bluuebunny/crossref_metadata_2025_split huggingface dataset:
DNA metabarcoding of gut contents reveals key habitat and seasonal drivers of trophic networks involving generalist predators in agricultural landscapes
Authors: Saqib Hafiz Sohaib Ahmed , Sun Linyang , Pozsgai Gabor , Liang Pingping , You Minsheng , Gurr Geoff M. , You Shijun 
Published: May 2022

ABSTRACTBACKGROUNDUnderstanding the networks of trophic interactions into which generalist predators are embedded is key to assessing their ecological role of in trophic networks and the biological control services they provide. The advent of affordable DNA metabarcoding approaches greatly facilitates quantitative understanding of trophic networks and their response to environmental drivers. Here, we examine how key environmental gradients interact to shape predation by Lycosidae in highly dynamic vegetable growing systems in China.RESULTSFor the sampled Lycosidae, crop identity, pesticide use, and seasons shape the abundance of preydetected in spider guts. For the taxonomic richness of prey, local- and landscape-scale factors gradients were more influential. Multivariate ordinations confirm that these crop-abundant spiders dynamically adjust their diet to reflect environmental constraints and seasonal availability to prey.CONCLUSIONThe plasticity in the diet composition is likely to account for the persistence of spiders in relatively ephemeral brassica crops. Our findings provide further insights into the optimization of habitat management for predator-based biological control practices.
Potential future climate change effects on global reptile distributions and diversity
Authors: Biber Matthias F. , Voskamp Alke , Hof Christian 
Published: May 2022

AbstractAimUntil recently, complete information on global reptile distributions has not been widely available. Here, we provide the first comprehensive climate impact assessment for reptiles on a global scale.LocationGlobal, excluding AntarcticaTime period1995, 2050, 2080Major taxa studiedReptilesMethodsWe modelled the distribution of 6,296 reptile species and assessed potential global as well as realm-specific changes in species richness, the change in global species richness across climate space, and species-specific changes in range extent, overlap and position under future climate change. To assess the future climatic impact on 3,768 range-restricted species, which could not be modelled, we compared the future change in climatic conditions between both modelled and non-modelled species.ResultsReptile richness was projected to decline significantly over time, globally but also for most zoogeographic realms, with the greatest decrease in Brazil, Australia and South Africa. Species richness was highest in warm and moist regions, with these regions being projected to shift further towards climate extremes in the future. Range extents were projected to decline considerably in the future, with a low overlap between current and future ranges. Shifts in range centroids differed among realms and taxa, with a dominating global poleward shift. Non-modelled species were significantly stronger affected by projected climatic changes than modelled species.Main conclusionsWith ongoing future climate change, reptile richness is likely to decrease significantly across most parts of the world. This effect as well as considerable impacts on species’ range extent, overlap, and position were visible across lizards, snakes and turtles alike. Together with other anthropogenic impacts, such as habitat loss and harvesting of species, this is a cause for concern. Given the historical lack of global reptile distributions, this calls for a reassessment of global reptile conservation efforts, with a specific focus on anticipated future climate change.
Significant phylogenetic signal is not enough to trust phylogenetic predictions
Authors: Molina-Venegas Rafael , Morales-Castilla Ignacio , Á. Rodríguez Miguel 
Published: May 2022

AbstractIn a recent study, Cantwell-Jones et al. (2022) proposed a list of 1044 species as promising key sources of B vitamins based primarily on phylogenetic predictions. To identify candidate plants, they fitted lambda models of evolution to edible species with known values in each of six B vitamins (232 to 280 species) and used the estimated parameters to predict B-vitamin profiles of edible plants lacking nutritional data (6460 to 6508 species). The latter species were defined as potential sources of a B vitamin if the predicted vitamin content was ≥15% towards recommended dietary allowances for active females between 31-50 years per 100 g of fresh edible plant material consumed. Unfortunately, the reliability of the predictions that informed the list of candidate species is questionable due to insufficient phylogenetic signal in the data (Pagel’s λ between 0.171 and 0.665) and a high incidence of species with missing values (over 95% of all the species analyzed in the study). We found that of the 1044 species proposed as promising B-vitamin sources, 626 to 993 species showed accuracies that were indistinguishable from those obtained under a white noise model of evolution (i.e. random predictions conducted in absence of any phylogenetic structure) in at least one of the vitamins, which proves the weakness of the inference drawn from imputed information in the original study. We hope this commentary serves as a cautionary note for future phylogenetic imputation exercises to carefully assess whether the data meet the requirements for the predictions to be valuable, or at least more accurate than expected by chance.
Allogeneic testes transplanted into partially castrated adult medaka (Oryzias latipes) can produce donor-derived offspring by natural mating over a prolonged period
Authors: Kayo Daichi , Kanda Shinji , Okubo Kataaki 
Published: May 2022

