bluuebunny/crossref_metadata_2025_split huggingface dataset:
Normal mammary epithelia accumulate DNA methylation changes with age that are consistent with breast cancer methylomes
Authors: Senapati Parijat , Miyano Masaru , Sayaman Rosalyn W. , Basam Mudaser , Trac Candi , Leung Amy , LaBarge Mark A. , Schones Dustin E. 
Published: June 2020

AbstractLuminal epithelial cells (LEps) are a key cell lineage implicated in age-related luminal breast cancers. Alterations to the epigenome are a hallmark of aging cells. However, the extent of age-associated DNA methylation alterations in LEps, and the corresponding functional consequences of these alterations, have remained unclear. We report here that aging leads to distinct methylation changes in LEps. Luminal lineage-specific genes gain promoter methylation, whereas myoepithelial-specific genes lose promoter methylation. Regulatory elements display methylation changes at lineage-specific TF binding sites consistent with the loss of lineage fidelity. CpG islands (CGIs) and transposable elements (TEs) have stochastic methylation gain and loss, respectively. PRC2 target genes that are hypermethylated in luminal breast cancer exhibit stochastic methylation increase with age. TEs with stochastic methylation loss are activated in breast cancer and potentially function as regulatory elements contributing to the loss of lineage fidelity with age. Each of these classes of methylation changes impact the regulation of genes associated with luminal breast cancer. Altogether, our results indicate that aging leads to DNA methylation changes that could determine breast cancer susceptibility.SignificanceMammary luminal epithelial cells lose lineage-specific expression with age and accumulate stochastic methylation changes that lead to loss of silencing at transposable elements. These age-dependent events potentially promote breast cancer susceptibility.
Evaluation of K18-hACE2mice as a model of SARS-CoV-2 infection
Authors: Moreau G. Brett , Burgess Stacey L. , Sturek Jeffrey M. , Donlan Alexandra N. , Petri William A. , Mann Barbara J. 
Published: June 2020

Abstract/SummaryMurine models of SARS-CoV-2 infection are critical for elucidating the biological pathways underlying COVID-19 disease. Because human ACE2 is the receptor for SARS-CoV-2, mice expressing the humanACE2gene have shown promise as a potential model for COVID-19. Five mice from the transgenic mouse strain K18-hACE2were intranasally inoculated with SARS-CoV-2 Hong Kong/VM20001061/2020. Mice were followed twice daily for five days and scored for weight loss and clinical symptoms. Infected mice did not exhibit any signs of infection until day four, when weight loss, but no other obvious clinical symptoms were observed. By day five all infected mice had lost around 10% of their original body weight, but exhibited variable clinical symptoms. All infected mice showed high viral titers in the lungs as well as altered lung histology associated with proteinaceous debris in the alveolar space, interstitial inflammatory cell infiltration and alveolar septal thickening. Overall, these results show that symptomatic SARS-CoV-2 infection can be established in the K18-hACE2transgenic background and should be a useful mouse model for COVID-19 disease.
Proteomic data from leaves of twenty-four sunflower genotypes underwater deficit
Authors: Balliau Thierry , Duruflé Harold , Blanchet Nicolas , Blein-Nicolas Mélisande , Langlade Nicolas B. , Zivy Michel 
Published: June 2020

AbstractThis article describes how the proteomic data were produced on sunflower plants subjected to water deficit. Twenty-four sunflower genotypes were selected to represent genetic diversity within cultivated sunflower. They included both inbred lines and their hybridsWater deficit was applied to plants in pots at the vegetative stage using the high-throughput phenotyping platform Heliaphen. Here, we provide proteomic data from sunflower leaves corresponding to the identification of 3062 proteins and the quantification of 1211 of them in these 24 genotypes grown in two watering conditions. These data differentiate both treatment and the different genotypes and constitute a valuable resource to the community to study adaptation of crops to drought and the molecular basis of heterosis.
Dopachrome tautomerase variants in patients with oculocutaneous albinism
Authors: Pennamen Perrine , Tingaud-Sequeira Angèle , Gazova Iveta , Keighren Margaret , McKie Lisa , Marlin Sandrine , Halem Souad Gherbi , Kaplan Josseline , Delevoye Cédric , Lacombe Didier , Plaisant Claudio , Michaud Vincent , Lasseaux Eulalie , Javerzat Sophie , Jackson Ian , Arveiler Benoit 
Published: June 2020

