bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of an Innovative Training Program for New Graduate Registered Nurses: a Comparison Study
Authors: Xu Fengqin , Wang Yinhe , Ma Liang , Yu Jiang , Li Dandan , Zhou Guohui , Xu Yuzi , Zhang Hailin , Cao Yang
Published: September 2020

New graduate registered nurses (NGRNs) face great challenge during the transition from school to clinical practice. The aim of the study is to evaluate the effects of a new training mode for newly recruited NGRNs in a Chinese teaching hospital. This is a quasi-randomized controlled study. One hundred and fifty NGRNs were randomly selected from a teaching hospital and assigned into two groups. The conventional training and a new training program were taken for the control group and the research group respectively. At the end of training, the two groups were evaluated and compared for theoretical knowledge and operation skills using a self-assessment questionnaire and the Chinese Registered Nurse Core Competency Scale. The theoretical knowledge (88.4 vs. 81.7, p< 0.001), operation skills (94.8 vs. 90.3, p< 0.001), and total core competencies scores (156.2 vs. 148.8, p< 0.05) in the research group were significantly higher than those in the control group. Compared to the control group, the research group had statistically significantly higher scores in education and consultation (2.47 vs. 2.40), clinical nursing (2.87 vs. 2.62), interpersonal relationship (2.56 vs. 2.43), and critical thinking and scientific research (2.78 vs. 2.61). The innovative pre-job training program for NGRNs conducted in Chinese clinical nursing skill training bases could significantly improve the training effect and is worthy of broader implementation.
Smartphone overuse and visual impairment in children and young adults: a systematic review and meta-analysis
Authors: Wang Jian , Li Mei , Zhu Daqiao , Cao Yang
Published: September 2020

Background

Smartphone overuse has been cited as a potentially modifiable risk factor that can result in visual impairment. However, associations between smartphone overuse and visual impairment have not been consistently reported.

Objective

The aim of this systematic review is to determine the association between smartphone overuse and visual impairment, including myopia, blurred vision, and poor vision, in children and young adults.

Methods

We conducted a systematic search in the Cochrane Library, Pubmed, EMBASE, Web of Science Core Collection, and ScienceDirect since the beginning of the databases to June 2020. Fourteen eligible studies (ten cross-sectional studies and four controlled trials) were identified, which included a total of 27110 subjects with mean ages ranging from 9.5 to 26.0 years. We used a random-effects model in the ten cross-sectional studies (n= 26962) and a fixed-effects model in the four controlled trials (n= 148) to combine odds ratios (OR) and effect sizes (ES). TheI2statistics was used to assess heterogeneity.

Results

A pooled OR of 1.05 (95% CI: 0.98, 1.13;p= 0.159) from cross-sectional studies suggests that smartphone overuse is not statistically significantly associated with myopia, poor vision, or blurred vision, however these visual impairments together are more apparent in children (OR = 1.06, 95% CI: 0.99, 1.14; p = 0.087) than in young adults (OR = 0.91, 95% CI: 0.57, 1.46; p = 0.707). In all the controlled trials, the smartphone overuse groups showed worse visual function scores compared with the less-use groups. The pooled ES is 0.76 (95% CI: 0.53, 0.99) and statistically significant (p< 0.001).

Conclusions

Our results indicate that longer smartphone use may increase the likelihood of ocular symptoms including myopia, asthenopia, and/or ocular surface disease, especially in children. Thus, regulating use time and restricting the prolonged use of smartphones may prevent ocular and visual symptoms. Further research on the patterns of use, with longer follow-up on the longitudinal associations will help inform detailed guidelines and recommendations for smartphone use in children and young adults.
A novel sample pooling strategy and its application for mass screening of SARS-CoV-2 in an outbreak of COVID-19 in Vietnam
Authors: Thanh Ton That , Nhan Nguyen Thi Thanh , Mai Huynh Kim , Trieu Nguyen Bao , Huy Le Xuan , Thuy Ho Thi Thanh , Chung Le Thanh , Anh Nguyen Ngoc , Hong Nguyen Thi Thu , Thang Bui Duc , Thu Nguyen Thi Hoai , Chi Le Thi Kim , Hanh Nguyen Thi , Hoang Nguyen Huy , Van Vinh Chau Nguyen , Thwaites Guy , Hung Do Thai , Van Tan Le , Yen Ngo Thi Kim
Published: September 2020

We present a sample pooling approach and the results of its application for mass screening of SARS-CoV-2 in >96,000 asymptomatic individuals. Our approach did not compromise the sensitivity of PCR, while increasing the throughput and reducing 77% of the costs. 22/32 asymptomatic cases would have been missed without mass screening.
Resurgence of SARS-CoV-2 in England: detection by community antigen surveillance
Authors:   REACT Study Investigators:, Riley Steven , Ainslie Kylie E. C. , Eales Oliver , Walters Caroline E. , Wang Haowei , Atchison Christina , Fronterre Claudio , Diggle Peter J. , Ashby Deborah , Donnelly Christl A. , Cooke Graham , Barclay Wendy , Ward Helen , Darzi Ara , Elliott Paul
Published: September 2020

Background

Based on cases and deaths, transmission of SARS-CoV-2 in England peaked in late March and early April 2020 and then declined until the end of June. Since the start of July, cases have increased, while deaths have continued to decrease.

