bluuebunny/crossref_metadata_2025_split huggingface dataset:
Reconceptualizing programmed transcriptional slippage in RNA viruses
Authors: Valli Adrian A. , Domingo-Calap María Luisa , González de Prádena Alfonso , García Juan Antonio , Cui Hongguang , Desbiez Cécile , Lopez-Moya Juan José 
Published: February 2024

ABSTRACTRNA viruses have evolved sophisticated strategies to exploit the limited encoded information within their typically compact genomes. One of such, named programmed transcriptional slippage (PTS), is defined by the insertion of an additional A at Anmotifs (n ≥ 6) of newly synthetized viral transcripts to get access to overlapping open reading frames (ORFs). Although key proteins from Ebolavirus and potyvirids (members of thePotyviridaefamily) are expressed via PTS, available information about this phenomenon is very scarce. Here, by using diverse experimental approaches and a collection of plant/virus combinations, we discover cases in which PTS does not fit with its current definition. In summary, we observe (i) high rate of single nucleotide deletions at slippage motifs, (ii) overlapping ORFs acceded by slippage at an U8stretch, and (iii) significant changes in slippage rates induced by factors not related to cognate viruses. Moreover, a survey of full-genome sequences from potyvirids shows a widespread occurrence of species-specific An/Un(n ≥ 6) motifs. Even though many of them, but not all, lead to the production of truncated proteins rather than access to overlapping ORFs, these results suggest that slippage motifs appear more frequently than expected and play relevant roles during virus evolution. In conclusion, our data prompt to broaden PTS definition in RNA viruses. Considering the potential of this phenomenon to expand the viral proteome by acceding to overlapping ORFs and/or producing truncated proteins, a revaluation of PTS significance during infections of RNA viruses is required.IMPORTANCEProgrammed transcriptional slippage (PTS) is used by RNA viruses as another strategy to maximise the coding information in their genomes. This phenomenon is based on a peculiar feature of viral replicases: they insert an untemplated A in An motifs (n ≥ 6) in a small fraction of newly synthesised viral RNAs. As a consequence, ribosomes can get access to overlapping open reading frames (ORFs) when translating those particular transcripts. Here, using plant-infecting RNA viruses as models, we discover cases challenging the previously stablished definition of viral PTS, prompting us to reconsider and redefine this expression strategy. An interesting conclusion from our study is that PTS might be more relevant during RNA virus evolution and infection processes than previously assumed.
(p)ppGpp-mediated GTP homeostasis ensures the survival and antibiotic tolerance ofStaphylococcus aureusduring starvation by preserving the proton motive force
Authors: Salzer Andrea , Ingrassia Sophia , Sauer Lisa , Rapp Johanna , Dobritz Ronja , Müller Jennifer , Link Hannes , Wolz Christiane 
Published: February 2024

AbstractUpon nutrient limitation bacteria enter a nongrowing state, which allow bacterial survival and antibiotic tolerance. The mechanisms whether and how the messenger molecule (p)ppGpp contributes to the transition in Firmicutes is debated. Here we show forStaphylococcus aureusthat (p)ppGpp-dependent restriction of the GTP pool is essential for the culturability of starved cells and for antibiotic tolerance. Elevated GTP levels in a starving (p)ppGpp-deficient mutant lead to a division-incompetent, dormant state characterized by reduced metabolic activity and alterations in membrane function and architecture. GTP level control of nucleotide sensitive promoters result in transcriptional downregulation of gene of the TCA cycle and electron transport chain. Increasing transcription ofqoxABCD, a terminal oxidase of the respiratory chain, through mutation of the transcriptional start site partially restored the culturability of the (p)ppGpp-deficient mutant. Furthermore, we showed that the maintenance of proton motive force under nutritional stress contributes to antibiotic tolerance, supporting the idea of applying (p)ppGpp or PMF inhibitors to combat antibiotic-tolerant bacteria.
A deterministic, c-di-GMP-dependent genetic program ensures the generation of phenotypically similar, symmetric daughter cells during cytokinesis
Authors: Pérez-Burgos María , Herfurth Marco , Kaczmarczyk Andreas , Harms Andrea , Huber Katrin , Jenal Urs , Glatter Timo , Søgaard-Andersen Lotte 
Published: February 2024

