bluuebunny/crossref_metadata_2025_split huggingface dataset:
The maintenance of genetic polymorphism underlying sexually antagonistic traits
Authors: Flintham Ewan , Savolainen Vincent , Otto Sarah , Reuter Max , Mullon Charles 
Published: October 2023

AbstractSelection often favours different trait values in males and females, leading to genetic conflicts between the sexes when traits have a shared genetic basis. Such sexual antagonism has been proposed to maintain genetic polymorphism. However, this notion is based on insights from population genetic models of single loci with fixed fitness effects. It is thus unclear how readily polymorphism emerges from sex-specific selection acting on continuous traits, where fitness effects arise from the genotype-phenotype map and the fitness landscape. Here we model the evolution of a continuous trait that has a shared genetic basis but different optima in males and females, considering a wide variety of genetic architectures and fitness landscapes. For autosomal loci, the long-term maintenance of polymorphism requires strong conflict between males and females that generates uncharacteristic sex-specific fitness patterns. Instead, more plausible sex-specific fitness landscapes typically generate stabilising selection leading to an evolutionarily stable state that consists of a single homozygous genotype. Except for sites tightly linked to the sex determining region, our results indicate that genetic variation due to sexual antagonism should arise only rarely and often be transient, making these signatures challenging to detect in genomic data.
Experimental and methodological framework for the assessment of nucleic acids in airborne microorganisms
Authors: Péguilhan Raphaëlle , Rossi Florent , Rué Olivier , Joly Muriel , Amato Pierre 
Published: October 2023

AbstractStudying airborne microorganisms is highly challenging due to ultra-low and spread biomass, and great spatial and temporal variabilities at short scales. Aeromicrobiology is still an emerging discipline of environmental microbiology, and some of the basic practices (replication, control of contaminants,etc) are not yet widely adopted, which potentially limits conclusions. Here we aim at evaluating the benefits of such practices in the study of the aeromicrobiome using molecular-based approaches, and recommend the following: (i) sample at high airflow rate, if possible into a fixative agent, in order to be able to capture specific situations ; (ii) replicate sampling and process samples individually to enable statistical analyses ; (iii) check for contaminants at different steps of the analytical process, and account for their potential stochasticity in sequence decontamination methods ; (iv) include internal references to verify qualitative and quantitative aspects of the data, and (v) eventually investigate multiple analytical procedures to identify potential impacts on the data. In our study, samples were collected at a remote mountain site using high-flow rate impingers collecting airborne material into nucleic acid preservation buffer. As high of ∼75% of the sequences were shared between independent triplicates, gathering 28 to 38% of the richness observed at the ASV level at a given sampling date, which also emphasizes spatial heterogeneity at short scale due to rare taxa. Thanks to replicates, daily variations in the diversity of bacteria could be distinguished statistically, and the inevitable presence of contaminating sequences in controls could be accounted for using established statistical methods. This work opens new perspectives and notably paves the way to untargeted molecular methods in the exploration of aeromicrobiome’s composition and functioning.Graphical abstract
In vivodisentanglement of diffusion frequency-dependence, tensor shape, and relaxation using multidimensional MRI
Authors: Johnson Jessica T.E. , Irfanoglu M. Okan , Manninen Eppu , Ross Thomas J. , Yang Yihong , Laun Frederik B. , Martin Jan , Topgaard Daniel , Benjamini Dan 
Published: October 2023