Methods

We report results from 594,000 swabs tested for SARS-CoV-2 virus obtained from a representative sample of people in England over four rounds collected regardless of symptoms, starting in May 2020 and finishing at the beginning of September 2020. Swabs for the most recent two rounds were taken between 24th July and 11th August and for round 4 between 22nd August and 7th September. We estimate weighted overall prevalence, doubling times between and within rounds and associated reproduction numbers. We obtained unweighted prevalence estimates by sub-groups: age, sex, region, ethnicity, key worker status, household size, for which we also estimated odds of infection. We identified clusters of swab-positive participants who were closer, on average, to other swab-positive participants than would be expected.

Findings

Over all four rounds of the study, we found that 72% (67%, 76%) of swab-positive individuals were asymptomatic at the time of swab and in the week prior. The epidemic declined between rounds 1 and 2, and rounds 2 and 3. However, the epidemic was increasing between rounds 3 and 4, with a doubling time of 17 (13, 23) days corresponding to an R value of 1.3 (1.2, 1.4). When analysing round 3 alone, we found that the epidemic had started to grow again with 93% probability. Using only the most recent round 4 data, we estimated a doubling time of 7.7 (5.5, 12.7) days, corresponding to an R value of 1.7 (1.4, 2.0). Cycle threshold values were lower (viral loads were higher) for rounds 1 and 4 than they were for rounds 2 and 3. In round 4, we observed the highest prevalence in participants aged 18 to 24 years at 0.25% (0.16%, 0.41%), increasing from 0.08% (0.04%, 0.18%) in round 3. We observed the lowest prevalence in those aged 65 and older at 0.04% (0.02%, 0.06%) which was stable compared with round 3. Participants of Asian ethnicity had elevated odds of infection. We identified clusters in and around London, transient clusters in the Midlands, and an expanding area of clustering in the North West and more recently in Yorkshire and the Humber.

Interpretation

Although low levels of transmission persisted in England through to mid-summer 2020, the prevalence of SARS-CoV-2 is now increasing. We found evidence of accelerating transmission at the end of August and beginning of September. Representative community antigen sampling can increase situational awareness and help improve public health decision making even at low prevalence.
Retrospective study of COVID-19 seroprevalence among tissue donors at the onset of the outbreak before implementation of strict lockdown measures in France
Authors: Germain Nicolas , Herwegh Stéphanie , Hatzfeld Anne-Sophie , Bocket Laurence , Prévost Brigitte , Danze Pierre-Marié , Marchetti Philippe
Published: September 2020

Background

The COVID-19 pandemic has altered organ and tissue donations as well as transplantation practices. SARS-CoV-2 serological tests could help in the selection of donors. We assessed COVID-19 seroprevalence in a population of tissue donors, at the onset of the outbreak in France, before systematic screening of donors for SARS-CoV-2 RNA.

Methods

235 tissue donors at the Lille Tissue bank between November 1, 2019 and March 16, 2020 were included. Archived serum samples were tested for SARS-CoV-2 antibodies using two FDA-approved kits.

Results: Most donors were at higher risks for severe COVID-19 illness including age over 65 years (142/235) and/or presence of co-morbidities (141/235). According to the COVID-19 risk assessment of transmission, 183 out of 235 tissue donors presented with a low risk level and 52 donors with an intermediate risk level of donor derived infection. Four out of the 235 (1.7%) tested specimens were positive for anti-SARS-CoV-2 antibodies: 2 donors with anti-N protein IgG and 2 other donors with anti-S protein total Ig. None of them had both type of antibodies. Conclusion: Regarding the seroprevalence among tissue donors, we concluded that the transmission probability to recipient via tissue products was very low at the beginning of the outbreak.
Mortality associated with third generation cephalosporin-resistance in Enterobacteriaceae infections: a multicentre cohort study in Southern China
Authors: Wang Jiancong , Zhou Mouqing , Hesketh Therese , Kritsotakis Evangelos I.
Published: September 2020

Background

Emerging third generation cephalosporin-resistant Enterobacteriaceae (3GCR-EB) pose a global healthcare concern. We assessed excess mortality in patients infected with 3GCR-EB compared to patients infected with third-generation cephalosporin-susceptible Enterobacteriaceae (3GCS-EB).

Methods

The study cohort comprised all inpatients with a community-onset or healthcare-associated infection caused by Enterobacteriaceae in three tertiary-care public hospitals in 2017. Excess in-hospital mortality was assessed using competing risk survival models, adjusting for baseline patient characteristics.

Results

Of 2,343 study patients (median age 60 years; 45.2% male), 1,481 (63.2%) had 3GCS-EB and 862 (36.8%) 3GCR-EB infection. 494 (57.0%) 3GCR-EB isolates were co-resistant to fluoroquinolones and 15 (1.7%) co-resistant to carbapenems. In-hospital mortality was similar in the 3GCS-EB and 3GCR-EB groups (2.4% vs. 2.8%; p=0.601). No increase in the hazard of in-hospital mortality was detected for 3GCR-EB infections compared to 3GCS-EB infections (sub-distribution hazard ratio [HR] 0.80; 95%CI, 0.41 - 1.55) in multivariable analysis adjusting for patient age, sex, intensive care admission, origin of infection and site of infection. Analysis of cause-specific hazards showed that 3GCR-EB infections significantly decreased the daily rate of hospital discharge (cause-specific HR=0.84; 95%CI, 0.76 - 0.92) thereby leading to lengthier hospitalizations.

