bluuebunny/crossref_metadata_2025 huggingface dataset:
PyINETA: Open-source platform for INADEQUATE-JRES integration in NMR metabolomics
Authors: Taujale Rahil , Uchimiya Mario , Clendinen Chaevien S. , Borges Ricardo M. , Turck Christoph W. , Edison Arthur S.
Published: July 2024

Annotating compounds with high confidence is a critical element in metabolomics.13C-detection NMR experiment INADEQUATE (incredible natural abundance double-quantum transfer experiment) stands out as a powerful tool for structural elucidation, whereas this valuable experiment is not often included in metabolomics studies. This is partly due to the lack of community platform that provides structural information based INADEQUATE. Also, it is often the case that a single study uses various NMR experiments synergistically to improve the quality of information or balance total NMR experiment time, but there is no public platform that can integrate the outputs of INADEQUATE and other NMR experiments either. Here, we introduce PyINETA, Python-based INADEQUATE network analysis. PyINETA is an open-source platform that provides structural information of molecules using INADEQUATE, conducts database search, and integrates information of INADEQUATE and a complementary NMR experiment13CJ-resolved experiment (13C-JRES). Those steps are carried out automatically, and PyINETA keeps track of all the pipeline parameters and outputs, ensuring the transparency of annotation in metabolomics. Our evaluation of PyINETA using a model mouse study showed that our pipeline successfully integrated INADEQUATE and13C-JRES. The results showed that13C-labeled amino acids that were fed to mice were transferred to different tissues, and, also, they were transformed to other metabolites. The distribution of those compounds was tissue-specific, showing enrichment of particular metabolites in liver, spleen, pancreas, muscle, or lung. The value of PyINETA was not limited to those known compounds; PyINETA also provided fragment information for unknown compounds. PyINETA is available on NMRbox.
Neuron synchronization analyzed through spatial-temporal attention
Authors: Yang Haoming , Pramod KC , Chen Panyu , Lei Hong , Sponberg Simon , Tarokh Vahid , Riffell Jeffrey A.
Published: July 2024

Across diverse organisms, the temporal dynamics of spiking responses between neurons, the neural synchrony, is crucial for encoding different stimuli. Neural synchrony is especially important in the insect antennal (olfactory) lobe (AL). Previous studies on synchronization, however, rely on pair-wise synchronization metrics including the cross-correlogram and cos-similarity between kernelized spikes train. These pair-wise analyses overlook an important aspect of synchronization which is the interaction at the population neuron level. There are also limited modeling techniques that incorporate the synchronization between neurons in modeling population spike trains. Inspired by recent advancements in machine learning, we leverage a modern attention mechanism to learn a generative normalizing flow that captures neuron population synchronization. Our method not only reveals the spiking mechanism of neurons in the AL region but also produces semi-interpretable attention weights that characterize neuron interactions over time. These automatically learned attention weights allow us to elucidate the known principles of neuron synchronization and further shed light on the functional roles of different cell types (the local interneurons (LNs), and projection neurons (PNs)) in the dynamic neural network in the AL. By varying the balance of excitation and inhibition in this neural circuit, our method further uncovers the pattern between the strength of synchronization and the ratio of an odorant in the mixture.

Author Summary

The olfactory system can accurately compute the mixture of volatile compounds emitted from distant sources, enabling the foraging species to exhibit fast and effective decisions. However, altering ratios of one of the compounds in the mixture could be perceived as a different odor. Leveraging the current understanding of neural synchronization on sensory neural regions of insects, we construct a spatial-temporal attention normalizing flow, which partially replicates the AL region’s functionality by learning the spiking mechanics of neurons. Beyond providing insights of the spiking mechanism of neurons in the AL region, our method also produces semi-interpretable attention weights that characterize neuron interaction over time. These automatically learned attention weights allow us to dissect out the principles of neuron synchronization and interaction mechanisms between projection neurons (PNs) and local neurons (LNs). Utilizing our accurate model of these AL functionality, we show evidence that the behavioral relevant compounds are closely clustered together while varying the intensities of one of the behavioral compounds in the mixture could attenuate the synchronization
Ventral Morphology and Ecological Implications ofCindarella eucalla(Artiopoda, Xandarellida) from Chengjiang Biota, China
Authors: Zhang Maoyin , Liu Yu , Mai Huijuan , Schmidt Michel , Hou Xianguang
Published: July 2024