AbstractGenerally, successful testis transplantation has been considered to require immune suppression in the recipient to avoid rejection of the transplanted tissue. In the present study, we demonstrate in medaka that allogeneic adult testicular tissue will engraft in adult recipients immediately after partial castration without the use of immunosuppressive drugs. The allografted testes are retained in the recipient’s body for at least three months and are able to produce viable sperm that yield offspring after natural mating. Some recipients showed a high frequency (over 60%) of offspring derived from spermatozoa produced by the transplanted testicular tissue. Histological analyses showed that allografted testicular tissues included both germ cells and somatic cells that had established within an immunocompetent recipient testis. The relative simplicity of this testis transplantation approach will benefit investigations of the basic processes of reproductive immunology and will improve the technique of gonadal tissue transplantation.
Population genomics provide insights into the global genetic structure of Colletotrichum graminicola, the causal agent of maize anthracnose
Authors: Rogério Flávia , Baroncelli Riccardo , Cuevas-Fernández Francisco Borja , Becerra Sioly , Crouch JoAnne , Bettiol Wagner , Azcárate-Peril M. Andrea , Malapi-Wight Martha , Ortega Veronique , Betran Javier , Tenuta Albert , Dambolena José S. , Esker Paul D. , Revilla Pedro , Jackson-Ziems Tamra A. , Hiltbrunner Jürg , Munkvold Gary , Buhiniček Ivica , Vicente-Villardón José L. , Sukno Serenella A. , Thon Michael R. 
Published: May 2022

AbstractBackgroundColletotrichum graminicola, the causal agent of maize anthracnose, is an important crop disease worldwide. Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. The genus Colletotrichum is largely recognized as asexual, but several species have been reported to have a sexual cycle. Here, we employed a population genomics approach to investigate the genetic diversity and reproductive biology of C. graminicola isolates infecting maize. We sequenced 108 isolates of C. graminicola collected in 14 countries using restriction site-associated DNA sequencing (RAD-Seq) and whole-genome sequencing (WGS).ResultsClustering analyses based on single-nucleotide polymorphisms showed populational differentiation at a global scale, with three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen, and geographic subdivision. Distinct levels of genetic diversity were observed between these clades, suggesting different evolutionary histories. Intra and inter-continental migration was predicted between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality and evidence of genetic recombination were detected from the analysis of linkage disequilibrium and the pairwise homoplasy index (PHI) test for clonality. We show evidence that even if rare (possibly due to losses of sex and meiosis-associated genes) C. graminicola can undergo sexual recombination based on lab assays and genomic analyses.ConclusionsOur results support hypotheses of intra and intercontinental pathogen migration and genetic recombination with great impact on C. graminicola population structure.
Climate and ant richness explain the global distribution of ant-plant mutualisms
Authors: Luo Yangqing , Taylor Amanda , Weigelt Patrick , Guénard Benoit , Economo Evan P. , Nowak Arkadiusz , Inderjit  , Kreft Holger 
Published: May 2022

