bluuebunny/crossref_metadata_2025 huggingface dataset:
Single-cell Multi-omics reveal heterogeneity and metastasis potential in different liver cancer cell lines
Authors: Wang Shanshan , Xie Jiarui , Zou Xuanxuan , Pan Taotao , Zhuang Zhenkun , Wang Zifei , Yuan Yue , Liu Longqi , Liu Shiping , Wu Liang
Published: November 2020

Hepatocellular carcinoma (HCC) is a malignant neo-plasm with a high recurrence and metastatic rate, accounted for poor prognosis. Commonly existed heterogeneity is concerned with neoplasia, cancer progression, therapeutic resistance and metastasis is the principal cause of cancer lethality. As development of multi-omics methods in single-cell technology provides multi-faceted insight into disease processes in the era of precision medicine. Here, we interrogated single-cell transcriptomes, proteomes and epigenetic information, revealing metastasis potential heterogeneity in 5 HCC cell lines across different metastasis capacity. We confirmed that higher mesenchymal (M) status but not proliferation rate was associated with stronger metastasis ability of cell lines. Besides, we identified a subgroup being common in several cell lines, showing a higher hypoxic signature. A gene set involving 14 genes were chosen to represent the hypoxia state, much consistent than previous reported gene set, and showed worse prognosis association in TCGA data. This hypoxic subgroup prefers glycolysis metabolism than OXPO, and showed non-cycling, quiescent state which could be resistant to many proliferation-targeting drugs. Our results provide a comprehensive understanding of characteristic associated with metastasis capacity of HCC cell line, which will guide the metastasis mechanism study of HCC.
Physical and psychiatric comorbidity among patients with severe mental illness as seen in Uganda
Authors: Mpango Richard Stephen , Ssembajjwe Wilber , Rukundo Godfrey Zari , Birungi Carol , Kalungi Allan , Gadow Kenneth D. , Patel Vikram , Nyirenda Moffat , Kinyanda Eugene
Published: November 2020

This study established the prevalence of physical and psychiatric comorbidity and associated risk factors among 1,201 out-patients with severe mental illness (SMI) attending Butabika and Masaka hospitals in Uganda. Participants completed an assessment battery; structured, standardized and locally translated instruments. SMIs were established using the MINI International Neuropsychiatric Interview version 7.2. We used logistic regression to determine the association between physical and psychiatric comorbidity and risk factors. Prevalence of physical and psychiatric comorbidity was 13.1 %. Childhood sexual abuse (aOR 1.06, 95% CI 1.03 -1.10, P=0.001), sexual abuse in adulthood (aOR 2.22, 95% CI 1.60 - 3.08, P<0.001), childhood physical abuse (aOR 1.07, 95% CI 1.03 - 1.10, P<0.001) and physical abuse in adulthood (aOR 1.69, 95% CI 1.30 - 2.20, P<0.001) were associated with an increased risk of having comorbid psychiatric and physical disorders. Emerging healthcare models in Uganda should optimise care for people with physical and psychiatric comorbidity.
Clinical and microbiological assessments of COVID-19 in healthcare workers: a prospective longitudinal study
Authors: Bal Antonin , Brengel-Pesce Karen , Gaymard Alexandre , Quéromès Grégory , Guibert Nicolas , Frobert Emile , Bouscambert Maude , Trabaud Mary-Anne , Allantaz-Frager Florence , Oriol Guy , Cheynet Valérie , d’Aubarede Constance , Massardier-Pilonchery Amélie , Buisson Marlyse , Lupo Julien , Pozzetto Bruno , Poignard Pascal , Lina Bruno , Fassier Jean-Baptiste , Morfin-Sherpa Florence , Trouillet-Assant Sophie
Published: November 2020

Background

A comprehensive assessment of COVID-19 in healthcare workers (HCWs) including the investigation of viral shedding duration is critical.

Methods

A longitudinal study including 319 HCWs was conducted. After SARS-CoV-2 screening with RT-PCR assay, other respiratory pathogens were tested with a multiplex molecular panel. For SARS-CoV-2 positive HCWs, the normalized viral load was determined weekly; viral culture and virus neutralization assays were also performed. For 190 HCWs tested negative, SARS-CoV-2 serological testing was performed one month after the inclusion.

Findings

Of the 319 HCWs included, 67 (21.0%) were tested positive for SARS-CoV-2; two of them developed severe COVID-19. The proportion of smell and taste dysfunction was significantly higher in SARS-CoV-2 positive HCWs than in negative ones (38.8% vs 9.5% and 37.3% vs 10.7%, respectively, p<0.001). Of the 67 positive patients, 9.1% were tested positive for at least another respiratory pathogen (vs19.5%, p=0.07). The proportion of HCWs with a viral load > 5.0 log10cp/ml (Ct value <25) was less than 15% at 8 days after symptom onset; 12% of them were still positive after 40 days (Ct >37). More than 90% of culturable virus had a viral load > 4.5 log10cp/ml (Ct < 26) and were collected within 10 days after symptom onset. From HCWs tested negative, 6/190 (3.2%) exhibited seroconversion for IgG antibodies.

Interpretation

Our data suggest that the determination of normalized viral load (or its estimation through Ct values) can be useful for discontinuing isolation of HCWs and facilitating their safe return to work. HCWs presenting mild COVID-19 are unlikely infectious 10 days after symptom onset.

