bluuebunny/crossref_metadata_2025 huggingface dataset:
An improved mathematical prediction of the time evolution of the Covid-19 Pandemic in Italy, with Monte Carlo simulations and error analyses
Authors: Ciufolini Ignazio , Paolozzi Antonio
Published: April 2020

We present an improved mathematical analysis of the time evolution of the Covid-19 pandemic in Italy and a statistical error analyses of its evolution, including Monte Carlo simulations with a very large number of runs to evaluate the uncertainties in its evolution. A previous analysis was based on the assumption that the number of nasopharyngeal swabs would be constant. However the number of daily swabs is now more than five times what it was when we did our previous analysis. Therefore, here we consider the time evolution of the ratio of the new daily cases to number of swabs, which is more representative of the evolution of the pandemic when the number of swabs is increasing or changing in time. We consider a number of possible distributions representing the evolution of the pandemic in Italy and we test their prediction capability over a period of up to four weeks. The results show that a distribution of the type of Planck black body radiation law provides very good forecasting. The use of different distributions provides an independent possible estimate of the uncertainty. We then consider five possible trajectories for the number of daily swabs and we estimate the potential dates of a substantial reduction in the number of new daily cases. We then estimate the spread in a substantial reduction, below a certain threshold, of the daily cases per swab among the Italian regions. We finally perform Monte Carlo simulations with 25000 runs to evaluate a random uncertainty in the prediction of the date of a substantial reduction in the number of diagnosed daily cases per swab.
Recombinant SARS-CoV-2 spike S1-Fc fusion protein induced high levels of neutralizing responses in nonhuman primates
Authors: Ren Wenlin , Sun Hunter , Gao George F. , Chen Jianxin , Sun Sean , Zhao Rongqing , Gao Guang , Hu Yalin , Zhao Gan , Chen Yuxin , Jin Xia , Fang Feng , Chen Jinggong , Wang Qi , Gong Sitao , Gao Wen , Sun Yufei , Su Junchi , He Ailiang , Cheng Xin , Li Min , Xia Chenxi , Li Maohua , Sun Le
Published: April 2020

The COVID-19 outbreak has become a global pandemic responsible for over 2,000,000 confirmed cases and over 126,000 deaths worldwide. In this study, we examined the immunogenicity of CHO-expressed recombinant SARS-CoV-2 S1-Fc fusion protein in mice, rabbits, and monkeys as a potential candidate for a COVID-19 vaccine. We demonstrate that the S1-Fc fusion protein is extremely immunogenic, as evidenced by strong antibody titers observed by day 7. Strong virus neutralizing activity was observed on day 14 in rabbits immunized with the S1-Fc fusion protein using a pseudovirus neutralization assay. Most importantly, in less than 20 days and three injections of the S1-Fc fusion protein, two monkeys developed higher virus neutralizing titers than a recovered COVID-19 patient in a live SARS-CoV-2 infection assay. Our data strongly suggests that the CHO-expressed SARS-CoV-2 S1-Fc recombinant protein could be a strong candidate for vaccine development against COVID-19.

Highlights

CHO-expressed S1-Fc protein is very immunogenic in various animals and can rapidly induce strong antibody production

S1-Fc protein solicits strong neutralizing activities against live virus

Stable CHO cell line expressing 50 mg/L of S1-Fc and a 3,000 L Bioreactor can produce 3 million doses of human COVID-19 vaccine every 10 days, making it an accessible and affordable option for worldwide vaccination
Identification of potential treatments for COVID-19 through artificial intelligence-enabled phenomic analysis of human cells infected with SARS-CoV-2
Authors: Heiser Katie , McLean Peter F. , Davis Chadwick T. , Fogelson Ben , Gordon Hannah B. , Jacobson Pamela , Hurst Brett , Miller Ben , Alfa Ronald W. , Earnshaw Berton A. , Victors Mason L. , Chong Yolanda T. , Haque Imran S. , Low Adeline S. , Gibson Christopher C.
Published: April 2020

To identify potential therapeutic stop-gaps for SARS-CoV-2, we evaluated a library of 1,670 approved and reference compounds in an unbiased, cellular image-based screen for their ability to suppress the broad impacts of the SARS-CoV-2 virus on phenomic profiles of human renal cortical epithelial cells using deep learning. In our assay, remdesivir is the only antiviral tested with strong efficacy, neither chloroquine nor hydroxychloroquine have any beneficial effect in this human cell model, and a small number of compounds not currently being pursued clinically for SARS-CoV-2 have efficacy. We observed weak but beneficial class effects of β-blockers, mTOR/PI3K inhibitors and Vitamin D analogues and a mild amplification of the viral phenotype with β-agonists.
Experimental and computational study on motor control and recovery after stroke: towards a constructive loop between experimental and virtual embodied neuroscience
Authors: Allegra Mascaro Anna Letizia , Falotico Egidio , Petkoski Spase , Pasquini Maria , Vannucci Lorenzo , Tort-Colet Núria , Conti Emilia , Resta Francesco , Spalletti Cristina , Ramalingasetty Shravan Tata , von Arnim Axel , Formento Emanuele , Angelidis Emmanouil , Blixhavn Camilla Hagen , Leergaard Trygve Brauns , Caleo Matteo , Destexhe Alain , Ijspeert Auke , Micera Silvestro , Laschi Cecilia , Jirsa Viktor , Gewaltig Marc-Oliver , Pavone Francesco S.
Published: April 2020

