bluuebunny/crossref_metadata_2025 huggingface dataset:
Neural network modelling reveals changes in directional connectivity between cortical and hypothalamic regions in obesity
Authors: Voigt Katharina , Razi Adeel , Harding Ian H. , Andrews Zane B. , Verdejo-Garcia Antonio
Published: May 2020

Obesity has been ascribed to corticostriatal regions taking control over homeostatic areas. To test this assumption, we applied an effective connectivity approach to reveal the direction of information flow between brain regions and the valence of connections (excitatory versus inhibitory) as a function of adiposity and homeostatic state. Forty-one participants (21 overweight/obese) underwent two resting-state fMRI scans: after overnight fasting (hunger) and following a standardised meal (satiety). We used spectral dynamic causal modelling to unravel hunger and adiposity related changes in directed connectivity between cortical, insular, striatal and hypothalamic regions. During hunger, as compared to satiety, we found increased excitation of the ventromedial prefrontal cortex over the ventral striatum and hypothalamus, suggesting enhanced top-down modulation compensating energy depletion. Adiposity was associated with increased excitation of the anterior insula over the hypothalamus across the hunger and satiety conditions. The interaction of hunger and adiposity yielded decreased intra-cortical excitation from the dorsolateral to the ventromedial prefrontal cortex. Our findings suggest that obesity is associated with persistent top-down excitation of the hypothalamus, regardless of homeostatic state, and hunger-related reductions of dorsolateral to ventromedial prefrontal inputs. These findings are compatible with eating without hunger and reduced self-regulation views of obesity.

Significance Statement

Obesity is a leading contributor to morbidity and mortality. Neurobiological theories propose that, in obese people, corticostriatal regions take over homeostatic areas. Neuroimaging-based functional connectivity is well-poised to unravel such abnormalities by examining between-regions communication, but existing studies have only measured signal covariance, not direction and valence of connectivity. We applied computational modelling to reveal the direction of information flow between brain regions and excitatory/inhibitory valence of connections in obese versus healthy-weight participants. Obesity associated with heightened top-down excitation from the insula to hypothalamus, and reduced excitation within prefrontal regions. Findings have two advantages relative to current knowledge: demonstrate theory-based directional abnormalities, i.e. cortical regions taking over homeostatic areas; and inform brain stimulation therapies targeting cortical input to lower-level regions.
Increased levels of anxiety among medical and non-medical university students during the COVID-19 pandemic in the United Arab Emirates.
Authors: Saddik Basema , Hussein Amal , Sharif-Askari Fatemeh Saheb , Kheder Waad , Temsah Mohamad-Hani , Koutaich Rim Adnan , Haddad Enad Sami , Al-Roub Nora Marwan , Marhoon Fatema Adel , Hamid Qutayba , Halwani Rabih
Published: May 2020

Introduction: The COVID-19 pandemic is likely to increase anxiety levels within the community and in particular medical students who are already considered psychologically vulnerable groups. Since the COVID-19 outbreak, no study has yet estimated the effect of this pandemic on university students in the UAE or its impact on the psychological well-being of medical students.
Methods: In this study, we surveyed 1485 medical (comprising medical and dental) and non-medical university students across 4 emirates within the UAE. We used an online platform to assess knowledge, sources of information, changes in hygienic behavior, perceptions of fear and worry and anxiety levels using the generalized anxiety disorder 7 (GAD-7) scale. The GAD-7 score was measured at three time points; during hospital visits for medical/dental students, before the introduction of online learning and after online learning for all students.
Results: The majority of students demonstrated high levels of knowledge and utilized reliable sources of
information. Non-medical students exercised higher compliance with social restrictions, while medical students practiced better hand hygiene. Almost half of students reported anxiety levels ranging from mild to severe with females reporting higher anxiety scores during hospital visits (OR=2.02, 95% CI,1.41 to 2.91) and medical students reporting lower anxiety levels in comparison to dental students (OR=0.61, 95% CI,0.45 to 0.84). Medical students reported higher levels of anxiety during their clinical rotations which decreased with the introduction of online learning, yet, non-medical student's anxiety levels increased with online learning.
Conclusions: This is the first study to provide important information on the initial response and anxiety levels in university students across the UAE during the COVID-19 pandemic. The findings from our study can be used to support the development of effective screening strategies and interventions to build psychological resilience among university students during the COVID-19 pandemic or any other public health emergencies in the future.
Metric and chronological time in human episodic memory
Authors: Evensmoen Hallvard Røe , Rimol Lars M. , Rise Henning Hoel , Hansen Tor Ivar , Nili Hamed , Winkler Anderson M. , Håberg Asta
Published: May 2020

The relative contributions of metric and chronological time in the encoding of episodic memories are unknown. One hundred one healthy young adults viewed 48 unique episodes of visual events and were later tested on recall of the order of events (chronological time) and the precise timing of events (metric time). The behavioral results show that metric recall accuracy correlates with chronological accuracy for events within episodes, but does not play a role on larger time-scales across episodes. Functional magnetic resonance imaging during encoding and recall showed that metric time was represented in the posterior medial entorhinal cortex, as well as the temporal pole and the cerebellum, whereas chronological time was represented in a widespread brain network including the anterior lateral entorhinal cortex, hippocampus, parahippocampal cortex and the prefrontal cortex. We conclude that metric time has a role in episodic memory on short time-scales and is mainly subserved by medial temporal lobe structures.
Huntington’s disease-specific mis-splicing captured by human-mouse intersect-RNA-seq unveils pathogenic effectors and reduced splicing factors
Authors: Elorza Ainara , Márquez Yamile , Cabrera Jorge R. , Sánchez-Trincado José Luis , Santos-Galindo María , Hernández Ivó H. , Díaz-Hernández Juan Ignacio , García-Escudero Ramón , Irimia Manuel , Lucas José J.
Published: May 2020

