear but increased in intensity and relocated to the cytoplasm in response to serum, sorbitol, angiotensin II, TGFβ, or H2O2and this was prevented by inhibition of p38α/β. Phos-tag SDS-PAGE revealed multiple slower migrating bands of MK5 immunoreactivity, indicating phosphorylation of MK5 at multiple sites. Phos-tag PAGE also revealed MK5 phosphorylation was increased with fibroblast activation and in hearts exposed to a chronic increase in afterload. MK5 and ERK3 co-immunoprecipitated and proximity ligation assays revealed ERK3 and MK5 in close proximity in myofibroblast cytoplasmic compartment. Furthermore, p38α/βinhibition decreased the abundance of MK5 immunoreactivity in ERK3 immunoprecipitates. Finally, deleting MK5 did not reduce the abundance of ERK3 immunoreactivity. These observations suggest that p38αand/or p38βare the primary mediators of T182-MK5 phosphorylation and hence MK5 activation in cardiac myofibroblasts.
The developmental and genetic architecture of the sexually selected male ornament of swordtails
Authors: Schartl Manfred , Kneitz Susanne , Ormanns Jenny , Schmidt Cornelia , Anderson Jennifer L , Amores Angel , Catchen Julian , Wilson Catherine , Geiger Dietmar , Du Kang , Garcia-Olazábal Mateo , Sudaram Sudha , Winkler Christoph , Hedrich Rainer , Warren Wesley C , Walter Ronald , Meyer Axel , Postlethwait John H
Published: July 2020

Sexual selection results in sex-specific characters like the conspicuously pigmented extension of the ventral tip of the caudal fin - the “sword” - in males of several species of Xiphophorus fishes. To uncover the genetic architecture underlying sword formation and to identify genes that are associated with its development, we characterized the sword transcriptional profile and combined it with genetic mapping approaches. Results showed that the male ornament of swordtails develops from a sexually non-dimorphic prepattern of transcription factors in the caudal fin. Among genes that constitute the exclusive sword transcriptome only two are located in the genomic region associated with this trait; the chaperone, fkbp9, and the potassium channel, kcnh8 that in addition to its neural function performs a role known to affect fin growth. This indicates that during evolution of swordtails a brain gene has been recruited for an additional function in establishing a male ornament.
What the Phage: A scalable workflow for the identification and analysis of phage sequences
Authors: Marquet Mike , Hölzer Martin , Pletz Mathias W. , Viehweger Adrian , Makarewicz Oliwia , Ehricht Ralf , Brandt Christian
Published: July 2020

Phages are among the most abundant and diverse biological entities on earth. Phage prediction from sequence data is a crucial first step to understanding their impact on the environment. A variety of bacteriophage prediction tools have been developed over the years. They differ in algorithmic approach, results, and ease of use. We, therefore, developed “What the Phage” (WtP), an easy-to-use and parallel multitool approach for phage prediction combined with an annotation and classification downstream strategy, thus, supporting the user’s decision-making process by summarizing the results of the different prediction tools in charts and tables. WtP is reproducible and scales to thousands of datasets through a workflow manager (Nextflow). WtP is freely available under a GPL-3.0 license (https://github.com/replikation/What_the_Phage).