bluuebunny/crossref_metadata_2025 huggingface dataset:
RNG2 tethers the conoid to the apical polar ring inToxoplasma gondii: a key mechanism in parasite motility and invasion
Authors: Haase Romuald , Ren Bingjian , Santos Pacheco Nicolas Dos , Visentin Rémy , Maco Bohumil , Flores Ricardo Mondragon , Vadas Oscar , Soldati-Favre Dominique
Published: August 2024

InToxoplasma gondii, the conoid is a dynamic organelle composed of spiraling tubulin fibers that extrudes during egress, gliding motility, and invasion. This organelle traverses the apical polar ring (APR) in response to calcium waves and plays a critical role in controlling parasite motility. While the actomyosin-dependent extrusion of the conoid is beginning to be understood, the mechanism by which it is anchored apically to the APR remains unclear. RNG2, a protein localized at both the conoid and the APR, has emerged as a key candidate for this function. By combining iterative ultrastructure expansion microscopy and immunoelectron microscopy we discovered that RNG2 forms 22 tethers between the APR and the conoid. The unique biochemical properties of RNG2, including several proteolytic processing events and its ability to form concatenations, enable it to function as a dynamic bridge between these structures. Conditional depletion of RNG2 resulted in the conoid organelle detaching from the APR without compromising the integrity of its structure, thereby confirming RNG2 essential tethering role. Although microneme secretion remains normal, parasites lacking RNG2 were unable to move and impaired in rhoptry discharge, highlighting the conoid’s crucial role in parasite motility and invasion. RNG2 is a pivotal protein that ensures conoid functionality inCoccidia.
Chemical crosslinking extends and complements UV crosslinking in analysis of RNA/DNA nucleic acid–protein interaction sites by mass spectrometry
Authors: Welp Luisa M. , Sachsenberg Timo , Wulf Alexander , Chernev Aleksandar , Horokhovskyi Yehor , Neumann Piotr , Pašen Martin , Siraj Arslan , Raabe Monika , Johannsson Sven , Schmitzova Jana , Netz Eugen , Pfeuffer Julianus , He Yi , Fritzemeier Kai , Delanghe Bernard , Viner Rosa , Vos Seychelle M. , Cramer Patrick , Ficner Ralf , Liepe Juliane , Kohlbacher Oliver , Urlaub Henning
Published: August 2024

UV (ultra-violet) crosslinking with mass spectrometry (XL-MS) has been established for identifying RNA-and DNA-binding proteins along with their domains and amino acids involved. Here, we explore chemical XL-MS for RNA-protein, DNA-protein, and nucleotide-protein complexesin vitroandin vivo. We introduce a specialized nucleotide-protein-crosslink search engine, NuXL, for robust and fast identification of such crosslinks at amino acid resolution. Chemical XL-MS complements UV XL-MS by generating different crosslink species, increasing crosslinked protein yields in vivo almost four-fold and thus it expands the structural information accessible via XL-MS. Our workflow facilitates integrative structural modelling of nucleic acid–protein complexes and adds spatial information to the described RNA-binding properties of enzymes, for which crosslinking sites are often observed close to their cofactor-binding domains.In vivoUV and chemical XL-MS data fromE. colicells analysed by NuXL establish a comprehensive nucleic acid–protein crosslink inventory with crosslink sites at amino acid level for more than 1500 proteins. Our new workflow combined with the dedicated NuXL search engine identified RNA crosslinks that cover most RNA-binding proteins, with DNA and RNA crosslinks detected in transcriptional repressors and activators.
Reliability of canopy photography for forest ecology and biodiversity studies
Authors: von Meijenfeldt Anouk , Chianucci Francesco , Rigo Francesca , Ottenburghs Jente , Hilpold Andreas , Mina Marco
Published: August 2024

Understory is a key component of forest biodiversity. The structure of the forest stand and the horizontal composition of the canopy play a major role on the light regime of the understory, which in turn affects the abundance and the diversity of the understory plant community. Reliable assessments of canopy structural attributes are essential for forest research and biodiversity monitoring programs, as well as to study the relationship between canopy and understory plant communities. Canopy photography is a widely used method but it is still not clear which photographic techniques is better suited to capture canopy attributes at stand-level that can be relevant in forest biodiversity studies. For this purpose, we collected canopy structure and understory plant diversity data on 51 forest sites in the north-eastern Italian Alps, encompassing a diversity of forest types. Canopy images were acquired using both digital cover (DCP) and hemispherical (DHP) photography. Canopy structural attributes were then compared to tree species composition data to evaluate whether they were appropriate to differentiate between forest types. Additionally, we tested what canopy attributes derived from DCP and DHP best explained the species composition of vascular plants growing in the understory. We found that hemispherical canopy photography was most suitable to capture differences in forest types, which was best expressed by variables such as leaf inclination angle and canopy openness. On our sites, DHP-based canopy attributes were also able to better distinguish between different conifer forests. Leaf clumping was the most important attribute for determining plant species distribution of the understory, indicating that diverse gap structures create different microclimate conditions enhancing diverse plant species with different ecological strategies. This study supports the reliability of canopy photography in forest ecology and biodiversity monitoring, but also provide insights for increasing understory diversity in managed forests of high conservation value.

