bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 RNA quantification using droplet digital RT-PCR
Authors: Kinloch Natalie N. , Ritchie Gordon , Dong Winnie , Cobarrubias Kyle D. , Sudderuddin Hanwei , Lawson Tanya , Matic Nancy , Montaner Julio S.G. , Leung Victor , Romney Marc G. , Lowe Christopher F. , Brumme Chanson J. , Brumme Zabrina L. 
Published: December 2020

AbstractQuantitative viral load assays have transformed our understanding of – and ability to manage − viral diseases. They hold similar potential to advance COVID-19 control and prevention, but SARS-CoV-2 viral load tests are not yet widely available. SARS-CoV-2 molecular diagnostic tests, which typically employ real-time reverse transcriptase-polymerase chain reaction (RT-PCR), yield semi-quantitative results only. Reverse transcriptase droplet digital PCR (RT-ddPCR), a technology that partitions each reaction into 20,000 nanolitre-sized droplets prior to amplification, offers an attractive platform for SARS-CoV-2 RNA quantification. We evaluated eight primer/probe sets originally developed for real-time RT-PCR-based SARS-CoV-2 diagnostic tests for use in RT-ddPCR, and identified three (Charité-Berlin E-Sarbeco and Pasteur Institute IP2 and IP4) as the most efficient, precise and sensitive for RT-ddPCR-based SARS-CoV-2 RNA quantification. Analytical efficiency of the E-Sarbeco primer/probe set, for example, was ~83%, while assay precision, as measured by the coefficient of variation, was ~2% at 1000 input copies/reaction. Lower limits of quantification and detection for this primer/probe set were 18.6 and 4.4 input SARS-CoV-2 RNA copies/reaction, respectively. SARS-CoV-2 RNA viral loads in a convenience panel of 48 COVID-19-positive diagnostic specimens spanned a 6.2log10range, confirming substantial viral load variationin vivo. We further calibrated RT-ddPCR-derived SARS-CoV-2 E gene copy numbers against cycle threshold (Ct) values from a commercial real-time RT-PCR diagnostic platform. The resulting log-linear relationship can be used to mathematically derive SARS-CoV-2 RNA copy numbers from Ctvalues, allowing the wealth of available diagnostic test data to be harnessed to address foundational questions in SARS-CoV-2 biology.
Leri: a web-server for identifying protein functional networks from evolutionary couplings
Authors: Cheung Ngaam J. , Peter Arun T. John , Kornmann Benoit 
Published: December 2020

ABSTRACTInformation on the co-evolution of amino acid pairs in a protein can be used for endeavors such as protein engineering, mutation design, and structure prediction. Here we report a method that captures significant determinants of proteins using estimated co-evolution information to identify networks of residues, termed “residue communities”, relevant to protein function. By taking advantage of recent developments in high-performance and parallel computing, we constructed a web-server,Leri, that identifies relevant residue communities to allow researchers to investigate how a protein evolves and folds for function(s). All the data of the computational results including high-quality images can be downloaded and presented for publication. This web-server, written in C++, is sufficiently rapid to enable the studies on proteins of up to 400 amino acids.
Annotation and analysis ofyellow genesinDiaphorina citri, vector for the Huanglongbing disease
Authors: Massimino Crissy , Vosburg Chad , Shippy Teresa , Hosmani Prashant S. , Flores-Gonzalez Mirella , Mueller Lukas A. , Hunter Wayne B. , Benoit Joshua B. , Brown Susan J. , D’Elia Tom , Saha Surya 
Published: December 2020