ABSTRACTPurposeAlbinism is a clinically and genetically heterogeneous condition. Despite analysis of the nineteen known genes, ∼30% patients remain unsolved. We aimed to identify new genes involved in albinism.MethodsWe sequenced a panel of genes with known or predicted involvement in melanogenesis in 230 unsolved albinism patients.ResultsWe identified variants in theDopachrome tautomerase(DCT) gene in two patients. One was compound heterozygous for a 14 bp deletion in exon 9 and c.118T>A p.(Cys40Ser). The second was homozygous for c.183C>G p.(Cys61Trp). Both patients had mild hair and skin hypopigmentation, and classical ocular features. CRISPR/Cas9 was used in C57BL/6J mice to create mutations identical to the missense mutations carried by the patients, along with one loss-of-function indel mutation. When bred to homozygosity the three mutations revealed hypopigmentation of the coat, milder for Cys40Ser compared to Cys61Trp or the frameshift mutation. Histological analysis identified significant hypopigmentation of the retinal pigmented epithelium (RPE) indicating that defective RPE melanogenesis could be associated with eye and vision defects.DCTloss of function in zebrafish embryos elicited hypopigmentation both in melanocytes and RPE cells.ConclusionsDCTis the gene for a new type of oculocutaneous albinism that we propose to name OCA8.
Spatial Variation of Microtubule Depolymerization in Large Asters Suggests Regulation by MAP Depletion
Authors: Ishihara Keisuke , Decker Franziska , Caldas Paulo , Pelletier James F. , Loose Martin , Brugués Jan , Mitchison Timothy J. 
Published: June 2020

AbstractMicrotubule plus end depolymerization rate is a potentially important target of physiological regulation, but it has been challenging to measure, so its role in spatial organization is poorly understood. Here we apply a method for tracking plus ends based on time difference imaging to measure depolymerization rates in large interphase asters growing inXenopusegg extract. We observed strong spatial regulation of depolymerization rates, which were almost two-fold higher in the aster interior compared to the periphery, and much less regulation of polymerization or catastrophe rates. We interpret these data in terms of a limiting component model, where aster growth results in lower levels of soluble tubulin and MAPs in the interior cytosol compared to that at the periphery. The steady-state polymer fraction of tubulin was ∼30%, so tubulin is not strongly depleted in the aster interior. We propose that the limiting component for microtubule assembly is a MAP that inhibits depolymerization, and that egg asters are tuned to low microtubule density.
Functional domain studies uncover novel roles for the ZTL Kelch repeat domain in clock function
Authors: Feke Ann M. , Gendron Joshua M. 
Published: June 2020

AbstractThe small LOV/F-box/Kelch family of E3 ubiquitin ligases plays an essential role in the regulation of plant circadian clocks and flowering time by sensing dusk. The family consists of three members, ZEITLUPE (ZTL), LOV KELCH PROTEIN 2 (LKP2), and FLAVIN-BINDING KELCH REPEAT F-BOX PROTEIN 1 (FKF1), which share a unique protein domain architecture allowing them to act as photoreceptors that transduce light signals via altering stability of target proteins. Despite intensive study of this protein family we still lack important knowledge about the biochemical and functional roles of the protein domains that comprise these unique photoreceptors. Here, we perform comparative analyses of transgenic lines constitutively expressing the photoreceptor LOV domain or the Kelch repeat protein-protein interaction domains of ZTL, FKF1, and LKP2. Expression of each domain alone is sufficient to disrupt circadian rhythms and flowering time, but each domain differs in the magnitude of effect. Immunoprecipitation followed by mass spectrometry with the ZTL Kelch repeat domain identified a suite of potential interacting partners. Furthermore, the ZTL Kelch repeat domain mediates interaction with the LOV domain of ZTL and the ZTL homologs LKP2 and FKF1. This suggests that the Kelch repeat domain of ZTL may mediate homo- and hetero-dimerization of the three LOV/F-box/Kelch proteins and provide added insight into the composition of the protein complexes and an additional role for the Kelch repeat domain.
Germline gene de-silencing by a transposon insertion is triggered by an altered landscape of local piRNA biogenesis
Authors: Miller Danny E. , Van Vaerenberghe Kelley , Li Angela , Grantham Emily K. , Cummings Celeste , Barragan Marilyn , Egidy Rhonda , Scott Allison R. , Hall Kate , Perera Anoja , Gilliland William D. , Blumenstiel Justin P. 
Published: June 2020