Artiopoda, an early arthropod group, displays post-antennal appendages resembling trilobite limbs, but relationships with other ealy arthropods remain enigmatic. Limited studies and morphological details hinder the understanding of internal relationships within Artiopoda. Recently, exceptionally well preserved arthropod fossils from the Chengjiang Biota were studied using X-ray computed tomography, revealing detailed morphologies. In this study,Cindarella eucalla, a xandarellid from the Chengjiang Biota, was re-investigated using X-ray computed tomography and fluorescent microscopy to reconstruct its morphology and understand its phylogeny and ecology. This study successfully reconstructed a three-dimensional model ofCindarella eucalla, revealing features, such as spindle-shaped trunk tergites with the anterior six covered by the head shield and axial spines extending from the last four, natant hypostome, four post-antennal cephalic appendage pairs, dorsoventral mismatch existed between trunk tergites and limb pairs. This research suggests thatCindarella eucallacould escape in a very short time when it encounters an enemy, and it probably lived in muddy environments with ample light. Phylogenetic analysis indicates that Xandarellids may have close relationship with concililiterga or a clade composed of Nektaspida + (Conciliterga + (Phytophilaspis pergamena+ Trilobita)).
EGFR meets hATG8s – Biophysical and structural insights supporting a unique role of GABARAP during receptor trafficking
Authors: Üffing Alina , Weiergräber Oliver H. , Schwarten Melanie , Hoffmann Silke , Willbold Dieter
Published: July 2024

The human ATG8 family member GABARAP is involved in numerous autophagy-related and - unrelated processes. We recently observed that specifically the deficiency of GABARAP enhances EGFR degradation upon ligand stimulation. Here, we report on two putative LC3-interacting regions (LIRs) within the EGFR, the first of which (LIR1) is selected as GABARAP binding sitein-silico. Indeed,in-vitrointeraction studies reveal preferential binding of LIR1 to GABARAP and GABARAPL1. Our X-ray data demonstrate interaction of core LIR1 residues FLPV with both hydrophobic pockets of GABARAP suggesting a canonical binding. Although LIR1 occupies the LIR docking site, GABARAP Y49 and L50 appear dispensable this case. Our data support the hypothesis that GABARAP affects the fate of EGFR at least in part through direct binding.
Detecting latent gene-environment interaction when analyzing binary traits
Authors: Zhang Ziang , Lawless Jerald F. , Paterson Andrew D. , Sun Lei
Published: July 2024

In genome-wide association studies (GWAS), it is desirable to test for interactions (GxE) between single-nucleotide polymorphisms (SNPs,G’s) and environmental variables (E’s). However, directly accounting for interaction is often infeasible, becauseEis latent. For quantitative traits (Y) that are approximately normally distributed, it has been shown that indirect testing onGxEcan be done by testing for heteroskedasticity ofYbetween genotypes. However, when traits are binary, the existing methodology based on testing the heteroskedasticity of the trait across genotypes cannot be generalized. In this paper, we propose an approach to indirectly testGxEfor binary traits based on the non-additive effectG, and subsequently propose a joint test that accounts for the main and interaction effects of each SNP during GWAS. We illustrate the statistical features including type-I-error control and power of the proposed method through extensive numerical studies. Applying our method to the UK Biobank dataset, we showcase the practical utility of the proposed method, revealing SNPs and genes with strong potential for latent interaction effects.
OpenTn5: Open-Source Resource for Robust and Scalable Tn5 Transposase Purification and Characterization
Authors: Soroczynski Jan , Anderson Lauren J. , Yeung Joanna L. , Rendleman Justin M. , Oren Deena A. , Konishi Hide A. , Risca Viviana I.
Published: July 2024

Tagmentation combines DNA fragmentation and sequencing adapter addition by leveraging the transposition activity of the bacterial cut-and-paste Tn5 transposase, to enable efficient sequencing library preparation. Here we present an open-source protocol for the generation of multi-purpose hyperactive Tn5 transposase, including its benchmarking in CUT&Tag, bulk and single-cell ATAC-seq. The OpenTn5 protocol yields multi-milligram quantities of pG-Tn5E54K, L372Pprotein per liter ofE. coliculture, sufficient for thousands of tagmentation reactions and the enzyme retains activity in storage for more than a year.
The penetration ring is a novel infection structure formed by the penetration peg for invading plant cell membrane in rice blast fungus
Authors: Fang Wenqin , Zai Xiaoyu , Chen Jia , Abubakar Yakubu Saddeeq , Wu Qiuqiu , Fang Zhenyu , Huang Xiuwei , Gan Xiang , Ebbole Daniel J. , Wang Zonghua , Zheng Wenhui
Published: July 2024

Many fungal pathogens develop specialized infection structures such as appressoria to penetrate plant cells. However, it is not clear whether special structures are formed after cell wall penetration before invading host cytoplasm membrane in hemibiotrophic pathogens. Here, we showed that a penetration ring consisting of Ppe1 secreted proteins is formed after appressorium-mediated cell wall penetration and remained at the base of penetration site after invading plant cytoplasm membrane in the rice blast fungusMagnaporthe oryzae. The same persistent Ppe1 ring is formed after the penetration of neighboring cells by transpressoria.PPE1is specifically expressed during plant infection and the Δppe1mutant is defective in penetration and invasive growth. Blockage of penetration peg formation impedes the development of the Ppe1 ring. Close examinations showed that the penetration ring is formed at the collar of penetration pegs between plant cell wall and cytoplasm membrane and it is persistent as a fixed ring even after invasive hyphae invaded neighboring cells. Furthermore, Ppe1 is a member of an expanded family of secreted proteins that are unique to fungal pathogens using extreme appressorium turgor for plant penetration. Other members of the Ppe1 family also localize to the penetration ring for anchoring on cytoplasm membrane during plant infection. Taken together, a penetration ring consisting of a family of secreted proteins is formed between plant cell wall and cytoplasm membrane, which may function as a novel physical structure at the interface between the tip of penetration pegs and plant cytoplasm membrane before the differentiation of invasive hyphae.