Deregulated alternative splicing has been implicated in a wide range of pathologies. Deep RNA-sequencing has revealed global mis-splicing signatures in multiple human diseases; however, for neurodegenerative diseases, these analyses are intrinsically hampered by neuronal loss and neuroinflammation in post-mortem brains. To infer splicing alterations relevant to Huntington’s disease (HD) pathogenesis, here we performed intersect-RNA-seq analyses of human post-mortem striatal tissue and of an early symptomatic mouse model in which neuronal loss and gliosis are not yet present. Together with a human/mouse parallel motif scan analysis, this approach allowed us to identify the shared mis-splicing signature triggered by the HD-causing mutation in both species and to infer upstream deregulated splicing factors. Moreover, we identified a plethora of downstream neurodegeneration-linked effector genes, whose aberrant splicing is associated with decreased protein levels in HD patients and mice. In summary, our intersect-RNA-seq approach unveiled the pathogenic contribution of mis-splicing to HD and could be readily applied to other neurodegenerative diseases for which bona fide animal models are available.
Lumi-Map, a real-time luciferase bioluminescence screen of mutants combined with MutMap, revealsArabidopsisgenes involved in PAMP-triggered immunity
Authors: Kato Hiroaki , Onai Kiyoshi , Abe Akira , Shimizu Motoki , Takagi Hiroki , Tateda Chika , Utsushi Hiroe , Singkarabanit-Ogawa Suthitar , Kitakura Saeko , Ono Erika , Zipfel Cyril , Takano Yoshitaka , Ishiura Masahiro , Terauchi Ryohei
Published: May 2020

Plants recognize pathogen-associated molecular patterns (PAMPs) to activate PAMP-triggered immunity (PTI). However, our knowledge of PTI signaling remains limited. In this report, we introduce Lumi-Map, a high-throughput platform for identifying causative single nucleotide polymorphisms (SNPs) to studying PTI signaling components. In Lumi-Map, a transgenic reporter plant line is produced that contains a fireflyluciferase(LUC) gene driven by a defense gene promoter, which generates luminescence upon PAMP treatment. The line is mutagenized and the mutants with altered luminescence patterns are screened by a high-throughput real-time bioluminescence monitoring system. Selected mutants are subjected to MutMap analysis, a whole genome sequencing (WGS)-based method of rapid mutation identification, to identify the causative SNP responsible for the luminescence pattern change. We generated nine transgenicArabidopsisreporter lines expressingLUCgene fused to multiple promoter sequences of defense-related genes. These lines generate luminescence upon activation of FLAGELLIN-SENSING 2 (FLS2) by flg22, a PAMP derived from bacterial flagellin. We selected theWRKY29-promoter reporter line to identify mutants in the signaling pathway downstream ofFLS2. After screening 24,000 ethylmethanesulfonate (EMS)-induced mutants of the reporter line, we isolated 22 mutants with alteredWRKY29expression upon flg22 treatment (abbreviated asawfmutants). While five flg22-insensitiveawfmutants harbored mutations inFLS2itself, Lumi-Map revealed three genes not previously associated with PTI. Lumi-Map has the potential to identify novel PAMPs and their receptors as well as signaling components downstream of the receptors.
Meta-Align: A Novel HMM-based Algorithm for Pairwise Alignment of Error-Prone Sequencing Reads
Authors: Tomii Kentaro , Kumar Shravan , Zhi Degui , Brenner Steven E.
Published: May 2020

Background

Insertion and deletion sequencing errors are relatively common in next-generation sequencing data and produce long stretches of mistranslated sequence. These frameshifting errors can cause very serious damages to downstream data analysis of reads. However, it is possible to obtain more precise alignment of DNA sequences by taking into account both coding frame and sequencing errors estimated by quality scores.

Results

Here we designed and proposed a novel hidden Markov model (HMM)-based pairwise alignment algorithm, Meta-Align, that aligns DNA sequences in the protein space, incorporating quality scores from the DNA sequences and allowing frameshifts caused by insertions and deletions. Our model is based on both an HMM transducer of a pair HMM and profile HMMs for all possible amino acid pairs. A Viterbi algorithm over our model produces the optimal alignment of a pair of metagenomic reads taking into account all possible translating frames and gap penalties in both the protein space and the DNA space. To reduce the sheer number of states of this model, we also derived and implemented a computationally feasible model, leveraging the degeneracy of the genetic code. In a benchmark test on a diverse set of simulated reads based on BAliBASE we show that Meta-Align outperforms TBLASTX which compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database using the BLAST algorithm. We also demonstrate the effects of incorporating quality scores on Meta-Align.

