bluuebunny/crossref_metadata_2025 huggingface dataset:
Non-apoptotic roles of apoptotic proteases: new tricks for an old dog
Authors: Su Tin Tin
Published: August 2020

This Open Question article highlights current advances in the study of non-apoptotic roles of apoptotic proteins. Apoptosis is a highly regulated and energy-requiring process in which cells actively kill themselves. Apoptosis helps remove extra cells to sculpt organs during embryo development and culls damaged cells throughout the body. Apoptosis relies on evolutionarily conserved proteins that include a family of proteases called caspases. Caspases activity has long been considered a hallmark of apoptosis. Yet an emerging body of literature indicates that caspase activity is required for a number of non-lethal processes that range from sculpting cells, removing protein aggregates, changing cell identity during differentiation or de-differentiation, and rebuilding tissues. Failure in each of these processes is associated with human disease. This article is not meant to be an exhaustive review but an introduction to the subject for an educated public, with caspases as a gateway example. I propose that it is time to explore non-apoptotic roles of caspases and other apoptotic proteins, in order to better understand their non-apoptosis function and to leverage new knowledge into new therapies.
Evaluating the impacts of release in São Paulo State (Brazil) on the epidemic of covid-19 based on mathematical model
Authors: Yang Hyun Mo , Junior Luis Pedro Lombardi , Yang Ariana Campos , Castro Fabio Fernandes Morato
Published: August 2020

To flatten the curve of the natural epidemic of covid-19, many countries adopted lockdown or isolation resulting in the containment of the SARS-CoV-2 transmission. However, an important question arises about the strategies of release of isolated persons to avoid overloaded hospitals and increased deaths. São Paulo State (Brazil) implemented the isolation of the population in non-essential activities on March 24, and the progressive flexibilization considering the characteristics of each location (release of the isolated population) initiated on June 15. A mathematical model based on the natural history of covid-19 was applied to describe the epidemiological scenario with isolation in São Paulo State, and assess the impact of release on the covid-19 epidemic. Using data collected from São Paulo State, we estimated the model parameters to obtain the curves of the epidemic, the number of deaths, and the clinical evolution of covid-19. The epidemic under isolation was the framework to evaluate the strategies of the release, that is, how these curves are changed with the release of isolated persons. We evaluated three strategies of release. First two strategies considered four releases in the isolated population in four equal proportions, but successive releases elapsed by 14 and 21 days. In each strategy the beginning of the release was on June 29 and July 13, when the effective reproduction numberRefwas evaluated. The third strategy aimed at the protection of the elder subpopulation. We observed that the delay to begin the release and the increased elapse between successive releases resulted in a better scenario by decreasing severe covid-19 cases and, consequently, to avoid overloaded hospitals. We also observed that the release delayed to achieve lower values forRefand infectious persons retarded in several months the quick increasing phase of the forthcoming epidemic. However, this epidemic can be flattened or even suppressed by isolation of infectious persons by mass testing and/or by rigid adoption of protective measures and social distancing.
Pharmacological inhibition of the kinin-kallikrein system in severe COVID-19 – A proof-of-concept study
Authors: Mansour Eli , Palma Andre C. , Ulaf Raisa G. , Ribeiro Luciana C. , Bernardes Ana Flavia , Nunes Thyago A. , Agrela Marcus V. , Bombassaro Bruna , Monfort-Pires Milena , Camargo Rafael L. , Araujo Eliana P. , Brunetti Natalia S. , Farias Alessandro S. , Falcão Antônio Luís E. , Santos Thiago Martins , Trabasso Plinio , Dertkigil Rachel P. , Dertkigil Sergio S. , Moretti Maria Luiza , Velloso Licio A.
Published: August 2020

Coronavirus disease-19 (COVID-19) can develop into a severe respiratory syndrome that results in up to 40% mortality. Acute lung inflammatory edema is a major pathological finding in autopsies explaining O2 diffusion failure and hypoxemia. Only dexamethasone has been shown to reduce mortality in severe cases, further supporting a role for inflammation in disease severity. SARS-CoV-2 enters cells employing angiotensin converting enzyme 2 (ACE2) as a receptor, which is highly expressed in lung alveolar cells. ACE2 is one of the components of the cellular machinery that inactivates the potent inflammatory agent bradykinin, and SARS-CoV-2 infection could interfere with the catalytic activity of ACE2, leading to accumulation of bradykinin. In this open-label, randomized clinical trial, we tested two pharmacological inhibitors of the kinin-kallikrein system that are currently approved for the treatment of hereditary angioedema, icatibant and inhibitor of C1 esterase/kallikrein, in a group of 30 patients with severe COVID-19. Neither icatibant nor inhibitor of C1 esterase/kallikrein resulted in significant changes in disease mortality and time to clinical improvement. However, both compounds promoted significant improvement of lung computed tomography scores and increased blood eosinophils, which has been reported as an indicator of disease recovery. In this small cohort, we found evidence for a beneficial role of pharmacological inhibition of the kinin-kallikrein system in two markers that indicate improved disease recovery.
Influenza epidemic model with dynamic social networks of agents with individual behaviour: A self organize perspective
Authors: López L. , Femández M. , Giovanini L.
Published: August 2020