AbstractDiffusion MRI with free gradient waveforms, combined with simultaneous relaxation encoding, referred to as multidimensional MRI (MD-MRI), offers microstructural specificity in complex biological tissue. This approach delivers intravoxel information about the microstructure, local chemical composition, and importantly, how these properties are coupled within heterogeneous tissue containing multiple microenvironments. Recent theoretical advances incorporated diffusion time dependency and integrated MD-MRI with concepts from oscillating gradients. This framework probes the diffusion frequency,ω, in addition to the diffusion tensor,D, and relaxation,R1,R2, correlations. AD(ω)-R1-R2clinical imaging protocol was then introduced, with limited brain coverage and 3 mm3voxel size, which hinder brain segmentation and future cohort studies. In this study, we introduce an efficient, sparsein vivoMD-MRI acquisition protocol providing whole brain coverage at 2 mm3voxel size. We demonstrate its feasibility and robustness using a well-defined phantom and repeated scans of five healthy individuals. Additionally, we test different denoising strategies to address the sparse nature of this protocol, and show that efficient MD-MRI encoding design demands a nuanced denoising approach. The MD-MRI framework provides rich information that allows resolving the diffusion frequency dependence into intravoxel components based on theirD(ω)-R1-R2distribution, enabling the creation of microstructure-specific maps in the human brain. Our results encourage the broader adoption and use of this new imaging approach for characterizing healthy and pathological tissues.
The benzoxazinoid breakdown product 5-Methoxy-2-Nitrophenol has a dual function in maize defense against herbivory
Authors: Schimmel Bernardus C. J. , Escobar-Bravo Rocío , Mateo Pierre , Chen Cindy , Glauser Gaétan , Ogi Vera , Wang Lei , Verdecia-Mogena Arletys , Robert Christelle A. M. , Erb Matthias 
Published: October 2023

ABSTRACTCatabolism of plant secondary metabolites can yield bioactive breakdown products. However, these compounds often remain poorly characterized. Here, we report on the discovery, biosynthesis, and biological relevance of 5-Methoxy-2-Nitrophenol (5M2NP), a secondary metabolite breakdown product which accumulates in damaged maize tissues. We used mutant plants, biochemical complementation, and metabolomic analyses to determine the biosynthetic origin of 5M2NP. Additionally, we assessed 5M2NP’s role in plant defense against herbivores. For this, we surveyed defense-associated responses (gene expression, phytohormones, volatile organic compounds) in wounded, 5M2NP-supplemented maize leaves, and performed bioassays with herbivorous insects. We found that 5M2NP accumulation upon tissue disruption is contingent upon a functional benzoxazinoid biosynthesis pathway. Labeling experiments demonstrated that 5M2NP is derived from DIMBOA. Physiological doses of exogenous 5M2NP increased the wound-induced expression of defense genes and emission of terpenoids. Additionally, 5M2NP exhibited antibiotic and antixenotic activities towards both generalist and specialist herbivores in nano-to micromolar quantities. We conclude that 5M2NP, which represents a novel class of plant-derived compounds, can act as a direct defense and a defense modulator. 5M2NP thus expands the functional repertoire of benzoxazinoids and likely contributes to their protective function against insect herbivores. The discovery of 5M2NP highlights the multifunctionality of plant secondary metabolites and their breakdown products.
The Hidden Diversity of Vascular Patterns in Flower Heads
Authors: Owens Andrew , Zhang Teng , Gu Philmo , Hart Jeremy , Stobbs Jarvis , Cieslak Mikolaj , Elomaa Paula , Prusinkiewicz Przemyslaw 
Published: October 2023

SummaryVascular systems are intimately related to the shape and spatial arrangement of the plant organs they support. We investigate the largely unexplored association between spiral phyllotaxis and the vascular system in Asteraceae flowers heads.We imaged heads of eight species using synchrotron-based X-ray micro-computed tomography and applied original virtual reality and haptic software to explore head vasculature in three dimensions. We then constructed a computational model to infer a plausible patterning mechanism.The vascular system in the head of the model plantGerbera hybridais qualitatively different from those ofBellis perennisandHelianthus annuus, characterized previously.Cirsium vulgare, Craspedia globosa, Echinacea purpurea, Echinops bannaticus, andTanacetum vulgarerepresent variants of the Bellis and Helianthus systems. In each species the layout of the main strands is stereotypical, but details vary. The observed vascular patterns can be generated by a common computational model with different parameter values.In spite of the observed differences of vascular systems in heads, they may be produced by a conserved mechanism. The diversity and irregularities of vasculature stand in contrast with the relative uniformity and regularity of phyllotactic patterns, confirming that phyllotaxis in heads is not driven by the vasculature.
Shifts in attention drive context-dependent subspace encoding in anterior cingulate cortex during decision making
Authors: Hajnal Márton Albert , Tran Duy , Szabó Zsombor , Albert Andrea , Safaryan Karen , Einstein Michael , Martelo Mauricio Vallejo , Polack Pierre-Olivier , Golshani Peyman , Orbán Gergő 
Published: October 2023

