bluuebunny/crossref_metadata_2025 huggingface dataset:
Hydrogen peroxide production byStreptococcus pneumoniaeresults in alpha-hemolysis by oxidation of oxy-hemoglobin to met-hemoglobin
Authors: McDevitt Erin , Khan Faidad , Scasny Anna , Eichembaun Zehava , McDaniel Larry S. , Vidal Jorge E.
Published: July 2020

Streptococcus pneumoniae(Spn) and other streptococci produce a greenish halo on blood agar plates referred to as α-hemolysis. This phenotype is utilized by clinical microbiology laboratories to report culture findings of α-hemolytic streptococci, including Spn, and other bacteria. The α-hemolysis halo on blood agar plates has been related to the hemolytic activity of pneumococcal pneumolysin (Ply), or to a lesser extent, to lysis of erythrocytes by Spn-produced hydrogen peroxide. We investigated the molecular basis of the α-hemolysis halo produced by Spn. Wild-type strains TIGR4, D39, R6, and EF3030, and isogenic derivative Δplymutants, produced a similar α-hemolytic halo on blood agar plates while cultures of hydrogen peroxide knockout ΔspxB/ΔlctOmutants lacked this characteristic halo. Spectroscopic studies demonstrated that culture supernatants of TIGR4 released hemoglobin-bound heme (heme-hemoglobin) from erythrocytes and oxidized oxy-hemoglobin to met-hemoglobin within 30 min of incubation. As expected, given Ply hemolytic activity, and that hydrogen peroxide contributes to the release of Ply, TIGR4 isogenic mutants Δplyand ΔspxB/ΔlctOhad a significantly decreased release of heme-hemoglobin from erythrocytes. However, TIGR4Δplythat produces hydrogen peroxide oxidized oxy-hemoglobin to met-hemoglobin, whereas TIGR4ΔspxB/ΔlctOfailed to produce oxidation of oxy-hemoglobin. We demonstrated that the so-called α-hemolysis halo is caused by the oxidation oxy-hemoglobin (Fe+2) to a non-oxygen binding met-hemoglobin (Fe+3) by Spn-produced hydrogen peroxide. Since Spn colonizes the human lung, oxidation of oxy-hemoglobin might have important implications for pathogenesis.

Importance

There is a misconception that α-hemolysis observed on blood agar plates cultures ofStreptococcus pneumoniae(Spn), and other α-hemolytic streptococci is produced by a hemolysin, or alternatively, by lysis of erythrocytes caused by hydrogen peroxide. We noticed in the course of our investigations that wild-type Spn strains and hemolysin (e.g., pneumolysin) knockout mutants, produced the α-hemolytic halo on blood agar plates. In contrast, hydrogen peroxide defective mutants prepared in four different strains lacked the characteristic α-hemolysis halo. We also demonstrated that wild-type strains and pneumolysin mutants oxidized oxy-hemoglobin to met-hemoglobin. Hydrogen peroxide knockout mutants, however, failed to oxidize oxy-hemoglobin. Therefore, the greenish halo formed on cultures of Spn and other so-called α-hemolytic streptococci is caused by the oxidation of oxy-hemoglobin produced by hydrogen peroxide. Oxidation of oxy-hemoglobin to the non-binding oxygen form, met-hemoglobin, might occur in the lungs during pneumococcal pneumonia.
Country distancing reveals the effectiveness of travel restrictions during COVID-19
Authors: Zhong Lu , Diagne Mamadou , Wang Weiping , Gao Jianxi
Published: July 2020

Travel restrictions are the current central strategy to globally stop the transmission of the novel coronavirus disease (COVID-19). Despite remarkably successful approaches in predicting the spatiotemporal patterns of the ongoing pandemic, we lack an intrinsic understanding of the travel restriction’s effectiveness. We fill this gap by developing a surprisingly simple measure,country distancing, that is analogical to theeffective resistancein series and parallel circuits and captures the propagation backbone tree from the outbreak locations globally. This approach enables us to map the effectiveness of travel restrictions to arrival time delay (ATD) or infected case reduction (ICR) systematically. Our method estimates that 50.8% of travel restrictions as of Apr-4 are ineffective, resulting in zero ATD or ICR worldwide. Instead, by imposing Hubei’s lockdown on Jan-23 and national lockdown on Feb-8, mainland China alone leads to 11.66 [95% credible interval (CI), 9.71 to 13.92] days of ATD per geographic area and 1,012,233 (95% CI, 208,210 −4,959,094) ICR in total as of Apr-4. Our result unveils the trade-off between thecountry distancingincrease and economic loss, offering practical guidance for strategic actsion about when and where to implement travel restrictions, tailed to the real-time national context.
Anxiety and perceived risk during COVID-19 outbreak
Authors: Malhotra Chetna , Chaudhry Isha , Ozdemir Semra , Teo Irene , Finkelstein Eric Andrew
Published: July 2020

The uncertainty around coronavirus disease-19 (COVID-19) has triggered anxiety among public. We aimed to assess the variation in anxiety and risk perceptions of COVID-19 among adults in Singapore. We administered a web-survey to a panel of residents between 31 March and 14 April 2020. We assessed anxiety using general anxiety disorder (GAD) scale and assessed participants’ risk perceptions regarding severity of the outbreak. Of the 1,017 participants, 23% reported moderate to severe anxiety [GAD score≥10]. A high proportion reported perceived likelihood of ICU admission (46%) and death (30%) upon getting COVID-19. Results from path analysis showed that younger participants, those with chronic conditions, those living with children and low perceived trust in government response to COVID-19 had a significantly higher anxiety mediated by their perceived risk of dying upon getting COVID-19. These results highlight the need for management of anxiety through adequate and effective risk communication for the general public.
Local measures enable COVID-19 containment with fewer restrictions due to cooperative effects
Authors: Bittihn Philip , Hupe Lukas , Isensee Jonas , Golestanian Ramin
Published: July 2020

