bluuebunny/crossref_metadata_2025 huggingface dataset:
Werner syndrome protein (WRN) regulates cell proliferation and the human papillomavirus 16 life cycle during epithelial differentiation
Authors: James Claire D. , Das Dipon , Morgan Ethan L. , Otoa Raymonde , Macdonald Andrew , Morgan Iain M.
Published: May 2020

Human papillomaviruses recruit a host of DNA damage response factors to their viral genome to facilitate homologous recombination replication in association with the viral replication factors E1 and E2. We previously demonstrated that SIRT1 deacetylation of WRN promotes recruitment of WRN to E1-E2 replicating DNA, and that WRN regulates both the levels and fidelity of E1-E2 replication. The deacetylation of WRN by SIRT1 results in an active protein able to complex with replicating DNA, but a protein that is less stable. Here we demonstrate an inverse correlation between SIRT1 and WRN in CIN cervical lesions when compared with normal control tissue, supporting our model of SIRT1 deacetylation destabilizing WRN protein. We CRISPR/Cas9 edited N/Tert-1 and N/Tert-1+HPV16 cells to knock out WRN protein expression and subjected the cells to organotypic raft cultures. In N/Tert-1 cells without WRN expression there was enhanced basal cell proliferation, DNA damage and thickening of the differentiated epithelium. In N/Tert-1+HPV16 cells, there was enhanced basal cell proliferation, increased DNA damage throughout the epithelium and increased viral DNA replication. Overall, the results demonstrate that the expression of WRN is required to control the proliferation of N/Tert-1 cells and controls the HPV16 life cycle in these cells. This complements our previous data demonstrating that WRN controls the levels and fidelity of HPV16 E1-E2 DNA replication. The results describe a new role for WRN, a tumor suppressor, in controlling keratinocyte differentiation and the HPV16 life cycle.

Importance

HPV16 is the major human viral carcinogen, responsible for around 3-4% of all cancers worldwide. Our understanding of how the viral replication machinery interacts with host factors to control/activate the DNA damage response to promote the viral life cycle remains incomplete. Recently, we demonstrated a SIRT1-WRN axis that controls HPV16 replication and here we demonstrate that this axis persists in clinical cervical lesions induced by HPV16. Here we describe the effects of WRN depletion on cellular differentiation with and without HPV16; WRN depletion results in enhanced proliferation and DNA damage irrespective of HPV16 status. Also, WRN is a restriction factor for the viral life cycle as replication is disrupted in the absence of WRN. Future studies will focus on enhancing our understanding of how WRN regulates viral replication. Our goal is to ultimately identify cellular factors essential for HPV16 replication that can be targeted for therapeutic gain.
Current tobacco smoking and risk from COVID-19: results from a population symptom app in over 2.4 million people
Authors: Hopkinson Nicholas S , Rossi Niccolo , El-Sayed Moustafa Julia , Laverty Anthony A , Quint Jennifer K , Freydin Maxim B , Visconti Alessia , Murray Benjamin , Modat Marc , Ourselin Sebastien , Small Kerrin , Davies Richard , Wolf Jonathan , Spector Timothy , Steves Claire J , Falchi Mario
Published: May 2020

Background: The association between current tobacco smoking, the risk of developing COVID-19 and the severity of illness is an important information gap.

Methods: UK users of the COVID Symptom Study app provided baseline data including demographics, anthropometrics, smoking status and medical conditions, were asked to log symptoms daily from 24th March 2020 to 23rd April 2020. Participants reporting that they did not feel physically normal were taken through a series of questions, including 14 potential COVID-19 symptoms and any hospital attendance. The main study outcome was the association between current smoking and the development of classic symptoms of COVID-19 during the pandemic defined as fever, new persistent cough and breathlessness. The number of concurrent COVID-19 symptoms was used as a proxy for severity. In addition, association of subcutaneous adipose tissue expression of ACE2, both the receptor for SARS-CoV-2 and a potential mediator of disease severity, with smoking status was assessed in a subset of 541 twins from the TwinsUK cohort.

Results: Data were available on 2,401,982 participants, mean(SD) age 43.6(15.1) years, 63.3% female, overall smoking prevalence 11.0%. 834,437 (35%) participants reported being unwell and entered one or more symptoms. Current smokers were more likely to develop symptoms suggesting a diagnosis of COVID-19; classic symptoms adjusted OR[95%CI] 1.14[1.10 to 1.18]; >5 symptoms 1.29[1.26 to 1.31]; >10 symptoms 1.50[1.42 to 1.58]. Smoking was associated with reduced ACE2 expression in adipose tissue (Beta(SE)= -0.395(0.149); p=7.01x10-3).

Interpretation: These data are consistent with smokers having an increased risk from COVID-19.
Risk of Ischemic Stroke in Patients with Covid-19 versus Patients with Influenza
Authors: Merkler Alexander E. , Parikh Neal S. , Mir Saad , Gupta Ajay , Kamel Hooman , Lin Eaton , Lantos Joshua , Schenck Edward J. , Goyal Parag , Bruce Samuel S. , Kahan Joshua , Lansdale Kelsey N. , LeMoss Natalie M. , Murthy Santosh B. , Stieg Philip E. , Fink Matthew E. , Iadecola Costantino , Segal Alan Z. , Campion Thomas R. , Diaz Ivan , Zhang Cenai , Navi Babak B.
Published: May 2020

