bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phylogenetic Analysis of SARS-CoV-2 Genomes in Turkey
Authors: Adebalı Ogün , Bırcan Aylin , Çırcı Defne , İşlek Burak , Kilinç Zeynep , Selçuk Berkay , Turhan Berk 
Published: May 2020

AbstractCOVID-19 has effectively spread worldwide. As of May 2020, Turkey is among the top ten countries with the most cases. A comprehensive genomic characterization of the virus isolates in Turkey is yet to be carried out. Here, we built a phylogenetic tree with globally obtained 15,277 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genomes. We identified the subtypes based on the phylogenetic clustering in comparison with the previously annotated classifications. We performed a phylogenetic analysis of the first thirty SARS-CoV-2 genomes isolated and sequenced in Turkey. We suggest that the first introduction of the virus to the country is earlier than the first reported case of infection. Virus genomes isolated from Turkey are dispersed among most types in the phylogenetic tree. We find two of the seventeen sub-clusters enriched with the isolates of Turkey, which likely have spread expansively in the country. Finally, we traced virus genomes based on their phylogenetic placements. This analysis suggested multiple independent international introductions of the virus and revealed a hub for the inland transmission. We released a web application to track the global and interprovincial virus spread of the isolates from Turkey in comparison to thousands of genomes worldwide.
Interplay of folded domains and the disordered low-complexity domain in mediating hnRNPA1 phase separation
Authors: Martin Erik W. , Thomasen F. Emil , Milkovic Nicole M. , Cuneo Matthew J. , Grace Christy R. , Nourse Amanda , Lindorff-Larsen Kresten , Mittag Tanja 
Published: May 2020

AbstractLiquid-liquid phase separation underlies the membrane-less compartmentalization of cells. Intrinsically disordered low-complexity domains (LCDs) often mediate phase separation, but how their phase behavior is modulated by folded domains is incompletely understood. Here, we interrogate the interplay between folded and disordered domains of the RNA-binding protein hnRNPA1. The LCD of hnRNPA1 is sufficient for mediating phase separationin vitro. However, we show that the folded RRM domains and a folded solubility-tag modify the phase behavior, even in the absence of RNA. Notably, the presence of the folded domains reverses the salt dependence of the driving force for phase separation relative to the LCD alone. Small-angle X-ray scattering experiments and coarse-grained MD simulations show that the LCD interacts transiently with the RRMs and/or the solubility-tag in a salt-sensitive manner, providing a mechanistic explanation for the observed salt-dependent phase separation. These data point to two effects from the folded domains: (1) electrostatically mediated interactions that compact hnRNPA1 and contribute to phase separation, and (2) increased solubility at higher ionic strengths mediated by the folded domains. The interplay between disordered and folded domains can modify the dependence of phase behavior on solution conditions and can obscure signatures of physicochemical interactions underlying phase separation.Graphical abstracthnRNPA1 phase separation is highly salt sensitive.Phase separation of the low-complexity domain (LCD) of hnRNPA1 increases with NaCl. In contrast, phase separation of full-length hnRNPA1 is saltsensitive. At low NaCl concentrations, electrostatic RRM-LCD interactions occur and can contribute positively to phase separation, but they are screened at high NaCl concentrations. The folded domains solubilize hnRNPA1 under these conditions and prevent phase separation.
TOR signaling modulates Cdk8-dependentGALgene expression inSaccharomyces cerevisiae
Authors: Hawe Nicole , Mestnikov Konstantin , Horvath Riley , Eji-Lasisi Mariam , Lam Cindy , Rohde John , Sadowski Ivan 
Published: May 2020