AbstractAttention is a cognitive faculty that selects part of a larger set of percepts, driven by cues such as stimulus saliency, internal goals or priors. The enhancement of the attended representation and inhibition of distractors have been proposed as potential neural mechanisms driving this selection process. Yet, how attention operates when the cue has to be internally constructed from conflicting stimuli, decision rules, and reward contingencies, is less understood. Here we recorded from populations of neurons in the anterior cingulate cortex (ACC), an area implicated in ongoing error monitoring and correction during decision conflicts, in a challenging attention-shifting task. In this task, mice had to attend to the rewarded modality when presented identical auditory and visual stimuli in two contexts without direct external cues. In the ACC, the irrelevant stimulus continuously became less decodable than the relevant stimulus as the trial progressed to the decision point. This contrasted strongly with our previous findings in V1 where both relevant and irrelevant stimuli were equally decodable throughout the trial. Using analytical tools and a recurrent neural network (RNN) model, we found that the linearly independent representation of stimulus modalities in ACC was well suited to context-gated suppression of a stimulus modality. We demonstrated that the feedback structure of lateral connections in the RNN consisted of excitatory interactions between cell ensembles representing the same modality and mutual inhibition between cell ensembles representing distinct stimulus modalities. Using this RNN model showing signatures of context-gated suppression, we predicted that the level of contextual modulation of individual neurons should be correlated with their relative responsiveness to the two stimulus modalities used in the task. We verified this prediction in recordings from ACC neurons but not from recordings from V1 neurons. Therefore, ACC effectively operates on low-dimensional neuronal subspaces to combine stimulus related information with internal cues to drive actions under conflict.
Cultivating efficiency: High-throughput growth analysis of anaerobic bacteria in compact microplate readers
Authors: Snoeyenbos-West Oona L.O. , Guerrero Christina R , Valencia Makaela , Carini Paul 
Published: October 2023

ABSTRACTAnaerobic microbes play crucial roles in environmental processes, industry, and human health. Traditional methods for monitoring the growth of anaerobes, including plate counts or subsampling broth cultures for optical density measurements, are time and resource intensive. The advent of microplate readers revolutionized bacterial growth studies by enabling high-throughput and real-time monitoring of microbial growth kinetics but their use in anaerobic microbiology has remained limited. Here, we present a workflow for using small-footprint microplate readers and the Growthcurver R package to analyze the kinetic growth metrics of anaerobic bacteria. We benchmarked the small-footprint Cerillo Stratus microplate reader against a BioTek Synergy HTX microplate reader in aerobic conditions usingEscherichia coliDSM 28618 cultures. The growth rates and carrying capacities obtained from the two readers were statistically indistinguishable. However, the area under the logistic curve was significantly higher in cultures monitored by the Stratus reader. We used the Stratus to quantify the growth responses of anaerobically grownE. coliandClostridium bolteaeDSM 29485 to different doses of the toxin sodium arsenite. The growth ofE. coliandC. bolteaewas sensitive to arsenite doses of 1.3 μM and 0.4 μM, respectively. Complete inhibition of growth was achieved at 38 μM arsenite forC. bolteae, and 338 μM inE. coli. These results show that the Stratus performs similarly to a leading brand of microplate reader and can be reliably used in anaerobic conditions. We discuss the advantages of the small format microplate readers and our experiences with the Stratus.Importance statementWe present a workflow that facilitates the production and analysis of growth curves for anaerobic microbes using small-footprint microplate readers and an R script. This workflow is a cost and space-effective solution to most high-throughput solutions for collecting growth data from anaerobic microbes. This technology can be used for applications in which high-throughput would advance discovery, including microbial isolation, bioprospecting, co-culturing, host-microbe interactions, and drug/toxin-microbial interactions.
Shared and Distinct Mechanisms of UBA1 Inactivation Across Different Diseases
Authors: Collins Jason C. , Magaziner Samuel J. , English Maya , Hassan Bakar , Chen Xiang , Balanda Nicholas , Anderson Meghan , Lam Athena , Fernandez-Pol Sebastian , Kwong Bernice , Greenberg Peter L. , Terrier Benjamin , Likhite Mary E. , Kosmider Olivier , Wang Yan , Samara Nadine L. , Walters Kylie J. , Beck David B. , Werner Achim 
Published: October 2023