Significance Statement

Like many other plant pathogens, the rice blast fungus forms melanized appressoria (specialized infection structures) to penetrate plant cells. In this study, we showed that a penetration ring is formed by penetration pegs after appressorium- or transpressorium-mediated penetration of plant cell wall. This ring of secreted proteins is persistent at the point of penetration pegs invading plant cytoplasm membrane to form invasive hyphae. Therefore, after the penetration of plant cell wall, the rice blast fungus forms a penetration ring that consists of a family of secreted proteins unique to pathogens using extreme appressorium turgor for penetration and may function as a physical structure for anchoring onto plant cytoplasm membrane and developing invasive hyphae in penetrated cells.
Post-weaning social isolation alters sociability in a sex-specific manner
Authors: Myers Teneisha , Birmingham Elizabeth A. , Rhoads Brigham T. , McGrath Anna G. , Miles Nylah A. , Schuldt Carmen B. , Briand Lisa A.
Published: July 2024

Adolescence is a critical period for brain development in humans and stress exposure during this time can have lasting effects on behavior and brain development. Social isolation and loneliness are particularly salient stressors that lead to detrimental mental health outcomes particularly in females, although most of the preclinical work on social isolation has been done in male animals. Our lab has developed a model of post-weaning adolescent social isolation that leads to increased drug reward sensitivity and altered neuronal structure in limbic brain regions. The current study utilized this model to determine the impact of adolescent social isolation on a three-chamber social interaction task both during adolescence and adulthood. We found that while post-weaning isolation does not alter social interaction during adolescence (PND45), it has sex-specific effects on social interaction in adulthood (PND60), potentiating social interaction in male mice and decreasing it in female mice. As early life stress can activate microglia leading to alterations in neuronal pruning, we next examined the impact of inhibiting microglial activation with daily minocycline administration during the first three weeks of social isolation on these changes in social interaction. During adolescence, minocycline dampened social interaction in male mice, while having no effect in females. In contrast, during adulthood, minocycline did not alter the impact of adolescent social isolation in males, with socially isolated males exhibiting higher levels of social interaction compared to their group housed counterparts. In females, adolescent minocycline treatment reversed the effect of social isolation leading to increased social interaction in the social isolation group, mimicking what is seen in naïve males. Taken together, adolescent social isolation leads to sex-specific effects on social interaction in adulthood and adolescent minocycline treatment alters the effects of social isolation in females, but not males.
Pymportx: Facilitating Next-Generation Transcriptomics Analysis in Python
Authors: Pena González Paula , Lozano-Paredes Dafne , Rojo-Álvarez José Luis , Bote-Curiel Luis , Sánchez-Arévalo Lobo Víctor Javier
Published: July 2024

The efficient importation of quantified gene expression data is pivotal in transcriptomics. Historically, the R package Tximport addressed this need by enabling seamless data integration from various quantification tools. However, the Python community lacked a corresponding tool, restricting cross-platform bioinformatics interoperability. We introduce Pymportx, a Python adaptation of Tximport, which replicates and extends the original package’s functionalities. Pymportx maintains the integrity and accuracy of gene expression data while improving processing speed and integration within the Python ecosystem. It supports new data formats and includes tools for enhanced data exploration and analysis. Available under the MIT license, Pymportx integrates smoothly with Python’s bioinformatics tools, facilitating a unified and efficient workflow across the R and Python ecosystems. This advancement not only broadens access to Python’s extensive toolset but also fosters interdisciplinary collaboration and the development of cutting-edge bioinformatics analyses.

Availability and Implementation

Pymportx is released as an open-source software under the MIT license. The source code is available on GitHub athttps://github.com/victorsanchezarevalo/Pymportx.
Influenza-induced alveolar macrophages protect against death by malaria-associated acute lung injury
Authors: Reed Jenna S. , Nayan Ritika , Deckers Margot , Evavold Brian D. , Lamb Tracey J.
Published: July 2024

