bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plant DNA polymerases alpha and delta mediate replication of geminiviruses
Authors: Wu Mengshi , Wei Hua , Tan Huang , Pan Shaojun , Liu Qi , Bejarano Eduardo R , Lozano-Durán Rosa 
Published: July 2020

ABSTRACTGeminiviruses are causal agents of devastating diseases in crops. Geminiviruses have circular single-stranded (ss)DNA genomes that are replicated in the nucleus of the infected plant cell through double-stranded (ds)DNA intermediates by the plant’s DNA replication machinery; which host DNA polymerase mediates geminiviral multiplication, however, has so far remained elusive. Here, we show that subunits of the nuclear replicative DNA polymerases α and δ physically interact with the geminivirus-encoded replication enhancer protein, C3, and are required for viral replication. Our results suggest that while DNA polymerase α is essential to generate the viral dsDNA intermediate, DNA polymerase δ mediates the synthesis of new copies of the geminiviral ssDNA genome, and that the virus-encoded C3 acts selectively recruiting DNA polymerase δ over ε to favour a productive replication.
Ivermectin inhibits extracellular vesicle secretion from parasitic nematodes
Authors: Loghry Hannah J. , Yuan Wang , Zamanian Mostafa , Wheeler Nicolas J. , Day Timothy A. , Kimber Michael J. 
Published: July 2020

AbstractLymphatic filariasis (LF) is a disease caused by parasitic filarial nematodes that is endemic in 49 countries and affects or threatens over 890 million people. Strategies to control LF rely heavily on mass administration of anthelmintic drugs including ivermectin (IVM), a macrocyclic lactone drug considered an Essential Medicine by the WHO. However, despite its widespread use the therapeutic mode of action of IVM against filarial nematodes is not clear. We have previously reported that filarial nematodes secrete extracellular vesicles (EVs) and that their cargo has immunomodulatory properties. Here we investigate the effects of IVM and other anti-filarial drugs on parasitic nematode EV secretion, motility, and protein secretion. We show that inhibition of EV secretion was a specific property of IVM, which had consistent and significant inhibitory effects across nematode life stages and species (with the exception of male parasites). IVM inhibited EV secretion, but not parasite motility, at therapeutically relevant concentrations. Protein secretion was inhibited by IVM in the microfilariae stage, but not in any other stage tested. Our data provides evidence that inhibiting the secretion of immunomodulatory EVs by parasitic nematodes could explain, at least in part, IVM mode of action and provides a phenotype for novel drug discovery.
Discordant transcriptional signatures of mitochondrial genes in Parkinson’s disease human myeloid cells
Authors: Navarro Elisa , Udine Evan , de Paiva Lopes Katia , Parks Madison , Riboldi Giulietta , Schilder Brian M. , Humphrey Jack , Snijders Gijsje J. L. , Vialle Ricardo A. , Zhuang Maojuan , Sikder Tamjeed , Argyrou Charalambos , Allan Amanda , Chao Michael , Farrell Kurt , Henderson Brooklyn , Simon Sarah , Raymond Deborah , Elango Sonya , Ortega Roberto A. , Shanker Vicki , Swan Matthew , Zhu Carolyn W. , Ramdhani Ritesh , Walker Ruth H. , Tse Winona , Sano Mary , Pereira Ana C. , Ahfeldt Tim , Goate Alison M. , Bressman Susan , Crary John F. , de Witte Lotje , Frucht Steven , Saunders-Pullman Rachel , Raj Towfique 
Published: July 2020

AbstractAn increasing number of identified Parkinson’s disease (PD) risk loci contain genes highly expressed in innate immune cells, yet their potential role in pathological mechanisms is not obvious. We have generated transcriptomic profiles of CD14+monocytes from 230 individuals with sporadic PD and age-matched healthy subjects. We identified dysregulation of genes involved in mitochondrial and proteasomal function. We also generated transcriptomic profiles of primary microglia from autopsied brains of 55 PD and control subjects and observed discordant transcriptomic signatures of mitochondrial genes in PD monocytes and microglia. We further identified PD susceptibility genes, whose expression, relative to each risk allele, is altered in monocytes. These findings reveal that transcriptomic mitochondrial alterations are detectable in PD monocytes and are distinct from brain microglia, and facilitates efforts to understand the roles of myeloid cells in PD.
Voluntary wheel running improves outcomes in an early life stress-induced model of urologic chronic pelvic pain syndrome in male mice
Authors: Fuentes Isabella M. , Jones Brittni M. , Brake Aaron D. , Pierce Angela N. , Eller Olivia C. , Supple Rachel M. , Wright Douglas E. , Christianson Julie A. 
Published: July 2020