Many countries worldwide that were successful in containing the first wave of the COVID-19 epidemic are faced with the seemingly impossible choice between the resurgence of infections and endangering the economic and mental well-being of their citizens. While blanket measures are slowly being lifted and infection numbers are monitored, a systematic strategy for balancing contact restrictions and the freedom necessary for a functioning society long-term in the absence of a vaccine is currently lacking. Here, we propose a regional strategy with locally triggered containment measures that can largely circumvent this trade-off and substantially lower the magnitude of restrictions the average individual will have to endure in the near future. For the simulation of future disease dynamics and its control, we use current data on the spread of COVID-19 in Germany, Italy, England, New York State and Florida, taking into account the regional structure of each country and their past lockdown efficiency. Overall, our analysis shows that tight regional control in the short term can lead to long-term net benefits due to small-number effects which are amplified by the regional subdivision and crucially depend on the rate of cross-regional contacts. We outline the mechanisms and parameters responsible for these benefits and suggest possible was to gain access to them, simultaneously achieving more freedom for the population and successfully containing the epidemic. Our open-source simulation code is freely available and can be readily adapted to other countries. We hope that our analysis will help create sustainable, theory-driven long-term strategies for the management of the COVID-19 epidemic until therapy or immunization options are available.
Adherence to protective measures among health care workers in the UK; a cross-sectional study
Authors: Smith Louise E. , Serfioti Danai , Weston Dale , Greenberg Neil , Rubin G James
Published: July 2020

Healthcare workers (HCWs) are frontline responders to emergency infectious disease outbreaks such as COVID-19. We investigated factors associated with adherence to personal protective behaviours in UK HCWs during the COVID-19 pandemic using an online cross-sectional survey of 1035 healthcare professionals in the UK. Data were collected between 12th and 16th June 2020. Adjusted logistic regressions were used to separately investigate factors associated with adherence to use of personal protective equipment, maintaining good hand hygiene, and physical distancing from colleagues. Adherence to personal protective measures was suboptimal (PPE use: 80.0%, 95% CI [77.3 to 82.8], hand hygiene: 67.8%, 95% CI [64.6 to 71.0], coming into close contact with colleagues: 74.7%, 95% CI [71.7 to 77.7]). Adherence to PPE use was associated with having adequate PPE resources, receiving training during the pandemic, lower perceived fatalism from COVID-19, higher perceived social norms and higher perceived effectiveness of PPE. Adherence to physical distancing was associated with one’s workplace being designed, using markings to facilitate physical distancing and receiving training during the pandemic. There were few associations with adherence to hand hygiene. Findings indicate HCWs should receive training on personal protective behaviours to decrease fatalism over contracting COVID-19 and increase perceived effectiveness of protective measures.
Serum anion gap is associated with all-cause mortality among critically ill patients with congestive heart failure
Authors: Tang Yiyang , Lin Wenchao , Zha Lihuang , Zeng Xiaofang , Liu Zhenghui , Yu Zaixin
Published: July 2020

Background

Congestive heart failure (CHF) is a complex clinical syndrome, with high morbidity and mortality. Serum anion gap (SAG) has been known to be associated with the severity of various cardiovascular diseases. However, the role of SAG indicators in CHF is unclear.

Methods and results

A retrospective analysis of data from MIMIC-III v1.4 was conducted in critically ill patients with CHF. Clinical information of each patient, including demographic data, comorbidities, vital signs, scores, and laboratory indicators, were successfully obtained. Cox proportional hazards models were performed to determine the relationship between SAG and mortality in CHF patient, the consistency of which was further verified by subgroup analysis.

Results

A total of 7426 subjects met the inclusion criteria. In multivariate analysis, after adjusting for age, gender, ethnicity, and other potential confounders, higher SAG was significantly related to an increase in 30-day and 90-day all-cause mortality of critically ill patients with CHF compared with lower SAG (tertile3 vs tertile1: adjusted HR, 95% CI: 1.74, 1.46–2.08; 1.53, 1.32–1.77). In subgroup analysis, the association between SAG and all-cause mortality present similarities in most strata.

Conclusion

SAG at admission can be a promising predictor of all-cause mortality in critically ill patients with CHF.
Expression of HER2/neu in premalignant lesions of oral cavity
Authors: Verma Vansh , Jha Ashesh Kumar , Patiri Karsing , Arora Nikhil
Published: July 2020

Context

Molecular alterations in premalignant lesions of oral cavity are not well known, many reports and have found increased HER2 expression to be correlated with poor prognosis in oral cancer. However, literature on expression of HER2 in premalignant lesions is limited and data is conflicting in nature. Overexpression of HER2 in premalignant lesions may denote its positive contribution in malignant transformation of these lesions.

Aims

To evaluate the expression of HER2 in premalignant lesions of oral cavity.

Settings and Design

In this prospective observational study of 2 months, patients attending OPD at Department of ENT and meeting the inclusion criteria were included.

