bluuebunny/crossref_metadata_2025_split huggingface dataset:
Plant-animal below-ground interaction modifies plant phenotype and its above-ground interaction: a review and new case study
Authors: Vaca-Benito Celia , Ferrón Camilo , Velázquez de Castro Antonio J. , Muñoz-Pajares A. Jesús , Abdelaziz Mohamed , García-Muñoz Ana 
Published: April 2024

AbstractEcological interactions play a role in promoting and maintaining biodiversity. These interactions form complex networks of interconnected species. Therefore, changes resulting from an interaction in one of the partners can have indirect consequences on subsequent interactions with other species. Since the mutualism-antagonism continuum is a gradient, a shift in the strength and sign of an interaction is possible, highlighting the dynamic nature of interaction networks. In flowering plants, a wide variety of below- and above-ground interactions are established with a single host plant. Changes in the host, derived from such interactions, can modulate the outcome of the remaining connections in both strength and sign, and the overall configuration of the network. Thus, a species can mediate community-wide consequences through its interaction with the host by altering the plant phenotype. We present a case study where a root infection has unexpected consequences on the pollination host, driving phenotypic changes. This study provides new data on the dynamism of species interactions and the importance of obtaining a global view of interaction networks. Disentangling the direct and indirect effects of interactions and their impact on the rest of the interactions in wild communities is essential for a good understanding of the evolutionary and ecological mechanisms that promote and maintain biodiversity.
Crystallographic Fragment Screen of Coxsackievirus A16 2A Protease identifies new opportunities for the development of broad-spectrum anti-enterovirals
Authors: Lithgo Ryan M. , Tomlinson Charles W.E. , Fairhead Michael , Winokan Max , Thompson Warren , Wild Conor , Aschenbrenner Jasmin Cara , Balcomb Blake H. , Marples Peter G. , Chandran Anu V , Golding Mathew , Koekemoer Lizbe , Williams Eleanor P. , Wang SiYl , Ni Xiaomin , MacLean Elizabeth , Giroud Charline , Godoy Andre Schutzer , Xavier Mary-Ann , Walsh Martin , Fearon Daren , von Delft Frank 
Published: April 2024

AbstractEnterovirusesare the causative agents of paediatric hand-foot-and-mouth disease, and a target for pandemic preparedness due to the risk of higher order complications in a large-scale outbreak. The 2A protease of these viruses is responsible for the self-cleavage of the poly protein, allowing for correct folding and assembly of capsid proteins in the final stages of viral replication. These 2A proteases are highly conserved betweenEnterovirusspecies, such asEnterovirus A71 and Coxsackievirus A16. Inhibition of the 2A protease deranges capsid folding and assembly, preventing formation of mature virions in host cells and making the protease a valuable target for antiviral activity. Herein, we describe a crystallographic fragment screening campaign that identified 75 fragments which bind to the 2A protease including 38 unique compounds shown to bind within the active site. These fragments reveal a path for the development of non-peptidomimetic inhibitors of the 2A protease with broad-spectrum anti-enteroviral activity.
An extended omnigenic model explains genome-phenome relationships for complex traits in global sorghum diversity
Authors: Hu Zhenbin , Wang Xu , Marla Sandeep R. , Poland Jesse , Morris Geoffrey P. 
Published: April 2024