Abstract Figure
An active model for the basilar membrane and the outer hair cells
Authors: Berger Jorge , Rubinstein Jacob
Published: August 2024

A model for the joint motion of the basilar membrane (BM) and the outer hair cells (OHC) in the cochlea is presented. The model consists of two one-dimensional mass distributions, one along the OHC and outer hair bundle (OHB) interface, and one along the BM. The motion of these masses is driven by the forces exerted on them by the elastic bodies connecting them and by the pressure difference in the fluids separated by the BM. The model includes a nonlinear motility of the OHC and its coupling with the vibrations of the BM. The model implies a Hopf bifurcation for the dynamical system governing the two coupled distributed oscillators. It is shown that when the system operates near the bifurcation point the BM motion is amplified up to a saturation level. The model provides very sharp frequency decomposition of the incident audio signal according to the place principle. It also acts as a powerful filter that distinguishes pure tones even in the presence of louder noisy background. In addition to simulations of the model, the unusual role played by the OHC friction is studied. Energy estimates are derived for the model functions.
Hawkmoth pheromone transduction involves G protein-dependent phospholipase Cβ signaling
Authors: Schneider Anna C. , Schröder Katrin , Chang Yajun , Nolte Andreas , Gawalek Petra , Stengl Monika
Published: August 2024

1

Evolutionary pressures adapted insect chemosensation to the respective insect’s physiological needs and tasks in their ecological niches. Solitary nocturnal moths rely on their acute olfactory sense to find mates at night. Pheromones are detected with maximized sensitivity and high temporal resolution through mechanisms that are mostly unknown. While the inverse topology of insect olfactory receptors and heteromerization with the coreceptor Orco suggest ionotropic transduction via odorant-gated receptor-ion channel complexes, contradictory data propose amplifying G protein-coupled transduction. Here, we usedin vivotip-recordings of pheromone-sensitive sensilla of maleManduca sextahawkmoths at specific times of day (rest vs. activity). Since the olfactory receptor neurons distinguish signal parameters in three consecutive temporal windows of their pheromone response (phasic; tonic; late, long-lasting), respective response parameters were analyzed separately. Disruption of G protein-coupled transduction and block of phospholipase C decreased and slowed the phasic response component during the activity phase of hawkmoths without affecting any other component of the response during activity and rest. A more targeted disruption of Gαsubunits by blocking Gαoor sustained activation of Gαsusing bacterial toxins affected the phasic pheromone response, while toxins targeting Gαqand Gα12/13were ineffective. Consistent with these data, the expression of phospholipase Cβ4 depended on zeitgeber time, which indicates circadian clock-modulated metabotropic pheromone transduction cascades that maximize sensitivity and temporal resolution of pheromone transduction during the hawkmoth’s activity phase. Thus, discrepancies in the literature on insect olfaction may be resolved by considering circadian timing and the distinct odor response components.

2 Significance statement

Insect chemosensory transduction is typically thought to be ionotropic, but data from different insect species suggests that metabotropic olfactory signaling may occur, either alongside or instead of ionotropic mechanisms. Nocturnal moths, known for their extraordinarily sensitive pheromone-detecting olfactory receptor neurons, likely use metabotropic signal amplification. To overcome limitations of previousin vitrostudies, we conducted tip-recordings of pheromone-sensitive sensilla in healthy hawkmoths at specific zeitgeber times. Disrupting G protein signaling and phospholipase Cβ reduced sensitivity and altered response kinetics, revealing strict temporal control of transduction. Thus, contradictory findings in insect olfaction may be reconciled by considering diverse evolutionary pressures for distinct chemosensory signals in different species, zeitgeber time, and disparate odor response parameters.
Dance displays in gibbons: Biological and linguistic perspectives on structured, intentional and rhythmic body movement
Authors: Coye C. , Caspar K.R. , Patel-Grosz P.
Published: August 2024

Female crested gibbons perform conspicuous sequences of twitching movements involving the rump and extremities. However, these dances have attracted little scientific attention and their structure and meaning remain largely obscure. Here we analyse close-range video recordings of captive crested gibbons, extracting descriptions of dance in fourNomascusspecies (N. annamensis, N. gabriellae, N. leucogenys,andN. siki). Additionally, we report results from a survey amongst relevant professionals clarifying behavioural contexts of dance in captive and wild crested gibbons. Our results demonstrate that dances inNomascusrepresent a common and intentional form of visual communication restricted to sexually mature females. While primarily used as a proceptive signal to solicit copulation, dances occur in a wide range of contexts related to arousal and/or frustration in captivity. A linguistically informed view of this sequential behaviour demonstrates that dances follow a grouping organisation and isochronous rhythm – patterns not described for visual displays in other non-human primates. We argue that applying the concept of dance to gibbons allows us to expand our understanding of the communicative behaviours of non-human apes and develop hypotheses on the rules and regularities characterizing this behaviour. We propose that gibbons dances likely evolved from less elaborate rhythmic proceptive signals, similar to those found in siamangs. Although dance displays in humans and crested gibbons share a number of key characteristics, they cannot be assumed to be homologous. Nevertheless, gibbon dances represent a model behaviour whose investigation could be extended to the study of complex gestural signals in hominoid primates.
ChimpanSEE, ChimpanDO: Grooming and play contagion in chimpanzees
Authors: Sandars Georgia , Brooker Jake Stephen , Clay Zanna
Published: August 2024