Lower respiratory tract infections are common in malaria-endemic areas, and there is some evidence that co-infections between various bacteria/viruses andPlasmodiummay affect disease prognosis. In this study, we report the novel finding that co-infection with influenza/A/X31 protects mice from death byPlasmodium bergheiNK65-Edinburgh, a model of severe malarial pulmonary leak which underpins malaria-associated acute lung injury (MA-ALI) and malaria-associated acute respiratory distress (MA-ARDS). Co-infected mice exhibit equivalent parasitemia as mice with malaria only, suggesting that the survival phenotype is due to differences in immune kinetics. We demonstrated that the pulmonary leak typical ofPbE is attenuated in co-infected mice without alteration in CD8 T cell activation and recruitment to the lung. Upon further examination of the immune response to influenza/A/X31 we identified a population of arginase 1-expressing alveolar macrophages that traffic to the lungs early during infection. In vitro these macrophages inhibit CD8 T cell activation and proliferation better than non-arginase expressing cells. Removal of arginase-1 expressing alveolar macrophagesin vivovia administration of the antimetabolite gemcitabine removed the protective effects of influenza/A/X31co-infection on MA-ALI. This study opens a route to better understanding of how to modulate the immunopathology observed in pulmonary leak associated with severe malaria, which must be achieved to rationally design therapeutic interventions for MA-ARDS / MA-ALI.
Ideal efficacy photoswitches for TRPC4/5 channels harness high potency for spatiotemporally-resolved control of TRPC function in live tissues
Authors: Müller Markus , Niemeyer Konstantin , Ojha Navin K. , Porav Sebastian A. , Vinayagam Deivanayagabarathy , Urban Nicole , Büchau Fanny , Oleinikov Katharina , Makke Mazen , Bauer Claudia C. , Johnson Aidan V. , Muench Stephen P. , Zufall Frank , Bruns Dieter , Schwarz Yvonne , Raunser Stefan , Leinders-Zufall Trese , Bon Robin S. , Schaefer Michael , Thorn-Seshold Oliver
Published: July 2024

Directly probing the endogenous biological roles of target proteins with high spatial and temporal resolution, as non-invasively and reproducibly as possible, is a shared conceptual goal for research across many fields, as well as for targeted therapies. Here we describe the rational conceptual design and test-case practical implementation of a photopharmacological paradigm to empower high-performance photomodulation studiesin vivo. TRPC4/5 ion channels are involved in many spatiotemporally resolved circuits, from pain and anxiety, to reproductive signaling, digestion, and obesity. To unpick their biology requires spatiotemporally precise tools, which were lacking. We developed “ideal efficacy photoswitch” ligands to control their diverse functionsin situ. TheseE⇆Z-photoswitchable ligands bias TRPC[4]/5 channel activity with exquisite photocontrol, from strong agonism under 360 nm, to low agonism at 385 nm, to strong antagonism at 410-460 nm. Cryo-EM structures of both TRPC4 and TRPC5 with bothZ-agonists andE-antagonists support the rationale for efficacy switching through competitiveE/Zisomer binding. Crucially, since theE/Zratio is exclusively determined by the light wavelength applied,their channel photocontrol is exclusively wavelength-dependent, yet drug-concentration-independent: so is reproducible from cell culture to >millimetre-depth tissues. Indeed, we were able to photocontrol both direct and downstream TRPC4/5 biology in cell lines or primary cells in culture, from calcium flux, to primary neuron excitability and adrenaline release; and even in tissues, photoswitching small intestine motility and peristalsis. The TRPC4/5 ligands we develop will thus unlock a range of high-precision investigations in TRP biology. More broadly, we propose that the success of this efficacy photoswitch program, from concept to tissue level translation, is mainly a consequence of how biology has evolved proteins for efficacy control. We therefore foresee that a variety of functionally responsive protein targets, not only sensory and signaling ion channels and receptors, will be amenable to similarly high-performance photocontrol evenin vivo, if a new generation of reagent development adopts this paradigm ofideal efficacy photoswitching.

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Fundamental frequency predominantly drives talker differences in auditory brainstem responses to continuous speech
Authors: Polonenko Melissa J. , Maddox Ross K.
Published: July 2024

Deriving human neural responses to natural speech is now possible, but the responses to male- and female-uttered speech have been shown to differ. These talker differences may complicate interpretations or restrict experimental designs geared toward more realistic communication scenarios. This study found that when a male and female talker had the same fundamental frequency, auditory brainstem responses (ABRs) were very similar. Those responses became smaller and later with increasing fundamental frequency, as did click ABRs with increasing stimulus rates. Modeled responses suggested that the speech and click ABR differences were reasonably predicted by peripheral and brainstem processing of stimulus acoustics.
Endemism shapes viral ecology and evolution in globally distributed hydrothermal vent ecosystems
Authors: Langwig Marguerite V. , Koester Faith , Martin Cody , Zhou Zhichao , Joye Samantha B. , Reysenbach Anna-Louise , Anantharaman Karthik
Published: July 2024

Viruses are ubiquitous in deep-sea hydrothermal environments, where they exert a major influence on microbial communities and biogeochemistry. Yet, viral ecology and evolution remain understudied in these environments. Here, we identified 49,962 viruses from 52 globally distributed hydrothermal vent samples (10 plumes, 40 deposits, and 2 diffuse flow), and reconstructed 5,708 viral metagenome-assembled genomes (vMAGs), the majority of which were bacteriophages. Hydrothermal viruses were largely endemic. However, some viruses were shared between geographically separated vents, predominantly between the Lau Basin and Brothers Volcano in the Pacific Ocean. Geographically distant viruses often shared proteins related to core functions such as structural proteins, and rarely, proteins of auxiliary functions. Common microbial hosts of viruses included members of Campylobacterota, Alpha-, and Gammaproteobacteria in deposits, and Gammaproteobacteria in plumes. Campylobacterota- and Gammaproteobacteria-infecting viruses reflected variations in hydrothermal chemistry and functional redundancy in their predicted microbial hosts, suggesting that hydrothermal geology is a driver of viral ecology and coevolution of viruses and hosts. Our study indicates that viral ecology and evolution in globally distributed hydrothermal vents is shaped by endemism, and thus may have increased susceptibility to the negative impacts of deep-sea mining and anthropogenic change in ocean ecosystems.
Bioenergetic stress potentiates antimicrobial resistance and persistence
Authors: Li B , Srivastava S , Shaikh M , Mereddy G , Garcia MR , Shah A , Ofori-Anyinam N , Chu T , Cheney N , Yang JH
Published: July 2024