ABSTRACTA central finding of complex trait genetics is the geometric distribution of effect sizes, but the biological basis of this phenomena is not understood. The omnigenic model (OM) could explain this architecture, with oligogenic variation arising from direct regulatory genes (core genes) and polygenic variation from indirect regulators (peripheraltransregulators). Plant yield is a canonical complex trait and here we tested the OM using genome-phenome analysis of biomass yield in global sorghum diversity. We used field-based phenomics to characterize dynamic growth and yield formation traits, then decomposed oligogenic and polygenic components of variation using genome-wide association studies (GWAS), genome-wide prediction (GWP), and tissue-specific transcriptome analyses. We identified major dynamic QTL, including several persistent (Dw1,Dw3) or transient (ELF3) QTL at known genes, consistent with the oligogenic-core of the OM. Next, we evaluated a key prediction on the peripheral-polygenic component – a positive correlation between GWP marker loadings and gene expression in relevant tissues. GWP loadings are indeed correlated with gene expression in relevant tissues. However, correlations are often higher with non-relevant tissues from earlier growth stages or tissues, which is not predicted by within-tissuetransregulation for the peripheral-polygenic component (the “omnigenic in space” model). Therefore, these findings suggest that genes expressed in early growth stages, with indirect effects on later traits, are contributing to polygenic variation (“omnigenic in time”). Together, our findings suggest that an extended OM, with regulatory effects both in space and in time, could explain the ubiquitous geometric genetic architecture of complex traits.
P66 is a bacterial mimic of CD47 that binds the anti-phagocytic receptor SIRPα and facilitates macrophage evasion byBorrelia burgdorferi
Authors: Tal Michal Caspi , Hansen Paige S. , Ogasawara Haley A. , Feng Qingying , Volk Regan F. , Lee Brandon , Casebeer Sara E. , Blacker Grace S. , Shoham Maia , Galloway Sarah D. , Sapiro Anne L. , Hayes Beth , Dulgeroff Laughing Bear Torrez , Raveh Tal , Pothineni Venkata Raveendra , Potula Hari-Hara SK , Rajadas Jayakumar , Bastounis Effie E. , Chou Seemay , Robinson William H. , Coburn Jenifer , Weissman Irving L. , Zaro Balyn W. 
Published: April 2024

Summary ParagraphInnate immunity, the first line of defense against pathogens, relies on efficient elimination of invading agents by phagocytes. In the co-evolution of host and pathogen, pathogens developed mechanisms to dampen and evade phagocytic clearance. Here, we report that bacterial pathogens can evade clearance by macrophages through mimicry at the mammalian anti-phagocytic “don’t eat me” signaling axis between CD47 (ligand) and SIRPα (receptor). We identified a protein, P66, on the surface ofBorrelia burgdorferithat, like CD47, is necessary and sufficient to bind the macrophage receptor SIRPα. Expression of the gene encoding the protein is required for bacteria to bind SIRPα or a high-affinity CD47 reagent. Genetic deletion ofp66increases phagocytosis by macrophages. Blockade of P66 during infection promotes clearance of the bacteria. This study demonstrates that mimicry of the mammalian anti-phagocytic protein CD47 byB. burgdorferiinhibits macrophage-mediated bacterial clearance. Such a mechanism has broad implications for understanding of host-pathogen interactions and expands the function of the established innate immune checkpoint receptor SIRPα. Moreover, this report reveals P66 as a novel therapeutic target in the treatment of Lyme Disease.
Interactome dynamics during heat stress signal transmission and reception
Authors: Park Sung-Gun , Keller Andrew , Kaiser Nathan K. , Bruce James E. 
Published: April 2024

