bluuebunny/crossref_metadata_2025_split huggingface dataset:
AUXIN RESPONSE FACTOR 6(ARF6)andARF8promote Gibberellin-mediated hypocotyl xylem expansion and cambium homeostasis
Authors: Ben-Targem Mehdi , Ripper Dagmar , Bayer Martin , Ragni Laura 
Published: November 2020

AbstractDuring secondary growth, the thickening of plant organs, wood (xylem) and bast (phloem) are continuously produced by the vascular cambium. In Arabidopsis hypocotyl and root, we can distinguish two phases of secondary growth based on cell morphology and production rate. The first phase, in which xylem and phloem are equally produced, precedes the xylem expansion phase in which xylem formation is enhanced and xylem fibers differentiate. It is known that Gibberellins (GA) trigger this developmental transition via the degradation of DELLA proteins and that the cambium master regulator BREVIPEDICELLUS/KNAT1 (BP/KNAT1) and the receptor like kinases ERECTA and ERL1 regulate this process downstream of GA. However, our understandings on the regulatory network underlying GA-mediated secondary growth, are still limited.Here, we demonstrate that DELLA-mediated xylem expansion is mainly achieved through RGA and GAI and that RGA and GAI promote cambium senescence. We further show that AUXIN RESPONSE FACTOR (ARF6) and ARF8, which physically interact with DELLAs, specifically repress phloem proliferation and induce cambium senescence during the xylem expansion phase. Moreover, the inactivation ofBPinarf6 arf8background revealed an essential role for ARF6 and ARF8 in cambium establishment and maintenance. Overall, our results shed light on a pivotal hormone cross-talk between GA and auxin in the context of plant secondary growth.
The two formyl peptide receptors differently regulate GPR84-mediated neutrophil NADPH-oxidase activity
Authors: Mårtensson Jonas , Sundqvist Martina , Manandhar Asmita , Ieremias Loukas , Zhang Linjie , Ulven Trond , Xie Xin , Björkman Lena , Forsman Huamei 
Published: November 2020

ABSTRACTNeutrophils express many G protein-coupled receptors (GPCRs) including the two formyl peptide receptors (FPR1 and FPR2) and the medium chain fatty acid receptor GPR84. The FPRs are known to define a hierarchy among neutrophil GPCRs, i.e., the GPCR-mediated response can be either suppressed or amplified by signals generated by FPRs. In this study, we investigated the position of GPR84 in the FPR-defined hierarchy regarding the activation of neutrophil NADPH-oxidase, an enzyme system designed to generate reactive oxygen species (ROS). When naïve neutrophils are activated by GPR84 agonists a modest ROS release was induced. However, vast amounts of ROS production was induced by these GPR84 agonists in FPR2-desensitized neutrophils, and the response is inhibited not only by a GPR84 antagonist but also by an FPR2 specific antagonist. This suggests that the amplified GPR84 agonist response is achieved through a reactivation of the desensitized FPR2. In addition, the GPR84-mediated FPR2 reactivation was independent of β-arrestin recruitment and sensitive to a protein phosphatase inhibitor. In contrast, the modest ROS production induced by GPR84 agonists was primarily suppressed in FPR1-desensitized neutrophils through hierarchical desensitization of GPR84 by FPR1 generated signals.In summary, our data show that FPRs control the NADPH-oxidase activity mediated through GPR84 in human neutrophils. While an amplified ROS generation is achieved by GPR84 agonists through reactivation of desensitized FPR2, FPR1 heterologously desensitizes GPR84 and by that suppresses the release of ROS induced by GPR84 agonists.
DNA methylation during development and regeneration of the annelidPlatynereis dumerilii
Authors: Planques Anabelle , Kerner Pierre , Ferry Laure , Grunau Christoph , Gazave Eve , Vervoort Michel 
Published: November 2020