Behavioural contagion—the onset of a species-typical behaviour soon after witnessing it in a conspecific—forms the foundation of behavioural synchrony and cohesive group living in social animals. Although past research has mostly focused on negative emotions or neutral contexts, the sharing of positive emotions in particular may be key for social affiliation. We investigated the contagion of two socially affiliative interactive behaviours, grooming and play, in chimpanzees. We collected naturalistic observations ofN= 41 sanctuary-living chimpanzees at Chimfunshi Wildlife Orphanage, conducting focal follows of individuals following observations of a grooming or play bout, compared with matched controls. We then tested whether the presence and latency of behavioural contagion was influenced by age, sex, rank, and social closeness. Our results offer evidence for the presence of grooming and play contagion in sanctuary-living chimpanzees. Grooming contagion appeared to be influenced by social closeness, whilst play contagion was more pronounced in younger individuals. These findings emphasise that contagion is not restricted to negatively valenced or self-directed behaviours, and that the predictors of contagious behaviour are highly specific to the behaviour and species in question. Examining the factors that influence this foundational social process contributes to theories of affective state matching and is key for understanding social bonding and group dynamics.
USP9X is a mechanosensitive deubiquitinase that controls tumor cell invasiveness and drug response through YAP stabilization
Authors: Biber Pierric , Carminati Alexandrine , Girard Christophe A. , Mohager Walaa , Ohanna Mickael , Lecacheur Margaux , Bouvet Oceane , Audebert Stephane , Khaled Mehdi , Tartare-Deckert Sophie , Deckert Marcel
Published: August 2024

Post-translational modification by ubiquitin is crucial for protein turnover. Deubiquitinases (DUBs) remove ubiquitin chains from target proteins to prevent their degradation by the proteasome, thus acting as gatekeepers of protein homeostasis alongside the ubiquitin-proteasome system (UPS). Tumor cells exhibit remarkable plasticity, enabling them to adapt to anticancer treatments and the conditions of the tumor microenvironment, including mechanical cues from the extracellular matrix (ECM). However, the role of DUBs in mechanotransduction remains unexplored. To identify DUBs involved in cancer cell mechanosignaling, we used melanoma cells grown on collagen matrices with varying stiffnesses and an activity-based ubiquitin probe to profile DUB activities. Our approach, combined with quantitative proteomics, revealed that ubiquitin-specific protease 9X (USP9X) is sensitive to ECM stiffness through discoidin domain receptors (DDR)/actomyosin signaling pathway. In silico analysis further indicated that the mechanosensor YAP is part of the USP9X interactome, and USP9X expression correlates with the YAP transcriptional signature in melanoma. We hypothesized that mechanical signals regulate YAP levels through USP9X DUB activity. Consistently, low collagen stiffness reduced YAP expression, and siRNA-mediated depletion or pharmacological inhibition of USP9X decreased YAP protein expression in tumor cells. Conversely, knockdown of the ubiquitin E3 ligase βTrCP increased YAP protein levels. Affinity purification of polyubiquitinated proteins using Tandem Ubiquitin Binding Entities (TUBEs) showed that combined USP9X and proteasome inhibition increased YAP poly-ubiquitination, revealing that USP9X deubiquitinates YAP to prevent its proteasomal degradation. Targeting USP9X impaired stiffness-mediated responses, including YAP nuclear translocation and transcriptional activity, cell migration and invasion, and drug resistance. An experimental metastasis assay showed that stable knockdown of USP9X impaired melanoma cell lung colonization. Finally, targeting USP9X in a syngeneic BRAF-mutant melanoma model counteracted targeted therapy-induced ECM remodeling, enhanced treatment efficacy, and delayed tumor relapse. Our findings reveal a novel role of USP9X in cancer cell mechanobiology and drug resistance through stiffness-dependent stabilization of the oncoprotein YAP, proposing USP9X as a targetable "mechano-DUB" in cancer.
Transitions from monotonic to tuned responses in recurrent neural network models during timing prediction
Authors: Hendrikx Evi , Manns Daniel , van der Stoep Nathan , Testolin Alberto , Zorzi Marco , Harvey Ben M.
Published: August 2024

The brain exhibits a gradual transition in responses to visual event duration and frequency through the visual processing hierarchy: from monotonically increasing to timing-tuned responses. Over their hierarchies, properties of both response types are progressively transformed. Here, we implement simulations based on artificial neural networks to investigate the requirements of neural systems for the emergence of such responses and their properties’ transformations. We see that recurrent networks develop monotonic responses whose properties’ progressions over network layers resemble those over brain areas. Responses to another sensory quantity, Furthermore, recurrent networks can further develop tuned responses, but only with training, a gradual transition between monotonic and tuned responses emerges. Particularly, if this training is done on predictable sequences, the tuned properties’ progressions resemble those observed in the brain. These results suggest that the emergence of visual timing-tuned responses and the subsequent hierarchical transformations of these responses result from recurrent neural computation and predictive processing of sensory event timing.
Diverse RNA Structures Induce PRC2 Dimerization and Inhibit Histone Methyltransferase Activity
Authors: Song Jiarui , Yao Liqi , Gooding Anne R. , Thron Valentin , Kasinath Vignesh , Cech Thomas R.
Published: August 2024