ABSTRACTHuanglongbing (HLB), also known as citrus greening disease, is caused by the bacteriumCandidatusLiberibacter asiaticus (CLas) and represents a serious threat to global citrus production. This bacteria is transmitted by the Asian citrus psyllid,Diaphorina citri(Hemiptera) and there are no effective in-planta treatments for CLas. Therefore, one strategy is to manage the psyllid population. Manual annotation of theD. citrigenome can identify and characterize gene families that could serve as novel targets for psyllid control. Theyellowgene family represents an excellent target asyellowgenes are linked to development and immunity due to their roles in melanization. Combined analysis of the genome with RNA-seq datasets, sequence homology, and phylogenetic trees were used to identify and annotate nineyellowgenes for theD. citrigenome. Phylogenetic analysis shows a unique duplication ofyellow-yinD. citri, with life stage specific expression for these two genes. Genomic analysis also indicated the loss of a gene vital to the process of melanization,yellow-f, and the gain of a gene which seems to be unique to hemipterans,yellow 9. We suggest thatyellow 9or the geneyellow 8(c), which consistently groups closely toyellow-f, may take on this role. Manual curation of genes inD. citrihas provided an in-depth analysis of theyellowfamily among hemipteran insects and provides new targets for molecular control of this psyllid pest. Manual annotation was done as part of a collaborative community annotation project (https://citrusgreening.org/annotation/index).
T cell activation, highly armed cytotoxic cells and a sharp shift in monocytes CD300 receptors expression is characteristic of patients with severe COVID-19
Authors: Zenarruzabeitia Olatz , Astarloa-Pando Gabirel , Terrén Iñigo , Orrantia Ane , Pérez-Garay Raquel , Seijas-Betolaza Iratxe , Nieto-Arana Javier , Imaz-Ayo Natale , Pérez-Fernández Silvia , Arana-Arri Eunate , Borrego Francisco 
Published: December 2020

SUMMARYCOVID-19 manifests with a wide diversity of clinical phenotypes characterized by dysfunctional and exaggerated host immune responses. Many results have been described on the status of the immune system of patients infected with SARS-CoV-2, but there are still aspects that have not been fully characterized. In this study, we have analyzed a cohort of patients with mild, moderate and severe disease. We performed flow cytometric studies and correlated the data with the clinical features and clinical laboratory values of patients. Both conventional and unsupervised data analyses concluded that patients with severe disease are characterized, among others, by a higher state of activation in all T cell subsets, higher expression of perforin and granzyme B in cytotoxic cells, expansion of adaptive NK cells and the accumulation of activated and immature dysfunctional monocytes which are identified by a low expression of HLA-DR and an intriguing abrupt change in the expression pattern of CD300 receptors. More importantly, correlation analysis showed a strong association between the alterations in the immune cells and the clinical signs of severity. These results indicate that patients with severe COVID-19 have a broad perturbation of their immune system, and they will help to understand the immunopathogenesis of severe COVID-19 as well as could be of special value for physicians to decide which specific therapeutic options are most effective for their patients.
Active learning tools improve the learning outcomes, scientific attitude and critical thinking in higher education: Experiences in an online course during the COVID-19 pandemic
Authors: Rossi Izadora Volpato , de Lima Jordana Dinorá , Sabatke Bruna , Ferreira Nunes Maria Alice , Ramirez Graciela Evans , Ramirez Marcel Ivan 
Published: December 2020

AbstractActive teaching methodologies have been placed as a hope for changing education at different levels, transiting from passive lecture-centered to student-centered learning. With the health measures of social distance, the COVID-19 pandemic forced a strong shift to remote education. With the challenge of delivering quality education through a computer screen, we validated and applied an online course model using active teaching tools for higher education. We incorporated published active-learning strategies into an online construct, with problem-based inquiry and design of inquiry research projects to serve as our core active-learning tool. The gains related to students’ science learning experiences and their attitudes towards science were assessed by applying questionnaires before, during and after the course. The course counted on the participation of 83 students, most of them (60,8%) from post-graduate students. Our results show that engagement provided by active learning methods can improve performance both in hard and soft skills. Students participation seems to be more relevant when activities require interaction of information, prediction and reasoning, such as open-ended questions and design of research projects. Therefore, our data shows that, in pandemic, active learning tools benefit students and improve their critical thinking and their motivation and positive positioning in science.
Graphic: Graph-Based Hierarchical Clustering for Single-Molecule Localization Microscopy
Authors: Pourya Mehrsa , Aziznejad Shayan , Unser Michael , Sage Daniel 
Published: December 2020

ABSTRACTWe propose a novel method for the clustering of point-cloud data that originate from single-molecule localization microscopy (SMLM). Our scheme has the ability to infer a hierarchical structure from the data. It takes a particular relevance when quantitatively analyzing the biological particles of interest at different scales. It assumes a prior neither on the shape of particles nor on the background noise. Our multiscale clustering pipeline is built upon graph theory. At each scale, we first construct a weighted graph that represents the SMLM data. Next, we find clusters using spectral clustering. We then use the output of this clustering algorithm to build the graph in the next scale; in this way, we ensure consistency over different scales. We illustrate our method with examples that highlight some of its important properties.
Type I and III IFNs produced by the nasal epithelia and dimmed inflammation are key features of alpacas resolving MERS-CoV infection
Authors: Te Nigeer , Rodon Jordi , Ballester Maria , Pérez Mónica , Pailler-García Lola , Segalés Joaquim , Vergara-Alert Júlia , Bensaid Albert 
Published: December 2020

