bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nanosized extracellular vesicles released byNeurospora crassahyphae
Authors: Medina-Castellanos Elizabeth , Salgado-Bautista Daniel A. , Martínez-Andrade Juan Manuel , Cadena-Nava Ruben Dario , Riquelme Meritxell 
Published: November 2022

ABSTRACTExtracellular vesicles (EVs) are nanosized structures containing proteins, lipids, and nucleic acids, released by living cells to the surrounding medium. EVs participate in diverse processes, such as intercellular communication, virulence, and disease. In pathogenic fungi, EVs carry enzymes that allow them to invade the host or undergo environmental adaptation successfully. InNeurospora crassa, a non-pathogenic filamentous fungus widely used as a model organism, the vesicle-dependent secretory mechanisms that lead to polarized growth are well studied. In contrast, biosynthesis of EVs in this fungus has been practically unexplored. In the present work, we analyzedN. crassaculture’s supernatant for the presence of EVs by dynamic light scattering (DLS), transmission electron microscopy (TEM) and proteomic analysis. We identified spherical membranous structures, with a predominant subpopulation averaging a hydrodynamic diameter (dh) of 68 nm and a particle diameter (dp) of 38 nm. EV samples stained with osmium tetroxide vapors were better resolved than those stained with uranyl acetate. Mass spectrometry analysis identified 252 proteins, including enzymes involved in carbohydrate metabolic processes, oxidative stress response, cell wall organization/remodeling, and circadian clock-regulated proteins. Some of these proteins have been previously reported in exosomes from human cells or in EVs of other fungi. In view of the results, it is suggested a putative role for EVs in cell wall biosynthesis and vegetative development inN. crassa.
Changes in functional composition and gene expression in eukaryotic plankton at the Atlantic-Arctic Polar front
Authors: Frémont Paul , Da Silva Corinne , Campese Lucia , Villar Émilie , Rastogi Achal , Aury Jean-Marc , Bowler Chris , Boss Lee Karp , Wincker Patrick , Pelletier Eric , Gehlen Marion , Iudicone Daniele , Jaillon Olivier 
Published: November 2022

AbstractPlanktonic communities are shaped by ocean currents and participate in multiple global biogeochemical cycles. Unraveling how the functions of communities respond to strong environmental gradients will improve our understanding of the interactions between climate change and marine ecosystems. Here, we investigate changes in functions and gene expression of eukaryotic plankton transiting between the North Atlantic Ocean (NAO) in winter and the Arctic Ocean (AO) in spring/summer using metatranscriptomes and metagenomes fromTaraOceans. In Arctic communities, functions involved in maintaining the protein pool and translation machinery appear to be more active. Four major phylogenetically distant algal groups are abundant in both basins and show similar strategies at transcriptional level, including increased expression of some functions related to cold acclimation. These results shade lights on gene expression strategies shared by cosmopolitan phototrophs of widely separated lineages.
Ultra-sensitive platelet proteome maps the O-glycosylation landscape and charts the response to thrombin dosage
Authors: Houlahan Callum B. , Kong Yvonne , Johnston Bede , Cielesh Michelle , Chau The Huong , Coleman Paul R. , Hao Huilin , Haltiwanger Robert S. , Thaysen-Andersen Morten , Passam Freda H. , Larance Mark 
Published: November 2022