Conclusions

Meta-Align will be particularly effective when applied to error-prone DNA sequences. The package of our software can be downloaded athttps://github.com/shravan-repos/Metaalign.
Ppd-1Remodels Spike Architecture by Regulating Floral Development in wheat
Authors: Liu Yangyang , Zhang Lili , Melzer Michael , Shen Liping , Sun Zhiwen , Wang Ziying , Schnurbusch Thorsten , Guo Zifeng
Published: May 2020

The determination of spike architecture is critical to grain yield in wheat (Triticum aestivum), yet the underlying mechanisms remain largely unknown. Here, we measured 51 traits associated with spike architecture and floral development in 197 wheat accessions with photoperiod sensitive and insensitive alleles. We included five distinct allele combinations at thePhotoperiod-1(Ppd-1) loci. A systematic dissection of all recorded phenotypes revealed connections between floral development, spike architecture and grain yield. Modifying the durations of spikelet primordia initiation did not necessarily affect spikelet number. In addition,Ppd-1loci clearly influenced rachis dry weight, pointing to the rachis vascular system as a potential target for higher yield.Ppd-1displayed opposite effects on the durations of pre and post-anthesis phases.Ppd-1controlled carpel size, but not anther size. Finally, the photoperiod-insensitive alleles ofPpd-1triggered floral degeneration. In parallel, we profiled the spike transcriptome at six stages and four positions in threePpd-1genotypes which consists of 234 samples. Integrating phenotypic and expression data suggested that loss of function inPpd-1loci delayed floral degeneration by regulating autophagy and extended floret development by regulating genes in different families. Therefore, we concluded thatPpd-1remodels spike architecture by regulating floral development in wheat.
The study of the determinants controlling Arpp19 phosphatase-inhibitory activity reveals a new Arpp19/PP2A-B55 feedback loop
Authors: Labbé Jean Claude , Vigneron Suzanne , Méchali Francisca , Robert Perle , Genoud Cindy , Goguet-Rubio Perrine , Barthe Phillipe , Labesse Gilles , Cohen-Gonsaud Martin , Castro Anna , Lorca Thierry
Published: May 2020

Arpp19 is a potent inhibitor of PP2A-B55 that regulates this phosphatase to ensure the stable phosphorylation of mitotic/meiotic substrates. At G2-M, Arpp19 is phosphorylated by Greatwall on S67. This phosphorylated Arpp19 form displays a high affinity to PP2A-B55 and a slow dephosphorylation rate, acting as an “unfair” competitor of PP2A-B55 substrates. The molecular determinants conferring slow dephosphorylation kinetics to S67 are unknown. PKA also phosphorylates Arpp19. This phosphorylation performed on S109 is essential to maintain prophase I-arrest in Xenopus oocytes although the underlying signaling mechanism is elusive. Here, we characterized the molecular determinants conferring slow dephosphorylation to S67 and controlling PP2A-B55 inhibitory activity of Arpp19. Moreover, we showed that phospho-S109 restricts S67 phosphorylation by increasing its catalysis by PP2A-B55. Finally, we discovered a double feed-back loop between these two phospho-sites which is essential to coordinate the temporal pattern of Arpp19-dependent PP2A-B55 inhibition and Cyclin B/Cdk1 activation during cell division.
Δ9-Tetrahydrocannabinolic Acid markedly alleviates liver fibrosis and inflammation in murine models of chemically- and obesity-induced liver injury
Authors: Carmona-Hidalgo Beatriz , González-Mariscal Isabel , García-Martín Adela , Ruiz-Pino Francisco , Appendino Giovanni , Tena-Sempere Manuel , Muñoz Eduardo
Published: May 2020

Background

Non-alcoholic fatty liver disease (NAFLD) is the most common liver disease in the Western world, and it is closely associated to obesity, type 2 diabetes mellitus, and dyslipidemia. Hepatocellular stellate cells (HSCs) activation by oxidative stress and inflammation is the hallmark of liver fibrosis and leads to cirrhosis and liver failure resistant to pharmacological management. Cannabinoids have been suggested as a potential therapy for liver fibrosis, prompting us to explore the antifibrotic and anti-inflammatory effects of Δ9-THCA-A, a major non-psychotropic cannabinoid fromCannabis sativaL., in animal models of NAFLD.

Methods

Non-alcoholic liver fibrosis was induced in mice by CCl4treatment or, alternatively, by 23-week high fat diet (HFD) feeding. Δ9-THCA was administered daily intraperitoneally during the CCl4treatment or during the last 3 weeks in HFD-fed mice. Liver fibrosis and inflammation were assessed by immunochemistry and qPCR. Blood glucose and plasma insulin, leptin and triglyceride levels were measured in HFD mice.

Results

Δ9-THCA significantly attenuated CCl4-induced liver fibrosis and inflammation and reduced T cell and macrophage infiltration. Mice fed HFD for 23 weeks developed severe obesity (DIO), fatty liver and marked liver fibrosis, accompanied by immune cell infiltration. Δ9-THCA, significantly reduced body weight and adiposity, improved glucose tolerance, and drastically attenuated DIO-induced liver fibrosis and immune cell infiltration.

