bluuebunny/crossref_metadata_2025 huggingface dataset:
CALGARY NORMATIVE STUDY: STUDY DESIGN OF A PROSPECTIVE LONGITUDINAL STUDY TO CHARACTERIZE POTENTIAL QUANTITATIVE MR BIOMARKERS OVER THE ADULT LIFESPAN
Authors: McCreary Cheryl R , Salluzzi Marina , Andersen Linda B , Gobbi David , Lauzon M Louis , Saad Feryal , Smith Eric E , Frayne Richard
Published: March 2020

Introduction

A number of magnetic resonance (MR) imaging methods have been proposed to be useful, quantitative biomarkers of neurodegeneration in aging. The Calgary Normative Study (CNS) is an ongoing single-centre, prospective, longitudinal study that seeks to develop, test and assess quantitative MR methods as potential biomarkers. The CNS has three objectives: first and foremost, to evaluate and characterize the dependence of the selected quantitative neuroimaging biomarkers on age over the adult lifespan; secondly, to evaluate the precision, variability and repeatability of quantitative neuroimaging biomarkers as part of biomarker validation providing proof of-concept and proof-of-principle; and thirdly, provide a shared repository of normative data for comparison to various disease cohorts.

Methods and Analysis

Quantitative MR mapping of the brain including longitudinal relaxation time (T1), transverse relaxation time (T2), T2*, magnetic susceptibility (QSM), diffusion and perfusion measurements, as well as morphological assessments are performed. The Montreal Cognitive Assessment (MoCA) and a brief, self-report medical history will be collected. Mixed regression models will be used to characterize changes in quantitative MR biomarker measures over the adult lifespan. In this report on study design, we report interim prevalence and demographic information of recruitment from 28 May 2013 to 31 December 2018.

Ethics and Dissemination

Participants provide signed informed consent. Changes in quantitative MR biomarkers measured over the adult lifespan as well as estimates of measurement variance and repeatability will be disseminated through peer-reviewed scientific publication.

STRENGTHS AND LIMITATIONS

Both cross-sectional and longitudinal quantitative MR data is being acquired in a large sample normal aging population to characterize changes in these potential neuroimaging biomarkers over the adult lifespan.

Clinical and multiple quantitative imaging data are being collected and shared with the research community.

Measures of repeatability and a process to update the imaging protocol are included in the study design.

Associated self-reported medical history and cognitive assessments are limited
Bactopia: a flexible pipeline for complete analysis of bacterial genomes
Authors: Petit Robert A. , Read Timothy D.
Published: March 2020

Sequencing of bacterial genomes using Illumina technology has become such a standard procedure that often data are generated faster than can be conveniently analyzed. We created a new series of pipelines called Bactopia, built using Nextflow workflow software, to provide efficient comparative genomic analyses for bacterial species or genera. Bactopia consists of a dataset setup step (Bactopia Datasets; BaDs) where a series of customizable datasets are created for the species of interest; the Bactopia Analysis Pipeline (BaAP), which performs quality control, genome assembly and several other functions based on the available datasets and outputs the processed data to a structured directory format; and a series of Bactopia Tools (BaTs) that perform specific post-processing on some or all of the processed data. BaTs include pan-genome analysis, computing average nucleotide identity between samples, extracting and profiling the 16S genes and taxonomic classification using highly conserved genes. It is expected that the number of BaTs will increase to fill specific applications in the future. As a demonstration, we performed an analysis of 1,664 publicLactobacillusgenomes, focusing onL. crispatus, a species that is a common part of the human vaginal microbiome. Bactopia is an open source system that can scale from projects as small as one bacterial genome to thousands that allows for great flexibility in choosing comparison datasets and options for downstream analysis. Bactopia code can be accessed athttps://www.github.com/bactopia/bactopia.
HLA-class II specificity assessed by high-density peptide microarray interactions
Authors: Osterbye Thomas , Nielsen Morten , Dudek Nadine L. , Ramarathinam Sri H. , Purcell Anthony W. , Schafer-Nielsen Claus , Buus Soren
Published: March 2020

The ability to predict and/or identify MHC binding peptides is an essential component of T cell epitope discovery; something that ultimately should benefit the development of vaccines and immunotherapies. In particular, MHC class I (MHC-I) prediction tools have matured to a point where accurate selection of optimal peptide epitopes is possible for virtually all MHC-I allotypes; in comparison, current MHC class II (MHC-II) predictors are less mature. Since MHC-II restricted CD4+ T cells control and orchestrate most immune responses, this shortcoming severely hampers the development of effective immunotherapies. The ability to generate large panels of peptides and subsequently large bodies of peptide-MHC-II interaction data is key to the solution of this problem; a solution that also will support the improvement of bioinformatics predictors, which critically relies on the availability of large amounts of accurate, diverse and representative data. Here, we have used recombinant HLA-DRB1*01:01 and HLA-DRB1*03:01 molecules to interrogate high-density peptide arrays,in casucontaining 70,000 random peptides in triplicates. We demonstrate that the binding data acquired contains systematic and interpretable information reflecting the specificity of the HLA-DR molecules investigated. Collectively, with a cost per peptide reduced to a few cents combined with the flexibility of recombinant HLA technology, this poses an attractive strategy to generate vast bodies of MHC-II binding data at an unprecedented speed and for the benefit of generating peptide-MHC-II binding data as well as improving MHC-II prediction tools.
Validation of melomind™ signal quality: a proof of concept resting-state and ERPs study
Authors: Spinelli Giuseppe , Odouard Alexandre , Nierat Marie-Cécile , Campion Sébastien , Bensoussan Mickael , Grosselin Fanny , Pandremmenou Katerina , Breton Audrey , Raux Mathieu , Attal Yohan , Similowski Thomas , Navarro-Suné Xavier
Published: March 2020

