bluuebunny/crossref_metadata_2025 huggingface dataset:
Inhibition of potassium ion channels reduces Semliki Forest virus genome replication
Authors: Russell Tristan , O’Brien Caoimhe , Gangotia Disha , Fulford Stefanie , Kenny Roísín , Alkhamees Abdullah , Premchand-Branker Shonnette , Fragkoudis Rennos , Barry Gerald
Published: May 2023

Introduction

Semliki forest virus(SFV) is a model virus used to investigate the Alphavirus genus, which includes human pathogens Chikungunya virus and Ross River virus. Viruses harness cellular machinery to facilitate various steps of their replicative cycles. Ion channels are one group of cellular proteins required for the efficient replication of some viruses, including Influenza A viruses, Ebola virus and members of theBetacoronavirusgenus. This study focussed on understanding SFV’s requirement for functional ion channels during replication.

Methods

The effect of ion channel inhibitors onin vitroSFV infections was measured to investigate the contribution of ion channels in its replication cycle.

Results

In vitroSFV infections carried out in the presence or absence of different ion channel inhibitors showed broad-range K+channel inhibitors reproducibly attenuated virus replication and reduced its cytotoxicity in two mammalian cell lines. These broad-range K+channel inhibitors disrupted an early, post-entry step causing a delay or reduction in SFV protein and RNA synthesis. Screens using inhibitors of specific K+channel families showed that two-pore domain K+channel (2pK) inhibitors attenuated SFV replication. Confocal microscopy revealed decreased detection of dsRNA and SFV protein in the presence of inhibitor but no change in RNA and protein colocalisation, which would indicate disruption of replication complexes. Broad-range K+and 2pK inhibitors decreased viral RNA replication and transcription from the subgenomic promoter.

Conclusions

K+channel inhibitors attenuatein vitroSFV replication by inhibiting an early, post-entry step of virus replication, potentially RNA synthesis.

Importance

No antiviral therapies have been approved for clinical use against diseases caused by members of the Alphavirus genus. Work presented in this manuscript shows for the first time that SFV genome replication and virus induced cytotoxicity can be reducedin vitroby treating infected cells with K+channel inhibitors. This work provides the basis for investigating the effectiveness of K+channel inhibitors against other alphaviruses bothin vitro and in vivoand, because many ion channel inhibiting drugs are already in clinical use, rapid repurposing against alphavirus infections would be possible.
Ascidian embryonic cells with properties of neural-crest cells and neuromesodermal progenitors of vertebrates
Authors: Ishida Tasuku , Satou Yutaka
Published: May 2023

Neural-crest cells and neuromesodermal progenitors (NMPs) are multipotent cells that are important for development of vertebrate embryos. In embryos of ascidians, which are the closest invertebrate relatives of vertebrates, several cells located at the border between the neural plate and the epidermal region have neural-crest-like properties; hence, the last common ancestor of ascidians and vertebrates may have had ancestral cells similar to neural-crest cells. However, these ascidian neural-crest-like cells do not produce cells that are commonly of mesodermal origin. Here, we showed that a cell population located in the lateral region of the neural plate has properties resembling those of vertebrate neural-crest cells and NMPs. Among them, cells withTbx6-relatedexpression contribute to muscle near the tip of the tail region, and cells withSox1/2/3expression give rise to the nerve cord. These observations and cross-species transcriptome comparisons indicate that these cells have properties like those of NMPs. Meanwhile, transcription factor genesDlx.b,Zic-r.b, andSnai,which are reminiscent of a gene circuit in vertebrate neural-crest cells, are involved in activation ofTbx6-related.b. Thus, the last common ancestor of ascidians and vertebrates may have had cells with properties of neural-crest cells and NMPs, and such ancestral cells may have produced cells commonly of ectodermal and mesodermal origins.
Analysis of cortical cell polarity by imaging flow cytometry
Authors: Jespersen Jesper Huitfeld , Harazin Andras , Bohn Anja Bille , Christensen Anni , Lorentzen Esben , Lorentzen Anna
Published: May 2023