Funding

Fondation des Hospices Civils de Lyon. bioMérieux provided diagnostic kits.
Nowcasting and forecasting provincial-level SARS-CoV-2 case positivity using google search data in South Africa
Authors: Nsoesie Elaine O. , Sy Karla Therese L. , Oladeji Olubusola , Sefala Raesetje , Nichols Brooke E.
Published: November 2020

Data from non-traditional data sources, such as social media, search engines, and remote sensing, have previously demonstrated utility for disease surveillance. Few studies, however, have focused on countries in Africa, particularly during the SARS-CoV-2 pandemic. In this study, we use searches of COVID-19 symptoms, questions, and at-home remedies submitted to Google to model COVID-19 in South Africa, and assess how well the Google search data forecast short-term COVID-19 trends. Our findings suggest that information seeking trends on COVID-19 could guide models for anticipating COVID-19 trends and coordinating appropriate response measures.
Effectiveness of an Ozone Disinfecting and Sanitizing Cabinet to Decontaminate a Surrogate Virus for SARS-CoV-2 on N-95 Masks
Authors: Beaudry Megan S. , Frederick Julia C. , Lott Megan E. J. , Norfolk William A. , Glenn Travis C. , Lipp Erin K.
Published: November 2020

Medical demands during the COVID-19 pandemic have triggered a grave shortage of medical-grade personal protective equipment (PPE), especially, N95 respirators. N95 respirators are critical for the personal protection of medical providers and others when being exposed to individuals with infections caused by the SARS-CoV-2 coronavirus. To address the shortage of N95 respirators, innovative methods are needed to decontaminate coronaviruses from N95 respirators, allowing them to be safely reused by healthcare workers. For this research, we use a commercial ozone disinfecting cabinet to examine the efficacy of ozone-based disinfection of a conservative surrogate virus for SARS-CoV-2, the MS2 bacteriophage. Treatment of mask materials with enhanced ozone treatment resulted in 2.38-log 10 (>99%) reduction of phage from household dust masks and a range of 1.43-log 10 (96.2%) to 4-log 10 (99.99%) reductions of phage from common N95 mask materials.
Age and diet shape the genetic architecture of body weight in Diversity Outbred mice
Authors: Wright Kevin M. , Deighan Andrew , Di Francesco Andrea , Freund Adam , Jojic Vladimir , Churchill Gary , Raj Anil
Published: November 2020

Abstract

Understanding how genetic variation shapes an age-dependent complex trait relies on accurate quantification of both the additive genetic effects and genotype-environment interaction effects in an age-dependent manner. We used a generalization of the linear mixed model to quantify diet-dependent genetic contributions to body weight and growth rate measured from early development through adulthood of 960 Diversity Outbred female mice subjected to five dietary interventions. We observed that heritability of body weight remained substantially high (h2≈ 0.8) throughout adulthood under the 40% calorie restriction diet, while heritability, although still appreciably high, declined with age under all other dietary regimes. We identified 14 loci significantly associated with body weight in an age-dependent manner and 19 loci that contribute to body weight in an age- and diet-dependent manner. We found the effect of body weight alleles to be dynamic with respect to genomic background, age, and diet, identifying the scope of pleiotropy and several instances of allelic heterogeneity. In many cases, we fine-mapped these loci to narrow genomic intervals containing a few genes and impute putative functional variants from the genome sequence of the DO founders. Of the loci associated with body weight in a diet-dependent manner, many have been previously linked to neurological function and behavior in mice or humans. These results enable us to more fully understand the dynamics of the genetic architecture of body weight with age and in response to different dietary interventions, and to predict the effectiveness of dietary intervention on overall health in distinct genetic backgrounds.
Vascular cognitive impairment in the mouse reshapes visual, spatial network functional connectivity
Authors: Hall Gerard R , Boehm-Sturm Philipp , Dirnagl Ulrich , Finke Carsten , Foddis Marco , Harms Christoph , Koch Stefan Paul , Kuchling Joseph , Madan Christopher R , Mueller Susanne , Sassi Celeste , Sotiropoulos Stamatios N , Trueman Rebecca C , Wallis Marcus , Yildirim Ferah , Farr Tracy D
Published: November 2020

Connectome analysis of neuroimaging data is a rapidly expanding field to identify disease specific biomarkers. Structural diffusion MRI connectivity has been useful in individuals with radiological features of small vessel disease, such as white matter hyperintensities. Global efficiency, a network metric calculated from the structural connectome, is an excellent predictor of cognitive decline. To dissect the biological underpinning of these changes, animal models are required. We tested whether the structural connectome is altered in a mouse model of vascular cognitive impairment. White matter damage was more pronounced by 6 compared to 3 months. Global efficiency remained intact, but the visual association cortex exhibited increased structural connectivity with other brain regions. Exploratory resting state functional MRI connectivity analysis revealed diminished default mode network activity in the model compared to shams. Further perturbations were observed in a primarily cortical hub and the retrosplenial and visual cortices, and the hippocampus were the most affected nodes. Behavioural deficits were observed in the cued water maze, supporting the suggestion that the visual and spatial memory networks are affected. We demonstrate specific circuitry is rendered vulnerable to vascular stress in the mouse, and the model will be useful to examine pathophysiological mechanisms of small vessel disease.