AbstractCdk8 of the RNA Polymerase II mediator complex regulates genes by phosphorylating sequence specific transcription factors. Despite conserved importance for eukaryotic transcriptional regulation, the signals regulating Cdk8 are unknown. Full induction of the yeastGALgenes requires phosphorylation of Gal4 by Cdk8, and we exploited this requirement for growth ofgal3yeast on galactose to identify mutants affecting Cdk8 activity. Several mutants from the screen produced defects in TOR signaling. A mutant designatedgalfour throttle (gft) 1,gft1, was identified as an allele ofhom3, encoding aspartokinase. Defects ingft1/hom3caused hypersensitivity to rapamycin, and constitutive nuclear localization of Gat1. Furthermore, mutations oftor1ortco89, encoding TORC1 components, also preventedGALexpression ingal3yeast, andtco89was determined to be allelic togft7. Disruption ofcdc55, encoding a subunit of PP2A regulated by TOR signaling, suppressed the effect ofgft1/hom3, gft7/tco89, andtor1mutations onGALexpression ingal3yeast, but not ofcdk8/srb10disruptions or Gal4 S699A mutation. Mutations ofgft1/hom3andtor1did not affect kinase activity of Cdk8in vitro, but caused loss of Gal4 phosphorylationin vivo. These observations demonstrate that TOR signaling regulatesGALinduction through the activity of PP2A/ Cdc55, and are consistent with the contention that Cdk8-dependent phosphorylation of Gal4 S699 is opposed by PP2A/ Cdc55 dephosphorylation. These results provide insight into how induction of transcription by a specific inducer can be modulated by global nutritional signals through regulation of Cdk8-dependent phosphorylation.
Direct and indirect effects of maternal, paternal, and offspring genotypes: Trio-GCTA
Authors: Eilertsen Espen Moen , Jami Eshim Shahid , McAdams Tom A. , Hannigan Laurie J. , Havdahl Alexandra S. , Magnus Per Minor , Evans David M. , Ystrom Eivind 
Published: May 2020

AbstractIndirect genetic effects from relatives may result in misleading quantifications of heritability, but can also be of interest in their own right. In this paper we propose Trio-GCTA, a model for separating direct and indirect genetic effects when genome-wide single nucleotide polymorphism data have been collected from parent-offspring trios. The model is applicable to phenotypes obtained from any of the family members. We discuss appropriate parameter interpretations and apply the method to four exemplar phenotypes; offspring birth weight, offspring temperament, maternal relationship satisfaction, and paternal body-mass index, using real data from the Norwegian Mother, Father and Child Cohort Study (MoBa).
The Receptor Kinase BRI1 promotes cell proliferation in Arabidopsis by phosphorylation- mediated inhibition of the growth repressing peptidase DA1
Authors: Dong Hui , Smith Caroline , Prior Rachel , Carter Ross , Dumenil Jack , Saalbach Gerhard , McKenzie Neil , Bevan Michael 
Published: May 2020

SummaryBrassinosteroids (BR) have centrally important functions in plant growth by promoting cell proliferation and cell expansion through phosphorylation-mediated regulatory cascades that are initiated by perception of BR by receptor-like kinases of the BRI1 family. These BR-mediated growth responses have been explained by transcriptional controls mediated by phosphorylation of BES1/BZR1 transcription factors. Here we link BRI1-mediated phosphorylation to another growth regulatory network that directly mediates protein stability. BRI1 and its co-receptor BAK1 phosphorylate and inhibit the activities of the growth repressor DA1 by promoting the formation of high molecular weight complexes. Phospho-mimic forms of DA1 are less active while phospho-dead mutants have increased growth-repressive activity, while their regulatory monoubiquitylation is unaffected. BR inhibition of DA1 activity maintains higher levels of DA1 substrates such as UBP15 that sustain the potential for cell proliferation during leaf growth. Reduced BR levels lead to activation of DA1 peptidase activity and a transition from cell proliferation to cell growth and differentiation. This dual monoubiquitylation-phosphorylation regulation supports the key role of BR levels in maintaining the proliferative potential of cells during organ growth.
Dengue and Zika virus infection are impaired by small molecule ER proteostasis regulator 147 in an ATF6-independent manner
Authors: Almasy Katherine M. , Davies Jonathan P. , Lisy Samantha M. , Tirgar Reyhaneh , Tran Sirena C. , Plate Lars 
Published: May 2020

ABSTRACTFlaviviruses, including Dengue and Zika, are widespread human pathogens, however, no broadly active therapeutics exist to fight infection. Here, we establish the recently discovered pharmacologic modulator of ER proteostasis147as an effective host-centered antiviral strategy. Compound147reduces infection by attenuating viral replication without causing toxicity in host cells.147is a preferential activator of the ATF6 pathway of the unfolded protein response, which requires targeting of cysteine residues primarily on protein disulfide isomerases (PDIs). We find that the antiviral activity of147is independent of ATF6 induction but does require modification of reactive thiols on protein targets. Targeting PDIs using RNAi and other PDI small molecule inhibitors was unable to recapitulate the antiviral effects, suggesting additional identified protein targets of147may mediate the activity. Importantly,147can impair infection of multiple strains of Dengue and Zika virus, indicating that it is suitable as a broad-spectrum antiviral agent.
Shifting carbon flux from non-transient starch to lipid allows oil accumulation in transgenic tobacco leaves
Authors: Chu Kevin L. , Jenkins Lauren M. , Bailey Sally R. , Kambhampati Shrikaar , Koley Somnath , Foley Kevin , Arp Jennifer J. , Czymmek Kirk J. , Bates Philip D. , Allen Doug K. 
Published: May 2020

