bluuebunny/crossref_metadata_2025_split huggingface dataset:
The Ralstonia solanacearum effector RipV1 acts as a novel E3 ubiquitin ligase to suppress plant PAMP‐triggered immunity responses and promote susceptibility in potato
Authors: Cheng Dong , Zhou Dan , Wang Yuqi , Wang Yudan , Qiu Huishan , Tan Xiaodan , Wang Bingsen , Huang Mengshu , Song Botao , Chen Huilan 
Published: February 2024

AbstractBacterial wilt caused by Ralstonia solanacearum is a destructive plant disease, particularly in potato (Solanum tuberosum). R. solanacearum deploys a diverse and potent arsenal of type III effectors to inhibit the plant immune system. However, the understanding of individual effectors promoting susceptibility in host plants and interfering with plant immunity responses is still limited. Here, we demonstrated that the type III effector RipV1 functioned as a novel E3 ubiquitin ligase (NEL) effector and exhibited E3 ubiquitin ligase activity in vitro. Transient expression of RipV1 suppressed plant pathogen‐associated molecular pattern (PAMP)‐triggered immunity (PTI) responses in Nicotiana benthamiana, such as the expression of PTI‐related genes and the reactive oxygen species (ROS) burst. Prolonged expression of RipV1 induced cell death in N. benthamiana leaves. Notably, mutating the conserved cysteine residue of RipV1 abolished its E3 ligase activity and its ability to suppress plant PTI responses. This study also revealed the indispensability of RipV1 for R. solanacearum's full virulence in potato. Transgenic potato plants overexpressing ripV1 but not the catalytic mutant ripV1‐C444A displayed enhanced susceptibility to R. solanacearum. RipV1 was observed to localize specifically to the plant plasma membrane, with its N‐terminus being pivotal in determining this localization. These findings showcase that RipV1 acts as a NEL effector and contributes to R. solanacearum virulence by suppressing plant PTI responses through its E3 activity.
Other People's Liberties
Authors: Halpin Andrew 
Published: February 2024

AbstractWhen we seek a fuller understanding of individual liberty including its relational character, we confront a conundrum. The evident advantages of a single individual possessing liberty cannot be simply transferred to a greater number of beneficiaries. This conundrum is confronted with the resources of Hohfeld's analytical framework, developed specifically to elucidate the practical outworkings of interpersonal relations within the law. Attention is also paid to concerns expressed by von Wright over a representation of liberty (permission) within the resources of standard deontic logic which fails to address its social aspect. The aggregate level of the Hohfeldian scheme is employed to represent a complete picture of liberty, but one that cannot guarantee benefits for a plurality of holders. The conclusion is reached that in order to extend the advantages of individual liberty to all, something other than liberty is required.
Stronger together: A workflow to design new fish polycultures
Authors: Lecocq Thomas , Amoussou Nellya , Aubin Joël , Butruille Grégoire , Liarte Sébastien , Pasquet Alain , Thomas Marielle 
Published: February 2024

AbstractPolyculture is a relevant practice for improving the sustainability of aquaculture, which raises interest in implementing it in a variety of production systems. However, polyculture is a complex approach that can result not only in complementarity among species but also competition among them and animal welfare issues. Potential polyculture benefits can be expected provided that compatibility and complementarity occur among the combined species. This places a premium on identifying the best species combinations for a given aquaculture system. Here, we developed a conceptual integrative workflow to standardise and plan the development of new fish polycultures. This workflow is designed to screen all possible combinations in a set of species based on three successive steps of assessment. Overall, these steps consider the compatibility and complementarity of co‐farmed species as well as stakeholder demands, sustainability and fish welfare. Step 1 consists of selecting the most promising compatible species combinations (i.e., ‘prospective combinations’) as a function of stakeholder opinion and expectations using databases and surveys. Step 2 validates the effectiveness of prospective combinations based on bioassays by considering species complementarity and animal welfare. Step 3 implements the best species combination(s) in aquaculture production, during which prototyping allows the sustainability of the resulting commercial production system to be studied. In conclusion, the workflow aims at being a valuable tool to innovate in aquaculture by exploiting the opportunities and the strengths of polyculture.
Comparing methods of social preference assessment in childhood
Authors: deMayo Benjamin , Olson Kristina R. 
Published: February 2024