Graphical abstract
A systemic whole-plant change in redox levels accompanies the rapid systemic response of Arabidopsis to wounding
Authors: Fichman Yosef , Mittler Ron
Published: November 2020

Reactive oxygen species (ROS) play a key role in regulating plant responses to different abiotic stresses, wounding and pathogen attack. In addition to triggering responses at the tissues directly subjected to stress, ROS were recently shown to mediate a rapid whole-plant systemic signal, termed the “ROS wave”, required for inducing a state of systemic acquired acclimation, or systemic wound response. However, whether the ROS wave that spreads from the local tissues subjected to wounding to the rest of the plant triggers alterations in redox levels, is mostly unknown at present. Here, using a genetically-encoded reporter for cellular glutathione redox changes, roGFP1, we show that the wounding-induced systemic ROS wave in Arabidopsis thaliana is accompanied by a rapid systemic wave of cytosolic redox oxidation, termed a “redox wave”. The ROS wave may therefore trigger changes in redox levels in systemic leaves that in turn can trigger transcriptional, metabolic and proteomic changes resulting in acclimation and/or systemic wound responses.

One sentence summary

The wounding-induced reactive oxygen species (ROS) wave is accompanied by a systemic whole-plant redox response.
BASE: a novel workflow to integrate non-ubiquitous genes in comparative genomics analyses for selection
Authors: Forni Giobbe , Ruggeri Angelo Alberto , Piccinini Giovanni , Luchetti Andrea
Published: November 2020

Inferring the selective forces that different ortholog genes underwent across different lineages can make us understand the evolutionary processes which shaped their extant diversity. The more widespread metric to estimate coding sequences selection regimes across across their sites and species phylogeny is the ratio of nonsynonymous to synonymous substitutions (dN/dS, also known asω). Nowadays, modern sequencing technologies and the large amount of already available sequence data allow the retrieval of thousands of genes orthology groups across large numbers of species. Nonetheless, the tools available to explore selection regimes are not designed to automatically process all orthogroups and practical usage is often restricted to those consisting of single-copy genes which are ubiquitous across the species considered (i.e.the subset of genes which is shared by all the species considered). This approach limits the scale of the analysis to a fraction of single-copy genes, which can be as lower as an order of magnitude in respect to non-ubiquitous ones (i.e.those which are not present across all the species considered). Here we present a workflow named BASE that - leveraging the CodeML framework - ease the inference and interpretation of selection regimes in the context of comparative genomics. Although a number of bioinformatics tools have already been developed to facilitate this kind of analyses, BASE is the first to be specifically designed to ease the integration of non-ubiquitous genes orthogroups. The workflow - along with all the relevant documentation - is available at github.com/for-giobbe/BASE.
DNAscent v2: Detecting Replication Forks in Nanopore Sequencing Data with Deep Learning
Authors: Boemo Michael A.
Published: November 2020

The detection of base analogues in Oxford Nanopore Technologies (ONT) sequencing reads has become a promising new method for the high-throughput measurement of DNA replication dynamics with single-molecule resolution. This paper introduces DNAscent v2, software that uses a residual neural network to achieve fast, accurate detection of the thymidine analogue BrdU with single-base resolution. DNAscent v2 comes equipped with an autoencoder that detects replication forks, origins, and termination sites in ONT sequencing reads from both synchronous and asynchronous cell populations, outcompeting previous versions and other tools across different experimental protocols. DNAscent v2 is open-source and available athttps://github.com/MBoemo/DNAscent.
Artemin and its cognate receptor, GFRα3, play a function role in osteoarthritis pain
Authors: Minnema Laura , Mishra Santosh K. , Lascelles B Duncan X
Published: November 2020

Osteoarthritis associated pain (OA-pain) is a significant global problem. OA-pain limits limb use and mobility, and is associated with widespread sensitivity. Therapeutic options are limited, and the ones that are available are often associated with side or adverse effects. The lack of therapeutic options is partly due to a lack of understanding of clinically relevant underlying neural mechanisms of OA-pain. In previous work in naturally occurring OA-pain in dogs, we identified potential signaling molecules (artemin/GFRα3) that were upregulated. Here, we use multiple approaches including knockout mice, immunological suppression in a mouse model of OA, and clinically relevant measures of sensitivity and limb use to explore the functional role of artemin/GFRα3 signaling in OA-pain. We found the monoiodoacetate (MIA)-induced OA model in mice is associated with decreased limb use and hypersensitivity. GFRα3 expression is increased in sensory neurons. Exogenous artemin induces heat, cold and mechanical hypersensitivity, and anti-artemin monoclonal antibody administration reverses this hypersensitivity and restores limb use in mice with MIA-induced OA pain. Our results provide a molecular basis of arthritis pain linked with artemin/GFRα3 signaling and indicate that further work is warranted to investigate the neuronal plasticity and the pathways that drive pain in OA.
Stability and Control of Biomolecular Circuits through Structure
Authors: Xiao Fangzhou , Khammash Mustafa , Doyle John C.
Published: November 2020