ABSTRACTPlatelet activation induces the secretion of proteins that promote platelet aggregation and inflammation. However, detailed analysis of the released platelet proteome is hampered by platelets’ tendency to pre-activate during their isolation and a lack of sensitive protocols for low abundance releasate analysis. Here we detail the most sensitive analysis to date of the platelet releasate proteome with the detection of >1,300 proteins. Unbiased scanning for post-translational modifications within releasate proteins highlighted O-glycosylation as being a major component. For the first time, we detected O-fucosylation on previously uncharacterised sites including multimerin-1 (MMRN1), a major alpha granule protein that supports platelet adhesion to collagen and is a carrier for platelet factor V. The N-terminal EMI domain of MMRN1, a key site for protein-protein interaction, was O-fucosylated at a conserved threonine within a new consensus sequence. Our data suggest that Protein O-fucosyltransferase 1 (POFUT1) is responsible for this modification. Secretion of MMRN1 was reduced in cells lacking POFUT1, supporting a key role of O-fucosylation in MMRN1 function. By comparing releasates from resting and thrombin-treated platelets, 202 proteins were found to be significantly released after high-dose thrombin stimulation. Complementary quantification of the platelet lysates identified >3,800 proteins, which confirmed the platelet origin of releasate proteins by anti-correlation analysis. Low-dose thrombin treatment yielded a smaller subset of significantly regulated proteins with fewer secretory pathway enzymes. The comprehensive platelet proteome resource provided here (larancelab.com/platelet-proteome) allows identification of novel regulatory mechanisms for drug targeting to address platelet dysfunction and thrombosis.Key PointsHigh-sensitivity proteome mapping of human platelets identifies O-glycosylation of platelet proteins at key functional sitesPlatelet O-fucosyltransferase POFUT1 regulates the secretion of adhesive protein multimerin-1 (MMRN1)
Gut microbiota bacterial strain richness is species specific and limits therapeutic engraftment
Authors: Chen-Liaw Alice , Aggarwala Varun , Mogno Ilaria , Haifer Craig , Li Zhihua , Eggers Joseph , Helmus Drew , Hart Amy , Wehkamp Jan , Lamousé-Smith Esi SN , Kerby Robert L. , Rey Federico E. , Colombel Jean Frédéric , Kamm Michael A , Borody Thomas J. , Grinspan Ari , Paramsothy Sudarshan , Kaakoush Nadeem O. , Dubinsky Marla C. , Faith Jeremiah J. 
Published: November 2022

AbstractDespite the fundamental role of strain variation in gut microbiota function, the number of unique strains of a species that can stably colonize the human gut is still unknown. In this work, we determine the strain richness of common gut species using thousands of sequenced bacterial isolates and metagenomes. We find that strain richness varies across species, is transferable by fecal microbiota transplantation, and is low in the gut compared to other environments. Therapeutic administration of supraphysiologic numbers of strains per species only temporarily increases recipient strain richness, which subsequently converges back to the population average. These results suggest that properties of the gut ecosystem govern the number of strains of each species colonizing the gut and provide a theoretical framework for strain engraftment and replacement in fecal microbiota transplantation and defined live biotherapeutic products.
Curvature Sensing and Membrane Remodeling of the VPS37A N-terminal Domain during Autophagy
Authors: Ye Yansheng , Liang Xinwen , Wang Guifang , Bewley Maria C , Liu Xiaoming , Flanagan John M. , Wang Hong-Gang , Takahashi Yoshinori , Tian Fang 
Published: November 2022

AbstractVPS37A, a component of ESCRT-I, is essential for recruiting a subset of ESCRT proteins that seal the phagophore during autophagosome biogenesis. In this study, we uncover two hydrophobic motifs in the VPS37A N-terminal 148 amino acids (VPS37A1-148) that selectively interact with highly curved membranes. Mutations in these motifs nearly abolish VPS37A membrane bindingin vitroand compromise its localization to the phagophore and autophagic fluxin vivo. We also determined the solution structure of residues 21 to 131 and demonstrated that it is the UEVL (ubiquitin E2 variant-like) domain. Intriguingly, this domain remodels highly curved liposomes to high-order structures. We suggest that the specific interactions between VPS37A1-148and the curved membrane may facilitate the recruitment of VPS37A to the phagophore and its subsequent closure. Our results support the premise that the distinct membrane architecture of the cup-like phagophore spatiotemporally regulates autophagosome biogenesis.
Mechanism of nucleic-acid-driven LLPS of TDP-43 PLD
Authors: Mei Dang , Li Tongyang , Zhou Shibo , Song Jianxing 
Published: November 2022