AbstractPatients with a history of early life stress (ELS) exposure have an increased risk of developing chronic pain and mood disorders later in life. The severity of ELS in patients with urologic chronic pelvic pain syndrome (UCPPS) is directly correlated with symptom severity and increased comorbidity, and is inversely related to likelihood of improvement. Voluntary exercise improves chronic pain symptoms and our group and others have shown that voluntary wheel running can improve outcomes in stress-induced UCPPS models, suggesting that exercise may negate some of the outcomes associated with ELS. Here we provide further evidence that voluntary wheel running can attenuate increased perigenital mechanical sensitivity, bladder output, and mast cell degranulation in the bladder and prostate in male mice that underwent neonatal maternal separation (NMS). Sedentary male NMS mice had reduced serum corticosterone, which was not impacted by voluntary wheel running, although stress-related regulatory gene expression in the hypothalamus and hippocampus was significantly increased following exercise. Neurogenesis in the dentate gyrus of the hippocampus was diminished in sedentary NMS mice and significantly increased in both exercised naïve and NMS mice. Sucrose consumption increased in exercised naïve but not NMS mice, and anxiety behaviors measured on an elevated plus maze were increased following exercise. Together these data suggest that voluntary wheel running is sufficient to normalize many of the UCPPS-related outcomes resulting from NMS. Exercise also increased hippocampal neurogenesis and stress-related gene expression within the hypothalamic-pituitary-adrenal axis, further supporting exercise as a non-pharmacological intervention for attenuating outcomes related to ELS exposure.
Dimerization of kringle 1 domain from hepatocyte growth factor/scatter factor provides a potent minimal MET receptor agonist
Authors: de Nola Giovanni , Leclercq Bérénice , Mougel Alexandra , Taront Solenne , Simonneau Claire , Forneris Federico , Adriaenssens Eric , Drobecq Hervé , Iamele Luisa , Dubuquoy Laurent , Melnyk Oleg , Gherardi Ermanno , de Jonge Hugo , Vicogne Jérôme 
Published: July 2020

AbstractHepatocyte Growth Factor/Scatter Factor (HGF/SF) and its cognate receptor MET play several essential roles in embryogenesis and regeneration in post-natal life of epithelial organs such as liver, kidney, lung, and pancreas, prompting a strong interest in harnessing HGF/SF-MET signalling for regeneration of epithelial organs after acute or chronic damage. The limited stability and tissue diffusion of native HGF/SF, however, which reflect the tightly controlled, local mechanism of action of the morphogen, have led to a major search for HGF/SF mimics for therapy. In this work, we describe the rational design, production and characterisation of K1K1, a novel minimal MET agonist consisting of two copies of the kringle 1 domain of HGF/SF placed in tandem. K1K1 is highly stable and displays biological activities equivalent or superior to native HGF/SF in a variety ofin vitroassay systems and in a mouse model of liver disease. These data suggest that this engineered ligand may find wide applications in acute and chronic diseases of the liver and other epithelial organs dependent on MET activation.
Integration of Transcriptome and Small RNA Sequencing to Decipher Molecular Interaction ofChenopodium quinoaVarieties with Cucumber Mosaic Virus
Authors: Soltani Nourolah , Staton Margaret , Gwinn Kimberly D. 
Published: July 2020