Importance: Case series without control groups suggest that Covid-19 may cause ischemic stroke, but whether Covid-19 is associated with a higher risk of ischemic stroke than would be expected from a viral respiratory infection is uncertain.
Objective: To compare the rate of ischemic stroke between patients with Covid-19 and patients with influenza, a respiratory viral illness previously linked to stroke.
Design: A retrospective cohort study.
Setting: Two academic hospitals in New York City.
Participants: We included adult patients with emergency department visits or hospitalizations with Covid-19 from March 4, 2020 through May 2, 2020. Our comparison cohort included adult patients with emergency department visits or hospitalizations with influenza A or B from January 1, 2016 through May 31, 2018 (calendar years spanning moderate and severe influenza seasons).
Exposures: Covid-19 infection confirmed by evidence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in the nasopharynx by polymerase chain reaction, and laboratory-confirmed influenza A or B.
Main Outcomes and Measures: A panel of neurologists adjudicated the primary outcome of acute ischemic stroke and its clinical characteristics, etiological mechanisms, and outcomes. We used logistic regression to compare the proportion of Covid-19 patients with ischemic stroke versus the proportion among patients with influenza.
Results: Among 2,132 patients with emergency department visits or hospitalizations with Covid-19, 31 patients (1.5%; 95% confidence interval [CI], 1.0%-2.1%) had an acute ischemic stroke. The median age of patients with stroke was 69 years (interquartile range, 66-78) and 58% were men. Stroke was the reason for hospital presentation in 8 (26%) cases. For our comparison cohort, we identified 1,516 patients with influenza, of whom 0.2% (95% CI, 0.0-0.6%) had an acute ischemic stroke. After adjustment for age, sex, and race, the likelihood of stroke was significantly higher with Covid-19 than with influenza infection (odds ratio, 7.5; 95% CI, 2.3-24.9).
Conclusions and Relevance: Approximately 1.5% of patients with emergency department visits or hospitalizations with Covid-19 experienced ischemic stroke, a rate 7.5-fold higher than in patients with influenza. Future studies should investigate the thrombotic mechanisms in Covid-19 in order to determine optimal strategies to prevent disabling complications like ischemic stroke.
Reproduction ratio and growth rates: measures for an unfolding pandemic
Authors: Aguiar Maíra , Van-Dierdonck Joseba Bidaurrazaga , Stollenwerk Nico
Published: May 2020

The initial exponential growth rate of an epidemic is an important measure that follows directly from data at hand, commonly used to infer the basic reproduction number. As the growth rates λ(t) of tested positive COVID-19 cases have crossed the threshold in many countries, with negative numbers as surrogate for disease transmission deceleration, lockdowns lifting are linked to the behavior of the momentary reproduction numbers r(t), often called R0. Important to note that this concept alone can be easily misinterpreted as it is bound to many internal assumptions of the underlying model and significantly affected by the assumed recovery period. Here we present our experience, as part of the Basque Country Modeling Task Force (BMTF), in monitoring the development of the COVID-19 epidemic, by considering not only the behaviour of r(t) estimated for the new tested positive cases - significantly affected by the increased testing capacities, but also the momentary growth rates for hospitalizations, ICU admissions, deceased and recovered cases, in assisting the Basque Health Managers and the Basque Government during the lockdown lifting measures. Two different data sets, collected and then refined during the COVID-19 responses, are used as an exercise to estimate the momentary growth rates and reproducetion numbers over time in the Basque Country, and the implications of using those concepts to make decisions about easing lockdown and relaxing social distancing measures are discussed. These results are potentially helpful for task forces around the globe which are now struggling to provide real scientific advice for health managers and governments while the lockdown measures are relaxed.
Trauma and posttraumatic stress interact with sex-specific risk loci for suicidality and converge on brain extracellular matrix biology and synaptic plasticity
Authors: Wendt Frank R , Pathak Gita A , Levey Daniel F , Nunez Yaira Z , Overstreet Cassie , Tyrrell Chelsea , Adhikari Keyrun , De Angelis Flavio , Tylee Daniel S , Goswami Aranyal , Krystal John H , Abdallah Chadi , Stein Murray B , Kranzler Henry R , Gelernter Joel , Polimanti Renato
Published: May 2020

We performed a multivariate gene-by-environment genome-wide interaction study (GEWIS) of suicidality in 123,633 individuals using a covariance matrix based on 26 environments related to traumatic experiences, posttraumatic stress, social support, and socioeconomic status. We discovered sex-specific risk loci exhibiting interaction effects driven by PTSD, including the male-specific rs2367967 (CWC22), which replicated in an independent cohort. Sex-specific cell-type transcriptome enrichment, gene-based analyses, and locus annotation point to extracellular matrix biology and synaptic plasticity as biological mediators of the effects of lifetime traumatic experiences on genetic risk for suicidality.
Mitochondrial D-loop sequence variation and maternal lineage in the endangered Cleveland Bay horse
Authors: Dell A.C. , Curry M.C. , Yarnell K.M. , Starbuck G.R. , Wilson P. B.
Published: May 2020