Conclusions

Δ9-THCA prevents liver fibrogenesisin vivo, providing a rationale for additional studies on the medicinal use of this cannabinoid, as well as cannabis preparations containing it, in the treatment of liver fibrosis and the management of NAFLD.
Allelic diversity study of functional genes in East Africa bread wheat highlights opportunities for genetic improvement
Authors: Wamalwa Mercy , Tadesse Zerihun , Muthui Lucy , Yao Nasser , Zegeye Habtemariam , Randhawa Mandeep , Wanyera Ruth , Uauy Cristobal , Shorinola Oluwaseyi
Published: May 2020

Wheat (Triticum aestivumL.) is a major staple crop in East Africa (EA) providing 9% and 10% of daily calories and protein intake, respectively. However, EA countries depend on import to meet 55% of their domestic wheat supplies due to increasing demands and low domestic yields. To determine the beneficial gene pool currently exploited for wheat improvement in EA, we examined the allelic diversity of 42 genes of breeding importance in a collection of 239 wheat cultivars and breeding lines from Kenya and Ethiopia using KASP markers. The assayed genes have been shown to control variations in plant height, thousand kernel weight (TKW), grain protein content, pre-harvest sprouting (PHS), disease resistance and flowering time. We observed the beneficial alleles of some major genes includingRht-D1, Gpc-B1, Yr5, Yr15, Sr26, andFhb1to be missing or present at low frequencies in this population. Furthermore, we validated the effects of the majorRht-1alleles andTaCKX-6Ain controlling variation in plant height and thousand kernel weight, respectively, under EA conditions. Our results uncover hitherto unexploited allelic diversity that can be used to improve the genetic potential of EA wheat germplasm. This will inform strategies to rapidly mobilize these beneficial alleles for wheat improvement in EA.
TripletProt: Deep Representation Learning of Proteins based on Siamese Networks
Authors: Nourani Esmaeil , Asgari Ehsaneddin , McHardy Alice C. , Mofrad Mohammad R.K.
Published: May 2020

We introduce TripletProt, a new approach for protein representation learning based on the Siamese neural networks. We evaluate TripletProt comprehensively in protein functional annotation tasks including sub-cellular localization (14 categories) and gene ontology prediction (more than 2000 classes), which are both challenging multi-class multi-label classification machine learning problems. We compare the performance of TripletProt with the state-of-the-art approaches including recurrent language model-based approach (i.e., UniRep), as well as protein-protein interaction (PPI) network and sequence-based method (i.e., DeepGO). Our TripletProt showed an overall improvement of F1 score in the above mentioned comprehensive functional annotation tasks, solely relying on the PPI network. TripletProt and in general Siamese Network offer great potentials for the protein informatics tasks and can be widely applied to similar tasks.
A Homology Independent Sequence Replacement Strategy in Human Cells Using a CRISPR Nuclease
Authors: Danner Eric , Lebedin Mikhail , de la Rosa Kathrin , Kühn Ralf
Published: May 2020

Precision genomic alterations largely rely on Homology Directed Repair (HDR), but targeting without homology using the Non-Homologous End Joining (NHEJ) pathway has gained attention as a promising alternative. Previous studies demonstrated precise insertions formed by the ligation of donor DNA into a targeted genomic double strand break in both dividing and non-dividing cells. Here we extend this idea and use NHEJ repair to replace genomic segments with donor sequences; we name this method ‘Replace’ editing (Rationalend-joiningprotocol deliveringatargeted sequenceexchange). Using CRISPR/Cas9 we create two genomic breaks and ligate a donor sequence in-between. This exchange of a genomic for a donor sequence uses neither microhomology nor homology arms. We target four loci and show successful exchange of exons in 16% to 54% of cells. Using linear amplification methods and deep sequencing pipelines we quantify the diversity of outcomes following Replace editing and profile mutations formed at the ligated interfaces. The ability to replace exons or other genomic sequences in cells not efficiently modified by HDR holds promise for both basic research and medicine.
Reimplementing Unirep in JAX
Authors: Ma Eric J. , Kummer Arkadij
Published: May 2020

UniRep is a recurrent neural network model trained on 24 million protein sequences, and has shown utility in protein engineering. The original model, however, has rough spots in its implementation, and a convenient API is not available for certain tasks. To rectify this, we reimplemented the model in JAX/NumPy, achieving near-100X speedups in forward pass performance, and implemented a convenient API for specialized tasks. In this article, we wish to document our model reimplementation process with the goal of educating others interested in learning how to dissect a deep learning model, and engineer it for robustness and ease of use.
3D ultrastructural study of synapses in the human entorhinal cortex
Authors: Domínguez-Álvaro M , Montero-Crespo M , Blazquez-Llorca L , DeFelipe J , Alonso-Nanclares L
Published: May 2020

The entorhinal cortex (EC) is a brain region that has been shown to be essential for memory functions and spatial navigation. However, detailed 3D synaptic morphology analysis and identification of postsynaptic targets at the ultrastructural level have not been performed before in the human EC. In the present study, we used Focused Ion Beam/Scanning Electron Microscopy (FIB/SEM) to perform a three-dimensional analysis of the synapses in the neuropil of medial EC in layers II and III from human brain autopsies. Specifically, we studied synaptic structural parameters of3561synapses, which were fully reconstructed in 3D. We analyzed the synaptic density, 3D spatial distribution, and type (excitatory and inhibitory), as well as the shape and size of each synaptic junction. Moreover, the postsynaptic targets of synapses could be clearly determined. The present work constitutes a detailed description of the synaptic organization of the human EC, which is a necessary step to better understand the functional organization of this region in both health and disease.

Significance Statement

The present study represents the first attempt to unveil the detailed synaptic organization of the neuropil of the human entorhinal cortex — a brain region that is essential for memory function and spatial navigation. Using 3D electron microscopy, we have characterized the synaptic morphology and identified the postsynaptic targets of thousands of synapses. The results provide a new, large, quantitative ultrastructure dataset of the synaptic organization of the human entorhinal cortex. These data provide critical information to better understand synaptic functionality in the human brain.