AbstractSaponins are secondary metabolites with antiviral properties. Low saponin (sweet) varieties of quinoa (Chenopodium quinoa) have been developed because seeds high in saponins taste bitter. The aim of this study was to elucidate the role of saponin in resistance of quinoa toCucumber mosaic virus(CMV). Differential gene expression was studied in time-series study of CMV infection. High-throughput transcriptome sequence data were obtained from 36 samples (3 varieties × +/- CMV × 1 or 4 days after inoculation × 3 replicates). Translation, lipid, nitrogen, amino acid metabolism, and mono- and sesquiterpenoid biosynthesis genes were upregulated in CMV infections. In ‘Red Head’, (bitter), CMV-induced systemic symptoms were concurrent with downregulation of a key saponin biosynthesis gene, TSARL1, four days after inoculation. In local lesion responses (sweet and semi-sweet), TSARL1 levels remained up-regulated. Known microRNAs (miRNA) (81) from 11 miR families and 876 predicted novel miRNAs were identified. Differentially expressed miRNA and short interfering RNA clusters (24nt) induced by CMV infection are predicted to target genomic and intergenic regions enriched in repetitive elements. This is the first report of integrated RNASeq and sRNASeq data in quinoa-virus interactions and provides comprehensive understanding of involved genes, non-coding regions, and biological pathways in virus resistance.
The hunt for ancient prions: Archaeal prion-like domains form amyloids and substitute for yeast prion domains
Authors: Zajkowski Tomasz , Lee Michael D. , Mondal Shamba S. , Carbajal Amanda , Dec Robert , Brennock Patrick D. , Piast Radoslaw W. , Snyder Jessica E. , Bense Nicholas B. , Dzwolak Wojciech , Jarosz Daniel F. , Rothschild Lynn J. 
Published: July 2020

AbstractPrions are proteins capable of acquiring an alternate conformation that can then induce additional copies to adopt this same alternate conformation. Although initially discovered in relation to mammalian disease, subsequent studies have revealed the presence of prions in Bacteria and Viruses, suggesting an ancient evolutionary origin. Here we explore whether prions exist in Archaea - the last domain of life left unexplored with regard to prions. After searching for potential prion-forming protein sequences computationally, we tested candidatesin vitroand in organisms from the two other domains of life:Escherichia coliandSaccharomyces cerevisiae. Out of the 16 candidate prion-forming domains tested, 8 bound to amyloid-specific dye, and six acted as protein-based elements of information transfer, driving non-Mendelian patterns of inheritance. We additionally identified short peptides from archaeal prion candidates that can form amyloid fibrils independently. Candidates that tested positively in our assays had significantly higher tyrosine and phenylalanine content than candidates that tested negatively, suggesting that the presence of these amino acids may help distinguish functional prion domains from nonfunctional ones. Our data establish the presence of amyloid-forming prion-like domains in Archaea. Their discovery in all three domains of life further suggests the possibility that they were present at the time of the last universal common ancestor (LUCA).Significance StatementThis work establishes that amyloid-forming, prion-like domains exist in Archaea and are capable of vertically transmitting their prion phenotype – allowing them to function as protein-based elements of inheritance. These observations, coupled with prior discoveries in Eukarya and Bacteria, suggest that prion-based self-assembly was likely present in life’s last universal common ancestor (LUCA), and therefore may be one of the most ancient epigenetic mechanisms.
Iterative Epigenomic Analyses in the Same Single Cell
Authors: Ohnuki Hidetaka , Venzon David J. , Lobanov Alexei , Tosato Giovanna 
Published: July 2020

AbstractGene expression in individual cells is epigenetically regulated by DNA modifications, histone modifications, transcription factors and other DNA-binding proteins. It has been shown that multiple histone modifications can predict gene expression and reflect future responses of bulk cells to extracellular cues. However, the predictive ability of epigenomic analysis is still limited for mechanistic research at a single cell level. To overcome this limitation, it is useful to acquire reliable signals from multiple epigenetic marks in the same single cell. Here, we propose a new approach for analysis of several components of the epigenome in the same single cell. The new method allows reanalysis of the same single cell. We found that reanalysis of the same single cell is feasible, and provides confirmation of the signals and allows application of statistical analysis to identify reliable signals using data sets generated only from the single cell. Reanalysis of the same single cell is also useful to acquire multiple-epigenetic marks from the same single cells. The method can acquire at least 4 epigenetic marks, H3K27ac, H3K27me3, mediator complex subunit 1 and a DNA modification. We predicted active signaling pathways in K562 single cells using the data. We confirmed that the prediction results showed a strong correlation with actual active signaling pathways shown by RNA-seq results. These results suggest that the new approach provides mechanistic insights for cellular phenotypes through multi-layered epigenome analysis in the same single cells.
The fiber knob protein of human adenovirus type 49 mediates highly efficient and promiscuous infection of cancer cell lines using a novel cell entry mechanism
Authors: Baker Alexander T. , Marlow Gareth , Davies James A. , Moses Elise , Mundy Rosie M. , Cole David K. , Rizkallah Pierre J. , Parker Alan L. 
Published: July 2020