Methods and Material

23 samples of Leukoplakia and 1 sample of oral lichen planus were stained by routine H&E to confirm clinical diagnosis and assess dysplasia if any, 5 samples of normal mucosa were used as control. Immunohistochemical staining for HER2 was done. ASCO/CAP 2018 guidelines were used for reporting the results.

Statistical analysis used

Percentage of lesions expressing cytoplasmic or membranous expression was calculated.

Results

1 sample of Leukoplakia with severe dysplasia expressed focal membranous staining. 20% leukoplakia lesions expressed cytoplasmic staining. Staining was not observed in oral lichen planus and leucoplakia without dysplasia.

Conclusions

Membranous expression in Severe dysplasia and higher expression in oral cancer is in concordance with the multistep theory of carcinogenesis. Larger studies are needed if HER2 is to be proposed as a marker for oral premalignant lesions. Significance of cytoplasmic staining in oral premalignant lesions needs to be elucidated.

Key Messages

To the best of our knowledge, this is the first report of focal membranous expression of HER2 in leucoplakia in India. 20% leucoplakia with dysplasia expressed cytoplasmic staining. The significance of cytoplasmic staining needs to be further explored.
CCOFEE-GI Study: Colombian COVID19 First Experience in Gastroentrology. Characterization of digestive manifestations in patients diagnosed with COVID-19 at a highly complex institution in Bogota D.C., Colombia
Authors: Mejía Alejandro Concha , Sánchez Reinaldo Rincón , Calderón-Zapata Douvan , Tafur Santiago Huertas , Durana Andrés Montoya , Camacho John Guzmán , Hernández Alan Ovalle , Varela Heinz Ibañez , Lombana Juan Pablo Osorio , Monsalve Edwin Silva , Cortés-Muñoz Fabian
Published: July 2020

The current pandemic caused by SARS-CoV-2 has posed an important threat to the human health, healthcare systems, economy, and structure of societies. In Colombia, the first case was diagnosed on March 6, 2020, with exponential progressive growth, and there were >200,000 confirmed cases as of July 20, 2020, in this cross-sectional, analytical, and observational study, we focused on the demographic, epidemiologic, and clinical characteristics of patients with confirmed SARS-CoV-2 infection at a highly complex institution in Latinamerica, with special emphasis on gastrointestinal symptoms. Methods: Demographic and clinical data were collected, results related to the outcomes such as hospitalization time, admission to ICU, need for orotracheal intubation, and death were also included. Statistical analyses were conducted using Stata software V.15.

Results

We included 72 patients RT-PCR positive for SARS-CoV-2 (34 women and 38 men) with age 47.5 ± 17.7 years; 17 (23.6%) presented at least one of the gastrointestinal symptoms (nausea/vomiting, abdominal pain, and/or diarrhea). 13 (76.47%) presented with diarrhea, 29.41% with nausea/vomiting, and five (29.41%) with abdominal pain. Diarrhea in 18.06% of all those infected with SARS-CoV-2 at the time of consultation, which was the most common digestive symptom. No significant differences were observed in requirement for endotracheal intubation, hospitalization, ICU admission, and fatal outcome between the NGIS and GIS groups (p:0.671, 0.483, 1,000, and 1,000). Conclusion: In our study, patients with gastrointestinal symptoms had no significant differences in disease severity, admission to ICU or death compared to those who did not have such symptoms.
Smoking is associated with significantly increased green autofluorescence intensity and asymmetry of the skin and the fingernails of natural populations, population at-risk of developing stroke, and population of acute ischemic stroke
Authors: Zhang Mingchao , Tao Yue , Wu Danhong , Ying Weihai
Published: July 2020

Tobacco smoking is an important risk factor for multiple major diseases including cancer and stroke. It is of significance to search for the biomarkers of smoking for non-invasive, rapid and economic monitoring of the pathological changes of smokers’ body. However, there has been no non-invasive method for monitoring the health state of smokers. Our current study has indicated that green autofluorescence (AF) of the fingernails and certain locations of the skin is a novel biomarker for smoking: Both the green AF intensity and the AF asymmetry of the fingernails and the skin of Dorsal Index Fingers of the smokers were significantly higher than those of the non-smokers in natural populations, the population at-risk of developing stroke and the acute ischemic stroke (AIS) patients. ROC analyses using the green AF intensity of either right or left Index Fingernails showed that the AUC values ranged from 0.8136 and 0.8644 for differentiating smokers and non-smokers in these populations. ROC analyses using the green AF intensity of the skin of the right Dorsal Index Fingers showed that the AUC values ranged between 0.7418 and 0.7478 for differentiating the smokers and the non-smokers in natural populations and the population at-risk of developing stroke. Collectively, our study has indicated that increased green AF intensity of the fingernails and certain locations of the skin is a novel biomarker for smoking. Based on this finding, pathological alterations of smokers’ body may be monitored non-invasively, rapidly and economically, which could be highly valuable for the health management of the large population of tobacco smokers.
Actinobacteria challenge the paradigm: a unique protein architecture for a well-known central metabolic complex
Authors: Bruch Eduardo M. , Vilela Pierre , Lexa-Sapart Norik , Yang Lu , Raynal Bertrand , Alzari Pedro M. , Bellinzoni Marco
Published: July 2020