Metastasis is the main cause of cancer-related death and therapies specifically targeting metastasis are highly needed. Cortical cell polarity (CCP) is a pro-metastatic property of circulating tumor cells (CTCs) affecting their ability to exit blood vessels and form new metastases that constitutes a promising point of attack to prevent metastasis. However, conventional fluorescence microscopy on single cells and manual quantification of CCP are time-consuming and unsuitable for screening of regulators. In this study, we developed an imaging flow cytometry (IFC)-based method for high-throughput screening of factors affecting CCP in melanoma cells. The artificial intelligence (AI)-supported analysis method we developed is highly reproducible, accurate, and orders of magnitude faster than manual quantification. Additionally, this method is flexible and can be adapted to include additional cellular parameters. In a small-scale pilot experiment using polarity-, cytoskeleton-or membrane-affecting drugs, we demonstrate that our workflow provides a straightforward and efficient approach for screening factors affecting CCP in cells in suspension and provide insights into the specific function of these drugs in this cellular system. The method and workflow presented here will facilitate large-scale studies to reveal novel cell-intrinsic as well as systemic factors controlling CCP during metastasis.
Alterations in the preneoplastic breast microenvironment ofBRCA1/2mutation carriers revealed by spatial transcriptomics
Authors: Caputo Anthony , Vipparthi Kavya , Bazeley Peter , Downs-Kelly Erinn , McIntire Patrick , Ni Ying , Hu Bo , Keri Ruth A. , Karaayvaz Mihriban
Published: May 2023

Breast cancer is the most common cancer in females, affecting one in every eight women and accounting for the majority of cancer-related deaths in women worldwide. Germline mutations in theBRCA1andBRCA2genes are significant risk factors for specific subtypes of breast cancer.BRCA1mutations are associated with basal-like breast cancers, whereasBRCA2mutations are associated with luminal-like disease. There are currently few chemoprevention strategies available forBRCA1/2mutation carriers, and irreversible prophylactic mastectomy is the primary option. Designing chemo-preventive strategies requires an in-depth understanding of the physiological processes underlying tumor initiation. Here, we employ spatial transcriptomics to investigate defects in mammary epithelial cell differentiation accompanied by distinct microenvironmental alterations in preneoplastic breast tissues fromBRCA1/2mutation carriers and normal breast tissues from non-carrier controls. We uncovered spatially defined receptor-ligand interactions in these tissues for the investigation of autocrine and paracrine signaling. We discovered that β1-integrin-mediated autocrine signaling inBRCA2-deficient mammary epithelial cells differs fromBRCA1-deficient mammary epithelial cells. In addition, we found that the epithelial-to-stromal paracrine signaling in the breast tissues ofBRCA1/2mutation carriers is greater than in control tissues. More integrin-ligand pairs were differentially correlated inBRCA1/2-mutant breast tissues than non-carrier breast tissues with more integrin receptor-expressing stromal cells. These results reveal alterations in the communication between mammary epithelial cells and the microenvironment inBRCA1andBRCA2mutation carriers, laying the foundation for designing innovative breast cancer chemo-prevention strategies for high-risk patients.
MISATO - Machine learning dataset of protein-ligand complexes for structure-based drug discovery
Authors: Siebenmorgen Till , Menezes Filipe , Benassou Sabrina , Merdivan Erinc , Kesselheim Stefan , Piraud Marie , Theis Fabian J. , Sattler Michael , Popowicz Grzegorz M.
Published: May 2023