AbstractBiotic interactions are known to play an important role in shaping species geographic distributions and diversity patterns. However, the role of mutualistic interactions in shaping global diversity patterns remains poorly quantified, particularly with respect to interactions with invertebrates. Moreover, it is unclear how the nature of different mutualisms interacts with abiotic drivers and affects diversity patterns of mutualistic organisms. Here, we present a global-scale biogeographic analysis of three different ant-plant mutualisms, differentiating between plants bearing domatia, extrafloral nectaries (EFNs), and elaiosomes, based on comprehensive geographic distributions of ∼15,000 flowering plants and ∼13,000 ant species. Domatia and extrafloral nectaries involve indirect plant defenses provided by ants, while elaiosomes attract ants to disperse seeds. Our results show distinct biogeographic patterns of different ant-plant mutualisms, with domatium- and EFN-bearing plant richness decreasing sharply from the equator towards the poles, while elaiosome-bearing plants prevail at mid-latitudes. Contemporary climate, especially mean annual temperature and precipitation, emerge as the most important predictor of ant-associated plant diversity. In hot and moist regions, typically the tropics, domatium- and EFN-bearing plant richness increases with related ant guild richness, while in warm regions plants with elaiosomes are strongly linked to interacting ants. Our results suggest that ant richness in combination with climate drives the spatial variation of plants bearing domatia, extrafloral nectaries, and elaiosomes, highlighting the importance of mutualistic interactions for understanding plant biogeography and its response to global change.
Pnpt1 mediates NLRP3 inflammasome activation by MAVS and metabolic reprogramming in macrophages
Authors: Hsu Chia George , Li Wenjia , Sowden Mark , Chávez Camila Lage , Berk Bradford C. 
Published: May 2022

AbstractPolyribonucleotide nucleotidyltransferase 1 (Pnpt1) plays critical roles in mitochondrial homeostasis by controlling mitochondrial RNA (mt-RNA) processing, trafficking and degradation. Pnpt1 deficiency results in mitochondrial dysfunction that triggers a Type I interferon response, suggesting a role in inflammation. However, the role of Pnpt1 in inflammasome activation remains largely unknown. In this study, we generated myeloid-specific Pnpt1-knockout mice, and demonstrated that Pnpt1 depletion enhanced interleukin-1 beta (IL-1β) and interleukin-18 (IL-18) secretion in mouse sepsis models. Using cultured peritoneal and bone marrow-derived macrophages we demonstrated that Pnpt1 regulated NLRP3 inflammasome dependent IL-1β release in response to lipopolysaccharides (LPS), followed by nigericin, ATP or poly (I:C) treatment. Pnpt1 deficiency in macrophages increased glycolysis after LPS, and mt-reactive oxygen species (mt-ROS) after NLRP3 inflammasome activation. Pnpt1 activation of the inflammasome was dependent on both increased glycolysis and expression of the mitochondrial antiviral-signaling protein (MAVS), but not NF-κB signaling. Collectively, these data strengthen the concept that Pnpt1 is an important mediator of inflammation as shown by activation of the NLRP3 inflammasome in mouse sepsis and cultured macrophages.
Cyst size variability in invasive American Artemia franciscana Kellogg, 1906 (Branchiopoda: Anostraca) in Asia: a commercial approach
Authors: Wu Xiao-Fang , Shen Chun-Yang , Fu Chun-Zheng , Yang Ning , Pei-Zheng Wang , Eimanifar Amin , Asem Alireza 
Published: May 2022

ABSTRACTArtemia is the most common live food which is used in aquaculture worldwide. This study reports on biometrical variation of introduced American Artemia franciscana cyst from 24 non-native localities and two native habitats in Asia and USA, respectively. Results showed the largest diameter of untreated cyst, diameter of decapsulated cyst and thicker chorion ordinarily belong to invasive populations. Because of the small cysts, which have an effect on increasing quantity per unit weight and could be the cause of increased hatching efficiency, commercial productions of A. franciscana cyst from native sources should potentially be considered higher quality than productions from non-indigenous environments. Principal Component Analysis revealed that all cyst batches from San Francisco Bay were classified in one group and the most invasive populations could arrange in other separated group. Although, diameter of decapsulated cyst and chorion thickness showed a negative and significant correlation among invasive populations, there was no significant relationship within native populations. These observations contrast with biometrical patterns of parthenogenetic populations.
ATXN2 is a target of N-terminal proteolysis
Authors: Chitre Monika , Emery Patrick 
Published: May 2022