ABSTRACTBackgroundMethylation of cytosines in DNA (5mC methylation) is a major epigenetic modification that modulates gene expression and is important for embryonic development and cell reprogramming in vertebrates. In mammals, 5mC methylation in promoter regions is linked to transcriptional repression. Transcription regulation by 5mC methylation notably involves the Nucleosome Remodeling and Deacetylase complex (NuRD complex) which bridges DNA methylation and histone modifications. Less is known about roles and mechanisms of 5mC methylation in non-vertebrate animals. In this paper, we study 5mC methylation in the marine annelid wormPlatynereis dumerilii,an emerging evolutionary and developmental biology model capable of regenerating the posterior part of its body upon amputation. The regenerated region includes both differentiated structures and a growth zone consisting of stem cells required for the continuous growth of the worm.ResultsUsingin silicoand experimental approaches, we show thatP. dumeriliidisplays a high level of DNA methylation comparable to that of mammalian somatic cells. 5mC methylation inP. dumeriliiis dynamic along the life cycle of the animal and markedly decreases at the transition between larval to post-larval stages. We identify a full repertoire of mainly singlecopy genes encoding the machinery associated to 5mC methylation or members of the NuRD complex inP. dumeriliiand show, through phylogenetic analyses, that this repertoire is close to the one inferred for the last common ancestor of bilaterians. These genes are dynamically expressed duringP. dumeriliidevelopment, growth and regeneration. Treatment with the DNA hypomethylating agent Decitabine, impairsP. dumeriliilarval development and regeneration, and has long-term effects on post-regenerative growth by affecting the functionality of stem cells of the growth zone.ConclusionsOur data indicate high-level of 5mC methylation in the annelidP. dumerilii,highlighting that this feature is not specific to vertebrates in the bilaterian clade. Analysis of DNA methylation levels and machinery gene expression during development and regeneration, as well as the use of a chemical inhibitor of DNA methylation, suggest an involvement of 5mC methylation inP. dumeriliidevelopment, regeneration and stem cell-based post-regenerative growth. We also present data indicating thatP. dumeriliiconstitutes a promising model to study biological roles and mechanisms of DNA methylation in non-vertebrate bilaterians and to provide new knowledge about evolution of the functions of this key epigenetic modification in bilaterian animals.
Properdin oligomers adopt rigid extended conformations supporting function
Authors: Pedersen Dennis V. , Pedersen Martin Nors , Mazarakis Sofia M.M. , Wang Yong , Lindorff-Larsen Kresten , Arleth Lise , Andersen Gregers R. 
Published: November 2020

AbstractProperdin stabilizes convertases formed upon activation of the complement cascade within the immune system. The biological activity of properdin depends on the oligomerization state, but whether properdin oligomers are rigid and how their structure links to function remains unknown. We show by combining electron microscopy and solution scattering, that properdin oligomers adopt extended rigid and well-defined conformations that are well approximated by single models of apparent n-fold rotational symmetry with dimensions of 23-36 nm. Properdin monomers are pretzel shaped molecules with limited flexibility. In solution, properdin dimers are curved molecules whereas trimers and tetramers are close to being planar molecules. Structural analysis indicates that simultaneous binding through all binding sites to surface linked convertases is unlikely for properdin trimer and tetramers. We show that multivalency alone is insufficient for full activity in a cell lysis assay. Hence, the observed rigid extended oligomer structure is an integral component of properdin function.
Small RNAs couple embryonic developmental programs to gut microbes
Authors: Ohno Hayao , Bao Zhirong 
Published: November 2020

AbstractMaternal exposure to microbes and other environmental factors is known to induce adaptive changes in the progeny, but little is understood about how development of the progeny is changed. We show thatCaenorhabditis elegansundergoes additional embryonic cell divisions in response to maternal gut microbes such as one producing the biopolymer γ-poly-DL-glutamic acid. The divisions coincide with anatomical changes including left-right asymmetric cell alignment, doubling the association between intestinal cells and primordial germ cells, and improved fecundity. The developmental changes are regulated by soma-to-germline transmission of endogenous RNAi and the miR-35 microRNA family, which targets the LIN-23/CDC-25 pathway. Our findings challenge the widespread assumption thatC. eleganshas an invariant cell lineage that consists of 959 somatic cells and provide insights into how organisms optimize embryogenesis to adapt to environmental changes through epigenetic controls.
Spatial and Temporal Localization of SPIRRIG and WAVE/SCAR Reveal Roles for These Proteins in Actin-Mediated Root Hair Development
Authors: Chin Sabrina , Kwon Taegun , Khan Bibi Rafeiza , Sparks J. Alan , Mallery Eileen L. , Szymanski Daniel B. , Blancaflor Elison B. 
Published: November 2020