AbstractPhenotypic heterogeneity in bacteria results from stochastic processes or deterministic genetic programs. These deterministic programs often incorporate the versatile second messenger c-di-GMP, and by deploying c-di-GMP metabolizing enzyme(s) asymmetrically during cell division give rise to daughter cells with different c-di-GMP levels. By contrast, less is known about how phenotypic heterogeneity is kept to a minimum. Here, we identify a deterministic c-di-GMP-dependent genetic program that is hardwired into the cell cycle ofMyxococcus xanthusto minimize phenotypic heterogeneity and guarantee the formation of phenotypically similar daughter cells during division. Cells lacking the diguanylate cyclase DmxA have an aberrant motility behaviour. DmxA is recruited to the cell division site and its activity switched on during cytokinesis, resulting in a dramatic but transient increase in the c-di-GMP concentration. During cytokinesis, this c-di-GMP burst ensures the symmetric incorporation and allocation of structural motility proteins and motility regulators at the new cell poles of the two daughters, thereby generating mirror-symmetric, phenotypically similar daughters with correct motility behaviours. These findings suggest a general c-di-GMP-dependent mechanism for minimizing phenotypic heterogeneity, and demonstrate that bacteria by deploying c-di-GMP metabolizing enzymes to distinct subcellular locations ensure the formation of dissimilar or similar daughter cells.
YraN is a helicase-associated nuclease fostering extended recombination events by natural transformation
Authors: Hardy Léo , Plantade Julie , Morales Violette , Mazzamuro Fanny , Rocha Eduardo P. C. , Polard Patrice , Charpentier Xavier 
Published: February 2024

AbstractNatural transformation is a widespread molecular pathway of horizontal gene transfer involving the uptake and recombination of exogenous DNA. Exogenous DNA follows a pathway involving genes sequentially required for its capture, internalization, protection, and recombination with the chromosome. Most of these genes were identified through the isolation of transformation-defective mutants and/or based on their expression preceding natural transformation. Yet, genes required for key steps of the pathway remain elusive. We sought to identify any missing component by comparing Tn-seq data obtained in two distantly-related transformable diderm species, the human pathogenLegionella pneumophilaand the cyanobacteriumSynechococcus elongatus. We identifiedyraN, a widespread and highly conserved gene of unknown function required for natural transformation. We provide evidence that YraN is a nuclease associated with the ComM helicase, which cooperate to process the D-loop formed by the invasion of the transforming DNA in the chromosomal DNA strands. We propose a model in which cleavage of the displaced strand by YraN can promote the recombination of transforming DNA, leading to extended recombination events. The identification of this YraN/ComM nuclease/helicase system supports the hypothesis that bacteria possess a conserved pathway for the transport and recombination of exogenous DNA.SignificanceMany bacteria use a dedicated pathway to internalize and integrate extracellular DNA into their chromosome. This allows them to naturally acquire genes, or gene variants, that can confer them new traits, hence the term of natural transformation. Although reported nearly a century ago by Frederick Griffith, several aspects of the mechanism of natural transformation remain elusive. Specifically, it is not clear whether or not all the conserved molecular players of the pathway have been identified. We queried two distinct bacterial species for any gene that would be required for natural transformation. We confirmed all core players of the pathway, but also uncovered a highly conserved one, YraN. We provide evidence that YraN is an endonuclease, which in association with the ComM helicase, promotes the efficient integration of the extracellular DNA in the bacterial chromosome.
Simulation and analysis of micro-textured rough curved surface based on fractal characterization method
Authors: Zhu Chunxia , Meng Xianling 
Published: February 2024

Purpose
Micro-texture is processed on the surface to reduce the friction of the contact surface, and its application is more and more extensive. The purpose of this paper is to create a texture function model to study the influence of surface parameters on the accuracy of the simulated surface so that it can more accurately reflect the characteristics of the real micro-textured surface.

Design/methodology/approach
The microstructure function model of rough surfaces is established based on fractal geometry and polar coordinate theory. The offset angle θ is introduced into the fractal geometry function to make the surface asperity normal perpendicular to the tangent of the surface. The 2D and 3D contour surfaces of the surface groove texture are analyzed by MATLAB simulation. The effects of fractal parameters (D and G) and texture parameter h on the curvature of the surface micro-texture model were studied.

Findings
This paper more accurately characterizes the textured 3D curved surface, especially the surface curvature. The scale coefficient G significantly affects curvature, and the influence of fractal dimension D and texture parameters on curvature can be ignored.