AbstractSpinocerebellar ataxia 2 (SCA2) is a neurodegenerative disorder caused by the expansion of the poly-glutamine (polyQ) tract of Ataxin-2 (ATXN2). Other polyQ-containing proteins such as ATXN7 and huntingtin are associated with the development of neurodegenerative diseases when their N-terminal polyQ domains are expanded. Furthermore, they undergo proteolytic processing events that produce N-terminal fragments that include the polyQ stretch, which are implicated in pathogenesis. Interestingly, N-terminal ATXN2 fragments were reported in a brain extract from a SCA2 patient, but it is currently unknown whether an expanded polyQ domain contributes to ATXN2 proteolytic susceptibility. Here, we used transient expression in HEK293 cells to determine whether ATXN2 is a target for specific N-terminal proteolysis. We found that ATXN2 proteins with either normal or expanded polyQ stretches undergo proteolytic cleavage releasing an N-terminal polyQ-containing fragment. We identified a short amino acid sequence downstream of the polyQ domain that is necessary for N-terminal cleavage of full-length ATXN2 and sufficient to induce proteolysis of a heterologous protein. However, this sequence is not required for cleavage of a short ATXN2 isoform produced from an alternative start codon located just upstream of the CAG repeats encoding the polyQ domain. Our study extends our understanding of ATXN2 posttranslational regulation by revealing that this protein can be the target of specific proteolytic cleavage events releasing polyQ-containing products that are modulated by the N-terminal domain of ATXN2. N-terminal ATXN2 proteolysis of expanded polyQ domains might contribute to SCA2 pathology, as observed in other neurodegenerative disorders caused by polyQ domain expansion.
The metastatic capacity of high-grade serous ovarian cancer cells changes along disease progression: inhibition by mifepristone
Authors: Ritch Sabrina J. , Noman Abu S. M. , Goyeneche Alicia A. , Telleria Carlos M. 
Published: May 2022

ABSTRACTBackgroundReductionist two-dimensional (2D) in vitro assays have long been the standard for studying the metastatic abilities of cancer cells. However, tri-dimensional (3D) organotypic models provide a more complex environment, closer to that seen in patients, and thereby provide a more accurate representation of their true capabilities. Our laboratory has previously shown that the antiprogestin and antiglucocorticoid mifepristone can reduce the growth, adhesion, migration, and invasion of various aggressive cancer cells assessed using 2D assays. In this study, we characterize the metastatic capabilities of high-grade serous ovarian cancer cells generated along disease progression, in both 2D and 3D assays, and the ability of cytostatic doses of mifepristone to inhibit them.MethodsHigh-grade serous ovarian cancer cells collected from two separate patients at different stages of their disease were used throughout the study. The 2D wound healing and Boyden chamber assays were used to study migration, while a layer of extracellular matrix was added to the Boyden chamber to study invasion. A 3D organotypic model, composed of fibroblasts embedded in collagen I and topped with a monolayer of mesothelial cells was used to further study cancer cell adhesion and mesothelial displacement. All assays were studied in cells representing different stages of disease progression in the absence or presence of cytostatic doses of mifepristone.Results2D in vitro assays demonstrated that the migration and invasive rates of the cells isolated from both patients decreased along disease progression. Conversely, in both patients, cells representing late-stage disease demonstrated a higher adhesion capacity to the 3D organotypic model than those representing an early-stage disease. This adhesive behavior is associated with the in vivo tumor capacity of the cells. Regardless of these differences in adhesive, migratory, and invasive behavior among the experimental protocols used, cytostatic doses of mifepristone were able to inhibit the adhesion, migration, and invasion rates of all cells studied, regardless of their basal capabilities over reductionist or organotypic metastatic in vitro model systems. Finally, we demonstrate that when cells acquire the capacity to grow spontaneously as spheroids, they do attach to a 3D organotypic model system when pre-incubated with conditioned media. Of relevance, mifepristone was able to cause dissociation or “cleavage” of these multicellular structures.ConclusionDifferences in cellular behaviours were observed between reductionist 2D and 3D assays when studying the metastatic capabilities of high-grade serous ovarian cancer cells representing disease progression. Mifepristone inhibited these metastatic capabilities in all assays studied.
Comparative genomic and crystal structure analyses identify a collagen glucosyltransferase from Acanthamoeba Polyphaga Mimivirus
Authors: Wu Wenhui , Kim Jeong Seon , Richards Stephen J. , Buhlheller Christoph , Bailey Aaron O. , Russell William , Chen Tiantian , Chen Tingfei , Chen Zhenhang , Liang Bo , Yamauchi Mitsuo , Guo Houfu 
Published: May 2022