AbstractRoot hairs are single cell protrusions that enable roots to optimize nutrient and water acquisition. They attain their tubular shapes by confining growth to the cell apex, a process called tip growth. The actin cytoskeleton and endomembrane systems are essential for tip growth; however, little is known about how these cellular components coordinate their activities during this process. Here, we show that SPIRRIG (SPI), a BEACH domain-containing protein involved in membrane trafficking, and BRK1 and SCAR2, subunits of the WAVE/SCAR (W/SC) actin nucleating promoting complex, display polarized localizations to root hairs at distinct developmental stages. SPI accumulates at the root hair apex via post-Golgi vesicles and positively regulates tip growth by maintaining tip-focused vesicle secretion and filamentous-actin integrity. BRK1 and SCAR2 on the other hand, mark the root hair initiation domain to specify the position of root hair emergence. Consistent with the localization data, tip growth was reduced inspiand the position of root hair emergence was disrupted inbrk1 and scar1234. BRK1 depletion coincided with SPI accumulation as root hairs transitioned from initiation to tip growth. Taken together, our work uncovers a role for SPI in facilitating actin-dependent root hair development through pathways that might intersect with W/SC.
Natural genetic diversity in the potato resistance geneRBconfers suppression avoidance from Phytophthora effector IPI-O4
Authors: Karki Hari S. , Abdullah Sidrat , Chen Yu , Halterman Dennis A. 
Published: November 2020

ABSTRACTRBis a potato gene that provides resistance to a broad spectrum of genotypes of the late blight pathogenPhytophthora infestans.RBbelongs to the CC-NB-LRR (coiled-coil, nucleotide-binding, leucine-rich repeat) class of resistance (R) genes, a major component of the plant immune system. It directly interacts with Class I and II IPI-O effectors fromP. infestansto initiate a hypersensitive resistance response, but this activity is suppressed in the presence of the Class III effector IPI-O4. Using natural genetic variation of RB within potato wild relatives, we identified two amino acids in the CC domain that alter interactions needed for suppression of resistance by IPI-O4. We have found that separate modification of these amino acids in RB can diminish or enhance the resistance capability of this protein againstP. infestansin bothNicotiana benthamianaand potato. Our results demonstrate that increased knowledge of the molecular mechanisms that determine resistance activation and R protein suppression by effectors can be utilized to tailor-engineer genes with the potential to provide increased durability.
Global gene expression analysis ofStreptococcus agalactiaeat exponential growth phase
Authors: Silvestre Inês , Borges Vítor , Duarte Sílvia , Nunes Alexandra , Sobral Rita , Vieira Luís , Gomes João Paulo , Borrego Maria José 
Published: November 2020

AbstractStreptococcus agalactiaeis a leading cause of neonatal infections and an increasing cause of infections in adults with underlying diseases. One of the firstS. agalactiaeisolates to be subjected to whole genome sequencing was NEM316, a strain responsible for a fatal case of septicemia that has been widely used as reference strain forin vitroassays. Whole transcriptome analyses may provide an essential contribute to the understanding of the molecular mechanisms responsible for bacteria adaptation and pathogenicity, still, so far, very few studies were dedicated to the analysis of global gene expression ofS. agalactiae. Here, we applied RNA-sequencing to perform a comparative overview of the global gene expression levels of theS. agalactiaereference strain NEM316 at the exponential growth phase. Genes were ranked by expression level and grouped by functional category and 46% of the top-100 expressed genes encode proteins involved in “Translation, ribosomal structure and biogenesis”. Among the group of highly expressed genes were also represented genes with no assigned functional category. Although this result warrants further investigation, most of them might be implicated in stress response. As very little is known about the molecular mechanisms behind the release of DNase’sin vitroandin vivo, we also performed preliminary assays to understand whether direct DNA exposure affects the gene expression of strain NEM316 at the exponential growth phase. No differentially expressed genes were detected, which indicates that follow-up studies are needed to disclose the complex molecular pathways (and stimuli) triggering the release of DNase’s. In general, we provide data on the global expression levels of NEM316 at exponential growth phase that may contribute to better understandS. agalactiaeadaptation and virulence.
alms1mutant zebrafish do not show hair cell phenotypes seen in other cilia mutants
Authors: Parkinson Lauren , Stawicki Tamara M. 
Published: November 2020