AbstractAmong evolved molecular mechanisms, cellular stress response to altered environmental conditions to promote survival is among the most fundamental. The presence of stress-induced unfolded or misfolded proteins and molecular registration of these events constitute early steps in cellular stress response. However, what stress-induced changes in protein conformations and protein-protein interactions within cells initiate stress response and how these features are recognized by cellular systems are questions that have remained difficult to answer, requiring new approaches. Quantitativein vivochemical cross-linking coupled with mass spectrometry (qXL-MS) is an emerging technology that provides new insight on protein conformations, protein-protein interactions and how the interactome changes during perturbation within cells, organelles, and even tissues. In this work, qXL-MS and quantitative proteome analyses were applied to identify significant time-dependent interactome changes that occur prior to large-scale proteome abundance remodeling within cells subjected to heat stress. Interactome changes were identified within minutes of applied heat stress, including stress-induced changes in chaperone systems as expected due to altered functional demand. However, global analysis of all interactome changes revealed the largest significant enrichment in the gene ontology molecular function term of RNA binding. This group included more than 100 proteins among multiple components of protein synthesis machinery, including mRNA binding, spliceosomes, and ribosomes. These interactome data provide new conformational insight on the complex relationship that exists between transcription, translation and cellular stress response mechanisms. Moreover, stress-dependent interactome changes suggest that in addition to conformational stabilization of RNA-binding proteins, adaptation of RNA as interacting ligands offers an additional fitness benefit resultant from generally lower RNA thermal stability. As such, RNA ligands also serve as fundamental temperature sensors that signal stress through decreased conformational regulation of their protein partners as was observed in these interactome dynamics.
Multiomic analysis reveals developmental dynamics of the human heart in health and disease
Authors: Cranley James , Kanemaru Kazumasa , Bayraktar Semih , Knight-Schrijver Vincent , Pett Jan Patrick , Polanski Krzysztof , Dabrowska Monika , Mulas Ilaria , Richardson Laura , Semprich Claudia I. , Kapuge Rakeshlal , Perera Shani , He Xiaoling , Ho Siew Yen , Yayon Nadav , Tuck Liz , Roberts Kenny , Palmer Jack A. , Davaapil Hongorzul , Gambardella Laure , Patel Minal , Tyser Richard , Sinha Sanjay , Teichmann Sarah A. 
Published: April 2024

AbstractDevelopmental dynamics encompass both the specification of cell types and their spatial organisation into multicellular niches. Here we harness the power of single-cell and spatial multiomics to unravel embryonic and foetal cardiac tissue niches, which lead to the development of a new tool, TissueTypist. We reveal that cardiac-resident macrophages likely originate from the yolk sac, forming heterogeneous subsets. CX3CR1+macrophages with a microglia-like profile localise in the sinoatrial node, which may contribute to axon guidance for the innervating autonomic neurons. Foetal pacemaker cells exhibit distinct characteristics compared to their adult counterparts, including the expression of genes that are known to promote parasympathetic innervation. We highlight the enhancer-mediated gene regulatory networks governing atrial and ventricular cardiomyocyte specification. The maturation of atrial cardiomyocytes into distinct left and right phenotypes, driven by transcription factors linked to atrial septal defect genes, underscores the significance of this process for healthy heart development. In the ventricle, cellular and transcriptional gradients along both pseudotime and the transmural axis provide a new molecular understanding of myocardial compaction. Finally, generating data from Trisomy 21 hearts and comparing this with the euploid atlas, we reveal a reduced abundance of specific cell types including compact cardiomyocytes. Overall, this extensive dataset and our precomputed models will form a valuable resource for the field.
The mechanoreceptor PIEZO1 is a novel oncogene in glioma by promoting astrocyte reactivity
Authors: Blanco-Carlon Pablo , Navarro Aguadero Miguel Ángel , Aguilar-Garrido Pedro , Otero-Sobrino Álvaro , Hernández-Sánchez María , Arroyo-Barea Andrés , Graña-Castro Osvaldo , Gargini Ricardo , García-Martín Rosa María , Hernández-Laín Aurelio , Pérez-Martínez Manuel , Gómez Alonso Jesús , Ortega Sagrario , Martínez-López Joaquín , Gallardo Miguel , Velasco-Estévez María 
Published: April 2024

