bluuebunny/crossref_metadata_2025 huggingface dataset:
A potent neutralizing nanobody against SARS-CoV-2 with inhaled delivery potential
Authors: Gai Junwei , Ma Linlin , Li Guanghui , Zhu Min , Qiao Peng , Li Xiaofei , Zhang Haiwei , Zhang Yanmin , Chen Yadong , Ji Weiwei , Zhang Hao , Cao Huanhuan , Li Xionghui , Gong Rui , Wan Yakun
Published: August 2020

The outbreak of COVID-19 has emerged as a global pandemic. The unprecedented scale and severity call for rapid development of effective prophylactics or therapeutics. We here reported Nanobody (Nb) phage display libraries derived from four camels immunized with the SARS-CoV-2 spike receptor-binding domain (RBD), from which 381 Nbs were identified to recognize SARS-CoV-2-RBD. Furthermore, seven Nbs were shown to block interaction of human angiotensin converting enzyme 2 (ACE2) with SARS-CoV-2-RBD-variants, bat-SL-CoV-WIV1-RBD and SARS-CoV-1-RBD. Among the seven candidates, Nb11-59 exhibited the highest activity against authentic SARS-CoV-2 with ND50 of 0.55 μg/mL. Nb11-59 can be produced on a large-scale in Pichia pastoris, with 20 g/L titer and 99.36% purity. It also showed good stability profile, and nebulization did not impact its stability. Overall, Nb11-59 might be a promising prophylactic and therapeutic molecule against COVID-19, especially through inhalation delivery.

Graphical Abstract
Brain-wide mapping of neural activity mediating collicular-dependent behaviors
Authors: Sans-Dublanc Arnau , Chrzanowska Anna , Reinhard Katja , Lemmon Dani , Montaldo Gabriel , Urban Alan , Farrow Karl
Published: August 2020

Neuronal cell-types are arranged in brain-wide circuits to guide behavior. In mice, the superior colliculus is comprised of a set of cell-types that each innervate distinct downstream targets. Here we reveal the brain-wide networks downstream of four collicular cell-types by combining functional ultrasound imaging (fUSi) with optogenetics to monitor neural activity at a resolution of ~100 μm. Each neuronal group triggered different behaviors, and activated distinct, partially overlapping sets of brain nuclei. This included regions not previously thought to mediate defensive behaviors, e.g. the posterior paralaminar nuclei of the thalamus (PPnT), that we show to play a role in suppressing habituation. Electrophysiological recordings support the fUSi findings and show that neurons in the downstream nuclei preferentially respond to innately threatening visual stimuli. This work provides insight into the functional organization of the networks governing defensive behaviors and demonstrates an experimental approach to explore the whole-brain neuronal activity downstream of targeted cell-types.
DC/L-SIGN recognition of spike glycoprotein promotes SARS-CoV-2 trans-infection and can be inhibited by a glycomimetic antagonist
Authors: Thépaut Michel , Luczkowiak Joanna , Vivès Corinne , Labiod Nuria , Bally Isabelle , Lasala Fátima , Grimoire Yasmina , Fenel Daphna , Sattin Sara , Thielens Nicole , Schoehn Guy , Bernardi Anna , Delgado Rafael , Fieschi Franck
Published: August 2020

The efficient spread of SARS-CoV-2 resulted in a pandemic that is unique in modern history. Despite early identification of ACE2 as the receptor for viral spike protein, much remains to be understood about the molecular events behind viral dissemination. We evaluated the contribution of C-type lectin receptors (CLRS) of antigen-presenting cells, widely present in air mucosa and lung tissue. DC-SIGN, L-SIGN, Langerin and MGL bind to diverse glycans of the spike using multiple interaction areas. Using pseudovirus and cells derived from monocytes or T-lymphocytes, we demonstrate that while virus capture by the CLRs examined does not allow direct cell infection, DC/L-SIGN, among these receptors, promote virus transfer to permissive ACE2+ cells. A glycomimetic compound designed against DC-SIGN, enable inhibition of this process. Thus, we described a mechanism potentiating viral capture and spreading of infection. Early involvement of APCs opens new avenues for understanding and treating the imbalanced innate immune response observed in COVID-19 pathogenesis
The tiny Cretaceous stem-birdOculudentavisrevealed as a bizarre lizard
Authors: Bolet Arnau , Stanley Edward L. , Daza Juan D. , Arias J. Salvador , Čerňanský Andrej , Vidal-García Marta , Bauer Aaron M. , Bevitt Joseph J. , Peretti Adolf , Evans Susan E.
Published: August 2020

Oculudentavis khaungraaewas described based on a tiny skull trapped in amber. The slender tapering rostrum with retracted osseous nares, large eyes, and short vaulted braincase led to its identification as the smallest avian dinosaur on record, comparable to the smallest living hummingbirds. Despite its bird-like appearance,Oculudentavisshowed several features inconsistent with its original phylogenetic placement. Here we describe a more complete, specimen that demonstratesOculudentavisis actually a bizarre lizard of uncertain position. The new interpretation and phylogenetic placement highlights a rare case of convergent evolution rarely seen among reptiles. Our results re-affirm the importance of Myanmar amber in yielding unusual taxa from a forest ecosystem rarely represented in the fossil record.
Identification of spacer and protospacer sequence requirements in theVibrio choleraeType I-E CRISPR/Cas System
Authors: Bourgeois Jacob , Lazinski David W. , Camilli Andrew
Published: August 2020