Genetic diversity and maternal ancestry line relationships amongst a sample of 96 Cleveland Bay horses were investigated using a 479bp length of mitochondrial D-loop sequence. The analysis yielded at total of 11 haplotypes with 27 variable positions, all of which have been described in previous equine mitochondrial DNA d-loop studies. Four main haplotype clusters were present in the Cleveland Bay breed describing 89% of the total sample. This suggests that only four principal maternal ancestry lines exist in the present-day global Cleveland Bay population. Comparison of these sequences with other domestic horse haplotypes shows a close association of the Cleveland Bay horse with Northern European (Clade C), Iberian (Clade A) and North African (Clade B) horse breeds. This indicates that the Cleveland Bay horse may not have evolved exclusively from the now extinct Chapman horse, as previous work as suggested. The Cleveland Bay horse remains one of only fivedomestic horse breeds classified as Critical on the Rare Breeds Survival Trust (UK) Watchlist and our results provide important information on the origins of this breed and represent a valuable tool for conservation purposes.
Abl kinase deficiency promotes AKT pathway activation and prostate cancer progression and metastasis
Authors: Marchal Melissa A , Moose Devon L , Varzavand Afshin , Taylor Destiney , Brown James A , Henry Michael D , Stipp Christopher S
Published: May 2020

Abl family kinases function as proto-oncogenes in various leukemias, and pro-tumor functions have been discovered for Abl kinases in solid tumors as well. However, a growing body of evidence indicates that Abl kinases can function to suppress tumor cell proliferation, motility, andin vivotumor growth in some settings. To investigate the role of Abl kinases in prostate cancer, we generated Abl-deficient cells in a pre-clinical model of spontaneously metastatic, androgen-indifferent prostate cancer. Loss of Abl family kinase expression resulted in a highly aggressive, metastatic phenotypein vivothat was associated with AKT pathway activation, increased growth on 3D collagen matrix, and enhanced cell motilityin vitro. Treatment of Abl kinase-expressing cells with the Abl kinase inhibitor imatinib phenocopied the malignant phenotypes observed in Abl-deficient tumor cells. In addition, inhibiting AKT pathway signaling abolished the increased 3D growth of Abl-deficient cells. Our data reveal that Abl family kinases can function as suppressors of prostate cancer progression and metastasis by restraining AKT signaling, a signaling pathway known to be associated with emergence of metastatic castration-resistant prostate cancer.
PrimPol primase mediates replication traverse of DNA interstrand crosslinks
Authors: González-Acosta Daniel , Blanco-Romero Elena , Mutreja Karun , Llanos Susana , Míguez Samuel , García Fernando , Muñoz Javier , Blanco Luis , Lopes Massimo , Méndez Juan
Published: May 2020

Interstrand crosslinks (ICLs) are DNA lesions frequently induced by chemotherapy that interfere with essential processes such as replication and transcription. ICL repair may be initiated by the convergence of two replication forks at the crosslink, which results in a termination-like DNA structure recognized and processed by the Fanconi Anemia (FA) pathway. An alternative possibility to generate a suitable substrate for ICL repair involves “ICL traverse”, a DNA damage tolerance mechanism in which a single fork arriving at the ICL can skip the lesion and restart DNA synthesis from a downstream point. This reaction requires FANCM translocase, the BLM/TOP3A/RMI1-2 (BTR) complex and other factors. Here we report that PrimPol, the second primase-polymerase identified in mammalian cells after Polα/Primase, interacts with BTR and participates in the ICL traverse reaction. A functional complementation assay reveals that the primase activity of PrimPol is required, confirming the need for re-priming events during ICL traverse. Genetic ablation of PRIMPOL strongly impaired this tolerance mechanism, making cells more dependent on fork convergence to initiate ICL repair. PRIMPOL KO cells and mice display hypersensitivity to ICL-inducing drugs, opening the possibility of targeting PrimPol activity to enhance the efficacy of chemotherapy based on DNA crosslinking agents.
A redesigned TetR-aptamer system to control gene expression inPlasmodium falciparum
Authors: Rajaram Krithika , Liu Hans B. , Prigge Sean T.
Published: May 2020

One of the most powerful approaches to understanding gene function involves turning genes on and off at will and measuring the impact at the cellular or organismal level. This particularly applies to the cohort of essential genes where traditional gene knockouts are inviable. InPlasmodium falciparum, conditional control of gene expression has been achieved by using multi-component systems in which individual modules interact with each other to regulate DNA recombination, transcription or posttranscriptional processes. The recently devised TetR-DOZI aptamer system relies on the ligand-regulatable interaction of a protein module with synthetic RNA aptamers to control the translation of a target gene. This technique has been successfully employed to study essential genes inP. falciparumand involves the insertion of several aptamer copies into their 3’ untranslated regions (UTRs) which provide control over mRNA fate. However, aptamer repeats are prone to recombination and one or more copies can be lost from the system, resulting in a loss of control over target gene expression. We rectified this issue by redesigning the aptamer array to minimize recombination while preserving the control elements. As proof of concept, we compared the original and modified arrays for their ability to knock down the levels of a putative essential apicoplast protein (PF3D7_0815700) and demonstrated that the modified array is highly stable and efficient. This redesign will enhance the utility of a tool that is quickly becoming a favored strategy for genetic studies inP. falciparum.