It’s well known the existence of an interplay between the spread of an infectious disease like influenza and behavioural changes of individuals. An outbreak can trigger behavioural responses, at group and individual levels, which in turn can influence the course of the epidemic. Daily life interactions can be modelled by adaptive temporal networks in an explicit contact space through an agent based model, where each agent represents the interacting individuals. In this paper we introduce an individual based model where the behaviour of each individual is determined both by the external stimuli and its own appreciation of the environment and can be built as a combination of three interacting blocks:i)individual behaviour,ii)social behaviour andiii)epidemic state or epidemiological behaviour. We fit the model for a real influenza epidemic and perform the model validation, comparing the results with the classical approaches.
A simple numerical and analytical analysis of Covid-19 progression, infection inhibition and control in various countries
Authors: Chakravarty U. , Chaturvedi Deepa , Joshi M.P.
Published: August 2020

Covid-19 disease outspread and its subsequent control and inhibition strategies in various countries have been different which led to quite drastic difference in the outcome of the disease progression. In this paper we present an analytical and numerical study of Covid-19 disease spread and control by applying the modified SIR model of epidemic outbreak to explain the Covid spread from February-July 2020 in various countries. Two approaches are evident from the disease progression; one focused on disease eradication and inhibition, and the other is less restrictive dynamic response. Both the approaches are analytically modeled to determine the parameters that characterize the effectiveness of dealing with the disease progression. The model successfully explains the Covid-19 evolution and control of various countries over a vast span of four-five months. The study is highly beneficial to simply analytically and numerically model this complex problem of epidemic proliferation. It assists to easily determine the mathematical parameters for the Covid-19 control measures, helps in predicting the end of the epidemic, and most importantly conceiving the judicious way of unlock process to restore communication between cities, states and countries.
Superspreading k-cores at the center of COVID-19 pandemic persistence
Authors: Serafino Matteo , Monteiro Higor S. , Luo Shaojun , Reis Saulo D. S. , Igual Carles , Neto Antonio S. Lima , Travizano Matías , Andrade José S. , Makse Hernán A.
Published: August 2020

The spread of COVID-19 caused by the recently discovered SARS-CoV-2 virus has become a worldwide problem with devastating consequences. To slow down the spread of the pandemic, mass quarantines have been implemented globally, provoking further social and economic disruptions. Here, we address this problem by implementing a large-scale contact tracing network analysis to find the optimal quarantine protocol to dismantle the chain of transmission of coronavirus with minimal disruptions to society. We track billions of anonymized GPS human mobility datapoints from a compilation of hundreds of mobile apps deployed in Latin America to monitor the evolution of the contact network of disease transmission before and after the confinements. As a consequence of the lockdowns, people’s mobility across the region decreases by ~53%, which results in a drastic disintegration of the transmission network by ~90%. However, this disintegration did not halt the spreading of the disease. Our analysis indicates that superspreading k-core structures persist in the transmission network to prolong the pandemic. Once the k-cores are identified, the optimal strategy to break the chain of transmission is to quarantine a minimal number of ’weak links’ with high betweenness centrality connecting the large k-cores. Our results demonstrate the effectiveness of an optimal tracing strategy to halt the pandemic. As countries race to build and deploy contact tracing apps, our results could turn into a valuable resource to help deploy protocols with minimized disruptions.
Comprehensive Systematic Review to Identify putative COVID-19 Treatments: Roles for Immunomodulator and Antiviral Treatments
Authors: Hill Thomas , Baker Mark , Isherwood Lawrence , Lee Lennard YW
Published: August 2020

Objectives

To identify putative COVID-19 treatments and identify the roles of immunomodulators and antivirals in disease management.

Design

Systematic review.

Data sources

PubMed, bioRxiv.org and medRxiv.org were searched for studies suggestive of effective treatments for COVID-19. Additional studies were identified via a snowballing method applied to the references of retrieved papers as well as a subsequent targeted search for drug names.

Review methods

Inclusion criteria included any case series or randomised control trials in any language that were published from 18th December 2019 to 18th April 2020 and described COVID-19 treatment. Of an initial 2140 studies identified from the initial search, 29 studies were found to meet the inclusion criteria and included in this comprehensive systematic review.

Results

19 studies of antiviral treatments for COVID-19 have been reported and seven studies for immunomodulatory treatments. Six randomised controlled trials have been published with one positive trial for Hydroxychloroquine. This small study consisted of 31 patients though subsequent studies showed contradictory findings. All the remaining studies were observational studies, retrospective case reviews or non-randomised trials and these results are difficult to interpret due to methodological issues.

