bluuebunny/crossref_metadata_2025_split huggingface dataset:
A transcriptional activator effector ofUstilago maydisregulates hyperplasia in maize during pathogen-induced tumor formation
Authors: Zuo Weiliang , Depotter Jasper R. L. , Stolze Sara Christina , Nakagami Hirofumi , Doehlemann Gunther 
Published: March 2023

AbstractUstilago maydiscauses common smut in maize, which is characterized by tumor formation in aerial parts of the host. Tumors result from thede novocell division of highly developed bundle sheath and subsequent cell enlargement. However, the molecular mechanisms underlying tumorigenesis are still largely unknown. Here, we characterize theU. maydiseffector Sts2 (Smalltumor onseedlings 2), which promotes the division of hyperplasia tumor cells. Upon infection, Sts2 is translocated into the maize cell nucleus, where it acts as a transcriptional activator, and the transactivation activity is crucial for its virulence function. Sts2 interacts with ZmNECAP1, a yet undescribed plant transcriptional activator, and it activates the expression of several leaf developmental regulators to potentiate tumor formation. Contrary, fusion of a suppressive SRDX-motif to Sts2 causes dominant negative inhibition of tumor formation, underpinning the central role of Sts2 for tumorigenesis. Our results not only disclose the virulence mechanism of a tumorigenic effector, but also reveal the essential role of leaf developmental regulators in pathogen-induced tumor formation.
Myosin VIII and XI isoforms interact withAgrobacteriumVirE2 protein and help direct transport from the plasma membrane to the perinuclear region during plant transformation
Authors: Liu Nana , Lee Lan-Ying , Yu Yanjun , Gelvin Stanton B. 
Published: March 2023

ABSTRACTVirulentAgrobacteriumstrains transfer single-strand T-DNA (T-strands) and virulence effector proteins into plant cells. VirE2, one of these virulence effectors, enters the plant cell and is thought to bind T-strands, protecting them from nuclease degradation and helping guide them to the nucleus. How VirE2 is trafficked inside the plant cell is not fully understood. Using bimolecular fluorescence complementation,in vitropull-down, yeast two-hybrid, andin vivoco-immunoprecipitation assays, we found that VirE2 binds directly to the cargo binding domains of several myosin VIII family members, and to myosin XI-K. We observed reduced susceptibility of severalArabidopsisactin mutants and a myosinVIII-1/2/a/bquadruple mutant toAgrobacterium-mediated transformation. Expression of cargo binding domains of myosin VIII-1, VIII-2, VIII-A, or VIII-B in transgenic plants inhibitsArabidopsisroot transformation. However, none of the myosin VIII proteins contribute to the intracellular trafficking of VirE2. Expression of myosinVIII-2,-A,-B, but notVIII-1, cDNAs in the myosinVIII-1/2/a/bmutant partially restored transformation. Furthermore, functional fluorescently-tagged VirE2, synthesized in plant cells, relocalized from the cellular periphery into the cytoplasm after delivery of T-strands fromAgrobacterium. Surprisingly, mutation of myosinXI-kand expression of the myosin XI-K cargo binding domain had no effect on transformation, although it blocked VirE2 movement along actin filaments. We hypothesize that myosin VIII proteins facilitate VirE2 tethering to the plasma membrane and are required for efficient localization of VirE2 to membrane sites from which they bind incoming T-strands. Myosin XI-K is important for VirE2 movement through the cytoplasm towards the nucleus.
A rapid method to quantify vein density in C4plants using starch staining
Authors: Simpson Conor J. C. , Singh Pallavi , Sogbohossou Deedi E.O. , Schranz M. Eric , Hibberd Julian M. 
Published: March 2023