The prokaryotic adaptive immune system CRISPR/Cas serves as defense against bacteriophage and invasive nucleic acid. A Type I-E CRISPR/Cas system has been detected in classical biotype isolates ofVibrio cholerae, the causative agent of the disease cholera. Experimental characterization of this system revealed a functional immune system that operates using a 5’-TT-3’ protospacer-adjacent motif (PAM) for interference. However, several designed spacers against the 5’-TT-3’ PAM do not interfere as expected, indicating further investigation of this system is necessary. In this study, we identified additional sequence requirements of a pyrimidine in the 5’ position of the spacer and purine in the complementary position of the protospacer using 873 unique spacers and 2267 protospacers mined from CRISPR arrays in deposited sequences ofV. cholerae. We present bioinformatic evidence that during acquisition the protospacer purine is captured in the prespacer and that a 5’-RTT-3’ PAM is necessary for spacer acquisition. Finally, we demonstrate experimentally that a 5’-RTT-3’ PAM is necessary for CRISPR interference by designing and manipulating spacer and cognate PAMs in a plasmid conjugation assay and discover functional consequences of base pairing with the 5’ spacer pyrimidine in spacer efficacy.

Importance

Bacterial CRISPR/Cas systems provide immunity by defending against phage and other invading elements. A thorough comprehension of the molecular mechanisms employed by these diverse systems will improve our understanding of bacteriophage-bacterial interactions and bacterial adaptation to foreign DNA. TheVibrio choleraeType I-E system was previously identified in an extinct classical biotype and was partially characterized for its function. Here, using both bioinformatic and functional assays, we extend that initial study. We have found that the Type I-E system still exists in modern strains ofV. cholerae. Furthermore, we defined additional sequence elements in both the CRISPR array and in target DNA that are required for immunity. CRISPR/Cas systems are now commonly used as precise and powerful genetic engineering tools. Knowledge of the sequences required for CRISPR/Cas immunity is a prerequisite for the effective design and experimental use of these systems. Our results greatly facilitate the effective use of one such system. Furthermore, we provide a publicly available script that assists in the detection and validation of CRISPR/Cas immunity requirements when such a system exists in any bacterial species.
Feature selection and causal analysis for microbiome studies in the presence of confounding using standardization
Authors: Goren Emily , Wang Chong , He Zhulin , Sheflin Amy M , Chiniquy Dawn , Prenni Jessica E , Tringe Susannah , Schachtman Daniel P , Liu Peng
Published: August 2020

Background

Microbiome studies have uncovered associations between microbes and human, animal, and plant health outcomes. This has led to an interest in developing microbial interventions for treatment of disease and optimization of crop yields which requires identification of microbiome features that impact the outcome in the population of interest. That task is challenging because of the high dimensionality of microbiome data and the confounding that results from the complex and dynamic interactions among host, environment, and microbiome. In the presence of such confounding, variable selection and estimation procedures may have unsatisfactory performance in identifying microbial features with an effect on the outcome.

Results

In this manuscript, we aim to estimate population-level effects of individual microbiome features while controlling for confounding by a categorical variable. Due to the high dimensionality and confounding-induced correlation between features, we propose feature screening, selection, and estimation conditional on each stratum of the confounder followed by a standardization approach to estimation of population-level effects of individual features.

Comprehensive simulation studies demonstrate the advantages of our approach in recovering relevant features. Utilizing a potential-outcomes framework, we outline assumptions required to ascribe causal, rather than associational, interpretations to the identified microbiome effects. We conducted an agricultural study of the rhizosphere microbiome of sorghum in which nitrogen fertilizer application is a confounding variable. In this study, the proposed approach identified microbial taxa that are consistent with biological understanding of potential plant-microbe interactions.

Conclusions

Standardization enables more accurate identification of individual microbiome features with an effect on the outcome of interest compared to other variable selection and estimation procedures when there is confounding by a categorical variable.
Discovery of COVID-19 Inhibitors Targeting the SARS-CoV2 Nsp13 Helicase
Authors: White Mark Andrew , Lin Wei , Cheng Xiaodong
Published: August 2020

The raging COVID-19 pandemic caused by SARS-CoV2 has infected millions of people and killed several hundred thousand patients worldwide. Currently, there are no effective drugs or vaccines available for treating coronavirus infections. In this study, we have focused on the SARS-CoV2 helicase (Nsp13), which is critical for viral replication and the most conserved non-structural protein within the coronavirus family. Using homology modeling and molecular dynamics approaches, we generated structural models of the SARS-CoV2 helicase in its apo- and ATP/RNA-bound conformations. We performed virtual screening of ~970,000 chemical compounds against the ATP binding site to identify potential inhibitors. Herein, we report docking hits of approved human drugs targeting the ATP binding site. Importantly, two of our top drug hits have significant activity in inhibiting purified recombinant SARS-CoV-2 helicase, providing hope that these drugs can be potentially repurposed for the treatment of COVID-19.
Comparison of polygenic risk scores for coronary artery disease highlights obstacles to overcome for clinical use
Authors: Trochet Holly , Pelletier Justin , Tadros Rafik , Hussin Julie G
Published: August 2020