Conclusion

Third-generation cephalosporin resistance in Enterobacteriaceae infection per se was not associated with increased in-hospital mortality in this study. However, 3GCR-EB infections were seen to place significant healthcare burden by increasing the length of hospitalization compared to 3GCS-EB infections.
NGPINT: A Next-generation protein-protein interaction software
Authors: Banerjee Sagnik , Velásquez-Zapata Valeria , Fuerst Gregory , Elmore J. Mitch , Wise Roger P.
Published: September 2020

Mapping protein-protein interactions at a proteome scale is critical to understanding how cellular signaling networks respond to stimuli. Since eukaryotic genomes encode thousands of proteins, testing their interactions one-by-one is a challenging prospect. High-throughput yeast-two hybrid (Y2H) assays that employ next-generation sequencing to interrogate cDNA libraries represent an alternative approach that optimizes scale, cost, and effort. We present NGPINT, a robust and scalable software to identify all putative interactors of a protein using Y2H in batch culture. NGPINT combines diverse tools to align sequence reads to target genomes, reconstruct prey fragments and compute gene enrichment under reporter selection. Central to this pipeline is the identification of fusion reads containing sequences derived from both the Y2H expression plasmid and the cDNA of interest. To reduce false positives, these fusion reads are evaluated as to whether the cDNA fragment forms anin-frametranslational fusion with the Y2H transcription factor. NGPINT successfully recognized 95% of interactions in simulated test runs. As proof of concept, NGPINT was tested using published data sets and recognized all validated interactions. NGPINT can be used in any organism with an available reference, thus facilitating the discovery of protein-protein interactions in non-model organisms.
Single-cell RNA sequencing of Tocilizumab-treated peripheral blood mononuclear cells as an in vitro model of inflammation
Authors: Zarinsefat Arya , Hartoularos George , Chandran Sindhu , Yee Chun J. , Vincenti Flavio , Sarwal Minnie M.
Published: September 2020

COVID-19 has posed a significant threat to global health. Early data has revealed that IL-6, a key regulatory cytokine, plays an important role in the cytokine storm of COVID-19. Multiple trials are therefore looking at the effects of Tocilizumab, an IL-6 receptor antibody that inhibits IL-6 activity, on treatment of COVID-19, with promising findings. As part of a clinical trial looking at the effects of Tocilizumab treatment on kidney transplant recipients with subclinical rejection, we performed single-cell RNA sequencing of comparing stimulated PBMCs before and after Tocilizumab treatment. We leveraged this data to create an in vitro cytokine storm model, to better understand the effects of Tocilizumab in the presence of inflammation. Tocilizumab-treated cells had reduced expression of inflammatory-mediated genes and biologic pathways, particularly amongst monocytes. These results support the hypothesis that Tocilizumab may hinder the cytokine storm of COVID-19, through a demonstration of biologic impact at the single-cell level.
NHR-49 Acts in Distinct Tissues to Promote Longevity versus Innate Immunity
Authors: Naim Nikki , Amrit Francis RG , Ratnappan Ramesh , DelBuono Nicholas , Loose Julia A , Ghazi Arjumand
Published: September 2020

Aging and immunity are inextricably linked and many genes that extend lifespan also enhance immunoresistance. However, it remains unclear if longevity-enhancing factors modulate immunity and longevity by distinct or shared mechanisms. Here, we demonstrate that theCaenorhabditis eleganspro-longevity factor, NHR-49, also promotes resistance againstPseudomonas aeruginosa, but modulates immunity and longevity by spatially and mechanistically distinct mechanisms. Fenofibrate, an agonist of NHR-49’s mammalian functional homolog, PPARα, enhanced worm immunoresistance in an NHR-49-dependent manner. NHR-49 expression is increased by germline ablation, an intervention that extends lifespan, but lowered by pathogen exposure. NHR-49 acted in multiple somatic tissues to promote longevity, whereas, it’s pro-immunity function was mediated by neuronal expression. The canonical NHR-49 target genes,acs-2andfmo-2, were upregulated by germline loss, but infection triggeredfmo-2downregulation andacs-2upregulation. Interestingly, neither gene conferred resistance against Gram-negativePseudomonas, unlike their reported roles in immunity against Gram-positive pathogens. Thus, NHR-49 is differentially regulated by interventions that bring about long-term changes (lifespan extension) vs. short-term stress (pathogen exposure) and in response it orchestrates distinct outputs, including pathogen-specific transcriptional programs. Overall, our study demonstrates the independent control of immunity and longevity by a conserved regulatory protein.
Orphan G protein-coupled receptor, GPR37L1: pharmacological toolbox empty once again
Authors: Ngo Tony , Wilkins Brendan P. , So Sean S. , Keov Peter , Chahal Kirti K. , Finch Angela M. , Coleman James L.J. , Kufareva Irina , Smith Nicola J.
Published: September 2020

Orphan G protein-coupled receptors (GPCRs) are largely intractable therapeutic targets, owing to the lack of chemical tools for exploring their pharmacology. The discovery of such tools, however, is hampered by a number of unknowns, such as effector coupling and appropriate positive controls. In our 2017 Nature Chemical Biology paper1, we developed a computational chemical tool discovery approach called GPCR Contact-Informed Neighboring Pocket (GPCR-CoINPocket). This method predicted pharmacological similarity of GPCRs in a ligand- and structure-independent manner, to enable the discovery of off-target activities of known compounds at orphan GPCRs and hence the identification of so-called surrogate ligands. Our orphan GPCR target for prospective surrogate ligand discovery efforts was GPR37L1, a brain-specific receptor linked to cerebellar development2and seizures3. We had previously demonstrated that GPR37L1 constitutively coupled to Gαs and generated ligand-independent increases in intracellular cAMP4§. Thus, the inverse agonist activities of computationally predicted surrogates were tested in the cAMP response element luciferase (CRE-luc) reporter gene assay in human embryonic kidney (HEK293) cells expressing either vector control or what we thought was untagged GPR37L1 in pcDNA3.1. However, we recently discovered that the GPR37L1 construct used in that study was incorrect: instead of pcDNA3.1, it carried the receptor inserted backwards into a yeast p426GPD vector (hereafter referred to as p426-r37L1). Here, we correct the cloning error and describe our subsequent unsuccessful efforts to re-test the computationally predicted GPR37L1 ligands (triggering an author-initiated retraction of1).

