bluuebunny/crossref_metadata_2025_split huggingface dataset:
Bipartite viral RNA genome heterodimerization influences genome packaging and virion thermostability
Authors: Zhou Yiyang , Routh Andrew L. 
Published: July 2022

AbstractDiverse RNA-RNA interactions occur throughout the lifecycle of RNA viruses, including genome dimerization or multimerization through non-covalent association of two or more genomic segments. Both homo-dimerization of retrovirus genomic RNA and hetero-multimerization of genomic segments of multipartite viruses are recognized as important factors that govern genome packaging. The heterodimer of the bipartite alphanodaviruses represents a unique case as its formation is conserved among different virus species but is only observed within the context of fully assembled virus particles. In spite of this, the RNA sequences involved in heterodimerization are unknown. It also remains unclear whether the formation of this heterodimer might impact any stage of the virus lifecycle. In this study, we used Flock House virus (FHV) as a model system to uncover the nucleotide composition of the heterodimer and dissected the impact of heterodimer formation upon numerous stages of the virus lifecycle. We developed a novel Next-Generation Sequencing (NGS) approach called “XL-ClickSeq” to probe candidate heterodimer sequences. We found that the heterodimer is formed via intermolecular base-pairing and its formation is retained in defective virus particles. One heterodimer site was identified by thermodynamic prediction that, upon mutagenic disruption, exhibited significant deficiencies in genome packaging and encapsidation specificity to viral genomic RNA. Furthermore, we demonstrate that disruption of this RNA secondary structure directly impacts the thermostability of mature virus particles. These results demonstrated that the intermolecular RNA-RNA interactions within the encapsidated genome of an RNA virus can have an important impact on virus particle integrity and stability and thus its transmission to a new host.
The kinase Rio1 and a ribosome collision-dependent decay pathway survey the integrity of 18S rRNA cleavage
Authors: Parker Melissa D. , Getzler Adam J. , Karbstein Katrin 
Published: July 2022

AbstractThe 18S rRNA sequence is highly conserved, particularly at its 3’-end. In contrast, the sequence around the 3’-end is degenerate with similar sites nearby. How RNA is correctly processed by the endonuclease Nob1 is not known, especially because in vitro experiments have shown it to be error-prone. Here we used yeast genetics, biochemistry, and next generation sequencing to investigate a role for Rio1 in monitoring the 3’-end of 18S rRNA. We demonstrate that Nob1 can miscleave its rRNA substrate and that miscleaved rRNA accumulates upon bypassing the Rio1-mediated quality control step, but not in healthy cells with intact quality control mechanisms. Mechanistically, we show that Rio1 binding to miscleaved rRNA is weakened. Accordingly, excess Pno1 results in accumulation of miscleaved rRNA. Ribosomes containing miscleaved rRNA enter the polysomes and produce dominant negative growth defects, suggesting that they cause defects during translation. Our data strongly suggest that ribosome collisions identify these miscleaved 18S rRNA-containing ribosomes as partially functional and target them for degradation. Altogether, the data support a model in which Rio1 inspects the 3’-end of the nascent 18S rRNA, only removing Nob1 and Pno1 from the ribosomes with precisely cleaved 18S rRNA to prevent miscleaved 18S rRNA-containing ribosomes from erroneously engaging in translation, where they induce ribosome collisions. The data also demonstrate how ribosome collisions “purify” the cells of altered ribosomes with different functionalities, with important implications for the concept of ribosome heterogeneity.
TNF licenses macrophages to undergo rapid caspase-1, -11, and -8-mediated cell death that restricts Legionella pneumophila infection
Authors: Pollock Tzvi , R. Vázquez Marrero Víctor , Brodsky Igor E. , Shin Sunny 
Published: July 2022