Highlight

Estimation of the number of synapses, as well as determination of their type, shapes, sizes and postsynaptic targets, provides critical data to better understand synaptic functionality. This study provides a new, large, quantitative ultrastructure dataset of the synaptic organization of the human entorhinal cortex using 3D electron microscopy.
G protein-coupled receptor signaling regulates ER-mitochondria contacts
Authors: Lim Youngshin , Cho Il-Taeg , Rennke Helmut G. , Cho Ginam
Published: May 2020

Interactions between the endoplasmic reticulum (ER) and mitochondria (Mito) are crucial for many cellular functions, and their interaction levels change dynamically depending on the cellular environment. Little is known about how the interactions between these organelles are regulated within the cell. Here we screened a compound library to identify chemical modulators for ER-Mito contacts. Multiple agonists of G-protein coupled receptors (GPCRs), beta-adrenergic receptors (β-ARs) in particular, scored in this screen. Analyses in multiple orthogonal assays validated that GPCR activation promotes physical and functional interactions between the two organelles. Furthermore, we have elucidated potential downstream effectors mediating GPCR-induced ER-Mito contacts. Given the role of GPCRs in sensing various extracellular signals and subsequently eliciting appropriate cellular responses, our data provide significant insights into the roles of ER-Mito contacts in maintaining cellular homeostasis and in responding to physiological demands or stresses.
Thermostable mutants of glycoside hydrolase family 6 cellobiohydrolase from the basidiomycetePhanerochaete chrysosporium
Authors: Yamaguchi Sora , Sunagawa Naoki , Tachioka Mikako , Igarashi Kiyohiko , Samejima Masahiro
Published: May 2020

Thermal inactivation of saccharifying enzymes is a crucial issue for the efficient utilization of cellulosic biomass as a renewable resource. Cellobiohydrolases (CBHs) is a kind of cellulase. In general, CBHs belonging to glycoside hydrolase (GH) family 6 (Cel6) act synergistically with CBHs of GH family 7 (Cel7) and other carbohydrate-active enzymes during the degradation of cellulosic biomass. However, while the catalytic rate of enzymes generally becomes faster at higher temperatures, Cel6 CBHs are inactivated at lower temperatures than Cel7 CBHs, and this represents a limiting factor for industrial utilization. In this study, we produced a series of mutants of the glycoside hydrolase family 6 cellobiohydrolasePcCel6A from the fungusPhanerochaete chrysosporium, and compared their thermal stability. Eight mutants from a random mutagenesis library and one rationally designed mutant were selected as candidate thermostable mutants and produced by heterologous expression in the yeastPichia pastoris. Comparison of the hydrolytic activities at 50 and 60°C indicated that the thermal stability ofPcCel6A is influenced by the number and position of cysteine residues that are not involved in disulfide bonds.
The SARS-CoV-2 conserved macrodomain is a mono-ADP-ribosylhydrolase
Authors: Alhammad Yousef M.O. , Kashipathy Maithri M. , Roy Anuradha , Gagné Jean-Philippe , McDonald Peter , Gao Philip , Nonfoux Louis , Battaile Kevin P. , Johnson David K. , Holmstrom Erik D. , Poirier Guy G. , Lovell Scott , Fehr Anthony R.
Published: May 2020

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other SARS-like-CoVs encode 3 tandem macrodomains within non-structural protein 3 (nsp3). The first macrodomain, Mac1, is conserved throughout CoVs, and binds to and hydrolyzes mono-ADP-ribose (MAR) from target proteins. Mac1 likely counters host-mediated anti-viral ADP-ribosylation, a posttranslational modification that is part of the host response to viral infections. Mac1 is essential for pathogenesis in multiple animal models of CoV infection, implicating it as a virulence factor and potential therapeutic target. Here we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose. SARS-CoV-2, SARS-CoV and MERS-CoV Mac1 exhibit similar structural folds and all 3 proteins bound to ADP-ribose with low μM affinities. Importantly, using ADP-ribose detecting binding reagents in both a gel-based assay and novel ELISA assays, we demonstrated de-MARylating activity for all 3 CoV Mac1 proteins, with the SARS-CoV-2 Mac1 protein leading to a more rapid loss of substrate compared to the others. In addition, none of these enzymes could hydrolyze poly-ADP-ribose. We conclude that the SARS-CoV-2 and other CoV Mac1 proteins are MAR-hydrolases with similar functions, indicating that compounds targeting CoV Mac1 proteins may have broad anti-CoV activity.

IMPORTANCE

SARS-CoV-2 has recently emerged into the human population and has led to a worldwide pandemic of COVID-19 that has caused greater than 900 thousand deaths worldwide. With, no currently approved treatments, novel therapeutic strategies are desperately needed. All coronaviruses encode for a highly conserved macrodomain (Mac1) that binds to and removes ADP-ribose adducts from proteins in a dynamic post-translational process increasingly recognized as an important factor that regulates viral infection. The macrodomain is essential for CoV pathogenesis and may be a novel therapeutic target. Thus, understanding its biochemistry and enzyme activity are critical first steps for these efforts. Here we report the crystal structure of SARS-CoV-2 Mac1 in complex with ADP-ribose, and describe its ADP-ribose binding and hydrolysis activities in direct comparison to SARS-CoV and MERS-CoV Mac1 proteins. These results are an important first step for the design and testing of potential therapies targeting this unique protein domain.
An integratedin silicoimmuno-genetic analytical platform provides insights into COVID-19 serological and vaccine targets
Authors: Ward Daniel , Higgins Matthew , Phelan Jody E. , Hibberd Martin L. , Campino Susana , Clark Taane G
Published: May 2020

Background

The COVID-19 pandemic, caused by the SARS-CoV-2 virus, has a major global health and socio-economic burden. It has instigated the mobilisation of resources into the development of control tools, such as diagnostics and vaccines. The poor performance of some diagnostic serological tools has emphasised the need for up to date immune-informatic analyses to inform the selection of viable targets for further study. This requires the integration and analysis of genetic and immunological data for SARS-CoV-2 and its homology with other human coronavirus species to understand cross-reactivity.