Due to omnipresent uncertainties and environmental disturbances, natural and engineered biological organisms face the challenging control problem of achieving robust performance using unreliable parts. The key to overcoming this challenge rests in identifying structures of biomolecular circuits that are largely invariant despite uncertainties, and building feedback control through such structures. In this work, we develop the tool of log derivatives to capture structures in how the production and degradation rates of molecules depend on concentrations of reactants. We show that log derivatives could establish stability of fixed points based on structure, despite large variations in rates and functional forms of models. Furthermore, we demonstrate how control objectives, such as robust perfect adaptation (i.e. step disturbance rejection), could be implemented through the structures captured. Due to the method’s simplicity, structural properties for analysis and design of biomolecular circuits can often be determined by a glance at the equations.
Age-related degradation of optic radiation white matter predicts visual, but not verbal executive functions
Authors: Webb Christina E. , Viera Perez Patricio M. , Hoagey David A. , Gonen Chen , Rodrigue Karen M. , Kennedy Kristen M.
Published: November 2020

Healthy aging is accompanied by degraded white matter connectivity, which has been suggested to contribute to cognitive dysfunction observed in aging, especially in relation to fluid measures of cognition. Prior research linking white matter microstructure and cognition, however, has largely been limited to major association and heteromodal white matter tracts. The optic radiations (OR), which transfer visual sensory-perceptual information from thalamic lateral geniculate nucleus to primary visual cortex, are generally considered lower-level input-relay white matter tracts. However, the role of this prominent white-matter visual relay system in supporting higher-order cognition is understudied, especially in regard to healthy aging. The present study used deterministic tractography to isolate OR fractional anisotropy (FA) in 130 participants aged 20-94 to assess age effects on OR tract white matter. We also examined associations between age-related differences in the OR and cognitive domains involving visual processing speed, and visual- and non-visual executive function (EF). OR microstructure, as indexed by FA, exhibited a significant linear decrease across age. A significant interaction between age, FA, and cognitive domain on cognitive task performance indicated that in older age, more degraded OR white matter was associated with poorer visual EF, but no age-related association between FA in the OR and visual processing speed or verbal EF was observed. These findings suggest the optic radiations are not merely sensory-perceptual relays, but also influence higher-order visual cognition differentially with age.
Northward range expansion of the European green crabCarcinus maenasin the SW Atlantic: a synthesis after ~20 years of invasion history
Authors: Malvé Mariano E. , Rivadeneira Marcelo M. , Gordillo Sandra
Published: November 2020

This study aims at synthesizing the recent invasion history ofCarcinus maenasin the SW Atlantic (~20 years), particularly the northward expansion, based on available published papers, technical reports, and new field surveys. Our analyses extend the known distribution range northwards ca. 330 km. totaling ~1000 km along the Argentinean coast since its last detection in Nuevo Gulf in 2015. The expansion rate appeared to slow down during the last 15 years (from 115km/yr. to 30 km/yr.) as the species continues moving northwards into the transition zone between the Magellan and Argentinean biogeographic provinces (41°–43°S). In addition, a species distribution model (SDM) is provided at a much finer spatial resolution than previous studies, which accurately foresees suitable areas of invasion in the southern San Jorge Gulf, and predicts a hotspot of invasibility around 40°–33°S° if the invasion continues northward. Potential impacts ofC. maenason native species, particularly economically important oyster beds are discussed.
Streamlined and quantitative detection of chimerism in mouse tissue using digital PCR
Authors: Suchy Fabian P. , Nishimura Toshiya , Wilkinson Adam C. , Higuchi Maimi , Bhadury Joydeep , Nakauchi Hiromitsu
Published: November 2020

Animal chimeras are widely used for biomedical discoveries, from developmental biology to cancer research. However, the accurate quantitation of mixed cell types in chimeric and mosaic tissues has challenges. Here, we have developed and characterized a droplet digital PCR single-nucleotide discrimination assay to detect chimerism among albino and non-albino mouse strains. In addition, we have validated that this assay is compatible with crude lysate from most organs, drastically streamlining sample preparation. This chimerism detection assay has many additional advantages over existing methods including its robust nature, minimal technical bias, and ability to report the total number of cells in a prepared sample. Importantly, the concepts developed and discussed here are readily adapted to other genomic loci to accurately measure mixed cell populations in any tissue.
Mechanistic inferences from analysis of measurements of protein phase transitions in live cells
Authors: Posey Ammon E. , Ruff Kiersten M. , Lalmansingh Jared M. , Kandola Tejbir S. , Lange Jeffrey J. , Halfmann Randal , Pappu Rohit V.
Published: November 2020

The combination of phase separation and disorder-to-order transitions can give rise to ordered, semi-crystalline fibrillar assemblies that underlie prion phenomena namely, the non-Mendelian transfer of information across cells. Recently, a method known as Distributed Amphifluoric Förster Resonance Energy Transfer (DAmFRET) was developed to study the convolution of phase separation and disorder-to-order transitions in live cells. In this assay, a protein of interest is expressed to a broad range of concentrations and the acquisition of local density and order, measured by changes in FRET, is used to map phase transitions for different proteins. The high-throughput nature of this assay affords the promise of uncovering sequence-to-phase behavior relationships in live cells. Here, we report the development of a supervised method to obtain automated and accurate classifications of phase transitions quantified using the DAmFRET assay. Systems that we classify as undergoing two-state discontinuous transitions are consistent with prion-like behaviors, although the converse is not always true. We uncover well-established and surprising new sequence features that contribute to two-state phase behavior of prion-like domains. Additionally, our method enables quantitative, comparative assessments of sequence-specific driving forces for phase transitions in live cells. Finally, we demonstrate that a modest augmentation of DAmFRET measurements, specifically time-dependent protein expression profiles, can allow one to apply classical nucleation theory to extract sequence-specific lower bounds on the probability of nucleating ordered assemblies. Taken together, our approaches lead to a useful analysis pipeline that enables the extraction of mechanistic inferences regarding phase transitions in live cells.
A Workflow of Integrated Resources to Catalyze Network Pharmacology Driven COVID-19 Research
Authors: Zahoránszky-Kőhalmi Gergely , Siramshetty Vishal B. , Kumar Praveen , Gurumurthy Manideep , Grillo Busola , Mathew Biju , Metaxatos Dimitrios , Backus Mark , Mierzwa Tim , Simon Reid , Grishagin Ivan , Brovold Laura , Mathé Ewy A. , Hall Matthew D. , Michael Samuel G. , Godfrey Alexander G. , Mestres Jordi , Jensen Lars J. , Oprea Tudor I.
Published: November 2020