Antimicrobial resistance (AMR) is a global health crisis and there is an urgent need to better understand AMR mechanisms. Antibiotic treatment alters several aspects of bacterial physiology, including increased ATP utilization, carbon metabolism, and reactive oxygen species (ROS) formation. However, how the “bioenergetic stress” induced by increased ATP utilization affects treatment outcomes is unknown. Here we utilized a synthetic biology approach to study the direct effects of bioenergetic stress on antibiotic efficacy. We engineered a genetic system that constitutively hydrolyzes ATP or NADH inEscherichiacoli. We found that bioenergetic stress potentiates AMR evolution via enhanced ROS production, mutagenic break repair, and transcription-coupled repair. We also find that bioenergetic stress potentiates antimicrobial persistence via potentiated stringent response activation. We propose a unifying model that antibiotic-induced antimicrobial resistance and persistence is caused by antibiotic-induced. This has important implications for preventing or curbing the spread of AMR infections.
IL-21 Shapes the B Cell Response in a Context-Dependent Manner
Authors: Kim Youngjun , Manara Francesca , Grassmann Simon , Belcheva Kalina T. , Reyes Kanelly , Kim Hyunu , Downs-Canner Stephanie , Yewdell William T. , Sun Joseph C. , Chaudhuri Jayanta
Published: July 2024

The cytokine interleukin-21 (IL-21) is a pivotal T cell-derived signal crucial for germinal center (GC) responses, but the precise mechanisms by which IL-21 influences B cell function remain elusive. Here, we investigated the B cell-intrinsic role of IL-21 signaling by employing a novel IL-21 receptor (Il21r) conditional knock-out mouse model andex vivoculture systems and uncovered a surprising duality of IL-21 signaling in B cells. While IL-21 stimulation of naïve B cells led to Bim-dependent apoptosis, it promoted robust proliferation of pre-activated B cells, particularly class-switched IgG1+B cellsex vivo. Consistent with this, B cell-specific deletion ofIl21rled to a severe defect in IgG1 responsesin vivofollowing immunization. Intriguingly,Il21r-deleted B cells are significantly impaired in their ability to transition from a pre-GC to a GC state following immunization. AlthoughIl21r-deficiency did not affect the proportion of IgG1+B cells among GC B cells, it greatly diminished the proportion of IgG1+B cells among the plasmablast/plasma cell population. Collectively, our data suggest that IL-21 serves as a critical regulator of B cell fates, influencing B cell apoptosis and proliferation in a context-dependent manner.
Does pre-speech auditory modulation reflect processes related to feedback monitoring or speech movement planning?
Authors: Li Joanne Jingwen , Daliri Ayoub , Kim Kwang S. , Max Ludo
Published: July 2024

Previous studies have revealed that auditory processing is modulated during the planning phase immediately prior to speech onset. To date, the functional relevance of this pre-speech auditory modulation (PSAM) remains unknown. Here, we investigated whether PSAM reflects neuronal processes that are associated with preparing auditory cortex for optimized feedback monitoring as reflected in online speech corrections. Combining electroencephalographic PSAM data from a previous data set with new acoustic measures of the same participants’ speech, we asked whether individual speakers’ extent of PSAM is correlated with the implementation of within-vowel articulatory adjustments during /b/-vowel-/d/ word productions. Online articulatory adjustments were quantified as the extent of change in inter-trial formant variability from vowel onset to vowel midpoint (a phenomenon known ascentering). This approach allowed us to also consider inter-trial variability in formant production and its possible relation to PSAM at vowel onset and midpoint separately. Results showed that inter-trial formant variability was significantly smaller at vowel midpoint than at vowel onset. PSAM was not significantly correlated with this amount of change in variability as an index of within-vowel adjustments. Surprisingly, PSAM was negatively correlated with inter-trial formant variability not only in the middle but also at the very onset of the vowels. Thus, speakers with more PSAM produced formants that were already less variable at vowel onset. Findings suggest that PSAM may reflect processes that influence speech acoustics as early as vowel onset and, thus, that are directly involved in motor command preparation (feedforward control) rather than output monitoring (feedback control).
A fast and robust gene knockout method forSalpingoeca rosettainforms the genetics of choanoflagellate multicellular development
Authors: Combredet Chantal , Brunet Thibaut
Published: July 2024