Methods

We have developed an online “immuno-analytics” resource to facilitate SARS-CoV-2 research, combining an extensive B/T-cell epitope mapping and prediction meta-analysis, and human CoV sequence homology mapping and protein database annotation, with an updated variant database and geospatial tracking for >7,800 non-synonymous mutation positions derived from >150,000 whole genome sequences. To demonstrate its utility, we present an integrated analysis of SARS-CoV-2 spike and nucleocapsid proteins, both being vaccine and serological diagnostic targets, including an analysis of changes in relevant mutation frequencies over time.

Results

Our analysis reveals that the nucleocapsid protein in its native form appears to be a sub-optimal target for use in serological diagnostic platforms. The most frequent mutations were the spike protein D614G and nsp12 L314P, which were common (>86%) across all the geographical regions. Some mutations in the spike protein (e.g. A222V and L18F) have increased in frequency in Europe during the latter half of 2020, detected using our automated algorithms. The tool also suggests that orf3a proteins may be a suitable alternative target for diagnostic serologic assays in a post-vaccine surveillance setting.

Conclusions

The immuno-analytics tool can be accessed online (http://genomics.lshtm.ac.uk/immuno) and will serve as a useful resource for biological discovery and surveillance in the fight against SARS-CoV-2. Further, the tool may be adapted to inform on biological targets in future outbreaks, including potential emerging human coronaviruses that spill over from animal hosts.
Performance of Abbott ID NOW COVID-19 rapid nucleic acid amplification test in nasopharyngeal swabs transported in viral media and dry nasal swabs, in a New York City academic institution
Authors: Basu Atreyee , Zinger Tatyana , Inglima Kenneth , Woo Kar-mun , Atie Onome , Yurasits Lauren , See Benjamin , Aguero-Rosenfeld Maria E.
Published: May 2020

The recent emergence of the SARS-CoV-2 pandemic has posed formidable challenges for clinical laboratories seeking reliable laboratory diagnostic confirmation. The swift advance of the crisis in the United States has led to Emergency Use Authorization (EUA) facilitating the availability of molecular diagnostic assays without the more rigorous examination to which tests are normally subjected prior to FDA approval. Our laboratory currently uses two real time RT-PCR platforms, the Roche Cobas SARS-CoV2 and the Cepheid Xpert Xpress SARS-CoV-2. Both platforms demonstrate comparable performance; however, the run times for each assay are 3.5 hours and 45 minutes, respectively. In search for a platform with shorter turnaround time, we sought to evaluate the recently released Abbott ID NOW COVID-19 assay which is capable of producing positive results in as little as 5 minutes. We present here the results of comparisons between Abbott ID NOW COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media and comparisons between Abbott ID NOW COVID-19 and Cepheid Xpert Xpress SARS-CoV-2 using nasopharyngeal swabs transported in viral transport media for Cepheid and dry nasal swabs for Abbott ID NOW. Regardless of method of collection and sample type, Abbott ID NOW COVID-19 had negative results in a third of the samples that tested positive by Cepheid Xpert Xpress when using nasopharyngeal swabs in viral transport media and 45% when using dry nasal swabs.
Systemic hypoferraemia and severity of hypoxaemic respiratory failure in COVID-19
Authors: Shah Akshay , Frost Joe , Aaron Louise , Donovan Killian , McKechnie Stuart , Stanworth Simon , Drakesmith Hal
Published: May 2020

Coronavirus disease 2019 (COVID-19) mortality is associated with hypoxaemia, multiorgan failure, and thromboinflammation. However severity of disease varies considerably and understanding physiological changes that may link to poor outcomes is important. Although increased serum ferritin has been observed in COVID-19 patients consistent with inflammation, other iron parameters have not been examined to our knowledge. Because iron is required for immunity and oxygen utilisation, and dysregulated iron homeostasis has been observed in COPD, we investigated serum iron concentrations in 30 patients with COVID-19 requiring ICU admission. All patients had low serum iron but patients with severe hypoxemic respiratory failure had more profound hypoferraemia. The area under the curve for receiver operating characteristic curves for serum iron to identify severe hypoxemia was 0.95; the optimal Youden Index for distinguishing between severe and non-severe hypoxemia was a serum iron concentration of 2.9 micromol/L. By linear regression, serum iron was associated with lymphocyte count and PaO2/FiO2. In conclusion, profound hypoferraemia identifies COVID-19 patients with severe hypoxaemia. Serum iron is a simple biomarker that could be usefully employed to stratify patients and monitor disease. Severe hypoferraemia may plausibly impair critical iron-dependent processes such as lymphocyte responses and hypoxia sensing, contributing to pathology, and is potentially treatable.
Connecting structure to function with the recovery of over 1000 high-quality activated sludge metagenome-assembled genomes encoding full-length rRNA genes using long-read sequencing
Authors: Singleton Caitlin M , Petriglieri Francesca , Kristensen Jannie M , Kirkegaard Rasmus H , Michaelsen Thomas Y , Andersen Martin H , Kondrotaite Zivile , Karst Søren M , Dueholm Morten S , Nielsen Per H , Albertsen Mads
Published: May 2020