Importance

Malaria elimination efforts have been repeatedly hindered by the evolution and spread of multidrug-resistant strains ofPlasmodium falciparum. The absence of a commercially available vaccine emphasizes the need for a better understanding ofPlasmodiumbiology in order to further translational research. This has been partly facilitated by targeted gene deletion strategies for the functional analysis of parasite genes. However, genes that are essential for parasite replication in erythrocytes are refractory to such methods, and require conditional knockdown or knockout approaches to dissect their function. One such approach is the TetR-DOZI system that employs multiple synthetic aptamers in the untranslated regions of target genes to control their expression in a tetracycline-dependent manner. Maintaining modified parasites with intact aptamer copies has been challenging since these repeats are frequently lost by recombination. By interspacing the aptamers with unique sequences, we created a stable genetic system that remains effective at controlling target gene expression.
Clinical And Analytical Performance Of An Automated Serological Test That Identifies S1/S2 Neutralizing IgG In Covid-19 Patients Semiquantitatively
Authors: Bonelli Fabrizio , Sarasini Antonella , Zierold Claudia , Calleri Mariella , Bonetti Alice , Vismara Chiara , Blocki Frank , Pallavicini Luca , Chinali Alberto , Campisi Daniela , Percivalle Elena , DiNapoli Anna Pia , Perno Carlo Federico , Baldanti Fausto
Published: May 2020

BACKGROUND

In the Covid-19 pandemic, highly selective serological testing is essential to define exposure to SARS-CoV-2 virus. Many tests have been developed, yet with variable speed to first result, and of unknown quality, particularly when considering the prediction of neutralizing capacity.

OBJECTIVES/METHODS

The LIAISON®SARS-CoV-2 S1/S2 IgG assay was designed to measure antibodies against the SARS-CoV-2 native S1/S2 proteins in a standardized automated chemiluminescent assay. Clinical and analytical performance of the test were validated in an observational study using residual samples (>1500) with positive or negative Covid-19 diagnosis.

RESULTS

The LIAISON®SARS-CoV-2 S1/S2 IgG assay proved highly selective and specific, and offers semiquantitative measures of serum or plasma levels of anti-S1/S2 IgG with neutralizing activity. The diagnostic sensitivity was 91.3% and 95.7% at >5 or ≥15 days from diagnosis respectively, and 100% when assessed against a neutralizing assay. The specificity ranged between 97% and 98.5%. The average imprecision of the assay was <5 % coefficient of variation. Assay performance at 2 different cut-offs was evaluated to optimize predictive values in settings with different % disease prevalence. CONCLUSIONS. The automated LIAISON®SARS-CoV-2 S1/S2 IgG assay brings efficient, sensitive, specific, and precise serological testing to the laboratory, with the capacity to test large amounts of samples per day: first results are available within 35 minutes with a throughput of 170 tests/hour. The test also provides a semiquantitative measure to identify samples with neutralizing antibodies, useful also for a large scale screening of convalescent plasma for safe therapeutic use.

IMPORTANCE

With the worldwide advance of the COVID-19 pandemic, efficient, reliable and accessible diagnostic tools are needed to support public health officials and healthcare providers in their efforts to deliver optimal medical care, and articulate sound demographic policy. DiaSorin has developed an automated serology based assay for the measurement of IgG specific to SARS CoV-2 Spike protein, and tested its clinical performance in collaboration with Italian health care professionals who provided access to large numbers of samples from infected and non-infected individuals. The assay delivers excellent sensitivity and specificity, and is able to identify samples with high levels of neutralizing antibodies. This will provide guidance in assessing the true immune status of subjects, as well as meeting the pressing need to screen donors for high titer convalescent sera for subsequent therapeutic and prophylactic use.
Morphologic Classification and Automatic Diagnosis of Bacterial Vaginosis by Deep Neural Networks
Authors: Wang Zhongxiao , Zhang Lei , Zhao Min , Wang Ying , Bai Huihui , Wang Yufeng , Rui Can , Fan Chong , Li Jiao , Li Na , Liu Xinhuan , Wang Zitao , Si Yanyan , Feng Andrea , Li Mingxuan , Zhang Qiongqiong , Yang Zhe , Wang Mengdi , Wu Wei , Cao Yang , Qi Lin , Zeng Xin , Geng Li , An Ruifang , Li Ping , Liu Zhaohui , Qiao Qiao , Zhu Weipei , Mo Weike , Liao Qinping , Xu Wei
Published: May 2020

Background

Bacterial vaginosis (BV) was the most common condition for women’s health caused by the disruption of normal vaginal flora and an overgrowth of certain disease-causing bacteria, affecting 30-50% of women at some time in their lives. Gram stain followed by Nugent scoring (NS) based on bacterial morphotypes under the microscope was long considered golden standard for BV diagnosis. This conventional manual method was often considered labor intensive, time consuming, and variable results from person to person.

Methods

We developed four convolutional neural networks (CNN) models, and evaluated their ability to automatic identify vaginal bacteria and classify Nugent scores from microscope images. All the CNN models were first trained with 23280 microscopic images labeled with Nugent scores from top experts. A separate set of 5815 images were evaluated by the CNN models. The best CNN model was selected to generalize its application on an independent sets of 1082 images collecting from three teaching hospitals. Different hardwares were used to take images in hospitals.

Results

Our model could classify three Nugent Scores from images with high three classification accuracy of 89.3% (with 82.4% sensitivity and 96.6% specificity) on the 5815 test images, which was better diagnostic yield than the top-level technologists and obstetricians in China. The ability of generalization for our model was strong that it obtained 75.1%, which was 6.6% higher than the average of technologists.