Wearable EEG systems have become accessible to researchers and clinicians over the last decade, thus requiring neurotechnology companies to seek for outstanding EEG signal quality. Here, we show that the melomind™ headset equipped with dry electrodes (myBrain Technologies, Paris, France) allows the recording of reliable electro-cortical dynamics as compared to a wet-based standard-EEG system (actiCAP, Brain Products GmbH, Gilching, Germany). EEGs were acquired simultaneously from the two systems while thirteen subjects underwent a visual oddball, a steady-state visually-evoked potentials (SSVEPs) and two resting-state (RS) tasks. RS were acquired with eyes-closed and eyes-open (2 minutes each) and repeated twice (before and after the cognitive tasks). During the oddball task, participants responded on a gamepad when a target-stimulus was displayed. In the SSVEPs, visual responses were elicited at 15 and 20 Hz through a series of 15-second stimuli presented 5 times each. The power of theta- [4-8 Hz], alpha- [8-13 Hz], and beta- [13-30 Hz] band was extracted from the two RS. The signal-to-noise-ratio in the 15 (± 1) and 20 (± 1) Hz range was computed from the SSVEPs. The shape of the N2/P300 complex was analysed from the oddball task. Strong correlations resulted between the parameters obtained from the two EEG systems (0.53 < Pearson’s r < 0.97). Bland and Altman analysis revealed small dissimilarities between the two systems, with values laying in the 95% confidence interval in all the tasks. Our results demonstrate that the melomind™ is an affordable solution to reliably assess humans’ electro-cortical dynamics at-rest and during cognitive tasks, thus paving the way to its use in neuroscience studies and brain-computer interfaces.
Delivery of cell-penetrating chromatin sensor-actuators to human osteosarcoma cells
Authors: Tekel Stefan J. , Brookhouser Nicholas , Haynes Karmella A.
Published: March 2020

The leading FDA-approved drugs for epigenetic cancer therapy are small molecule compounds that activate silenced tumor suppressors by inhibiting enzymes that generate aberrant repressive chromatin. Although promising, this approach is limited because chromatin-modifying enzymes often target non-chromatin proteins and can serve dual functions as gene repressors and activators. Previously, we have demonstrated that a transgenically expressed synthetic polycomb-derived transcription factor (PcTF) could activate genes in silenced chromatin via specific interactions with histone H3 trimethylated at lysine 27 (H3K27me3). Efficient non-viral intracellular delivery remains a challenge for protein-based biologics. Herein, we report the delivery of cell-penetrating PcTF (CP-PcTF) to cultured cells. We expressed and purified recombinant PcTF that was fused in frame with a nuclear localization signal and a cell penetrating peptide tag (TAT). We demonstrated rapid and efficient uptake of soluble CP-PcTF by osteosarcoma U-2 OS cells grown in 2-D monolayers and 3-D spheroids. However, CP-PcTF had a modest effect on gene expression and cell proliferation compared to transgenically-expressed PcTF from our previous work. Overall, these results suggest that TAT is a very effective delivery vehicle for the recombinant transcriptional regulator PcTF, and that further technical development is needed to deliver functional PcTF into cell nuclei.
Designing of a next generation multiepitope based vaccine (MEV) against SARS-COV-2: Immunoinformatics andin silicoapproaches
Authors: ul Qamar Muhammad Tahir , Rehman Abdur , Ashfaq Usman Ali , Awan Muhammad Qasim , Fatima Israr , Shahid Farah , Chen Ling-Ling
Published: March 2020

Coronavirus disease 2019 (COVID-19) associated pneumonia caused by severe acute respiratory coronavirus 2 (SARS-COV-2) was first reported in Wuhan, China in December 2019. Till date, no vaccine or completely effective drug is available to cure COVID-19. Therefore, an effective vaccine against SARS-COV-2 is crucially needed. This study was conducted to design an effective multiepitope based vaccine (MEV) against SARS-COV-2. Seven antigenic proteins were taken as targets and different epitopes (B-cell, T-cell and IFN-γ inducing) were predicted. Highly antigenic and overlapping epitopes were shortlisted. Selected epitopes indicated significant interactions with the HLA-binding alleles and 99.29% coverage of the world’s population. Finally, 505 amino acids long MEV was designed by connecting sixteen MHC class I and eleven MHC class II epitopes with suitable linkers and adjuvant. Linkers and adjuvant were added to enhance the immunogenicity response of the MEV. The antigenicity, allergenicity, physiochemical properties and structural details of MEV were analyzed in order to ensure safety and immunogenicity. MEV construct was non-allergenic, antigenic, stable and flexible. Molecular docking followed by molecular dynamics (MD) simulation analysis, demonstrated a stable and strong binding affinity of MEV with human pathogenic toll-like receptors (TLR), TLR3 and TLR8. Codon optimization andin silicocloning of MEV ensured increased expression in theEscherichia coliK-12 system. Designed MEV in present study could be a potential candidate for further vaccine production process against COVID-19. However, to ensure its safety and immunogenic profile, the proposed MEV needs to be experimentally validated.
Chromosome-Scale Genome Assembly Provides Insights into Speciation of Allotetraploid and Massive Biomass Accumulation of Elephant Grass (Pennisetum purpureumSchum.)
Authors: Zhang Shengkui , Xia Zhiqiang , Zhang Wenqing , Li Can , Wang Xiaohan , Lu Xianqin , Zhao Xianyan , Ma Haizhen , Zhou Xincheng , Zhang Weixiong , Zhu Tingting , Liu Pandao , Liu Guodao , Yang Hubiao , Arango Jacobo , Peters Michael , Wang Wenquan , Xia Tao
Published: March 2020