AbstractC4photosynthesis has evolved multiple times in the angiosperms and typically involves alterations to the biochemistry, cell biology and development of leaves. One common modification found in C4plants compared with the ancestral C3state is an increase in vein density such that the leaf contains a larger proportion of bundle sheath cells. Recent findings indicate that there may be significant intra-specific variation in traits such as vein density in C4plants but to use such natural variation for trait-mapping, rapid phenotyping would be required. Here we report a high-throughput method to quantify vein density that leverages the bundle sheath specific accumulation of starch found in C4species. Starch staining allowed high-contrast images to be acquired that permitted image analysis using a MATLAB-based program. The method works for the dicotyledonGynandropsis gynandrawhere significant variation in vein density was detected between natural accessions, and the monocotyledonZea mayswhere no variation was apparent in the genotypically diverse lines assessed. We anticipate this approach will be useful to map genes controlling vein density in C4species demonstrating natural variation for this trait.One sentence summaryPreferential accumulation of starch in bundle sheath cells of C4plants allows high-throughput phenotyping of vein density.
Knockout of endoplasmic reticulum localized molecular chaperone HSP90.7 impairs seeding development and cellular auxin homeostasis in Arabidopsis
Authors: Noureddine Jenan , Mu Bona , Hamidzada Homaira , Mok Wai Lam , Bonea Diana , Nambara Eiji , Zhao Rongmin 
Published: March 2023

SUMMARYThe Arabidopsis endoplasmic reticulum localized heat shock protein HSP90.7 modulates tissue differentiation and stress responses; however, complete knockout lines have not been previously reported. In this study, we identified and analyzed a mutant allele,hsp90.7-1, which did not express any protein and showed seedling lethality. Microscopic analyses revealed its essential role in male and female fertility, trichomes and root hairs development, proper chloroplast function, and in apical meristem maintenance and differentiation. Comparative transcriptome and proteome analyses also revealed a role of the protein in a multitude of cellular processes. Particularly, the auxin responsive pathway was specifically down-regulated in thehsp90.7-1mutant seedlings. We measured a much-reduced auxin content in both root and shoot tissues. Through comprehensive histological and molecular analyses, we demonstrated PIN1 and PIN5 expressions were dramatically reduced in the mutant, and the TAA-YUCCA primary auxin biosynthesis pathway was also down-regulated, thus revealing a critical new role of HSP90.7 in the regulation of auxin responses. This study therefore not only fulfilled a gap in understanding the essential role of HSP90 paralogs in eukaryotes, but also provided a mechanistic insight on this molecular chaperone in regulating plant growth and development via modulating cellular auxin homeostasis.
Comparative transcriptomics reveals divergence in pathogen response gene families amongst 20 forest tree species
Authors: Lu Mengmeng , Cao Min , Yang Jie , Swenson Nathan G. 
Published: March 2023

AbstractForest trees provide critical ecosystem services for humanity that are under threat due to ongoing global change. Measuring and characterizing genetic diversity is key to understanding adaptive potential and developing strategies to mitigate negative consequences arising from climate change. In the area of forest genetic diversity, genetic divergence caused by large-scale changes at the chromosomal level has been largely understudied. In this study, we used the RNA-seq data of twenty co-occurring forest trees species from genera includingAcer,Alnus,Amelanchier,Betula,Cornus,Corylus,Dirca,Fraxinus,Ostrya,Populus,Prunus,Quercus,Ribes,Tilia, andUlmussampled from Upper Peninsula of Michigan. These data were used to infer the origin and maintenance of gene family variation, species divergence time, as well as gene family expansion and contraction. We identified a signal of common whole genome duplication events shared by core eudicots. We also found rapid evolution, namely fast expansion or fast contraction of gene families, in plant-pathogen interaction genes amongst the studied diploid species. Finally, the results lay the foundation for further research on the genetic diversity and adaptive capacity of forest trees, which will inform forest management and conservation policies.
Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem
Authors: Coclet Clement , Sorensen Patrick O. , Karaoz Ulas , Wang Shi , Brodie Eoin L. , Eloe-Fadrosh Emiley A. , Roux Simon 
Published: March 2023