Being able to replicate real experiments with computational simulations is a unique opportunity to refine and validate models with experimental data and redesign the experiments based on simulations. However, since it is technically demanding to model all components of an experiment, traditional approaches to modeling reduce the experimental setups as much as possible. In this study, our goal is to replicate all the relevant features of an experiment on motor control and motor rehabilitation after stroke. To this aim, we propose an approach that allows continuous integration of new experimental data into a computational modeling framework. First, results show that we could reproduce experimental object displacement with high accuracy via the simulated embodiment in the virtual world by feeding a spinal cord model with experimental registration of the cortical activity. Second, by using computational models of multiple granularities, our preliminary results show the possibility of simulating several features of the brain after stroke, from the local alteration in neuronal activity to long-range connectivity remodeling. Finally, strategies are proposed to merge the two pipelines. We further suggest that additional models could be integrated into the framework thanks to the versatility of the proposed approach, thus allowing many researchers to achieve continuously improved experimental design.
UMI-Gen: a UMI-based reads simulator for variant calling evaluation in paired-end sequencing NGS libraries
Authors: Sater Vincent , Viailly Pierre-Julien , Lecroq Thierry , Ruminy Philippe , Bérard Caroline , Prieur-Gaston Élise , Jardin Fabrice
Published: April 2020

Motivation

With Next Generation Sequencing becoming more affordable every year, NGS technologies asserted themselves as the fastest and most reliable way to detect Single Nucleotide Variants (SNV) and Copy Number Variations (CNV) in cancer patients. These technologies can be used to sequence DNA at very high depths thus allowing to detect abnormalities in tumor cells with very low frequencies. A lot of different variant callers are publicly available and usually do a good job at calling out variants. However, when frequencies begin to drop under 1%, the specificity of these tools suffers greatly as true variants at very low frequencies can be easily confused with sequencing or PCR artifacts. The recent use of Unique Molecular Identifiers (UMI) in NGS experiments offered a way to accurately separate true variants from artifacts. UMI-based variant callers are slowly replacing raw-reads based variant callers as the standard method for an accurate detection of variants at very low frequencies. However, benchmarking done in the tools publication are usually realized on real biological data in which real variants are not known, making it difficult to assess their accuracy.

Results

We present UMI-Gen, a UMI-based reads simulator for targeted sequencing paired-end data. UMI-Gen generates reference reads covering the targeted regions at a user customizable depth. After that, using a number of control files, it estimates the background error rate at each position and then modifies the generated reads to mimic real biological data. Finally, it will insert real variants in the reads from a list provided by the user.

Availability

The entire pipeline is available athttps://gitlab.com/vincent-sater/umigen-masterunder MIT license.

Contact

vincent.sater@gmail.com
Functional and Genetic Analysis of Viral Receptor ACE2 Orthologs Reveals a Broad Potential Host Range of SARS-CoV-2
Authors: Liu Yinghui , Hu Gaowei , Wang Yuyan , Zhao Xiaomin , Ji Fansen , Ren Wenlin , Gong Mingli , Ju Xiaohui , Zhu Yuanfei , Cai Xia , Wu Jianping , Lan Xun , Xie Youhua , Wang Xinquan , Yuan Zhenghong , Zhang Rong , Ding Qiang
Published: April 2020

The pandemic of Coronavirus Disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a major global health threat. Epidemiological studies suggest that bats are the natural zoonotic reservoir for SARS-CoV-2. However, the host range of SARS-CoV-2 and intermediate hosts that facilitate its transmission to humans remain unknown. The interaction of coronavirus with its host receptor is a key genetic determinant of host range and cross-species transmission. SARS-CoV-2 uses angiotensin-converting enzyme 2 (ACE2) as the receptor to enter host cells in a species-dependent manner. It has been shown that human, palm civet, pig and bat ACE2 can support virus entry, while the murine ortholog cannot. In this study, we characterized the ability of ACE2 from diverse species to support viral entry. We found that ACE2 is expressed in a wide range of species, with especially high conservation in mammals. By analyzing amino acid residues of ACE2 critical for virus entry, based on structure of SARS-CoV spike protein interaction with human, bat, palm civet, pig and ferret ACE2, we identified approximately eighty ACE2 proteins from mammals that could potentially mediate SARS-CoV-2 entry. We chose 48 representative ACE2 orthologs among eighty orthologs for functional analysis and it showed that 44 of these mammalian ACE2 orthologs, including those of domestic animals, pets, livestock, and animals commonly found in zoos and aquaria, could bind SARS-CoV-2 spike protein and support viral entry. In contrast, New World monkey ACE2 orthologs could not bind SARS-CoV-2 spike protein and support viral entry. We further identified the genetic determinant of New World monkey ACE2 that restricts viral entry using genetic and functional analyses. In summary, our study demonstrates that ACE2 from a remarkably broad range of species can facilitate SARS-CoV-2 entry. These findings highlight a potentially broad host tropism of SARS-CoV-2 and suggest that SARS-CoV-2 might be distributed much more widely than previously recognized, underscoring the necessity to monitor susceptible hosts to prevent future outbreaks.
A Substantia Innominata-midbrain Circuit Controls a General Aggressive Response
Authors: Zhu Zhenggang , Ma Qingqing , Miao Lu , Yang Hongbin , Pan Lina , Li Kaiyuan , Zeng Ling-Hui , Zhang Xiaoxing , Wu Jintao , Hao Sijia , Lin Shen , Ma Xiulin , Mai Weihao , Feng Xiang , Hao Yizhe , Sun Li , Duan Shumin , Yu Yan-qin
Published: April 2020