α-ketoacid dehydrogenase complexes are large, tripartite enzymatic machineries carrying out key reactions in central metabolism. Extremely conserved across the tree of life, they have so far all considered to be structured around a high molecular weight hollow core, consisting of up to 60 subunits of the acyltransferase component. We provide here evidence that Actinobacteria break the rule by possessing an acetyltranferase component reduced to its minimally active, trimeric unit, characterized by a unique C-terminal helix that affects the oligomerization and the full 3D architecture of the complex. We show that this unique feature is characterized by an insertion, which together with OdhA is found spread over Actinobacteria. This phylum includes organisms or great interest for agriculture, industrial bio-production and many human pathogens asMycobacterium tuberculosis. Moreover, components of this complex are key forM. tuberculosissurvival in the human host, and its unique core and protein-protein interactions represent potentially “druggable” targets.
Phase Unwrapping with a Rapid Opensource Minimum Spanning TreE AlgOrithm (ROMEO)
Authors: Dymerska Barbara , Eckstein Korbinian , Bachrata Beata , Siow Bernard , Trattnig Siegfried , Shmueli Karin , Robinson Simon Daniel
Published: July 2020

Purpose

To develop a rapid and accurate MRI phase unwrapping technique for challenging phase topographies encountered at high magnetic fields, around metal implants or post-operative cavities, that is sufficiently fast to be applied to large group studies including Quantitative Susceptibility Mapping and functional MRI (with phase-based distortion correction).

Methods

The proposed path-following phase unwrapping algorithm, ROMEO, estimates the coherence of the signal both in space - using MRI magnitude and phase information - and over time, assuming approximately linear temporal phase evolution. This information is combined to form a quality map that guides the unwrapping along a three-dimensional path through the object using a computationally efficient minimum spanning tree algorithm. ROMEO was tested against the two most commonly used exact phase unwrapping methods: PRELUDE and BEST PATH in simulated topographies and at several field strengths: in 3 T and 7 T in vivo human head images and 9.4 T ex vivo rat head images.

Results

ROMEO was more reliable than PRELUDE and BEST PATH, yielding unwrapping results with excellent temporal stability for multi-echo or multi-time-point data. ROMEO does not require image masking and delivers results within seconds even in large, highly wrapped multi-echo datasets (e.g. 9 seconds for a 7 T head dataset with 31 echoes and a 208 x 208 x 96 matrix size).

Conclusion

Overall, ROMEO was both faster and more accurate than PRELUDE and BEST PATH delivering exact results within seconds, which is well below typical image acquisition times, enabling potential on-console application.
Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster
Authors: Shibu Preetha , McCuaig Frazer , McCartney Anne L. , Kujawska Magdalena , Hall Lindsay J. , Hoyles Lesley
Published: July 2020

As part of ongoing studies with clinically relevant Klebsiella spp., we characterized the genomes of three clinical GES-5-positive ST138 strains originally identified as Klebsiella oxytoca. blaOXY gene, average nucleotide identity and phylogenetic analyses showed the strains to be Klebsiella michiganensis. Affiliation of the strains to ST138 led us to demonstrate that the current multi-locus sequence typing scheme for K. oxytoca can be used to speciate members of this genetically diverse complex of bacteria. The strains encoded the kleboxymycin biosynthetic gene cluster (BGC), previously only found in K. oxytoca strains and one strain of Klebsiella grimontii. The finding of this BGC, associated with antibiotic-associated haemorrhagic colitis, in K. michiganensis led us to carry out a wide-ranging study to determine the prevalence of this BGC in Klebsiella spp. Of 7,170 publicly available Klebsiella genome sequences screened, 88 encoded the kleboxymycin BGC. All BGC-positive strains belonged to the K. oxytoca complex, with strains of four (K. oxytoca, K. pasteurii, K. grimontii, K. michiganensis) of the six species of the complex found to encode the complete BGC. In addition to being found in K. grimontii strains isolated from preterm infants, the BGC was found in K. oxytoca and K. michiganensis metagenome-assembled genomes recovered from neonates. Detection of the kleboxymycin BGC across the K. oxytoca complex may be of clinical relevance and this cluster should be included in databases characterizing virulence factors, in addition to those characterizing BGCs.

IMPACT STATEMENT

Members of the Klebsiella oxytoca complex are difficult to speciate using phenotypic and chemotaxonomic methods. Consequently, many genomes deposited in public databases are misclassified as K. oxytoca. Here we demonstrate that the current multi-locus sequence typing (MLST) system for the complex can be used to accurately speciate many strains, which will be of use to clinical laboratories in resource-limited settings which rely on the MLST scheme for typing and epidemiological tracking of isolates. In addition, extended analyses of the genomes of Klebsiella spp. have revealed the kleboxymycin biosynthetic gene cluster (BGC) is restricted to species of the Klebsiella oxytoca complex (K. oxytoca, K. michiganensis, K. pasteurii and K. grimontii). Species- and/or gene-specific differences in the cluster’s sequences may be relevant to virulence of K. oxytoca and related species. The finding of the kleboxymycin BGC in the preterm infant gut microbiota may have implications for disease presentation in a subset of neonates.
Genomic network analysis of an environmental and livestock IncF plasmid population
Authors: Matlock William , Chau Kevin K. , AbuOun Manal , Stubberfield Emma , Barker Leanne , Kavanagh James , Pickford Hayleah , Gilson Daniel , Smith Richard P. , Gweon H. Soon , Hoosdally Sarah J. , Swann Jeremy , Sebra Robert , Bailey Mark J. , Peto Timothy E. A. , Crook Derrick W. , Anjum Muna F. , Read Daniel S. , Walker A. Sarah , Stoesser Nicole , Shaw Liam P. ,   on behalf of the REHAB consortium
Published: July 2020