SummaryMost cellular ubiquitin signaling is initiated by UBA1, which activates and transfers ubiquitin to tens of E2 enzymes. Clonally acquiredUBA1missense mutations cause an inflammatory-hematologic overlap disease called VEXAS (vacuoles, E1, X-linked, autoinflammatory, somatic) syndrome. Despite extensive clinical investigation into this lethal disease, little is known about the underlying molecular mechanisms. Here, by dissecting VEXAS-causingUBA1mutations, we discovered that p.Met41 mutations alter cytoplasmic isoform expression, whereas other mutations reduce catalytic activity of nuclear and cytoplasmic isoforms by diverse mechanisms, including aberrant oxyester formation. Strikingly, non-p.Met41 mutations most prominently affect transthioesterification, revealing ubiquitin transfer to cytoplasmic E2 enzymes as a shared property of pathogenesis amongst different VEXAS syndrome genotypes. A similar E2 charging bottleneck exists in some lung cancer-associatedUBA1mutations, but not in spinal muscular atrophy-causingUBA1mutations, which instead, render UBA1 thermolabile. Collectively, our results highlight the precision of conformational changes required for faithful ubiquitin transfer, define distinct and shared mechanisms of UBA1 inactivation in diverse diseases, and suggest that specific E1-E2 modules control different aspects of tissue differentiation and maintenance.
Social bond dynamics and the evolution of helping
Authors: Leimar Olof , Bshary Redouna 
Published: October 2023

AbstractEmpiricists often struggle to apply game theory models to real-life cases of animal cooperation. One reason is that many examples of cooperation occur in stable groups, where costs and benefits of helping depend on several factors. Among these are variable investments, fitness interdependencies, learning, memory, reciprocity, and partner choice, including the formation of social bonds with specific group members. Here, we present a game theory model exploring the conditions under which social bonds between group members can promote cooperation, with reciprocal acts of helping. In the model, bonds build up from exchanges of help in a similar way as the strength of association increases in learning, as in the Rescorla-Wagner rule. The bonds in turn affect partner choice and influence helping amounts. The model has a mechanism of reciprocity for bonded pairs, which can evolve towards either loose or strict reciprocation. Several aspects of the model are inspired by observations of food sharing in vampire bats. We find that small social neighbourhoods are required for the evolutionary stability of helping, either as small group sizes, or if members of larger groups can form temporary (daily) smaller groupings. The evolutionary outcome is a fairly low cost helping, while the benefit of receiving help can be substantial. Individuals in need request help based on bond strength, but there is also an evolved preference for initiating bonds with new group members. In contrast, if different groups come into temporary contact with each other, the evolved tendency is to avoid forming bonds between groups.Popular science summaryThe search for evolutionary explanations of cooperation between members of social groups has long been a high profile endeavour. A case of particular interest is when individuals develop a network of friends and exchange help through these social bonds. The question of helping between friends was given emphasis already from the start of the evolutionary study of cooperation, more than 50 years ago, but it has remained without any decisive progress since that time. Here we present a game-theory analysis of helping through the build-up of social bonds. We find that there is reciprocity in socially bonded pairs, which is neither immediate nor very strict, and that relatively small social neighbourhoods are required for the evolutionary stability of helping.
Non-coding variants impactcis-regulatory coordination in a cell type-specific manner
Authors: Pushkarev Olga , van Mierlo Guido , Kribelbauer Judith F. , Saelens Wouter , Gardeux Vincent , Deplancke Bart 
Published: October 2023