Note

We, the authors, are working with the Nature Chemical Biology Editors to retract our 2017 paper ‘Orphan receptor ligand discovery by pickpocketing pharmacological neighbors’1. The present manuscript is under review at Nature Chemical Biology as a Matters Arising accompaniment to the anticipated author-initiated retraction. We initiated the steps towards the retraction upon discovering a regrettable cloning error that put into question the in vitro findings reported in1. This action was unanimously agreed upon by all authors. The computational aspects of the original manuscript1are unaffected by this error.
Functional interrogation of a SARS-CoV-2 host protein interactome identifies unique and shared coronavirus host factors
Authors: Hoffmann H.-Heinrich , Schneider William M. , Sánchez-Rivera Francisco J. , Luna Joseph M. , Ashbrook Alison W. , Soto-Feliciano Yadira M. , Leal Andrew A. , Le Pen Jérémie , Ricardo-Lax Inna , Michailidis Eleftherios , Hao Yuan , Stenzel Ansgar F. , Peace Avery , Allis C. David , Lowe Scott W. , MacDonald Margaret R. , Poirier John T. , Rice Charles M.
Published: September 2020

The ongoing SARS-CoV-2 pandemic has devastated the global economy and claimed nearly one million lives, presenting an urgent global health crisis. To identify host factors required for infection by SARS-CoV-2 and seasonal coronaviruses, we designed a focused high-coverage CRISPR-Cas9 library targeting 332 members of a recently published SARS-CoV-2 protein interactome. We leveraged the compact nature of this library to systematically screen four related coronaviruses (HCoV-229E, HCoV-NL63, HCoV-OC43 and SARS-CoV-2) at two physiologically relevant temperatures (33 °C and 37 °C), allowing us to probe this interactome at a much higher resolution relative to genome scale studies. This approach yielded several new insights, including unexpected virus and temperature specific differences in Rab GTPase requirements and GPI anchor biosynthesis, as well as identification of multiple pan-coronavirus factors involved in cholesterol homeostasis. This coronavirus essentiality catalog could inform ongoing drug development efforts aimed at intercepting and treating COVID-19, and help prepare for future coronavirus outbreaks.

HIGHLIGHTS

Focused CRISPR screens targeting host factors in the SARS-CoV-2 interactome were performed for SARS-CoV-2, HCoV-229E, HCoV-NL63, and HCoV-OC43 coronaviruses.

Focused interactome CRISPR screens achieve higher resolution compared to genome-wide screens, leading to the identification of critical factors missed by the latter.

Parallel CRISPR screens against multiple coronaviruses uncover host factors and pathways with pan-coronavirus and virus-specific functional roles.

The number of host proteins that interact with a viral bait protein is not proportional to the number of functional interactors.

Novel SARS-CoV-2 host factors are expressed in relevant cell types in the human airway.
Cardiac Cell Type-Specific Gene Regulatory Programs and Disease Risk Association
Authors: Hocker James D. , Poirion Olivier B. , Zhu Fugui , Buchanan Justin , Zhang Kai , Chiou Joshua , Wang Tsui-Min , Hou Xiaomeng , Li Yang E. , Zhang Yanxiao , Farah Elie N. , Wang Allen , McCulloch Andrew D. , Gaulton Kyle J. , Ren Bing , Chi Neil C. , Preissl Sebastian
Published: September 2020

Background

Cis-regulatory elements such as enhancers and promoters are crucial for directing gene expression in the human heart. Dysregulation of these elements can result in many cardiovascular diseases that are major leading causes of morbidity and mortality worldwide. In addition, genetic variants associated with cardiovascular disease risk are enriched withincis-regulatory elements. However, the location and activity of thesecis-regulatory elements in individual cardiac cell types remains to be fully defined.

Methods

We performed single nucleus ATAC-seq and single nucleus RNA-seq to define a comprehensive catalogue of candidatecis-regulatory elements (cCREs) and gene expression patterns for the distinct cell types comprising each chamber of four non-failing human hearts. We used this catalogue to computationally deconvolute dynamic enhancers in failing hearts and to assign cardiovascular disease risk variants to cCREs in individual cardiac cell types. Finally, we applied reporter assays, genome editing and electrophysiogical measurements inin vitrodifferentiated human cardiomyocytes to validate the molecular mechanisms of cardiovascular disease risk variants.