Polygenic risk scores, or PRS, are a tool to estimate individuals’ liabilities to a disease or trait measurement based solely on genetic information. One commonly discussed potential use is in the clinic to identify people who are at greater risk of developing a disease. In this paper, we compare three PRS models that incorporate a large number of genetic markers for coronary artery disease (CAD). In the UK Biobank, the cohort which was used at some point in the creation or validation of each score, we calculated the association between CAD, the scores, and population structure for the white British subset. After adjusting for geographic and socioeconomic factors, CAD was not associated with the first principal components of genetic diversity, which reflect fine-scale population structure. In contrast, all three scores were confounded by these genetic components, highlighting that PRS may be influenced by genetic factors not directly causal for CAD, thereby raising concerns about their biases in clinical application.Furthermore, we investigated the differences in risk stratification using four different UK Biobank assessment centers as separate cohorts, and tested how missing genetic data affected risk stratification through simulation. We show that missing data impact classification for extreme individuals for high- and low-risk, and quantiles of risk are sensitive to individual-level genotype missingness. Distributions of scores varied between assessment centers, revealing that thresholding based on quantiles can be problematic for consistency across centers and populations. Based on these results, we discuss potential avenues of improvements of PRS methodologies for usage in clinical practice.
Anatomical modeling of brain vasculature in two-photon microscopy by generalizable deep learning
Authors: Tahir Waleed , Kura Sreekanth , Zhu Jiabei , Cheng Xiaojun , Damseh Rafat , Tadesse Fetsum , Seibel Alex , Lee Blaire S. , Lesage Frédéric , Sakadžié Sava , Boas David A. , Tian Lei
Published: August 2020

Objective and Impact Statement

Segmentation of blood vessels from two-photon microscopy (2PM) angiograms of brains has important applications in hemodynamic analysis and disease diagnosis. Here we develop a generalizable deep learning technique for accurate 2PM vascular segmentation of sizable regions in mouse brains acquired from multiple 2PM setups. The technique is computationally efficient, thus ideal for large-scale neurovascular analysis.

Introduction

Vascular segmentation from 2PM angiograms is an important first step in hemodynamic modeling of brain vasculature. Existing segmentation methods based on deep learning either lack the ability to generalize to data from different imaging systems, or are computationally infeasible for large-scale angiograms. In this work, we overcome both these limitations by a method that is generalizable to various imaging systems, and is able to segment large-scale angiograms.

Methods

We employ a computationally efficient deep learning framework with a loss function that incorporates a balanced binary-cross-entropy loss and a total variation regularization on the network’s output. Its effectiveness is demonstrated on experimentally acquired in-vivo angiograms from mouse brains of dimensions up to 808×808×702 μm.

Results

To demonstrate the superior generalizability of our framework, we train on data from only one 2PM microscope, and demonstrate high-quality segmentation on data from a different microscope without any network tuning. Overall, our method demonstrates 10× faster computation in terms of voxels-segmented-per-second and 3× larger depth compared to the state-of-the-art.

Conclusion

Our work provides a generalizable and computationally efficient anatomical modeling framework for brain vasculature, which consists of deep learning based vascular segmentation followed by graphing. It paves the way for future modeling and analysis of hemodynamic response at much greater scales that were inaccessible before.
Nonstructural protein 1 of SARS-CoV-2 is a potent pathogenicity factor redirecting host protein synthesis machinery toward viral RNA
Authors: Yuan Shuai , Peng Lei , Park Jonathan J. , Hu Yingxia , Devarkar Swapnil C. , Dong Matthew B. , Wu Shenping , Chen Sidi , Lomakin Ivan , Xiong Yong
Published: August 2020

The COVID-19 pandemic affects millions of people worldwide with a rising death toll. The causative agent, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), uses its nonstructural protein 1 (Nsp1) to redirect host translation machinery to the viral RNA by binding to the ribosome and suppressing cellular, but not viral, protein synthesis through yet unknown mechanisms. We show here that among all viral proteins, Nsp1 has the largest impact on host viability in the cells of human lung origin. Differential expression analysis of mRNA-seq data revealed that Nsp1 broadly alters the transcriptome in human cells. The changes include repression of major gene clusters in ribosomal RNA processing, translation, mitochondria function, cell cycle and antigen presentation; and induction of factors in transcriptional regulation. We further gained a mechanistic understanding of the Nsp1 function by determining the cryo-EM structure of the Nsp1-40S ribosomal subunit complex, which shows that Nsp1 inhibits translation by plugging the mRNA entry channel of the 40S. We also determined the cryo-EM structure of the 48S preinitiation complex (PIC) formed by Nsp1, 40S, and the cricket paralysis virus (CrPV) internal ribosome entry site (IRES) RNA, which shows that this 48S PIC is nonfunctional due to the incorrect position of the 3’ region of the mRNA. Results presented here elucidate the mechanism of host translation inhibition by SARS-CoV-2, provide insight into viral protein synthesis, and furnish a comprehensive understanding of the impacts from one of the most potent pathogenicity factors of SARS-CoV-2.

Highlights

ORF screen identified Nsp1 as a major cellular pathogenicity factor of SARS-CoV-2

Nsp1 broadly alters the gene expression programs in human cells

Nsp1 inhibits translation by blocking mRNA entry channel

Nsp1 prevents physiological conformation of the 48S PIC
Trans-cinnamaldehyde potently killsEnterococcus faecalisbiofilm cells and prevents biofilm recovery
Authors: Ali Islam A. A. , Cheung Becky P. K. , Matinlinna Jukka. P. , Lévesque Celine M. , Neelakantan Prasanna
Published: August 2020