As the closest living relatives of animals, choanoflagellates offer crucial insights into the evolutionary origin of animals. Notably, certain choanoflagellate species engage in facultative multicellular development that resembles the early stages of embryogenesis. In the past few years,Salpingoeca rosettahas emerged as a tractable model for choanoflagellate cell biology and multicellular development, in particular through mutant screens and CRISPR/Cas9-mediated gene knockout (KO). However, existing KO pipelines have variable and sometimes low efficiency, frequently requiring isolation and genotyping of hundreds of clones without guarantee to obtain a KO strain. Here, we present a robust method for gene inactivation inS. rosettathat relies on insertion by CRISPR/Cas9 of a single 1.9 kb cassette encoding both a premature termination sequence and an antibiotic resistance gene. We show that this approach allows robust, fast and efficient isolation of KO clones after antibiotic selection. As a proof of principle, we first knocked out all three genes previously reported to regulateS. rosettamulticellular development in a published mutant screen (rosetteless,couscousandjumble), and confirmed that all three KOs abolished multicellular development. To showcase the potential of this method forde novocharacterization of candidate developmental genes, we then inactivated three homologs of genes in the Hippo pathway:hippo,wartsandyorkie, which together control cell proliferation and multicellular size in animals. Interestingly,wartsKO rosettes were consistently about twice as large as their wild-type counterparts, showing our KO pipeline can reveal novel loss-of-function phenotypes of biological interest. Thus, this method has the potential to accelerate choanoflagellate functional genetics.
Single influenza A viruses induce nanoscale cellular reprogramming at the virus-cell interface
Authors: Broich Lukas , Wullenkord Hannah , Osman Maria Kaukab , Fu Yang , Reuther Peter , Brönstrup Mark , Sieben Christian
Published: July 2024

Viruses, as nanoscale entities with limited proteomes, must efficiently infect target cells using their available resources. During infection, individual virions induce specific cellular signaling within the virus-cell interface, a nanoscale patch of the plasma membrane in contact with the virus. However, virus-induced receptor recruitment and cellular activation are transient processes that occur within minutes and at the nanoscale level. Hence, the temporal and spatial kinetics of such early events often remain poorly understood due to technical limitations. To address this challenge, we developed a novel protocol to covalently immobilize unmodified influenza A viruses on glass surfaces before exposing them to live epithelial cells. This approach extends the observation time for virus-plasma membrane interaction while preserving the viruses’ native state for uncompromised cell interaction. Using single-molecule super-resolution microscopy, we investigated virus-receptor interaction showing that viral receptors are not immobilized by the virus but rather slowed down, which leads to a specific local receptor accumulation and turnover. We further followed the dynamics of clathrin-mediated endocytosis at the single-virus level and demonstrate the recruitment of adaptor protein 2 (AP-2), previously thought to be uninvolved in influenza A virus infection. Finally, we examined the nanoscale organization of the actin cytoskeleton at the virus-binding site, showing a local and dynamic response of the cellular actin cortex to the infecting virus. Our findings provide novel insights into the fundamental process of virus-cell interaction and demonstrate the versatility and potential impact of our approach on virus-cell biology.
Coca in history and the future
Authors: Cáceres Santa María Baldomero
Published: July 2024

Purpose

This study aims to question the psychiatric framework currently adopted by governments toward the traditional plants of great cultures, stigmatized by the paradigm of the unfounded psychiatric doctrine and to propose the need for a change of outlook.

Design/methodology/approach

Documentary research of the “black history” of coca. Documentary research on academic contributions to the revaluation of coca.

Findings

This brief chronicle of the coca leaf in history, duly documented, proves that its medicinal and energetic prestige was proven and praised by the naturalistic and experimental medicine of the 19th century, a precedent buried by the psychiatric pathologizing version that invented “drug addictions” without any experimental support.

Research limitations/implications

Psychiatry can be revealed as the authoritarian and unpunished inquisition of the 20th century, in its arbitrary pathologizing version of coca leaf consumption and in most of its professional work. A scientific revolution is taking place (Kuhn, 1962), given that the psychopathological paradigm does not respond to the facts surrounding coca leaf consumption and virtues. The medical perspective must replace the negative psychiatric perspective that the law maintains

Practical implications

The author concludes that the way out would be to denounce before the Social and Economic Council of the United Nations, with evidence in hand, the fraud in the 1950 UN Commission on Coca Report, due to concealment on information.

Social implications

Taking advantage of the hygienic and medicinal virtues of plants stigmatized by psychiatry, such as the coca leaf, would put an end to an omnipresent war and give way to peace in the producing areas.

Originality/value

The questioning of the psychiatric frame of reference adopted by governments to deal with coca leaf consumption has led to the “war on drugs.”
Social capital development in online education and its impact on academic performance and satisfaction
Authors: Wong Teik Aun , Tan Kevin Tee Liang , Darmaraj Sheila Rose , Loo Joshua Teck Khun , Ng Alex Hou Hong
Published: July 2024

Purpose

The first objective is to investigate and determine the social capital development of students in online education. The second objective is to analyze the influence of social capital on students’ academic success and educational satisfaction. The third objective is to generate recommendations to foster social capital development.