AbstractTransposable elements (TE) are selfish genetic elements that can cause harmful mutations. InDrosophila, it has been estimated that half of all spontaneous visible marker phenotypes are mutations caused by TE insertions. Because of the harm posed by TEs, eukaryotes have evolved systems of small RNA-based genome defense to limit transposition. However, as in all immune systems, there is a cost of autoimmunity and small RNA-based systems that silence TEs can inadvertently silence genes flanking TE insertions. In a screen for essential meiotic genes inDrosophila melanogaster, a truncatedDocretrotransposon within a neighboring gene was found to trigger the germline silencing ofald, theDrosophila Mps1homolog, a gene essential for meiosis. A subsequent screen for modifiers of this silencing identified a new insertion of aHoboDNA transposon in the same neighboring gene. Here we describe how the originalDocinsertion triggers flanking piRNA biogenesis and local gene silencing and how the additionalHoboinsertion leads to de-silencing by reducing flanking piRNA biogenesis triggered by the originalDocinsertion. These results support a model of TE-mediated silencing by piRNA biogenesis incisthat depends on local determinants of transcription. This may explain complex patterns of off-target gene silencing triggered by TEs within populations and in the laboratory. It also provides a mechanism of sign epistasis among TE insertions.Author SummaryTransposable elements (TEs) are selfish DNA elements that can move through genomes and cause mutation. In some species, the vast majority of DNA is composed of this form of selfish DNA. Because TEs can be harmful, systems of genome immunity based on small RNA have evolved to limit the movement of TEs. However, like all systems of immunity, it can be challenging for the host to distinguish self from non-self. Thus, TE insertions occasionally cause the small RNA silencing machinery to turn off the expression of critical genes. The rules by which this inadvertent form of autoimmunity causes gene silencing are not well understood. In this article, we describe a phenomenon whereby a TE insertion, rather than silencing a nearby gene, rescues the silencing of a gene caused by another TE insertion. This reveals a mode of TE interactionviasmall RNA silencing that may be important for understanding how TEs exert their effects on gene expression in populations and across species.
Population Bottlenecks and Intra-host Evolution during Human-to-Human Transmission of SARS-CoV-2
Authors: Wang Daxi , Wang Yanqun , Sun Wanying , Zhang Lu , Ji Jingkai , Zhang Zhaoyong , Cheng Xinyi , Li Yimin , Xiao Fei , Zhu Airu , Zhong Bei , Ruan Shicong , Li Jiandong , Ren Peidi , Ou Zhihua , Xiao Minfeng , Li Min , Deng Ziqing , Zhong Huanzi , Li Fuqiang , Wang Wen-jing , Zhang Yongwei , Chen Weijun , Zhu Shida , Xu Xun , Jin Xin , Zhao Jingxian , Zhong Nanshan , Zhang Wenwei , Zhao Jincun , Li Junhua , Xu Yonghao 
Published: June 2020

AbstractThe emergence of the novel human coronavirus, SARS-CoV-2, causes a global COVID-19 (coronavirus disease 2019) pandemic. Here, we have characterized and compared viral populations of SARS-CoV-2 among COVID-19 patients within and across households. Our work showed an active viral replication activity in the human respiratory tract and the co-existence of genetically distinct viruses within the same host. The inter-host comparison among viral populations further revealed a narrow transmission bottleneck between patients from the same households, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions.Author summaryIn this study, we compared SARS-CoV-2 populations of 13 Chinese COVID-19 patients. Those viral populations contained a considerable proportion of viral sub-genomic messenger RNAs (sgmRNA), reflecting an active viral replication activity in the respiratory tract tissues. The comparison of 66 identified intra-host variants further showed a low viral genetic distance between intra-household patients and a narrow transmission bottleneck size. Despite the co-existence of genetically distinct viruses within the same host, most intra-host minor variants were not shared between transmission pairs, suggesting a dominated role of stochastic dynamics in both inter-host and intra-host evolutions. Furthermore, the narrow bottleneck and active viral activity in the respiratory tract show that the passage of a small number of virions can cause infection. Our data have therefore delivered a key genomic resource for the SARS-CoV-2 transmission research and enhanced our understanding of the evolutionary dynamics of SARS-CoV-2.
The Gb3-enriched CD59/flotillin plasma membrane domain regulates host cell invasion byPseudomonas aeruginosa
Authors: Brandel Annette , Aigal Sahaja , Lagies Simon , Schlimpert Manuel , Lehmann Anika , Hummel Daniel , Fisch Daniel , Meléndez Ana Valeria , Madl Josef , Eierhoff Thorsten , Kammerer Bernd , Römer Winfried 
Published: June 2020

