bluuebunny/crossref_metadata_2025_split huggingface dataset:
A chromosome-level assembly of the cat flea genome uncovers rampant gene duplication and genome size plasticity
Authors: Driscoll Timothy P. , Verhoeve Victoria I. , Gillespie Joseph J. , Johnston J. Spencer , Guillotte Mark L. , Rennoll-Bankert Kristen E. , Rahman M. Sayeedur , Hagen Darren , Elsik Christine G. , Macaluso Kevin R. , Azad Abdu F. 
Published: April 2020

AbstractBackgroundFleas (Insecta: Siphonaptera) are small flightless parasites of birds and mammals; their blood-feeding can transmit many serious pathogens (i.e. the etiological agents of bubonic plague, endemic and murine typhus). The lack of flea genome assemblies has hindered research, especially comparisons to other disease vectors. Accordingly, we sequenced the genome of the cat flea,Ctenocephalides felis, an insect with substantial human health and veterinary importance across the globe.ResultsBy combining Illumina and PacBio sequencing with Hi-C scaffolding techniques, we generated a chromosome-level genome assembly forC.felis. Unexpectedly, our assembly revealed extensive gene duplication across the entire genome, exemplified by ∼38% of protein-coding genes with two or more copies and over 4,000 tRNA genes. A broad range of genome size determinations (433-551 Mb) for individual fleas sampled across different populations supports the widespread presence of fluctuating copy number variation (CNV) inC. felis. Similarly broad genome sizes were also calculated for individuals ofXenopsylla cheopis(Oriental rat flea), indicating that this remarkable “genome-in-flux” phenomenon could be a siphonapteran-wide trait. Finally, from theC. felissequence reads we also generated closed genomes for two novel strains ofWolbachia, one parasitic and one symbiotic, found to co-infect individual fleas.ConclusionRampant CNV inC.felishas dire implications for gene-targeting pest control measures and stands to complicate standard normalization procedures utilized in comparative transcriptomics analysis. Coupled with co-infection by novelWolbachiaendosymbionts – potential tools for blocking pathogen transmission – these oddities highlight a unique and underappreciated disease vector.
Microbial interactions in the mosquito gut determineSerratiacolonization and blood feeding propensity
Authors: Kozlova Elena V. , Hegde Shivanand , Roundy Christopher M. , Golovko George , Saldaña Miguel A. , Hart Charles E. , Anderson Enyia R , Hornett Emily A , Khanipov Kamil , Popov Vsevolod L. , Pimenova Maria , Zhou Yiyang , Fovanov Yuriy , Weaver Scott C. , Routh Andrew L. , Heinz Eva , Hughes Grant L. 
Published: April 2020

AbstractHow microbe-microbe interactions dictate microbial complexity in the mosquito gut is unclear. Previously we found thatSerratia, a gut symbiont that alters vector competence and is being considered for vector control, poorly colonizedAedes aegyptiyet was abundant inCulex quinquefasciatusreared under identical conditions. To investigate the incompatibility betweenSerratiaandAe. aegypti, we characterized two distinct strains ofSerratia marcescensfromCx. quinquefasciatusand examined their ability to infectAe. aegypti. BothSerratiastrains poorly infectedAe. aegypti, but when microbiome homeostasis was disrupted, the prevalence and titers ofSerratiawere similar to the infection in its native host. Examination of multiple genetically diverseAe. aegyptilines found microbial interference toS. marcescenswas commonplace, however one line ofAe. aegyptiwas susceptible to infection. Microbiome analysis of resistant and susceptible lines indicated an inverse correlation betweenEnterobacteriaceaebacteria andSerratia, and experimental co-infections in a gnotobiotic system recapitulated the interference phenotype. Furthermore, we observed an effect on host behaviour;Serratiaexposure toAe. aegyptidisrupted their feeding behaviour, and this phenotype was also reliant on interactions with their native microbiota. Our work highlights the complexity of host-microbe interactions and provides evidence that microbial interactions influence mosquito behaviour.
Molecular basis for the recognition of steroidogenic acute regulatory protein by the 14-3-3 protein family
Authors: Tugaeva Kristina V. , Titterington James , Sotnikov Dmitriy V. , Maksimov Eugene G. , Antson Alfred A. , Sluchanko Nikolai N. 
Published: April 2020