While aggressive behaviors are universal and essential for survival, ‘uncontrollable’ and abnormal aggressive behaviors in animals or humans may have severe adverse consequences or social costs. Neural circuits regulating specific forms of aggression under defined conditions have been described, but how brain circuits govern a general aggressive response remains unknown. Here, we found that posterior substantia innominata (pSI) neurons responded to several aggression-provoking cues with the graded activity of differential dynamics, predicting the aggressive state and the topography of aggression in mice. Activation of pSI neurons projecting to the periaqueductal gray (PAG) increased aggressive arousal and robustly initiated/promoted all the types of aggressive behavior examined in an activity level-dependent manner. Inactivation of the pSI circuit largely blocked diverse aggressive behaviors but not mating. By encoding a general aggressive response, the pSI-PAG circuit universally drives multiple aggressive behaviors and may provide a potential target for alleviating human pathological aggression.

In Brief

Zhu et al. find that the posterior substantia innominata neurons universally drive aggressive behaviors by representing aggressive state and topography of aggression in mice.

Highlights

pSI neuronal dynamics reflect aggressive state and the topography of aggression

The pSI-PAG circuit promotes arousal and elicits thirteen aggressive behaviors

The pSI controls various aggressive behaviors in an activity level-dependent manner

Inactivation of the pSI circuit blocks diverse aggressive behaviors but not mating
Network and pathway expansion of genetic disease associations identifies successful drug targets
Authors: MacNamara Aidan , Nakic Nikolina , Amin Ali , Guo Cong , Sieber Karsten B. , Hurle Mark , Gutteridge Alex
Published: April 2020

It is widely accepted that genetic evidence of disease association acts as a sound basis for the selection of drug targets for complex common diseases and that propagation of genetic evidence through gene or protein interaction networks can accurately infer novel disease associations at genes for which no direct genetic evidence can be observed. However, an empirical test of the utility of combining these beliefs for drug discovery has been lacking.

In this study, we examine genetic associations arising from an analysis of 648 UK Biobank GWAS and evaluate whether targets identified as proxies of direct genetic hits are enriched for successful drug targets, as measured by historical clinical trial data.

We find that protein networks formed from specific functional linkages such as protein complexes and ligand-receptor pairs are suitable for even naïve guilt-by-association network propagation approaches. In addition, more sophisticated approaches applied to global protein-protein interaction networks and pathway databases, also successfully retrieve targets enriched for clinically successful drug targets. We conclude that network propagation of genetic evidence should be used for drug target identification.
Diffusion-MRI-based regional cortical microstructure at birth for predicting neurodevelopmental outcomes of 2-year-olds
Authors: Ouyang Minhui , Peng Qinmu , Jeon Tina , Heyne Roy , Chalak Lina , Huang Hao
Published: April 2020

Brain cerebral cortical architecture encoding regionally differential dendritic arborization and synaptic formation at birth underlies human behavior emergence at 2 years of age. Brain changes in 0-2 years are most dynamic across lifespan. Effective prediction of future behavior with brain microstructure at birth will reveal structural basis of behavioral emergence in typical development, and identify biomarkers for early detection and tailored intervention in atypical development. Here, we aimed to evaluate the neonate whole-brain cortical microstructure quantified by diffusion MRI for predicting future behavior. We found that individual cognitive and language functions assessed at age of 2 years were robustly predicted by neonate cortical microstructure using support vector regression. Remarkably, cortical regions contributing heavily to the prediction models exhibited distinctive functional selectivity for cognition and language. These findings highlight regional cortical microstructure at birth as potential sensitive biomarker in predicting future neurodevelopmental outcomes and identifying individual risks of brain disorders.
Concurrent neuroimaging and neurostimulation reveals a causal role for dlPFC in coding of task-relevant information
Authors: Jackson Jade B. , Feredoes Eva , Rich Anina N. , Lindner Michael , Woolgar Alexandra
Published: April 2020

The way in which the brain prioritises processing of information relevant for our current goals is widely contested. Many studies implicate the dorsolateral prefrontal cortex (dlPFC), and propose that it drives brain-wide focus by biasing processing in favour of relevant information. An alternative, however, is that dlPFC is involved in the inhibition of irrelevant information. Here, we address this longstanding debate using the inferentially powerful approach of applying transcranial magnetic stimulation during functional magnetic resonance imaging (concurrent TMS-fMRI) and testing for changes in information coding using multivariate pattern analysis (MVPA). We ask whether dlPFC plays a causal role in prioritising information processing, and whether this is throughselectionof relevant information orinhibitionof irrelevant information. Participants attended to one object feature whilst ignoring another feature of the same object. We reasoned that, if dlPFC is necessary forselection, active (disruptive) TMS shoulddecreasecoding of attended information compared to the low intensity (control) condition. Conversely, if right dlPFC is crucial forinhibition, active TMS shouldincreasecoding of irrelevant information relative to the control condition. The results showed that active TMS decreased coding ofrelevantinformation throughout the frontoparietal multiple demand regions, and that this impact was significantly stronger than the effect of TMS onirrelevantinformation coding, which was not statistically detectable. These data provide causal evidence for a specific role of dlPFC in supporting the representation of task-relevant information and demonstrate the crucial insights into high level cognitive-neural mechanisms possible with the combination of TMS-fMRI and MVPA.
Blocking gephyrin phosphorylation or microglia BDNF signaling prevents synapse loss and reduces infarct volume after ischemia
Authors: Cramer Teresa , Gill Raminder , Thirouin Zahra S , Vaas Markus , Sampath Suchita , Martineau Fanny , Noya Sara B. , Colameo David , Chang Philip K.-Y. , Wu Peiyou , Barker Philip A , Brown Steven A. , Paolicelli Rosa C. , Klohs Jan , McKinney R. Anne , Tyagarajan Shiva K.
Published: April 2020