Results

We defined >287,000 candidatecis-regulatory elements (cCREs) in human hearts at single-cell resolution, which notably revealed gene regulatory programs controlling specific cell types in a cardiac region/structure-dependent manner and during heart failure. We further report enrichment of cardiovascular disease risk variants in cCREs of distinct cardiac cell types, including a strong enrichment of atrial fibrillation variants in cardiomyocyte cCREs, and reveal 38 candidate causal atrial fibrillation variants localized to cardiomyocyte cCREs. Two such risk variants residing within a cardiomyocyte-specific cCRE at theKCNH2/HERGlocus resulted in reduced enhancer activity compared to the non-risk allele. Finally, we found that deletion of the cCRE containing these variants decreasedKCNH2expression and prolonged action potential repolarization in an enhancer dosage-dependent manner.

Conclusions

This comprehensive atlas of human cardiac cCREs provides the foundation for not only illuminating cell type-specific gene regulatory programs controlling human hearts during health and disease, but also interpreting genetic risk loci for a wide spectrum of cardiovascular diseases.
Phylogeographic model selection using convolutional neural networks
Authors: da Fonseca Emanuel Masiero , Colli Guarino R. , Werneck Fernanda P. , Carstens Bryan C.
Published: September 2020

The field of phylogeography has evolved rapidly in terms of the analytical toolkit to analyze the ever-increasing amounts of genomic data. Despite substantial advances, researchers have not fully explored all potential analytical tools to tackle the challenge posed by the huge size of genomic datasets. For example, deep learning techniques, such as convolutional neural networks (CNNs), widely employed in image and video classification, are largely unexplored for phylogeographic model selection. In non-model organisms, the lack of information about their ecology, natural history, and evolution can lead to uncertainty about which set of demographic models should be considered. Here we investigate the utility of CNNs for assessing a large number of competing phylogeographic models using South American lizards as an example, and approximate Bayesian computation (ABC) to contrast the performance of CNNs. First, we evaluated three demographic scenarios (constant, expansion, and bottleneck) for each of four recovered lineages and found that the overall model accuracy was higher than 98% for all lineages. Next, we evaluated a set of 26 models that accounted for evolutionary relationships, gene flow, and changes in effective population size among these lineages and recovered an overall accuracy of 87%. In contrast, ABC was unable to single out a best fit model among 26 competing models. Finally, we used the CNN model to investigate the evolutionary history of two South American lizards. Our results indicate the presence of hidden genetic diversity, gene flow between non-sister populations, and changes in effective population sizes through time, likely in response to Pleistocene climatic oscillations. Our results demonstrate that CNNs can be easily and usefully incorporated into the phylogeographer’s toolkit.
Constitutively active TrkB kinase signalling reduces actin filopodia dynamics and cell migration
Authors: Gupta Rohini , Bauer Melanie , Wohlleben Gisela , Luzak Vanessa , Wegat Vanessa , Segebarth Dennis , Bady Elena , Langlhofer Georg , Wachter Britta , Havlicek Steven , Lüningschrör Patrick , Villmann Carmen , Polat Bülent , Monoranu Camelia M. , Kuper Jochen , Blum Robert
Published: September 2020

Trk receptors and gene fusions ofNTRKare targets in precision oncology. Classical Trk signalling concepts fail to explain ligand-independent signalling of intracellular TrkB orNTRKfusion proteins. Here, we show that abundance of the intracellular domain of TrkB is sufficient for ligand-independent autophosphorylation. This constitutive TrkB signalling reduced actin filopodia dynamics, could phosphorylate FAK, and changed cell morphology. Mutating Y705in the kinase domain of TrkB alone specifically blocked these pathways. Engineered intracellular kinase domain proteins and a cancer-related intracellularNTRK2-fusion protein (SQSTM1-NTRK2) also underwent constitutive activation. In migrating glioblastoma-like U87MG cells, self-active TrkB kinase reduced cell migration. Moreover, we found evidences for constitutively active, intracellular TrkB in tissue of human grade IV glioblastoma. Structural modelling of the kinase domain let us postulate that ‘release from cis-autoinhibition by abundance’ is sufficient for TrkB/FAK/Actin signalling via Y705. These constitutive signalling pathways could be fully blocked within minutes by clinically approved, anti-tumorigenic Trk inhibitors. In conclusion, our data provide an explanation and biological function for TrkB kinase domain signalling in the absence of a ligand.
The Novel PII-Interacting Regulator PirC (Sll0944) Identifies 3-Phosphoglycerate Mutase (PGAM) as Central Control Point of Carbon Storage Metabolism in Cyanobacteria
Authors: Orthwein Tim , Scholl Jörg , Spät Philipp , Lucius Stefan , Koch Moritz , Macek Boris , Hagemann Martin , Forchhammer Karl
Published: September 2020

Nitrogen limitation imposes a major transition in the life-style of non-diazotrophic cyanobacteria, which is regulated via a complex interplay of regulatory factors, involving, the nitrogen-specific transcription factor NtcA and the pervasive signal processor PII. Immediately upon nitrogen-limitation, newly fixed carbon is re-directed towards glycogen synthesis. How the metabolic switch for distributing fixed carbon to either glycogen or cellular building blocks is operated was poorly understood. Here we identify fromSynechocystissp. PCC 6803 a novel PII interactor, PirC, (Sll0944) that controls 3-phosphoglycerate mutase (PGAM), the enzyme that deviates newly fixed CO2towards lower glycolysis. PirC acts as competitive inhibitor of PGAM and this interaction is tuned by PII/2-oxoglutarate. High oxoglutarate release PirC from PII-complex to inhibit PGAM. Accordingly, PirC deficient mutant, as compared to the wild-type, shows strongly reduced glycogen levels upon nitrogen deprivation whereas polyhydroxybutyrate granules are over-accumulated. Metabolome analysis revealed an imbalance in 3-phosphoglycerate to pyruvate levels in the PirC mutant, conforming that PirC controls the carbon flux in cyanobacteria via mutually exclusive interaction with either PII or PGAM.
mTOR S-nitrosylation inhibits autophagy and lysosomal proteolysis
Authors: Tan Bryce W.Q. , Tan Sijie , Tan Byorn W.L. , Navakkode Sheeja , Ng Cheng Yang , Yuan Steven , Liang Mui Cheng , Liu Chao , Yin Shi , Chai Chou , Chew Katherine C.M. , Tai Yee Kit , Sajikumar Sreedharan , Lam Yulin , Liao Ping , Shen Han-Ming , Lim Kah-Leong , Wong Esther , Soong Tuck Wah
Published: September 2020