Large language models (LLMs) have greatly enhanced our ability to understand biology and chemistry. Yet, relatively few robust methods have been reported for structure-based drug discovery. Highly precise biomolecule-ligand interaction datasets are urgently needed in particular for LLMs, that require extensive training data. We present MISATO, the first dataset that combines quantum mechanics properties of small molecules and associated molecular dynamics simulations of about 20000 experimental protein-ligand complexes. Starting from the PDBbind dataset, semi-empirical quantum mechanics was used to systematically refine these structures. The largest collection to date of molecular dynamics traces of protein-ligand complexes in explicit water are included, accumulating to 170 μs. We give ML baseline models and simple Python data loaders, and aim to foster a thriving community around MISATO (https://github.com/t7morgen/misato-dataset). An easy entry point for ML experts is provided without the need of deep domain expertise to enable the next generation of drug discovery AI models.
Revealing the Oligomerization of Channelrhodopsin-2 in the Cell Membrane using Photo-Activated Localization Microscopy
Authors: Bestsennaia Ekaterina , Maslov Ivan , Balandin Taras , Alekseev Alexey , Yudenko Anna , Shamseye Assalla Abu , Zabelskii Dmitrii , Baumann Arnd , Catapano Claudia , Karathanasis Christos , Gordeliy Valentin , Heilemann Mike , Gensch Thomas , Borshchevskiy Valentin
Published: May 2023

Microbial rhodopsins are retinal membrane proteins that found a broad application in optogenetics. The oligomeric state of rhodopsins is important for their functionality and stability. Of particular interest is the oligomeric state in the cellular native membrane environment. Fluorescence microscopy provides powerful tools to determine the oligomeric state of membrane proteins directly in cells. Among these methods is quantitative photoactivated localization microscopy (qPALM) allowing the investigation of molecular organization at the level of single protein clusters. Here, we apply qPALM to investigate the oligomeric state of the first and most used optogenetic tool Channelrhodopsin-2 (ChR2) in the plasma membrane of eukaryotic cells. ChR2 appeared predominantly as a dimer in the cell membrane and did not form higher oligomers. The disulfide bonds between Cys34 and Cys36 of adjacent ChR2 monomers were not required for dimer formation and mutations disrupting these bonds resulted in only partial monomerization of ChR2. The monomeric fraction increased when the total concentration of mutant ChR2 in the membrane was low. The dissociation constant was estimated for this partially monomerized mutant ChR2 as 2.2±0.9 proteins/μm2. Our findings are important for understanding the mechanistic basis of ChR2 activity as well as for improving existing and developing future optogenetic tools.
Environment and taxonomy shape the genomic signature of prokaryotic extremophiles
Authors: Millán Arias Pablo , Butler Joseph , Randhawa Gurjit S. , Soltysiak Maximillian P. M. , Hill Kathleen A. , Kari Lila
Published: May 2023

This study provides comprehensive quantitative evidence suggesting that adaptations to extreme temperatures and pH imprint a discernible environmental component in the genomic signature of microbial extremophiles. Both supervised and unsupervised machine learning algorithms were used to analyze genomic signatures, each computed as thek-mer frequency vector of a 500 kbp DNA fragment arbitrarily selected to represent a genome. Computational experiments classified/clustered genomic signatures extracted from a curated dataset of ∼700 extremophile (temperature, pH) bacteria and archaea genomes, at multiple scales of analysis, 1 ≤k≤6. The supervised learning resulted in high accuracies for taxonomic classifications at 2 ≤k≤6, and medium to medium-high accuracies for environment category classifications of the same datasets at 3 ≤k≤6. Fork= 3, our findings were largely consistent with amino acid compositional biases and codon usage patterns in coding regions, previously attributed to extreme environment adaptations. The unsupervised learning of unlabelled sequences identified several exemplars of hyperthermophilic organisms with large similarities in their genomic signatures, in spite of belonging to different domains in the Tree of Life.
Future movement plans interact in sequential arm movements
Authors: Kashefi Mehrdad , Reschechtko Sasha , Ariani Giacomo , Shahbazi Mahdiyar , Tan Alice , Diedrichsen Jörn , Pruszynski J. Andrew
Published: May 2023