Elephant grass (Pennisetum purpureumSchum., A’A’BB, 2n=4x=28), which is characterized as robust growth and high biomass, and widely distributed in tropical and subtropical areas globally, is an important forage, biofuels and industrial plant. We sequenced its allopolyploid genome and assembled 2.07 Gb (96.88%) into A’ and B sub-genomes of 14 chromosomes with scaffold N50 of 8.47 Mb. A total of 38,453 and 36,981 genes were annotated in A’ and B sub-genomes, respectively. A phylogenetic analysis with species inPennisetumidentified that the speciation of the allotetraploid occurred approximately 15 MYA after the divergence betweenS.italicaandP. glaucum. Double whole-genome duplication (WGD) and polyploidization events resulted in large scale gene expansion, especially in the key steps of growth and biomass accumulation. Integrated transcriptome profiling revealed the functional differentiation between sub-genomes; A’ sub-genome contributed more to plant growth, development and photosynthesis whereas B sub-genome primarily offered functions of effective transportation and resistance to stimulation. The results uncovered enhanced cellulose and lignin biosynthesis pathways with 645 and 666 genes expanded in A’ and B sub-genomes, respectively. Our findings provided deep insights into the speciation and genetic basis of fast growth and high biomass accumulation in the species. The genetic, genomic, and transcriptomic resources generated in this study will pave the way for further domestication and selection of these economical species and making them more adaptive to industrial utilization.
Precautions are Needed for COVID-19 Patients with Coinfection of Common Respiratory Pathogens
Authors: Xing Quan-sheng , Li Guo-ju , Xing Yu-han , Chen Ting , Li Wen-jie , Ni Wei , Deng Kai , Gao Ru-qin , Chen Chang-zheng , Gao Yang , Li Qiang , Yu Gui-ling , Tong Jian-ning , Li Wei , Hao Gui-liang , Sun Yue , Zhang Ai , Wu Qin , Li Zi-pu , Pan Si-lin
Published: March 2020

Background

With the ongoing outbreak of Coronavirus Disease 2019 (COVID-19), infected patients within and beyond the epidemic area, Wuhan, China, showed different epidemiological and clinical characteristics. There is a paucity of data concerning coinfection with other common respiratory pathogens in COVID-19 patients outside of Wuhan.

Methods

We conducted a double-centre study recruiting 68 patients with severe acute respiratory coronavirus 2 (SARS-CoV-2) infection confirmed by nucleic acid testing in Qingdao and Wuhan from January 17 to February 16, 2020. Indirect immunofluorescence was performed to detect the specific IgM antibody against common respiratory pathogens in collected acute phase serum.

Results

Of the 68 patients with SARS-CoV-2 infection, 30 (44.12%) were from Qingdao. The median age of Qingdao and Wuhan patients were 50 (IQR: 37-59) and 31 (IQR: 28-38) years, respectively, and the majority of patients were female in Qingdao (60.00%) and Wuhan (55.26%). Among COVID-19 patients in Qingdao, 24 (80.00%) of them had IgM antibodies against at least one respiratory pathogen, whereas only one (2.63%) of the patients in Wuhan had positive results for serum IgM antibody detection (P<0.0001). The most common respiratory pathogens detected in Qingdao COVID-19 patients were influenza virus A (60.00%) and influenza virus B (53.33%), followed by mycoplasma pneumoniae (23.33%) and legionella pneumophila (20.00%). While the pattern for coinfection in patients with community-acquired pneumonia in Qingdao was quite different, with a positive rate of only 20.90%.

Interpretation

We reported a large proportion of COVID-19 patients with coinfection of seasonal respiratory pathogens in Qingdao, northeast China, which differed greatly from the patients in Wuhan, central China. Precautions are needed when dealing with COVID-19 patients beyond the epidemic centre who have coinfection with other respiratory pathogens. We highly recommend adding SARS-CoV-2 to routine diagnostic testing in capable hospitals to prevent misdetection of the virus.
Smartphone addiction and its association with common mental disorders among students attending the university of Dschang, West region, Cameroon
Authors: Sonkoue Martial Pianta , Kadia Benjamin Momo , Esong Miranda Baame , Douanla Cyrielle Djouda , Ateudjieu Jerome
Published: March 2020

Background

Smartphones are an integral part of modern communication but addiction to these devices could predispose to common mental disorders.

Objectives

To determine the prevalence of smartphone addiction and common mental disorders as well as the association between smartphone addiction and these mental disorders in Dschang university students who use smartphones.

Methods

A cross-sectional study was conducted. Randomly selected students completed a survey comprising Patient Health Questionnaires seven and nine (PHQ-9 and PHQ-7) to screen for depression and anxiety respectively, and the Smartphone Addiction Scale-Short Version (SAS-SV) to grade smartphone use. The association between smartphone use and common mental disorders was assessed using logistic regression modelling.