AbstractPlant leaf biomass is composed predominantly of carbohydrate and protein with less than 5% dry weight allocated to lipid and less than 1% of total lipid in the form of triacylglycerols (TAGs). The combined overexpression of multiple genes involved in different aspects of TAG synthesis and stabilization can result in TAG accumulation to over 30% dry weight in tobacco leaves, presumably requiring many metabolic adjustments within plant cells. The metabolic consequences to the combined source and sink capacities of high oil accumulating transgenic tobacco leaves compared to wild-type were inspected across development and photoperiod by utilizing foliar biomass components and13CO2flux through central carbon intermediates. Lipid biosynthesis was investigated through assessment of acyl-acyl carrier protein (ACP) pools using a recently derived quantification method that was extended to accommodate isotopic labeling. Lipids accumulated stepwise over plant development in the high-oil leaves, with13CO2-labeling studies confirming increased carbon flux to lipids. The large increase in lipid content was concurrent with a decrease in foliar starch, with limited contribution from non-sucrose soluble sugars, indicating a redirection of carbon from starch to lipids. Starch accumulated non-transiently with plant age in wild-type leaves, suggesting an inherent capacity for a developmentally-regulated carbon sink in tobacco leaves that may have enabled the programmed altered carbon partitioning to lipids in transgenics. These studies provide insight into the metabolic plasticity of dual source-sink leaves over development and may in part explain recent successful leaf lipid engineering efforts in tobacco.One sentence summaryEngineering high oil accumulation in tobacco leaves is enabled by inherent source-sink plasticity associated with non-transient foliar starch accumulation over development.
Chitosan inhibits septin-mediated plant infection by the rice blast fungusMagnaporthe oryzaein a Protein Kinase C and Nox1 NADPH oxidase-dependent manner
Authors: Lopez-Moya Federico , Martin-Urdiroz Magdalena , Oses-Ruiz Miriam , Fricker Mark D. , Littlejohn George R. , Lopez-Llorca Luis V. , Talbot Nicholas J. 
Published: May 2020

SummaryChitosan is a partially deacetylated linear polysaccharide composed of β-1,4-linked units of D-glucosamine and N-acetyl glucosamine. As well as acting as a structural component of fungal cell walls, chitosan can be applied as a potent antifungal agent. However, the mode-of-action of chitosan in fungal pathogens is poorly understood.Here, we report that chitosan is effective for control of rice blast disease. Chitosan application impairs growth of the blast fungusMagnaporthe oryzaeand has a pronounced effect on appressorium-mediated plant infection. Chitosan inhibits septin-mediated F-actin re-modelling at the appressorium pore, thereby preventing re-polarisation of the infection cell and rice leaf cuticle penetration.We found that chitosan causes plasma membrane permeabilization ofM. oryzaeand affects NADPH oxidase-dependent synthesis of reactive oxygen species, essential for septin ring formation and fungal pathogenicity. Our data further show that the toxicity of chitosan toM. oryzaerequires the protein kinase C-dependent cell wall integrity pathway and the Nox1 NADPH oxidase. A conditionally lethal, analogue (PP1)-sensitive mutant of Pkc1 is partially remediated for growth in the presence of chitosan and PP1, while Δnox1mutants increase their glucan/chitin cell wall ratio, rendering them resistant to chitosan.Taken together, our data show that chitosan is a potent fungicide for control of the rice blast fungus which involves the cell wall integrity pathway, disrupts plasma membrane and inhibits septin-mediated plant infection.
Structure and Dynamic Basis of Molecular Recognition Between Acyltransferase and Carrier Protein inE. coliFatty Acid Synthesis
Authors: Misson Laetitia E. , Mindrebo Jeffrey T. , Davis Tony D. , Patel Ashay , McCammon J. Andrew , Noel Joseph P. , Burkart Michael D. 
Published: May 2020

