bluuebunny/crossref_metadata_2025_split huggingface dataset:
Character evolution of modern fly-speck fungi and implications for interpreting thyriothecial fossils
Authors: Renard Ludovic Le , Firmino André L. , Pereira Olinto L. , Stockey Ruth A. , Berbee Mary. L. 
Published: March 2020

AbstractPREMISE OF THE STUDYFossils show that fly-speck fungi have been reproducing with small, black thyriothecia on leaf surfaces for ∼250 million years. We analyze morphological characters of extant thyriothecial fungi to develop a phylogenetic framework for interpreting fossil taxa.METHODSWe placed 59 extant fly-speck fungi in a phylogeny of 320 Ascomycota using nuclear ribosomal large and small subunit sequences, including newly determined sequences from nine taxa. We reconstructed ancestral character states using BayesTraits and maximum likelihood after coding 11 morphological characters based on original observations and literature. We analyzed the relationships of three previously published Mesozoic fossils using parsimony and our morphological character matrix, constrained by the molecular phylogeny.KEY RESULTSThyriothecia evolved convergently in multiple lineages of superficial, leaf- inhabiting ascomycetes. The radiate and ostiolate scutellum organization is restricted to Dothideomycetes. Scutellum initiation by intercalary septation of a single hypha characterizes Asterinales and Asterotexiales, and initiation by coordinated growth of two or more adjacent hyphae characterizes Aulographaceae (orderincertae sedis). Scutella in Microthyriales are initiated apically on a lateral hyphal branch. Patterns of hyphal branching in scutella contribute to distinguishing among orders. Parsimony resolves three fossil taxa as Dothideomycetes; one is further resolved as a member of a Microthyriales-Zeloasperisporiales clade within Dothideomycetes.CONCLUSIONSThis is the most comprehensive systematic study of thyriothecial fungi and their relatives to date. Parsimony analysis of the matrix of character states of modern taxa provides an objective basis for interpreting fossils, leading to insights into morphological evolution and geological ages of Dothideomycetes clades.
Light microscopy of proteins in their ultrastructural context
Authors: M’Saad Ons , Bewersdorf Joerg 
Published: March 2020

AbstractResolving the distribution of specific proteins at the nanoscale in the structural context of the cell is a major challenge in fluorescence microscopy. Here we present a new concept that decrowds the intracellular space through 13 to 21-fold physical expansion while simultaneously retaining the proteins. This combination makes labeling of the proteome efficient enough that local protein densities are revealed and the cellular nanoarchitecture can be visualized by standard light microscopy.
Discovery of the world’s highest-dwelling mammal
Authors: Storz Jay F. , Quiroga-Carmona Marcial , Opazo Juan C. , Bowen Thomas , Farson Matthew , Steppan Scott J. , D’Elía Guillermo 
Published: March 2020

AbstractEnvironmental limits of animal life are invariably revised upwards when the animals themselves are investigated in their natural habitats. Here we report results of a scientific mountaineering expedition to survey the high-altitude rodent fauna of Volcán Llullaillaco in the Puna de Atacama of northern Chile, an effort motivated by video documentation of mice (genusPhyllotis) at a record altitude of 6205 m. Among numerous trapping records at altitudes >5000 m, we captured a specimen of the yellow-rumped leaf-eared mouse (Phyllotis xanthopygus rupestris) on the very summit of Llullaillaco at 6739 m. This summit specimen represents an altitudinal world record for mammals, far surpassing all specimen-based records from the Himalayas and elsewhere in the Andes. This discovery suggests that we may have generally underestimated the altitudinal range limits and physiological tolerances of small mammals simply because the world’s highest summits remain relatively unexplored by biologists.
Ocular conjunctival inoculation of SARS-CoV-2 can cause mild COVID-19 in Rhesus macaques
Authors: Deng Wei , Bao Linlin , Gao Hong , Xiang Zhiguang , Qu Yajin , Song Zhiqi , Gong Shunran , Liu Jiayi , Liu Jiangning , Yu Pin , Qi Feifei , Xu Yanfeng , Li Fengli , Xiao Chong , Lv Qi , Xue Jing , Wei Qiang , Liu Mingya , Wang Guanpeng , Wang Shunyi , Yu Haisheng , Liu Xing , Zhao Wenjie , Han Yunlin , Qin Chuan 
Published: March 2020