ABSTRACTSteroidogenesis in adrenals and gonads starts from cholesterol transport to mitochondria by the steroidogenic acute regulatory protein STARD1, containing a mitochondrial import sequence followed by a cholesterol-binding START domain. Although mutations in this protein have been linked to lipoid congenital adrenal hyperplasia, the mechanism of steroidogenesis regulation by the STARD1 remains debatable, hypothetically involving a molten-globule structural transition and interaction with 14-3-3 proteins. We show that, while the isolated START domain does not interact with 14-3-3, interaction is enabled by STARD1 phosphorylation at Ser57, close to the mitochondrial peptide cleavage site. Biochemical analysis of the STARD1 affinity towards 14-3-3 and crystal structures of 14-3-3 complexes with Ser57 and Ser195 phosphopeptides, suggest distinct roles of site-specific phosphorylations in recruiting 14-3-3, to modulate STARD1 activity, processing and import to mitochondria. Phosphorylation at Ser195 creates a unique conditional site, that could only bind to 14-3-3 upon partial unfolding of the START domain.
Integrin-linked kinase is a key signal factor involved in Nogo-66-induced inhibition of neurite outgrowth
Authors: Yu Ya-ping , Wang Qiang-ping , Shen Jian-Ying , Xiong Nan-xiang , Yu Hua , Fu Peng , Wang Lei , Yuan Ye , Zhao Hong-yang , Zhang Fang-cheng , Pool Hendrik 
Published: April 2020

AbstractNogo-66, the extracellular domain of Nogo-A, has been identified as the most important myelin-associated neuronal growth inhibitor. Evidence suggested that Nogo-66 exert its neurite inhibition effect via a Nogo-66/Protein kinase B (PKB)/Glycogen synthase kinase-3β (GSK-3β)/tau signaling pathway. Integrin-linked kinase (ILK) is a serine/threonine kinase mediating axon upstream growth of PKB and GSK-3β. However, the contribution of ILK to the Nogo-66-induced inhibition of neurite, is not clear. In this study, we set out to reveal the role of ILK on Nogo-66 signalingin vitroandin vivo. To deteremine this directly, Recombinant adenoviruses were constructed to upregulate or downregulate the expresioon of ILK in Neuro 2a (N2a)and analysis the change of downstream molecule and neurite length. The results showed that Nogo-66 inhibited the phosphorylation of ILK, while ILK regulated the phosphorylation of PKB and GSK-3β, and the expression of tau in Nogo-66-treated N2a cells. ILK overexpression through lentivirus vector transfection reduced the inhibitory effect of neurite outgrowth induced by Nogo-66 in cortical neurons. The Tau expression in the complete spinal cord transection rat model was promoted by the overexpression of ILK. Our findings indicated that ILK is a key signal factor involved in Nogo-66-induced inhibition of neurite outgrowth. The mechanism of Nogo-66 signaling pathway was further explained and a proper target for the promotion of neural regeneration was also provided by this study.
Regional transmission and reassortment of 2.3.4.4b highly pathogenic avian influenza (HPAI) viruses in Bulgarian poultry 2017/18
Authors: Venkatesh Divya , Brouwer Adam , Ellis Richard , Goujgoulova Gabriela , Seekings James , Brown Ian H. , Lewis Nicola S. 
Published: April 2020

AbstractBetween 2017 and 2018, several farms across Bulgaria reported outbreaks of H5 HPAI viruses. In this study we use genomic and traditional epidemiological analyses to trace the origin and subsequent spread of these outbreaks within Bulgaria. Both methods indicate two separate incursions, one restricted to the North-Eastern region of Dobrich, and another largely restricted to Central and Eastern Bulgaria including places such as Plovdiv, Sliven and Stara Zagora, as well as one virus from the Western region of Vidin. Both outbreaks likely originate from different European 2.3.4.4b virus ancestors circulating in 2017. The viruses were likely introduced by wild birds or poultry trade links in 2017 and have continued to circulate, but due to lack of contemporaneous sampling and sequences from wild bird viruses in Bulgaria, the precise route and timing of introduction cannot be determined. Analysis of whole genomes indicates complete lack of reassortment in all segments but the MP, which presents as multiple smaller clusters associated with different European 2.3.4.4b viruses. Ancestral reconstruction of host states of the HA gene of viruses involved in the outbreaks suggests that transmission is driven by domestic ducks into galliform poultry. Thus, according to present evidence we suggest that surveillance of domestic ducks as epidemiologically relevant species for subclinical infection. Monitoring spread due to movement between farms within regions and links to poultry production systems in European countries can help to predict and prevent future outbreaks.
Spatiotemporal development of cuticular ridges on leaf surfaces ofHevea brasiliensisalters insect attachment
Authors: Surapaneni Venkata A. , Bold Georg , Speck Thomas , Thielen Marc 
Published: April 2020