IncF plasmids are diverse and of great clinical significance, often carrying genes conferring antimicrobial resistance (AMR) such as extended-spectrum β-lactamases, particularly inEnterobacteriaceae. Organising this plasmid diversity is challenging, and current knowledge is largely based on plasmids from clinical settings. Here, we present a network community analysis of a large survey of IncF plasmids from environmental (influent, effluent, and upstream/downstream waterways surrounding wastewater treatment works) and livestock settings. We use a tractable and scalable methodology to examine the relationship between plasmid metadata and network communities. This reveals how niche (sampling compartment and host genera) partition and shape plasmid diversity. We also perform pangenome-style analyses on network communities. We show that such communities define unique combinations of core genes, with limited overlap. Building plasmid phylogenies based on alignments of these core genes, we demonstrate that plasmid accessory function is closely linked to core gene content. Taken together, our results suggest that stable IncF plasmid backbone structures can persist in environmental settings while allowing dramatic variation in accessory gene content that may be linked to niche adaptation. The recent association of IncF plasmids with AMR likely reflects their suitability for rapid niche adaptation.
Musical expertise shapes functional and structural brain networks independent of absolute pitch ability
Authors: Leipold Simon , Klein Carina , Jäncke Lutz
Published: July 2020

Professional musicians are a popular model for investigating experience-dependent plasticity in human large-scale brain networks. A minority of musicians possess absolute pitch, the ability to name a tone without reference. The study of absolute pitch musicians provides insights into how a very specific talent is reflected in brain networks. Previous studies of the effects of musicianship and absolute pitch on large-scale brain networks have yielded highly heterogeneous findings regarding the localization and direction of the effects. This heterogeneity was likely influenced by small samples and vastly different methodological approaches. Here, we conducted a comprehensive multimodal assessment of effects of musicianship and absolute pitch on intrinsic functional and structural connectivity using a variety of commonly employed and state-of-the-art multivariate methods in the largest sample to date (n = 153 female and male human participants; 52 absolute pitch musicians, 51 non-absolute pitch musicians, and 50 non-musicians). Our results show robust effects of musicianship in inter- and intrahemispheric connectivity in both structural and functional networks. Crucially, most of the effects were replicable in both musicians with and without absolute pitch when compared to non-musicians. However, we did not find evidence for an effect of absolute pitch on intrinsic functional or structural connectivity in our data: The two musician groups showed strikingly similar networks across all analyses. Our results suggest that long-term musical training is associated with robust changes in large-scale brain networks. The effects of absolute pitch on neural networks might be subtle, requiring very large samples or task-based experiments to be detected.

Significance Statement

A question that has fascinated neuroscientists, psychologists, and musicologists for a long time is how musicianship and absolute pitch, the rare talent to name a tone without reference, are reflected in large-scale networks of the human brain. Much is still unknown as previous studies have reported widely inconsistent results based on small samples. Here, we investigate the largest sample of musicians and non-musicians to date (n = 153) using a multitude of established and novel analysis methods. Results provide evidence for robust effects of musicianship on functional and structural networks that were replicable in two separate groups of musicians and independent of absolute pitch ability.
Adopting STING agonist cyclic dinucleotides as a potential adjuvant for SARS-CoV-2 vaccine
Authors: Wu Jun-Jun , Chen Yong-Xiang , Li Yan-Mei
Published: July 2020

A novel STING agonist CDGSF unilaterally modified with phosphorothioate and fluorine was synthesized. CDGSF displayed better STING activity over dithio CDG. Immunization of SARS-CoV-2 Spike protein with CDGSF as an adjuvant elicited an exceptional high antibody titer and a robust T cell response, which were better than the group using aluminium hydroxide as a adjuvant. These results highlighted the adjuvant potential of STING agonist in SARS-CoV-2 vaccine preparation for the first time.
Multiplexed quantitative screens of single cell shape and YAP/TAZ localisation identify DOCK5 as a coincident detector of polarity and adhesion during migration
Authors: Pascual-Vargas Patricia , Arias-Garcia Mar , Roumeliotis Theodoros I. , Choudhary Jyoti S. , Bakal Chris
Published: July 2020

YAP and TAZ are transcriptional co-activators that are often constitutively active in triple negative breast cancer (TNBC) cells driving proliferation, invasion, and drug resistance. Through multiplexed quantitative genetic screens for YAP/TAZ localisation and cell shape, we found that the RhoGEF DOCK5 is essential for YAP/TAZ activation in metastatic cells and is required for the maintenance of polarity during migration. DOCK5 regulates cell shape and thus YAP/TAZ through different genetic interactions with CDC42, RAC, and RHOA GTPases. DOCK5 regulates focal adhesion (FA) morphogenesis in RAC-dependent fashions that promote RHOA mediated actomyosin engagement of FA. Using unbiased systems-level quantification of protein levels by mass spectrometry we show that DOCK5 maintains polarity by stabilising protein levels of the CDC42 effector GSK3β. We conclude DOCK5 acts as a coincidence detector to promote leading edge persistence in subcellular locations where there is both RAC and RHOA dependent FA morphogenesis and active CDC42 mediated cell polarisation.
Intercellular signaling dynamics from a single cell atlas of the biomaterials response
Authors: Cherry Christopher , Maestas David R , Han Jin , Andorko James I , Cahan Patrick , Fertig Elana J , Garmire Lana X , Elisseeff Jennifer H
Published: July 2020