AbstractThe opportunistic pathogenPseudomonas aeruginosais responsible for a high number of acute and chronic hospital-acquired infections. As it develops more and more resistances against existing antibiotics,P. aeruginosahas been placed highest on the global priority list of antibiotic-resistant bacteria for which alternative treatments are urgently needed. Former studies have highlighted the crucial role of the bacterial lectin LecA and the host cell glycosphingolipid globotriaosylceramide (Gb3) for the cellular uptake ofP. aeruginosainto epithelial cells via the lipid zipper mechanism. To further characterize the host cell plasma membrane domain for LecA-driven attachment and invasion, we analyzed the protein and lipid composition of pulled-down membrane domains for novel interaction partners of LecA by mass spectrometry. We unraveled a predilection of LecA for binding to saturated Gb3 species in the extracellular membrane leaflet and an induction of dynamic phosphatidylinositol (3,4,5)-trisphosphate clusters at the intracellular leaflet co-localizing with sites of LecA binding. Moreover, we identified the GPI-anchored protein CD59 and flotillins, known as cargo and eponymous component of flotillin-assisted endocytosis, as LecA interaction partners. Depletion of each of these host cell proteins resulted in more than 50% of reduction in invasiveness of theP. aeruginosastrain PAO1 highlighting the importance of this LecA-induced plasma membrane domain. Our strategy to reduce the complexity of host-pathogen interactions by first identifying interaction partners of a single virulence factor and subsequently transferring these findings to the bacterium has been proven to be a successful approach in elucidating the molecular mechanisms of bacterial infections.
The infection cushion: a fungal “weapon” of plant-biomass destruction
Authors: Choquer Mathias , Rascle Christine , Gonçalves Isabelle R , de Vallée Amélie , Ribot Cécile , Loisel Elise , Smilevski Pavlé , Ferria Jordan , Savadogo Mahamadi , Souibgui Eytham , Gagey Marie-Josèphe , Dupuy Jean-William , Rollins Jeffrey A , Marcato Riccardo , Noûs Camille , Bruel Christophe , Poussereau Nathalie 
Published: June 2020

SummaryGrey mold disease affects fruits, vegetables and ornamental plants around the world, causing considerable losses every year. Its causing agent, the necrotrophic fungusBotrytis cinerea, produces infection cushions (IC) that are compound appressorial structures dedicated to the penetration of the plant tissues.A microarray analysis was performed to identify genes up-regulated in mature IC. The expression data were supported by RT-qPCR analysis performedin vitroandin planta, proteomic analysis of the IC secretome and mutagenesis of two candidate genes.1,231 up-regulated genes and 79 up-accumulated proteins were identified. They highlight a secretion of ROS, secondary metabolites including phytotoxins, and proteins involved in virulence: proteases, plant cell wall degrading enzymes and necrosis inducers. The role in pathogenesis was confirmed for two up-regulated fasciclin genes. DHN-melanin pathway and chitin deacetylases genes are up-regulated and the conversion of chitin into chitosan was confirmed by differential staining of the IC cell wall. In addition, up-regulation of sugar transport and sugar catabolism encoding genes was found.These results support a role for theB. cinereaIC in plant penetration and suggest other unexpected roles for this fungal organ, in camouflage, necrotrophy or nutrition of the pathogen.
The GET pathway safeguards against non-imported mitochondrial protein stress
Authors: Xiao Tianyao , Shakya Viplendra P.S. , Hughes Adam L. 
Published: June 2020

SUMMARYDeficiencies in mitochondrial import cause the toxic accumulation of non-imported mitochondrial precursor proteins. Numerous fates for non-imported mitochondrial precursors have been identified, including proteasomal destruction, deposition into protein aggregates, and mis-targeting to other organelles. Amongst organelles, the endoplasmic reticulum (ER) has emerged as a key destination for non-imported mitochondrial proteins, but how ER-targeting of these proteins is achieved remains unclear. Here, we show that the guided entry of tail-anchored proteins (GET) complex is required for ER-targeting of endogenous mitochondrial multi-transmembrane proteins. Without a functional GET pathway, non-imported mitochondrial proteins destined for the ER are alternatively sequestered into Hsp42-dependent protein foci. The ER targeting of non-imported mitochondrial proteins by the GET complex prevents cellular toxicity and facilitates re-import of mitochondrial proteins from the ER via the recently identified ER-SURF pathway. Overall, this study outlines an important and unconventional role for the GET complex in mitigating stress associated with non-imported mitochondrial proteins.
Phosphorylation of the GARP Subunit Vps53 by Snf1 Leads to the Formation of a Golgi – Mitochondria Contact Site (GoMiCS) in Yeast
Authors: Wycislo Susanne A. , Sundag Celine , Walter Stefan , Schuck Sebastian , Fröhlich Florian 
Published: June 2020