AbstractGlioblastoma is the most common and aggressive brain tumour in adults. Despite advances in its molecular characterization, there is a gap-of-knowledge in the identification ofbona fidedrivers and potential therapeutic targets that could change the clinical picture. Mechanoreception, the sensing of mechanical cues by cells, has proven to be an important factor in cell biology, particularly in cancer. Piezo1 is a mechanoreceptor found in all cells and seems to play a role in different cancer types, such as gastric, breast or lung cancer. However, there is still lack of understanding about its role in the onset and progression of glioblastoma. Here, we show that Piezo1 acts as an oncogene in glioma by potentially promoting chronic astrocyte reactivity. We developed a novel transgenic murine model of Piezo1 overexpression in astrocytes. These animals had a significant reduction in overall survival and developed glioma with a penetrance of 30%. We also developed a PIEZO1-overexpressing U251 cell line and found that it had a more aggressive and reactive-like phenotype. Finally, we correlated the levels of PIEZO1 with the clinical outcome of a cohort of glioblastoma patients and observed that PIEZO1 is a biomarker of worse prognosis. However, PIEZO1 only correlated with worse prognosis in male patients, suggesting a sexual dimorphism. In conclusion, we identified Piezo1 as abona fidedriver of glioma, revealing its implication in astrocyte reactivity and identifying it as a biomarker for glioma in the clinic.
Aerobic Adaptation and Metabolic Dynamics ofPropionibacterium freudenreichiiDSM 20271: Insights from Comparative Transcriptomics and Surfaceome Analysis
Authors: Loivamaa Iida , Sillanpää Annika , Deptula Paulina , Chamlagain Bhawani , Edelmann Minnamari , Auvinen Petri , Nyman Tuula A. , Savijoki Kirsi , Piironen Vieno , Varmanen Pekka 
Published: April 2024

AbstractPropionibacterium freudenreichii(PFR) DSM 20271 is a bacterium known for its ability to thrive in diverse environments and to produce vitamin B12. Despite its anaerobic preference, recent studies have elucidated its ability to prosper in the presence of oxygen, prompting a deeper exploration of its physiology under aerobic conditions. Here, we investigated the response of DSM 20271 to aerobic growth by employing comparative transcriptomic and surfaceome analyses alongside metabolite profiling. Cultivation under controlled partial pressure of oxygen (pO2) conditions revealed significant increases in biomass formation and altered metabolite production, notably of B12 vitamin, pseudovitamin-B12, propionate and acetate, under aerobic conditions. Transcriptomic analysis identified differential expression of genes involved in lactate metabolism, TCA cycle, and electron transport chain, suggesting metabolic adjustments to aerobic environments. Moreover, surfaceome analysis unveiled growth environment-dependent changes in surface protein abundance, with implications for sensing and adaptation to atmospheric conditions. Supplementation experiments with key compounds highlighted the potential for enhancing aerobic growth, emphasizing the importance of iron and α-ketoglutarate availability. Furthermore, in liquid culture, FeSO4supplementation led to increased heme production and reduced vitamin B12 production, highlighting the impact of oxygen and iron availability on the metabolic pathways. These findings deepen our understanding ofPFR’s physiological responses to oxygen availability and offer insights for optimizing its growth in industrial applications.ImportanceThe study of the response ofPropionibacterium freudenreichiito aerobic growth is crucial for understanding how this bacterium adapts to different environments and produces essential compounds like vitamin B12. By investigating its physiological changes under aerobic conditions, we can gain insights into its metabolic adjustments and potential for enhanced growth. These findings not only deepen our understanding ofP. freudenreichiiresponses to oxygen availability but also offer valuable information for optimizing its growth in industrial applications. This research sheds light on the adaptive mechanisms of this bacterium, providing a foundation for further exploration and potential applications in various fields.
Toward nanophotonic optical isolation via inverse design of energy transfer in nonreciprocal media
Authors: Cisowski Claire M. , Waller Madeline C. , Bennett Robert 
Published: April 2024

In this paper we generalize the adjoint method of inverse design to nonreciprocal media. As a test case, we use three-dimensional topology optimization via the level-set method to optimize one-way energy transfer for pointlike source and observation points. To achieve this we introduce a suite of tools, chiefly what we term the “Faraday-adjoint” method which allows for efficient shape optimization in the presence of magneto-optical media. We carry out an optimization based on a very general equation that we derive for energy transfer in a nonreciprocal medium, and link finite-different time-domain numerics to analytics via a modified Born series generalized to a tensor permittivity. This paper represents a stepping stone towards practical nanophotonic optical isolation, often regarded as the “holy grail” of integrated photonics.