Biomaterials serve as the basis of implants, tissue engineering scaffolds, and multiple other biomedical therapeutics. New technologies, such as single cell RNA sequencing (scRNAseq), are enabling characterization of the biomaterial response to an unprecedented level of detail, facilitating new discoveries in the complex cellular environment surrounding materials. We performed scRNAseq and integrated data sets from multiple experiments to create a single cell atlas of the biomaterials response that contains 42,156 cells from biological extracellular matrix (ECM)-derived and synthetic polyester (polycaprolactone, PCL) scaffold biomaterials implanted in murine muscle wounds. We identified 18 clusters of cells, including natural killer (NK) cells, multiple subsets of fibroblasts, and myeloid cells, many of which were previously unknown in the biomaterial response. To determine intra and intercellular signaling occurring between the numerous cell subsets, including immune-stromal interactions in the biomaterial response, we developed Domino (github.com/chris-cherry/domino), a computational tool which allows for identification of condition specific intercellular signaling patterns connected to transcription factor activation from single cell data. The Domino networks self-assembled into signaling modules and cellular subsets involved in signaling independent of clustering, defining interactions between immune, fibroblast, and tissue-specific modules with biomaterials-specific communication patterns. Further compilation and integration of biomaterials single cell data sets will delineate the impact of materials chemical and physical properties and biological factors, such as anatomical placement, age, or systemic disease, that will direct biomaterials design.
Structure of human sodium leak channel NALCN in complex with FAM155A
Authors: Xie Jiongfang , Ke Meng , Xu Lizhen , Lin Shiyi , Zhang Jiabei , Yang Fan , Wu Jianping , Yan Zhen
Published: July 2020

NALCN, a sodium leak channel mainly expressed in the central nervous systems, is responsible for the resting Na+ permeability that controls neuronal excitability. Dysfunctions of the NALCN channelosome, NALCN with several auxiliary subunits, are associated with a variety of human diseases. Here, we reported the cryo-EM structure of human NALCN in complex with FAM155A, at an overall resolution of 3.1 angstrom. FAM155A forms extensive interactions with the extracellular loops of NALCN that help stabilize NALCN in the membrane. A Na+ ion-binding site, reminiscent of a Ca2+ binding site in Cav channels, is identified in the unique EEKE selectivity filter. Despite its ‘leaky’ nature, the intracellular gate is sealed by S6I, II-III linker and III-IV linker. Our study establishes the molecular basis of Na+ permeation and voltage sensitivity, and provides important clues to the mechanistic understanding of NALCN regulation and NALCN channelosome-related diseases.
Introgression, hominin dispersal and megafaunal survival in Late Pleistocene Island Southeast Asia
Authors: Teixeira João C. , Jacobs Guy S. , Stringer Chris , Tuke Jonathan , Hudjashov Georgi , Purnomo Gludhug A. , Sudoyo Herawati , Cox Murray P. , Tobler Ray , Turney Chris S.M. , Cooper Alan , Helgen Kristofer M.
Published: July 2020

The hominin fossil record of Island Southeast Asia (ISEA) indicates that at least two endemic ‘super-archaic’ species –Homo luzonensisandH. floresiensis– were present around the time anatomically modern humans (AMH) arrived in the region >50,000 years ago. Contemporary human populations carry signals consistent with interbreeding events with Denisovans in ISEA – a species that is thought to be more closely related to AMH than the super-archaic endemic ISEA hominins. To query this disparity between fossil and genetic evidence, we performed a comprehensive search for super-archaic introgression in >400 modern human genomes. Our results corroborate widespread Denisovan ancestry in ISEA populations but fail to detect any super-archaic admixture signals. By highlighting local megafaunal survival east of the Wallace Line as a potential signature of deep, pre-H. sapienshominin-faunal interaction, we propose that this understudied region may hold the key to unlocking significant chapters in Denisovan prehistory.
An organoid and multi-organ developmental cell atlas reveals multilineage fate specification in the human intestine
Authors: Yu Qianhui , Kilik Umut , Holloway Emily M. , Tsai Yu-Hwai , Wu Angeline , Wu Joshua H. , Czerwinski Michael , Childs Charlie , He Zhisong , Glass Ian A. , Higgins Peter D. R. , Treutlein Barbara , Spence Jason R. , Camp J. Gray
Published: July 2020

Human intestinal organoids (HIOs) generated from pluripotent stem cells provide extraordinary opportunities to explore development and disease. Here, we generate a single-cell transcriptome reference atlas from HIOs and from multiple developing human organs to quantify the specificity of HIO cell fate acquisition, and to explore alternative fates. We identify epithelium-mesenchyme interactions, transcriptional regulators involved in cell fate specification, and stem cell maturation features in the primary tissue that are recapitulated in HIOs. We use an HIO time course to reconstruct the molecular dynamics of intestinal stem cell emergence, as well as the specification of multiple mesenchyme subtypes. We find that the intestinal master regulator CDX2 correlates with distinct phases of epithelial and mesenchymal development, and CDX2 deletion perturbs the differentiation of both intestinal epithelium and mesenchyme. Collectively our data provides a comprehensive and quantitative assessment of HIO development, and illuminates the molecular machinery underlying endodermal and mesodermal cell fate specification.
Phenotypic plasticity underlies local invasion and distant metastasis in colon cancer
Authors: Sacchetti Andrea , Teeuwssen Miriam , Verhagen Mathijs , Joosten Rosalie , Xu Tong , Stabile Roberto , van der Steen Berdine , Watson Martin M. , Gusinac Alem , Kim Won Kyu , Ubink Inge , van de Werken Harmen J.G. , Fumagalli Arianna , Paauwe Madelon , van Rheenen Jacco , Sansom Owen , Kranenburg Onno , Fodde Riccardo
Published: July 2020