AbstractWhile MERS-CoV (Middle East respiratory syndrome Coronavirus) provokes a lethal disease in humans, camelids, the main virus reservoir, are asymptomatic carriers, suggesting a crucial role for innate immune responses in controlling the infection. Experimentally infected camelids clear infectious virus within one week and mount an effective adaptive immune response. Here, transcription of immune response genes was monitored in the respiratory tract of MERS-CoV infected alpacas. Concomitant to the peak of infection, occurring at 2 days post inoculation (dpi), type I and III interferons (IFNs) were maximally transcribed only in the nasal mucosa of alpacas, provoking the induction of interferon stimulated genes (ISGs) along the whole respiratory tract. Simultaneous to mild focal infiltration of leukocytes in nasal mucosa and submucosa, upregulation of the anti-inflammatory cytokine IL10 and dampened transcription of pro-inflammatory genes under NF-κB control were observed. In the lung, early (1 dpi) transcription of chemokines (CCL2 and CCL3) correlated with a transient accumulation of mainly mononuclear leukocytes. A tight regulation of IFNs in lungs with expression of ISGs and controlled inflammatory responses, might contribute to virus clearance without causing tissue damage. Thus, the nasal mucosa, the main target of MERS-CoV in camelids, is central in driving an efficient innate immune response based on triggering ISGs as well as the dual anti-inflammatory effects of type III IFNs and IL10.Author summaryMiddle East respiratory syndrome coronavirus (MERS-CoV) is the etiological agent of a respiratory disease causing high mortality in humans. In camelids, the main MERS-CoV reservoir host, viral infection leads to subclinical disease. Our study describes transcriptional regulations of innate immunological pathways underlying asymptomatic clinical manifestations of alpacas in response to MERS-CoV. Concomitant to the peak of infection, these animals elicited a strong transient interferon response and induction of the anti-inflammatory cytokine IL10 in the nasal mucosa. This was associated to a dimmed regulation of pro-inflammatory cytokines and induction of interferon stimulated genes along the whole respiratory mucosa, leading to the rapid clearance of the virus. Thus, innate immune responses occurring in the nasal mucosa appear to be the key in controlling MERS-CoV disease by avoiding a cytokine storm. Understanding on how asymptomatic host reservoirs counteract MERS-CoV infection will aid in the development of antiviral drugs and vaccines.
Quantifying absolute gene expression profiles reveals distinct regulation of central carbon metabolism genes in yeast
Authors: Yu Rosemary , Vorontsov Egor , Sihlbom Carina , Nielsen Jens 
Published: December 2020

AbstractIn addition to specific regulatory circuits, gene expression is also regulated by global physiological cues such as the cell growth rate and metabolic parameters. Here we examine these global control mechanisms by analyzing an orthogonal multi-omics dataset consisting of absolute-quantitative abundances of the transcriptome, proteome, and intracellular amino acids in 22 steady-state yeast cultures. Our model indicates that transcript and protein abundance are coordinately controlled by the cell growth rate via RNA polymerase II and ribosome abundance, but are independently controlled by metabolic parameters relating to amino acid and nucleotide availability. Genes in central carbon metabolism, however, are regulated independently of these global physiological cues. Our findings can be used to augment gene expression profiling analyses in the distantly related yeastSchizosaccharomyces pombeand a human cancer cell model. Our results provide a framework to analyze gene expression profiles to gain novel biological insights, a key goal of systems biology.
From egg to adult: a developmental table of the antMonomorium pharaonis
Authors: Rajakumar Arjuna , Pontieri Luigi , Li Ruyan , Larsen Rasmus Stenbak , Vásquez-Correa Angelly , Frandsen Johanne KL , Rafiqi Ab Matteen , Zhang Guojie , Abouheif Ehab 
Published: December 2020