AbstractThe inflammatory cytokine tumor necrosis factor (TNF) is associated with host defense against many intracellular pathogens, including Legionella pneumophila. Legionella causes the severe pneumonia Legionnaires’ Disease and predominantly affects individuals with a suppressed immune system, such as those receiving therapeutic TNF blockade to treat autoinflammatory disorders. TNF induces pro-inflammatory gene expression, cellular proliferation, and survival signals in certain contexts, but can also trigger programmed cell death in others. It remains unclear, however, which of the many downstream activities of TNF contribute to control of intracellular bacterial pathogens like Legionella. In this study, we demonstrate that TNF signaling licenses macrophages to die rapidly in response to Legionella infection. We find that TNF-licensed cells undergo rapid gasdermin-dependent, pyroptotic death downstream of inflammasome activation. We also find that TNF signaling upregulates components of the inflammasome response, and that the caspase-11 mediated non-canonical inflammasome is the first inflammasome to be activated, with caspase-1 and caspase-8 mediating delayed pyroptotic death. We find that all three caspases are collectively required for optimal TNF-mediated restriction of bacterial replication in macrophages. Furthermore, caspase-8 is required for control of pulmonary Legionella infection. These findings reveal a TNF-dependent mechanism in macrophages for the activation of rapid cell death that is collectively mediated by caspases-1, -8, and -11 and subsequent restriction of Legionella infection.
Unexpected higher convergence of human-great ape enteric viromes in central African forest than in a European zoo: A One Health analysis
Authors: Narat Victor , Salmona Maud , Kampo Mamadou , Heyer Thibaut , Mercier-Delarue Severine , Ranger Noémie , Rupp Stephanie , Ambata Philippe , Njouom Richard , Simon François , Le Goff Jérôme , Giles-Vernick Tamara 
Published: July 2022

AbstractHuman-animal pathogenic transmissions threaten both human and animal health, and the processes catalyzing zoonotic spillover and spillback are complex. Prior field studies offer partial insight into these processes but overlook animal ecologies and human perceptions and practices facilitating human-animal contact. Conducted in Cameroon and a European zoo, this holistic study elucidates these processes, integrating metagenomic, historical, anthropological and great ape ecological analyses, and real-time evaluation of human-great ape contact types and frequencies. Surprisingly, we find more enteric virome sharing between Cameroonian humans and great apes than in the zoo, a virome convergence between Cameroonian humans and gorillas, and adenovirus and enterovirus taxa as most frequently shared between Cameroonian humans and great apes. In addition to physical contact from hunting, meat handling and fecal exposure, overlapping human cultivation and gorilla pillaging in forest gardens explain these unexpected findings. Our multidisciplinary study identifies environmental co-use as a complementary mechanism for viral sharing.
A ready-to-use logistic Verhulst model implemented in R shiny to estimate growth parameters of microorganisms
Authors: Garel Marc , Izard Lloyd , Vienne Marthe , Nerini David , Ali Badr Al , Tamburini Christian , Martini Séverine 
Published: July 2022

AbstractIn microbiology, the estimation of the growth rate of microorganisms is a critical parameter to describe a new strain or characterize optimal growth conditions. Traditionally, this parameter is estimated by selecting subjectively the exponential phase of the growth, and then determining the slope of this curve section, by linear regression. However, for some experiments, the number of points to describe the growth can be very limited, and consequently such linear model will not fit, or the parameters estimation can much lower and strongly variable. In this paper, we propose a tools to estimate growth parameters using a logistic Verhulst model that take into account the entire growth curve for the estimation of the growth rate. The efficiency of such model is compared to the linear model. Finally, the novelty of our work is to propose a “Shiny-web application”, online, without any programming or modelling skills, to allow estimating growth parameters including growth rate, maximum population, and beginning of the exponential phase, as well as an estimation of their variability. The final results can be displayed in the form of a scatter plot representing the model, its efficiency and the estimated parameters are downloadable.
miR167-ARF8, an auxin-responsive module involved in the formation of root-knot nematode-induced galls in tomato
Authors: Noureddine Yara , Rocha Martine da , An Jing , Médina Clémence , Mejias Joffrey , Mulet Karine , Quentin Michael , Abad Pierre , Zouine Mohamed , Favery Bruno , Jaubert-Possamai Stéphanie 
Published: July 2022