Methyltransferase PRC2 (Polycomb Repressive Complex 2) introduces histone H3K27 trimethylation, a repressive chromatin mark, to tune the differential expression of genes. PRC2 is precisely regulated by accessory proteins, histone post-translational modifications and, notably, RNA. Research on PRC2-associated RNA has mostly focused on the tight-binding G-quadruplex (G4) RNAs, which inhibit PRC2 enzymatic activity in vitro and in cells. Our recent cryo-EM structure provided a molecular mechanism for G4 RNA inactivating PRC2 via dimerization, but it remained unclear how diverse RNAs associate with and regulate PRC2.

Here, we show that a single-stranded G-rich RNA and an atypical G4 structure called pUG-fold unexpectedly also mediate near-identical PRC2 dimerization resulting in inhibition of PRC2 methyltransferase activity. The conformational flexibility of arginine-rich loops within subunits EZH2 and AEBP2 of PRC2 can accommodate diverse RNA secondary structures, resulting in protein-RNA and protein-protein interfaces similar to those observed previously with G4 RNA. Furthermore, we address a recent report that failed to detect PRC2-associated RNAs in living cells by demonstrating the insensitivity of PRC2-RNA interaction to photochemical crosslinking. Our results support the significance of RNA-mediated PRC2 regulation by showing that this interaction is not limited to a single RNA secondary structure, consistent with the broad PRC2 transcriptome containing many G-tract RNAs incapable of folding into G4 structures.
TRAIL receptor agonist TLY012 in combination with PD-1 inhibition promotes tumor regression in an immune-competent mouse model of pancreatic ductal adenocarcinoma
Authors: Louie Anna D. , Huntington Kelsey E. , Lee Young , Mompoint Jared , Wu Laura Jinxuan , Lee Seulki , Miner Thomas J. , El-Deiry Wafik S.
Published: August 2024

Pancreatic ductal adenocarcinoma (PDAC) has an immunosuppressed, apoptosis-resistant phenotype. TLY012 is a pegylated recombinant Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL), an orphan drug for chronic pancreatitis and systemic sclerosis. Innate immune TRAIL signaling suppresses cancer. We hypothesized that combination of immune checkpoint-blocking anti-PD-1 antibody and TLY012 would have synergistic anti-tumor efficacy in immune-competent PDAC-bearing mice. PDAC tumor-bearing C57Bl/6 mice treated 10 mg/kg anti-mouse PD-1 antibody twice weekly and 10 mg/kg TLY012 three times weekly had reduced tumor growth and tumor volume at 70 days compared to either drug alone (all p<0.005). B-cell activating factor (BAFF), which promotes PDAC tumors, decreased to 44% of control mice with dual treatment at 7 days and remained decreased at 3 months. Long-term dual treatment showed the highest levels of proinflammatory cytokines interferon gamma (average 5.6 times control level, p=0.046), CCL5 (average 14.1 times control level, p=0.048), and interleukin-3 (IL-3, average 71.1 times control level, p=0.0053). Flow cytometry showed trends toward decreased circulating regulatory T cells, increased NK cells, and a higher proportion of CD8+ T cells within tumors in dual treatment group. In summary, combination of anti-PD-1 and TLY012 prevented growth of PDAC in an immunocompetent mouse model while increasing tumor-infiltrating CD8+ T cells, decreasing circulating T-regulatory cells and altering cytokine expression of CCL5, interferon gamma and IL-3 to promote proinflammatory, antitumor effects. Combining TLY012 and anti-mouse PD-1 creates changes in immune cell and cytokine levels to induce a more proinflammatory immune environment that contributes to decreased PDAC tumor growth.
RepeatAscarischallenge reduces worm intensity through gastric cellular reprograming
Authors: Wu Yifan , Suarez-Reyes Charlie , Kneubehl Alexander R. , Weatherhead Jill E.
Published: August 2024

Ascariasis (roundworm) is the most prevalent parasitic nematode infection worldwide, impacting approximately 500 million people predominantly in low- and middle-income countries (LMICs). While people of all ages are infected withAscaris, infection intensity (defined by worm burden) paradoxically peaks in pre-school and school aged children but then declines with age. The cause of age-dependentAscarisworm intensity is not well understood but may be dependent on cellular changes in mucosal barrier sites. We have previously found that the gastric mucosa is a critical barrier site forAscarisinfection. Following oral ingestion ofAscariseggs, larvae use AMCase secreted by gastric chief cells and acid secreted by gastric parietal cells to hatch. Once hatched, larvae translocate across the gastric mucosa to initiate the larval migratory cycle. However, inducing mucosal injury with administration of Tamoxifen induces mucosa cellular changes that impairsAscarishatching and reduces larval translocation across the gastric mucosa. In this study we established a repeatedAscaris suumchallenge mouse model and evaluated if repeated Ascaris challenge also lead to cellular changes in the gastric mucosal barrier. We found that repeatedAscarischallenge caused cellular changes in the gastric mucosa which reduced worm intensity in the liver independent of the adaptive immune response. Thus, in endemic regions, where individuals experience recurrent infection throughout their lives, gastric cellular changes may be a key mechanism leading to the observed age-dependentAscarisworm intensity changes from childhood to adulthood.
Developmental transformations of Purkinje cells tracked by DNA electrokinetic mobility
Authors: Brandenburg C. , Crutcher G.W. , Romanowski A.J. , Donofrio S.G. , Duraine L.R. , Owusu-Mensah R.N.A. , Sugihara I. , Blatt G.J. , Sillitoe R.V. , Poulopoulos A.
Published: August 2024