Phenotypic plasticity represents the most relevant hallmark of the carcinoma cell as it bestows it with the capacity of transiently altering its morphologic and functional features whileen routeto the metastatic site. However, the study of phenotypic plasticity is hindered by the rarity of these events within primary lesions and by the lack of experimental models. Here, we identified a subpopulation of phenotypic plastic colon cancer cells: EpCAMlocells are motile, invasive, chemo-resistant, and highly metastatic. EpCAMlobulk and single-cell RNAseq analysis indicated 1. enhanced Wnt/β-catenin signaling, 2. a broad spectrum of degrees of EMT activation including hybrid E/M states (partial EMT) with highly plastic features, and 3. high correlation with the CMS4 subtype, accounting for colon cancer cases with poor prognosis and a pronounced stromal component. Of note, a signature of genes specifically expressed in EpCAMlocancer cells is highly predictive of overall survival in tumors other than CMS4, thus highlighting the relevance of quasi-mesenchymal tumor cells across the spectrum of colon cancers. Enhanced Wnt and the downstream EMT activation represent key events in eliciting phenotypic plasticity along the invasive front of primary colon carcinomas. Distinct sets of epithelial and mesenchymal genes define transcriptional trajectories through which state transitions arise. pEMT cells, often earmarked by the extracellular matrix glycoprotein SPARC together with nuclear ZEB1 and β-catenin along the invasive front of primary colon carcinomas, are predicted to represent the origin of these (de)differentiation routes through biologically-distinct cellular states, and to underlie the phenotypic plasticity of colon cancer cells.
Quantitative detection of sleep apnea with wearable watch device
Authors: Hayano Junichiro , Yamamoto Hiroaki , Nonaka Izumi , Komazawa Makoto , Itao Kenichi , Udea Norihiro , Tanaka Haruhito , Yuda Emi
Published: July 2020

The spread of wearable watch devices with photoplethysmography (PPG) sensors has made it possible to use continuous pulse wave data during daily life. We examined if PPG pulse wave data can be used to detect sleep apnea, a common but underdiagnosed health problem associated with impaired quality of life and increased cardiovascular risk. In 41 patients undergoing diagnostic polysomnography (PSG) for sleep apnea, PPG was recorded simultaneously with a wearable watch device. The pulse interval data were analyzed by an automated algorithm called auto-correlated wave detection with adaptive threshold (ACAT) which was developed for electrocardiogram (ECG) to detect the cyclic variation of heart rate (CVHR), a characteristic heart rate pattern accompanying sleep apnea episodes. The median (IQR) apnea-hypopnea index (AHI) was 17.2 (4.4-28.4) and 22 (54%) subjects had AHI ≥15. The hourly frequency of CVHR (Fcv) detected by the ACAT algorithm closely correlated with AHI (r= 0.81), while none of the time-domain, frequency-domain, or non-linear indices of pulse interval variability showed significant correlation. The Fcv was greater in subjects with AHI ≥15 (19.6 ± 12.3 /h) than in those with AHI <15 (6.4 ± 4.6 /h), and was able to discriminate them with 82% sensitivity, 89% specificity, and 85% accuracy. The classification performance was comparable to that obtained when the ACAT algorithm was applied to ECG R-R intervals during the PSG. The analysis of wearable watch PPG by the ACAT algorithm could be used for the quantitative screening of sleep apnea.
Absence of reliable physiological signature of illusory body ownership revealed by fine-grained autonomic measurement during the rubber hand illusion
Authors: Critchley Hugo D , Botan Vanessa , Ward Jamie
Published: July 2020

The neural representation of a ‘biological self’ is linked theoretically to the control of bodily physiology. In an infleuntial model, selfhood relates to internal agency and higher-order interoceptive representation, inferred from the predicted impact of efferent autonomic nerves on afferent viscerosensory feedback. Here we tested if an altered representation of physical self (illusory embodiment of an artificial hand) is accompanied by sustained shifts in autonomic activity.

Participants (N=37) underwent procedures for induction of the rubber hand illusion (synchronous stroking of own unseen hand and observed stroking of artificial hand) and a control condition (asychronous stroking). We recorded electrodermal activity, electrocardiography, and non-invasive measurement of multiunit skin sympathetic nerve activity (SKNA) from the chest. We compared measures between task conditions, and between individuals who did and did not experience the illusion. Bayes factors quantified the strength of evidence for and against null hypotheses.

Subjective reports and observed proprioceptive drift confirmed the efficacy of synchronous vs asynchronous condition in inducing illusory hand ownership. Stringent discriminant analysis classified 24 /37 individuals as experiencing the rubber hand illusion. Electrodermal activity, heart rate, heart rate variability, and SKNA measures revealed no autonomic differences between synchronous vs asynchronous conditions, nor between individuals who did or did not experience the rubber hand illusion. Bayes factors confirmed there was substantial evidence for no physiological differences.