Microglia interact with neurons to facilitate synapse plasticity; however, signal transducers between microglia and neuron remain unknown. Here, usingin vitroorganotypic hippocampal slice cultures and transient MCAO in genetically-engineered micein vivo, we report that at 24 h post-ischemia microglia release BDNF to downregulate glutamatergic and GABAergic synapses within the peri-infarct area. Analysis of the CA1 hippocampal formationin vitroshows that proBDNF and mBDNF downregulate glutamatergic dendritic spines and gephyrin scaffold stability through p75NTRand TrkB receptors respectively. Post-MCAO, we report that in the peri- infarct area and in the corresponding contralateral hemisphere similar neuroplasticity occur through microglia activation and gephyrin phosphorylation at Ser268, Ser270in vivo. Targeted deletion of theBdnfgene in microglia orGphnS268A/S270A (phospho-null) point-mutations protect against ischemic brain damage, neuroinflamation and synapse downregulation normally seen post-MCAO. Collectively, we report that gephyrin phosphorylation and microglia derived BDNF faciliate synapse plasticity after transient ischemia.
Predicting cell fate commitment of embryonic differentiation by single-cell graph entropy
Authors: Zhong Jiayuan , Han Chongyin , Zhang Xuhang , Chen Pei , Liu Rui
Published: April 2020

Cell fate commitment occurs during early embryonic development, that is, the embryonic differentiation sometimes undergoes a critical phase transition or “tipping point” of cell fate commitment, at which there is a drastic or qualitative shift of the cell populations. In this study, we presented a novel computational approach, the single-cell graph entropy (SGE), to explore the gene-gene associations among cell populations based on single-cell RNA sequencing (scRNA-seq) data. Specifically, by transforming the sparse and fluctuating gene expression data to the stable local network entropy, the SGE score quantitatively characterizes the criticality of gene regulatory networks among cell populations, and thus can be employed to predict the tipping point of cell fate or lineage commitment at the single cell level. The proposed SGE method was applied to five scRNA-seq datasets. For all these datasets of embryonic differentiation, SGE effectively captures the signal of the impending cell fate transitions, which cannot be detected by gene expressions. Some “dark” genes that are non-differential but sensitive to SGE values were revealed. The successful identification of critical transition for all five datasets demonstrates the effectiveness of our method in analyzing scRNA-seq data from a network perspective, and the potential of SGE to track the dynamics of cell differentiation.
Engineering highly multivalent sperm-binding IgG antibodies for potent non-hormonal female contraception
Authors: Shrestha Bhawana , Schaefer Alison , Saada Jamal , Yong Zhu , Jacobs Timothy M. , Chavez Elizabeth C. , Omsted Stuart S. , Vincent Kathleen , Moench Thomas R. , Lai Samuel K.
Published: April 2020

Many women risk unintended pregnancy due to dissatisfaction with available hormonal contraceptive methods. This led us to pursue topical sperm-binding monoclonal antibodies as a strategy for safe, non-hormonal contraception. Motivated by the greater agglutination potencies of polymeric immunoglobulins such as IgM and the exceptional bioprocessing ease in manufacturing IgG, we engineered IgGs possessing 6-10 Fabs against a unique surface antigen universally present on human sperm. These highly multivalent IgGs (HM-IgGs) are at least 10- to 16-fold more potent and faster than the parent IgG at agglutinating sperm, while preserving Fc-mediated trapping of individual spermatozoa in mucus. The increased potencies translate to effective (>99.9%) reduction of progressively motile sperm in the sheep vagina using 33 micrograms of the 10 Fab HM-IgG. HM-IgGs produce at comparable yields and possess identical thermal stability to the parent IgG, with greater homogeneity. HM-IgGs represent not only promising biologics for non-hormonal contraception but also a promising platform for generating potent agglutinating mAb for diverse medical applications.
CeMbio - TheC. elegansmicrobiome resource
Authors: Dirksen Philipp , Assié Adrien , Zimmermann Johannes , Zhang Fan , Tietje Adina-Malin , Marsh Sarah Arnaud , Félix Marie-Anne , Shapira Michael , Kaleta Christoph , Schulenburg Hinrich , Samuel Buck S.
Published: April 2020

The study of microbiomes by sequencing has revealed a plethora of correlations between microbial community composition and various life-history characteristics of the corresponding host species. However, inferring causation from correlation is often hampered by the sheer compositional complexity of microbiomes, even in simple organisms. Synthetic communities offer an effective approach to infer cause-effect relationships in host-microbiome systems. Yet the available communities suffer from several drawbacks, such as artificial (thus non-natural) choice of microbes, microbe-host mismatch (e.g. human microbes in gnotobiotic mice), or hosts lacking genetic tractability. Here we introduce CeMbio, a simplified naturalCaenorhabditis elegansmicrobiota derived from our previous meta-analysis of the natural microbiome of this nematode. The CeMbio resource is amenable to all strengths of theC. elegansmodel system, strains included are readily culturable, they all colonize the worm gut individually, and comprise a robust community that distinctly affects nematode life-history. Several tools have additionally been developed for the CeMbio strains, including diagnostic PCR primers, completely sequenced genomes, and metabolic network models. With CeMbio, we provide a versatile resource and toolbox for the in-depth dissection of naturally relevant host-microbiome interactions inC. elegans.