AbstractFatty acid synthases (FASs) and polyketide synthases (PKSs) iteratively elongate and often reduce two-carbon ketide units inde novofatty acid and polyketide biosynthesis. Cycles of chain extensions in FAS and PKS are initiated by an acyltransferase (AT), which loads monomer units onto acyl carrier proteins (ACPs), small, flexible proteins that shuttle covalently linked intermediates between catalytic partners. Formation of productive ACP-AT interactions is required for catalysis and specificity within primary and secondary FAS and PKS pathways. Here, we use theEscherichia coliFAS AT, FabD, and its cognate ACP, AcpP, to interrogate type II FAS ACP-AT interactions. We utilize a covalent crosslinking probe to trap transient interactions between AcpP and FabD to elucidate the first x-ray crystal structure of a type II ACP-AT complex. Our structural data are supported using a combination of mutational, crosslinking, and kinetic analyses, and long timescale molecular dynamics (MD) simulations. Together, these complementary approaches reveal key catalytic features of FAS ACP-AT interactions. These mechanistic inferences suggest that AcpP adopts multiple, productive conformations at the AT binding interface, allowing the complex to sustain high transacylation rates. Furthermore, MD simulations support rigid body subdomain motions within the FabD structure that may play a key role in AT activity and substrate selectivity.Significance StatementThe essential role of acyltransferases (ATs) in fatty acid synthase (FAS) and polyketide synthase (PKS) pathways, namely the selection and loading of starter and extender units onto acyl carrier proteins (ACPs), relies on catalytically productive ACP-AT interactions. Here, we describe and interrogate the first structure of a type II FAS malonyl-CoA:ACP-transacylase (MAT) in covalent complex with its cognate ACP. We combine structural, mutational, crosslinking and kinetic data with molecular dynamics simulations to describe a highly flexible and robust protein-protein interface, substrate-induced active site reorganization, and key subdomain motions that likely govern FAS function. These findings strengthen a mechanistic understanding of molecular recognitions between ACPs and partner enzymes and provide new insights for engineering AT-dependent biosynthetic pathways.
Effects of Different Strategies for Exploiting Genomic Selection in Perennial Ryegrass Breeding Programs
Authors: Esfandyari Hadi , Fè Dario , Tessema Biructawit Bekele , Janss Lucas L. , Jensen Just 
Published: May 2020

AbstractGenomic selection (GS) is a potential pathway to accelerate genetic gain for perennial ryegrass(Lolium perenneL.). The main objectives of the present study were to investigate the level of genetic gain and accuracy by applying GS in commercial perennial ryegrass breeding programs. Different scenarios were compared to a conventional breeding program. Simulated scenarios differed in the method of selection and structure of the breeding program. Two scenarios (Phen-Y12 and Phen) for phenotypic selection and three scenarios (GS-Y12, GS and GS-SP) were considered for genomic breeding schemes. All breeding schemes were simulated for 25 cycles. The amount of genetic gain achieved was different across scenarios. Compared to phenotypic scenarios, GS scenarios resulted in a significantly larger genetic gain for the simulated traits. This was mainly due to more efficient selection of plots and single plants based on GEBV. Also, GS allows for reduction in cycle time, which led to at least a doubling or a trebling of genetic gain compared to the traditional program. Reduction in additive genetic variance levels were higher with GS scenarios than with phenotypic selection. The results demonstrated that implementation of GS in ryegrass breeding is possible and presents an opportunity to make very significant improvements in genetic gains.
The role of incoherent feedforward circuits in regulating precision of event timing
Authors: Dey Supravat , Kannoly Sherin , Bokes Pavol , Dennehy John J , Singh Abhyudai 
Published: May 2020

AbstractTriggering of cellular events often relies on the level of a key gene product crossing a critical threshold. Achieving precision in event timing in spite of noisy gene expression facilitates high-fidelity functioning of diverse processes from biomolecular clocks, apoptosis and cellular differentiation. Here we investigate the role of an incoherent feedforward circuit in regulating the time taken by a bacterial virus (bacteriophage lambda) to lyse an infectedEscherichia colicell. Lysis timing is the result of expression and accumulation of a single lambda protein (holin) in theE. colicell membrane up to a critical threshold level, which triggers the formation of membrane lesions. This easily visualized process provides a simple model system for characterizing event-timing stochasticity in single cells. Intriguingly, lambda’s lytic pathway synthesizes two functionally opposite proteins: holin and antiholin from the same mRNA in a 2:1 ratio. Antiholin sequesters holin and inhibits the formation of lethal membrane lesions, thus creating an incoherent feedforward circuit. We develop and analyze a stochastic model for this feedforward circuit that considers correlated bursty expression of holin/antiholin, and their concentrations are diluted from cellular growth. Interestingly, our analysis shows the noise in timing is minimized when both proteins are expressed at an optimal ratio, hence revealing an important regulatory role for antiholin. These results are in agreement with single cell data, where removal of antiholin results in enhanced stochasticity in lysis timing.
Ramifications of the diverse mRNA patterns inAcanthamoeba royreba
Authors: Tyndall Richard , Ali Ibne , Newsome Anthony 
Published: May 2020