Conclusion

The CNN model over performed human healthcare practitioners on accuracy, efficiency and stability for BV diagnosis using microscopic image-based Nugent scores. The deep learning model may offer translational application in automating diagnosis of bacterial vaginosis with proper supporting hardware.
S-nitrosylated and non-nitrosylated COX2 has differential expression and distinct subcellular localization in normal and breast cancer tissue
Authors: Jindal Sonali , Pennock Nathan D. , Klug Alex , Narasimhan Jayasri , Calhoun Andrea , Roberts Michelle R. , Tamimi Rulla M. , Eliassen A. Heather , Weinmann Sheila , Borges Virginia F. , Schedin Pepper
Published: May 2020

Immunohistochemical staining in breast cancer shows both gain and loss of COX2 expression with disease risk and progression. We investigated four common COX2 antibody clones and found high specificity for purified human COX2 for three clones; however, recognition of COX2 in cell lysates was clone dependent. Biochemical characterization revealed two distinct forms of COX2, with SP21 recognizing an S-nitrosylated form and CX229 and CX294 appearing to recognize the same non-nitrosylated COX2 antigen. We found S-nitrosylated and non-nitrosylated COX2 occupy different subcellular locations in normal and breast cancer tissue, implicating distinct synthetic/trafficking pathways and function. Dual stains of ~2000 breast cancer cases show early onset breast cancer has increased expression of both forms of COX2 compared to postmenopausal cases. Our results highlight the strengths of using multiple, highly characterized antibody clones for COX2 immunohistochemical studies and raise the prospect that S-nitrosylation of COX2 may play a role in breast cancer biology.
IndigenousBacillus paramycoidesandAlcaligenes faecalis: potential solution for the bioremediation of wastewaters
Authors: Rashid Aneeba , Mirza Safdar A. , Keating Ciara , Ali Sikander , Campos Luiza C.
Published: May 2020

Farmers near towns and cities are using wide range of untreated wastewaters for crop irrigation in Pakistan due to severe freshwater shortage. The present study aimed to treat different types of wastewater including domestic, hospital, textile, pharmaceutical and mixed wastewaters using indigenous bacterial isolates to remove contaminants and render these wastewaters safer for irrigation. 37 bacterial strains were isolated from the 5 wastewater samples collected from different sites in Lahore, Pakistan. Under optimum growth conditions, the isolates D6, D7 and P1 showed maximum decolourisation potential of 96, 96, 93 %, respectively against hospital wastewater. GCMS analysis of the untreated hospital wastewater confirmed the presence of pharmaceutic pollutants i.e. Phenol, Salicylic acid, Caffeine, Naproxen, Octadecene and Diazepam. These organic compounds were biodegraded into derivate Ticlopidine in the case of isolate D6, derivatives Tetradecene and Griseofulvin in the case of isolate D7, and derivatives Lidocaine and Butalbital in the case of isolate P1. 16S rDNA sequencing was used to identify these isolates. Isolates D6 and D7 showed 100 and 99.86 % homology toBacillus paramycoides, a novel strain fromBacillus cereusgroup (Liu et al., 2017). Isolate P1 showed 97.47 % homology toAlcaligenes faecalis. These strains therefore could represent a low-cost and low-tech alternative to bioremediate complex wastewaters prior to irrigation to support the achievement of the Sustainable Development Goal 6 - clean water and sanitation in Pakistan.
The calcium binding protein S100β marks hedgehog-responsive resident vascular stem cells within vascular lesions
Authors: Luca Mariana Di , Fitzpatrick Emma , Burtenshaw Denise , Liu Weimin , Helt Jay-Christian , Hakimjavadi Roya , Corcoran Eoin , Gusti Yusof , Sheridan Daniel , Harman Susan , Lally Catriona , Redmond Eileen M. , Cahill Paul A.
Published: May 2020

A hallmark of subclinical atherosclerosis is the accumulation of vascular smooth muscle cell (SMC)-like cells leading to intimal thickening. While medial SMCs contribute, the participation of hedgehog responsive resident vascular stem cells (vSCs) to lesion formation remains unclear. Using transgenic eGFP mice and genetic lineage tracing of S100β vSCsin vivo, we identified S100β/Sca1 cells derived from a S100β non-SMC parent population within lesions that co-localise with smooth muscle ⍰-actin (SMA) cells following iatrogenic flow restriction, an effect attenuated following hedgehog inhibition with the smoothened inhibitor, cyclopamine.In vitro, S100β/Sca1 cells isolated from atheroprone regions of the mouse aorta expressed hedgehog signalling components, acquired the di-methylation of histone 3 lysine 4 (H3K4me2) stable SMC epigenetic mark at the Myh11 locus and underwent myogenic differentiation in response to recombinant sonic hedgehog (SHh). Both S100β and PTCH1 cells were present in human vessels while S100β cells were enriched in arteriosclerotic lesions. Recombinant SHh promoted myogenic differentiation of human induced pluripotent stem cell-derived S100β neuroectoderm progenitorsIn vitro. We conclude that hedgehog responsive S100β vSCs contribute to lesion formation and support targeting hedgehog signalling to treat subclinical arteriosclerosis.
Development of follicular dendritic cells in lymph nodes depends on retinoic acid mediated signaling
Authors: Koning Jasper J. , Rajaraman Anusha , Reijmers Rogier M. , Konijn Tanja , Pan Junliang , Ware Carl F. , Butcher Eugene C. , Mebius Reina E.
Published: May 2020

Specialized stromal cells occupy and help define B- and T cell domains, which is crucial for proper functioning of our immune system. Signaling through lymphotoxin and TNF-receptors is crucial for development of different stromal subsets which are thought to arise from a common precursor. However, mechanisms that control the selective generation of the different stromal phenotypes are not known.

Here we show that in mice, retinoic acid mediated signaling is important for the differentiation of precursors towards the Cxcl13posfollicular dendritic cell (FDC) lineage, while blocking lymphotoxin mediated Ccl19posfibroblastic reticular cell (FRC) lineage differentiation. Consequently, we see at day of birth Cxcl13posCcl19neg/lowand Cxcl13neg/lowCcl19poscells within neonatal lymph nodes.