ABSTRACTViruses, including phages, impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time, and their response to strong seasonal change in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental DNA and RNA viruses, including phages, across dynamics seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes. We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of RNA viruses target fungal hosts and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active phages which changed across seasons, consistent with a “seed-bank” viral community structure in which new phage activity, for example replication and host lysis, is sequentially triggered by changes in environmental conditions. Zooming in at the population level, we further identified virus-host dynamics matching two existing ecological models: “Kill-The-Winner” which proposes that lytic phages are actively infecting abundant bacteria, and “Piggyback-The-Persistent” which argues that when the host is growing slowly it is more beneficial to remain in a lysogenic state. The former was associated with summer months of high and rapid microbial activity, and the latter to winter months of limited and slow host growth. Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. Moving forward, while as our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry.
Leaf traits predict performance under varying levels of drought stress in cultivated sunflower (Helianthus annuusL.)
Authors: Earley Ashley M. , Nolting Kristen M. , Burke John M. 
Published: March 2023

ABSTRACTDrought is a major agricultural challenge and is expected to worsen with climate change. Exploring plant traits and how they respond to drought has the potential to improve understanding of drought tolerance and inform breeding efforts to develop more drought tolerant plants. Given their importance in plant-water relations, we explored variation and plasticity in leaf traits in response to water limitation in cultivated sunflower (Helianthus annuusL.). A set of four sunflower genotypes was grown under four different levels of water availability and leaf vein and stomatal traits were measured along with total biomass (as an indicator of performance), leaf mass per area (LMA), chlorophyll content, and various mass fraction traits related to resource allocation (e.g., leaf, root, and stem mass fraction). Traits exhibited numerous bivariate correlations within treatments that generally followed expectations based on the literature. For example, stomatal size and density were negatively correlated while stomatal density and vein length per area (VLA) were positively correlated. Most traits exhibited substantial plasticity, as evidenced by significant shifts in trait values across environments and multivariate analyses revealed differentiation in trait space across treatment levels. This included an overall reduction in growth/productivity in response to stress, accompanied by a shift in traits relating to gas exchange and hydraulics including stomatal and vein density (increased), stomatal size (decreased), and theoretical gsmax (increased). We found that variation in performance across treatments (estimated as total biomass) can be largely explained by a small number of putatively size-independent traits (i.e., VLA, stomatal length and density and LMA;R2= 0.74). Moreover, on average, more extreme changes in VLA were associated with more extreme decreases in performance across environments. A small number of leaf traits can predict plant performance, with plasticity in VLA being the best predictor of changes in productivity.
Distinct activation mechanisms of β-arrestin 1 revealed by19F NMR spectroscopy
Authors: Zhai Ruibo , Wang Zhuoqi , Chai Zhaofei , Li Conggang , Jin Changwen , Hu Yunfei 
Published: March 2023

ABSTRACTβ-Arrestins (βarrs) are functionally versatile proteins that play critical roles in the G-protein-coupled receptor (GPCR) signaling pathways. While the classical theory of GPCR-mediated βarr activation centers around the formation of a stable complex between βarr and the phosphorylated receptor tail, emerging evidences highlight the indispensable contribution from membrane lipids for many receptors. Due to the intrinsic complexity of βarr conformational dynamics, detailed molecular mechanisms of its activation by different binding partners remain elusive. Herein we present a comprehensive study of the structural changes of βarr1 in critical structural regions during activation using19F NMR method. We demonstrate that phosphopeptides derived from different classes of GPCRs show distinct abilities in inducing βarr1 activation. We further show that the membrane phosphoinositide PIP2independently modulates βarr1 conformational dynamics without displacing its autoinhibitory carboxyl tail, leading to a distinct partially activated state. Our results delineate two activation mechanisms of βarr1 by different binding partners, uncovering a highly multifaceted conformational energy landscape for this protein family.
EhrlichiaWnt short linear motif ligand mimetic deactivates the Hippo pathway to engage the anti-apoptotic Yap-GLUT1-BCL-xL axis
Authors: Byerly Caitlan D. , Patterson LaNisha L. , Pittner Nicholas A. , Solomon Regina N. , Patel Jignesh G. , Rogan Madison R. , McBride Jere W. 
Published: March 2023