AbstractA central question in social cognitive development concerns the degree to which children prefer social ingroup members relative to social outgroup members. Forced‐choice measures and continuous rating scales are often used to assess these preferences, but little work has examined the extent to which these two methods yield similar or divergent estimates. In Study 1, we used a within‐subjects design to assess gender‐, race‐, and accent‐based preferences in 5–6‐year‐old predominantly white children (N = 100) with both a forced‐choice and a rating measure (on a 1–6 scale); replicating prior work, children expressed ingroup preference along all three dimensions regardless of how they were assessed. In Study 2, we replicated the discrepancy between forced‐choice and rating in children's ingroup gender preferences in a more racially diverse sample (N = 55). In both studies, while responses on forced‐choice and rating measures were correlated, estimates of ingroup preference were stronger in each domain when assessed with a forced‐choice measure. We discuss the implications for researchers who wish to assess social group preferences.
Alternative targeting methods for social assistance programs: Evidence from Tunisia
Authors: Nasri Khaled , Amara Mohamed , Helmi Imane 
Published: February 2024

AbstractSocial assistance programmes are crucial in alleviating poverty, reducing inequality, and addressing social exclusion. The efficacy of these programmes hinges on the precision and efficiency of their targeting methods. Governments, especially in developing countries, can enhance the impact of social assistance programmes and ensure equitable resource distribution by accurately identifying the right individuals or households. This paper proposes two approaches to targeting beneficiaries of social benefits in Tunisia, including cash transfers and healthcare programmes. The first approach, a Mixed Means Test, extends the Proxy Means Test model by integrating individual/household assessments with explicit geographical targeting methods. The second is a multidimensional targeting strategy that explicitly considers the various deprivations faced by the households. Utilising data from the 2015 National Survey on Household Budget, Consumption, and Standard of Living, our results indicate that the targeting performance of the Mixed Means Test surpasses existing programmes both nationally and regionally, notably minimising inclusion and exclusion errors in the poorest regions of Tunisia. However, the multidimensional targeting approach identifies a higher number of potential beneficiaries compared to the current selection process in Tunisia. Including these households in social programmes may be hindered by limited monetary resources and the country's financial constraints. To address this, the multidimensional targeting approach enables the categorisation of potential beneficiaries into three mutually exclusive and collectively exhaustive groups based on their degree of deprivation.
First 3D reconstruction of the male genitalia of a Cretaceous fossil cricket: Diving into the evolutionary history of the Oecanthidae family (Orthoptera: Grylloidea) with the incorporation of new fossils in its phylogeny and a total‐evidence dating approach
Authors: Ferreira Jules , Desutter‐Grandcolas Laure , Nel André , Josse Hugo , de Campos Lucas Denadai 
Published: February 2024

AbstractFossils are valuable indicators of the evolutionary history of the clades to which they belong to, especially when they are incorporated as terminal taxa in a total‐evidence phylogeny. According to their state of preservation, fossils are often incompletely described for key morphological characters, such as genitalic structures. Here, the internal parts of the genitalia of a male fossil cricket from Cretaceous amber, †Picogryllus carentonensis Josse & Desutter‐Grandcolas (Oecanthidae, Podoscirtinae), together with other key morphological characters (i.e., metanotal structures and tibial spurs), were reconstructed for the first time by 3D microtomography. Total‐evidence phylogeny and dating combining morphological data (fossils and extant taxa), molecular data (extant taxa only) and time calibration (fossil dates) were performed to evaluate the tempo and mode of evolution of the cricket family Oecanthidae. Divergence time estimates were thus refined and the patterns of transformation for key morphological structures contrasted through the analysis of phylogenetic morphological partitions. Our results show that Oecanthidae date back to the Upper Jurassic (Oxfordian, around 162 Ma) and attest to the presence of the Podoscirtinae in Western Europe during the Lower Cretaceous. Morphological evolution may have been driven by the conquest of new resources (as shown by leg evolution in ancestral Oecanthidae) and/or the ‘conquest of silence’ (as shown by repetitive and definitive losses of acoustic structures). By contrast, genitalia evolution proved more diffuse.
Character sums over sparse elements of finite fields
Authors: Mérai László , Shparlinski Igor E. , Winterhof Arne 
Published: February 2024