Originality/value
The micro-texture model of the rough surface was successfully established, and the range of fractal parameters was determined. It provides a new method for the study of surface micro-texture tribology.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-09-2023-0298/
The market reaction of real estate companies to the announcement of the Russian–Ukrainian invasion
Authors: Yudaruddin Rizky , Lesmana Dadang 
Published: February 2024

PurposeThis study aims to investigate the market reaction in the real estate market to the announcement of Russia’s invasion of Ukraine.Design/methodology/approachThis study uses the event study method to assess the market reaction to the announcement that Russia is invading Ukraine. The sample in this study comprises 2,325 companies in the real estate market. We also conduct a cross-sectional analysis to determine the influence of the North Atlantic Treaty Organization (NATO) members and company characteristics on market reactions during the invasion.FindingsThe global market reacts significantly negative toward Russia’s invasion of Ukraine. This indicates that the war poses a high geopolitical risk that prompts financial markets down. The authors also demonstrate that emerging and frontier markets react significantly negative to the invasion before and after its announcement. Meanwhile, developed markets tend to react only before the invasion is announced. Furthermore, we find that the NATO members react more strongly than other markets.Social implicationsThis result implies that war prompts investors to flee from the stock exchange, while the deeper the country’s involvement, the more investors worry about the risks.Originality/valueThis study is the first to discuss the market reaction to the Russian invasion of Ukrainian, specifically in the real estate market.
Applying the engineering design process to teach the physics course for engineering students using the flipped classroom combined with an instructional design model
Authors: Ngo Van Thien 
Published: February 2024

PurposeThis study aims to examine the perceptions of students about learning science and physics using the engineering design process (EDP).Design/methodology/approachThe study employed a mixed-methods research design: The quantitative session features a pre–post-test control group study. In the qualitative aspect, the study conducted semistructured interviews for data collection. In the experimental group, the flipped classroom (FC) model and an instructional design are combined to design, develop and implement a physics course using the steps of the EDP, while the conventional method was applied to the control group. The respondents are students of the Department of Mechanical Engineering at Cao Thang Technical College in Vietnam for the academic year 2022–2023. The control and experimental groups are composed of 80 students each. An independent sample Mann–Whitney U test is applied to the quantitative data, while thematic analysis is employed for the qualitative data.FindingsThe results demonstrate a statistically significant difference between the experimental and control groups in terms of perceptions about learning science and physics using the EDP, which, when combined with a FC, enhances physics learning for engineering students.Research limitations/implications This study implemented the EDP in teaching physics to first-year engineering students in the Department of Mechanical Engineering using the combined FC and instructional design models. The results revealed that a difference exists in the perception of the students in terms of integrating the EDP into learning physics between the experimental and control groups. The experimental group, which underwent the EDP, obtained better results than did the control group, which used the conventional method. The results demonstrated that the EDP encouraged the students to explore and learn new content knowledge by selecting the appropriate solution to the problem. The EDP also helped them integrate new knowledge and engineering skills into mechanical engineering. This research also introduced a new perspective on physics teaching and learning using the EDP for engineering college students.Practical implicationsThe research findings are important for teaching and learning physics using EDP in the context of engineering education. Thus, educators can integrate the teaching and learning of physics into the EDP to motivate and engage student learning.Originality/valueUsing the EDP combined with a FC designed under stages of the analyze, design, develop, implement and evaluate (ADDIE) model has enhanced the learning of physics for engineering college students.
Murine models of idiopathic inflammatory myopathies
Authors: Okiyama Naoko , Konishi Risa , Ichimura Yuki 
Published: February 2024

AbstractIdiopathic inflammatory myopathies (IIMs) are divided into polymyositis and dermatomyositis (DM) with specific cutaneous manifestation. Several myositis‐specific autoantibodies (MSAs) have been identified in IIMs and were found to be associated with distinct clinical features, including anti‐synthetase syndrome (ASyS) and immune‐mediated necrotizing myopathy (IMNM). Moreover, MSA‐related clinical features have been identified even within DM. Although MSAs are valuable for the diagnosis of IIMs, the pathogenic roles of these antibodies remain unknown. To investigate the pathogenesis of IIMs, classical murine models of autoimmune myositis, experimental autoimmune myositis, and C protein‐induced myositis have been established by immunization with muscle‐specific antigens, myosin, and myosin‐binding skeletal C protein, respectively. To according to MSA‐related autoimmunity, a murine model of ASyS was generated by immunization with a murine recombinant histidyl‐transfer RNA (tRNA) synthetase, Jo‐1, in which muscle and lung inflammation are induced depending on acquired immunity. Furthermore, it was found that the transfer of human Immunoglobulin G (IgGs) from patients with IMNM, comprising anti‐signal recognition particles and anti‐3‐hydroxy‐3‐methylglutaryl coenzyme A reductase antibodies, induced complement‐mediated myositis in recipient mice. We found that CD8+ T cell‐mediated myositis can be established depending on autoimmunity against transcriptional intermediary factor 1γ (TIF1γ), an autoantigen for MSAs induced by recombinant human TIF1γ immunization. These new murine models reflecting MSA‐associated IIMs will reveal the immunological mechanisms underlying IIMs.
Trait‐based mechanistic approach highlights global patterns and losses of herbivore biomass functional diversity
Authors: Berzaghi Fabio , Zhu Dan , Alroy John , Ciais Philippe 
Published: February 2024