AbstractThe outbreak of Corona Virus Disease 2019 caused by the severe acute respiratory syndrome coronavirus (SARS-CoV-2) is highly transmitted. The potential extra-respiratory transmission routes remain uncertain. Five rhesus macaques were inoculated with 1×106TCID50of SARS-CoV-2 via conjunctival (CJ), intratracheal (IT), and intragastric (IG) routes, respectively. Remarkably, the CJ inoculated-macaques developed mild interstitial pneumonia and viral load was detectable in the conjunctival swabs at 1 days post-inoculation (dpi). Only via IT inoculation, viral load was detected in the anal swab at 1-7 dpi and macaque showed weight loss. However, viral load was undetectable after IG inoculation. Comparatively, viral load was higher in the nasolacrimal system but lesions of lung were relatively mild and local via CJ inoculation compared with that via IT inoculation, demonstrating distinct characteristics of virus dispersion. Both the two routes affected the alimentary tract. Therefore the clinicians need to protect eye while working with patients.
FITNESS BENEFITS TO BACTERIA OF CARRYING PROPHAGES AND PROPHAGE-ENCODED ANTIBIOTIC-RESISTANCE GENES PEAK IN DIFFERENT ENVIRONMENTS
Authors: Wendling Carolin C. , Refardt Dominik , Hall Alex R. 
Published: March 2020

AbstractBacteria can acquire antibiotic resistance genes (ARGs) via prophages, phage genomes integrated into bacterial chromosomes. Such prophages may influence bacterial fitness via increased antibiotic resistance, protection from further phage infection, or by switching to a lytic lifecycle that releases free phages which can infect phage-susceptible competitors. We expect these effects to depend on environmental conditions because of, for example, environment-dependent induction of the lytic lifecycle. However, our understanding of how costs and benefits of prophage-encoded ARGs vary across environments remains limited. Here, by studying prophages with and without ARGs inEscherichia coli, we distinguished between effects of prophages alone and ARGs they carry. In competition with prophage-free strains, fitness benefits from prophages and ARGs peaked in different environments. Prophage carriage was most beneficial in conditions where induction of the lytic lifecycle was common, whereas ARGs were more beneficial in the presence of antibiotics and when prophage induction was lower. Acquisition of prophage-encoded ARGs by competing phage-susceptible strains was most common when prophage induction, and therefore the amount of free phages, was high. Thus, selection on prophages and ARGs varies independently across environments, which is important for predicting the spread of mobile/integrating genetic elements and their role in antibiotic resistance evolution.
Targeted genome editing inNicotiana tabacumusing inducible CRISPR/Cas9 system
Authors: Ren Chong , Liu Yanfei , Wang Xida , Guo Yuchen , Fan Peige , Li Shaohua , Liang Zhenchang 
Published: March 2020

AbstractTargeted genome editing has been achieved in multiple plant species using the clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR/Cas9) system, in which theCas9gene is usually driven by constitutive promoters. However, constitutive expression ofCas9is not necessary and can be harmful to plant development. In this study, we developed an estrogen-inducible CRISPR/Cas9 system by taking advantage of the chimeric transcription activator XVE and tested the efficacy of this inducible system inNicotiana tabacumby targeting the phytoene desaturase (NtPDS) gene, whose mutation resulted in albino phenotypes. Treatment of four independent transgenic lines with exogenous estradiol successfully induced targeted mutagenesis inNtPDS. Sanger sequencing assay uncovered the presence of indel mutations (nucleotides insertions or deletions) at the target site as expected, and at least two types of mutations were identified for each line. Transgenic plants with mutatedNtPDSgene after estradiol treatment exhibited pale green or incomplete albino leaves. Moreover, the expression ofCas9in transgenic plants was strongly induced by estradiol treatment. Our results demonstrate the efficacy of XVE-based CRISPR/Cas9 system inN. tabacum, and the system reported here promises to be a useful approach for conditional genome editing, which would facilitate the study of genes of interest, especially those developmentally important genes.
Tales of 1,008 Small Molecules: Phenomic Profiling through Live-cell Imaging in a Panel of Reporter Cell Lines
Authors: Cox Michael J. , Jaensch Steffen , Van de Waeter Jelle , Cougnaud Laure , Seynaeve Daan , Benalla Soulaiman , Koo Seong Joo , Van Den Wyngaert Ilse , Neefs Jean-Marc , Malkov Dmitry , Bittremieux Mart , Steemans Margino , Peeters Pieter J. , Wegner Jörg Kurt , Ceulemans Hugo , Gustin Emmanuel , Chong Yolanda T. , Göhlmann Hinrich W.H. 
Published: March 2020