Enterococcus faecalisis a biofilm-forming, nosocomial pathogen that is frequently isolated from failed root canal treatments. Contemporary root canal disinfectants are ineffective in eliminating these biofilms and preventing reinfection. As a result, there is a pressing need to identify novel and safe antibiofilm molecules. The effect of short-term (5 and 15 min) and long-term (24 h) treatments of TC on the viability ofE. faecalisbiofilms was compared with currently used root canal disinfectants. Treatment for 15 min with TC reduced biofilm metabolic activity as effective as 1% sodium hypochlorite and 2% chlorhexidine. Treatment with TC for 24 h was significantly more effective than 2% chlorhexidine in reducing the viable cell counts of biofilms. This serendipitous effect of TC was sustained for 10 days under growth-favoring conditions. For the first time, our study highlights the strong antibacterial activity of TC againstE. faecalisbiofilms, and notably, its ability to prevent biofilm recovery after treatment.
Bmp8a Is a Novel Player in Regulation of Antiviral Immunity
Authors: Zhong Shenjie , Li Haoyi , Wang Yun-Sheng , Wang Ying , Ji Guangdong , Li Hong-Yan , Zhang Shicui , Liu Zhenhui
Published: August 2020

Bone morphogenetic protein (BMP) is a kind of classical multi-functional growth factor that plays a vital role in the formation and maintenance of bone, cartilage, muscle, blood vessels, and the regulation of energy balance. Whether BMP plays a role in antiviral immunity is unknown. Here we demonstrate that Bmp8a is a newly-identified positive regulator for antiviral immune responses. Thebmp8a−/−zebrafish, when infected with the viruses of GCRV, SVCV or TSVDV, show significantly reduced antiviral immunity, increased viral load and morbidity. We also show for the first time that Bmp8a interacts with Alk6a, which promotes the phosphorylation of Tbk1 and Irf3 through p38 MAPK pathway, and induces the production of type I IFNs in response to virus infection. Upon virus infection,bmp8aexpression is activated through the binding of Stat1a/Stat1b to the GAS motifs inbmp8apromoter region, enlarging the antiviral innate immune signal. Our study uncovers a previously unrecognized role of Bmp8a in regulation of antiviral immune responses and provides a new target for controlling viral infection.
On the numbers of infected and deceased in the second Corona wave
Authors: Janssen Rainer , Mimkes Juergen
Published: August 2020

In Germany and other countries, a second wave of corona infections has been observed since July 2020, after the first wave has subsided. We have investigated both waves by a modified SIR-SI infection model, adapted to the data to the Robert-Koch-Institute (RKI) or the Johns-Hopkins-University (JHU).

The first wave is characterized by the SIR model: in a perfect lockdown only a small part of the society is infected and the infections end after a certain time. The SI part considers the incompleteness of any lockdown: at the end of the first wave infections do not completely go down to zero, but continue to rise again, but only slowly due to mouth protection, hygiene and distance keeping. During this first wave the number of deceased people follows the number of infected persons with a fixed time interval and percentage: mostly symptomatic ill people have been tested. This applied to nearly all countries observed, with different intervals and percentages.

In the present second wave, the number of daily infections has risen again significantly in some countries, and it may be questioned whether this is due to the increased number of tests. The answer may be given by looking at the daily number of deaths. In Germany, Austria, Italy, Great Britain and others this number has still remained at a constant level for six weeks. In these countries a second wave of died people has not yet arrived. The increased number of tests include obviously mostly asymptomatically infected persons, who do not fall ill or die from coronavirus. However, in some countries, like USA or Israel, the second wave did arrive. The numbers of infected and deceased people both have grown. A real second wave is a permanent threat to all countries.
Disentangling craving- and valence-driven brain responses to smoking cues in individuals with nicotine use disorder
Authors: Haugg Amelie , Manoliu Andrei , Sladky Ronald , Hulka Lea M. , Kirschner Matthias , Brühl Annette B. , Seifritz Erich , Quednow Boris B. , Herdener Marcus , Scharnowski Frank
Published: August 2020

Tobacco smoking is one of the leading causes of preventable death and disease worldwide. Most smokers want to quit, but relapse rates are high. To improve current smoking cessation treatments, a better understanding of the underlying mechanisms of nicotine dependence and related craving behavior is needed. Studies on cue-driven cigarette craving have been a particularly useful tool for investigating the neural mechanisms of drug craving. Here, functional neuroimaging studies in humans have identified a core network of craving-related brain responses to smoking cues that comprises of amygdala, anterior cingulate cortex, orbitofrontal cortex, posterior cingulate cortex, and ventral striatum.

However, most functional Magnetic Resonance Imaging (fMRI) cue-reactivity studies do not adjust their stimuli for emotional valence, a factor assumed to confound craving-driven brain responses to smoking cues. Here, we investigated the influence of emotional valence on key addiction brain areas by disentangling craving- and valence-related brain responses with parametric modulators in 32 smokers. For one of the suggested key regions for addiction, the amygdala, we observed significantly stronger brain responses to the valence aspect of the presented images than to the craving aspect. Our results emphasize the need for carefully selecting stimulus material for cue-reactivity paradigms, in particular with respect to emotional valence. Further, they can help designing future research on teasing apart the diverse psychological dimensions that comprise nicotine dependence, and, therefore, can lead to a more precise mapping of craving-associated brain areas, an important step towards more tailored smoking cessation treatments.
The impact of COVID-19 on the reproductive health of people living in Australia: findings from an online survey
Authors: Coombe Jacqueline , Kong Fabian , Bittleston Helen , Williams Hennie , Tomnay Jane , Vaisey Alaina , Malta Sue , Goller Jane , Temple-Smith Meredith , Bourchier Louise , Lau Andrew , Hocking Jane S
Published: August 2020

Introduction

Australia introduced ‘lockdown’ measures to control COVID-19 on 22 March 2020. For two months, Australians were asked to remain at home and only leave for essential activities. We investigate the impact this had on sexual and reproductive health (SRH).