Conclusions

To date, an impressive number of studies have been performed in a short space of time, indicative of a resilient clinical trials infrastructure. However, there is a lack of high quality evidence to support any novel treatments for COVID-19 to be incorporated into the current standard of care. The majority of the studies of treatments for COVID-19 could only be found in pre-print servers. Future clinical reviews should therefore be Comprehensive Systematic Reviews involving pre-print studies to prevent potential unnecessary replications of clinical studies.
PROTOCOL – Are investigators’ access to trial data and rights to publish restricted and are trial participants informed about this? A comparison of trial protocols and informed consent materials
Authors: Paludan-Müller Asger Sand , Jørgensen Karsten Juhl , Gøtzsche Peter C.
Published: August 2020

This is a protocol for the project entitled: “Are investigators’ access to trial data and rights to publish restricted and are trial participants informed about this? A comparison of trial protocols and informed consent materials”
ResistoXplorer: a web-based tool for visual, statistical and exploratory data analysis of resistome data
Authors: Dhariwal Achal , Junges Roger , Chen Tsute , Petersen Fernanda Cristina
Published: August 2020

The study of resistomes using whole metagenomic sequencing enables high throughput identification of resistance genes in complex microbial communities, such as the human microbiome. Over recent years, sophisticated and diverse pipelines have been established to facilitate raw data processing and annotation. Despite the progress, there are no easy-to-use tools for comprehensive visual, statistical, and functional analysis of resistome data. Thus, exploration of the resulting large complex datasets remains a key bottleneck requiring robust computational resources and technical expertise, which creates a significant hurdle for advancements in the field. Here, we introduce ResistoXplorer, a user-friendly tool that integrates recent advancements in statistics and visualization, coupled with extensive functional annotations and phenotype collection, to enable high-throughput analysis of common outputs generated from metagenomic resistome studies. ResistoXplorer contains three modules- the ‘Antimicrobial Resistance Gene Table’ module offers various options for composition profiling, functional profiling and comparative analysis of resistome data; the ‘Integration’ module supports integrative exploratory analysis of resistome and microbiome abundance profiles derived from metagenomic samples; finally, the ‘Antimicrobial Resistance Gene List’ module enables users to intuitively explore the associations between antimicrobial resistance genes and the microbial hosts using network visual analytics to gain biological insights. ResistoXplorer is publicly available athttp://www.resistoxplorer.no.
Consequences of aneuploidy in human fibroblasts with trisomy 21
Authors: Hwang Sunyoung , Cavaliere Paola , Li Rui , Zhu Lihua Julie , Dephoure Noah , Torres Eduardo M.
Published: August 2020

An extra copy of chromosome 21 causes Down syndrome, the most common genetic disease in humans. The mechanisms by which the aneuploid status of the cell, independent of the identity of the triplicated genes, contributes to the pathologies associated with this syndrome are not well defined. To characterize aneuploidy driven phenotypes in trisomy 21 cells, we performed global transcriptome, proteome, and phenotypic analysis of primary human fibroblasts from individuals with Patau (trisomy 13), Edwards (trisomy 18), or Down syndromes. On average, mRNA and protein levels show a 1.5 fold increase in all trisomies with a subset of proteins enriched for subunits of macromolecular complexes showing signs of post-transcriptional regulation. Furthermore, we show several aneuploidy-associated phenotypes are present in trisomy 21 cells, including lower viability and an increased dependency on the serine-driven lipid biosynthesis pathway to proliferate. Our studies present a novel paradigm to study how aneuploidy contributes to Down syndrome.
Influenza A virus diffusion through mucus gel networks
Authors: Kaler Logan , Iverson Ethan , Bader Shahed , Song Daniel , Scull Margaret A. , Duncan Gregg A.
Published: August 2020

In this study, influenza A virus (IAV) and nanoparticle diffusion in human airway mucus was quantified using fluorescent video microscopy and multiple particle tracking. In previous work, it was determined that mucin-associated sialic acid acts as a decoy receptor for IAV hemagglutinin binding, and that virus passage through the mucus gel layer is facilitated through the sialic-acid cleaving enzyme, neuraminidase (NA), also present on the IAV envelope. However, our data suggests the mobility of IAV in mucus is significantly influenced by the mesh structure of the gel, as measured by nanoparticle probes, and NA activity is not required to facilitate virus passage through mucus gels. Using newly developed analyses, the binding affinity of IAV to the 3D mucus meshwork was estimated for individual virions with dissociation constants in the mM range, indicative of weak and reversible IAV-mucus interactions. We also found IAV diffusion significantly increased in mucus when treated with a mucolytic agent to break mucin-mucin disulfide bonds. In addition, IAV diffusion was significantly limited in a synthetic mucus model as crosslink density was systematically increased and network pore size was reduced. The results of this work provide important insights on how the balance of adhesive and physical barrier properties of mucus influence the dissemination of IAV within the lung microenvironment.
Genotypic diversity and dynamic nomenclature ofParechovirus A
Authors: Parker Edyth , Han Alvin , Brouwer Lieke , Wolthers Katja , Benschop Kimberley , Russell Colin A.
Published: August 2020

Human parechoviruses (PeV-A) can cause severe sepsis and neurological syndromes in neonates and children and are currently classified into 19 genotypes based on genetic divergence in the VP1 gene. However, the genotyping system has notable limitations including an arbitrary distance threshold and reliance on insufficiently robust phylogenetic reconstruction approaches leading to inconsistent genotype definitions. In order to improve the genotyping system, we investigated the molecular epidemiology of human parechoviruses, including the evolutionary history of the different PeV-A lineages as far as is possible. We found that PeV-A lineages suffer from severe substitution saturation in the VP1 gene which limit the inference of deep evolutionary timescales among the extant PeV-A and suggest that the degree of evolutionary divergence among current PeV-A lineages has been substantially underestimated, further confounding the current genotyping system. We propose an alternative nomenclature system based on robust, amino-acid level phylogenetic reconstruction and clustering with the PhyCLIP algorithm which delineates highly divergent currently designated genotypes more informatively. We also describe a dynamic nomenclature framework that combines PhyCLIP’s progressive clustering with phylogenetic placement for genotype assignment.
simATAC: a single-cell ATAC-seq simulation framework
Authors: Navidi Zeinab , Zhang Lin , Wang Bo
Published: August 2020