AbstractPhenomic profiles are high-dimensional sets of readouts that can comprehensively capture the biological impact of chemical and genetic perturbations in cellular assay systems. Phenomic profiling of compound libraries can be used for compound target identification or mechanism of action (MoA) prediction and other applications in drug discovery. To devise an economical set of phenomic profiling assays, we assembled a library of 1,008 approved drugs and well-characterized tool compounds manually annotated to 218 unique MoAs, and we profiled each compound at four concentrations in live-cell, high-content imaging screens against a panel of 15 reporter cell lines, which expressed a diverse set of fluorescent organelle and pathway markers in three distinct cell lineages. For 41 of 83 testable MoAs, phenomic profiles accurately ranked the reference compounds (AUC-ROC ≥0.9). MoAs could be better resolved by screening compounds at multiple concentrations than by including replicates at a single concentration. Screening additional cell lineages and fluorescent markers increased the number of distinguishable MoAs but this effect quickly plateaued. There remains a substantial number of MoAs that were hard to distinguish from others under the current study’s conditions. We discuss ways to close this gap, which will inform the design of future phenomic profiling efforts.
Detection of M-Protein in Acetonitrile Precipitates of Serum using MALDI-TOF Mass Spectrometry
Authors: Mehra Nikita , Gopisetty Gopal , Jayavelu S , Arivazhagan Rajamanickam , Sundersingh Shirley , Karunakaran Parathan , Kalaiyarasi Jayachandran Perumal , Kannan Krishnarathinam , Radhakrishnan Venkatraman , Sagar Tenali Gnana , Rajkumar Thangarajan 
Published: March 2020

AbstractPurpose of the researchMultiple myeloma and plasmacytomas belong to a group of disorders, namely plasma cell dyscrasias and are identified by the presence of a monoclonal protein (M-protein). MALDI-TOF-mass spectrometry (MS) has demonstrated superior analytical sensitivity for the detection of M-protein and is now used for screening of M-protein at some centres. We present the results of an alternative methodology for M-protein analysis by MALDI-TOF MS.MethodsSerum samples from patients with newly diagnosed multiple myeloma or plasmacytoma with positive M-protein detected by serum protein electrophoresis, immunofixation electrophoresis and serum free light chain analysis, underwent direct reagent-based extraction process using Acetonitrile (ACN) precipitation. Serumκandλlight chains were validated using immunoenrichment by anti-κand anti-λbiotin-labelled antibodies immobilised on streptavidin magnetic beads. MALDI-TOF MS measurements were obtained for intact proteins using alpha-cyano-4-hydroxycinnamic acid as matrix. The images obtained were overlaid on apparently healthy donor serum samples to confirm the presence of M-protein.Principle resultsCharacteristic M-protein peaks were observed in the ACN precipitates of serum in the predicted mass ranges forκandλ. Theκandλpeaks were confirmed by immunoenrichment analysis. Twenty-seven patient samples with either newly diagnosed multiple myeloma or plasmacytoma with monoclonal gammopathy detected by the standard methods were chosen for Acetonitrile precipitation and analysed by MALDI-TOF MS. All 27 patient samples demonstrated a peak suggestive of M-protein with mass/charge(m/z)falling within theκandλrange. The concordance rate with serum immunofixation electrophoresis and free light chain analysis was above 90%.Major conclusionsWe report the results of a low-cost reagent-based extraction process using Acetonitrile precipitation to enrich forκandλlight chains, which can be used for the screening and qualitative analysis of M-protein.
The COMPASS-like complex modulates fungal development and pathogenesis by regulating H3K4me3-mediated targeted gene expression inMagnaporthe oryzae
Authors: Zhou Sida , Sun Wanyu , Zhao Xinyu , Xu Yang , Zhang Mengyu , Yin Yue , Pan Song , He Dan , Shen Mi , Yang Jun , Liu Xiuying , Zheng Qi , Wang Weixiang 
Published: March 2020