AbstractCuticular ridges on plant surfaces can control insect adhesion and wetting behaviour and might also offer stability to underlying cells during growth. The growth of the plant cuticle and its underlying cells possibly results in changes in the morphology of cuticular ridges and may also affect their function. We present spatial and temporal patterns in cuticular ridge development on the leaf surfaces of the model plant,Hevea brasiliensis. We have identified, by confocal laser scanning microscopy of polymer leaf replicas, an acropetally directed progression of ridges during the ontogeny ofHevea brasiliensisleaf surfaces. The use of Colorado potato beetles(Leptinotarsa decemlineata)as a model insect species has shown that the changing dimensions of cuticular ridges on plant leaves during ontogeny have a significant impact on insect traction forces and act as an effective indirect defence mechanism. The traction forces of walking insects are significantly lower on mature leaf surfaces compared with young leaf surfaces. The measured walking traction forces exhibit a strong negative correlation with the dimensions of the cuticular ridges.
COVID-19 Knowledge Graph: a computable, multi-modal, cause-and-effect knowledge model of COVID-19 pathophysiology
Authors: Domingo-Fernández Daniel , Baksi Shounak , Schultz Bruce , Gadiya Yojana , Karki Reagon , Raschka Tamara , Ebeling Christian , Hofmann-Apitius Martin , Kodamullil Alpha Tom 
Published: April 2020

AbstractSummaryThe past few weeks have witnessed a worldwide mobilization of the research community in response to the novel coronavirus (COVID-19). This global response has led to a burst of publications on the pathophysiology of the virus, yet without coordinated efforts to organize this knowledge, it can remain hidden away from individual research groups. By extracting and formalizing this knowledge in a structured and computable form, as in the form of a knowledge graph, researchers can readily reason and analyze this information on a much larger scale. Here, we present the COVID-19 Knowledge Graph, an expansive cause-and-effect network constructed from scientific literature on the new coronavirus that aims to provide a comprehensive view of its pathophysiology. To make this resource available to the research community and facilitate its exploration and analysis, we also implemented a web application and released the KG in multiple standard formats.AvailabilityThe COVID-19 Knowledge Graph is publicly available under CC-0 license athttps://github.com/covid19kgandhttps://bikmi.covid19-knowledgespace.de.Contactalpha.tom.kodamullil@scai.fraunhofer.deSupplementary informationSupplementary data are available online.
Mating-type locus rearrangement leads to shift from homothallism to heterothallism inCitrus-associatedPhyllostictaspecies
Authors: Petters-Vandresen Desirrê Alexia Lourenço , Rossi Bruno Janoski , Groenewald Johannes Z. , Crous Pedro W. , Machado Marcos Antonio , Stukenbrock Eva H. , Glienke Chirlei 
Published: April 2020