Results

We recruited 634 participants. The prevalence of smartphone addiction was 20.98% [C.I:17.99%-24.32%]. The prevalence of depression and anxiety were 34.86% [95% CI: 31.25-38.65] and 19.27% [95% CI: 16.81-22.99] respectively. The odds of depression in students with addiction was 5 times the odds of depression in students without addiction [OR: 4.96, 95% CI: 3.30-7.45, p<0.001]. The odds of anxiety in students with addiction was 2 times the odds of anxiety in students without addiction [OR: 2.44, 95% CI: 1.58-3.77, p<0.001]. After adjusting for age, sex, faculty, cycle of study, marital status, religion, chronic diseases, sexual abuse and suicidal ideation, there remained a statistically-significant association between smartphone addiction and both depression [OR: 4.46, 95%CI; 2.92-6.84, p<0.001] and anxiety [OR: 2.08, 95% CI; 1.31-3.30, p=0.002].

Conclusion

In this setting, it is crucial to foster strategies of prevention and promotion in mental health especially among problematic smartphone users.
An integrated transcriptomic and epigenomic atlas of mouse primary motor cortex cell types
Authors: Yao Zizhen , Liu Hanqing , Xie Fangming , Fischer Stephan , Booeshaghi A. Sina , Adkins Ricky S , Aldridge Andrew I. , Ament Seth A. , Pinto-Duarte Antonio , Bartlett Anna , Behrens M. Margarita , Van den Berge Koen , Bertagnolli Darren , Biancalani Tommaso , Bravo Héctor Corrada , Casper Tamara , Colantuoni Carlo , Creasy Heather , Crichton Kirsten , Crow Megan , Dee Nick , Dougherty Elizabeth L , Doyle Wayne I. , Dudoit Sandrine , Fang Rongxin , Felix Victor , Fong Olivia , Giglio Michelle , Goldy Jeff , Hawrylycz Mike , de Bézieux Hector Roux , Herb Brian R. , Hertzano Ronna , Hou Xiaomeng , Hu Qiwen , Crabtree Jonathan , Kancherla Jayaram , Kroll Matthew , Lathia Kanan , Li Yang Eric , Lucero Jacinta D. , Luo Chongyuan , Mahurkar Anup , McMillen Delissa , Nadaf Naeem , Nery Joseph R. , Niu Sheng-Yong , Orvis Joshua , Osteen Julia K. , Pham Thanh , Poirion Olivier , Preissl Sebastian , Purdom Elizabeth , Rimorin Christine , Risso Davide , Rivkin Angeline C. , Smith Kimberly , Street Kelly , Sulc Josef , Nguyen Thuc Nghi , Tieu Michael , Torkelson Amy , Tung Herman , Vaishnav Eeshit Dhaval , Svensson Valentine , Vanderburg Charles R. , Ntranos Vasilis , van Velthoven Cindy , Wang Xinxin , White Owen R. , Huang Z. Josh , Kharchenko Peter V. , Pachter Lior , Ngai John , Regev Aviv , Tasic Bosiljka , Welch Joshua D. , Gillis Jesse , Macosko Evan Z. , Ren Bing , Ecker Joseph R. , Zeng Hongkui , Mukamel Eran A.
Published: March 2020

Single cell transcriptomics has transformed the characterization of brain cell identity by providing quantitative molecular signatures for large, unbiased samples of brain cell populations. With the proliferation of taxonomies based on individual datasets, a major challenge is to integrate and validate results toward defining biologically meaningful cell types. We used a battery of single-cell transcriptome and epigenome measurements generated by the BRAIN Initiative Cell Census Network (BICCN) to comprehensively assess the molecular signatures of cell types in the mouse primary motor cortex (MOp). We further developed computational and statistical methods to integrate these multimodal data and quantitatively validate the reproducibility of the cell types. The reference atlas, based on more than 600,000 high quality single-cell or -nucleus samples assayed by six molecular modalities, is a comprehensive molecular account of the diverse neuronal and non-neuronal cell types in MOp. Collectively, our study indicates that the mouse primary motor cortex contains over 55 neuronal cell types that are highly replicable across analysis methods, sequencing technologies, and modalities. We find many concordant multimodal markers for each cell type, as well as thousands of genes and gene regulatory elements with discrepant transcriptomic and epigenomic signatures. These data highlight the complex molecular regulation of brain cell types and will directly enable design of reagents to target specific MOp cell types for functional analysis.
The 2019 coronavirus (SARS-CoV-2) surface protein (Spike) S1 Receptor Binding Domain undergoes conformational change upon heparin binding
Authors: Mycroft-West Courtney , Su Dunhao , Elli Stefano , Li Yong , Guimond Scott , Miller Gavin , Turnbull Jeremy , Yates Edwin , Guerrini Marco , Fernig David , Lima Marcelo , Skidmore Mark
Published: March 2020

Many pathogens take advantage of the dependence of the host on the interaction of hundreds of extracellular proteins with the glycosaminoglycans heparan sulphate to regulate homeostasis and use heparan sulphate as a means to adhere and gain access to cells. Moreover, mucosal epithelia such as that of the respiratory tract are protected by a layer of mucin polysaccharides, which are usually sulphated. Consequently, the polydisperse, natural products of heparan sulphate and the allied polysaccharide, heparin have been found to be involved and prevent infection by a range of viruses including S-associated coronavirus strain HSR1. Here we use surface plasmon resonance and circular dichroism to measure the interaction between the SARS-CoV-2 Spike S1 protein receptor binding domain (SARS-CoV-2 S1 RBD) and heparin. The data demonstrate an interaction between the recombinant surface receptor binding domain and the polysaccharide. This has implications for the rapid development of a first-line therapeutic by repurposing heparin and for next-generation, tailor-made, GAG-based antivirals.
An ultrasensitive, rapid, and portable coronavirus SARS-CoV-2 sequence detection method based on CRISPR-Cas12
Authors: Lucia Curti , Federico Pereyra-Bonnet , Alejandra Gimenez Carla
Published: March 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has received global attention due to the recent outbreak in China. In this work, we report a CRISPR-Cas12 based diagnostic tool to detect synthetic SARS-CoV-2 RNA sequences in a proof-of-principle evaluation. The test proved to be sensitive, rapid, and potentially portable. These key traits of the CRISPR method are critical for virus detection in regions that lack resources to use the currently available methods.
Structural basis of transcription-translation coupling and collision in bacteria
Authors: Webster Michael William , Takacs Maria , Zhu Chengjin , Vidmar Vita , Eduljee Ayesha , Abdelkareem Mo’men , Weixlbaumer Albert
Published: March 2020