ABSTRACTHistone H3K4 methylation is catalysed by the multi-protein complex known as the Set1/COMPASS or MLL/COMPASS-like complex, an element that is highly evolutionarily conserved from yeast to humans. However, the components and mechanisms by which the COMPASS-like complex targets the H3K4 methylation of plant pathogenic genes in fungi remain elusive. Here we present a comprehensive analysis combining biochemical, molecular, and genome-wide approaches to characterize the roles of the COMPASS-like family inMagnaporthe oryzae, a model plant fungal pathogen. We purified and identified six conserved subunits of COMPASS from the rice blast fungusM. oryzae, i.e., MoBre2 (Cps60/ASH2L), MoSpp1 (Cps40/Cfp1), MoSwd2 (Cps35), MoSdc1 (Cps25/DPY30), MoSet1 (MLL/ALL) and MoRbBP5 (Cps50), using an affinity tag on MoBre2. We determined the SPRY domain of MoBre2 can recognize directly with DPY30 domain of MoSdc1in vitro.Furthermore, we found that deletion of the genes encoding COMPASS subunits of MoBre2, MoSpp1 and MoSwd2 caused similar defects regarding invasive hyphal development and pathogenicity. Genome-wide profiling of H3K4me3 revealed that the it has remarkable co-occupancy at the TSS regions of target genes. Significantly, these target genes are often involved in spore germination and pathogenesis. Decreased gene expression caused by the deletion ofMoBre2,MoSwd2orMoSpp1gene was highly correlated with decrease in H3K4me3. Taken together, these results suggest that MoBre2, MoSpp1, and MoSwd2 function as a whole COMPASS complex, contributing to fungal development and pathogenesis by regulating H3K4me3-targeted genes inM. oryzae.
Lack of Reinfection in Rhesus Macaques Infected with SARS-CoV-2
Authors: Bao Linlin , Deng Wei , Gao Hong , Xiao Chong , Liu Jiayi , Xue Jing , Lv Qi , Liu Jiangning , Yu Pin , Xu Yanfeng , Qi Feifei , Qu Yajin , Li Fengdi , Xiang Zhiguang , Yu Haisheng , Gong Shuran , Liu Mingya , Wang Guanpeng , Wang Shunyi , Song Zhiqi , Liu Ying , Zhao Wenjie , Han Yunlin , Zhao Linna , Liu Xing , Wei Qiang , Qin Chuan 
Published: March 2020

AbstractA global pandemic of Corona Virus Disease 2019 (COVID-19) caused by severe acute respiratory syndrome CoV-2 (SARS-CoV-2) is ongoing spread. It remains unclear whether the convalescing patients have a risk of reinfection. Rhesus macaques were rechallenged with SARS-CoV-2 during an early recovery phase from initial infection characterized by weight loss, interstitial pneumonia and systemic viral dissemination mainly in respiratory and gastrointestinal tracts. The monkeys rechallenged with the identical SARS-CoV-2 strain have failed to produce detectable viral dissemination, clinical manifestations and histopathological changes. A notably enhanced neutralizing antibody response might contribute the protection of rhesus macaques from the reinfection by SARS-CoV-2. Our results indicated that primary SARS-CoV-2 infection protects from subsequent reinfection.One Sentence SummaryNeutralizing antibodies against SARS-CoV-2 might protect rhesus macaques which have undergone an initial infection from reinfection during early recovery days.
Classification and Specific Primer Design for Accurate Detection of SARS-CoV-2 Using Deep Learning
Authors: Lopez-Rincon Alejandro , Tonda Alberto , Mendoza-Maldonado Lucero , Mulders Daphne G.J.C. , Molenkamp Richard , Perez-Romero Carmina A. , Claassen Eric , Garssen Johan , Kraneveld Aletta D. 
Published: March 2020