Motivation

In the event of an outbreak due to an emerging pathogen, time is of the essence to contain or to mitigate the spread of the disease. Drug repositioning is one of the strategies that has the potential to deliver therapeutics relatively quickly. The SARS-CoV-2 pandemic has shown that integrating critical data resources to drive drug-repositioning studies, involving host-host, hostpathogen and drug-target interactions, remains a time-consuming effort that translates to a delay in the development and delivery of a life-saving therapy.

Results

Here, we describe a workflow we designed for a semi-automated integration of rapidly emerging datasets that can be generally adopted in a broad network pharmacology research setting. The workflow was used to construct a COVID-19 focused multimodal network that integrates 487 host-pathogen, 74,805 host-host protein and 1,265 drug-target interactions. The resultant Neo4j graph database named “Neo4COVID19” is accessible via a web interface and via API calls based on the Bolt protocol. We believe that our Neo4COVID19 database will be a valuable asset to the research community and will catalyze the discovery of therapeutics to fight COVID-19.

Availability

https://neo4covid19.ncats.io
Analysis of Genomes of Bacterial Isolates from Lameness Outbreaks in Broilers
Authors: Ekesi N. Simon , Dolka Beata , Alrubaye Adnan A.K. , Rhoads Douglas D.
Published: November 2020

We investigated lameness outbreaks at commercial broiler farms in Arkansas. From Bacterial Chondronecrosis with Osteomyelitis (BCO) lesions, we obtained different isolates of distinct bacterial species. Genome assemblies forEscherichia coliandStaphylococcus aureusisolates show that BCO-lameness pathogens on farms can differ significantly. Genomes assembled fromEscherichia coliisolates from three different farms were quite different from each other, and more similar to isolates from different hosts and geographical locations. The S aureus genomes were closely related to chicken isolates from Europe, and appear to have been restricted to chicken hosts for more than 40 years. Detailed analyses of genomes from this clade of chicken isolates with a sister clade of human isolates, suggests the acquisition of a particular pathogenicity island in the transition from human to chicken pathogen and that pathogenesis in chickens may depend on this mobile element. Phylogenomics is consistent with more frequent host shifts forE. coli, whileS. aureusappears to be highly host restricted. Isolate-specific genome characterizations will help further our understanding of the disease mechanisms and spread of BCO-lameness, a significant animal welfare issue.

Importance

Detailed inspection of the genome sequences of different bacterial species associated with causing lameness in broiler chickens reveals that one species,E. coli, appears to easily switch hosts from humans to chickens and other host species. Conversely, isolates ofS. aureusappear to be restricted to specific hosts. One potential mobile DNA element has been identified that may be critical for causing disease in chickens forS. aureus.
Rapid High Throughput Whole Genome Sequencing of SARS-CoV-2 by using One-step RT-PCR Amplification with Integrated Microfluidic System and Next-Gen Sequencing
Authors: Li Tao , Chung Hye Kyung , Pireku Papa K. , Beitzel Brett F. , Sanborn Mark A. , Tang Cynthia Y. , Hammer Richard , Ritter Detlef , Wan XiuFeng , Berry Irina Maljkovic , Hang Jun
Published: November 2020

The long-lasting global COVID-19 pandemic demands timely genomic investigation of SARS-CoV-2 viruses. Here we report a simple and efficient workflow for whole genome sequencing utilizing one-step RT-PCR amplification on a microfluidic platform, followed by MiSeq amplicon sequencing. The method uses Fluidigm IFC and instruments to amplify 48 samples with 39 pairs of primers in a single step. Application of this method on RNA samples from both viral isolate and clinical specimens demonstrate robustness and efficiency of this method in obtaining the full genome sequence of SARS-CoV-2.
Characteristics of three different chemiluminescence assays for testing for SARS-CoV-2 antibodies
Authors: Weber Myriam C. , Risch Martin , Thiel Sarah L. , Grossmann Kirsten , Nigg Susanne , Wohlwend Nadia , Lung Thomas , Hillmann Dorothea , Ritzler Michael , Ferrara Francesca , Bigler Susanna , Egli Konrad , Bodmer Thomas , Imperiali Mauro , Salimi Yacir , Fleisch Felix , Cusini Alexia , Heer Sonja , Renz Harald , Paprotny Matthias , Kohler Philipp , Vernazza Pietro , Risch Lorenz , Kahlert Christian R.
Published: November 2020