Real world actions often comprise of a series of movements that cannot be entirely planned before initiation. When these actions are executed rapidly, the planning of multiple future movements needs to occur simultaneously with the ongoing action. How the brain solves this task remains unknown. Here we address this question with a new sequential arm reaching paradigm that manipulates how many future reaches are available for planning while controlling execution of the ongoing reach. We show that participants plan at least two future reaches simultaneously with an ongoing reach. Further, the planning processes of the two future reaches are not independent of one another. Evidence that the planning processes interact is two-fold. First, correcting for a visual perturbation of the ongoing reach target is slower when more future reaches are planned. Second, the curvature of the current reach is modified based on the next reach only when their planning processes temporally overlap. These interactions between future planning processes may enable smooth production of sequential actions by linking individual segments of a long sequence at the level of motor planning.
Morphogenesis inTrypanosoma cruziepimastigotes proceeds via a highly asymmetric cell division
Authors: Campbell Paul C. , Graffenried Christopher L. de
Published: May 2023

Trypanosoma cruziis a protist parasite that is the causative agent of Chagas’ disease, a neglected tropical disease endemic to the Americas.T. cruzicells are highly polarized and undergo morphological changes as they cycle within their insect and mammalian hosts. Work on related trypanosomatids has described cell division mechanisms in several life-cycle stages and identified a set of essential morphogenic proteins that serve as markers for key events during trypanosomatid division. Here, we use Cas9-based tagging of morphogenic genes, live-cell imaging, and expansion microscopy to study the cell division mechanism of the insect-resident epimastigote form ofT. cruzi,which represents an understudied trypanosomatid morphotype. We find thatT. cruziepimastigote cell division is highly asymmetric, producing one daughter cell that is significantly smaller than the other. Daughter cell division rates differ by 4.9 h, which may be a consequence of this size disparity. Many of the morphogenic proteins identified inT. bruceihave altered localization patterns inT. cruziepimastigoes, which may reflect fundamental differences in the cell division mechanism of this life cycle stage, which widens and shortens the cell body to accommodate the duplicated organelles and cleavage furrow rather than elongating the cell body along the long axis of the cell, as is the case in life-cycle stages that have been studied inT. brucei. This work provides a foundation for further investigations ofT. cruzicell division and shows that subtle differences in trypansomatid cell morphology can alter how these parasites divide.

Author Summary

Trypanosoma cruzicauses Chagas’ disease, which is among the most neglected of tropical diseases, affecting millions of people in South and Central America along with immigrant populations around the world.T. cruziis related to other important pathogens such asTrypanosoma bruceiandLeishmania spp,which have been the subject of molecular and cellular characterizations that have provided an understanding of how these organisms shape their cells and undergo division. Work inT. cruzihas lagged due to an absence of molecular tools for manipulating the parasite and the complexity of the original published genome; these issues have recently been resolved. Building on work inT. brucei, we have studied the localization of key cell cycle proteins and quantified changes in cell shape during division in an insect-resident form ofT. cruzi. This work has uncovered unique adaptations to the cell division process inT. cruziand provides insight into the range of mechanisms this family of important pathogens can employ to colonize their hosts.
A hierarchical Bayesian brain parcellation framework for fusion of functional imaging datasets
Authors: Zhi Da , Shahshahani Ladan , Nettekoven Caroline , Pinho Ana Lúısa , Bzdok Danilo , Diedrichsen Jörn
Published: May 2023

One important barrier in the development of complex models of human brain organization is the lack of a large and comprehensive task-based neuro-imaging dataset. Therefore, current atlases of functional brain organization are mainly based on single and homogeneous resting-state datasets. Here, we propose a hierarchical Bayesian framework that can learn a probabilistically defined brain parcellation across numerous task-based and resting-state datasets, exploiting their combined strengths. The framework is partitioned into a spatial arrangement model that defines the probability of a specific individual brain parcellation, and a set of dataset-specific emission models that defines the probability of the observed data given the individual brain organization. We show that the framework optimally combines information from different datasets to achieve a new population-based atlas of the human cerebellum. Furthermore, we demonstrate that, using only 10 min of individual data, the framework is able to generate individual brain parcellations that outperform group atlases.
Gut physiology of rainbow trout (Oncorhynchus mykiss) is influenced more by short-term fasting followed by refeeding than by feeding fishmeal-free diets
Authors: Frohn Laura , Peixoto Diogo , Terrier Frédéric , Costas Benjamin , Bugeon Jérôme , Cartier Christel , Richard Nadège , Pinel Karine , Skiba-Cassy Sandrine
Published: May 2023