ABSTRACTMost membrane-less organelles (MLOs) formed by LLPS contain both nucleic acids and IDR-rich proteins. Currently while IDRs are well-recognized to drive LLPS, nucleic acids are thought to exert non-specific electrostatic/salt effects. TDP-43 functions by binding RNA/ssDNA and its LLPS was characterized without nucleic acids to be driven mainly by PLD-oligomerization, which may further transit into aggregation characteristic of various neurodegenerative diseases. Here by NMR, we discovered unexpectedly for TDP-43 PLD: 1) ssDNAs drive and then dissolve LLPS by multivalently and specifically binding Arg/Lys. 2) LLPS is driven by nucleic-acid-binding coupled with PLD-oligomerization. 3) ATP and nucleic acids universally interplay in modulating LLPS by competing for binding Arg/Lys. However, the unique hydrophobic region within PLD renders LLPS to exaggerate into aggregation. The study not only unveils the first residue-resolution mechanism of the nucleic-acid-driven LLPS of TDP-43 PLD, but also decodes a general principle that not just TDP-43 PLD, all Arg/Lys-containing IDRs are cryptic nucleic-acid-binding domains that may phase separate upon binding nucleic acids. Strikingly, ATP shares a common mechanism with nucleic acids in binding IDRs, thus emerging as a universal mediator for interactions between IDRs and nucleic acids, which may underlie previously-unrecognized roles of ATP at mM in physiology and pathology.
Extreme diversity of mycoviruses present in four strains ofRhizoctonia cerealis, the pathogen of wheat sharp eyespot
Authors: Li Wei , Sun Haiyan , Cao Shulin , Zhang Aixiang , Zhang Haotian , Shu Yan , Chen Huaigu 
Published: November 2022

AbstractRhizoctonia cerealisis the pathogen of wheat sharp eyespot, which occurs throughout temperate wheat growing regions of the world. In this project, the genomes of viruses from four strains ofR. cerealiswere analyzed based on Illumina high-throughput RNA-Seq data. Ribosomal RNA-depleted total RNA and purified dsRNA from cultivated mycelia of each isolate were used for cDNA library construction and sequencing. After filtering out reads that mapped to the fungal genome, viral genomes were assembled using the remaining reads from the rRNA-depleted and dsRNA-Seq data. In total, 131 viral genome sequences containing complete ORFs, belonging to 117 viruses, were obtained. Based on phylogenetic analysis, some of them were identified as novel members of the familiesCurvulaviridae, Endornaviridae, Hypoviridae, Mitoviridae, MymonaviridaeandPhenuiviridae, while others were unclassified viruses. We compared the integrity and reliability of the viral sequences obtained by the two sequencing methods and, for the first time, estimated the density of some viruses in host cells. Most of these viruses fromR. cerealiswere sufficiently different from those deposited in databases. We propose the establishment of a new family,Rhizoctobunyaviridae, and two new genera,RhizoctobunyavirusandIotahypovirus. We further clarified the distribution and co-infection of these viruses in the fourR. cerealisstrains. In conclusion, the diversity of mycoviruses inR. cerealisis extremely rich. We report a series of novel viruses and provide important insight into virus evolution.
Protein kinase gene declines linearly with elevation: a shared genomic feature across species and continents in lichenized fungi suggests role in climate adaptation
Authors: Merges Dominik , Dal Grande Francesco , Valim Henrique , Singh Garima , Schmitt Imke 
Published: November 2022

AbstractIntraspecific genomic variability affects a species’ adaptive potential towards climatic conditions. Variation in gene content across populations and environments may point at genomic adaptations to specific environments. The lichen symbiosis, a stable association of fungal and photobiont partners, offers an excellent system to study environmentally driven gene content variation. Many species have remarkable environmental tolerances, and often form populations in different climate zones. Here we combine comparative and population genomics to assess the presence and absence of genes in high elevation and low elevation genomes of two lichenized fungi of the genusUmbilicaria. The two species have non-overlapping ranges, but occupy similar climatic niches in North America (U. phaea) and Europe (U. pustulata): high elevation populations are located in the cold temperate zone and low elevation populations in the Mediterranean zone. We assessed gene content variation along replicated elevation gradients in each of the two species, based on a total of 2050 individuals across 26 populations. Specifically, we assessed shared orthologs across species within the same climate zone, and tracked which genes increase or decrease in abundance within populations along elevation. In total, we found 16 orthogroups with shared orthologous genes in genomes at low elevation and 13 at high elevation. Coverage analysis revealed one ortholog that is exclusive to genomes at low elevation. Conserved domain search revealed domains common to the protein kinases (PKs) superfamily. We traced the discovered ortholog in populations along five replicated elevation gradients on both continents. The protein kinase gene linearly declined in abundance with increasing elevation, and was absent in the highest populations. We consider the parallel loss of an ortholog in two species and in two geographic settings a rare find, and a step forward in understanding the genomic underpinnings of climatic tolerances in lichenized fungi. In addition, the tracking of gene content variation provides a widely applicable framework for retrieving biogeographical determinants of gene presence/absence patterns. Our work provides insights into gene content variation of lichenized fungi in relation to climatic gradients, suggesting a new research direction with implications for understanding evolutionary trajectories of complex symbioses in relation to climatic change.
Regeneration in calcareous sponge relies on ‘purse-string’ mechanism and the rearrangements of actin cytoskeleton
Authors: Skorentseva Kseniia V. , Bolshakov Fyodor V. , Saidova Alina A. , Lavrov Andrey I. 
Published: November 2022