Microorganisms are critical to water recycling, pollution removal and resource recovery processes in the wastewater industry. While the structure of this complex community is increasingly understood based on 16S rRNA gene studies, this structure cannot currently be linked to functional potential due to the absence of high-quality metagenome-assembled genomes (MAGs) with full-length rRNA genes for nearly all species. Here, we sequence 23 Danish full-scale wastewater treatment plant metagenomes, producing >1 Tbp of long-read and >0.9 Tbp of short-read data. We recovered 1083 high-quality MAGs, including 57 closed circular genomes. The MAGs accounted for ~30% of the community, and meet the stringent MIMAG high-quality draft requirements including full-length rRNA genes. We show how novel high-quality MAGs in combination with >13 years of amplicon data, Raman microspectroscopy and fluorescence in situ hybridisation can be used to uncover abundant undescribed lineages belonging to important functional groups.
Knowledge syntheses in medical education: A bibliometric analysis
Authors: Maggio Lauren A. , Costello Joseph A. , Norton Candace , Driessen Erik W. , Artino Anthony R.
Published: May 2020

Purpose

This bibliometric analysis maps the landscape of knowledge syntheses in medical education. It provides scholars with a roadmap for understanding where the field has been and where it might go in the future. In particular, this analysis details the venues in which knowledge syntheses are published, the types of syntheses conducted, citation rates they produce, and altmetric attention they garner.

Method

In 2020, the authors conducted a bibliometric analysis of knowledge syntheses published in 14 core medical education journals from 1999 to 2019. To characterize the studies, metadata was extracted from Pubmed, Web of Science, Altmetrics Explorer, and Unpaywall.

Results

The authors analyzed 963 knowledge syntheses representing 3.1% of total articles published (n=30,597). On average, 45.9 knowledge syntheses were published annually (SD=35.85, Median=33), and there was an overall 2,620% increase in the number of knowledge syntheses published from 1999 to 2019. The journals each published, on average, a total of 68.8 knowledge syntheses (SD=67.2, Median=41) withMedical Educationpublishing the most (n=189; 19%). Twenty-one knowledge synthesis types were identified; the most prevalent types were systematic reviews (n=341; 35.4%) and scoping reviews (n=88; 9.1%). Knowledge syntheses were cited an average of 53.80 times (SD=107.12, Median=19) and received a mean Altmetric Attention Score of 14.12 (SD=37.59, Median=6).

Conclusions

There has been considerable growth in knowledge syntheses in medical education over the past 20 years, contributing to medical education’s evidence base. Beyond this increase in volume, researchers have introduced methodological diversity in these publications, and the community has taken to social media to share knowledge syntheses. Implications for the field, including the impact of synthesis types and their relationship to knowledge translation, are discussed.
A miR-494 dependent feedback loop regulates ER stress
Authors: Chatterjee Namita , Espinosa-Diez Cristina , Anand Sudarshan
Published: May 2020

Defects in stress responses are important contributors in many chronic conditions including cancer, cardiovascular disease, diabetes, and obesity-driven pathologies like non-alcoholic steatohepatitis (NASH). Specifically, endoplasmic reticulum (ER) stress is linked with these pathologies and control of ER stress can ameliorate tissue damage. MicroRNAs have a critical role in regulating diverse stress responses including ER stress. Here we show that miR-494 plays a functional role during ER stress. ER stress inducers (tunicamycin & thapsigargin) robustly increase the expression of miR-494in vitroin an ATF6 dependent manner. Surprisingly, miR-494 pretreatment dampens the induction and magnitude of ER stress in response to tunicamycin in endothelial cells. Conversely, inhibition of miR-494 increases ER stressde novoand amplifies the effects of ER stress inducers. Using Mass Spectrometry (TMT-MS) we identified 23 proteins that are downregulated by both tunicamycin and miR-494. Among these, we found 6 transcripts which harbor a putative miR-494 binding site. We validated the anti-apoptotic geneBIRC5(survivin) as one of the targets of miR-494 during ER stress. Finally, induction of ER stressin vivoincreases miR-494 expression in the liver. Pretreatment of mice with a miR-494 plasmid via hydrodynamic injection decreased ER stress in response to tunicamycin in part by decreasing inflammatory chemokines and cytokines. In summary, our data indicates that ER stress driven miR-494 may act in a feedback inhibitory loop to dampen downstream ER stress signaling. We propose that RNA-based approaches targeting miR-494 or its targets may be attractive candidates for inhibiting ER stress dependent pathologies in human disease.
Structures of the stator complex that drives rotation of the bacterial flagellum
Authors: Deme Justin C. , Johnson Steven , Vickery Owen , Muellbauer Amy , Monkhouse Holly , Griffiths Thomas , James Rory Hennell , Berks Ben C. , Coulton James W. , Stansfeld Phillip J. , Lea Susan M.
Published: May 2020