Supplementing a fishmeal-free diet with yeast extract improves rainbow trout (Oncorhynchus mykiss) growth performance and modulates the hepatic and intestinal transcriptomic response. These effects are often observed in the long term, but are not well documented after short periods of fasting. Fasting for a few days is a common practice in fish farming, especially before handling the fish, such as for short sorting, tank transfers and vaccinations. In the present study, rainbow trout were subjected to a four-day fast and then refed, for eight days, a conventional diet containing fishmeal (control diet) or alternative diets composed of terrestrial animal by-products supplemented or not with a yeast extract. During the refeeding period alone, most of the parameters considered did not differ significantly in response to the different feeds. Only the expression of claudin-15 was upregulated in fish fed the yeast-supplemented diet compared to the control diet. Conversely, fasting followed by refeeding significantly influenced most of the parameters analyzed. In the proximal intestine, the surface area of villi significantly increased and the density of goblet cell tended to decrease during refeeding. Although no distinct plasma immune response or major signs of gut inflammation were observed, some genes involved in the structure, complement pathway, antiviral functions, coagulation and endoplasmic reticulum stress response of the liver and intestine were significantly regulated by refeeding after fasting. These results indicate that short-term fasting, as commonly practiced in fish farming, significantly alters the physiology of the liver and intestine regardless of the composition of the diet.
Differential early-life survival underlies the adaptive significance of temperature-dependent sex determination in a long-lived reptile
Authors: Bock Samantha , Loera Yeraldi , Johnson Josiah , Smaga Christopher , Haskins David Lee , Tuberville Tracey , Singh Randeep , Rainwater Thomas , Wilkinson Philip , Parrott Benjamin B
Published: May 2023

Many ectotherms rely on temperature cues experienced during development to determine offspring sex. The first descriptions of temperature-dependent sex determination (TSD) were made over 50 years ago, yet an understanding of its adaptive significance remains elusive, especially in long-lived taxa.

One novel hypothesis predicts that TSD should be evolutionarily favored when two criteria are met – (a) incubation temperature influences annual juvenile survival and (b) sexes mature at different ages. Under these conditions, a sex-dependent effect of incubation temperature on offspring fitness arises through differences in age at sexual maturity, with the sex that matures later benefiting disproportionately from temperatures that promote juvenile survival.

The American alligator (Alligator mississippiensis) serves as an insightful model in which to test this hypothesis, as males begin reproducing nearly a decade after females. Here, through a combination of artificial incubation experiments and mark-recapture approaches, we test the specific predictions of the survival-to-maturity hypothesis for the adaptive value of TSD by disentangling the effects of incubation temperature and sex on annual survival of alligator hatchlings across two geographically distinct sites.

Hatchlings incubated at male-promoting temperatures consistently exhibited higher survival compared to those incubated at female-promoting temperatures. This pattern appears independent of hatchling sex, as females produced from hormone manipulation at male-promoting temperatures exhibit similar survival to their male counterparts.

Additional experiments show that incubation temperature may affect early-life survival primarily by affecting the efficiency with which maternally transferred energy resources are used during development.