Single-cell Assay for Transposase-Accessible Chromatin sequencing (scATAC-seq) identifies regulated chromatin accessibility modules at the single-cell resolution. Robust evaluation is critical to the development of scATAC-seq pipelines, which calls for reproducible datasets for benchmarking. We hereby present the simATAC framework, an R package that generates scATAC-seq count matrices that highly resemble real scATAC-seq datasets in library size, sparsity, and chromatin accessibility signals. simATAC deploys statistical models derived from analyzing 90 real scATAC-seq cell groups. simATAC provides a robust and systematic approach to generate in silico scATAC-seq samples with known cell labels for assessing analytical pipelines.
Whole-brain mapping of monosynaptic inputs to midbrain cholinergic neurons
Authors: Huerta-Ocampo Icnelia , Dautan Daniel , Gut Nadine K. , Khan Bakhtawer , Mena-Segovia Juan
Published: August 2020

The cholinergic midbrain is involved in a wide range of motor and cognitive processes. Cholinergic neurons of the pedunculopontine (PPN) and laterodorsal tegmental nucleus (LDT) send long-ranging axonal projections that target sensorimotor and limbic areas in the thalamus, the dopaminergic midbrain and the striatal complex following a topographical gradient, where they influence a range of functions including attention, reinforcement learning and action-selection. Nevertheless, a comprehensive examination of the afferents to PPN and LDT cholinergic neurons is still lacking, partly due to the neurochemical heterogeneity of this region. Here we characterize the whole-brain input connectome to cholinergic neurons across distinct functional domains (i.e. PPN vs LDT) using conditional transsynaptic retrograde labeling in ChAT::Cre male and female rats. The quantification of input neurons revealed that both PPN and LDT receive similar substantial inputs from the superior colliculus and the output of the basal ganglia (i.e. substantia nigra pars reticulata). In addition, we found that PPN cholinergic neurons receive preferential inputs from basal ganglia structures than from the cortex, whereas LDT cholinergic neurons receive preferential inputs from cortical areas. Our results provide the first characterization of inputs to PPN and LDT cholinergic neurons. The differences in afferents to each cholinergic structure support their differential roles in behavior.

Significance statement

Acetylcholine is a widespread neuromodulator that regulates a wide variety of functions including learning, goal-directed behavior and execution of movements. In this study we characterized the distribution of presynaptic neurons that modulate the activity of functionally distinct midbrain cholinergic neurons located in the pedunculopontine nucleus (PPN) and the laterodorsal tegmental nucleus (LDT) by using a transsynaptic, modified-rabies virus strategy. We reveal that input neurons are widely distributed throughout the brain but segregated into specific functional domains. Motor related areas innervate preferentially the PPN, whereas limbic related areas preferentially innervate the LDT. Our results suggest that input neurons located along distinct functional domains have differential impact over cholinergic midbrain regions.
Developmentally regulated activation of defense allows for rapid inhibition of infection in age-related resistance toPhytophthora capsiciin cucumber fruit
Authors: Mansfeld Ben N. , Colle Marivi , Zhang Chunqiu , Lin Ying-Chen , Grumet Rebecca
Published: August 2020

Background

Age-related resistance (ARR) is a developmentally regulated phenomenon conferring resistance to pathogens or pests. Although ARR has been observed in several host-pathogen systems, the underlying mechanisms are largely uncharacterized. In cucumber, rapidly growing fruit are highly susceptible toPhytophthora capsicibut become resistant as they complete exponential growth. We previously demonstrated that ARR is associated with the fruit peel and identified gene expression and metabolomic changes potentially functioning as preformed defenses.

Results

Here, we compare the response to infection in fruit at resistant and susceptible ages using microscopy, quantitative bioassays, and weighted gene co-expression analyses. We observed strong transcriptional changes unique to resistant aged fruit 2-4 hours post inoculation (hpi). Microscopy and bioassays confirmed this early response, with evidence of pathogen death and infection failure as early as 4 hpi and cessation of pathogen growth by 8-10 hpi. Expression analyses identified candidate genes involved in conferring the rapid response including those encoding transcription factors, hormone signaling pathways, and defenses such as reactive oxygen species metabolism and phenylpropanoid biosynthesis.