Prokaryotic messenger RNAs (mRNAs) are translated as they are transcribed. The pioneering ribosome potentially contacts RNA polymerase (RNAP), forming a supramolecular complex known as the expressome. The basis of expressome assembly and its consequences for transcription and translation are poorly understood. Here we present a series of structures representing uncoupled, coupled and collided expressome states determined by electron cryomicroscopy. A bridge between the ribosome and RNAP can be formed by the transcription factor NusG, stabilizing an otherwise variable interaction interface. Shortening of the intervening mRNA causes a substantial rearrangement that aligns the ribosome entrance-channel to the RNAP exit-channel. In this collided complex, NusG-linkage is no longer possible.

These structures reveal mechanisms of coordination between transcription and translation and provide a framework for future study.

One Sentence Summary

Structures of the molecular assembly executing gene expression shed light on transcription translation coupling.
Induced Polarization in MD Simulations of the 5HT3Receptor Channel
Authors: Klesse Gianni , Rao Shanlin , Tucker Stephen J. , Sansom Mark S.P.
Published: March 2020

Ion channel proteins form water-filled nanoscale pores within lipid bilayers and their properties are dependent on the complex behavior of water in a nano-confined environment. Using the pore of the 5HT3 receptor (5HT3R) we compare additive with polarizable models in describing the behavior of water in nanopores. Molecular Dynamics simulations were performed with four conformations of the channel: two closed state structures, an intermediate state, and an open state, each embedded in a phosphatidylcholine bilayer. Water density profiles revealed that for all water models, the closed and intermediate states exhibited strong dewetting within the central hydrophobic gate region of the pore. However, the open state conformation exhibited varying degrees of hydration, ranging from partial wetting for the TIP4P/2005 water model, to complete wetting for the polarizable AMOEBA14 model. Water dipole moments calculated using polarizable force fields also revealed that water molecules remaining within dewetted sections of the pore resemble gas phase water. Free energy profiles for Na+ and for Cl− ions within the open state pore revealed more rugged energy landscapes using polarizable force fields, and the hydration number profiles of these ions were also sensitive to induced polarization resulting in a substantive reduction of the number of waters within the first hydration shell of Cl− whilst it permeates the pore. These results demonstrate that induced polarization can influence the complex behavior of water and ions within nanoscale pores and provides important new insights into their chemical properties.

ToC Graphic
Expression of the endocannabinoid system in the human airway epithelial cells – Impact of sex and chronic respiratory disease status
Authors: Fantauzzi Matthew F. , Aguiar Jennifer A. , Tremblay Benjamin J-M. , Yanagihara Toyoshi , Chandiramohan Abiram , Revill Spencer , Ryu Min Hyung , Carlsten Chris , Ask Kjetil , Stämpfli Martin , Doxey Andrew C. , Hirota Jeremy A.
Published: March 2020

Recreational and medicinal cannabis consumption in the past 12 months has been reported in 1/5th of Canadians, with greater use in males relative to females. Cannabis smoking is the dominant route of delivery in consumers, with the airway epithelium functioning as the site of first contact for inhaled phytocannabinoids. The endocannabinoid system is responsible for mediating the physiological effects of inhaled phytocannabinoids. Acute cannabis smoke inhalation can result in bronchodilation, which may have applications in chronic respiratory disease management. In contrast, chronic cannabis smoke inhalation is associated with reduced lung function and bronchitis, which challenges potential applications in the lung. The contribution of the endocannabinoid system in the airway epithelium to either beneficial or harmful physiological responses remains to be clearly defined in males and females and those with underlying chronic respiratory disease.

To begin to address this knowledge gap, a curated dataset of 1090 unique human bronchial brushing gene expression profiles was created from Gene Expression Omnibus deposited microarray datasets. The dataset included 616 healthy subjects, 136 subjects with asthma, and 338 subjects with COPD. A 27-gene endocannabinoid signature was analyzed across all samples with sex and disease specific-analyses performed. Immunohistochemistry and immunoblots were performed to confirm in situ and in vitro protein expression of select genes in human airway epithelial cells.

We confirm three receptors for cannabinoids, CB1, CB2, and TRPV1, are expressed at the protein level in human airway epithelial cells in situ and in vitro, justifying examining the downstream endocannabinoid pathway more extensively at the gene expression level. Sex status was associated with differential expression of 6/27 genes. In contrast, disease status was associated with differential expression of 18/27 genes in asthmatics and 22/27 genes in COPD subjects. We confirm at the protein level that TRPV1, the most differentially expressed candidate in our analyses, was up-regulated in airway epithelial cells from asthmatics relative to healthy subjects.