Mammalian Target of Rapamycin (mTOR) is a master regulator of autophagy and lysosomes, and its downstream kinase-dependent pathways have been extensively characterized. Here, we report an unexpected kinase-independent regulation of autophagy and lysosomes by S-nitrosylation at Cys423 position of mTOR that resulted in suppression of VPS34 and PIKfyve-dependent phosphoinositide synthesis. Physiologically, S-nitrosylation of mTOR reduced basal lysosomal proteolysis via nitric oxide synthase (NOS)-mediated synthesis of NO from lysosomal arginine precursor, a marker of cellular nutrition status. Significantly, we found increased lysosomal NOS-mTOR complexes in APP-PS1 Alzheimer’s disease (AD) murine model, and increased mTOR S-nitrosylation in AD patient-derived fibroblasts. Lastly, we demonstrated that pharmacological inhibition of NOS or overexpression of mTORCys423Alamutant reversed lysosomal and autophagic dysfunction in AD patient-derived fibroblasts, suggesting novel therapeutic strategies for autophagosome-lysosomal activation.
A key linear epitope for a potent neutralizing antibody to SARS-CoV-2 S-RBD
Authors: Li Tingting , Han Xiaojian , Wang Yingming , Gu Chenjian , Wang Jianwei , Hu Chao , Li Shenglong , Wang Kai , Luo Feiyang , Huang Jingjing , Long Yingyi , Song Shuyi , Wang Wang , Hu Jie , Wu Ruixin , Mu Song , Hao Yanan , Chen Qian , Gao Fengxia , Shen Meiying , Long Shunhua , Gong Fang , Li Luo , Wu Yang , Xu Wei , Cai Xia , Qu Di , Yuan Zhenghong , Gao Qingzhu , Zhang Guiji , He Changlong , Nai Yaru , Deng Kun , Du Li , Tang Ni , Xie Youhua , Huang Ailong , Jin Aishun
Published: September 2020

The spread of SARS-CoV-2 confers a serious threat to the public health without effective intervention strategies1–3. Its variant carrying mutated Spike (S) protein D614G (SD614G) has become the most prevalent form in the current global pandemic4,5. We have identified a large panel of potential neutralizing antibodies (NAbs) targeting the receptor-binding domain (RBD) of SARS-CoV-2 S6. Here, we focused on the top 20 potential NAbs for the mechanism study. Of them, the top 4 NAbs could individually neutralize both authentic SARS-CoV-2 and SD614Gpseudovirus efficiently. Our epitope mapping revealed that 16/20 potent NAbs overlapped the same steric epitope. Excitingly, we found that one of these potent NAbs (58G6) exclusively bound to a linear epitope on S-RBD (termed as 58G6e), and the interaction of 58G6e and the recombinant ACE2 could be blocked by 58G6. We confirmed that 58G6e represented a key site of vulnerability on S-RBD and it could positively react with COVID-19 convalescent patients’ plasma. We are the first, as far as we know, to provide direct evidences of a linear epitope that can be recognized by a potent NAb against SARS-CoV-2 S-RBD. This study paves the way for the applications of these NAbs and the potential safe and effective vaccine design.
A bootstrap approach is a superior statistical method for the comparison of cell-to-cell movement data
Authors: Johnston Matthew G. , Faulkner Christine
Published: September 2020

Plasmodesmata are an increasing focus of plant research, and plant physiologists frequently aim to understand the dynamics of intercellular movement and plasmodesmal function. For this, experiments that measure the spread of GFP between cells are commonly performed to indicate whether plasmodesmata are more open or closed in different conditions or in different genotypes.

We propose cell-to-cell movement data sets are better analysed by a bootstrap method that tests the null hypothesis that means (or medians) are the same between two conditions, instead of the commonly used Mann-Whitney-Wilcoxon test. We found that that with hypothetical distributions similar to cell-to-cell movement data, the Mann-Whitney-Wilcoxon produces a false positive rate of 17% while the bootstrap method maintains a false positive at the set rate of 5% under the same circumstances. Here we present this finding, as well as our rationale, an explanation of the bootstrap method and an R script for easy use. We have further demonstrated its use on published datasets from independent laboratories.
Changes in cellular signaling patterns before and after stroke in the middle cerebral arteries of stroke prone spontaneously hypertensive rats
Authors: Chokshi Killol , Warren Julie , Squires Krista , Kitselman Kayla A. , Doré Jules , Daneshtalab Noriko
Published: September 2020