Methods

Australians aged 18+ were eligible to participate in an online survey from 23 April-11 May 2020. Questions included contraceptive use, pregnancy intentions and access to SRH services. We report on the experiences of 518 female participants aged <50 years. Pregnancy intentions and contraceptive use were analysed using descriptive statistics. Odds ratios and 95% confidence intervals were calculated to investigate difficulty accessing SRH products and services. Qualitative data were analysed using descriptive thematic analysis.

Results

Most participants (55.4%, 287/518) were aged 18-24 years. Most (76.1%, 379/498) indicated they were trying to avoid pregnancy. The oral contraceptive pill was the most common single method used (20.8%; 107/514). Nearly 20% (101/514) reported they were not using contraception. Older women (OR=0.4; 95%CI: 0.1, 0.9 for 25-34 vs 18-24 years) and those employed (OR=0.4; 95%CI: 0.2, 0.7) had less trouble accessing contraception during lockdown. Women aged 25-34 (OR=0.4; 95%CI: 0.3, 0.7) or 35-49 years (OR=0.3; 95%CI: 0.1, 0.6) were less likely to experience difficulty accessing feminine hygiene products. Qualitative analysis suggested that COVID-19 affected pregnancy plans, with participants delaying childbearing, or deciding to remain childfree.

Conclusion

COVID-19 lockdown impacted the SRH of Australian women. Findings highlight the importance of continued access to SRH services and products during global emergencies.

KEY MESSAGES

Nearly a third of participants reported difficulties accessing their usual feminine hygiene products during lockdown in Australia.

Participants reported delaying childbearing or deciding to remain childfree due to the COVID-19 pandemic.

Ensuring continued access to sexual and reproductive health services and products for all who require them during global emergencies is essential.
The Diagnostic Accuracy of Subjective Dyspnea in Detecting Hypoxemia Among Outpatients with COVID-19
Authors: Berezin Linor , Zhabokritsky Alice , Andany Nisha , Chan Adrienne K. , Gershon Andrea , Lam Philip W. , Leis Jerome A. , MacPhee Scott , Mubareka Samira , Simor Andrew E. , Daneman Nick
Published: August 2020

Objectives

The majority of patients with mild-to-moderate COVID-19 can be managed using virtual care. Dyspnea is challenging to assess remotely, and the accuracy of subjective dyspnea measures in capturing hypoxemia have not been formally evaluated for COVID-19. We explored the accuracy of subjective dyspnea in diagnosing hypoxemia in COVID-19 patients.

Methods

This is a retrospective cohort study of consecutive outpatients with COVID-19 who met criteria for home oxygen saturation monitoring at a university-affiliated acute care hospital in Toronto, Canada from April 3, 2020 to June 8, 2020. Hypoxemia was defined by oxygen saturation <95%. Dyspnea measures were treated as diagnostic tests, and we determined their sensitivity (SN), specificity (SP), negative/positive predictive value (NPV/PPV), and positive/negative likelihood ratios (+LR/-LR) for detecting hypoxemia.

Results

During the study period 64/298 (21.5%) of patients met criteria for home oxygen saturation monitoring, and of these 14/64 (21.9%) were diagnosed with hypoxemia. The presence/absence of dyspnea had limited accuracy for diagnosing hypoxemia, with SN 57% (95% CI 30-81%), SP 78% (63%-88%), NPV 86% (72%-94%), PPV 42% (21%-66%), +LR 2.55 (1.3-5.1), -LR 0.55 (0.3-1.0). An mMRC dyspnea score >1 (SP 97%, 95%CI 82%-100%), Roth Maximal Count <12 (SP 100%, 95%CI 75-100%), and Roth Counting time < 8 seconds (SP 93%, 95%CI 66%-100%) had high SP that could be used to rule in hypoxemia, but displayed low SN (≤50%).

Conclusions

Subjective dyspnea measures have inadequate accuracy for ruling out hypoxemia in high-risk patients with COVID-19. Safe home management of patients with COVID-19 should incorporate home oxygenation saturation monitoring.
Cell Programmed Nutrient Partitioning in the Tumor Microenvironment
Authors: Reinfeld BI , Madden MZ , Wolf MM , Chytil A , Bader JE , Patterson AR , Cohen AS , Ali A , Do BT , Muir A , Lewis CA , Hongo RA , Young KL , Brown RE , Todd VM , Huffstater T , Abraham A , O’Neil RT , Wilson MH , Xin F , Tantawy MN , Merryman WD , Johnson RW , Williams CS , Mason EF , Mason FM , Beckermann KE , Vander Heiden MG , Manning HC , Rathmell JC , Rathmell WK
Published: August 2020