AbstractBACKGROUNDInteractions amongcis-regulatory elements (CREs) play a crucial role in gene regulation. Various approaches have been developed to map these interactions genome-wide, including those relying on interindividual epigenomic variation to identify groups of covariable regulatory elements, referred to as chromatin modules (CMs). While CM mapping allows to investigate the relationship between chromatin modularity and gene expression, the computational principles used for CM identification vary in their application and outcomes.RESULTSWe comprehensively evaluate and streamline existing CM mapping tools and present guidelines for optimal utilization of epigenome data from a diverse population of individuals to assess regulatory coordination across the human genome. We showcase the effectiveness of our recommended practices by analysing distinct cell types and demonstrate cell type-specificity of CRE interactions in CMs and their relevance for gene expression. Integration of genotype information revealed that many non-coding disease-associated variants affect the activity of CMs in a cell type-specific manner by affecting the binding of cell type-specific transcription factors. We provide example cases that illustrate in detail how CMs can be used to deconstruct GWAS loci, understand variable expression of cell surface receptors in immune cells and reveal how genetic variation can impact the expression of prognostic markers in chronic lymphocytic leukaemia.CONCLUSIONSOur study presents an optimal strategy for CM mapping, and reveals how CMs capture the coordination of CREs and its impact on gene expression. Non-coding genetic variants can disrupt this coordination, and we highlight how this may lead to disease predisposition in a cell type-specific manner.
Apparel behavioural intentions of urban bottom-of-the-pyramid consumers: exploring the role of store atmospherics
Authors: van Niekerk Bianca Maria , Roberts-Lombard Mornay , Cunningham Nicole 
Published: October 2023

Purpose
This study aims to explore the impact of store atmospherics on urban bottom-of-the-pyramid consumers’ behavioural intentions to purchase apparel in an emerging African market context. This study also considers purchase antecedents to attitude, perceived behavioural control and social norms as determinants of urban bottom-of-the-pyramid consumers’ apparel behavioural intentions.

Design/methodology/approach
Using non-probability sampling, specifically purposive and interlocking sampling, data collection was secured from 881 economically active Namibian urban bottom-of-the-pyramid respondents through interviewer-administered questionnaires. Covariance-based structural equation modelling assessed the significant relationships among all constructs in the conceptual model.

Findings
This study found that for favourable apparel behavioural intentions of urban bottom-of-the-pyramid consumers to occur, apparel retailers should emphasise trust, perceived awareness and self-identity through apparel assortment and groupings, easy-to-read visible signage, together with competent, friendly and respectful sales personnel in their store atmospherics.

Practical implications
The findings of this study may guide apparel retailers in other emerging African markets to develop regional integration, market-based solutions and inclusive economic growth focusing on “non-essential” products, such as apparel, among urban bottom-of-the-pyramid consumers.

Originality/value
This study expands the intellectual boundaries of urban bottom-of-the-pyramid consumers’ behavioural intentions towards “non-essential” products. The theoretical framework supports the integration of both the stimulus-organism-response model and the theory of planned behaviour into one single model for empirical investigation. Additionally, adopting a novel theoretical framework helped identify the impact of store atmospherics from a bottom-of-the-pyramid perspective in an emerging African market context, such as Namibia.