Our data demonstrate that endocannabinoid system is expressed in human airway epithelial cells with expression impacted by disease status and minimally by sex. The data suggest that cannabis consumers may have differential physiological responses in the respiratory mucosa, which could impact both acute and chronic effects of cannabis smoke inhalation.
Stochastic bond dynamics facilitates alignment of malaria parasite at erythrocyte membrane upon invasion
Authors: Hillringhaus Sebastian , Dasanna Anil K. , Gompper Gerhard , Fedosov Dmitry A.
Published: March 2020

Malaria parasites invade healthy red blood cells (RBCs) during the blood stage of the disease. Even though parasites initially adhere to RBCs with a random orientation, they need to align their apex toward the membrane in order to start the invasion process. Using hydrodynamic simulations of a RBC and parasite, where both interact through discrete stochastic bonds, we show that parasite alignment is governed by the combination of RBC membrane deformability and dynamics of adhesion bonds. The stochastic nature of bond-based interactions facilitates a diffusive-like re-orientation of the parasite at the RBC membrane, while RBC deformation aids in the establishment of apexmembrane contact through partial parasite wrapping by the membrane. This bond-based model for parasite adhesion quantitatively captures alignment times measured experimentally and demonstrates that alignment times increase drastically with increasing rigidity of the RBC membrane. Our results suggest that the alignment process is mediated simply by passive parasite adhesion.
Forecasting the Cumulative Number of COVID-19 Deaths in China: a Boltzmann Function-based Modeling Study
Authors: Gao Yuanyuan , Li Zhongyan , Ying Qi , Long Cheng , Fu Xinmiao
Published: March 2020

The COVID-19 outbreak is on-going in China. Here we estimated the potential total numbers of COVID-19 deaths in China, outside Hubei (in China), Hubei Province, Wuhan City and outside Wuhan (in Hubei) by Boltzmann function-based analyses, which are 3342 (95% CI, 3214, 3527), 111 (109, 114), 3245 (3100, 3423), 2613 (2498, 2767) and 627 (603, 654), respectively. The results may help to evaluate the severity of COVID-19 outbreaks and facilitate timely mental service for the families of passed patients.
Diversification of molecularly defined myenteric neuron classes revealed by single cell RNA-sequencing
Authors: Morarach Khomgrit , Mikhailova Anastassia , Knoflach Viktoria , Memic Fatima , Kumar Rakesh , Li Wei , Ernfors Patrik , Marklund Ulrika
Published: March 2020

Autonomous functions of the gastrointestinal tract require the combined activity of functionally distinct neurons of the enteric nervous system (ENS). However, the range of enteric neuron diversity and how it emerges during development remain largely unknown. We here make a novel molecular definition of 12 enteric neuron classes (ENCs) within the myenteric plexus of the mouse small intestine. We identify communication features and provide histochemical markers for discrete motor, sensory, and interneurons together with genetic tools for class-specific targeting. Transcriptome analysis of embryonic ENS reveals a largely post-mitotic principle of diversification, where only ENC1 or ENC8 phenotypic traits arise through a binary neurogenic trajectory, and other identities form through subsequent differentiation. We propose generic and class-specific transcriptional regulators and functionally connect the transcription factorPbx3to one post-mitotic identity conversion. Our results offers a conceptual and molecular resource for dissecting ENS circuits, and predicting key regulators for the directed differentiation of distinct enteric neuron classes.
Interaction of RSC chromatin remodelling complex with nucleosomes is modulated by H3 K14 acetylation and H2B SUMOylationin vivo
Authors: Jain Neha , Tamborrini Davide , Evans Brian , Chaudhry Shereen , Wilkins Bryan J. , Neumann Heinz
Published: March 2020

Chromatin remodelling complexes are multi-subunit nucleosome translocases that reorganize chromatin in the context of DNA replication, repair and transcription. A key question is how these complexes find their target sites on chromatin. Here, we use genetically encoded photo-crosslinker amino acids to map the footprint of Sth1, the catalytic subunit of the RSC (remodels the structure of chromatin) complex, on the nucleosome in living yeast. We find that the interaction of the Sth1 bromodomain with the H3 tail depends on K14 acetylation by Gcn5. This modification does not recruit RSC to chromatin but mediates its interaction with neighbouring nucleosomes. We observe a preference of RSC for H2B SUMOylated nucleosomesin vivoand show that this modification moderately enhances RSC binding to nucleosomesin vitro. Furthermore, RSC is not ejected from chromatin in mitosis, but its mode of nucleosome binding differs between interphase and mitosis. In sum, ourin vivoanalyses show that RSC recruitment to specific chromatin targets involves multiple histone modifications most likely in combination with other components such as histone variants and transcription factors.

Key Points

In vivophoto-crosslinking reveals the footprint of the ATPase subunit of RSC on the nucleosome.

RSC binds to H3 K14ac nucleosomes via the C-terminal bromodomain of its ATPase-subunit Sth1.

RSC preferentially localizes to H2B-SUMOylated nucleosomes.
Ultrastructural comparison of dendritic spine morphology preserved with cryo and chemical fixation
Authors: Tamada Hiromi , Blanc Jerome , Korogod Natalya , Petersen Carl CH , Knott Graham W
Published: March 2020

Previously we showed that cryo fixation of brain tissue gave a truer representation of brain ultrastructure in comparison with a standard chemical fixation method (Korogod et al 2005). Extracellular space matched physiological measurements, there were larger numbers of docked vesicles and less glial coverage of synapses and blood capillaries. Here, using the same preservation approaches we compared the morphology of dendritic spines. We show that the length of the spine and the volume of its head is unchanged, however, the spine neck width is thinner by more than 30 % after cryo fixation. In addition, the weak correlation between spine neck width and head volume seen after chemical fixation was not present in cryo-fixed spines. Our data suggest that spine neck geometry is independent of the spine head volume, with cryo fixation showing enhanced spine head compartmentalization and a higher predicted electrical resistance between spine head and parent dendrite.
Adipose-tissue derived signals control bone remodelling
Authors: Madel Maria-Bernadette , Fu He , Pierroz Dominique D. , Schiffrin Mariano , Winkler Carine , Wilson Anne , Pochon Cécile , Toffoli Barbara , Jouzeau Jean-Yves , Gilardi Federica , Ferrari Serge , Bonnet Nicolas , Blin-Wakkach Claudine , Desvergne Béatrice , Moulin David
Published: March 2020