ABSTRACTIn this paper, deep learning is coupled with explainable artificial intelligence techniques for the discovery of representative genomic sequences in SARS-CoV-2. A convolutional neural network classifier is first trained on 553 sequences from available repositories, separating the genome of different virus strains from the Coronavirus family with considerable accuracy. The network’s behavior is then analyzed, to discover sequences used by the model to identify SARS-CoV-2, ultimately uncovering sequences exclusive to it. The discovered sequences are first validated on samples from other repositories, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. Next, one of the sequences is selected to generate a primer set, and tested against other state-of-the-art primer sets on existing datasets, obtaining competitive results. Finally, the primer is synthesized and tested on patient samples (n=6 previously tested positive), delivering a sensibility similar to routine diagnostic methods, and 100% specificity. In this paper, deep learning is coupled with explainable artificial intelligence techniques for the discovery of representative genomic sequences in SARS-CoV-2. A convolutional neural network classifier is first trained on 553 sequences from NGDC, separating the genome of different virus strains from the Coronavirus family with accuracy 98.73%. The network’s behavior is then analyzed, to discover sequences used by the model to identify SARS-CoV-2, ultimately uncovering sequences exclusive to it. The discovered sequences are validated on samples from NCBI and GISAID, and proven able to separate SARS-CoV-2 from different virus strains with near-perfect accuracy. Next, one of the sequences is selected to generate a primer set, and tested against other state-of-the-art primer sets, obtaining competitive results. Finally, the primer is synthesized and tested on patient samples (n=6 previously tested positive), delivering a sensibility similar to routine diagnostic methods, and 100% specificity. The proposed methodology has a substantial added value over existing methods, as it is able to both identify promising primer sets for a virus from a limited amount of data, and deliver effective results in a minimal amount of time. Considering the possibility of future pandemics, these characteristics are invaluable to promptly create specific detection methods for diagnostics.
Differential Antibody Recognition by Novel SARS-CoV-2 and SARS-CoV Spike Protein Receptor Binding Domains: Mechanistic Insights and Implications for the Design of Diagnostics and Therapeutics
Authors: D’Annessa Ilda , Marchetti Filippo , Colombo Giorgio 
Published: March 2020

AbstractThe appearance of the novel betacoronavirus SARS-CoV-2 represents a major threat to human health, and its diffusion around the world is causing dramatic consequences. The knowledge of the 3D structures of SARS-CoV-2 proteins can facilitate the development of therapeutic and diagnostic molecules. Specifically, comparative analyses of the structures of SARS-CoV-2 proteins and homologous proteins from previously characterized viruses, such as SARS-CoV, can reveal the common and/or distinctive traits that underlie the mechanisms of recognition of cell receptors and of molecules of the immune system.Herein, we apply our recently developed energy-based methods for the prediction of antibody-binding epitopes and protein-protein interaction regions to the Receptor Binding Domain (RBD) of the Spike proteins from SARS-CoV-2 and SARS-CoV. Our analysis focusses only on the study of the structure of RBDs in isolation, without making use of any previous knowledge of binding properties. Importantly, our results highlight structural and sequence differences among the regions that are predicted to be immunoreactive and bind/elicit antibodies. These results provide a rational basis to the observation that several SARS-CoV RDB-specific monoclonal antibodies fail to appreciably bind the SARS-CoV-2 counterpart. Furthermore, we correctly identify the region of SARS-CoV-2 RBD that is engaged by the cell receptor ACE2 during viral entry into host cells.The data, sequences and structures we present here can be useful for the development of novel therapeutic and diagnostic interventions.
Flexibility and constraint in preimplantation gene regulation in mouse
Authors: Conine Colin C. , Krykbaeva Marina , Song Lina , Brewster Robert C. , Friedman Nir , Rando Oliver J. 
Published: March 2020

ABSTRACTAlthough many features of embryonic development exhibit remarkable stability in the face of environmental perturbations, it is also clear that some aspects of early embryogenesis can be modulated by non-genetic influences during and after fertilization. Among potential perturbations experienced during reproduction, understanding the consequences of differing ex vivo fertilization methods at a molecular level is imperative for comprehending both the basic biology of early development and the potential consequences of assisted reproduction. Here, we set out to explore stable and flexible aspects of preimplantation gene expression using single-embryo RNA-sequencing of mouse embryos fertilized by natural mating, in vitro fertilization, or intracytoplasmic sperm injection, as well as oocytes parthenogenetically activated to develop (parthenotes). This dataset comprises a resource of over eight hundred individual embryos, which we use for three primary analyses. First, we characterize the effects of each fertilization method on early embryonic gene regulation, most notably finding decreased expression of trophectoderm markers at later stages of preimplantation development in ICSI embryos. Second, we find massive gene misregulation in parthenotes beyond the expected defects in imprinted gene expression, and show that many of these changes can be suppressed by sperm total RNA. Finally, we make use of the single-embryo resolution of our dataset to identify both stably-expressed genes and highly-variable genes in the early mouse embryo. Together, our data provide a detailed survey of the molecular consequences of different fertilization methods, establish parthenotes as a “tabula rasa” for understanding the role for sperm RNAs in preimplantation gene regulation, and identify subtypes of preimplantation embryos based on their expression of epivariable gene modules.