Published by the American Physical Society
2024
Toward a sustainable research agenda on food eco-labelling in the business and management research domain
Authors: Geldres-Weiss Valeska V. , Nicolas Carolina , Massa Nathaniel P. 
Published: April 2024

PurposeThis study aims to critically review the research on food eco-labels to identify research gaps and recommend future research directions in business and management.Design/methodology/approachA hybrid integrated review combines bibliometric analysis with an in-depth framework-based study of theory–context–characteristics–methodology (TCCM) and reviews quality research published over 21 years between 2002 and 2022.FindingsWe identify key research themes and the knowledge structure of food eco-label research. Future researchers should explore food eco-label dynamics and phenomena in areas related to consumer behaviour, information, consumer knowledge, environmental concerns, trust, packaging and willingness-to-pay as antecedent factors.Research limitations/implicationsThis review contributes to the business and management literature by quantifying existing research and consolidating its evolution. The articles were sourced from the established Web of Science (WoS) database. Other databases should be included in future reviews. We also focus on research published in business and management. Further studies could include research beyond such specialised domains.Practical implicationsConsumers need more information on the objectives and meaning of food eco-labels. The dissemination of knowledge on eco-labels, as well as effective communication and information on eco-labels, are relevant to future research issues.Social implicationsThe knowledge derived from this research holds significant potential in shaping policies and devising tools aimed at reducing the carbon footprint linked to food production and consumption. Considering the substantial impact of these activities on our planet’s carbon footprint, addressing food security and sustainability emerges as a crucial concern for humanity. Recognising the importance of eco-label communication and information becomes particularly pertinent for future generations, who stand to bear the most substantial impact of climate change and sustainable development. These generations are also more inclined toward embracing and implementing sustainable practices.Originality/valueThere are no comprehensive, integrated reviews exploring the methods, variables and constructs used in studies on food eco-labels based on all articles published in WoS journals in the business and management domains. This is the first comprehensive literature review using a hybrid approach (bibliometric review with TCCM framework) in the field of food eco-label research.
Madrasah management strategies through Madrasah Reform program: an evidence from Indonesia
Authors: Haddade Hasyim , Nur Askar , Achruh Andi , Rasyid Muhammad Nur Akbar , Ibrahim Andi 
Published: April 2024

PurposeImproving the quality of madrasah in the digital era is a must. This can be committed by strengthening aspects of madrasah governance through implementing management strategies that refer more to the integration of technology and Islamic education. This research focuses on madrasah management strategies through the Madrasah Reform program.Design/methodology/approachThis research uses a case study research design that focuses attention on strategic aspects of developing madrasah through the Madrasah Reform program. The informants in this study were 18 people consisting of three madrasah heads from Madrasah Ibtidaiyah (MI), Madrasah Tsanawiyah (MTs) and Madrasah Aliyah (MA), five teachers and 10 students. Data collection in this study used in-depth and semi-structured interviews with madrasah heads and teachers regarding the implementation of the Madrasah Reform program and also regarding madrasah management strategies at three levels of education.FindingsThis study shows that the strategy of managing madrasahs through the Madrasah Reform program in three madrasahs in Indonesia has had a positive impact on improving the quality of madrasahs, although there are still aspects that require development.Research limitations/implicationsThis research implies that the quality of madrasah in the digital era is determined by management strategies based on the use of educational technology.Practical implicationsThis program has implications for the development of the quality of human resources in educational institutions, especially in relation to digital literacy among students and teaching staff. The use of digital technology, which is one of the main projections of the Madrasah Reform program, is continuously able to change the face of education in a more modern direction, both in terms of governance and the learning process, so that the output of this program, especially what occurs at Madrasah Madani, is significant development in the aspects of digital literacy and technology. Which is the main criterion in facing a digital-based educational context.Social implicationsFor a policy aspect, the success of the Madrasah Reform program at Madrasah Madani can be used as a blueprint or model for implementing this program in Islamic educational institutions, specifically Madrasas in South Sulawesi and in general at Madrasas throughout Indonesia.Originality/valueThis proves that Madrasah Reform program is a program that can be implemented in madrasahs to improve the quality of madrasah management in the digital era while continuing to carry out simultaneous improvements and evaluations of the program.