AbstractThe crucial step in any regeneration process is epithelization, i.e. the restoration of epithelium structural and functional integrity. Epithelialization requires cytoskeletal rearrangements, primarily of actin filaments and microtubules. Sponges (phylum Porifera) are early branching metazoans with pronounced regenerative abilities. Calcareous sponges have a unique step during regeneration: formation of a temporary structure, regenerative membrane which initially covers a wound. It forms due to the morphallactic rearrangements of exo- and choanoderm epithelial-like layers. The current study quantitatively evaluates morphological changes and characterises underlying actin cytoskeleton rearrangements during regenerative membrane formation in asconoid calcareous spongeLeucosolenia variabilis, through a combination of time-lapse imaging, immunocytochemistry, and confocal laser scanning microscopy. Regenerative membrane formation has non-linear stochastic dynamics with numerous fluctuations. The pinacocytes at the leading edge of regenerative membrane form a contractile actomyosin cable. Regenerative membrane formation either depend on its contraction or being coordinated through it. The cell morphology changes significantly during regenerative membrane formation. Exopinacocytes flatten, their area increases, while circularity decreases. Choanocytes transdifferentiate into endopinacocytes, losing microvilli collar and flagellum. Their area increases and circularity decreases. Subsequent redifferentiation of endopinacocytes into choanocytes is accompanied by inverse changes in cell morphology. All transformations are based on actin filament rearrangements similar to those characteristic of higher metazoans. Altogether, we provide here a qualitative and quantitative description of cell transformations during reparative epithelial morphogenesis in a calcareous sponge.Summary statementFirst detailed description of actin cytoskeleton rearrangements during wound healing in calcareous sponge. ‘Purse-string’ mechanism presumably involved. Cytoskeletal rearrangements resemble those characteristic of Eumetazoans.
Intracellular calcium elevations drive the nucleation of FIP200- and ATG13-containing pre-autophagosomal structures that become omegasomes
Authors: Smith Matthew , Schoenfelder Priya , Manifava Maria , Polson Hannah , Tooze Sharon , Roderick H Llewelyn , Ktistakis Nicholas T. 
Published: November 2022

AbstractCa2+ modulates autophagy at multiple steps including the induction and maturation of autophagosomes, but the magnitude and spatiotemporal properties of this calcium signal and its ultimate effect on the autophagic machinery are unclear. Focusing on the induction step leading to omegasome formation, we report that low but sustained elevations in cytosolic calcium levels induce omegasome formation but treatments that only transiently elevate calcium do not. The calcium-induced structures are early intermediates that mature into omegasomes but do not constitute full autophagosomes because they are partially devoid of late autophagy proteins ATG16 and LC3. In addition to omegasomes, all four components of the ULK complex (ULK1, FIP200, ATG13, ATG101) respond to calcium modulation: they translocate to early autophagy puncta in complete medium upon calcium elevation, and are inhibited from translocation during starvation by calcium chelation with BAPTA-2 AM. The principal early step affected by calcium lies downstream of mTORC1 inactivation and upstream of VPS34 activation, coinciding biochemically with phosphorylation of ATG13 at serine 318, which is known to require ULK1 activity. However, although the calcium-mediated step requires ATG9, FIP200 and ATG13, it does not require ULK1/2, suggesting that calcium does not directly regulate ULK1 activity but rather it regulates the mechanism by which the ULK complex components ATG13 and FIP200, together with ATG9, nucleate pre-autophagosomal precursors. This calcium-induced nucleation is sufficient to drive autophagy induction up to the omegasome step, but not beyond it.
Paenibacillus glycinicolasp. nov.,Paenibacillus triticicolasp. nov.,Pseudescherichia oryzaesp. nov.,Pseudomonas gossypiisp. nov., andTardiphaga zeaesp. nov., five novel bacterial species from agricultural crops
Authors: Seaton Sarah , Auker Emily , Connolly Allison , Tesfaye Mekdem , Inderbitzin Patrik , Barnett Stephen J. , M. Franco Christopher M. , Trujillo Martha E. 
Published: November 2022