The tumor microenvironment (TME) includes transformed cancer and infiltrating immune cells1,2. Cancer cells can consume large quantities of glucose through Warburg metabolism3,4that can be visualized with positron emission tomography (PET). While infiltrating immune cells also rely on glucose, disruptions to metabolism can contribute to tumor immunological evasion5–9. How immune cell metabolism is programmed or restrained by competition with cancer cells for nutrients, remains uncertain. Here we used PET tracers to measure the accessibility of glucose and glutamine to cell subsets in the TME. Surprisingly, myeloid cells including macrophages were the greatest consumers of intra-tumoral glucose, followed by T cells and cancer cells. Cancer cells, in contrast, had the highest glutamine uptake. This distinct nutrient partitioning was programmed through selective mTORC1 signaling and glucose or glutamine-related gene expression. Inhibition of glutamine uptake enhanced glucose uptake across tumor resident cell types and shifted macrophage phenotype, demonstrating glucose is not limiting in the TME. Thus, cancer cells are not the only cells in tumors which exhibit high glucose uptakein vivoand instead preferentially utilize glutamine over other cell types. We observe that intrinsic cellular programs can play a major role in the use of some nutrients. Together, these data argue cell selective partitioning of glucose and glutamine can be exploited to develop therapies and imaging strategies to alter the metabolic programs of specific cell populations in the TME.
Modulation of macrophage inflammatory function through selective inhibition of the epigenetic reader protein SP140
Authors: Ghiboub Mohammed , Koster Jan , Craggs Peter D. , Li Yim Andrew Y.F. , Shillings Anthony , Hutchinson Sue , Bingham Ryan P. , Gatfield Kelly , Hageman Ishtu L. , Yao Gang , O’Keefe Heather P. , Coffin Aaron , Patel Amish , Sloan Lisa A. , Mitchell Darren J. , Lunven Laurent , Watson Robert J. , Blunt Christopher E. , Harrison Lee A. , Bruton Gordon , Kumar Umesh , Hamer Natalie , Spaull John R. , Zwijnenburg Danny A. , Welting Olaf , Hakvoort Theodorus B.M. , van Limbergen Johan , Henneman Peter , Prinjha Rab K. , de Winther Menno PJ. , Harker Nicola R. , Tough David F. , de Jonge Wouter J.
Published: August 2020

Speckled 140 KDa (SP140) is a nuclear body protein, mainly expressed in immune cells, which contains multiple domains suggestive of an epigenetic reader function; namely a bromodomain, a PHD domain and a SAND domain. Single nucleotide polymorphisms and epigenetic modifications in theSP140locus have been linked to autoimmune and inflammatory diseases including Crohn’s disease (CD). However, little is known about the cellular function of SP140; this is due in part to the fact that, unlike for other many other epigenetic proteins, no small molecule inhibitors have been available to investigate the biological role of SP140. We report the discovery of the first small molecule SP140 inhibitor (GSK761) and utilize this to elucidate SP140 function in innate immune cells. We show that SP140 is highly expressed in CD68+CD mucosal macrophages and inin vitro-generated inflammatory macrophages. SP140 inhibition through GSK761 reduced monocyte differentiation into inflammatory macrophages and lipopolysaccharide (LPS)-induced inflammatory activation, whilst inducing the generation of CD206+regulatory macrophages that mark anti-TNF remission induction in CD patients. ChIP-seq analyses revealed that SP140 preferentially occupies transcriptional start sites (TSS) in inflammatory macrophages, with enrichment at gene loci encoding pro-inflammatory cytokines/chemokines and inflammatory pathways. GSK761 specifically reduced SP140 binding and thereby expression of SP140-dependent downstream inflammatory genes. Notably, in CD14+macrophages isolated from CD intestinal-mucosa, GSK761 inhibited the spontaneous expression of cytokines, includingTNF. Together, this study identifies SP140 as a druggable epigenetic reader and therapeutic target for CD.
Rapid SARS-CoV-2 Adaptation to Available Cellular Proteases
Authors: Chaudhry M. Zeeshan , Eschke Kathrin , Hoffmann Markus , Grashoff Martina , Abassi Leila , Kim Yeonsu , Brunotte Linda , Ludwig Stephan , Kröger Andrea , Klawonn Frank , Pöhlmann Stefan , Cicin-Sain Luka
Published: August 2020

Since the pandemic spread of SARS-CoV-2, the virus has exhibited remarkable genome stability, but recent emergence of novel variants show virus evolution potential. Here we show that SARS-CoV-2 rapidly adapts to Vero E6 cells that leads to loss of furin cleavage motif in spike protein. The adaptation is achieved by asymptotic expansion of minor virus subpopulations to dominant genotype, but wildtype sequence is maintained at low percentage in the virus swarm, and mediate reverse adaptation once the virus is passaged on human lung cells. The Vero E6-adapted virus show defected cell entry in human lung cells and the mutated spike variants cannot be processed by furin or TMPRSS2. However, the mutated S1/S2 site is cleaved by cathepsins with higher efficiency. Our data show that SARS-CoV-2 can rapidly adapt spike protein to available proteases and advocate for deep sequence surveillance to identify virus adaptation potential and novel variant emergence.

Significance Statement

Recently emerging SARS-CoV-2 variants B1.1.1.7 (UK), B.1.351 (South Africa) and B.1.1.248 (Brazil) harbor spike mutation and have been linked to increased virus pathogenesis. The emergence of these novel variants highlight coronavirus adaptation and evolution potential, despite the stable consensus genotype of clinical isolates. We show that subdominant variants maintained in the virus population enable the virus to rapidly adapt upon selection pressure. Although these adaptations lead to genotype change, the change is not absolute and genome with original genotype are maintained in virus swarm. Thus, our results imply that the relative stability of SARS-CoV-2 in numerous independent clinical isolates belies its potential for rapid adaptation to new conditions.
Early Alpine occupation backdates westward human migration in Late Glacial Europe
Authors: Bortolini Eugenio , Pagani Luca , Oxilia Gregorio , Posth Cosimo , Fontana Federica , Badino Federica , Saupe Tina , Montinaro Francesco , Margaritora Davide , Romandini Matteo , Lugli Federico , Papini Andrea , Boggioni Marco , Perrini Nicola , Oxilia Antonio , Cigliano Riccardo Aiese , Barcelona Rosa , Visentin Davide , Fasser Nicolò , Arrighi Simona , Figus Carla , Marciani Giulia , Silvestrini Sara , Bernardini Federico , Sartorio Jessica C. Menghi , Fiorenza Luca , Moggi Cecchi Jacopo , Tuniz Claudio , Kivisild Toomas , Gianfrancesco Fernando , Peresani Marco , Scheib Christiana L. , Talamo Sahra , D’Esposito Maurizio , Benazzi Stefano
Published: August 2020