Results from this study provide the first explicit empirical support for the adaptive value of TSD in a crocodilian and point to developmental energetics as a potential unifying mechanism underlying persistent survival consequences of incubation temperature.
BAP1 deficient human and mouse uveal melanomas up-regulate a shared EMT pathway
Authors: Farag Roula , Jain Fagun , Longakit Anne Nathalie , Luty Amy , Van Raamsdonk Catherine D.
Published: May 2023

Monosomy 3 is a negative indicator for uveal melanoma (UM). A key tumor suppressor on chromosome 3 is the deubiquitinaseBAP1, which usually has a second hit in cases with monosomy 3. Here, we investigated the role ofBap1loss in the GNAQQ209Lmouse UM model. We found that heterozygousBap1mutations increased the proportion of lung lesions reaching an unusually large size and permitted the growth of liver lesions. Comparison of RNAseq data from mouse and human UM identified a set of 270 genes differentially expressed in the same direction whenBAP1is mutant. The most significant pathway in this gene set was Epithelial to Mesenchymal Transition (EMT). The expression of five apical junction complex genes known to be down-regulated in association with EMT was very significantly correlated with survival in human UM patients. Activation of EMT throughBap1deficiency could increase melanoma plasticity and adaptation to new microenvironments.
Liquid plug propagation in computer-controlled microfluidic airway-on-a-chip with semi-circular microchannels
Authors: Viola Hannah L. , Vasani Vishwa , Washington Kendra , Lee Ji-Hoon , Selva Cauviya , Li Andrea , Llorente Carlos J. , Murayama Yoshinobu , Grotberg James B. , Romanò Francesco , Takayama Shuichi
Published: May 2023

This paper introduces a two-inlet, one-outlet lung-on-a-chip device with semi-circular cross-section microchannels and computer-controlled fluidic switching that enables a broader systematic investigation of liquid plug dynamics in a manner relevant to the distal airways. A leak-proof bonding protocol for micro-milled devices facilitates channel bonding and culture of confluent primary small airway epithelial cells. Production of liquid plugs with computer-controlled inlet channel valving and just one outlet allows more stable long-term plug generation and propagation compared to previous designs. The system also captures both plug speed and length as well as pressure drop concurrently. In one demonstration, the system reproducibly generates surfactant-containing liquid plugs, a challenging process due to lower surface tension that makes the plug formation less stable. The addition of surfactant decreases the pressure required to initiate plug propagation, a potentially significant effect in diseases where surfactant in the airways is absent or dysfunctional. Next, the device recapitulates the effect of increasing fluid viscosity, a challenging analysis due to higher resistance of viscous fluids that makes plug formation and propagation more difficult particularly in airway-relevant length scales. Experimental results show that increased fluid viscosity decreases plug propagation speed for a given air flow rate. These findings are supplemented by computational modeling of viscous plug propagation that demonstrate increased plug propagation time, increased maximum wall shear stress, and greater pressure differentials in more viscous conditions of plug propagation. These results match physiology as mucus viscosity is increased in various obstructive lung diseases where it is known that respiratory mechanics can be compromised due to mucus plugging of the distal airways. Finally, experiments evaluate the effect of channel geometry on primary human small airway epithelial cell injury in this lung-on-a-chip. There is more injury in the middle of the channel relative to the edges highlighting the role of channel shape, a physiologically relevant parameter as airway cross-sectional geometry can also be non-circular. In sum, this paper describes a system that pushes the device limits with regards to the types of liquid plugs that can be stably generated for studies of distal airway fluid mechanical injury.
Transcriptional Profiling and Genetic Analysis of a Cystic Fibrosis Airway-Relevant Model Shows Asymmetric Responses to Growth in a Polymicrobial Community
Authors: Kesthely Christopher A. , Rogers Rendi R. , Hafi Bassam El , Jean-Pierre Fabrice , O’Toole George A.
Published: May 2023