Several tests based on chemiluminescence immunoassay techniques have become available to test for SARS-CoV-2 antibodies. There is currently insufficient data on serology assay performance beyond 35 days after symptoms onset. We aimed to evaluate SARS-CoV-2 antibody tests on three widely used platforms. A chemiluminescent microparticle immunoassay (CMIA; Abbott Diagnostics, USA), a luminescence immunoassay (LIA; Diasorin, Italy), and an electrochemiluminescence immunoassay (ECLIA; Roche Diagnostics, Switzerland) were investigated. In a multi-group study, sensitivity was assessed in a group of participants with confirmed SARS-CoV-2 (n=145), whereas specificity was determined in two groups of participants without evidence of COVID-19 (i.e. healthy blood donors, n=191, and healthcare workers, n=1002). Receiver operating characteristic (ROC) curves, multilevel likelihood ratios (LR), and positive (PPV) and negative (NPV) predictive values were characterized. Finally, analytical specificity was characterized in samples with evidence of Epstein–Barr virus (EBV) (n=9), cytomegalovirus (CMV) (n=7) and endemic common cold coronavirus infections (n=12) taken prior to the current SARS-CoV-2 pandemic. The diagnostic accuracy was comparable in all three assays (AUC 0.98). Using the manufacturers’ cut-offs, the sensitivities were 90%, 95% confidence interval,[84,94] (LIA), 93% [88,96] (CMIA), and 96% [91,98] (ECLIA). The specificities were 99.5% [98.9,99.8](CMIA) 99.7% [99.3,99,9] (LIA) and 99.9% [99.5,99.98] (ECLIA). The LR at half of the manufacturers’ cut-offs were 60 (CMIA), 82 (LIA), and 575 (ECLIA) for positive and 0.043 (CMIA) and 0.035 (LIA, ECLIA) for negative results. ECLIA had higher PPV at low pretest probabilities than CMIA and LIA. No interference with EBV or CMV infection was observed, whereas endemic coronavirus in some cases provided signals in LIA and/or CMIA. Although the diagnostic accuracy of the three investigated assays is comparable, their performance in low-prevalence settings is different. Introducing gray zones at half of the manufacturers’ cut-offs is suggested, especially for orthogonal testing approaches that use a second assay for confirmation.
A Randomized Controlled Trial to Increase Cancer Screening and Reduce Depression among Low-Income Women
Authors: Tobin Jonathan N. , Weiss Elisa S. , Cassells Andrea , Lin TJ , Carrozzi Gianni , Barsanti Franco , Morales Alejandra , Mailing Alison , Espejo Maria , Gilbert Erica , Casano Louann , O’Hara-Cicero Ellen , Weed John , Dietrich Allen J.
Published: November 2020

Background

Women from low-income, racial/ethnic minority backgrounds receive fewer cancer screenings than other womenandhave higher rates of depression, which can interfere with cancer screening participation.

Objective

Assess the comparative effectiveness of two interventions to improve breast, cervical, and colorectal cancer screening and reduce depression among underserved women with depressive symptoms.

Design

Randomized comparative effectiveness trial

Setting

Six Federally Qualified Health Centers

Participants

N=757, 50-64 years with depression symptoms and overdue for cancer screening.

Interventions

Participants were randomized to collaborative depression care plus cancer screening intervention (Collaborative Care Intervention, CCI) or cancer screening intervention alone (Prevention Care Management, PCM). Both of these evidence-based, telephone interventions were delivered in English or Spanish, for up to 12 months, by care managers.

Measurements

Electronic Health Records provided cancer screening data (primary outcome). PHQ-9 measured depression at study entry (T0), 6- and 12-months post-baseline (T1 and T2, respectively; secondary outcome).

Results

Analyses revealed statistically significant increases in up-to-date status for all cancer screenings; depression improved in both intervention groups. There were no statistically significant differences between the two interventions in improving cancer screening rates or reducing depression.

Limitations

Depressive symptom improvement may be explained by typical symptom remission. The study duration (12-months) was insufficient to evaluate intervention effects on long-term cancer screening behavior and depression. This study was not powered for site-level analysis.

Conclusions

CCI and PCM both improved breast, cervical, and colorectal cancer screening and depression in clinical settings in underserved communities, however neither intervention showed an advantage in outcomes. Decisions about which approach to implement may depend on the nature of the practice and alignment of the interventions with other ongoing priorities and resources.

Funding source

This study was funded by Patient Centered Outcomes Research Institute (PCORI) (IH-12-11-4522) with additional infrastructure support from Agency for Healthcare Research and Quality (AHRQ) (5P30-HS-021667).
Relationship of sleep homeostasis to seizures and cognition in children with focal epilepsy
Authors: Eriksson Maria H , Baldeweg Torsten , Pressler Ronit , Boyd Stewart G , Huber Reto , Cross J Helen , Bölsterli Bigna K , Chan Samantha YS
Published: November 2020

Objective

Sleep disruption and cognitive impairment are important co-morbidities in childhood epilepsy, yet a mechanistic link has not been substantiated. Slow wave activity during sleep and its homeostatic decrease across the night is associated with synaptic renormalisation, and shows maturational changes over the course of childhood. Here, we aimed to investigate the effect of epilepsy on sleep homeostasis in the developing brain.

Methods

We examined the relationship of sleep homeostasis as reflected in slow wave activity to seizures, cognition and behaviour, comparing 22 children (aged 6 to 16 years) with focal epilepsy to 21 age-matched healthy controls. Participants underwent overnight sleep EEG and IQ testing and performed memory consolidation tasks. Their parents completed standard behavioural questionnaires.