AbstractCurrently, eightPhyllostictaspecies are known to be associated withCitrushosts, incorporating endophytic and pathogenic lifestyles. As sexual reproduction is a key factor involved in host-interaction, it could be related to the differences in lifestyle. To evaluate this hypothesis, we characterized the mating-type loci of sixCitrus-associatedPhyllostictaspecies from whole genome assemblies. Mating-type genes are highly variable in their sequence content, but the genomic locations and organization of the mating-type loci are conserved.Phyllosticta citriasiana, P. citribraziliensisandP. paracitricarpaare heterothallic, andP. citrichinaensiswas confirmed to be homothallic. In addition, theP. citrichinaensis MAT1-2idiomorph occurs in a separate location from the mating-type locus. Ancestral state reconstruction suggests that homothallism is the ancestral thallism state inPhyllosticta, with a shift to heterothallism inPhyllostictaspecies that are pathogenic toCitrus. Moreover, the homothallic strategies ofP. capitalensisandP. citrichinaensisresult from independent evolutionary events. As the pathogenic speciesP. citriasiana, P. citricarpaandP. paracitricarpaare heterothallic and incapable of selfing, disease management practices focused in preventing the occurrence of sexual reproduction could assist in the control of Citrus Black Spot and Citrus Tan Spot diseases. This study emphasizes the importance of studyingCitrus-Phyllostictainteractions under evolutionary and genomic perspectives, as these approaches can provide valuable information about the association betweenPhyllostictaspecies and their hosts, and also serve as guidance for the improvement of disease management practices.
Suitability of resampled multispectral datasets for mapping flowering plants in the Kenyan savannah
Authors: Makori David M. , Abdel-Rahman Elfatih M. , Landmann Tobias , Mutanga Onisimo , Odindi John , Nguku Evelyn , Tonnang Henry E. Z , Raina Suresh 
Published: April 2020

AbstractPollination services and honeybee health in general are important in the African savannahs particularly to farmers who often rely on honeybee products as a supplementary source of income. Therefore, it is imperative to understand the floral cycle, abundance and spatial distribution of melliferous plants in the African savannah landscapes. Furthermore, placement of apiaries in the landscapes could benefit from information on spatiotemporal patterns of flowering plants, by optimising honeybees’ foraging behaviours, which could improve apiary productivity. This study sought to assess the suitability of simulated multispectral data for mapping melliferous (flowering) plants in the African savannahs. Bi-temporal AISA Eagle hyperspectral images, resampled to four sensors (i.e. WorldView-2, RapidEye, Spot-6 and Sentinel-2) spatial and spectral resolutions, and a 10-cm ultra-high spatial resolution aerial imagery coinciding with onset and peak flowering periods were used in this study. Ground reference data was collected at the time of imagery capture. The advanced machine learning random forest (RF) classifier was used to map the flowering plants at a landscape scale and a classification accuracy validated using 30% independent test samples. The results showed that 93.33%, 69.43%, 67.52% and 82.18% accuracies could be achieved using WorldView-2, RapidEye, Spot-6 and Sentinel-2 data sets respectively, at the peak flowering period. Our study provides a basis for the development of operational and cost-effective approaches for mapping flowering plants in an African semiarid agroecological landscape. Specifically, such mapping approaches are valuable in providing timely and reliable advisory tools for guiding the implementation of beekeeping systems at a landscape scale.
Ecological and anthropogenic drivers of large carnivore depredation on sheep in Europe
Authors: Gervasi Vincenzo , Linnell John D. C. , Berce Tomaž , Boitani Luigi , Cerne Rok , Cretois Benjamin , Ciucci Paolo , Duchamp Christophe , Gastineau Adrienne , Grente Oksana , Hilfiker Daniela , Huber Djuro , Iliopoulos Yorgos , Karamanlidis Alexandros A. , Marucco Francesca , Mertzanis Yorgos , Männil Peep , Norberg Harri , Pagon Nives , Pedrotti Luca , Quenette Pierre-Yves , Reljic Slaven , Salvatori Valeria , Talvi Tõnu , von Arx Manuela , Gimenez Olivier 
Published: April 2020