AbstractThe canonical function of the Golgi-associated retrograde protein (GARP) complex is the tethering of transport carriers. GARP belongs to the complexes associated with tethering containing helical rods (CATCHR) family and is a hetero-tetrameric complex consisting of the subunits Vps51, Vps52, Vps53 and Vps54. How the activity of GARP is regulated and if it possesses other functions besides tethering remains largely unknown. Here we identify the GARP subunit Vps53 as a novel regulatory target of theS. cerevisiaeAMP kinase (AMPK) homolog Snf1. We find that Vps53 is both anin vivoandin vitrotarget of Snf1 and show that phosphorylation depends on the nature and quantity of the available carbon source. Phosphorylation of Vps53 does not affect the canonical trafficking pathway, but results in altered mitochondrial dynamics and the formation of a previously unknown contact site between the Golgi apparatus and mitochondria, termed GoMiCS. Our results provide an example of a subunit of a CATCHR complex with a constitutive function in membrane trafficking and an inducible role in organelle contact site formation. We anticipate our results to be the starting point for the characterization of this novel contact site.
Tipiracil binds to uridine site and inhibits Nsp15 endoribonuclease NendoU from SARS-CoV-2
Authors: Kim Youngchang , Wower Jacek , Maltseva Natalia , Chang Changsoo , Jedrzejczak Robert , Wilamowski Mateusz , Kang Soowon , Nicolaescu Vlad , Randall Glenn , Michalska Karolina , Joachimiak Andrzej 
Published: June 2020

ABSTRACTSARS-CoV-2 Nsp15 is a uridylate-specific endoribonuclease with C-terminal catalytic domain belonging to the EndoU family. It degrades the polyuridine extensions in (−) sense strand of viral RNA and some non-translated RNA on (+) sense strand. This activity seems to be responsible for the interference with the innate immune response and evasion of host pattern recognition. Nsp15 is highly conserved in coronaviruses suggesting that its activity is important for virus replication. Here we report first structures with bound nucleotides and show that SARS-CoV-2 Nsp15 specifically recognizes U in a pattern previously predicted for EndoU. In the presence of manganese ions, the enzyme cleaves unpaired RNAs. Inhibitors of Nsp15 have been reported but not actively pursued into therapeutics. The current COVID-19 pandemic brought to attention the repurposing of existing drugs and the rapid identification of new antiviral compounds. Tipiracil is an FDA approved drug that is used with trifluridine in the treatment of colorectal cancer. Here, we combine crystallography, biochemical and whole cell assays, and show that this compound inhibits SARS-CoV-2 Nsp15 and interacts with the uridine binding pocket of the enzyme’s active site, providing basis for the uracil scaffold-based drug development.
Development of a Coronavirus Disease 2019 Nonhuman Primate Model Using Airborne Exposure
Authors: Johnston Sara C. , Jay Alexandra , Raymond Jo Lynne , Rossi Franco , Zeng Xiankun , Scruggs Jennifer , Dyer David , Frick Ondraya , Moore Joshua , Berrier Kerry , Esham Heather , Shamblin Joshua , Sifford Willie , Fiallos Jimmy , Klosterman Leslie , Stevens Stephen , White Lauren , Bowling Philip , Garcia Terrence , Jensen Christopher , Ghering Jeanean , Nyakiti David , Bellanca Stephanie , Kearney Brian , Giles Wendy , Alli Nazira , Paz Fabian , Akers Kristen , Danner Denise , Barth James , Johnson Joshua A. , Durant Matthew , Kim Ruth , Pitt Margaret LM , Nalca Aysegul 
Published: June 2020

AbstractAirborne transmission is predicted to be a prevalent route of human exposure with SARS-CoV-2. Aside from African green monkeys, nonhuman primate models that replicate airborne transmission of SARS-CoV-2 have not been investigated. A comprehensive and comparative evaluation of COVID-19 in African green monkeys, rhesus macaques, and cynomolgus macaques following airborne exposure to SARS-CoV-2 was performed to define parameters critical to disease progression and the extent to which they correlate with human COVID-19. Respiratory abnormalities and viral shedding were noted for all animals, indicating successful infection. Cynomolgus macaques developed fever, and thrombocytopenia was measured for African green monkeys and rhesus macaques. Type II pneumocyte hyperplasia and alveolar fibrosis were more frequently observed in lung tissue from cynomolgus macaques and African green monkeys. The data indicate that, in addition to African green monkeys, macaques can be successfully infected by airborne SARS-CoV-2, providing viable macaque natural transmission models for medical countermeasure evaluation.One Sentence SummaryNonhuman primates develop COVID-19 following airborne virus exposure.