Furthermore, ablation of retinoic acid receptor signaling in stromal precursors early after birth reduces Cxcl13 expression, while in addition, complete blockade of retinoic acid signaling prevents formation of FDC networks in lymph nodes.
Micro RNAs are minor constituents of extracellular vesicles and are hardly delivered to target cells
Authors: Albanese Manuel , Chen Yen-Fu Adam , Hüls Corinna , Gärtner Kathrin , Tagawa Takanobu , Mejias-Perez Ernesto , Keppler Oliver T. , Göbel Christine , Zeidler Reinhard , Shein Mikhail , Schütz Anne K. , Hammerschmidt Wolfgang
Published: May 2020

Mammalian cells release different types of vesicles, collectively termed extracellular vesicles (EVs). EVs contain cellular microRNAs (miRNAs) with an apparent potential to deliver their miRNA cargo to recipient cells to affect the stability of individual mRNAs and the cells’ transcriptome. The extent to which miRNAs are exported via the EV route and whether they contribute to cell-cell communication are controversial. To address these issues, we analyzed the capacity of EVs to deliver packaged miRNAs into target cells and to exert biological functions. We applied well-defined approaches to produce and characterize purified EVs with or without specific viral miRNAs. We found that only a small fraction of EVs carried miRNAs. EVs readily bound to different target cell types, but there was no EV-cell membrane fusion or delivery of cargo. Importantly, the functionality of cells exposed to miRNA-carrying EVs was not affected. These results suggest EV-borne miRNAs do not act as effectors and question their relevancy in paracrine cell-to-cell communication.

AUTHOR SUMMARY

The majority of metazoan cells release vesicles of different types and origins, such as exosomes and microvesicles, now collectively termed extracellular vesicles (EVs). EVs have gained much attention because they contain microRNAs (miRNAs) and thus could regulate their specific mRNA targets in recipient or acceptor cells that take up EVs. Using a novel fusion assay with superior sensitivity and specificity, we revisited this claim but found no convincing evidence for an efficient functional uptake of EVs in many different cell lines and primary human blood cells. Even EVs engineered to fuse and deliver their miRNA cargo to recipient cells had no measurable effect on target mRNAs in very carefully controlled, quantitative experiments. Our negative results clearly indicate that EVs do not act as vehicles for miRNA-based cell-to-cell communication.
Resistance to serine inBacillus subtilis: Identification of the serine transporter YbeC and of a metabolic network that links serine and threonine metabolism
Authors: Klewing Anika , Koo Byoung Mo , Krüger Larissa , Poehlein Anja , Reuß Daniel , Daniel Rolf , Gross Carol A. , Stülke Jörg
Published: May 2020

The Gram-positive bacteriumBacillus subtilisuses serine not only as building block for proteins but also as an important precursor in many anabolic reactions. Moreover, a lack of serine results in the initiation of biofilm formation. However, in excess serine inhibits the growth ofB. subtilis. To unravel the underlying mechanisms, we isolated suppressor mutants that can tolerate toxic serine concentrations by three targeted and non-targeted genome-wide screens. All screens as well as genetic complementation inEscherichia coliidentified the so far uncharacterized permease YbeC as the major serine transporter ofB. subtilis. In addition to YbeC, the threonine transporters BcaP and YbxG make minor contributions to serine uptake. A strain lacking these three transporters was able to tolerate 100 mM serine whereas the wild type strain was already inhibited by 1 mM of the amino acid. The screen for serine-resistant mutants also identified mutations that result in increased serine degradation and in increased expression of threonine biosynthetic enzymes suggesting that serine toxicity results from interference with threonine biosynthesis.

Originality-Significance Statement

Serine is an important precursor for many biosynthetic reactions, and lack of this amino acid can induce biofilm formation inBacillus subtilis. However, serine is toxic for the growth ofB. subtilis. To understand the reason(s) for this toxicity and to identify the so far unknown serine transporter(s) of this bacterium, we performed exhaustive mutant screens to isolate serine-resistant mutants. This screen identified YbeC, the major serine transporter ofB. subtilis. Moreover, we observed an intimate link between serine and threonine metabolism that is responsible for serine toxicity by inhibiting threonine biosynthesis.
Silica particles trigger the production of exopolysaccharides in harsh environment plant growth-promoting rhizobacteria and increase their ability to enhance drought tolerance
Authors: Fetsiukh Anastasiia , Conrad Julian , Bergquist Jonas , Ayele Fantaye , Timmusk Salme
Published: May 2020

In coming decades drought is expected to expand globally owing to increased evaporation and reduced rainfall. In order to reduce the vulnerability of agricultural systems we need to understand the crop plant growth environment. Understanding, predicting and controlling the rhizosphere has potential to harness plant microbe interactions, improve plant responses to environmental stress and mitigate effects of climate change. Our plant growth-promoting rhizobacteria (PGPR) are isolated from the natural laboratory ‘Evolution Canyon’ Israel (EC). The endophytic rhizobacteria from the wild progenitors of cereals have been co-habituated with their hosts for long periods of time. The study revealed that silica particles (SN) triggered the PGPR production of exopolysaccharides (EPS) containing D-glucuronate (D-GA). This leads to increased plant biomass accumulation in drought-stressed growth environments. The PGPR increased EPS content increases the water holding capacity (WHC) and osmotic pressure of the biofilm matrix. Light- and electron-microscopic studies show that in the presence of SN particles, bacterial morphology is changed, indicating that SNs are associated with significant reprogramming in bacteria.