Abstract

Mammalian herbivores play a pivotal role in Earth System processes by affecting biogeochemical cycles and ecosystem functioning, potentially leading to significant repercussions on atmosphere–biosphere feedbacks. Global dynamic models of mammalian populations can improve our understanding of their ecological role at large scales and the consequences of their extinctions. However, such models are still lacking and mammals are poorly integrated in Earth System Science.

We developed a mechanistic global model of terrestrial herbivore populations simulated with 37 functional groups defined through the analysis of eco‐physiological traits across all extant herbivores (2599 species). We coupled this model with a global vegetation model to predict herbivores' maximum potential biomass in pre‐industrial and at present‐day and to study the environmental drivers explaining the distribution of herbivore biomass. Present‐day biomass was estimated by accounting for anthropogenic activity causing habitat and range losses.

We show that natural ecosystems could have sustained a potential wild herbivore wet biomass of 330 Mt (95% CI: 245–417), comprised of 193 Mt (95% CI: 177–208) by large species (body mass >1–10 kg, depending on functional group) and 138 Mt (95% CI: 68–209) by small species. We estimate that the remaining present‐day large herbivores biomass is 82 Mt (95% CI: 32–133), reduced by 57% due to anthropogenic activity; consequently, small herbivores currently dominate global herbivore biomass with 98 Mt (95% CI: 91–106, −29%). Losses vary greatly across climatic zones and functional groups, suggesting that size is not the only discriminant feature of biomass decline.

Actual evapotranspiration is the most important driver of total, large and small herbivore biomass and explains 64%, 59% and 49% of its variation, respectively. Distribution of modelled and observed large herbivores' biomass suggested a high dependency on energy and water with more biomass in hot and wet areas. These results challenge the notion that large herbivore biomass peaks primarily in ecosystems with intermediate precipitation levels such as savannas.

Outside Africa and the Tropics, pre‐industrial biomass hotspots occur in areas today dominated by humans; this could undermine the recovery of larger species biomass in certain areas. Our herbivore biomass estimates provide a quantitative benchmark for setting conservation and rewilding goals at large spatial scales. The herbivore model and functional classification create new opportunities to integrate mammals into Earth System Science and models.

Read the free Plain Language Summary for this article on the Journal blog.
Fungal symbiont diversity drives growth of Holcus lanatus depending on soil nutrient availability
Authors: Sinanaj Besiana , Pressel Silvia , Bidartondo Martin I. , Field Katie J. 
Published: February 2024

Abstract

Arbuscular mycorrhizal (AM) fungi frequently colonise plant roots and can affect plant morphology and physiology through their contribution to plant nutrition. However, the functional role of AM fungi in the presence of other microbial symbionts, including widespread Mucoromycotina ‘fine root endophytes’ (MFRE) fungi, remains largely unknown.

While both AM fungi and MFRE transfer nutrients, including nitrogen, from inorganic and organic sources to host plants, their combined effects on co‐colonised plants have only been investigated in liverworts. Here, we compare the morphology and physiology of the grass Holcus lanatus grown with an AM fungal community versus a more diverse symbiotic fungal community containing both AM fungi and MFRE.

Holcus lanatus plants were grown in the presence of either a diverse MFRE+AM fungi soil inoculum or a multi‐species AM fungal inoculum. Plant traits associated with growth were quantified, along with fungal transfer of 15N tracer to plants from a variety of sources (ammonium chloride, alanine, glycine and algal necromass).

Holcus lanatus grown with the AM fungal community had greater root and shoot growth during early development and prior to the addition of 15N‐labelled sources, compared with plants grown with the more diverse symbiotic fungal community. When nitrogen sources were made available to the fungal symbionts in the pot microcosms, plants growing with the MFRE+AM fungi soil inoculum had a faster growth rate than plants growing with the AM fungal community. At harvest, H. lanatus grown with the AM fungal community had a larger biomass, and there were no differences in 15N tracer assimilation in plants across the two fungal community treatments.

Our results demonstrate that the diversity of fungal inocula in conjunction with soil nutrient availability determine the benefits derived by plants from diverse fungal symbionts. Our research contributes to understanding host plant outcomes in diverse multi‐symbiont scenarios.

Read the free Plain Language Summary for this article on the Journal blog.