Conclusion

The early pathogen death and rapid defense response in resistant-aged fruit provide insight into potential mechanisms for ARR, implicating both pre-formed biochemical defenses and developmentally regulated capacity for pathogen recognition as key factors shaping age-related resistance.
A data-driven epidemiological model to explain the Covid-19 pandemic in multiple countries and help in choosing mitigation strategies
Authors: Beira M. J. , Kumar A. , Perfeito L. , Gonçalves-Sá J. , Sebastião P. J.
Published: August 2020

Accurate models are fundamental to understand the dynamics of the COVID-19 pandemic and to evaluate different mitigation strategies. Here, we present a multi-compartmental model that fits the epidemiological data for eleven countries, despite the reduced number of fitting parameters. This model consistently explains the data for the daily infected, recovered, and dead over the first six months of the pandemic. The good quality of the fits makes it possible to explore different scenarios and evaluate the impact of both individual and collective behaviors and government-level decisions to mitigate the epidemic. We identify robust alternatives to lockdown, such as self-protection measures, and massive testing. Furthermore, communication and risk perception are fundamental to modulate the success of different strategies. The fitting/simulation tool is publicly available for use and test of other models, allowing for comparisons between different underlying assumptions, mitigation measures, and policy recommendations.
Exploring the Feasibility of Using Real-World Data from a Large Clinical Data Research Network to Simulate Clinical Trials of Alzheimer’s Disease
Authors: Chen Zhaoyi , Zhang Hansi , Guo Yi , George Thomas J , Prosperi Mattia , Hogan William R , He Zhe , Shenkman Elizabeth A , Wang Fei , Bian Jiang
Published: August 2020

In this study, we explored the feasibility of using real-world data (RWD) from a large clinical research network to simulate real-world clinical trials of Alzheimer’s disease (AD). The target trial (i.e.,NCT00478205) is a Phase III double-blind, parallel-group trial that compared the 23 mg donepezil sustained release with the 10 mg donepezil immediate release formulation in patients with moderate to severe AD. We followed the target trial’s study protocol to identify the study population, treatment regimen assignments, and outcome assessments, and to set up a number of different simulation scenarios and parameters. We considered two main scenarios: (1) a one-arm simulation: simulating a standard-of-care arm that can serve as an external control arm; and (2) a two-arm simulation: simulating both intervention and control arms with proper patient matching algorithms for comparative effectiveness analysis. In the two-arm simulation scenario, we used propensity score matching controlling for baseline characteristics to simulate the randomization process. In the two-arm simulation, higher SAE rates were observed in the simulated trials than the rates reported in original trial, and a higher SAE rate was observed in the 23mg arm than the 10 mg standard-of-care arm. In the one-arm simulation scenario, similar estimates of SAE rates were observed when proportional sampling was used to control demographic variables. In conclusion, trial simulation using RWD is feasible in this example of AD trial in terms of safety evaluation. Trial simulation using RWD could be a valuable tool for post-market comparative effectiveness studies and for informing future trials’ design. Nevertheless, such approach may be limited, for example, by the availability of RWD that matches the target trials of interest, and further investigations are warranted.
A novel stress response pathway regulates rRNA biogenesis
Authors: Szaflarski Witold , Sowiński Mateusz , Leśniczak Marta , Ojha Sandeep , Aulas Anaïs , Dave Dhwani , Malla Sulochan , Anderson Paul , Ivanov Pavel , Lyons Shawn M.
Published: August 2020

Production of ribosomes is an energy-intensive process owing to the intricacy of these massive macromolecular machines. Each human ribosome contains 80 ribosomal proteins and four non-coding RNAs. Accurate assembly requires precise regulation of protein and RNA subunits. In response to stress, the integrated stress response (ISR) rapidly inhibits global translation. How rRNA is coordinately regulated with the rapid inhibition of ribosomal protein synthesis is not known. Here we show that stress specifically inhibits the first step of rRNA processing. Unprocessed rRNA is stored within the nucleolus, and, when stress resolves, it re-enters the ribosome biogenesis pathway. Retention of unprocessed rRNA within the nucleolus aids in the maintenance of this organelle. This response is independent of the ISR or inhibition of cellular translation but represents an independent stress-response pathway that we term Ribosome Biogenesis Stress Response (RiBiSR). Failure to coordinately regulate ribosomal protein translation and rRNA production results in nucleolar fragmentation. Our study unveils a novel stress response pathway that aims at conserving energy, preserving the nucleolus, and prevents further stress by regulation of rRNA processing.
SARS-CoV-2 ORF9b Antagonizes Type I and III Interferons by Targeting Multiple Components of RIG-I/MDA-5-MAVS, TLR3-TRIF, and cGAS-STING Signaling Pathways
Authors: Han Lulu , Zhuang Meng-Wei , Zheng Yi , Zhang Jing , Nan Mei-Ling , Wang Pei-Hui , Gao Chengjiang
Published: August 2020