AbstractWe estimate mixed character sums of polynomial values over elements of a finite field with sparse representations in a fixed ordered basis over the subfield . First we use a combination of the inclusion–exclusion principle with bounds on character sums over linear subspaces to get nontrivial bounds for large . Then we focus on the particular case , which is more intricate. The bounds depend on certain natural restrictions. We also provide families of examples for which the conditions of our bounds are fulfilled. In particular, we completely classify all monomials as argument of the additive character for which our bound is applicable. Moreover, we also show that it is applicable for a large family of rational functions, which includes all reciprocal monomials.
A Novel Methodology to Estimate the Cell Temperature of Photovoltaic Thermal Modules: Test With Experimental Data, Prospects, and Limits
Authors: Mussard Maxime , Vaudrey Alexandre , Zhu Junjie , Foss Sean Erik 
Published: February 2024

Abstract
The efficient use and understanding of photovoltaic thermal (PVT) modules require accurately evaluating the temperature of their photovoltaic cells. But due to their specific composition, measuring this temperature directly is usually very complicated, if not impossible in practice. In this article, we present an original methodology to estimate the temperature of the cells of a PVT module. In order to do this, we simultaneously conduct experiments on both PVT and PV modules equipped with identical PV cells, and compare their electrical performance. The temperature of the PV module’s back side is measured and used to estimate the temperature of the PV cells. The latter is then combined with the electrical power output difference between PV and PVT modules in order to obtain, through a specifically developed thermal model, the cell temperature of the PVT module. In addition, an experimental comparative analysis of different PVT modules is presented. The methodology and the results are promising but the experimental measurements used are subject to significant uncertainties that impact the accuracy of the estimation. The model uses an innovative approach to estimate the PV cell temperature of PVT modules, and recommendations are provided to optimize experimental data measurement accuracy in order to use this model in the best possible conditions.
Sphingosine induction of the
Pseudomonas aeruginosa
hemolytic phospholipase C/sphingomyelinase (PlcH)
Authors: Mackinder Jacob R. , Hinkel Lauren A. , Schutz Kristin , Eckstrom Korin , Fisher Kira , Wargo Matthew J. 
Published: February 2024

ABSTRACT

Hemolytic phospholipase C, PlcH, is an important virulence factor for
Pseudomonas aeruginosa
. PlcH preferentially hydrolyzes sphingomyelin and phosphatidylcholine, and this hydrolysis activity drives tissue damage and inflammation and interferes with the oxidative burst of immune cells. Among other contributors, transcription of
plcH
was previously shown to be induced by phosphate starvation via PhoB and the choline metabolite, glycine betaine, via GbdR. Here, we show that sphingosine can induce
plcH
transcription and result in secreted PlcH enzyme activity. This induction is dependent on the sphingosine-sensing transcriptional regulator SphR. The SphR induction of
plcH
occurs from the promoter for the gene upstream of
plcH
that encodes the neutral ceramidase, CerN, and transcriptional readthrough of the
cerN
transcription terminator. Evidence for these conclusions came from mutation of the SphR binding site in the
cerN
promoter, mutation of the
cerN
terminator, enhancement of
cerN
termination by adding the
rrnB
terminator, and reverse transcriptase PCR (RT-PCR) showing that the intergenic region between
cerN
and
plcH
is made as RNA during sphingosine, but not choline, induction. We also observed that, like glycine betaine induction, sphingosine induction of
plcH
is under catabolite repression control, which likely explains why such induction was not seen in other studies using sphingosine in rich media. The addition of sphingosine as a novel inducer for PlcH points to the regulation of
plcH
transcription as a site for the integration of multiple host-derived signals.