Results

Children with epilepsy had lower slow wave activity at the start of non-rapid eye movement (NREM) sleep, though similar overnight decline and slow wave activity in the final hour of NREM sleep. Both groups displayed an antero-posterior shift in peak slow wave activity overnight, though individual patients showed persistent local increases at scalp locations matching those of focal interictal discharges. Patients who had seizures during their admission had lower early-night slow wave activity, the group without seizures showing similar activity to controls. We found a positive correlation between full scale IQ and early-night slow wave activity in patients but not controls.

Interpretation

Reduced early night slow wave activity in children with focal epilepsies is correlated with lower cognitive ability and more seizures and may reflect a reduction in learning-related synaptic potentiation.
Transcription and splicing dynamics during early Drosophila development
Authors: Prudêncio Pedro , Savisaar Rosina , Rebelo Kenny , Martinho Rui Gonçalo , Carmo-Fonseca Maria
Published: November 2020

Widespread co-transcriptional splicing has been demonstrated from yeast to human. However, most studies to date addressing the kinetics of splicing relative to transcription used either Saccharomyces cerevisiae or metazoan cultured cell lines. Here, we adapted native elongating transcript sequencing technology (NET-seq) to measure co-transcriptional splicing dynamics during the early developmental stages of Drosophila melanogaster embryos. Our results reveal the position of RNA polymerase II (Pol II) when both canonical and recursive splicing occur. We found heterogeneity in splicing dynamics, with some RNAs spliced immediately after intron transcription, whereas for other transcripts no splicing was observed over the first 100 nucleotides of the downstream exon. Introns that show splicing completion before Pol II has reached the end of the downstream exon are necessarily intron-defined. We studied the splicing dynamics of both nascent pre-mRNAs transcribed in the early embryo, which have few and short introns, as well as pre-mRNAs transcribed later in embryonic development, which contain multiple long introns. As expected, we found a relationship between the proportion of spliced reads and intron size. However, intron definition was observed at all intron sizes. We further observed that genes transcribed in the early embryo tend to be isolated in the genome whereas genes transcribed later are often overlapped by a neighboring convergent gene. In isolated genes, transcription termination occurred soon after the polyadenylation site, while in overlapped genes Pol II persisted associated with the DNA template after cleavage and polyadenylation of the nascent transcript. Taken together, our data unravels novel dynamic features of Pol II transcription and splicing in the developing Drosophila embryo.
Spatially resolved transcriptomics reveals the architecture of the tumor/microenvironment interface
Authors: Hunter Miranda V. , Moncada Reuben , Weiss Joshua M. , Yanai Itai , White Richard M.
Published: November 2020

During tumor progression, cancer cells come into contact with novel non-tumor cell types, but it is unclear how tumors adapt to these new environments. Here, we integrate spatially resolved transcriptomics, single-cell RNA-seq, and single-nucleus RNA-seq to characterize tumor-microenvironment interactions at the tumor boundary. Using a zebrafish model of melanoma, we identify a distinct “interface” cell state where the tumor contacts neighboring tissues. This interface is composed of specialized tumor and microenvironment cells that upregulate a common set of cilia genes, and cilia proteins are enriched only where the tumor contacts the microenvironment. Cilia gene expression is regulated by ETS-family transcription factors, which normally act to suppress cilia genes outside of the interface. An ETS-driven interface is conserved in human patient samples, suggesting it is a conserved feature of human melanoma. Our results demonstrate the power of spatially resolved transcriptomics in uncovering mechanisms that allow tumors to adapt to new environments.
Chromosome Integrity is Required for the Initiation of Meiotic Sex Chromosome Inactivation inCaenorhabditis elegans
Authors: Rappaport Yisrael , Achache Hanna , Falk Roni , Murik Omer , Ram Oren , Tzur Yonatan B.
Published: November 2020

During meiosis of heterogametic cells, such as XY meiocytes, sex chromosomes of many species undergo transcriptional silencing known as meiotic sex chromosome inactivation (MSCI). Silencing also occurs in aberrantly unsynapsed autosomal chromatin. The silencing of unsynapsed chromatin, is assumed to be the underline mechanism for MSCI. Initiation of MSCI is disrupted in meiocytes with sex chromosome-autosome translocations. Whether this is due to aberrant synapsis or the lack of sex chromosome integrity has never been determined. To address this, we used CRISPR to engineerCaenorhabditis elegansstable strains with broken X chromosomes that didn’t undergo translocations with autosomes. In early meiotic nuclei of these mutants, the X fragments lack silent chromatin modifications and instead the fragments are enriched with transcribing chromatin modifications. Moreover, the level of active RNA polymerase II staining on the X fragments in mutant nuclei is similar to that on autosomes, indicating active transcription on the X. Contrary to previous models, which predicted that any unsynapsed chromatin is silenced during meiosis, X fragments that did not synapse were robustly stained with RNA polymerase II and gene expression levels were high throughout the broken X. Therefore, lack of synapsis does not trigger MSCI if sex chromosome integrity is lost. Moreover, our results suggest that a unique character of the chromatin of sex chromosomes underlies their lack of meiotic silencing due to both unsynapsed chromatin and sex chromosome mechanisms when their integrity is lost.
Mevalonate pathway-mediated ER homeostasis is required for haploid stability in human somatic cells
Authors: Yaguchi Kan , Sato Kimino , Yoshizawa Koya , Banhegyi Gabor , Margittai Eva , Uehara Ryota
Published: November 2020