Brain development relies on orchestrated placement and timing of neurogenesis in progenitor zones to produce the expansive cellular diversity of the brain. We took advantage of bioelectric interactions between DNA and embryonic tissue to perform “stereo-tracking”, a developmental targeting strategy that differentially labels cells positioned at different depths within intact progenitor zones. This three-dimensional labeling was achieved by delivery of plasmids with distinct electrokinetic mobilities into neural progenitor zonesin utero. We applied stereo-tracking with light sheet imaging in the cerebellum and identified that Purkinje cells follow embryonically committed developmental trajectories linking distinct progenitor zone fields to the topography of the mature cerebellar cortex. In the process of stereo-tracking, we identified a previously unreported subcellular structure on the axon initial segment of Purkinje cells. These structures, we termed “axon bubbles”, are developmentally timed and differentially labeled by lipid-modified proteins. Our findings demonstrate key rules that orchestrate the stereotyped transformations from fetal progenitors into mature networks of neuronal circuits, and demonstrate the potential of progenitor zone stereo-tracking to reveal new biology within intact developing systems.
Variational inference of single cell time series
Authors: Xu Bingxian , Braun Rosemary
Published: August 2024

Time course single–cell RNA sequencing (scRNA-seq) enables researchers to probe genome–wide expression dynamics at the the single cell scale. However, when gene expression is affected jointly by time and cellular identity, analyzing such data — including conducting cell type annotation and modeling cell type–dependent dynamics — becomes challenging. To address this problem, we propose SNOW (SiNgle cell flOW map), a deep learning algorithm to deconvolve single cell time series data into time– dependent and time–independent contributions. SNOW has a number of advantages. First, it enables cell type annotation based on the time–independent dimensions. Second, it yields a probabilistic model that can be used to discriminate between biological temporal variation and batch effects contaminating individual timepoints, and provides an approach to mitigate batch effects. Finally, it is capable of projecting cells forward and backward in time, yielding time series at the individual cell level. This enables gene expression dynamics to be studied without the need for clustering or pseudobulking, which can be error prone and result in information loss. We describe our probabilistic framework in detail and demonstrate SNOW using data from three distinct time course scRNA-seq studies. Our results show that SNOW is able to construct biologically meaningful latent spaces, remove batch effects, and generate realistic time–series at the single–cell level. By way of example, we illustrate how the latter may be used to enhance the detection of cell type–specific circadian gene expression rhythms, and may be readily extended to other time–series analyses.
Rapid Visual Engagement in Neural Processing of Detailed Touch Interactions
Authors: Smit Sophie , Ramírez-Haro Almudena , Quek Genevieve L. , Varlet Manuel , Moerel Denise , Grootswagers Tijl
Published: August 2024

Touch perception is an inherently multisensory process in which vision plays an essential role. However, our understanding of how vision encodes sensory and emotional-affective aspects of observed touch, and the timing of these processes, is still limited. Here we address this gap by investigating the neural dynamics of visual touch observation by analysing electroencephalographic (EEG) data from participants viewing detailed hand interactions from the Validated Touch-Video Database. We examined how the brain encodes basic body cues such as hand orientation and viewing perspective, in addition to sensory aspects, including the type of touch (e.g., stroking vs. pressing; hand vs. object touch) and the object involved (e.g., knife, brush), as well as emotional-affective dimensions. Using multivariate decoding, information about body cues was present within 60 ms, with sensory and emotional details, including valence, arousal, and pain present around 130 ms, demonstrating efficient early visual processing. Threat was most clearly identified by approximately 265 ms, similarly involving visual regions, suggesting that such evaluations require slightly extended neural engagement. Our findings reveal that bottom-up, automatic visual processing is integral to complex tactile assessments, important for rapidly extracting both the personal relevance and the sensory and emotional dimensions of touch.
Sex and morph variation in activity from early ontogeny to maturity in ruffs (Calidris pugnax)
Authors: Rohr-Bender Veronika A. , Kupán Krisztina , Lopez-Nava Guadalupe , Forstmeier Wolfgang , Hertel Anne , Razumov Vitali , Martin Katrin , Kempenaers Bart , Küpper Clemens
Published: August 2024