IMPORTANCE

PlcH is a secreted phospholipase C/sphingomyelinase that is important for the virulence of
Pseudomonas aeruginosa
. Here, we show that sphingosine, which presents itself or as a product of
P. aeruginosa
sphingomyelinase and ceramidase activity, leads to the induction of plcH transcription. This transcriptional induction occurs from the promoter of the upstream ceramidase gene generating a conditional operon. The transcript on which plcH resides, therefore, is different depending on which host molecule or condition leads to induction, and this may have implications for PlcH post-transcriptional regulation. This work also adds to our understanding of
P. aeruginosa
with host-derived sphingolipids.
NLRP1 restricts porcine deltacoronavirus infection via IL-11 inhibiting the phosphorylation of the ERK signaling pathway
Authors: He Haojie , Li Yongfeng , Chen Yunyan , Chen Jianfei , Li Zhongyuan , Li Liang , Shi Da , Zhang Xin , Shi Hongyan , Xue Mei , Feng Li 
Published: February 2024

ABSTRACT

Continuously emerging highly pathogenic coronaviruses remain a major threat to human and animal health. Porcine deltacoronavirus (PDCoV) is a newly emerging enterotropic swine coronavirus that causes large-scale outbreaks of severe diarrhea disease in piglets. Unlike other porcine coronaviruses, PDCoV has a wide range of species tissue tropism, including primary human cells, which poses a significant risk of cross-species transmission. Nucleotide-binding oligomerization domain-like receptor (NLR) family pyrin domain-containing 1 (NLRP1) has a key role in linking host innate immunity to microbes and the regulation of inflammatory pathways. We now report a role for NLRP1 in the control of PDCoV infection. Overexpression of NLRP1 remarkably suppressed PDCoV infection, whereas knockout of NLRP1 led to a significant increase in PDCoV replication. A mechanistic study revealed that NLRP1 suppressed PDCoV replication in cells by upregulating IL-11 expression, which in turn inhibited the phosphorylation of the ERK signaling pathway. Furthermore, the ERK phosphorylation inhibitor U0126 effectively hindered PDCoV replication in pigs. Together, our results demonstrated that NLRP1 exerted an anti-PDCoV effect by IL-11-mediated inhibition of the phosphorylation of the ERK signaling pathway, providing a novel antiviral signal axis of NLRP1-IL-11-ERK. This study expands our understanding of the regulatory network of NLRP1 in the host defense against virus infection and provides a new insight into the treatment of coronaviruses and the development of corresponding drugs.

IMPORTANCE

Coronavirus, which mainly infects gastrointestinal and respiratory epithelial cells
in vivo
, poses a huge threat to both humans and animals. Although porcine deltacoronavirus (PDCoV) is known to primarily cause fatal diarrhea in piglets, reports detected in plasma samples from Haitian children emphasize the potential risk of animal-to-human spillover. Finding effective therapeutics against coronaviruses is crucial for controlling viral infection. Nucleotide-binding oligomerization-like receptor (NLR) family pyrin domain-containing 1 (NLRP1), a key regulatory factor in the innate immune system, is highly expressed in epithelial cells and associated with the pathogenesis of viruses. We demonstrate here that NLRP1 inhibits the infection of the intestinal coronavirus PDCoV through IL-11-mediated phosphorylation inhibition of the ERK signaling pathway. Furthermore, the ERK phosphorylation inhibitor can control the infection of PDCoV in pigs. Our study emphasizes the importance of NLRP1 as an immune regulatory factor and may open up new avenues for the treatment of coronavirus infection.
Structure-function analysis of the ATPase domain of African swine fever virus topoisomerase
Authors: Kuang Wenhua , Zhao Yan , Li Jinyue , Deng Zengqin 
Published: February 2024