Dataset accession numbers

Whole genome sequencing data (PRJNA624308); microbiome sequencing [PRJEB37101 and PRJEB37035]; data supplement on the GSA Figshare Portal.
Differential and sequential immunomodulatory role of neutrophils and Ly6Chiinflammatory monocytes during antiviral antibody therapy
Authors: Lambour Jennifer , Naranjo-Gomez Mar , Boyer-Clavel Myriam , Pelegrin Mireia
Published: April 2020

Antiviral monoclonal antibodies (mAbs) can generate protective immunity through Fc-Fcγ Rs interactions. Using a mouse model of retroviral infection, we previously showed a crucial role for immune complexes (ICs) in the enhancement of T-cell responses through FcγR-mediated activation of dendritic cells (DCs). However, IC-FcγR interactions involve different cells of the immune system other than DCs such as neutrophils and monocytes. These two myeloid cell-types are innate effector cells rapidly recruited to sites of infection. In addition to being key cells to fight against invading pathogens, they are also endowed with immunomodulatory properties. While the role of DCs in enhancing antiviral immune responses upon mAb treatment has been addressed in several studies, the role of neutrophils and monocytes has been much less studied. Here we addressed how mAb therapy affects the functional activation of neutrophils and inflammatory monocytes in retrovirus-infected mice. We found that both cell-types activatedin vitroby viral ICs secreted high levels of chemokines able to recruit monocytes and neutrophils themselves. Moreover, inflammatory cytokines potentiated chemokines and cytokines release by IC-activated cells and induced FcγRIV upregulation. Similarly, infection and mAb-treatment upregulated FcγRIV expression on neutrophils and inflammatory monocytes and enhanced their cytokines and chemokines secretion. Notably, upon antibody therapy neutrophils and inflammatory monocytes displayed distinct functional activation states and sequentially modulated the antiviral immune response through the secretion of Th1-type polarizing cytokines and chemokines. Our work provides novel findings on the immunomodulatory role of neutrophils and monocytes in the enhancement of immune responses upon antiviral mAb therapy.
Normative theory of patch foraging decisions
Authors: Kilpatrick Zachary P , Davidson Jacob D , Hady Ahmed El
Published: April 2020

Foraging is a fundamental behavior as animals’ search for food is crucial for their survival. Patch leaving is a canonical foraging behavior, but classic theoretical conceptions of patch leaving decisions lack some key naturalistic details. Optimal foraging theory provides general rules for when an animal should leave a patch, but does not provide mechanistic insights about how those rules change with the structure of the environment. Such a mechanistic framework would aid in designing quantitative experiments to unravel behavioral and neural underpinnings of foraging. To address these shortcomings, we develop a normative theory of patch foraging decisions. Using a Bayesian approach, we treat patch leaving behavior as a statistical inference problem. We derive the animals’ optimal decision strategies in both non-depleting and depleting environments. A majority of these cases can be analyzed explicitly using methods from stochastic processes. Our behavioral predictions are expressed in terms of the optimal patch residence time and the decision rule by which an animal departs a patch. We also extend our theory to a hierarchical model in which the forager learns the environmental food resource distribution. The quantitative framework we develop will therefore help experimenters move from analyzing trial based behavior to continuous behavior without the loss of quantitative rigor. Our theoretical framework both extends optimal foraging theory and motivates a variety of behavioral and neuroscientific experiments investigating patch foraging behavior.
scLM: automatic detection of consensus gene clusters across multiple single-cell datasets
Authors: Song Qianqian , Su Jing , Miller Lance D. , Zhang Wei
Published: April 2020

In gene expression profiling studies, including single-cell RNA-seq (scRNAseq) analyses, the identification and characterization of co-expressed genes provides critical information on cell identity and function. Gene co-expression clustering in scRNA-seq data presents certain challenges. We show that commonly used methods for single cell data are not capable of identifying co-expressed genes accurately, and produce results that substantially limit biological expectations of co-expressed genes. Herein, we present scLM, a gene co-clustering algorithm tailored to single cell data that performs well at detecting gene clusters with significant biologic context. scLM can simultaneously cluster multiple single-cell datasets, i.e. consensus clustering, enabling users to leverage single cell data from multiple sources for novel comparative analysis. scLM takes raw count data as input and preserves biological variations without being influenced by batch effects from multiple datasets. Results from both simulation data and experimental data demonstrate that scLM outperforms the existing methods with considerably improved accuracy. To illustrate the biological insights of scLM, we apply it to our in-house and public experimental scRNA-seq datasets. scLM identifies novel functional gene modules and refines cell states, which facilitates mechanism discovery and understanding of complex biosystems such as cancers. A user-friendly R package with all the key features of the scLM method is available athttps://github.com/QSong-WF/scLM.
Development of a Novel Class of Self-Assembling dsRNA Cancer Therapeutics: a Proof of Concept Investigation
Authors: Asthana Vishwaratn , Stern Brett S. , Tang Yuqi , Bugga Pallavi , Li Ang , Ferguson Adam , Asthana Anantratn , Bao Gang , Drezek Rebekah A.
Published: April 2020