Intraspecific variation provides the substrate for the evolution of organisms. Ruffs show exceptional phenotypic variation in physiology, appearance and behaviour linked to variation between sexes and male alternative reproductive tactics (ARTs). The male ARTs are associated with the evolution of separate morphs, which are encoded by an autosomal supergene. However, the effects of the supergene on females and chicks are much less well understood. In particular, it is still unknown, whether females also show morph-specific behavioural variation, when behavioural differences emerge during ontogeny, and whether behavioural differences can be detected outside of the breeding context. To address these knowledge gaps, we repeatedly measured the activity in an unfamiliar environment, also known as exploration behaviour, of 109 hand-raised young ruffs throughout their first two years of life. We used automated tracking in an open field arena, and quantified the distance moved within 10 minutes to examine behavioural differences between sexes, morphs and individuals. The activity of young ruffs rapidly increased during the first month after their crouching reflex, a response to potential threats, subsided. Repeatability of individual activity was initially low but increased throughout juvenile ontogeny and was high (R = 0.5) from day 21 onwards. Variation in activity was clearly sex-linked with females moving more than males, indicating potential energetic trade-offs accompanying the strong sexual size dimorphism. In contrast, morph differences in activity remained inconsistent and elusive, both in females and in males. Our results indicate that in species where much of the known behavioural variation is linked to mating tactics, a non-reproductive behaviour can show between-individual variation and clear sex differences, whereas morph differences appear less pronounced.
GPRC6A as a novel kokumi receptor responsible for enhanced taste preferences by ornithine
Authors: Yamamoto Takashi , Ueji Kayoko , Mizuta Haruno , Inui-Yamamoto Chizuko , Kumamoto Natsuko , Shibata Yasuhiro , Ugawa Shinya
Published: August 2024

The concept of “kokumi,” which refers to an enhanced and more delicious flavor of food, has recently generated considerable interest in food science. However, kokumi has not been well studied in gustatory physiology, and the underlying neuroscientific mechanisms remain largely unexplored. Our previous research demonstrated that ornithine (L-ornithine), which is abundant in shijimi clams, enhanced taste preferences in mice. The present study aimed to build on these findings and investigate the mechanisms responsible for kokumi in rats. In two-bottle preference tests, the addition of ornithine, at a low concentration that did not increase the favorability of this substance alone, enhanced the animals’ preferences for umami, sweet, fatty, salty, and bitter solutions, with the intake of monosodium glutamate showing the most significant increase. Additionally, a mixture of umami and ornithine synergistically induced significant responses in the chorda tympani nerve, which transmits taste information to the brain from the anterior part of the tongue. The observed preference enhancement and increase in taste-nerve response were abolished by antagonists of the G-protein-coupled receptor family C group 6 subtype A (GPRC6A). Furthermore, immunohistochemical analysis indicated that GPRC6A was expressed in a subset of type II taste cells in rat fungiform papillae. These results provide new insights into flavor-enhancement mechanisms, confirming that ornithine is a kokumi substance and GPRC6A is a novel kokumi receptor.
Root Anatomy: Preparing, Imaging, and Analyzing Maize Root Cross-Sections
Authors: Sidhu Jagdeep Singh , Schneider Hannah M.
Published: August 2024

Root anatomy plays a critical structural and functional role in the maize root system, and regulates edaphic stress tolerance. The function and genetic basis of several maize root anatomical traits for stress tolerance have been demonstrated. Leveraging root anatomical traits in maize thus holds great potential for developing cultivars with greater nutrient and water efficiency. Key for such approaches is the ability to characterize the root anatomy of plants of interest. Here, we outline a systematic method for preparing, imaging, and analyzing maize root cross-sections. The protocol describes root sectioning (by hand or using a vibratome), preparation of microscope slides and toluidine blue staining, imaging under a light microscope, and both manual and semiautomated methods for anatomical feature extraction from images. The protocol enables the visualization and quantification of various anatomical tissues and traits, and its simplicity, adaptability, and accessibility make it an ideal choice for both small- and large-scale phenotyping studies in maize and other plant species. This standardized protocol provides researchers with a comprehensive methodology to accurately dissect root structures, enabling in-depth analyses that are essential for understanding plant growth, development, and adaptive value for stress tolerance.
Scaling law for a buckled elastic filament in a shear flow
Authors: Sznajder Paweł , Zdybel Piotr , Liu Lujia , Ekiel-Jeżewska Maria L.
Published: August 2024

We analyze the three-dimensional (3D) buckling of an elastic filament in a shear flow of a viscous fluid at low Reynolds number and high Péclet number. We apply the Euler-Bernoulli beam (elastica) theoretical model. We show the universal character of the full 3D spectral problem for a small perturbation of a thin filament from a straight position of arbitrary orientation. We use the eigenvalues and eigenfunctions for the linearized elastica equation in the shear plane, found earlier by Liu [] with the Chebyshev spectral collocation method, to solve the full 3D eigenproblem. We provide a simple analytic approximation of the eigenfunctions, represented as Gaussian wave packets. As the main result of the paper, we derive the square-root dependence of the eigenfunction wave number on the parameter χ̃=−ηsin2ϕsin2θ, where η is the elastoviscous number and the filament orientation is determined by the zenith angle θ with respect to the vorticity direction and the azimuthal angle ϕ relative to the flow direction. We also compare the eigenfunctions with shapes of slightly buckled elastic filaments with a non-negligible thickness with the same Young's modulus, using the bead model and performing numerical simulations with the precise numerical codes.