ABSTRACTMultiple cilia-associated genes have been shown to affect hair cells in zebrafish (Danio rerio),including the human deafness genedcdc2,the radial spoke genersph9,and multiple intraflagellar transport (IFT) and transition zone genes. Recently a zebrafishalms1mutant was generated. TheALMS1gene is the gene mutated in the ciliopathy Alström Syndrome a disease that causes hearing loss among other symptoms. The hearing loss seen in Alström Syndrome may be due in part to hair cell defects asAlms1mutant mice show stereocilia polarity defects and a loss of hair cells. Hair cell loss is also seen in postmortem analysis of Alström patients. The zebrafishalms1mutant has metabolic defects similar to those seen in Alström syndrome andAlms1mutant mice. We wished to investigate if it also had hair cell defects. We, however, failed to find any hair cell related phenotypes inalms1mutant zebrafish. They had normal lateral line hair cell numbers as both larvae and adults and normal kinocilia formation. They also showed grossly normal swimming behavior, response to vibrational stimuli, and FM1-43 loading. Mutants also showed a normal degree of sensitivity to both short-term neomycin and long-term gentamicin treatment. These results indicate that cilia-associated genes differentially affect different hair cell types.
Zika Virus Capsid Anchor Forms Cytotoxic Amyloid-like Fibrils
Authors: Saumya Kumar Udit , Gadhave Kundlik , Kumar Amit , Giri Rajanish 
Published: November 2020

AbstractCapsid-anchor (CA) of Zika virus (ZIKV) is a small, single-pass transmembrane sequence that separates the capsid (C) protein from downstream pre-membrane (PrM) protein. During ZIKV polyprotein processing, CA is cleaved-off from C and PrM and left as a membrane-embedded peptide. CA plays an essential role in the assembly and maturation of the virus. However, its independent folding behavior is still unknown. Since misfolding and aggregation propensity of transmembrane proteins are now increasingly recognized and has been linked to several proteopathic disorders. Therefore, in this study, we investigated the amyloid-forming propensity of CA at physiological conditions. We observed aggregation behavior of CA peptide using dyebinding assays and ThT kinetics. The morphological analysis of CA aggregates explored by high-resolution microscopy (TEM and AFM) revealed characteristic amyloid-like fibrils. Further, the effect on mammalian cells exhibited the cytotoxic nature of the CA amyloid-fibrils. Our findings collectively shed light on the amyloidogenic phenomenon of flaviviral protein, which may contribute to their infection.Graphical Abstract:Schematic representation of Zika virus Capsid anchor forming amyloid aggregates with cytotoxic and hemolytic properties.
The solution structures of higher-order human telomere G-quadruplex multimers
Authors: Monsen Robert C. , Chakravarthy Srinivas , Dean William L. , Chaires Jonathan B. , Trent John O. 
Published: November 2020

ABSTRACTHuman telomeres contain the repeat DNA sequence 5’(TTAGGG), with duplex regions that are several kilobases long terminating in a 3’ single-stranded overhang. The structure of the single-stranded overhang is not known with certainty, with disparate modes proposed in the literature. We report here the results of an integrated structural biology approach that combines small-angle X-ray scattering, circular dichroism (CD), analytical ultracentrifugation, size-exclusion column chromatography and molecular dynamics simulations that provide the most detailed characterization to date of the structure of the telomeric overhang. We find that the single-stranded sequences 5’(TTAGGG)n, with n=8, 12, and 16, fold into multimeric structures containing the maximal number (2, 3, and 4, respectively) of contiguous G4 units with no long gaps between units. The G4 units are a mixture of hybrid-1 and hybrid-2 conformers. In the multimeric structures, G4 units interact, at least transiently, at the interfaces between units to produce distinctive CD signatures. Global fitting of our hydrodynamic and scattering data to a worm-like chain (WLC) model indicates that these multimeric G4 structures are semi-flexible, with a persistence length of about 34 Å. Investigations of its flexibility using MD simulations reveal stacking, unstacking, and coiling movements, which yield unique sites for drug targeting.
The Nab2 RNA binding protein promotes sex-specific splicing ofSex lethalinDrosophilaneuronal tissue
Authors: Jalloh Binta , Rounds J. Christopher , Brown Brianna E. , Lancaster Carly L. , Leung Sara W. , Banerjee Ayan , Morton Derrick J. , Bienkowski Rick S. , Kremsky Isaac J. , Fasken Milo B. , Corbett Anita H. , Moberg Kenneth H. 
Published: November 2020