AbstractAnts are one of the most ecologically and evolutionarily successful groups of animals and exhibit a remarkable degree of phenotypic diversity. This success is largely attributed to the fact that all ants are eusocial and live in colonies with a reproductive division of labor between morphologically distinct queen and worker castes. Yet, despite over a century of studies on caste determination and evolution in ants, we lack a complete ontogenetic series from egg to adult for any ant species. We therefore present a developmental table for the Pharaoh antMonomorium pharaonis, a species whose colonies simultaneously produce both reproductive queens and completely sterile workers. In total,M.pharaonisembryonic, larval, and pupal development lasts 45 days. During embryogenesis, the majority of developmental events are conserved betweenM.pharaonisand the fruit flyDrosophila melanogaster. However, we discovered two types of same-stage embryos prior to gastrulation: (1) embryos with internalized germ cells; and (2) embryos with germ cells outside of the blastoderm at the posterior pole. Moreover, we found two-types of embryos following germ band extension: (1) fertile embryos with primordial germ cells; and (2) sterile embryos with no germ cells. Together, our data shows that the queen (fertile) and worker (sterile) phenotypes are already determined and differentiated by early embryogenesis. During larval development, previous studies and our data find 3 larval instars reproductives and workers. However, there is considerable variation within each caste-specific instar, making it difficult to lineate instar boundaries. Here, we propose that developmental and anatomical markers can segregate larvae into gyne (unmatted queen), male and worker castes, including during the 1stlarval instar. Overall, we hope that the ontogenetic series we present here will serve as a blueprint for the generation of future ant developmental tables.
Phylogenetic and population structure analyses uncover pervasive misclassification and help assessing the biosafety of Pseudomonas alloputida for biotechnological applications
Authors: Passarelli-Araujo Hemanoel , Jacobs Sarah H. , Franco Glória R. , Venancio Thiago M. 
Published: December 2020

AbstractThe Pseudomonas putida group comprises strains with biotechnological and clinical relevance. P. alloputida was proposed as a new species and highlighted the misclassification of P. putida. Nevertheless, the population structure of P. alloputida remained unexplored. We retrieved 11,025 Pseudomonas genomes and used P. alloputida Kh7T to delineate the species. The P. alloputida population structure comprises at least 7 clonal complexes (CCs). Clinical isolates are mainly found in CC4 and acquired resistance genes are present at low frequency in plasmids. Virulence profiles support the potential of CC7 members to outcompete other plant or human pathogens through a type VI secretion system. Finally, we found that horizontal gene transfer had an important role in shaping the ability of P. alloputida to bioremediate aromatic compounds such as toluene. Our results provide the grounds to understand P. alloputida genetic diversity and safety for environmental applications.
KLF10 integrates circadian timing and sugar signaling to coordinate hepatic metabolism
Authors: Ruberto Anthony A. , Gréchez-Cassiau Aline , Guérin Sophie , Martin Luc , Revel Johana S. , Mehiri Mohamed , Subramaniam Malayannan , Delaunay Franck , Teboul Michèle 
Published: December 2020

AbstractThe mammalian circadian timing system and metabolism are highly interconnected, and disruption of this coupling is associated with negative health outcomes. Krüppel-like factors (KLFs) are transcription factors that govern metabolic homeostasis in various organs. Many KLFs show a circadian expression in the liver. Here, we show that the loss of the clock-controlled KLF10 in hepatocytes results in extensive reprogramming of the mouse liver circadian transcriptome, which in turn, alters the temporal coordination of pathways associated with energy metabolism. We also show that glucose and fructose induceKlf10,which helps mitigate glucose intolerance and hepatic steatosis in mice challenged with a sugar beverage. Functional genomics further reveal that KLF10 target genes are primarily involved in central carbon metabolism. Together, these findings show that in the liver, KLF10 integrates circadian timing and sugar metabolism related signaling, and serves as a transcriptional brake that protects against the deleterious effects of increased sugar consumption.
GPCR-mediated Activation of PLCγ2 Initiates Dysregulated Recruitment of Neutrophils in Cold-induced Urticaria in PLAID Patients
Authors: Xu Xuehua , Wen Xi , Bhimani Smit , Moosa Amer , Parsons Dustin , Jin Tian 
Published: December 2020