AbstractHumans and Acanthamoeba Polyphaga Mimivirus share numerous homologous genes, including collagens and collagen-modifying enzymes. To explore the homology, we performed a genome-wide comparison between human and mimivirus using DELTA-BLAST (Domain Enhanced Lookup Time Accelerated BLAST) and identified 52 new mimiviral proteins that are homologous with human proteins. To gain functional insights into mimiviral proteins, their human protein homologs were organized into Gene Ontology (GO) and REACTOME pathways to build a functional network. Collagen and collagen-modifying enzymes form the largest subnetwork with most nodes. Further analysis of this subnetwork identified a putative collagen glycosyltransferase R699. Protein expression test suggested that R699 is highly expressed in E coli, unlike the human collagen-modifying enzymes. Enzymatic activity assays showed that R699 catalyzes the conversion of unique galactosylhydroxylysine within the GXXXUG motif (U=galactosylhydroxylysine) to glucosylgalactosylhydroxylysine on collagen using uridine diphosphate glucose (UDP-Glc) as a sugar donor, suggesting R699 is a mimiviral collagen galactosylhydroxylysyl glucosyltransferase (GGT) with defined substrate specificity. Structural study of R699 produced the first crystal structure of a collagen GGT with a visible UDP-Glc. Sugar moiety of the UDP-Glc resides in a previously unrecognized pocket. Mn2+ coordination and nucleoside-diphosphate binding site are conserved among GGT family members and critical for R699’s collagen GGT activity. To facilitate further analysis of human and mimiviral homologous proteins, we presented an interactive and searchable genome-wide comparison website for quickly browsing human and Acanthamoeba Polyphaga Mimivirus homologs, which is available at RRID Resource ID: SCR_022140 or https://guolab.shinyapps.io/app-mimivirus-publication/.
Nitric oxide-induced tyrosine nitration of TrkB impairs BDNF signaling and restrains neuronal plasticity
Authors: Biojone Caroline , Casarotto Plinio C , Cannarozzo Cecilia , Fred Senem Merve , Herrera-Rodríguez Rosa , Lesnikova Angelina , Voipio Mikko , Castrén Eero 
Published: May 2022

AbstractNitric oxide has been long recognized as an important modulator of neural plasticity, but characterization of the molecular mechanisms involved - specially the guanylyl cyclase-independent ones - has been challenging. There is evidence that NO could modify BDNF-TRKB signaling, a key mediator of neuronal plasticity. However, the mechanism underlying the interplay of NO and TRKB remains unclear. Here we show that nitric oxide induces nitration of the tyrosine 816 in the TRKB receptorin vivoandin vitro,and that post-translational modification inhibits TRKB phosphorylation and binding of phospholipase Cγ1 (PLCγ1) to this same tyrosine residue. Additionally, nitration triggers clathrin-dependent endocytosis of TRKB through the adaptor protein AP2M and ubiquitination, thereby increasing translocation of TRKB away from the neuronal surface and directing it towards lysosomal degradation. Accordingly, inhibition of nitric oxide increases TRKB phosphorylation and TRKB-dependent neurite branching in neuronal cultures.In vivo,chronic inhibition of neuronal nitric oxide synthase (nNOS) dramatically reduced TRKB nitration and facilitated TRKB signaling in the primary visual cortex, and promoted a shift in ocular dominance upon monocular deprivation in the visual cortex - an indicator of increased plasticity. Altogether, our data describe and characterize a new molecular brake on plasticity, namely nitration of TRKB receptors.Significance statementWe described the nitration of TRKB receptors at the tyrosine residue 816 as a new post-translational modification (PTM) that restrains the signaling of the neurotrophic factor BDNF in neurons. This new PTM leads to endocytosis and degradation of the TRKB receptors. Intriguingly, this mechanism is tonically active under physiological conditionsin vivo,and it is important for restricting ocular dominance plasticity in the visual cortex. This mechanism directly links two major systems involved in brain plasticity, BDNF/TRKB and nitric oxide. Our data provides a model forhowNO production from nNOS can compromise TRKB function, and for the effects of nNOS inhibitors promoting plasticity.