Severe acute respiratory syndrome corona-virus 2 (SARS-CoV-2), the etiologic agent of the coronavirus disease 2019 (COVID-19), has a catastrophic effect on human health and society. Clinical findings indicated that the suppression of innate antiviral immunity, especially the type I and III interferon (IFN) production, contributes to the pathogenesis of COVID-19. However, how SARS-CoV-2 evades antiviral immunity still needs further investigations. Here, we reported that the open reading frame 9b (ORF9b) protein encoded by the SARS-CoV-2 genome inhibits the activation of type I and III IFN response by targeting multiple molecules of innate antiviral signaling pathways. SARS-CoV-2 ORF9b impaired the induction of type I and III IFNs by Sendai virus or the dsRNA mimic poly (I:C). SARS-CoV-2 ORF9b inhibits the activation of type I and III IFNs induced by the components of cytosolic dsRNA-sensing pathways of RIG-I/MDA5-MAVS signaling, including RIG-I, MDA-5, MAVS, TBK1, and IKKε rather than IRF3-5D, the active form of IRF3. SARS-CoV-2 ORF9b also suppressed the induction of type I and III IFNs by TRIF and STING, the adaptor protein of endosome RNA-sensing pathway of TLR3-TRIF signaling and the adaptor protein of cytosolic DNA-sensing pathway of cGAS-STING signaling, respectively. Mechanistically, SARS-CoV-2 ORF9b protein interacts with RIG-I, MDA-5, MAVS, TRIF, STING, TBK1, and prevents TBK1 phosphorylation, thus impeding the phosphorylation and nuclear trans-localization of IRF3 activation. Overexpression of SARS-CoV-2 ORF9b facilitates the replication of the vesicular stomatitis virus. Therefore, SARS-CoV-2 ORF9b negatively regulates antiviral immunity, thus, facilitate virus replication. This study contributes to our understanding of the molecular mechanism of how SARS-CoV-2 impaired antiviral immunity and providing an essential clue to the pathogenesis of COVID-19.
Healthcare workers’ high COVID-19 infection rate: the source of infections and potential for respirators and surgical masks to reduce occupational infections
Authors: Oksanen Lotta-Maria A. H. , Sanmark Enni , Oksanen Sampo A. , Anttila Veli-Jukka , Paterno Jussi J. , Lappalainen Maija , Lehtonen Lasse , Geneid Ahmed
Published: August 2020

Objective

To analyse the work-related exposure to SARS-CoV-2 and trace the source of COVID-19 infections in tertiary hospitals’ healthcare workers in light of the used PPE and their ability to maintain social distances and follow governmental restrictions.

Design

Cross-sectional study

Setting

Tertiary hospitals in Uusimaa region, Finland

Participants

Of 1072 enrolled, 866 HCWs (588 nurses, 170 doctors and 108 laboratory and medical imaging nurses) from the Helsinki University Hospital completed the questionnaire by July 15th, 2020. The average age of participants was 42.4 years and 772 (89.0%) were women. The participants answered a detailed questionnaire of their PPE usage, ability to follow safety restrictions, exposure to COVID-19, the source of potential COVID-19 infection and both mental and physical symptoms during the first wave of COVID-19 in Finland.

Main outcome measures

All participants with COVID-19 symptoms were tested with either RT-PCR or antibody tests. The infections were traced and categorised based on the location and source of infection. The possibility to maintain social distance and PPE usage during exposure were analyzed.

Results

Of the HCWs that participated, 41 (4.7%) tested positive for SARS-CoV-2, marking a substantially higher infection rate than that of the general population (0.3%); 22 (53.6%) of infections were confirmed or likely occupational, including 7 (31.8%) from colleagues. Additionally, 5 (26.3%) of other infections were from colleagues outside the working facilities. 14 (63.6%) of occupational infections occurred while using a surgical mask. No occupational infections were found while using an FFP2/3 respirator and aerosol precautions while treating suspected or confirmed COVID-19 patients.

Conclusions

While treating suspected or confirmed COVID-19 patients, HCWs should wear an FFP2/3 respirator and recommended PPE. Maintaining safety distances in the workplace and controlling infections between HCWs should be priorities to ensure safe working conditions.
No metabolic “default mode” of human brain function
Authors: Jonasson Lars S , Grill Filip , Hahn Andreas , Rischka Lucas , Lanzenberger Rupert , Lundmark Vania Panes , Riklund Katrine , Axelsson Jan , Rieckmann Anna
Published: August 2020

The finding of reduced activity in the default mode network (DMN) during externally focused cognitive control has been highly influential to our understanding of human brain function, but ‘deactivations’ have also prompted major questions of interpretation. Using hybrid functional PET-MR imaging, this study shows that fMRI task activations and deactivations do not reflect antagonistic patterns of synaptic metabolism. FMRI activations were accompanied by concomitant increases in metabolism during cognitive control, but, unlike the BOLD response, metabolism in the core DMN did not change between rest and task. Metabolic increases along the borders of the DMN during task performance further revealed a set of regions that guide engagement and suppression of neighboring networks during cognitive control. Collectively, dissociations between metabolism and BOLD signal specific to the DMN reveal functional heterogeneity in this network and demonstrate that BOLD deactivations during cognitive control should not be interpreted to reflect reduced synaptic activity.
Critical role of the periplasm in copper homeostasis in Gram-negative bacteria
Authors: Ishihara Jun-ichi , Mekubo Tomohiro , Kusaka Chikako , Kondo Suguru , Aiba Hirofumi , Ishikawa Shu , Ogasawara Naotake , Oshima Taku , Takahashi Hiroki
Published: August 2020