AbstractThe current dogma is that chemoattractants G protein coupled receptors (GPCRs) activate β phospholipase C (PLCβ) while receptor tyrosine kinases (RTKs) activate γ phospholipase C (PLCγ). Here, we show that chemoattractant/GPCR-mediated membrane recruitment of PLCγ2 constitutes GPCR-mediated phospholipase C (PLC) signaling and is essential for neutrophil polarization and migration during GPCR-mediated chemotaxis. In response to a chemoattractant stimulation, cells lacking PLCγ2 (plcg2kd) displayed altered dynamics of diacylglycerol (DAG) production and calcium response; increased Ras/PI3K/Akt activation; elevated GSK3 phosphorylation and cofilin activation; impaired dynamics of actin polymerization; and consequently defects in cell polarization and migration during chemotaxis. At low temperature, neutrophils expressing the gain-of-function mutant of PLCγ2 (Δ686) displayed better chemotaxis than the cells expressing wild-type PLCγ2. The study provides a molecular mechanism for the dysregulated recruitment and activation of neutrophils in cold-induced urticaria in PLCγ2-associated antibody deficiency and immune dysregulation (PLAID) patients bearing gain-of-function mutations of PLCγ2.
Sesbanimide R, a novel cytotoxic polyketide produced by magnetotactic bacteria
Authors: Awal Ram Prasad , Haack Patrick A. , Bader Chantal D. , Riese Cornelius N. , Schüler Dirk , Müller Rolf 
Published: December 2020

AbstractGenomic information from various magnetotactic bacteria suggested that besides their common ability to form magnetosomes they potentially also represent a source of bioactive natural products. By using targeted deletion and transcriptional activation, we connected a large biosynthetic gene cluster (BGC) of thetrans-AT PKS type to the biosynthesis of a novel polyketide in the alphaproteobacteriumMagnetospirillum gryphiswaldense.Structure elucidation by mass spectrometry and NMR revealed that this secondary metabolite resembles sesbanimides which were very recently reported from other taxa. However, sesbanimide R exhibits an additional arginine moiety the presence of which reconciles inconsistencies in the previously proposed sesbanimide biosynthesis pathway when comparing the chemical structure and the potential biochemistry encoded in the BGC. In contrast to sesbanimides D, E and F, we were able to assign the stereocenter of the arginine moiety experimentally and two of the remaining three stereocenters by predictive biosynthetic tools. Sesbanimide R displayed strong cytotoxic activity against several carcinoma cell lines.ImportanceThe finding of this study contributes a new secondary metabolite member to the glutarimide-containing polyketides. The determined structure of sesbanimide R correlates with its cytotoxic bioactivity characteristic for members of this family. Sesbanimide R represents the first natural product isolated from magnetotactic bacteria and identifies this highly diverse group as a so far untapped source for the future discovery of novel secondary metabolites.
Dynamic evolution of the MutS family in animals: multiple losses of MSH paralogues and gain of a viral MutS homologue in octocorals
Authors: Muthye Viraj , Lavrov Dennis V. 
Published: December 2020

AbstractMutS is a key component of the Mismatch Repair (MMR) pathway. Members of the MutS family of proteins are present in bacteria, archaea, eukaryotes, and viruses. Six MutS homologues (MSH1-6), have been identified in yeast, three of which function in nuclear MMR, while MSH1 has been associated with mitochondrial DNA repair. MSH1 is believed to be lacking in animals, potentially reflecting the loss of MMR in animal mitochondria, and correlated with higher rates of mitochondrial sequence evolution. An intriguing exception has been found in octocorals, a group of marine animals from phylum Cnidaria, which encode a MutS-homologue (mtMutS) in their mitochondrial genome. It has been suggested that this protein functions in mitochondrial DNA repair, which would explain some of the lowest rates of mitochondrial sequence evolution observed in this group. To place the acquisition of mtMutS in a functional context, we investigated the evolution of the whole MutS family in animals. Our study confirmed the acquisition of octocoral mtMutS by horizontal gene transfer from a giant virus. Surprisingly, we found orthologues of yeast MSH1 in all hexacorals (the sister group of octocorals) and several sponges and placozoans. By contrast, MSH1 orthologues were lacking in octocorals, medusozoan cnidarians, ctenophores, and bilaterian animals. Furthermore, while we were able to identify MSH2 and MSH6 in all animals, MSH4, MSH5, and, especially, MSH3 were missing in multiple species. Overall, our analysis reveals a dynamic evolution of MSH family in animals, with multiple losses of MSH1, MSH3, some losses of MSH4 and MSH5, and a gain of octocoral mtMutS.