AbstractRoot-knot nematodes (RKN) from genus Meloidogyne induce the dedifferentiation of root vascular cells into giant multinucleate feeding cells. These feeding cells result from an extensive reprogramming of gene expression in targeted root cells, as shown by transcriptomic analyses of galls or giant cells from various plant species.Small non-coding RNAs, and messenger RNAs from tomato (Solanum lycopersicum) galls and uninfected roots were sequenced. De novo microRNA prediction in the tomato genome identified microRNAs expressed in galls and uninfected roots. Statistical analyses identified 174 miRNA genes differentially expressed in galls at 7 and/or 14 days post infection (dpi).Integrative analyses combining small non-coding RNA and transcriptome datasets with the specific sequencing of cleaved transcripts identified miRNA targets in tomato galls. Functional analyses of promoter-GUS fusions and CRISPR-Cas9 mutants highlighted the role of the miR167-regulated transcription factor AUXIN RESPONSE FACTOR 8 (ARF8) in giant cell formation.
Proton and alpha radiation-induced mutational profiles in human cells
Authors: Delhomme Tiffany M. , Munteanu Maia , Buonanno Manuela , Grilj Veljko , Biayna Josep , Supek Fran 
Published: July 2022

AbstractIonizing radiation (IR) is known to be DNA damaging and mutagenic, however less is known about which mutational footprints result from exposures of human cells to different types of IR. We were interested in the mutagenic effects of particle radiation exposures on genomes of various human cell types, in order to gauge the genotoxic risks of galactic cosmic radiation, and of certain types of tumor radiotherapy. To this end, we exposed cultured cell lines from the human blood, breast and lung to intermittent proton and alpha particle (helium nuclei) beams at doses sufficient to considerably affect cell viability. Whole-genome sequencing revealed that mutation rates were not overall markedly increased upon proton and alpha exposures. However, there were changes in mutation spectra and distributions, such as the increases in clustered mutations and of certain types of indels and structural variants. The spectrum of mutagenic effects of particle beams may be cell-type and/or genetic background specific. Overall, the mutational effects of recurrent exposures to proton and alpha radiation on human cells in culture appear subtle, however further work is warranted to understand effects of long-term exposures on various human tissues.
Identification of an A20 critical region harboring missense variations that lead to autoinflammation
Authors: El Khouri Elma , Louvrier Camille , Assrawi Eman , Nguyen Alexandre , Piterboth William , Deshayes Samuel , Desdoits Alexandra , Copin Bruno , Le Moal Florence Dastot , Karabina Sonia-Athina , Amselem Serge , Aouba Achille , Giurgea Irina 
Published: July 2022

ABSTRACTA20 haploinsufficiency (HA20) is an autoinflammatory disease caused by heterozygous loss-of-function variations in TNFAIP3, the gene encoding the A20 protein. Diagnosis of HA20 is challenging due to its heterogeneous clinical presentation and the lack of pathognomonic symptoms. While the pathogenic effect of TNFAIP3 truncating variations is clearly established, that of missense variations is difficult to determine. Herein, we identified a novel TNFAIP3 variation, p.(Leu236Pro), located in the A20 Ovarian Tumor (OTU) domain and demonstrated its pathogenicity. In the patients’ primary cells, we observed reduced A20 levels explained by enhanced degradation. We showed a disrupted ability of A20_Leu236Pro to inhibit the NF-κB pathway. Review of previously reported TNFAIP3 missense variations revealed that only 3/7 are pathogenic. Through structural modeling we showed that the residues involved in OTU pathogenic missense variations establish common interactions. Interpretation of newly identified missense variations is challenging, requiring, as illustrated here, functional demonstration of their pathogenicity. Together with functional studies, in-silico structure analysis is a valuable approach that allowed us to unveil a region within the OTU domain critical for A20 function.
De novo assembly and annotation of the singing mouse genome
Authors: Smith Samantha K. , Frazel Paul W. , Khodadadi-Jamayran Alireza , Zappile Paul , Marier Christian , Okhovat Mariam , Brown Stuart , Long Michael A. , Heguy Adriana , Phelps Steven M 
Published: July 2022