Copper is essential for life, but is toxic in excess; that is, cells must keep an optimal internal copper concentration. Under aerobic conditions, less toxic Cu(II) taken up by bacterial cells is reduced to more toxic Cu(I) in the cytoplasm. Copper homeostasis is achieved in the cytoplasm and the periplasm as a unique feature of Gram-negative bacteria. The copper efflux pumps, CopA and CusCBA export Cu(I) from the cytoplasm or the periplasm to outside of the cells inEscherichia coli. In addition, the periplasmic proteins, such as a multi-copper oxidase CueO, play a role in the periplasmic detoxification. While the efflux pumps are highly conserved in Gram-negative bacteria, the periplasmic proteins are diversified, indicating that copper homeostasis in the periplasm could contribute to adaptation to various living environments. However, the role of the periplasm and periplasmic proteins in regard to whole-cell copper homeostasis remains unknown. In this study, we addressed the role of the periplasm and periplasmic proteins in copper homeostasis to adapt to various ecological niches. We have used a systems approach, alternating rounds of experiments and models, to further elucidate the dynamics of copper efflux system. We measured the response to copper of the main specific copper export systems in the wild typeE. colistrain, and a series of deletion mutant strains. We interpreted these data using a detailed mathematical model and Bayesian model fitting routines, and verified copper homeostasis. Compared with the simulation and the growth in response to copper, we found that the growth was associated with copper abundance in the periplasm. In particular, CueO unique to Gram-negative bacteria contributes both to protection against Cu(I) toxicity and to incorporating copper into the periplasmic components/proteins, resulting in maximizing the growth. These results suggest that Gram-negative bacteria have evolved to utilize the periplasm as a sensor and store for copper, in order to enable Gram-negative bacteria to adapt to a wide range of environmental copper concentrations.
Baculovirus-vectored precision delivery of large DNA cargoes in human genomes
Authors: Aulicino Francesco , Pelosse Martin , Toelzer Christine , Capin Julien , Meysami Parisa , Dillingham Mark Simon , Schaffitzel Christiane , Berger Imre
Published: August 2020

Precise gene editing and genome engineering by CRISPR technology requires simultaneous delivery of multiple DNA-encoded components into living cells rapidly exceeding the cargo capacity of currently utilized viral vector systems. Here we exploit the unmatched heterologous DNA cargo capacity of baculovirus to resolve this bottleneck. We implement hybrid DNA techniques (MultiMate) for rapid and error-free assembly of currently up to 25 functional DNA modules in a single baculoviral vector enabling CRISPR-based genome engineering. Utilizing homology-independent targeted integration (HITI), we achieve up to 30% correct genome interventions in human cells, including precision docking of large DNA payloads in theACTBlocus. We demonstrate baculovirus-vectored delivery of prime-editing toolkits for seamless DNA search-and-replace interventions achieving, with a single vector, highly efficient cleavage-free trinucleotide insertion in theHEK3locus without any detectable indels. Our approach thus unlocks a wide range of editing and engineering applications in human cell genomes.
The immune landscape of primary central nervous system diffuse large B cell lymphoma
Authors: Alame Melissa , Cornillot Emmanuel , Cacheux Valère , Rigau Valérie , Costes-Martineau Valérie , Lacheretz-Szablewski Vanessa , Colinge Jacques
Published: August 2020

Primary central nervous system diffuse large B-cell lymphoma (PCNSL) is a rare and aggressive entity that resides in an immune-privileged site. The tumor microenvironment (TME) and the disruption of the immune surveillance influence lymphoma pathogenesis and immunotherapy resistance. Despite growing knowledge on heterogeneous therapeutic responses, no comprehensive description of the PCNSL TME is available. We investigated the immune subtypes of PCNSL and their association with molecular signaling and survival. Bulk mRNA-sequencing (n=20) and microarray (n=34) data were exploited to identify three immune subtypes of PCNSL: immune-rich, poor, and intermediate. The immune-rich subtype was associated to better survival and characterized by hyper-activation of STAT3 signaling and inflammatory signaling,e.g., IFNγ and TNF-α, resembling the hot subtype described in primary testicular lymphoma and solid cancer. WNT/β-catenin, HIPPO, and NOTCH signaling were hyper-activated in the immune-poor subtype. HLA down-modulation was clearly associated with a low or intermediate immune infiltration and the absence of T-cell activation. Moreover, HLA class I down-regulation was also correlated with worse survival with implications on immune-intermediate PCNSL that frequently feature reduced HLA expression. A ligand-receptor intercellular network revealed high expression of two immune checkpoints,i.e., CTLA-4/CD86 and TIM-3/LAGLS9. Immunohistopathology and digital imaging showed that TIM-3 and galectin-9 proteins were clearly upregulated in PCNSL. Altogether, our study reveals that patient stratification according to immune subtypes, HLA status, and immune checkpoint molecule quantification should be considered prior to immune checkpoint inhibitor therapy. Moreover, TIM-3 protein should be considered an axis for future therapeutic development.
Bone Marrow Stromal Cells in a Mouse Model of Metal Implant Osseointegration
Authors: Vesprey Alexander , Suh Eun Sung , Aytürk Didem Göz , Yang Xu , Rogers Miracle , Sosa Branden , Niu Yingzhen , Kalajzic Ivo , Ivashkiv Lionel B. , Bostrom Mathias P.G. , Ayturk Ugur M.
Published: August 2020