AbstractFree-living amoebae are distributed worldwide and can be found in a variety of environments. While most Acanthamoebae have been isolated from soil and water,A. royrebaandA. culbertsoniwere isolated from mammalian cell cultures.A. royreba’sisolation from placental and tumoral tissue, its unusual ability to grow in mammalian cell culture media at 35°C, and the presence of a primitive centriole, prompted us to investigate the potential for mammalian information inA. royreba.While some soil amoeba contain small amounts of fungal and bacterial information, presumably from the microbes they phagocytosed, the informational content ofA. royreba,in some instances, was very different with > 70% of the mRNA being non-amoebic. Here we show that the proteins and mRNA content associated withA. royrebaare extremely diverse and represent multiple Kingdoms, Orders, Phyla, and Genera from around the globe. The information inA. royreba,such as placental proteins from numerous mammals, the preponderance of non-amoebic mRNA, and its ability to tolerate harsh environments including Megarad irradiation, leads to a discussion regarding the possible role of this amoebae as an immunological gatekeeper protecting fetal or malignant tissue from destruction and its potential as a vehicle for panspermia.
Suppression of liquid-liquid phase separation by 1,6-hexanediol partially compromises the 3D genome organization in living cells
Authors: Ulianov Sergey V. , Velichko Artem K. , Magnitov Mikhail D. , Luzhin Artem V. , Golov Arkadiy K. , Ovsyannikova Natalia , Kireev Igor I. , Tyakht Alexander V. , Gavrilov Alexey A. , Kantidze Omar L. , Razin Sergey V. 
Published: May 2020

AbstractLiquid-liquid phase separation (LLPS) contributes to the spatial and functional segregation of molecular processes. However, the role played by LLPS in chromatin folding in living cells remains unclear. Here, using stochastic optical reconstruction microscopy (STORM) and Hi-C techniques, we studied the effects of 1,6-hexanediol (1,6-HD)-mediated LLPS modulation on higher-order chromatin organization in living cells. We found that 1,6-HD treatment caused the enlargement of nucleosome nanodomains and their more uniform distribution in the nuclear space. At a megabase-scale, chromatin underwent moderate but irreversible perturbations that resulted in the partial mixing of A and B compartments. The removal of 1,6-HD from the culture medium did not allow chromatin to acquire initial configurations, but increased further mixing of the chromatin compartments and resulted in more compact repressed chromatin than in untreated cells. 1,6-HD treatment also weakened enhancer-promoter interactions but did not considerably affect CTCF-dependent loops. Our results suggest that 1,6-HD-sensitive LLPS plays a limited role in chromatin spatial organization by constraining its folding patterns and facilitating compartmentalization at different levels.
Repurposing of Miglustat to inhibit the coronavirus Severe Acquired Respiratory Syndrome SARS-CoV-2
Authors: Rajasekharan Sreejith , Bonotto Rafaela Milan , Kazungu Yvette , Alves Lais Nascimento , Poggianella Monica , Orellana Pamela Martinez , Skoko Natasa , Polez Sulena , Marcello Alessandro 
Published: May 2020

AbstractRepurposing clinically available drugs to treat the new coronavirus disease COVID-19 is an urgent need in these early stages of the SARS-CoV-2 pandemic, when very few treatment options are available. The iminosugar Miglustat is a well-characterized drug for the treatment of rare genetic lysosome storage diseases such as Gaucher and Niemann-Pick type C, and has also been described to be active against a variety of enveloped viruses. The activity of Miglustat is here demonstrated for SARS-CoV-2 at concentrations achievable in the plasma by current clinical regimens without cytotoxicity. The drug acts at the post-entry level and leads to a marked decrease of viral proteins and release of infectious virus. The mechanism resides in the inhibitory activity towards α-glucosidases that are involved in early stages of glycoprotein N-linked oligosaccharide processing in the endoplasmic reticulum, leading to a marked decrease of the viral Spike protein. The wealth of available data on the clinical use of Miglustat for the treatment of lysosomal storage disorders and the antiviral properties against SARS-CoV-2 make it an ideal candidate for drug repurposing.