Cancer has proven to be an extremely difficult challenge to treat. Several fundamental issues currently underlie cancer treatment including differentiating self from non-self, functional coupling of the recognition and therapeutic components of various therapies, and the propensity of cancerous cells to develop resistance to common treatment modalities via evolutionary pressure. Given these limitations, there is an increasing need to develop an all-encompassing therapeutic that can uniquely target malignant cells, decouple recognition from treatment, and overcome evolutionarily driven cancer resistance. We describe herein, a new class of programmable self-assembling dsRNA-based cancer therapeutics, that uniquely targets aberrant genetic sequences, and in a functionally decoupled manner, undergoes oncogenic RNA activated displacement (ORAD), initiating a therapeutic cascade that induces apoptosis and immune activation. As a proof-of-concept, we show that RNA strands targeting the EWS/Fli1 fusion gene in Ewing Sarcoma cells that are end-blocked with phosphorothioate bonds and additionally sealed with a 2’-U modified DNA protector can be used to induce specific and potent killing of cells containing the target oncogenic sequence, but not wildtype.
Modulation of the vesicle code transmitting the visual signal in the retina
Authors: Moya-Díaz José , James Ben , Lagnado Leon
Published: April 2020

Multivesicular release (MVR) allows retinal bipolar cells to transmit visual signals as changes in both the rate and amplitude of synaptic events. How do neuromodulators reguate this vesicle code? By imaging larval zebrafish, we find that the variability of calcium influx is a major source of synaptic noise. Dopamine increases synaptic gain up to 15-fold while Substance P reduces it 7-fold, both by acting on the presynaptic calcium transient to alter the distribution of amplitudes of multivesicular events. An increase in gain is accompanied by a decrease in the temporal precision of transmission and a reduction in the efficiency with which vesicles transfer visual information. The decrease in gain caused by Substance P was also associated with a shift in temporal filtering from band-pass to low-pass. This study demonstrates how neuromodulators act on the synaptic transformation of the visual signal to alter the way information is coded with vesicles.
The ancient fusogen EnvP(b)1 is expressed in human tissues and its structure informs the evolution of gammaretrovirus envelope proteins
Authors: McCarthy Kevin R. , Timpona Joseph L. , Jenni Simon , Brusic Vesna , Johnson Welkin E. , Whelan Sean P.J. , Robinson-McCarthy Lindsey R.
Published: April 2020

Host genomes have acquired diversity from viruses through the capture of viral elements, often from endogenous retroviruses (ERVs). These viral elements contribute new transcriptional control elements and new protein encoding genes, and their refinement through evolution can generate novel physiological functions for the host. EnvP(b)1 is an endogenous retroviral envelope gene found in human and other primate genomes. We show that EnvP(b)1 arose very early in the evolution of primates, i.e. at least 40-47 million years ago, but has nevertheless retained its ability to fuse primate cells. We have detected similar sequences in the genome of a lemur species, suggesting that a progenitor virus may have circulated 55+ million years ago. We demonstrate that EnvP(b)1 protein is expressed in multiple human tissues and is fully processed, rendering it competent to fuse cells. This activated fusogen is expressed in multiple healthy human tissues and is under purifying selection, suggesting that its expression is selectively advantageous. We determined a structure of the inferred receptor binding domain of human EnvP(b)1, revealing close structural similarities between this Env protein and those of currently circulating leukemia viruses, despite poor sequence conservation. This observation highlights a common scaffold from which novel receptor binding specificities have evolved. The evolutionary plasticity of this domain may underlie the diversity of related Envs in circulating viruses and coopted elements alike. The function of EnvP(b)1 in primates remains unknown.

SIGNIFICANCE STATEMENT

Organisms can access genetic and functional novelty by capturing viral elements within their genomes, where they can evolve to drive new cellular or organismal processes. We demonstrate that a retrovirus envelope gene, EnvP(b)1, has been maintained as a functional protein for 40 to ≥55 million years and is expressed as a protein in multiple healthy human tissues. We believe it has an unknown function in primates. We determined the structure of its inferred receptor binding domain and compared it with the same domain in modern viruses. We find a common conserved architecture that underlies the varied receptor binding activity of divergent Env genes. The modularity and versatility of this domain may underpin the evolutionary success of this clade of fusogens.
Autonomic/Central Coupling Boosts Working Memory in Healthy Young Adults
Authors: Chen Pin-Chun , Whitehurst Lauren N. , Naji Mohsen , Mednick Sara C.
Published: April 2020