Long bones from mammals host blood cell formation and contain multiple cell types, including adipocytes. Physiological functions of bone marrow adipocytes are poorly documented. Herein, we used adipocyte-deficient PPARγ-whole body null mice to investigate the consequence of total adipocyte deficiency on bone homeostasis in mice. We first highlight the dual bone phenotype of PPARγ null mice: on the one hand the increase bone formation and subsequent trabecularization extending in the long bone diaphysis, due to the well-known impact of PPARγ deficiency on osteoblasts formation and activity; on the other hand, an increased osteoclastogenesis in the cortical bone. We then further explore the cause of this unexpected increased osteoclastogenesis using two independent models of lipoatrophy, which recapitulated this phenotype. This demonstrates that hyperosteoclastogenesis is not intrinsically linked to PPARγ deficiency, but is a consequence of the total lipodystrophy. We further showed that adiponectin, a cytokine produced by adipocytes and mesenchymal stromal cells is a potent inhibitor of osteoclastogenesisin vitroandin vivo. Moreover, pharmacological activation of adiponectin receptors by the synthetic agonist AdipoRon inhibits mature osteoclast activity both in mouse and human cells by blocking podosome formation through AMPK activation. Finally, we demonstrated that AdipoRon treatment blocks bone erosion in vivo in a murine model of inflammatory bone loss, providing potential new approaches to treat osteoporosis.
Evidence for host-dependent RNA editing in the transcriptome of SARS-CoV-2
Authors: Di Giorgio Salvatore , Martignano Filippo , Torcia Maria Gabriella , Mattiuz Giorgio , Conticello Silvestro G.
Published: March 2020

The COVID-19 outbreak has become a global health risk and understanding the response of the host to the SARS-CoV-2 virus will help to contrast the disease. Editing by host deaminases is an innate restriction process to counter viruses, and it is not yet known whether it operates against Coronaviruses. Here we analyze RNA sequences from bronchoalveolar lavage fluids derived from infected patients. We identify nucleotide changes that may be signatures of RNA editing: Adenosine-to-Inosine changes from ADAR deaminases and Cytosine-to-Uracil changes from APOBEC ones. A mutational analysis of genomes from different strains of human-hosted Coronaviridae reveals mutational patterns compatible to those observed in the transcriptomic data. Our results thus suggest that both APOBECs and ADARs are involved in Coronavirus genome editing, a process that may shape the fate of both virus and patient.

For the casual Reader

Just to make a few things clear:

- RNA editing and DNA editing are PHYSIOLOGICAL processes. Organisms uses them to (a) try to fight viruses, (b) increase heterogeneity inside cells (on many levels), (c) recognise their own RNA.

- our work suggests that: (a) cells use RNA editing in trying to deal with Coronaviruses. We don't know to what extent they succeed (and it would be nice if we could help them). (b) Whatever happens, mutations inserted by RNA editing fuel viral evolution. We don't know whether viruses actively exploit this.

- If you (scientist or not) think our work suggests ANYTHING ELSE, contact us. It can be a first step to help fight these !@#$ coronavirus, or towards a Nobel prize - but we need to discuss it thoroughly.

- If you think these cellular processes are fascinating, join the club and contact us. We can have a nice cup of tea while chatting how wondrous nature is at coming up with extraordinary solutions…
Conserved His-Gly motif of acid-sensing ion channels resides in a reentrant ‘loop’ implicated in gating and ion selectivity
Authors: Yoder Nate , Gouaux Eric
Published: March 2020

Acid-sensing ion channels (ASICs) are proton-gated members of the epithelial sodium channel/degenerin (ENaC/DEG) superfamily of ion channels and are expressed throughout central and peripheral nervous systems. The homotrimeric splice variant ASIC1a has been implicated in nociception, fear memory, mood disorders and ischemia. Here we extract full-length chicken ASIC1a (cASIC1a) from cell membranes using styrene maleic acid (SMA) copolymer, yielding structures of ASIC1a channels in both high pH resting and low pH desensitized conformations by single-particle cryo-electron microscopy (cryo-EM). The structures of resting and desensitized channels reveal a reentrant loop at the amino terminus of ASIC1a that includes the highly conserved ‘His-Gly’ (HG) motif. The reentrant loop lines the lower ion permeation pathway and buttresses the ‘Gly-Ala-Ser’ (GAS) constriction, thus providing a structural explanation for the role of the His-Gly dipeptide in the structure and function of ASICs.
Staining the Blot for Total Protein with Ponceau S
Authors: Litovchick Larisa
Published: March 2020