Design/methodology/approach

A quantitative research approach is employed, with 264 respondents comprising students from colleges and universities in Malaysia. The data gathering instrument is an online questionnaire administered with the informed consent of participants. Data analysis is performed using structural equation modeling (SEM).

Findings

The results show that the faculty capital and peer capital components of social capital have not been compromised in online education, but the family capital component has declined. As such, it is concluded that there is a general decline in overall social capital in online education. These findings form the basis for recommendations on promoting social capital development among students in colleges and universities internationally.

Research limitations/implications

This study focused on study periods during the COVID-19 pandemic where online learning and communication were strictly enforced, providing a unique opportunity to explore how students adapted their social capital development. However, this is not meant to be a representation of scenarios where students are given the option of either physical or online education or a combination of both.

Practical implications

Academic and institutional management implications are evident, and recommendations are made based on the findings.

Social implications

The findings and subsequent recommendations have considerable social implications in terms of social sustainability of education practices and policies.

Originality/value

The COVID-19 pandemic that started in March 2020 and subsequent prolonged periods of physical lockdowns in many countries have forced colleges and universities that customarily practice classroom education to shift to online education temporarily. This situation created a novel “natural experiment” when classes or programs from the same college or university that are customarily conducted in classrooms (in person) were conducted online during the pandemic, thus contributing to the originality of the findings.
Good news urban tourism researchers! 19 ways to enhance the usefulness of your observational video analysis research
Authors: Nicely Annmarie
Published: July 2024

Purpose

The present article encourages urban tourism researchers use pre-recorded (like YouTube, TikTok and security camera footage) and self-recorded video data in research. The author highlighted the benefits of doing so for urban tourism scholars, as well as ways in which these investigators can use the observational video analysis technique to produce convincing findings and advance their field.

Design/methodology/approach

To accomplish the purpose, the author reviewed 25 scholarly articles on the topic from several fields.

Findings

One benefit of observational video analysis research (OVAR), the author highlighted, was the ability of scholars in different locations to simultaneously observe interactions, the focus of the study, in their natural setting and discuss them. This practice is not possible with traditional ethnographic research. Also, one way the author mentioned researchers can accomplish rigor in their OVAR project is through multimodal transcription. With multimodal transcription, verbal and non-verbal happenings in videos are transliterated and later analyzed.

Research limitations/implications

It is hoped because of the present article, increased use of the technique in urban tourism research will be seen.

Originality/value

The present article is the first, to the best of the author’s knowledge, to detail how rigor can be accomplished in OVAR in urban tourism.
Insights into elder abuse: a bibliometric analysis
Authors: Yueh Kuan-Yu , Chang Wen-Jung
Published: July 2024

Purpose

This paper aims to explore the trends in academic research on elder abuse from 1990 to 2023 using bibliometric analysis. It seeks to identify research trends, hotspots and gaps and proposes future research directions.

Design/methodology/approach

Using bibliometric analysis method, this study analyzes 2,404 documents related to elder abuse from the Scopus database. Visual analysis is conducted using VOSviewer software to reveal research trends, thematic clusters and their interrelationships.

Findings

The study shows a rising concern for elder abuse, especially in nursing homes, domestic settings and among dementia patients. However, research on prevention and intervention measures is lacking, despite increasing international collaboration. Yet, deeper exploration of cross-cultural and regional differences remains limited.

Practical implications

This study reveals that improving care conditions for nursing home residents and dementia patients requires increased funding, professional training for caregivers, the strengthening of regulations and the establishment of clear guidelines for reporting abuse. Additionally, promoting international cooperation, sharing best practices, raising public awareness and supporting ongoing research are essential measures to ensure the safety and dignity of older adults.

Originality/value

To the best of the authors’ knowledge, this study represents the first systematic review of elder abuse research using bibliometric analysis, providing researchers and policymakers with a comprehensive knowledge framework of the field’s development trends and research hotspots.
The impact of open branding on consumer brand attitudes: the moderating role of power distance belief
Authors: Li Yao , Zhang Cheng , Zhou Mi
Published: July 2024

Purpose

This study investigates the impact of open branding on consumer brand attitudes, as mediated by brand warmth and brand competence, and moderated by power distance belief.

Design/methodology/approach

This study employs two one-factor (brand strategy: open branding vs closed branding) between-subject experimental designs and a 2 × 2, namely (open branding vs closed branding) × (power distance belief: high vs low) between-subject experimental design to test the hypotheses.

Findings

The study indicates that open branding can enhance consumer brand attitudes, and that brand warmth and brand competence mediate the impact of open branding on consumer brand attitudes. Furthermore, power distance beliefs (PDB) moderated these relationships. Specifically, the impact of open branding on consumers brand attitudes is stronger for consumers with low PDB than for those with high PDB.