The somatic haploidy is unstable in diplontic animals, but cellular processes determining haploid stability remain elusive. Here, we found that inhibition of mevalonate pathway by pitavastatin, a widely used cholesterol-lowering drug, drastically destabilized the haploid state in HAP1 cells. Interestingly, cholesterol supplementation did not restore haploid stability in pitavastatin-treated cells, and cholesterol inhibitor U18666A did not phenocopy haploid destabilization. These results ruled out the involvement of cholesterol in haploid stability. Besides cholesterol perturbation, pitavastatin induced endoplasmic reticulum (ER) stress, the suppression of which by a chemical chaperon significantly restored haploid stability in pitavastatin-treated cells. Our data demonstrate the involvement of the mevalonate pathway in the stability of the haploid state in human somatic cells through managing ER stress, highlighting a novel link between ploidy and ER homeostatic control.
The N-terminal domain of spike glycoprotein mediates SARS-CoV-2 infection by associating with L-SIGN and DC-SIGN
Authors: Soh Wai Tuck , Liu Yafei , Nakayama Emi E. , Ono Chikako , Torii Shiho , Nakagami Hironori , Matsuura Yoshiharu , Shioda Tatsuo , Arase Hisashi
Published: November 2020

The widespread occurrence of SARS-CoV-2 has had a profound effect on society and a vaccine is currently being developed. Angiotensin-converting enzyme 2 (ACE2) is the primary host cell receptor that interacts with the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein. Although pneumonia is the main symptom in severe cases of SARS-CoV-2 infection, the expression levels of ACE2 in the lung is low, suggesting the presence of another receptor for the spike protein. In order to identify the additional receptors for the spike protein, we screened a receptor for the SARS-CoV-2 spike protein from the lung cDNA library. We cloned L-SIGN as a specific receptor for the N-terminal domain (NTD) of the SARS-CoV-2 spike protein. The RBD of the spike protein did not bind to L-SIGN. In addition, not only L-SIGN but also DC-SIGN, a closely related C-type lectin receptor to L-SIGN, bound to the NTD of the SARS-CoV-2 spike protein. Importantly, cells expressing L-SIGN and DC-SIGN were both infected by SARS-CoV-2. Furthermore, L-SIGN and DC-SIGN induced membrane fusion by associating with the SARS-CoV-2 spike protein. Serum antibodies from infected patients and a patient-derived monoclonal antibody against NTD inhibited SARS-CoV-2 infection of L-SIGN or DC-SIGN expressing cells. Our results highlight the important role of NTD in SARS-CoV-2 dissemination through L-SIGN and DC-SIGN and the significance of having anti-NTD neutralizing antibodies in antibody-based therapeutics.
Molecular mechanism of high affinity sugar transport in plants unveiled by structures of glucose/H+symporter STP10
Authors: Bavnhøj Laust , Paulsen Peter Aasted , Flores-Canales Jose C. , Schiøtt Birgit , Pedersen Bjørn Panyella
Published: November 2020

Sugars are essential sources of energy and carbon, and also function as key signaling molecules in plants. Sugar Transport Proteins (STP) are proton-coupled symporters, solely responsible for uptake of glucose from the apoplastic compartment into cells in all plant tissues. They are integral to organ development in symplastically isolated tissues such as seeds, pollen and fruit. Additionally, STPs play a significant role in plant responses to both environmental stressors such as dehydration, and prevalent fungal infections like rust and mildew. Here, we present two high-resolution crystal structures of the outward-occluded and inward-open conformations ofArabidopsis thalianaSTP10 with glucose and protons bound. The two structures describe key states in the STP transport cycle. Together within vivobiochemical analysis and Molecular Dynamics simulations they pinpoint structural elements that explain how STPs exhibit high affinity for sugar binding on the extracellular side and how it is considerably lowered on the intracellular side to facilitate substrate release. These structural elements, conserved in all STPs across plant species, clarify the basis of proton-to-glucose coupling, essential for symport. The results advance our understanding of a key molecular mechanism behind plant organ development, and sets the stage for novel bioengineering strategies in crops that could target seeds, fruits and plant resistance to fungal infections.
Immunocompetent Mouse Model for Crimean-Congo Hemorrhagic Fever Virus
Authors: Hawman David W. , Meade-White Kimberly , Leventhal Shanna , Feldmann Friederike , Okumura Atsushi , Smith Brian , Scott Dana , Feldmann Heinz
Published: November 2020

Crimean-Congo hemorrhagic fever (CCHF) is a severe tick-borne febrile illness with wide geographic distribution. CCHF is caused by infection with the Crimean-Congo hemorrhagic fever virus (CCHFV) and case fatality rates can be as high as 30%. Despite causing severe disease in humans, our understanding of the host and viral determinants of CCHFV pathogenesis are limited. A major limitation in the investigation of CCHF has been the lack of suitable small animal models. Wild-type mice are resistant to clinical isolates of CCHFV and consequently, mice must be deficient in type I interferon responses to study the more severe aspects of CCHFV. We report here a mouse-adapted variant of CCHFV that recapitulates in adult, immunocompetent mice the severe CCHF observed in humans. This mouse-adapted variant of CCHFV significantly improves our ability to study host and viral determinants of CCHFV-induced disease in a highly tractable mouse model.