Before probing blots for the presence of an antigen, the total composition of the transferred proteins can be determined by staining the nitrocellulose or polyvinylidene fluoride (PVDF) membrane. Staining for proteins is useful to determine the position of the non-prestained molecular weight markers or individual lanes on the gel and to ensure that efficient transfer has occurred. It can be also used to verify equal loading of the samples in the gel when a comparison of the protein of interest between the different samples is important. The conventional procedures such as Coomassie Blue and silver staining methods used for staining polyacrylamide gels are incompatible with immunoblotting. Ponceau S is the more common staining method in immunoblotting protocols because it is compatible with antibody–antigen binding, is cost efficient, and provides a good contrast between the stained bands and background. In this protocol, nitrocellulose or PVDF membrane is rinsed with ultrapure H2O after the transfer of proteins. Ponceau S dye is applied as an acidic aqueous solution, and the proteins on the membrane are stained with red color. The membrane is briefly destained with water and can be photographed or scanned to obtain the image of the total protein staining. Individual lane positions or the molecular weight standards can be marked with a pencil, if required.
Quantifying and Storing RNA
Authors: Green Michael R. , Sambrook Joseph
Published: March 2020

Quantifying RNA is an important and necessary step before most RNA analysis techniques. Methods for quantifying RNA can be classified into two categories: ultraviolet (UV) spectrophotometric methods, which are based on the absorption spectra of the purine and pyrimidine bases; and fluorescent dye-based methods, which measure the fluorescence intensity of dyes that selectively fluoresce when bound to nucleic acids. If the RNA sample is pure (i.e., without significant amounts of contaminants such as proteins, phenol, agarose, or other nucleic acids), UV spectrophotometric measurement of the amount of UV irradiation absorbed by the bases is simple and accurate. However, if the sample contains significant quantities of impurities or if the concentration of RNA is very low, it is better to use fluorescent dye-based methods. An overview of spectrophotometric and fluorescent dye-based RNA quantification methods is given here, as are several options for storing purified RNA preparations. Proper storage of RNA samples is important; it can help minimize RNase contamination and consequent sample degradation.
The crystal structure of the catalytic domain of tau tubulin kinase 2 in complex with a small-molecule inhibitor
Authors: Marcotte Douglas J. , Spilker Kerri A. , Wen Dingyi , Hesson Thomas , Patterson Thomas A. , Kumar P. Rajesh , Chodaparambil Jayanth V.
Published: March 2020

Tau proteins play an important role in the proper assembly and function of neurons. Hyperphosphorylation of tau by kinases such as tau tubulin kinase (TTBK) has been hypothesized to cause the aggregation of tau and the formation of neurofibrillary tangles (NFTs) that lead to the destabilization of microtubules, thereby contributing to neurodegenerative diseases such as Alzheimer's disease (AD). There are two TTBK isoforms with highly homologous catalytic sites but with distinct tissue distributions, tau phosphorylation patterns and loss-of-function effects. Inhibition of TTBK1 reduces the levels of NFT formation involved in neurodegenerative diseases such as AD, whereas inhibition of TTBK2 may lead to the movement disorder spinocerebellar ataxia type 11 (SCA11). Hence, it is critical to obtain isoform-selective inhibitors. Structure-based drug design (SBDD) has been used to design highly potent and exquisitely selective inhibitors. While structures of TTBK1 have been reported in the literature, TTBK2 has evaded structural characterization. Here, the first crystal structure of the TTBK2 kinase domain is described. Furthermore, the crystal structure of human TTBK2 in complex with a small-molecule inhibitor has successfully been determined to elucidate the structural differences in protein conformations between the two TTBK isoforms that could aid in SBDD for the design of inhibitors that selectively target TTBK1 over TTBK2.
Disturbance observer-based coordinated control for three dimensional formation of unmanned autonomous helicopter
Authors: Mei Rong
Published: March 2020

Purpose

This paper aims to study the issue of the three-dimensional formation coordinated control for the unmanned autonomous helicopter (UAH) by using the sliding mode disturbance observer. Under the designed formation coordinated controller, the desired formation can be maintained and the closed-loop system stability is analyzed by using the Lyapunov theory.

Design/methodology/approach

Considering the unknown time-varying external 10; disturbance in formation flight of UAHs, a sliding mode disturbance observer has been employed to estimate them.

Findings

This work is supported in part by the National Natural Science Foundation of China under Grant 61803207, and in part by the Fundamental Research Funds for the Central Universities under Grant LGZD201806.

Originality/value

A sliding mode disturbance observer has been designed to estimate the unknown time-varying external disturbance in formation flight of UAHs. Aiming at the leading UAH maneuver in three-dimensional space during the formation flight progress, the formation coordinated controller has been proposed based on the output of the disturbance observer to maintain the formation.
Reference publication year spectroscopy (RPYS) of computer science papers from Eastern Europe
Authors: Fiala Dalibor , Bornmann Lutz
Published: March 2020

Purpose

The current article presents the results of a case study dealing with the historical roots of Eastern European researchers in computer science.

Design/methodology/approach

The study is based on an analysis of cited references stemming from a collection of around 80,000 computer science papers by Eastern European researchers published from 1989 to 2014. By using a method called “reference publication year spectroscopy” (RPYS) for historical analyses based on bibliometric data, we analyze around 800,000 references cited in those papers. The study identifies the peak years, including most frequently cited publications (from 1952, 1965 and 1975), and focuses on these outstanding works for the field. The research shows how these influential papers were cited in Eastern Europe and in general, and on which scientific fields they have the most impact.

Findings

A noteworthy publication that seems to have a tremendous effect on Eastern European computer science is Zadeh's “Fuzzy sets” article which appeared in Information and Control in 1965. The study demonstrates that computer scientists from Eastern Europe are more conservative in their citation behaviour and tend to refer to older and more established research than their counterparts from the West.

Originality/value

Which are the historical roots of researchers working in a particular field or on a specific topic? Are there certain publications – landmark papers – which are important for their research? We guess that these are questions bothering researchers in many fields.