Background

Hemorrhagic stroke is associated with loss of middle cerebral artery (MCA) autoregulation in the stroke-prone spontaneously hypertensive rat (SHRsp). The signaling mechanism associated with the functional loss has yet to be defined. We hypothesize that physiological alterations coincide with changes to cerebrovascular inflammatory and contractile signaling and altered calcium signaling. METHODS: SHRsp rats were fed a high salt (4% NaCl) diet and sacrificed at 9 weeks of age for pre-stroke and after evidence of stroke for post-stroke samples. The MCAs were isolated for measuring protein levels using immunofluorescence (IF) & western blot (WB) for inflammatory signaling and contractile proteins. Tissues surrounding the MCA were analyzed for neuro-inflammation, neuronal damage, total and activated inflammatory proteins (ERK1/2 and p38MAPK), cerebrovascular contraction (PKC and MLC), and transient receptor potential V4 (TRPV4) expression. RESULTS: Our data show increase in activated inflammatory proteins after stroke with an associated decrease in expression of activated contractile proteins and TRPV4 channel expression compared to pre-stroke MCA. The post-stroke samples also show significant increase in neuro-inflammation and neuronal damage compared to pre-stroke samples.

CONCLUSION

An increase in activated/total (p38 MAPK &ERK1/2) is accompanied by a decrease in activated/total PKC & TRPV4 channel expression in post-stroke SHRsps. The decrease in vessel structural integrity and altered vascular tone of the MCAs may affect its ability to contract in response to pressure. Significant neuro-inflammation and neuronal damage in the brain tissues surrounding the MCA in post-stroke samples suggest MCA dysfunction is accompanied with neuronal and neural damage during stroke.
Experimental-based Computational Modeling Distinguishes Early Cardiac Outflow Tract Compensation Mechanisms
Authors: Lindsey Stephanie E. , Vignon-Clementel Irene E. , Butcher Jonathan T.
Published: September 2020

Mechanical forces are essential for proper growth and remodeling of the primitive pharyngeal arch arteries (PAAs) into the great vessels of the heart. Despite general acknowledgement of a link between abnormal hemodynamics and cardiac malformations, the direct correlation between hemodynamics and pharyngeal arch artery morphogenesis remains poorly understood. The elusiveness behind understanding hemodynamic-malformation links is largely due to the difficulty of performing isolated hemodynamic perturbations and quantifying key hemodynamic indices in-vivo. To overcome this issue, minimally invasive occlusion experiments were combined with three-dimensional anatomical models of development and in-silico testing of experimental phenomenon. This combined experimental-computational approach led to a mechanistic understanding of physiological compensation mechanisms in abnormal cardiac morphogenesis. Using our experimental-based framework, we detail morphological and hemodynamic changes twenty-four hours post vessel occlusion. To gain mechanistic insights into the dynamic vessel adaptation process, we perform in-silico occlusions which allow for quantification of instantaneous changes in mechanical loading. We follow the propagation of small defects in a single embryo Hamburger Hamilton (HH) Stage 18 embryo to a more serious defect in an HH29 embryo. Results demonstrate that abnormal PAA hemodynamics can precipitate abnormal cardiac function given the correct timing and location of injury. Following vessel occlusion, morphology changes along the arches are no longer a simple flow-mediated response but rather work to maintain a range of wall shear stress values. Occlusion of the presumptive aortic arch overrides natural growth mechanisms and prevents it from becoming the dominant arch of the aorta.

Author Summary

The developing great vessels transport flow from the heart to the rest of the body. Proper spatial temporal morphogenesis of the primitive paired vessels into the definitive outflow tract of the heart is critical for normal cardiac function. Malpatterning of the great vessels is highly prevalent in congenital heart defects and occurs in conjunction with other intracardiac malformations, such as impaired ventricle and valve development. In this work, we combine experimental-based computational modeling with theoretical adaptation principles. Our combined experimental-computational framework allows for the delineation of immediate and longer-term vascular remodeling as well as the physical mechanisms behind such changes. We show that a small flow obstruction originating within the developing vessels can propagate into structurally serious malformations with impaired functionality.
In silico prediction of COVID-19 test efficiency with DinoKnot
Authors: Newman Tara , Chang Hiu Fung Kevin , Jabbari Hosna
Published: September 2020

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a novel coronavirus spreading across the world causing the disease COVID-19. The diagnosis of COVID-19 is done by quantitative reverse-transcription polymer chain reaction (qRT-PCR) testing which utilizes different primer-probe sets depending on the assay used. Using in silico analysis we aimed to determine how the secondary structure of the SARS-CoV-2 RNA genome affects the interaction between the reverse primer during qRT-PCR and how it relates to the experimental primer-probe test efficiencies. We introduce the program DinoKnot (Duplex Interaction of Nucleic acids with pseudoKnots) that follows the hierarchical folding hypothesis to predict the secondary structure of two interacting nucleic acid strands (DNA/RNA) of similar or different type. DinoKnot is the first program that utilizes stable stems in both strands as a guide to find the structure of their interaction. Using DinoKnot we predicted the interaction of the reverse primers used in four common COVID-19 qRT-PCR tests with the SARS-CoV-2 RNA genome. In addition, we predicted how 12 mutations in the primer/probe binding region may affect the primer/probe ability and subsequent SARS-CoV-2 detection. While we found all reverse primers are capable of interacting with their target area, we identified partial mismatching between the SARS-CoV-2 genome and some reverse primers. We predicted three mutations that may prevent primer binding, reducing the ability for SARS-CoV-2 detection. We believe our contributions can aid in the design of a more sensitive SARS-CoV-2 test.