Metal implants are commonly used in orthopaedic surgery. The mechanical stability and longevity of implants depend on adequate bone deposition along the implant surface. The cellular and molecular mechanisms underlying peri-implant bone formation (i.e. osseointegration) are incompletely understood. Herein, our goal was to determine the specific bone marrow stromal cell populations that contribute to bone formation around metal implants. To do this, we utilized a mouse tibial implant model that is clinically representative of human joint replacement procedures. Using a lineage-tracing approach with theActa2.creERT2andTmem100.creERT2transgenic alleles, we found thatPdgfra- andLy6a/Sca1-expressing stromal cells (PαS cells) multiply and differentiate in the peri-implant environment to give rise to osteocytes in newly formed bone tissue. Single cell RNA-seq analysis indicated that PαS cells are quiescent in uninjured bone tissue; however, they express markers of proliferation and osteogenic differentiation shortly after implantation surgery. Our findings indicate that PαS cells are mobilized to repair bone tissue and facilitate implant osseointegration following surgery. Biologic therapies targeting PαS cells might improve osseointegration in patients undergoing orthopaedic procedures.
Simultaneous deep generative modeling and clustering of single cell genomic data
Authors: Liu Qiao , Chen Shengquan , Jiang Rui , Wong Wing Hung
Published: August 2020

Recent advances in single-cell technologies, including single-cell ATAC-seq (scATAC-seq), have enabled large-scale profiling of the chromatin accessibility landscape at the single cell level. However, the characteristics of scATAC-seq data, including high sparsity and high dimensionality, have greatly complicated the computational analysis. Here, we proposed scDEC, a computational tool for single cell ATAC-seq analysis with deep generative neural networks. scDEC is built on a pair of generative adversarial networks (GANs), and is capable of learning the latent representation and inferring the cell labels, simultaneously. In a series of experiments, scDEC demonstrates superior performance over other tools in scATAC-seq analysis across multiple datasets and experimental settings. In the downstream applications, we demonstrated that the generative power of scDEC helps to infer the trajectory and intermediate state of cells during differentiation and the latent features learned by scDEC can potentially reveal both biological cell types and within-cell-type variations.
A High-Performance Genetically Encoded Fluorescent Biosensor for Imaging Physiological Peroxynitrite
Authors: Chen Zhijie , Zhang Shen , Li Xinyu , Ai Hui-wang
Published: August 2020

Peroxynitrite is a highly reactive nitrogen species (RNS) that plays critical roles in signal transduction, stress response, and numerous human diseases. Advanced molecular tools that permit the selective, sensitive, and non-invasive detection of peroxynitrite is essential for understanding its pathophysiological functions. Here, we present pnGFP-Ultra, a high performance, reaction-based, genetically encodable biosensor for imaging peroxynitrite in live cells. pnGFP-Ultra features ap-boronophenylalanine-modified chromophore as the sensing moiety and exhibits a remarkable 123-fold fluorescence turn-on response towards peroxynitrite while displaying virtually no cross-reaction with other reactive oxygen/nitrogen species, including hydrogen peroxide. To facilitate the expression of pnGFP-Ultra in mammalian cells, we engineered a highly efficient noncanonical amino acid (ncAA) expression system that is broadly applicable to the mammalian expression of proteins containing various ncAAs. pnGFP-Ultra robustly detected peroxynitrite production during interferon γ and lipopolysaccharide-induced immune responses in macrophages, and in amyloid β-activated primary glial cells. Thus, pnGFP-Ultra fills an important technical gap and represents an important new addition to the molecular toolbox in probing RNS biology.

In Brief

Chen et al. report pnGFP-Ultra, a high-performance fluorescent biosensor for minimally invasive and selective imaging of peroxynitrite production in live cells.

Highlights

pnGFP-Ultra is a genetically encoded peroxynitrite biosensor with a 123-fold fluorescence turn-on response

pnGFP-Ultra exhibits high selectivity toward peroxynitrite, with virtually no crossreaction with hydrogen peroxide

An optimized plasmid-based system increases noncanonical amino acid incorporation in mammalian cells by >10 fold

pnGFP-Ultra robustly detects peroxynitrite production in macrophages and primary glial cells
Associations of early social experience with offspring DNA methylation and later life stress phenotype
Authors: Laubach Zachary M. , Greenberg Julia R. , Turner Julie W. , Montgomery Tracy , Pioon Malit O. , Smale Laura , Cavalcante Raymond , Padmanabhan Karthik R. , Lalancette Claudia , vonHoldt Bridgett , Faulk Christopher D. , Dolinoy Dana C. , Holekamp Kay E. , Perng Wei
Published: August 2020

In a wild population of spotted hyenas, we tested the hypothesis that maternal care during the first year of life and social connectedness during two periods of early development lead to differences in DNA methylation and fecal glucocorticoid metabolites (fGCMs) later in life. We found that although maternal care and social connectedness during the communal den dependent period were not associated with fGCMs, greater social connectedness after hyenas leave their communal den is associated with lower adult fGCMs. Additionally, more maternal care and social connectedness after leaving the communal den corresponded with higher global (%CCGG) DNA methylation. Finally, we identified multiple DNA methylation biomarkers near genes involved in inflammation that may link maternal care and stress phenotype. Our findings suggest that both maternal care during the first year of life and social connections after leaving the den influence DNA methylation and contribute to a developmentally plastic stress response.