The end of the Last Glacial Maximum (LGM) in Europe (~16.5 ka ago) set in motion major changes in human culture and population structure1. In Southern Europe, Early Epigravettian material culture was replaced by Late Epigravettian art and technology about 18-17 ka ago at the beginning of southern Alpine deglaciation, although available genetic evidence from individuals who lived ~14 ka ago2–5 opened up questions on the impact of migrations on this cultural transition only after that date. Here we generate new genomic data from a human mandible uncovered at the Late Epigravettian site of Riparo Tagliente (Veneto, Italy), that we directly dated to 16,980-16,510 cal BP (2σ). This individual, affected by a low-prevalence dental pathology named focal osseous dysplasia, attests that the very emergence of Late Epigravettian material culture in Italy was already associated with migration and genetic replacement of the Gravettian-related ancestry. In doing so, we push back by at least 3,000 years the date of the diffusion in Southern Europe of a genetic component linked to Balkan/Anatolian refugia, previously believed to have spread during the later Bølling/Allerød warming event (~14 ka ago4,6). Our results suggest that demic diffusion from a genetically diverse population may have substantially contributed to cultural changes in LGM and post-LGM Southern Europe, independently from abrupt shifts to warmer and more favourable conditions.
The role of toxin:antitoxin systems and insertion sequences in the loss of virulence inShigella sonnei
Authors: Martyn Jessica E. , Pilla Giulia , Hollingshead Sarah , Lobanovska Mariya , Winther Kristoffer S. , Lea Susan , McVicker Gareth , Tang Christoph M.
Published: August 2020

TheShigellaplasmid, pINV, contains a 30 kb pathogenicity island (PAI) encoding a Type III secretion system (T3SS) which is essential for virulence. During growth in the laboratory, avirulent colonies ofShigella(which do not express a T3SS) arise spontaneously. Avirulence inShigella flexnerimostly follows loss of the PAI, following recombination between insertion sequences (ISs) on pINV; toxin:antitoxin (TA) systems on pINV promote its retention through post-segregational killing (PSK). We show that avirulence inShigella sonneimainly results from plasmid loss, consistent with previous findings; IS-mediated PAI deletions can occur inS. sonnei, but through different ISs than inS. flexneri. We investigated the molecular basis for frequent loss of theS. sonneiplasmid, pINVSsonn. Introduction into pINVSsonnof CcdAB and GmvAT, toxin:antitoxin TA systems in pINV fromS. flexneribut notS. sonnei, reduced plasmid loss and the emergence of avirulent bacteria. However, plasmid loss remained the leading cause of avirulence. We show that a single amino acid difference in the VapC toxin of the VapBC TA system in pINV also contributes to high frequency plasmid loss inS. sonneicompared toS. flexneri. Our findings demonstrate that the repertoire of ISs, complement of TA systems, and polymorphisms in TA systems influence plasmid dynamics and virulence loss inS. sonnei. Understanding the impact of polymorphisms should be informative about how TA systems contribute to PSK, and could be exploited for generating strains with stable plasmids.
Protein mimetic amyloid inhibitor potently abrogates cancer-associated mutant p53 aggregation and restores tumor suppressor function
Authors: Palanikumar Loganathan , Karpauskaite Laura , Hassan Sarah , Alam Maheen , Al-Sayegh Mohamed , Chehade Ibrahim , Maity Debabrata , Ali Liaqat , Falls Zackary , Samudrala Ram , Kalmouni Mona , Hunashal Yamanappa , Ahmed Jemil , Karapetyan Shake , Pasricha Renu , Esposito Gennaro , Afzal Ahmed J. , Hamilton Andrew D. , Kumar Sunil , Magzoub Mazin
Published: August 2020

Missense mutations in p53 are severely deleterious and occur in over 50% of all human cancers. The vast majority of these mutations are located in the inherently unstable DNA-binding domain (DBD), many of which destabilize the domain further and expose its aggregation-prone hydrophobic core, prompting self-assembly of mutant p53 into inactive cytosolic amyloid-like aggregates. Screening an oligopyridylamide library, previously shown to inhibit amyloid formation associated with Alzheimer’s disease and type II diabetes, identified a tripyridylamide, ADH-6, that potently abrogates self-assembly of the aggregation-nucleating subdomain of mutant p53 DBD. Moreover, ADH-6 effectively targets and dissociates mutant p53 aggregates in human cancer cells, which restores p53’s transcriptional activity, leading to cell cycle arrest and apoptosis. Notably, ADH-6 treatment substantially shrinks xenografts harboring mutant p53 and prolongs survival, while exhibiting no toxicity to healthy tissue. This study demonstrates the first successful application of a bona fide small-molecule amyloid inhibitor as an anticancer agent.
Comprehensive characterization of single cell full-length isoforms in human and mouse with long-read sequencing
Authors: Tian Luyi , Jabbari Jafar S. , Thijssen Rachel , Gouil Quentin , Amarasinghe Shanika L. , Kariyawasam Hasaru , Su Shian , Dong Xueyi , Law Charity W. , Lucattini Alexis , Chung Jin D. , Naim Timur , Chan Audrey , Ly Chi Hai , Lynch Gordon S. , Ryall James G. , Anttila Casey J.A. , Peng Hongke , Anderson Mary Ann , Roberts Andrew W. , Huang David C.S. , Clark Michael B. , Ritchie Matthew E.
Published: August 2020