Published by the American Physical Society
2024
Determining pair distribution functions of thin films using laboratory-based X-ray sources
Authors: Bylin Johan , Kapaklis Vassilios , Pálsson Gunnar K.
Published: August 2024

This article demonstrates the feasibility of obtaining accurate pair distribution functions of thin amorphous films down to 80 nm, using modern laboratory-based X-ray sources. The pair distribution functions are obtained using a single diffraction scan without the requirement of additional scans of the substrate or of the air. By using a crystalline substrate combined with an oblique scattering geometry, most of the Bragg scattering of the substrate is avoided, rendering the substrate Compton scattering the primary contribution. By utilizing a discriminating energy filter, available in the latest generation of modern detectors, it is demonstrated that the Compton intensity can further be reduced to negligible levels at higher wavevector values. Scattering from the sample holder and the air is minimized by the systematic selection of pixels in the detector image based on the projected detection footprint of the sample and the use of a 3D-printed sample holder. Finally, X-ray optical effects in the absorption factors and the ratios between the Compton intensity of the substrate and film are taken into account by using a theoretical tool that simulates the electric field inside the film and the substrate, which aids in planning both the sample design and the measurement protocol.
Bis[μ-3-(pyridin-2-yl)pyrazolato]bis[acetato(3,5-dimethyl-1H-pyrazole)nickel(II)]
Authors: Pilavadi Thangamuniyandi , Krishnan Soundararajan , Loganathan Nagarajan
Published: August 2024

The title compound, [Ni2(C8H6N3)2(C2H3O2)2(C5H8N2)2] or [Ni(μ-OOCCH3)(2-PyPz)(Me2PzH)]2 (1) [2-PyPz = 3-(pyridin-2-yl) pyrazole; Me2PzH = 3,5-dimethyl pyrazole] was synthesized from Ni(OOCCH3)2·4H2O, 2-PyPzH, Me2PzH and triethylamine as a base. Compound 1 {[Ni2(C30H34N10Ni2O4)]} at 100 K has monoclinic (P21/n) symmetry and the molecules have crystallographic inversion symmetry. Molecules of 1 comprise an almost planar dinuclear NiII core with an N4O2 coordination environment. The equatorial plane consists of N3,O coordination derived from one of the bidentate acetate O atoms and three of the N atoms of the chelating 2-PyPz ligand while the axial positions are occupied by neutral Me2PzH and the second O atom of the acetate unit. The Ni atoms are bridged by the nitrogen atom of a deprotonated 2-PyPz ligand. Compound 1 exhibits various inter- and intramolecular C—H...O and N—H...O hydrogen bonds.
Pyridinium tosylate
Authors: Hosten Eric Cyriel , Betz Richard
Published: August 2024

The title compound (systematic name: pyridinium 4-methylbenzenesulfonate), C5H6N+·C7H7O3S−, is the pyridinium salt of para-toluenesulfonic acid. In the crystal, classical N—H...O hydrogen bonds as well as C—H...O contacts connect the cationic and anionic entities into sheets lying parallel to the ab plane.
Financial structure and innovation: firm-level evidence from Africa
Authors: Ayalew Misraku Molla , Zhang Joseph H.
Published: August 2024

Purpose

The purpose of this paper is to examine the effect of the financial structure on innovation.

Design/methodology/approach

We utilize the matched firm-level data from two sources: the World Bank Enterprise Survey and the Innovation Follow-Up Survey. A total of 3,664 firms from 11 African countries are included.

Findings

The authors find a financially constrained and low technology-intensive firm that uses internal finance more than its peers is less likely to innovate. Our results also show that a firm that uses new equity and debt finance more than its peers is more likely to innovate. The results particularly suggest the significant effect of bank and trade credit finance on firms’ innovation. The extent and, in some cases, the direction of the effect of dependence on internal finance, new equity finance and debt finance on innovation vary due to the heterogeneity in firm size, age and ownership status. Corporate innovation is also associated with firm size, R&D, cooperation, staff training, public support, exportation and group membership.

Practical implications

The management of companies, particularly financially constrained firms, should reduce their dependence on internal finance, which negatively affects their innovation. As a remedy, they could improve their reliance on new equity finance and debt finance, especially bank finance and trade credit finance, which positively affect their innovativeness.

Social implications

A pending policy task for African business leaders is to design and evaluate reforms that help create strong financial sectors willing to provide capital to a broad range of firms, particularly small and young firms.

Originality/value

This study adds new evidence to the recent surge of debate on the trade-off between going public, using debt or heavily using internal sources to finance innovative projects, and which of these is more important in promoting firm-level innovation.
Fast fashion consumption as a female competition strategy: implications for sustainable consumption
Authors: Font Carina Mae , Font Xavier
Published: August 2024

Purpose

This research considers new and unexplored explanations of why consumers continue to engage in environmentally damaging, fast fashion consumption. It explains why rational arguments alone do not prevent fast fashion consumption or encourage consumers to move toward greater adoption of sustainable fashion consumption behaviours.