Practical implications

Brand managers should consider adopting an open branding strategy to enhance consumers brand attitudes when encountering consumers’ unauthorized use of brand-related intellectual property. Additionally, when implementing an open-branding strategy, brand managers should use appropriate language to enhance consumers’ perceptions of brand warmth and brand competence.

Originality/value

This study contributes to the interactive marketing literature by empirically examining the impact of open branding on consumer brand attitudes. Furthermore, it investigates the underlying mechanism of how and the boundary conditions when open branding increases consumer brand attitudes, enriching the current knowledge.
Refugees and mental wellbeing. A call for community approaches in Aotearoa New Zealand
Authors: Brannelly Tula , Bhatia Anjali , Malihi Arezoo Zarintaj , Vanderpyl Lucie , Brennan Buster , Gonzalez Perez Leo , Saeid Fahima , Holroyd Eleanor , Charania Nadia
Published: July 2024

Purpose

The purpose of this paper is to examine community based, trauma informed to support refugee mental health and wellbeing, recognising that refugee status is met through forced displacement in which refugees have experience of personal human rights abuses and have survived atrocities in which family and community have been lost.

Design/methodology/approach

A co-production approach was taken to review existing literature and policy to produce a position statement on how to better meet the needs of people who experience mental distress who are refugees. The co-production was between refugee and mental health researchers and refugee representatives.

Findings

Understanding the mental health needs of refugees has conventionally focused on incidence of mental illness such as post-traumatic stress disorder and depression. If mental health and illness are understood as a continuum, diagnosis of mental illness indicates a significant problem, and furthermore access to services is predicated on risks associated with mental illness. When accessing mental health services, refugees have an added issue in a lack of communication availability and recognition of the trauma that they have survived.

Originality/value

In this paper, a different position is advocated, that understanding the mental health of refugees can be framed more effectively as a process of recovery from trauma that emerges during resettlement, and over a long period of time before people are able to talk about the trauma they experienced. Community-based responses that enable recovery from trauma are more readily able to meet the mental health and wellbeing needs of refugee communities.
A Speech to Win an Election: A Response to Rachel Reeves's Mais Lecture
Authors: Corry Dan
Published: July 2024

Rachel Reeves gave the Mais lecture in March 2024. While it was rightly cautious and light on detail given the impending general election, it gives us strong clues as to what kind of Chancellor of the Exchequer she will be.
“Ideology and Religion” how left‐right ideology plays a key role in attitudes toward Israel and Palestine in Sweden
Authors: Owiredu Maria
Published: July 2024

This research underscores the key role of ideology in shaping the Swedish public's stance towards Israel and Palestine. With the help of a survey conducted by the Surveyinstitute in 2020, this paper studies the Swedish population's attitudes toward the actions of Israel and Palestine in the Israel‐Palestine conflict. The findings reveal a distinct ideological divide along the left‐right scale in the attitudes of the Swedish population towards Israel and Palestine's actions. This ideological chasm extends to additional actors, such as Sweden, the United States, and the EU, in the Israel‐Palestine conflict. While religion does exert influence, particularly among practicing individuals, the study concludes that ideology is the most relevant factor in attitudes toward the actions of Israel and Palestina from a Swedish perspective.
Autonomous partners: asymmetry and masculinity in Amazonian river trade
Authors: Aguiar Furuie Vinicius de
Published: July 2024

Trade on the Iriri River, in the eastern Brazilian Amazonia, is structured around a credit‐barter system between clients and bosses known as aviamento in Portuguese. Nowadays, bosses are river traders born in the riversides who offer goods on credit to riverside dwellers, who later pay these debts with fish and products they collect from the forest. While the system, found in the Amazon basin since colonial times, is perhaps most known for fostering debt‐peonage during the Rubber Boom (1870‐1912), it can also create relations of mutual dependency that promote the autonomy of trade partners within an asymmetrical exchange. When that is the case, this trade is central to how clients and bosses define themselves as hard‐working, reliable, and transparent, personifying qualities they deem essential to masculine honour. In such partnerships (and more dramatically when they break down), the asymmetry of the relation can be challenged through a notion of male equivalence in which men must defend their honour and adhere to a code of conduct that ultimately excludes women and children from trade.
The economics of ethnic marriages: Endogamy and the social status of minority groups
Authors: Bro Naim , Morav Liran
Published: July 2024

This study examines the relationship between ethnic endogamy and socioeconomic status (SES) within the socioeconomically divergent Jewish and Native‐Chilean Mapuche communities of Santiago, Chile. By leveraging the Hispanic naming convention to analyze dual ethnic surnames, we trace endogamy patterns across comprehensive datasets that go back to 1884 up to the present. Our quantile regression analysis reveals that individuals from the lower SES brackets of the Jewish community and the higher brackets of the Mapuche community are more likely to have mixed ethnic backgrounds. This finding shows a nuanced interplay between socioeconomic standing and marital choices, suggesting that these factors significantly influence the persistence and transformation of SES within minority groups. The study introduces the Ecological Model of Ethnic Disaffiliation, providing a theoretical framework that explains how socioeconomic outliers within ethnic groups could lead to a narrowing of their socioeconomic range over generations.