In contrast to earlier reports, our cardiac and electrodermal autonomic data, including fine grained SKNA measurement, provide substantial evidence for the absence of a reliable change in physiological state during induction or experience of the rubber hand illusion. If illusory body ownership is coupled to, or facilitated by, changes in efferent autonomic activity and afferent viscerosensory feedback, our findings suggest that such changes in bodily physiology are not sustained as an obligatory component of the illusion.
The bakers’s yeast Msh4-Msh5 associates with double-strand break hotspots and chromosome axis during meiosis to promote crossovers
Authors: Nandanan Krishnaprasad G. , Pankajam Ajith V. , Salim Sagar , Shinohara Miki , Lin Gen , Chakraborty Parijat , Steinmetz Lars M. , Shinohara Akira , Nishant Koodali T.
Published: July 2020

Segregation of homologous chromosomes during the first meiotic division requires at least one obligate crossover/exchange event between the homolog pairs. In the baker’s yeastSaccharomyces cerevisiaeand mammals, the mismatch repair-related factors, Msh4-Msh5 and Mlh1-Mlh3 generate the majority of the meiotic crossovers from programmed double-strand breaks (DSBs). To understand the mechanistic role of Msh4-Msh5 in meiotic crossing over, we performed genome-wide ChIP-sequencing and cytological analysis of the Msh5 protein in cells synchronized for meiosis. We observe that Msh5 associates with DSB hotspots, chromosome axis, and centromeres. We found that the initial recruitment of Msh4-Msh5 occurs following DSB resection. A two-step Msh5 binding pattern was observed: an early weak binding at DSB hotspots followed by enhanced late binding upon the formation of double Holliday junction structures. Msh5 association with the chromosome axis is Red1 dependent, while Msh5 association with the DSB hotspots and axis is dependent on DSB formation by Spo11. Msh5 binding was enhanced at strong DSB hotspots consistent with a role for DSB frequency in promoting Msh5 binding. These data on thein vivolocalization of Msh5 during meiosis have implications for how Msh4-Msh5 may work with other crossover and synapsis promoting factors to ensure Holliday junction resolution at the chromosome axis.

AUTHOR SUMMARY

During meiosis, crossovers facilitate physical linkages between homologous chromosomes that ensure their accurate segregation. Meiotic crossovers are initiated from programmed DNA double-strand breaks (DSBs). In the baker’s yeast and mammals, DSBs are repaired into crossovers primarily through a pathway involving the highly conserved mismatch repair related Msh4-Msh5 complex along with other crossover promoting factors.In vitroand physical studies suggest that the Msh4-Msh5 heterodimer facilitates meiotic crossover formation by stabilizing Holliday junctions. We investigated the genome-widein vivobinding sites of Msh5 during meiotic progression. Msh5 was enriched at DSB hotspots, chromosome axis, and centromere sites. Our results suggest Msh5 associates with both DSB sites on the chromosomal loops and with the chromosome axis to promote crossover formation. These results on thein vivodynamic localization of the Msh5 protein provide novel insights into how the Msh4-Msh5 complex may work with other crossover and synapsis promoting factors to facilitate crossover formation.
The ParA’s function is realized by two separate proteins in the partitioning system ofMyxococcusplasmid pMF1
Authors: Sheng Duohong , Chen Xiaojing , Li Yajie , Wang Jingjing , Zhuo Li , Li Yuezhong
Published: July 2020

Theparoperon in the sole myxobacterial plasmid pMF1 includes a function-unknownparCgene in front of the classicalparAandparBgenes. Removal ofparCseverely reduced plasmid stability, but ex-situ compensations ofparCdid not restore theparsystem function. Individual expression ofparAformed insoluble proteins, while co-expression ofparCbeforeparAproduced a soluble ParC-ParA heterodimer. ParA alone had no ATPase activity and no polymerization, while ParC addition aided ParA to restore the activities. Fusing ParC and ParA in different ways all produced soluble proteins and some restored ATPase activity or increased plasmid stability. Protein interaction model analysis and experiments revealed that ParC structurally mimics the N-terminal of Ia-type SopA (ParA), endowing theMyxococcusParA protein to play functions by shifting of ParC between two sites on ParA surface. The present results highlight that ParC functions as a part of ParA to support its soluble expression and function, and the separation of ParC and ParA into two proteins in structure enables the ParC ‘fragment’ to shift in a larger range around ParA to function during partitioning.

Author summary

Our work on ParC here provides a new example for the evolution of multi-domain protein. ParC and ParA are two proteins, but their expression and function act as a whole, which proposes a new regulatory model for bacterialparsystem, and also provides research ideas and materials for the study of functional coordination and evolution of ParA domains in the future.
Opposing macroevolutionary and trait-mediated patterns of threat and naturalization in flowering plants
Authors: Schmidt J. P. , Davies T. J. , Farrell M. J.
Published: July 2020

Due to expanding global trade and movement, new plant species are establishing in exotic ranges at increasing rates while the number of native species facing extinction from multiple threats grows. Yet, how species losses and gains globally may together be linked to traits and macroevolutionary processes is poorly understood. Here we show that, adjusting for diversification rate and age, the proportion of threatened species across flowering plant families is negatively related to the proportion of naturalized species. Moreover, naturalization is positively associated with climate variability, short generation time, autonomous seed production, and interspecific hybridization, but negatively with age and diversification; whereas threat is negatively associated with climate variability and hybridization, and positively with biotic pollination, age and diversification. Such a pronounced signature of naturalization and threat across plant families suggests that both trait syndromes have coexisted over deep evolutionary time and that neither strategy is necessarily superior to the other.