The bacterial flagellum is the proto-typical protein nanomachine and comprises a rotating helical propeller attached to a membrane-embedded motor complex1. The motor consists of a central rotor surround by stator units that couple ion flow across the cytoplasmic membrane to torque generation. Here we present the structures of stator complexes from multiple bacterial species, allowing interpretation of the extensive body of data on stator mechanism. The structures reveal an unexpected asymmetric A5B2subunit assembly in which the five A subunits enclose the two B subunits. Comparison to novel structures of other ion-driven motors indicates that this A5B2architecture is fundamental to bacterial systems that couple energy from ion-flow to generate mechanical work at a distance, and suggests that such events involve rotation in the motor structures.
Supramolecular assembly of theE. coliLdcI upon acid stress
Authors: Jessop Matthew , Liesche Clarissa , Felix Jan , Desfosses Ambroise , Baulard Megghane , Adam Virgile , Fraudeau Angélique , Huard Karine , Effantin Grégory , Kleman Jean-Philippe , Bacia-Verloop Maria , Bourgeois Dominique , Gutsche Irina
Published: May 2020

Pathogenic and commensal bacteria often have to resist the harsh acidity of the host stomach. The inducible lysine decarboxylase LdcI buffers the cytosol and the local extracellular environment to ensure enterobacterial survival at low pH. Here, we investigate the acid-stress response regulation ofE. coliLdcI by combining biochemical and biophysical characterisation with negative stain and cryo-electron microscopy, and wide-field and super-resolution fluorescence imaging. Due to deleterious effects of fluorescent protein fusions on native LdcI decamers, we opt for three-dimensional localisation of nanobody-labelled endogenous wild-type LdcI in acid-stressedE. colicells, and show that it organises into distinct patches at the cell periphery. Consistent with recent hypotheses thatin vivoclustering of metabolic enzymes often reflects their polymerisation as a means of stimulus-induced regulation, we show that LdcI assembles into filamentsin vitroat physiologically relevant low pH. We solve the structures of these filaments and of the LdcI decamer formed at neutral pH by cryo-electron microscopy, and reveal the molecular determinants of LdcI polymerisation, confirmed by mutational analysis. Finally, we propose a model for LdcI function inside the enterobacterial cell, providing a structural and mechanistic basis for further investigation of the role of its supramolecular organisation in the acid stress response.

Significance statement

Bacteria possess a sophisticated arsenal of defence mechanisms that allow them to survive in adverse conditions. Adaptation to acid stress and hypoxia is crucial for the enterobacterial transmission in the gastrointestinal tract of their human host. When subjected to low pH,E. coliand many other enterobacteria activate a proton-consuming resistance system based on the acid-stress inducible lysine decarboxylase LdcI. Here we develop generally-applicable tools to uncover the spatial localisation of LdcI inside the cell by super-resolution fluorescence microscopy, and investigate thein vitrosupramolecular organisation of this enzyme by cryo-EM. We build on these results to propose a mechanistic model for LdcI function and offer tools for furtherin vivoinvestigations.
Upregulated-flotillins and sphingosine kinase 2 derail vesicular trafic to stabilize AXL and promote epithelial-mesenchymal transition
Authors: Genest Mallory , Comunale Franck , Planchon Damien , Govindin Pauline , Vacher Sophie , Bièche Ivan , Robert Bruno , Malhotra Himanshu , Schoenit Andreas , Tashireva Liubov A. , Gauthier-Rouvière Cécile , Bodin Stéphane
Published: May 2020

Altered endocytosis and vesicular trafficking are major players during tumorigenesis. Flotillin overexpression, a feature observed in many invasive tumors, and identified as a marker of poor prognosis, induces a deregulated endocytic and trafficking pathway called Upregulated Flotillin-Induced Trafficking (UFIT). Here, we found that, in non tumoral mammary epithelial cells, induction of the UFIT pathway promotes epithelial-to-mesenchymal transition (EMT) and accelerates the endocytosis of several transmembrane receptors, including AXL, in flotillin-positive late endosomes. AXL overexpression, frequently observed in cancer cells, is linked to EMT and metastasis formation. In flotillin-overexpressing non-tumoral mammary epithelial cells and in invasive breast carcinoma cells, we found that the UFIT-pathway-mediated AXL endocytosis allows its stabilization and depends on sphingosine-kinase 2, a lipid kinase recruited in flotillin-rich plasma membrane-domains and endosomes.

Thus, the deregulation of vesicular trafficking following flotillin upregulation, and through sphingosine kinase 2, emerges as a new mechanism of AXL overexpression and EMT-inducing signaling pathway activation.
Mediocremonas mediterraneus, a New Member within the Developea
Authors: Weiler Bradley A. , Sà Elisabet L. , Sieracki Michael E. , Massana Ramon , del Campo Javier
Published: May 2020

The Stramenopiles are a large and diverse group of eukaryotes that possess various lifestyles required to thrive in a broad array of environments. The stramenopiles branch with the alveolates, rhizarians, and telonemids, forming the supergroup TSAR. Here, we present a new genus and species of aquatic nanoflagellated stramenopile:Mediocremonas mediterraneus, a free-swimming heterotrophic predator.M. mediterraneuscell bodies measure between 2.0-4.0 μm in length and 1.2-3.7 μm in width, possessing two flagella and an oval body morphology. The growth and grazing rate ofM. mediterraneusin batch cultures ranges from 0.68 to 1.83 d-1and 1.99 to 5.38 bacteria h-1, respectively.M. mediterraneuswas found to be 93.9% phylogenetically similar withDevelopayella elegansand 94.7% withDevelorapax marinus, two members within the class Developea. The phylogenetic position of the Developea and the ability ofM. mediterraneusto remain in culture makes it a good candidate for further genomic studies that could help us to better understand phagotropy in marine systems as well as the transition from heterotrophy to phototrophy within the stramenopiles.