ABSTRACTFive novel species from healthy plants and other substrates are described. These arePaenibacillus glycinicolasp. nov. fromGlycine maxin Iowa, United States;Paenibacillus triticicolasp. nov. fromTriticum aestivumin Australia,Allium cepain Texas, garden soil in Wisconsin, cow’s milk in New York state,Panicum virgatumin Michigan, sweet sorghum in Nebraska, andZea maysin Ohio;Pseudescherichia oryzaesp. nov. fromOryza sativain Arkansas;Pseudomonas gossypiisp. nov. from a healthyBos taurusin Kansas,Capsicum annuumfrom Arizona,Gossypium hirsutumin New Mexico, Oklahoma, and Texas, andZea maysfrom Arkansas; andTardiphaga zeaesp. nov. fromZea maysin Iowa. No pathogenic strains are known for any of the novel species.
Environmentally sustainable airport development: Ukrainian case of decarbonization
Authors: Mishchenko Andriy , Dalkıran Alper , Novakovska Iryna , Skrypnyk Liliia , Ishchenko Nataliia 
Published: November 2022

PurposeThe world society as a whole and Ukraine are realizing that climate change and decarbonization are critical issues. This study aims to determine whether the aviation and transportation industries in Ukraine have rearranged their priorities as a result of this investigation. The process of decarbonization and adaptation begins with a legislative point of view and then moves on to technology, improvements, infrastructure, energy and emissions stages to meet the primary goals.Design/methodology/approachAn analysis of the content of the literature about decarbonization and the legislation and application processes for airport de-carbonization in Ukraine. The study focuses on the landing and take-off cycle of the airports. The statistics on the transportation of the Ukrainian territory have been looked at over time to determine whether or not there have been any shifts.FindingsThere are significant reduction figures found in the Poltava region. Double-figure emissions reductions in four years of series are 5.9%, 41.0% and 19.3%, in the respective years of 2018, 2019 and 2020, which is a 55.3% reduction compared with 2020 to 2017.Practical implicationsBecause the transportation industry and aviation generate a significant amount of carbon dioxide, steps must be taken to cut emissions. The decarbonization process ought to proceed in the form of a series of actions to achieve carbon reduction goals with a broader range of participants. In addition, an aviation subsidy for biofuels may be required to initiate the shift by having the taxation change.Originality/valueAs far as the literature surveys, to the best of the authors’ knowledge, this is the first comprehensive Ukrainian decarbonization analysis that considers legislation, technology, improvements, infrastructure, energy and emissions in addition to just those four categories.
Neural graph collaborative filtering for privacy preservation based on federated transfer learning
Authors: Liu Yaqi , Fang Shuzhen , Wang Lingyu , Huan Chong , Wang Ruixue 
Published: November 2022

Purpose
In recent years, personalized recommendations have facilitated easy access to users' personal information and historical interactions, thereby improving recommendation effectiveness. However, due to privacy risk concerns, it is essential to balance the accuracy of personalized recommendations with privacy protection. Accordingly, this paper aims to propose a neural graph collaborative filtering personalized recommendation framework based on federated transfer learning (FTL-NGCF), which achieves high-quality personalized recommendations with privacy protection.

Design/methodology/approach
FTL-NGCF uses a third-party server to coordinate local users to train the graph neural networks (GNN) model. Each user client integrates user–item interactions into the embedding and uploads the model parameters to a server. To prevent attacks during communication and thus promote privacy preservation, the authors introduce homomorphic encryption to ensure secure model aggregation between clients and the server.

Findings
Experiments on three real data sets (Gowalla, Yelp2018, Amazon-Book) show that FTL-NGCF improves the recommendation performance in terms of recall and NDCG, based on the increased consideration of privacy protection relative to original federated learning methods.

Originality/value
To the best of the authors’ knowledge, no previous research has considered federated transfer learning framework for GNN-based recommendation. It can be extended to other recommended applications while maintaining privacy protection.