AbstractEhrlichia chaffeensisTRP120 effector has evolved short linear motif (SLiM) ligand mimicry to repurpose multiple evolutionarily conserved cellular signaling pathways including Wnt, Notch and Hedgehog. In this investigation, we demonstrate thatE. chaffeensisand recombinant TRP120 deactivate Hippo signaling resulting in activation of Hippo transcription coactivator Yap and target gene expression. Moreover, a homologous 6 amino acid (QDVASH) SLiM shared by TRP120 and Wnt3a/5a ligands phenocopied Yap and β-catenin activation induced byE. chaffeensis,rTRP120 and Wnt5a. Similar Hippo gene expression profiles were also stimulated byE. chaffeensis,rTRP120, SLiM and Wnt5a. Single siRNA knockdown of Hippo transcription co-activator/factors (Yap and TEAD) significantly decreasedE. chaffeensisinfection. Yap activation was abolished in THP-1 Wnt Frizzled-5 (Fzd5) receptor knockout cells (KO), demonstrating Fzd5 receptor dependence. In addition, TRP120 Wnt-SLiM antibody blocked Hippo deactivation (Yap activation). Expression of anti-apoptotic Hippo target geneSLC2A1(encodes glucose transporter 1; GLUT1) was upregulated byE. chaffeensisand corresponded to increased levels of GLUT1. Conversely, siRNA knockdown ofSLC2A1significantly inhibited infection. Higher GLUT1 levels correlated with increased BCL-xL and decreased Bax levels. Moreover, blocking Yap activation with the inhibitor Verteporfin induced apoptosis that corresponded to significant reductions in levels of GLUT1 and BCL-xL, and activation of Bax and Caspase-3 and -9. This study identifies a novel shared Wnt/Hippo SLiM ligand mimetic and demonstrates thatE. chaffeensisdeactivates the Hippo pathway to engage the anti-apoptotic Yap-GLUT1-BCL-xL axis.
Distinguishing integrated sub-viral fragments from infectious Rubus yellow net virus in Scottish commercial red raspberry cultivars
Authors: McGavin Wendy , Jones Sue , MacFarlane Stuart 
Published: March 2023

SummaryShort read sequencing of two field-grown plants of red raspberry cv Glen Dee identified sequences derived from Rubus yellow net virus (RYNV). Surprisingly, PCR primers designed to target these sequences amplified RYNV-specific DNA fragments from some high health nuclear stock raspberry plants, previously tested as free from RYNV infection. The complete sequence of a Scottish isolate of RYNV (RYNV LG) was determined and a panel of primers covering the entire virus genome was designed to demonstrate that nuclear stock plants of cultivars Glen Dee, Glen Ericht, Glen Fyne and Glen Moy all contain partial fragments of the RYNV genome as integrated elements but do not contain the entire RYNV genome.The complete, circular genome of RYNV could be detected in RYNV LG-infected plants by rolling circle amplification but was not detected in Glen Dee plants. Grafting experiments showed that infectious RYNV could be transferred from RYNV LG plants but not from Glen Dee or Glen Moy plants, further demonstrating that these cultivars contain only partial, integrated RYNV elements. Grafting of RYNV LG to the certification-approved indexing speciesR. occidentalis(black raspberry) andR. macraei, showed that RYNV LG induced recognisable symptoms in both plants but thatR. macraeiwas more susceptible and produced more recognizable symptoms. Effective testing for RYNV in high health certified raspberry plants can be achieved by combining graft testing with multifragment PCR.
The zero-leverage policy and family firms
Authors: Fardnia Pedram , Kooli Maher , Kumar Sonal 
Published: March 2023