AbstractBackgroundDeveloping genomic resources for a diverse range of species is an important step towards understanding the mechanisms underlying complex traits.Specifically, organisms that exhibit unique, accessible phenotypes-of-interests, allow researchers to address questions that may be ill-suited to traditional model organisms. We sequenced the genome and transcriptome of Alston’s singing mouse (Scotinomys teguina), an emerging model for social cognition and vocal communication. In addition to producing advertisement songs used for mate attraction and male-male competition, these rodents are diurnal, live at high-altitudes, and are obligate insectivores, providing opportunities to explore diverse physiological, ecological, and evolutionary questions.ResultsUsing PromethION, Illumina, and PacBio sequencing, we produced an annotated genome and transcriptome, which were validated using gene expression and functional enrichment analyses. To assess the usefulness of our assemblies, we performed single nuclei sequencing on cells of the orofacial motor cortex, a brain region implicated in song coordination, identifying 12 cell types.ConclusionsThese resources will provide the opportunity to identify the molecular basis of complex traits in singing mice as well as to contribute data that can be used for large-scale comparative analyses.
Success in collaborative construction through the lens of project delivery elements
Authors: Moradi Sina , Kähkönen Kalle 
Published: July 2022

PurposeThe emergence of collaborative delivery models and working practices in construction industry has created a potential area for project success research. Previous studies have addressed success factors of various collaborative delivery models (e.g. alliance and partnering). However, there is currently very limited research-based knowledge concerning core success factors for different collaborative delivery models, exploring the commonalities. Thus, this study aims to conceptualize a success model for collaborative construction projects by identifying and structuring their core success factors through the lens of project delivery elements.Design/methodology/approachA systematic literature review was conducted, and thematic as well as content analysis of the relevant studies led to the identification of mentioned success factors in the literature for different collaborative delivery models. Then, those common success factors were structured in a model based on factors' relation to project delivery elements.FindingsThe obtained results present eight core success factors (e.g. equality, mutual trust and commitment to win–win philosophy) for collaborative construction projects, structured in a model based on their contribution toward project organization, contractual relationships, and operational system in construction project delivery. Moreover, the differences between success factors for traditional and collaborative construction projects are discussed.Originality/valueThis study's findings provide insightful theoretical contributions on collaborative construction project success and providing a departure point for future studies based on the discussed differences between success factors of collaborative and traditional construction projects. The findings can be also practically insightful for the project professionals in collaborative construction projects to succeed in managing project organization, contractual relationships, and operational system.
The method and its applications of determining possibility function of grey set
Authors: Li Li , Li Xican 
Published: July 2022