Working memory (WM) is an executive function that can improve with training. However, the precise mechanism for this improvement is not known. Studies have shown greater WM gains after a period of sleep than a similar period of wake (Kuriyama et al. 2008a; Zinke, Noack, and Born 2018), with WM improvement correlated with slow wave activity (SWA; 0.5-1Hz) during slow wave sleep (SWS) (Sattari et al. 2019; Pugin et al. 2015; Ferrarelli et al. 2019). A different body of literature has suggested an important role for autonomic activity during wake for WM (Hansen et al. 2004; Mosley, Laborde, and Kavanagh 2018). A recent study from our group reported that the temporal coupling of autonomic and central events (ACEs) during sleep was associated with memory consolidation (Naji et al. 2019). We found that heart rate bursts (HR bursts) during non-rapid eye movement (NREM) sleep are accompanied by increases in SWA and sigma (12-15Hz) power, as well as increases in the high-frequency (HF) component of the RR interval, reflecting vagal rebound. In addition, ACEs predict long-term, episodic memory improvement. Building on these previous results, we examined whether ACEs may also contribute to gains in WM. We tested 104 young adults in an operation span task (OSPAN) in the morning and evening, with either a nap (with electroencephalography (EEG) and electrocardiography (ECG)) or wake between testing sessions. We identified HR bursts in the ECG and replicated the increases in SWA and sigma prior to peak of the HR burst, as well as vagal rebound after the peak. Furthermore, we showed sleep-dependent WM improvement, which was predicted by ACE activity. Using regression analyses, we discovered that significantly more variance in WM improvement could be explained with ACE variables than with overall sleep activity not time-locked with ECG. These results provide the first evidence that coordinated autonomic and central events play a significant role in sleep-related WM improvement and implicate the potential of autonomic interventions during sleep for cognitive enhancement.
Gray matter networks associated with cognitive deficit in ADHD across adolescence and adulthood
Authors: Liu Jingyu , Duan Kuaikuai , Jiang Wenhao , Rootes-Murdy Kelly , Schoenmacker Gido , Buitelaar Jan K. , Hoogman Martine , Oosterlaan Jaap , Hoekstra Pieter J. , Heslenfeld Dirk J. , Hartman Catharina A. , Calhoun Vince D. , Arias-Vasquez Alejandro , Turner Jessica A.
Published: April 2020

Attention-deficit/hyperactivity disorder (ADHD) is a childhood-onset neuropsychiatric disorder, and its existence in adulthood is well established. Beyond symptoms of inattention and hyperactivity/impulsivity, patients commonly present with impairments in cognition. How neuronal underpinnings of symptoms and cognitive deficits differ across adolescence and adulthood is not clear. In this cross sectional study, we investigated gray matter of two cohorts, 486 adults and 508 adolescents, each including participants with ADHD and healthy controls. Independent component analysis was applied to the gray matter of each cohort, separately, to extract cohort specific networks. Then, we identified gray matter networks associated with symptoms, working memory and/or diagnosis in each cohort, and projected them onto the other cohort for comparison. Two components in the inferior, middle/superior frontal regions identified in adults and one component in the insula and inferior frontal region identified in adolescents were significantly associated with working memory deficits in both cohorts. One component in bilateral cerebellar tonsil and culmen identified in adults and one component in left cerebellar region identified in adolescents were significantly associated with inattentive symptoms in both cohorts. All these components presented significant or nominal level of gray matter reduction for ADHD patients in adolescents, but only one showed nominal reduction for patients in adults. Our findings suggest gray matter reduction may not be a sensitive marker for persist ADHD. However, the patterns of certain brain regions are associated with deficits in working memory or attention persistently from childhood into adulthood, which might help understand the mechanism of disease persistence.
Genome-wide study of the effect of blood collection tubes on the cell-free DNA methylome
Authors: Van Paemel Ruben , De Koker Andries , Caggiano Christa , Morlion Annelien , Mestdagh Pieter , De Wilde Bram , Vandesompele Jo , De Preter Katleen
Published: April 2020

Background

The methylation pattern of cfDNA, isolated from liquid biopsies, is gaining substantial interest for diagnosis and monitoring of diseases. We have evaluated the impact of type of blood collection tube and time delay between blood draw and plasma preparation on bisulfite-based cfDNA methylation profiling.

Methods

15 tubes of blood were drawn from three healthy volunteer subjects (BD Vacutainer K2E EDTA spray tubes, Streck Cell-Free DNA BCT tubes, PAXgene Blood ccfDNA tubes, Roche Cell-Free DNA Collection tubes and Biomatrica LBgard blood tubes in triplicate). Samples were either immediately processed or stored at room temperature for 24 or 72 hours before plasma preparation. DNA fragment size was evaluated by capillary electrophoresis. Reduced representation bisulfite sequencing was performed on the cell-free DNA isolated from these plasma samples. We evaluated the impact of blood tube and time delay on several quality control metrics.

Results

All preservation tubes performed similar on the quality metrics that were evaluated. Furthermore, a considerable increase in cfDNA concentration and the fraction of it derived from NK cells was observed after a 72-hour time delay in EDTA tubes.

Conclusion

The methylation pattern of cfDNA is robust and reproducible in between the different preservation tubes. EDTA tubes processed as soon as possible, preferably within 24 hours, are the most cost effective. If immediate processing is not possible, preservation tubes are valid alternatives.
Mapping the Immunodominance Landscape of SARS-CoV-2 Spike Protein for the Design of Vaccines against COVID-19
Authors: Zhang Bao-zhong , Hu Ye-fan , Chen Lin-lei , Tong Yi-gang , Hu Jing-chu , Cai Jian-piao , Chan Kwok-Hung , Dou Ying , Deng Jian , Gong Hua-rui , Kuwentrai Chaiyaporn , Li Wenjun , Wang Xiao-lei , Chu Hin , Su Cai-hui , Hung Ivan Fan-Ngai , Cheung Yau Thomas Chung , To Kelvin Kai-Wang , Yuen Kwok Yung , Huang Jian-Dong
Published: April 2020