The results here show that the production of EPS containing D-GA is induced by SN treatment. The findings encourage formulation of cells considering microencapsulation with materials that ensure higher WHC and hyperosmolarity under field conditions. Our results illustrate the importance of considering natural soil nanoparticles in the application of PGPR. Osmotic pressure involvement of holobiont cohabitation is discussed.
CD8+ T cell cross-reactivity against SARS-CoV-2 conferred by other coronavirus strains and influenza virus
Authors: Lee Chloe H. , Pereira Pinho Mariana , Buckley Paul , Woodhouse Isaac , Ogg Graham , Simmons Alison , Napolitani Giorgio , Koohy Hashem
Published: May 2020

While individuals infected with coronavirus disease 2019 (COVID-19) manifested a broad range in susceptibility and severity to the disease, the pre-existing immune memory of related pathogens can influence the disease outcome. Here, we investigated the potential extent of T cell cross-reactivity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that can be conferred by other coronaviruses and influenza virus, and generated a map of public and private predicted CD8+ T cell epitopes between coronaviruses. Moreover, to assess the potential risk of self-reactivity and/or diminished T cell response for peptides identical or highly similar to the host, we identified predicted epitopes with high sequence similarity with human proteome. Lastly, we compared predicted epitopes from coronaviruses with epitopes from influenza virus deposited in IEDB to support vaccine development against different virus strains. We believe the comprehensivein silicoprofile of private and public predicted epitopes across coronaviruses and influenza viruses will facilitate design of vaccines capable of protecting against various viral infections.
FGFR Signaling Coordinates the Balance Between Glycolysis and Fatty Acid β-Oxidation in Lymphatic Endothelial Cells
Authors: Song Hongyuan , Zhu Jie , Fang Longhou , Yu Pengchun
Published: May 2020

The balance between glycolysis and oxidative phosphorylation is believed to be critical for maintaining cellular bioenergetics, yet the regulation of such balance in lymphatic endothelial cells (LECs) remains unclear. Here we found that chemical inhibition of fibroblast growth factor receptor (FGFR) activity or knockdown of FGFR1, which has been shown to suppress glycolysis and consequently ATP production, induces substantial upregulation of fatty acid β-oxidation (FAO), but not glucose oxidation or glutamine oxidation in LECs. Mechanistically, blockade of FGFR-AKT signaling promotes the expression of CPT1A, a rate-limiting enzyme of FAO, in a PPARα-dependent manner. Metabolic analysis further showed that CPT1A depletion impairs ATP generation in FGFR1-deficient rather than wild-type LECs. This result suggests that FAO, which makes a minor contribution to cellular energy under normal conditions, can compensate for energy deficiency caused by FGFR inhibition. Consequently, CPT1A silencing potentiates the effect of FGFR1 knockdown on impeding LEC proliferation and migration. Collectively, our study identified an FGFR-regulated metabolic balance that is important for LEC growth.
Non-canonical cell death by reassortant reovirus
Authors: Stewart Roxana M. Rodríguez , Raghuram Vishnu , Berry Jameson T.L. , Mainou Bernardo A.
Published: May 2020

Triple-negative breast cancer (TNBC) constitutes 12% of all breast cancer and is associated with worse prognosis compared to other subtypes of breast cancer. Current therapies are limited to cytotoxic chemotherapy, radiation, and surgery, leaving a need for targeted therapeutics to improve outcomes for TNBC patients. Mammalian orthoreovirus (reovirus) is a nonenveloped, segmented, dsRNA virus in theReoviridaefamily. Reovirus preferentially kills transformed cells and is in clinical trials to assess its efficacy against several types of cancer. We previously engineered a reassortant reovirus, r2Reovirus, that infects TNBC cells more efficiently and induces cell death with faster kinetics than parental reoviruses. In this study, we sought to understand the mechanisms by which r2Reovirus induces cell death in TNBC cells. We show that r2Reovirus infection of TNBC cells of a mesenchymal-stem like (MSL) lineage downregulates the MAPK/ERK pathway and induces non-conventional cell death that is caspase dependent, but caspase 3-independent. Infection of different MSL lineage TNBC cells with r2Reovirus results in caspase 3-dependent cell death. We map the enhanced oncolytic properties of r2Reovirus in TNBC to epistatic interactions between the Type 3 Dearing M2 gene segment and Type 1 Lang genes. These findings suggest that the genetic composition of the host cell impacts the mechanism of reovirus-induced cell death in TNBC. Together, our data show that understanding host and virus determinants of cell death can identify novel properties and interactions between host and viral gene products that can be exploited for the development of improved viral oncolytics.