PurposeGrey set is the important foundation of the grey mathematics and grey system theory, and the possibility function is the way of expressing grey set. This paper aims to establish the method of determining the possibility function of grey set and discusses its extended applications.Design/methodology/approachFirst, the grey kernel and the grey support set of grey set are defined, and the properties of grey kernel are analyzed. Second, according to the decomposition theorem of grey set, a method of determining the possibility function of grey set is put forward in this paper, which is called the method of increasing information and taking maximum and minimum (IITMM), and then it is further simplified as the method of increasing information and taking maximum (IITM), and an simple example is given to illustrate the calculation procedure. Finally, the grey information cluster method (GICM) based on IITM is proposed and applied to the ecological and geographical environment analysis of pine caterpillar.FindingsThe results show that the grey kernel of grey set still has grey uncertainty; the method of IITM has simple calculation and strict mathematical basis, and it can synthesize the information of the research object and accords with the principle of using minimum information; the GICM and the fuzzy cluster method have the same classification effect.Practical implicationsThe researches show that method of IITM can be used not only to determine the possibility function of the grey set effectively, but also be used for the evaluation and cluster analysis of connotative objects. The classification result of the GICM presented in this paper is more precise than that of the fuzzy cluster method.Originality/valueThe paper succeeds in realizing both the IITM method for determining the possibility function of grey set and the GICM based on IITM for the connotative objects.
How omnichannel integration promotes customer word-of-mouth behaviors: the mediating roles of perceived personal preference fit and perceived social relatedness
Authors: Li Yang , Tan Ran , Gong Xiang 
Published: July 2022

PurposeThis study aims to investigate the psychological mediating mechanisms through which omnichannel integration affects customer word-of-mouth (WOM) behaviors in omnichannel retailing.Design/methodology/approachGuided by prior omnichannel retailing studies, the authors identify taxonomy of customer WOM behaviors with three archetypes, namely, face-to-face WOM, online store WOM, and social media WOM. Then, the authors draw on social exchange theory (SET) to explain how omnichannel integration influences customer WOM behaviors through the mediating roles of perceived personal preference fit and perceived social relatedness. The authors empirically tested the model using structural equation modeling and multiple mediation analysis with a field survey of 335 omnichannel customers.FindingsPerceived personal preference fit positively influences face-to-face WOM and social media WOM, whereas perceived social relatedness is positively associated with face-to-face WOM, online store WOM, and social media WOM. Furthermore, transactional integration and relational integration positively affect perceived personal preference fit, whereas relational integration has a positive effect on perceived social relatedness. Finally, perceived personal preference fit mediates the effects of transactional integration and relational integration on face-to-face WOM and social media WOM. Perceived social relatedness mediates the effects of relational integration on face-to-face WOM, online store WOM, and social media WOM.Originality/valueThe authors' study advances the omnichannel retailing literature by proposing a taxonomy of customer WOM behaviors in omnichannel retailing and identifying the mediating mechanisms through which omnichannel integration influences customer WOM behaviors.
An empirical analysis of the profitability of backshoring initiatives to Europe
Authors: Ancarani Alessandro , Di Mauro Carmela , Gitto Simone 
Published: July 2022

PurposeThe study investigates the profitability of manufacturing firms backshoring (BS) to Europe. In particular, the article analyses the relation between BS drivers and post-relocation profitability and tests whether this relation is moderated by innovation policies that firms adopt in conjunction with BS.Design/methodology/approachThe empirical model links the post-relocation profitability to BS drivers, firms’ involvement in product innovation and/or adoption of new manufacturing technologies. Data concerning BS initiatives to Europe between 2012 and 2018 extracted from secondary sources have been matched to firms’ balance sheet data.FindingsResults show that responsiveness-driven BS is associated with higher profitability when the relocation is coupled with product innovation. A second key finding is that the adoption of new manufacturing technologies has a positive impact on post-BS profitability.Research limitations/implicationsThe restriction of the dataset to firms for which information on post- and pre-BS financial performance was available has led to a small sample size. Availability of longer time series of profitability data will allow estimating long-term impact, especially for innovation.Practical implicationsThe study provides first evidence on the impact of BS on financial performance and throws light on the relevance of innovation as a lever supporting manufacturing relocation to high-cost countries.Originality/valueThe study advances empirical research on BS by offering evidence of its impact on profitability and by linking it to previous research on BS drivers. Further, the study throws light on the role of different drivers as “success factors” of BS and on how they interact with innovation efforts. The study also offers insights to business leaders who are evaluating the potential benefits on company profitability of a return to a high cost-environment and provides useful indications on the conditions under which BS pays off.