PurposeThe purpose of the study is to examine the zero-leverage (ZL) phenomenon in family and non-family firms.Design/methodology/approachThe authors consider three hypotheses and empirically test them using a sample of the largest US firms over the 2001–2016 period.FindingsThe authors find that, on average, 19.20% of family firms have zero debt vs 10.42% for non-family firms. The authors also find that family firms strategically choose to be ZL to maintain financial flexibility for future investments and exercise control over the decision-making process, consistent with the hypotheses of financial flexibility and control considerations. However, non-family firms are more likely to have zero debt if they have financial constraints and the credit market does not lend them money at affordable credit rates, consistent with the financial constraint hypothesis.Originality/valueThis paper contributes to different strands of literature. First, the authors contribute to the literature examining family firms' financial decisions. Second, the authors complement previous studies by exploring the reasons for the ZL behavior of family firms compared to non-family firms. The authors also examine the previously unexplored impact of ownership concentration on the ZL question.
Non‐destructive characterization of pulse flours—A review
Authors: Sivakumar Chitra , Findlay Catherine Rui Jin , Karunakaran Chithra , Paliwal Jitendra 
Published: March 2023

AbstractThe consumption of plant‐based proteins sourced from pulses is sustainable from the perspective of agriculture, environment, food security, and nutrition. Increased incorporation of high‐quality pulse ingredients into foods such as pasta and baked goods is poised to produce refined food products to satisfy consumer demand. However, a better understanding of pulse milling processes is required to optimize the blending of pulse flours with wheat flour and other traditional ingredients. A thorough review of the state‐of‐the‐art on pulse flour quality characterization reveals that research is required to elucidate the relationships between the micro‐ and nanoscale structures of these flours and their milling‐dependent properties, such as hydration, starch and protein quality, components separation, and particle size distribution. With advances in synchrotron‐enabled material characterization techniques, there exist a few options that have the potential to fill knowledge gaps. To this end, we conducted a comprehensive review of four high‐resolution nondestructive techniques (i.e., scanning electron microscopy, synchrotron X‐ray microtomography, synchrotron small‐angle X‐ray scattering, and Fourier‐transformed infrared spectromicroscopy) and a comparison of their suitability for characterizing pulse flours. Our detailed synthesis of the literature concludes that a multimodal approach to fully characterize pulse flours will be vital to predicting their end‐use suitability. A holistic characterization will help optimize and standardize the milling methods, pretreatments, and post‐processing of pulse flours. Millers/processors will benefit by having a range of well‐understood pulse flour fractions to incorporate into food formulations.
Thrombocytopenia during avacopan administration: A case report
Authors: Morimoto Nobuhisa , Mori Takayasu , Shioji Shingo , Watanabe Hatsumi , Sakai Keigo , Mori Katsuo , Yamamura Ayumi , Hanioka Asami , Akagi Yuichiro , Fujiki Tamami , Mandai Shintaro , Mori Yutaro , Ando Fumiaki , Susa Koichiro , Iimori Soichiro , Naito Shotaro , Sohara Eisei , Uchida Shinichi 
Published: March 2023

AbstractAvacopan is a novel C5a receptor antagonist recently approved for the treatment of microscopic polyangiitis and granulomatosis with polyangiitis. To our knowledge, thrombocytopenia induced by avacopan has not been reported. We report a case of a 78‐year‐old man with microscopic polyangiitis who developed rapidly progressive glomerulonephritis (RPGN) and vasculitis neuropathy. After developing RPGN, he was treated with prednisolone, which was ineffective. As the dosage of corticosteroids was decreased, he developed impaired dorsiflexion of the left ankle, tingling and numbness in his feet, consistent with vasculitis neuropathy. After a 3‐day administration of methylprednisolone, we started avacopan and prednisolone 20 mg/d to reduce the corticosteroid dosage. One week after starting avacopan, platelet counts began to decrease, eventually leading to the cessation of the drug. The possibility of thrombotic microangiopathy and heparin‐induced thrombocytopenia was considered unlikely given the clinical course and laboratory studies. After 3 weeks of avacopan cessation, platelet counts began to increase, suggesting avacopan as the most probable cause of thrombocytopenia. Our case highlights the importance of postmarketing surveillance of avacopan to identify its adverse events that were not reported in clinical trials to ensure its safe use. Clinicians should carefully monitor platelet counts when using avacopan.