Importance

Triple negative breast cancer (TNBC) is unresponsive to hormone therapies, leaving patients afflicted with this disease with limited treatment options. We previously engineered an oncolytic reovirus (r2Reovirus) with enhanced infective and cytotoxic properties in TNBC cells. However, how r2Reovirus promotes TNBC cell death is not known. In this study, we show that reassortant r2Reovirus can promote non-conventional caspase-dependent but caspase 3-independent cell death and that the mechanism of cell death depends on the genetic composition of the host cell. We also map the enhanced oncolytic properties of r2Reovirus in TNBC to interactions between a Type 3 M2 gene segment and Type 1 genes. Our data show that understanding the interplay between the host cell environment and the genetic composition of oncolytic viruses is crucial for the development of efficacious viral oncolytics.
Rapture-ready darters: choice of reference genome and genotyping method (whole-genome or sequence capture) influence population genomic inference inEtheostoma
Authors: Reid Brendan N. , Moran Rachel L. , Kopack Christopher J. , Fitzpatrick Sarah W.
Published: May 2020

Researchers studying non-model organisms have an increasing number of methods available for generating genomic data. However, the applicability of different methods across species, as well as the effect of reference genome choice on population genomic inference, are still difficult to predict in many cases. We evaluated the impact of data type (whole-genome vs. reduced representation) and reference genome choice on data quality and on population genomic and phylogenomic inference across several species of darters (subfamily Etheostomatinae), a highly diverse radiation of freshwater fish. We generated a high-quality reference genome and developed a hybrid RADseq/sequence capture (Rapture) protocol for the Arkansas darter (Etheostoma cragini). Rapture data from 1900 individuals spanning four darter species showed recovery of most loci across darter species at high depth and consistent estimates of heterozygosity regardless of reference genome choice. Loci with baits spanning both sides of the restriction enzyme cut site performed especially well across species. For low-coverage whole-genome data, choice of reference genome affected read depth and inferred heterozygosity. For similar amounts of sequence data, Rapture performed better at identifying fine-scale genetic structure compared to whole-genome sequencing. Rapture loci also recovered an accurate phylogeny for the study species and demonstrated high phylogenetic informativeness across the evolutionary history of the genusEtheostoma. Low cost and high cross-species effectiveness regardless of reference genome suggest that Rapture and similar sequence capture methods may be worthwhile choices for studies of diverse species radiations.
A flexible planning methodology for product family assembly line based on improved NSGA_II
Authors: Wu Yongming , Zhao Xudong , Xu Yanxia , Chen Yuling
Published: May 2020

Purpose

The product family assembly line (PFAL) is a mixed model-assembly line, which is widely used in mass customization and intelligent manufacturing. The purpose of this paper is to study the problem of PFAL, a flexible (evolution) planning method to respond to product evolution for PFAL, to focus on product data analysis and evolution planning method.

Design/methodology/approach

The evolution balancing model for PFAL is established and an improved NSGA_II (INSGA_II) is proposed. From the perspective of data analysis, dynamic characteristics of PFAL are researched and analyzed. Especially the tasks, which stability is considered, can be divided into a platform and individual task. In INSGA_II algorithm, a new density selection and a decoding method based on sorting algorithms are proposed to compensate for the lack of traditional algorithms.

Findings

The effectiveness and feasibility of the method are validated by an example of PFAL evolution planning for a family of similar mechanical products. The optimized efficiency is significantly improved using INSGA_II proposed in this paper and the evolution planning model proposed has a stronger ability to respond to product evolution, which maximizes business performance over an effective period of time.

Originality/value

The assembly line designers and managers in discrete manufacturing companies can obtain an optimal solution for PFAL planning through the evolution planning model and INSGA-II proposed in this paper. Then, this planning model and optimization method have been successfully applied in the production of small wheel loaders.
Building career capital: developing business leaders' career mobility
Authors: Brown Cathy , Hooley Tristram , Wond Tracey
Published: May 2020

Purpose

Career theorists have been increasingly occupied with role transitions across organisations, neglecting role transitions undertaken within single organisations. By exploring in depth the aspects of career capital that role holders need to facilitate their own organisational role transition, this article builds upon career capital theory.

Design/methodology/approach

Adopting an interpretivist approach, this study explores the experiences of 36 business leaders who have undertaken a recent role transition within a UK construction business.

Findings

The article empirically characterises 24 career capital aspects, clustered into Knowing Self, Knowing How and Knowing Whom. It argues that these aspects are important to internal role transitions and compares them to mainstream career capital theory. In addition, the concepts of connecting, crossing and investing career capital are introduced to explain how career capital supports such transitions.

Research limitations/implications

This study proposes a new career capital framework and refocuses debate on organisational careers. It is based on a single organisation, and it would be beneficial for future researchers to explore its applicability within other organisations.

Practical implications

The article explores the implications of the new career capital framework for business leaders and organisational managers who wish to build individual and organisational career mobility.

Originality/value

This study proposes a new, empirically grounded, career capital theoretical framework particularly attending to organisational role transitions.
Analyzing the intention of the households to drop off mobile phones to the collection boxes: empirical study in Malaysia
Authors: Afroz Rafia , Muhibbullah Mohammad , Farhana Puteri , Morshed Mohammad Niaz
Published: May 2020

Purpose

To achieve proper waste management, the disposal of electronic waste (e-waste) is one suitable method. Most developing countries, including Malaysia, are facing lack of e-waste recycling facilities and low household participation. Using a survey method using a questionnaire, this study aims to examine the intention of Malaysian households to drop-off their mobile phones to the nearest collection boxes (n= 600).

Design/methodology/approach

This study expanded the theory of planned behavior by adding environmental awareness and knowledge. In addition, the cost of disposal and the convenience of the available disposal infrastructure were measured as two parts of the perceived behavioral control.

Findings

The results of this study show that environmental knowledge and awareness have a significant impact on attitudes toward recycling intention of the households. In addition, it was also found that the attitude and cost of disposal infrastructure is positively related to household intention.

Originality/value

These results show that if e-waste collection boxes are provided to the nearest community and e-waste management information is distributed, this will increase household participation in e-waste management.