Author summary

The current testing for the disease COVID-19 that is caused by the novel cornonavirus SARS-CoV-2 uses oligonucleotides called primers that bind to specific target regions on the SARS-CoV-2 genome to detect the virus. Our goal was to use computational tools to predict how the structure of the SARS-CoV-2 RNA genome affects the ability of the primers to bind to their target region. We introduce the program DinoKnot (Duplex interaction of nucleic acids with pseudoknots) that is able to predict the interactions between two DNA or RNA molecules. We used DinoKnot to predict the efficiency of four common COVID-19 tests, and the effect of mutations in the SARS-CoV-2 virus on ability of the COVID-19 tests in detecting those strains. We predict partial mismatching between some primers and the SARS-CoV-2 genome but that all primers are capable of interacting with their target areas. We also predict three mutations that prevent primer binding and thus SARS-CoV-2 detection. We discuss the limitations of the current COVID-19 testing and suggest the design of a more sensitive COVID-19 test that can be aided by our findings.
Monsters with a shortened vertebral column: A population phenomenon in radiating fishLabeobarbus(Cyprinidae)
Authors: Golubtsov Alexander S. , Korostelev Nikolai B. , Levin Boris A.
Published: September 2020

The phenomenon of a massive vertebral deformity was recorded in the radiatingLabeobarbusassemblage from the middle reaches of the Genale River (south-eastern Ethiopia, East Africa). Within this sympatric assemblage, five trophic morphs – generalized, lipped, piscivorous and two scraping feeders – were reported between 1993 and 2019. In 2009, a new morph with prevalence of ∼10% was discovered. The new morph, termed ‘short’, had an abnormally shortened vertebral column and a significantly heightened body. This type of deformity is common in farmed Atlantic salmon and other artificially reared fish, but is rare in nature. In the GenaleLabeobarbusassemblage, the deformity was present exclusively within the generalized and lipped morphs. The short morph had between seven and 36 deformed (compressed and/or fused) vertebrae. Their body height was positively correlated with number of deformed vertebrae. In another collection in 2019, the short morph was still present at a frequency of 11%. Various environmental and genetic factors could contribute to the development of this deformity in the GenaleLabeobarbus, but based on the available data, it is impossible to confidently identify the key factor(s). Whether the result of genetics, the environment, or both, this high-bodied phenotype is assumed to be an anti-predator adaptation, as there is evidence of its selective advantage in the generalized morph. The Genale “monstrosity” is the first reported case of a massive deformity of the vertebral column in a natural population of African fishes.

“We have also what are called monstrosities; but they graduate into varieties. By a monstrosity I presume is meant some considerable deviation of structure in one part, either injurious to or not useful to the species, and not generally propagated. If it could be shown that monstrosities were even propagated for a succession of generations in a state of nature, modifications might be effected (with the aid of natural selection) more abruptly than I am inclined to believe they are.” Darwin (1860, pp. 46, 426).
The methylome and comparative transcriptome after high intensity sprint exercise in human skeletal muscle
Authors: Maasar Mohd Firdaus , Turner Daniel C. , Gorski Piotr P. , Seaborne Robert A. , Strauss Juliette A. , Shepherd Sam O. , Cocks Matt , Pillon Nicolas J. , Zierath Juleen R. , Hulton Andrew T. , Drust Barry , Sharples Adam P.
Published: September 2020

The methylome and transcriptome signature following exercise that is physiologically and metabolic relevant to sporting contexts such as team sports or health prescription scenarios (e.g. high intensity interval training/HIIT) has not been investigated. To explore this, we undertook two different sport/exercise relevant high-intensity sprint running protocols in humans using a repeated measures design of: 1) Change of direction (COD) versus; 2) straight line (ST) sprint exercise. We took skeletal muscle biopsies from the vastus lateralis 30 minutes and 24 hours post exercise followed by 850K methylation arrays and comparative analysis with recent sprint and acute aerobic exercise meta-analysis transcriptomes. Despite matched intensity (speed x distance and number of accelerations/decelerations) between COD and ST exercise, COD exercise elicited greater movement (GPS Playerload™), physiological (HR), metabolic (lactate) as well as central and peripheral (differential RPE) loading compared with ST exercise. The exercise response alone across both conditions evoked extensive alterations in the methylome immediately post and 24 hrs after exercise, particularly in MAPK, AMPK and axon guidance pathways. COD evoked a considerably greater hypomethylated signature across the genome compared with ST sprint exercise, particularly enriched in: Protein binding, MAPK, AMPK, insulin, and axon guidance pathways. A finding that was more prominent immediately post exercise. Comparative methylome analysis with sprint running transcriptomes identified considerable overlap, with 49% of the genes altered at the expression level also differentially methylated after COD exercise. After differential methylated region analysis, we discovered that VEGFA and its downstream nuclear transcription factor, NR4A1 had enriched hypomethylation within their promoter regions. VEGFA and NR4A1 were also significantly upregulated in the sprint transcriptome and meta-analysis of exercise transcriptomes. We confirmed increased mRNA expression of VEGFA, and considerably larger increases in the expression of canonical metabolic genes, PGC1-α and NR4A3, 3 hrs post COD vs. ST exercise. Overall, we demonstrate that increased physiological load via change of direction sprint exercise in human skeletal muscle evokes considerable epigenetic modifications that are associated with changes in expression of genes responsible for adaptation to exercise. These data imply that introducing changes in direction into high intensity running protocols could serve as an important modulator of a favourable epigenomic and transcriptomic landscape in response to exercise in athletes and trigger greater skeletal muscle remodelling through enhanced gene expression.