AbstractThe human adenovirus (HAdV) phylogenetic tree is diverse, divided across seven species and comprising over 100 individual types. Species D HAdV are rarely isolated with low rates of pre-existing immunity, making them appealing for therapeutic applications. Several species D vectors have been developed as vaccines against infectious diseases where they induce robust immunity in pre-clinical models and early phase clinical trials. However, many aspects of the basic virology of species D HAdV, including their basic receptor usage and means of cell entry, remain understudied.Here, we investigated HAdV-D49, which previously has been studied for vaccine and vascular gene transfer applications. We generated a pseudotyped HAdV-C5 presenting the HAdV-D49 fiber knob protein (HAdV-C5/D49K). This pseudotyped vector was efficient at infecting cells devoid of all known HAdV receptors, indicating HAdV-D49 uses an unidentified cellular receptor. Conversely, a pseudotyped vector presenting the fiber knob protein of the closely related HAdV-D30 (HAdV-C5/D30K), differing in four amino acids to HAdV-D49, failed to demonstrate the same tropism. These four amino acid changes resulted in a change in isoelectric point of the knob protein, with HAdV-D49K possessing a basic apical region compared to a more acidic region in HAdV-D30K. Structurally and biologically we demonstrate that HAdV-D49 knob protein is unable to engage CD46, whilst potential interaction with CAR is extremely limited by extension of the DG loop. HAdV-C5/49K efficiently transduced cancer cell lines of pancreatic, breast, lung, oesophageal and ovarian origin, indicating it may have potential for oncolytic virotherapy applications, especially for difficult to transduce tumour types.ImportanceAdenoviruses are powerful tools experimentally and clinically. To maximise efficacy, the development of serotypes with low pre-existing levels of immunity in the population is desirable. Consequently, attention has focussed on those derived from species D, which have proven robust vaccine platforms. This widespread usage is despite limited knowledge in their basic biology and cellular tropism.We investigated the tropism of HAdV-D49, demonstrating it uses a novel cell entry mechanism that bypasses all known HAdV receptors. We demonstrate, biologically, that a pseudotyped HAdV-C5/D49K vector efficiently transduces a wide range of cell lines, including those presenting no known adenovirus receptor. Structural investigation suggests that this broad tropism is the result of a highly basic electrostatic surface potential, since a homologous pseudotyped vector with a more acidic surface potential, HAdV-C5/D30K, does not display a similar pan-tropism. Therefore, HAdV-C5/D49K may form a powerful vector for therapeutic applications capable of infecting difficult to transduce cells.
Identification of novel mutations contributing to azole tolerance ofAspergillus fumigatus throughin vitroexposure to tebuconazole
Authors: Toyotome Takahito , Onishi Kenji , Sato Mio , Kusuya Yoko , Hagiwara Daisuke , Watanabe Akira , Takahashi Hiroki 
Published: July 2020

AbstractAzole resistance ofAspergillus fumigatusis a global problem. The major resistant mechanism is acyp51Aalteration such as mutation(s) in the gene and the acquisition of a tandem repeat in the promoter. Although other azole tolerances and resistant mechanisms such ashmg1mutation are known, few reports describe studies elucidating non-cyp51Aresistance mechanisms. This study explored genes contributing to azole tolerance inA. fumigatusbyin vitromutant selection with tebuconazole, an azole fungicide. After three-round selection, we obtained four isolates with low susceptibility to tebuconazole. These isolates also showed low susceptibility to itraconazole and voriconazole. Comparison of the genome sequences of the obtained isolates and the parental strain revealed a non-synonymous mutation in MfsD (Afu1g11820, R337L mutation) in all isolates. Furthermore, non-synonymous mutations in AgcA (Afu7g05220, E535Stop mutation), UbcD (Afu3g06030, T98K mutation), AbcJ (Afu3g12220, G297E mutation), and RttA (Afu7g04740, A83T mutation), a protein responsible for tebuconazole tolerance, were found in at least one isolate. Clarification by constructing the MfsD R337L mutant suggests that the mutation contributes to azole tolerance. Disruption of theagcAgene and reconstruction of the A83T point mutation in RttA led to decreased susceptibility to azoles. The reversion of T98K mutation to wild type in UbcD led to the level of azole susceptibility comparable to the parental strain. These results suggest that these mutations contribute to lowered susceptibility to medical azoles and to agricultural azole fungicides.
How does childhood maltreatment influence cardiovascular disease? A sequential causal mediation analysis
Authors: Soares Ana G , Howe Laura D , Heron Jon , Hammerton Gemma , Rich-Edwards Janet , Magnus Maria C , Halligan Sarah L , Fraser Abigail 
Published: July 2020