The ongoing coronavirus disease 2019 (COVID-19) pandemic is a serious threat to global public health, and imposes severe burdens on the entire human society. The severe acute respiratory syndrome (SARS) coronavirus-2 (SARS-CoV-2) can cause severe respiratory illness and death. Currently, there are no specific antiviral drugs that can treat COVID-19. Several vaccines against SARS-CoV-2 are being actively developed by research groups around the world. The surface S (spike) protein and the highly expressed internal N (nucleocapsid) protein of SARS-CoV-2 are widely considered as promising candidates for vaccines. In order to guide the design of an effective vaccine, we need experimental data on these potential epitope candidates. In this study, we mapped the immunodominant (ID) sites of S protein using sera samples collected from recently discharged COVID-19 patients. The SARS-CoV-2 S protein-specific antibody levels in the sera of recovered COVID-19 patients were strongly correlated with the neutralising antibody titres. We used epitope mapping to determine the landscape of ID sites of S protein, which identified nine linearized B cell ID sites. Four out of the nine ID sites were found in the receptor-binding domain (RBD). Further analysis showed that these ID sites are potential high-affinity SARS-CoV-2 antibody binding sites. Peptides containing two out of the nine sites were tested as vaccine candidates against SARS-CoV-2 in a mouse model. We detected epitope-specific antibodies and SARS-CoV-2-neutralising activity in the immunised mice. This study for the first time provides human serological data for the design of vaccines against COVID-19.
Arabidopsis O-fucosyltransferase SPINDLY regulates root hair patterning independently of gibberellin signalling
Authors: Mutanwad Krishna Vasant , Zangl Isabella , Lucyshyn Doris
Published: April 2020

Root hairs are able to sense soil composition and play an important role for water and nutrient uptake. InArabidopsis thaliana, root hairs are distributed in the epidermis in a specific pattern, regularly alternating with non-root hair cells in continuous cell files. This patterning is regulated by internal factors such as a number of hormones, as well as external factors like nutrient availability. Thus, root-hair patterning is an excellent model for studying the plasticity of cell fate determination in response to environmental changes. Here, we report that loss-of-function mutants in the Protein O-Fucosyltransferase SPINDLY (SPY) form ectopic root hairs. Using a number of transcriptional reporters, we show that patterning inspy-22is affected upstream of the central regulators GLABRA2 (GL2) and WEREWOLF (WER). O-fucosylation of nuclear and cytosolic proteins is an important post-translational modification that is still not very well understood. So far, SPY is best characterized for its role in gibberellin signalling via fucosylation of the growth-repressing DELLA protein REPRESSOR OF GA (RGA). Our data suggest that the formation of ectopic root hairs inspy-22is independent of RGA and gibberellin signalling.
Targeted CRM1-inhibition perturbs leukemogenic NUP214 fusion proteins and exerts anti-cancer effects in leukemia cell lines withNUP214rearrangements
Authors: Mendes Adélia , Jühlen Ramona , Martinelli Valérie , Fahrenkrog Birthe
Published: April 2020

Chromosomal translocations fusing the locus of nucleoporinNUP214each with the proto-oncogenesSETandDEKare recurrent in, largely intractable, acute leukemias. The molecular basis underlying the pathogenesis of SET-NUP214 and DEK-NUP214 are still poorly understood, but both chimeras inhibit protein nuclear export mediated by the ß-karyopherin CRM1. In this report, we show that SET-NUP214 and DEK-NUP214 both disturb the localization of proteins essential for nucleocytoplasmic transport, in particular for CRM1-mediated protein export. Endogenous and exogenous SET-NUP214 and DEK-NUP214 form nuclear bodies. These nuclear bodies disperse upon targeted inhibition of CRM1 and the two fusion proteins re-localize throughout the nucleoplasm. Moreover, SET-NUP214 and DEK-NUP214 nuclear bodies reestablish shortly after removal of CRM1 inhibitors. Likewise, cell viability, metabolism, and proliferation of leukemia cell lines harboring SET-NUP214 and DEK-NUP214 are compromised by CRM1 inhibition, which is even sustained after clearance from CRM1 antagonists. Our results indicate CRM1 as a possible therapeutic target in NUP214-related leukemia. This is especially important, since no specific or targeted treatment options for NUP214 driven leukemia are available yet.
P2X-GCaMPs as versatile tools for imaging extracellular ATP signaling
Authors: Ollivier Matthias , Beudez Juline , Linck Nathalie , Grutter Thomas , Compan Vincent , Rassendren Francois
Published: April 2020

Adenosine 5’ triphosphate (ATP) is an extracellular signaling molecule involved in numerous physiological and pathological processes. Yet,in situcharacterization of the spatiotemporal dynamic of extracellular ATP is still challenging due to the lack of sensor with appropriate specificity, sensitivity and kinetics. Here we report the development of biosensors based on the fusion of cation permeable ATP receptors (P2X) to genetically encoded calcium sensors (GECI). By combining the features of P2X receptors with the high signal to noise ratio of GECIs, we generated ultrasensitive green and red fluorescent sniffers that detect nanomolar ATP concentrationsin situand also enable the tracking of P2X receptor activity. We provide the proof of concept that these sensors can dynamically track ATP release evoked by neuronal depolarization or by extracellular hypotonicity. Targeting these P2X-based biosensors to diverse cell types should advance our knowledge of extracellular ATP dynamicsin vivo.