Design/methodology/approach

This research compared the effects of a “neutral” control and an “intrasexual rivalry” experimental condition on: (1) likelihood to buy, and (2) willingness to pay, of frequent female fast fashion shoppers (N = 184).

Findings

Women use fast fashion as a conspicuous signal to other women, although this is not necessarily why they waste fast fashion purchases. Mating motives appear to produce a significant increase in fast fashion buying behaviour with women feeling intrasexual pressure to engage in consumption, and utilising consumption themselves as a self-promotion strategy.

Practical implications

Retailers tackling wasteful fast fashion consumption can demonstrate that sustainable consumption provides a superior conspicuous signal to fast fashion consumption, instead of solely using rational messaging.

Originality/value

Grounded in evolutionary psychology, this study uses three theories of intrasexual rivalry, conspicuous consumption and conspicuous waste to understand how both the volume and variety of fast fashion consumed are used as conspicuous signals in a mate attraction context.
Are indeterminate sentenced prisoners prepared for open prison? Practical implications/applications of an exploratory study in an English open prison
Authors: Edgell Toni , Lorimer Hannah
Published: August 2024

Purpose

Research indicates the challenges indeterminate sentenced prisoners (ISPs) face within open prison may have a potentially devastating impact on rehabilitation and prison sentence progression. The authors conducted a study in an English open prison to explore whether the closed prison environment within England and Wales is sufficiently preparing ISPs for the transition to open conditions. There is currently a gap in existing research concerning this issue, which this paper aims to narrow for the purpose of informing good practice and improving sentence progression and rehabilitation outcomes within His Majesty’s Prison and Probation Service.

Design/methodology/approach

Qualitative and exploratory. Reflexive thematic analysis was conducted to identify themes (Braun and Clarke, 2019).

Findings

Findings indicated the need for policy in closed prisons to better prepare ISPs for open prison and the need for policy in open prisons to better support ISPs during the liminal phase.

Practical implications

Findings aimed to inform consideration for improvements to enhance preparation for, and transition to, open conditions. A 17-month follow-up after dissemination of the research found evidence for the practical application of the findings at a local level within HMPPS and potential for wider applications linking to strategy and ISP initiatives.

Originality/value

If applied more widely across HMPPS in both closed and open prisons, the research findings have the potential to improve sentence progression and rehabilitation outcomes for ISPs.
Unlocking organisational citizenship and innovation: a servant leadership approach for psychological empowerment
Authors: Kamil Nurul Liyana Mohd , Abukhalifa Anas Mahmoud Salem , Eliyana Anis , Pratama Andika Setia
Published: August 2024

Purpose

The study sought to investigate how servant leadership affects employees' organisational citizenship and innovative behaviour by emphasising the mediation role of psychological empowerment. Relying on social exchange and self-determination theories, the present research examined the associations between these key elements in organisational dynamics.

Design/methodology/approach

Two waves of data were obtained from 325 supervisor-subordinate dyads working for 15 nonprofit organisations.

Findings

The results uncovered a significant and positive connection between leaders with a strong servant mindset and employees' organisational citizenship and innovative behaviour. Psychological empowerment was found to serve as a mediator in the anticipated correlations. Cultivating leaders with an enduring servant attitude was found to significantly boost employees' organisational citizenship and innovation, supported by improved psychological empowerment.

Originality/value

This study is distinctive as it fills a gap in research on the relationships between servant leadership, psychological empowerment and work outcomes in the global nonprofit sector, particularly in the Eastern context. This disposition, when given the opportunity, will contribute to strengthening working productivity.
Capturing the care of complex community‐based health center patients: A comparison of multimorbidity indices and clinical classification software
Authors: Navale Suparna M. , Koroukian Siran , Cook Nicole , Templeton Anna , McGrath Brenda M. , Crocker Laura , Bensken Wyatt P. , Quiñones Ana R. , Schiltz Nicholas K. , Wei Melissa Y. , Stange Kurt C.
Published: August 2024

Objective

To compare morbidity burden captured from multimorbidity indices and aggregated measures of clinically meaningful categories captured in primary care community‐based health center (CBHC) patients.

Data Sources and Study Setting

Electronic health records of patients seen in 2019 in OCHIN's national network of CBHCs serving patients in rural and underserved communities.

Study Design

Age‐stratified analyses comparing the most common conditions captured by the Charlson, Elixhauser, and Multimorbidity Weighted (MWI) indices, and Classification Software Refined (CCSR) and Chronic Condition Indicator (CCI) algorithms.

Data Collection/Extraction Methods

Active ICD‐10 conditions on patients' problem list in 2019.

Principal Findings

Approximately 35%–56% of patients with at least one condition are not captured by the Charlson, Elixhauser, and MWI indices. When stratified by age, this range broadens to 9%–90% with higher percentages in younger patients. The CCSR and CCI reflect a broader range of acute and chronic conditions prevalent among CBHC patients.

Conclusion

Three commonly used indices to capture morbidity burden reflect conditions most prevalent among older adults, but do not capture those on problem lists for younger CBHC patients. An index with an expanded range of care conditions is needed to understand the complex care provided to primary care populations across the lifespan.