AbstractTheDrosophilapolyadenosine RNA binding protein Nab2, which is orthologous to a human protein lost in a form of inherited intellectual disability, controls axon projection, locomotion, and memory. Here we define an unexpectedly specific role for Nab2 in regulating splicing of ∼150 exons/introns in the head transcriptome and link the most prominent of these, female retention of a male-specific exon in the sex determination factorSex-lethal(Sxl), to a role in m6A-dependent mRNA splicing. Genetic evidence indicates that aberrantSxlsplicing underlies multiple phenotypes inNab2mutant females. At a molecular level, Nab2 associates withSxlpre-mRNA and ensures proper female-specific splicing by preventing m6A hypermethylation by Mettl3 methyltransferase. Consistent with these results, reducing Mettl3 expression rescues developmental, behavioral and neuroanatomical phenotypes inNab2mutants. Overall these data identify Nab2 as a required regulator of m6A-regulatedSxlsplicing and imply a broader link between Nab2 and Mettl3-regulated brain RNAs.
Single cell transcriptomics reveals the effect of PD-L1/TGF-β blockade on the tumor microenvironment
Authors: Lim Yoong Wearn , Coles Garry L. , Sandhu Savreet K. , Johnson David S. , Adler Adam S. , Stone Erica L. 
Published: November 2020

AbstractBackgroundThe anti-tumor activity of anti-PD-1/PD-L1 therapies correlates with T cell infiltration in tumors. Thus, a major goal in oncology is to find strategies that enhance T cell infiltration and efficacy of anti-PD-1/PD-L1 therapy. TGF-β has been shown to contribute to T cell exclusion and anti-TGF-β improves anti-PD-L1 efficacyin vivo. However, TGF-β inhibition has frequently been shown to induce toxicity in the clinic, and the clinical efficacy of combination PD-L1 and TGF-β blockade has not yet been proven. To identify strategies to overcome resistance to PD-L1 blockade, the transcriptional programs associated with PD-L1 and/or TGF-β blockade in the tumor microenvironment should be further elucidated.ResultsFor the first time, we used single-cell RNA sequencing to characterize the transcriptomic effects of PD-L1 and/or TGF-β blockade on nearly 30,000 single cells in the tumor and surrounding microenvironment. Combination treatment led to upregulation of immune response genes, including multiple chemokine genes such as CCL5, in CD45+ cells, and down-regulation of extracellular matrix genes in CD45-cells. Analysis of publicly available tumor transcriptome profiles showed that the chemokine CCL5 was strongly associated with immune cell infiltration in various human cancers. Further investigation within vivomodels showed that intratumorally administered CCL5 enhanced cytotoxic lymphocytes and the anti-tumor activity of anti-PD-L1.ConclusionsTaken together, our data could be leveraged translationally to improve anti-PD-L1 plus anti-TGF-β combination therapy, for example through companion biomarkers, and/or to identify novel targets that could be modulated to overcome resistance.
Functional microstructure of CaV-mediated calcium signaling in the axon initial segment
Authors: Lipkin Anna M , Cunniff Margaret M , Spratt Perry WE , Lemke Stefan M , Bender Kevin J 
Published: November 2020

ABSTRACTThe axon initial segment (AIS) is a specialized neuronal compartment in which synaptic input is converted into action potential output. This process is supported by a diverse complement of sodium, potassium, and calcium channels (CaV). Different classes of sodium and potassium channels are scaffolded at specific sites within the AIS, conferring unique functions, but how calcium channels are functionally distributed within the AIS is unclear. Here, we utilize conventional 2-photon laser scanning and diffraction-limited, high-speed spot 2-photon imaging to resolve action potential-evoked calcium dynamics in the AIS with high spatiotemporal resolution. In mouse layer 5 prefrontal pyramidal neurons, calcium influx was mediated by a mix of CaV2 and CaV3 channels that differentially localized to discrete regions. CaV3 functionally localized to produce nanodomain hotspots of calcium influx that coupled to ryanodine-dependent stores, whereas CaV2 localized to non-hotspot regions. Thus, different pools of CaVs appear to play distinct roles in AIS function.