ABSTRACT

Type II topoisomerase utilizes the energy from ATP hydrolysis to alter DNA topology during genome replication and transcription. The ATPase domain of this enzyme is required for ATP hydrolysis and plays a crucial role in coupling DNA binding and ATP turnover with the DNA strand passage reaction. The African swine fever virus (ASFV) specifically encodes a topoisomerase II (topo II), which is critical for viral replication and an attractive target for antiviral development. Here, we present a high-resolution crystal structure of the ASFV topo II ATPase domain complexed with the substrate analog AMPPNP. Structural comparison reveals that the ASFV topo II ATPase domain shares a conserved overall structure with its homologs from eukaryotes and prokaryotes but also has three characteristic regions, including the intra-molecular interface formed by the ATP-lid and QTK loop as well as helix α9, the K-loop in the transducer domain, and the antennae-like α-helix at the ATP binding domain. Mutating the key residues within these three regions impairs or abolishes the basal and DNA-stimulated ATPase activities and reduces or eliminates the relaxation activity of the holoenzyme. Our data indicate that all three regions are functionally important for the ATPase and relaxation activities and strongly suggest that ATP hydrolysis, DNA binding, and strand passage are highly coupled and managed by the allosteric coordination of multiple domains of the type II topoisomerase. Moreover, we find a promising druggable pocket in the dimeric interface of the ASFV topo II ATPase domain, which will benefit future anti-ASFV drug development.

IMPORTANCE
The ATPase domain of type II topoisomerase provides energy by hydrolyzing ATP and coordinates with the DNA-binding/cleavage domain to drive and control DNA transport. The precise molecular mechanisms of how these domains respond to DNA binding and ATP hydrolysis signals and communicate with each other remain elusive. We determine the first high-resolution crystal structure of the ATPase domain of African swine fever virus (ASFV) topo II in complex with AMPPNP and biochemically investigate its function in ATPase and DNA relaxation activities. Importantly, we find that mutations at three characteristic regions of the ASFV ATPase domain produce parallel effects on the basal/DNA-stimulated ATPase and relaxation activities, implying the tight coupling of the ATP hydrolysis and strand passage process. Therefore, our data provide important implications for understanding the strand passage mechanism of the type II topoisomerase and the structural basis for developing ATPase domain-targeting antivirals against ASFV.
Temperature impacts SARS-CoV-2 spike fusogenicity and evolution
Authors: Dufloo Jérémy , Sanjuán Rafael 
Published: February 2024

ABSTRACT

SARS-CoV-2 infects both the upper and lower respiratory tracts, which are characterized by different temperatures (33°C and 37°C, respectively). In addition, fever is a common COVID-19 symptom. SARS-CoV-2 has been shown to replicate more efficiently at low temperatures, but the effect of temperature on different viral proteins remains poorly understood. Here, we investigate how temperature affects the SARS-CoV-2 spike function and evolution. We first observed that increasing temperature from 33°C to 37°C or 39°C increased spike-mediated cell–cell fusion. We then experimentally evolved a recombinant vesicular stomatitis virus expressing the SARS-CoV-2 spike at these different temperatures. We found that spike-mediated cell–cell fusion was maintained during evolution at 39°C but was lost in a high proportion of viruses that evolved at 33°C or 37°C. Consistently, sequencing of the spikes evolved at 33°C or 37°C revealed the accumulation of mutations around the furin cleavage site, a region that determines cell–cell fusion, whereas this did not occur in spikes evolved at 39°C. Finally, using site-directed mutagenesis, we found that disruption of the furin cleavage site had a temperature-dependent effect on spike-induced cell–cell fusion and viral fitness. Our results suggest that variations in body temperature may affect the activity and diversification of the SARS-CoV-2 spike.

IMPORTANCE

When it infects humans, SARS-CoV-2 is exposed to different temperatures (e.g., replication site and fever). Temperature has been shown to strongly impact SARS-CoV-2 replication, but how it affects the activity and evolution of the spike protein remains poorly understood. Here, we first show that high temperatures increase the SARS-CoV-2 spike fusogenicity. Then, we demonstrate that the evolution of the spike activity and variants depends on temperature. Finally, we show that the functional effect of specific spike mutations is temperature-dependent. Overall, our results suggest that temperature may be a factor influencing the activity and adaptation of the SARS-CoV-2 spike
in vivo
, which will help understanding viral tropism, pathogenesis, and evolution.