SUMMARYSharing space with large carnivores on a human-dominated continent like Europe results in multiple conflictful interactions with human interests, of which depredation on livestock is the most widespread. Wildlife management agencies maintain compensation programs for the damage caused by large carnivores, but the long-term effectiveness of such programs is often contested. Therefore, understanding the mechanisms driving large carnivore impact on human activities is necessary to identify key management actions to reduce it.We conducted an analysis of the impact by all four European large carnivores on sheep husbandry in 10 European countries, during the period 2010-2015. We ran a hierarchical Simultaneous Autoregressive model, to assess the influence of ecological and anthropogenic factors on the spatial and temporal patterns in the reported depredation levels across the continent.On average, about 35,000 sheep were compensated in the ten countries as killed by large carnivores annually, representing about 0.5% of the total sheep stock. Of them, 45% were recognized as killed by wolves, 24% by wolverines, 19% by lynx and 12% by bears. At the continental level, we found a positive relationship between wolf distribution and the number of compensated sheep, but not for the other three species. Impact levels were lower in the areas where large carnivore presence has been continuous compared to areas where they disappeared and recently returned. The model explained 62% of the variation in the number of compensated sheep per year in each administrative unit. Only 13% of the variation was related to the ecological components of the process.Synthesis and Applications:Large carnivore distribution and local abundance alone are poor predictors of large carnivore impact on livestock at the continental level. A few individuals can produce high damage, when the contribution of environmental, social and economic systems predisposes for it, whereas large populations can produce a limited impact when the same components of the system reduce the probability that depredations occur. Time seems to play in favour of a progressive reduction in the costs associated with coexistence, provided that the responsible agencies focus their attention both on compensation and co-adaptation.
Genomics of experimental diversification ofPseudomonas aeruginosain cystic fibrosis lung-like conditions
Authors: Schick Alana , Kassen Rees 
Published: April 2020

AbstractPseudomonas aeruginosais among the most problematic opportunistic pathogens for adults with cystic fibrosis (CF), causing repeated and resilient infections in the lung and surrounding airways. Evidence suggests that long-term infections are associated with diversification into specialized types but the underlying cause of that diversification and the effect it has on the persistence of infections remains poorly understood. Here, we use evolve and resequence experiments to investigate the genetic changes accompanying rapid,de novophenotypic diversification in lab environments designed to mimic two aspects of human lung ecology: spatial structure and complex nutritional content. After ∼220 generations of evolution, we find extensive genetic variation present in all environments, including those that most closely resemble the CF lung, attributable to a combination of high mutation supply rates resulting from large population sizes and the complex ecological conditions imposed by resource complexity and spatial structure. We use the abundance and frequency of nonsynonymous and synonymous mutations to estimate the ratio of mutations that are selectively neutral (hitchhikers) to those that are under selection (drivers). A significantly lower proportion of driver mutations in spatially structured populations suggests that reduced dispersal generates subpopulations with reduced effective population size, decreasing the supply of beneficial mutations and causing more divergent evolutionary trajectories. The genes most commonly mutated tend to impact regulatory functions linked to a range of CF-associated phenotypes, including one gene that confers antibiotic resistance despite the absence of antibiotic selection in our experiment, but do not appear to be specific to CF-like conditions arising from antimicrobial treatment, immune system suppression, or competition from other microbial species. Our results are consistent with models of adaptation that see the first mutations fixed during adaptation to a stressful environment being those that are broadly beneficial across a range of environments.
Customer incivility and service sabotage in the hotel industry
Authors: Cheng Bao , Guo Gongxing , Tian Jian , Shaalan Ahmed 
Published: April 2020

PurposeUsing equity theory, this study aims to examine the role of customer incivility in effecting service sabotage among hotel employees by recognizing the mediating role of revenge motivation and the moderating effect of emotion regulation.Design/methodology/approachA multi-wave, multi-source questionnaire survey was conducted with 291 employee–supervisor dyads at chain hotels in Shenzhen, China. Previously developed and validated measures for customer incivility, revenge motivation, emotion regulation and service sabotage were adopted to test the hypotheses.FindingsCustomer incivility increased employees’ revenge motivation and service sabotage. Emotion regulation acted as a boundary condition for customer incivility’s direct effect on revenge motivation and its indirect effect on service sabotage through revenge motivation. Cognitive reappraisal mitigated the detrimental influence of customer incivility, whereas expressive suppression worsened its adverse effects.Practical implicationsManagers should monitor and deter the emergence of uncivil behaviors, provide psychological support for employees experiencing customer incivility and encourage these employees to use cognitive reappraisal rather than expressive suppression as an emotion regulation strategy.Originality/valueTo the authors’ knowledge, no prior research has investigated the customer incivility–service sabotage relationship in the hotel industry. This study sheds light on how customer incivility can motivate service sabotage among hotel employees. Furthermore, the authors used equity theory rather than the commonly adopted resources perspective to offer new insights into the customer incivility–service sabotage relationship.