ABSTRACTBackgroundChildhood maltreatment has been consistently associated with cardiovascular disease (CVD). However, the mechanisms of this relationship are not yet fully understood. We explored the relative contribution of anxiety/depression, smoking, body mass index (BMI) and inflammation (C-reactive protein, CRP) to the association between childhood maltreatment and CVD in men and women aged 40-69 years in the United Kingdom (UK).MethodsWe used data from 40,596 men and 59,511 women from UK Biobank. To estimate the indirect effects of childhood maltreatment (physical, sexual and emotional abuse, and emotional and physical neglect) on incident CVD via each of the mediators, we applied a sequential mediation approach.ResultsAll forms of maltreatment were associated with increased CVD risk (hazard ratios (HR) ranging from 1.09 to 1.27). Together anxiety/depression, smoking, BMI and CRP mediated 26%-90% of the association between childhood maltreatment and CVD, and the contribution of these mediators differed by type of maltreatment and sex. Anxiety/depression mediated the largest proportion of the association of sexual abuse, emotional abuse and emotional neglect with CVD (accounting for 16%-43% of the total effect), especially in women. In men, BMI contributed the most to the indirect effect of associations of physical abuse and physical neglect with CVD; in women anxiety/depression and BMI had similar contributions.ConclusionsThese findings add to the understanding of how childhood maltreatment affects CVD risk and identify modifiable mediating factors which could potentially reduce the burden of CVD in people exposed to maltreatment in early life.
In-silico modeling of COVID-19 ARDS: pathophysiological insights and potential management implications
Authors: Das Anup , Saffaran Sina , Chikhani Marc , Scott Timothy E , Laviola Marianna , Yehya Nadir , Laffey John G. , Hardman Jonathan G. , Bates Declan G. 
Published: July 2020

AbstractObjectivesPatients with COVID-19 Acute Respiratory Distress Syndrome (CARDS) appear to present with at least two distinct phenotypes: severe hypoxemia with relatively well-preserved lung compliance and lung gas volumes (Type 1) and a more conventional ARDS phenotype displaying the typical characteristics of the ‘baby lung’ (Type 2). We aimed to test plausible hypotheses regarding the pathophysiological mechanisms underlying CARDS, and to evaluate the resulting implications for ventilatory management.DesignWe adapted a high-fidelity computational simulator, previously validated in several studies of ARDS, to (a) develop quantitative insights into the key pathophysiologic differences between CARDS and conventional ARDS, and (b) assess the impact of different PEEP, FiO2 and tidal volume settings.SettingInterdisciplinary Collaboration in Systems Medicine Research Network.SubjectsThe simulator was calibrated to represent CARDS patients with both normal and elevated body mass indices undergoing invasive mechanical ventilation.Measurements and Main ResultsAn ARDS model implementing disruption of hypoxic pulmonary vasoconstriction and vasodilation leading to hyperperfusion of collapsed lung regions failed to replicate clinical data on Type 1 CARDS patients. Adding mechanisms to reflect disruption of alveolar gas-exchange due to the effects of pneumonitis, and heightened vascular resistance due to the emergence of microthrombi, produced levels of V/Q mismatch and hypoxemia consistent with data from Type 1 CARDS patients, while preserving close to normal lung compliance and gas volumes. Atypical responses to PEEP increments between 5 and 15 cmH2O were observed for this Type 1 CARDS model across a range of measures: increasing PEEP resulted in reduced lung compliance and no improvement in oxygenation, while Mechanical Power, Driving Pressure and Plateau Pressure all increased. FiO2 settings based on ARDSnet protocols at different PEEP levels were insufficient to achieve adequate oxygenation. Incrementing tidal volumes from 5 to 10 ml/kg produced similar increases in multiple indicators of ventilator induced lung injury in the Type 1 CARDS model to those seen in a conventional ARDS model.ConclusionsOur model suggests that use of standard PEEP/ FiO2 tables, higher PEEP strategies, and higher tidal volumes, may all be potentially deleterious in Type 1 CARDS patients, and that a highly personalized approach to treatment is advisable.