Alternative splicing shapes the phenotype of cells in development and disease. Long-read RNA-sequencing recovers full-length transcripts but has limited throughput at the single-cell level. Here we developed single-cell full-length transcript sequencing by sampling (FLT-seq), together with the computational pipelineFLAMESto overcome these issues and perform isoform discovery and quantification, splicing analysis and mutation detection in single cells. WithFLT-seqandFLAMES, we performed the first comprehensive characterization of the full-length isoform landscape in single cells of different types and species and identified thousands of unannotated isoforms. We found conserved functional modules that were enriched for alternative transcript usage in different cell populations, including ribosome biogenesis and mRNA splicing. Analysis at the transcript-level allowed data integration with scATAC-seq on individual promoters, improved correlation with protein expression data and linked mutations known to confer drug resistance to transcriptome heterogeneity. Our methods reveal previously unseen isoform complexity and provide a better framework for multi-omics data integration.
Rapid evolution drives the rise and fall of carbapenem resistance during an acutePseudomonas aeruginosainfection
Authors: Wheatley Rachel , Caballero Julio Diaz , Kapel Natalia , Quinn Angus , del Barrio-Tofiño Ester , López-Causapé Carla , Hedge Jessica , Torrens Gabriel , Van der Schalk Thomas , Britto Xavier Basil , Fernández-Cuenca Felipe , Arenzana Angel , Recanatini Claudia , Timbermont Leen , Sifakis Frangiscos , Ruzin Alexey , Ali Omar , Lammens Christine , Goossens Herman , Kluytmans Jan , Kumar-Singh Samir , Oliver Antonio , Malhotra-Kumar Surbhi , MacLean Craig
Published: August 2020

It is well established that antibiotic treatment selects for resistance in pathogenic bacteria. However, the evolutionary responses of pathogen populations to antibiotic treatment during infections remain poorly resolved, especially in acute infections. Here we map the evolutionary responses to treatment in high definition through genomic and phenotypic characterization of >100 isolates from a patient withP. aeruginosapneumonia. Antibiotic therapy (meropenem, colistin) caused a rapid crash of theP. aeruginosapopulation in the lung, but this decline was followed by the spread of meropenem resistance mutations that restrict antibiotic uptake (oprD) or modify LPS biosynthesis (wbpM). Low fitness strains with high-level meropenem resistance (oprD) were then replaced by high fitness strains with ‘anti-resistance’ mutations in the MexAB-OprM efflux pump, causing a rapid decline in resistance to both meropenem and a collateral loss of resistance to a broad spectrum of antibiotics. In contrast, we did not observe any evolutionary responses to antibiotic treatment in the intestinal population ofP. aeruginosa. Carbapenem antibiotics are key to the treatment of infections caused by Gram negative pathogens, and our work highlights the ability of natural selection to drive both the rapid rise and fall of carbapenem resistance during acute infections.
Modeling Risks and Mitigation Options for the Chronic Wasting Disease (CWD) in Scandinavia
Authors: Franklin Oskar , Moltchanova Elena , Krasovskiy Andrey , Kraxner Florian
Published: August 2020

Chronic wasting disease (CWD) is a contagious neural prion-disease affecting deer populations in North America with severe ecological and societal consequences. CWD is fatal and infectious prions spread and remain in the environment for many years even without animals present. The recent appearance of CWD in reindeers in Norway called for a drastic culling operation to prevent further spreading of the disease. This appears to have stopped the spreading of CWD among reindeers, but due to the persistence of CWD prions in the environment a reappearance of new cases among reindeer or other species in the future cannot be excluded. To evaluate the risks and the effectiveness of alternative management (monitoring and culling) options, we developed a model of CWD dynamics and management. The model includes stochastic population and spatial dynamics of the four relevant deer species in northern Sweden and Norway: reindeer (Rangifer tarandus), roe deer (Capreolus capreolus), red deer (Cervus elaphus) and moose (Alces alces). Transmission of CWD is modelled via direct contacts and via the environment. The model was parameterized and calibrated based on CWD studies from USA, data from the Norwegian CWD cases, and local deer population and vegetation data. The results indicate that without management, a CWD epidemic can be initiated by a single infected reindeer and would spread to other deer species. It would lead to dramatic population declines of reindeer and red deer and would also reduce the populations of roe deer and moose. The disease prevalence would stabilise at a about 50% after 50 years, as observed in some areas in the USA. A management strategy to cull only visibly sick animals, even with very efficient detection, cannot prevent a catastrophic development but merely slow the outbreak. To prevent an outbreak and the establishment of CWD it is necessary to cull all individuals, not only visibly sick ones, of an affected species in a relatively large area (30×30 km in our model) once a case is detected. Further, to prevent a slow buildup of CWD in the environment and eliminate the risk of outbreaks in the future it is necessary to expand this area of culling even further. Although the model has not yet been thoroughly validated due to scarcity of data, the results suggest that the drastic culling done in Norway was appropriate and necessary to prevent establishment of CWD and that further monitoring and potential culling is required to prevent outbreaks in the future.