Bacterial infections in the lungs of persons with cystic fibrosis are typically composed of multispecies biofilm-like communities, which modulate clinically relevant phenotypes that cannot be explained in the context of a single species culture. Most analyses to-date provide a picture of the transcriptional responses of individual pathogens, however, there is relatively little data describing the transcriptional landscape of clinically-relevant multispecies communities. Harnessing a previously described cystic fibrosis-relevant, polymicrobial community model consisting ofPseudomonas aeruginosa, Staphylococcus aureus, Streptococcus sanguinisandPrevotella melaninogenica, we performed an RNA-Seq analysis to elucidate the transcriptional profiles of the community grown in artificial sputum medium (ASM) as compared to growth in monoculture, without mucin, and in fresh medium supplemented with tobramycin. We provide evidence that, although the transcriptional profile ofP. aeruginosais community agnostic, the transcriptomes ofS. aureusandS. sanguinisare community aware. Furthermore,P. aeruginosaandP. melaninogenicaare transcriptionally sensitive to the presence of mucin in ASM, whereasS. aureusandS. sanguinislargely do not alter their transcriptional profiles in the presence of mucin when grown in a community. OnlyP. aeruginosashows a robust response to tobramycin. Genetic studies of mutants altered in community-specific growth provide complementary data regarding how these microbes adapt to a community context.

Importance

Polymicrobial infections constitute the majority of infections in the cystic fibrosis (CF) airway, but their study has largely been neglected in a laboratory setting. Our lab previously reported a polymicrobial community that can explain clinical outcomes in the lungs of persons with CF. Here we obtain transcriptional profiles of the community versus monocultures to provide transcriptional information about how this model community responds to CF-related growth conditions and perturbations. Genetic studies provide complementary functional outputs to assess how the microbes adapt to life in a community.
Mechanism of the Temperature-Dependent Self-Assembly and Polymorphism of Chitin
Authors: Romany Aarion , Payne Gregory F. , Shen Jana
Published: May 2023

Chitin is the second most abundant natural biopolymer; its crystalline structures have been extensively studied; however, the mechanism of chitin’s self-assembly is unknown. Here we applied all-atom molecular dynamics to study chitin’s self-assembly process at different temperatures. Strikingly, at 278 K, an amorphous aggregate was formed, whereas at 300 K single-sheet and at 323 K both single- and multi-sheet nanofibril regions were formed. The nanofibrils contain antiparallel, parallel or mixed orientation chains, with antiparallel being slightly preferred, recapitulating chitin’s polymorphism observed in nature. The inverse temperature dependence is consistent with the recent experiment. The analysis suggested that the multi-sheet nanofibrils are assembled by stacking the single nanofibril sheets, which are formed through two types of pathways in which hydrophobic collapse either precedes or is concomitant with increasing number of interchain hydrogen bonds and solvent expulsion. Furthermore, the antiparallel and parallel chains are mediated by different interchain hydrogen bonds. The analysis also suggested that the inverse temperature dependence may be attributed to the hydrophobic effect reminiscent of the low critical solution temperature phase behavior. The present study provides a rich, atomic-level view of chitin’s polymorphic self-assembly process, paving the way for the rational design of chitin-derived novel materials.
Microbiota produced indole metabolites disrupt host cell mitochondrial energy production and inhibitCryptosporidium parvumgrowth
Authors: Funkhouser-Jones Lisa J. , Xu Rui , Wilke Georgia , Fu Yong , Shriefer Lawrence A. , Makimaa Heyde , Rodgers Rachel , Kennedy Elizabeth A. , VanDussen Kelli L. , Stappenbeck Thaddeus S. , Baldridge Megan T. , Sibley L. David
Published: May 2023

Cryptosporidiosis is a leading cause of life-threatening diarrhea in young children in resource-poor settings. Susceptibility rapidly declines with age, associated with changes in the microbiota. To explore microbial influences on susceptibility, we screened 85 microbiota- associated metabolites enriched in the adult gut for their effects onC. parvumgrowth in vitro. We identified eight inhibitory metabolites in three main classes: secondary bile salts/acids, a vitamin B6precursor, and indoles. Growth restriction ofC. parvumby indoles did not depend on the host aryl hydrocarbon receptor (AhR) pathway. Instead, treatment impaired host mitochondrial function and reduced total cellular ATP, as well as directly reduced the membrane potential in the parasite mitosome, a degenerate mitochondria. Oral administration of indoles, or reconstitution of the gut microbiota with indole producing bacteria, delayed life cycle progression of the parasite in vitro and reduced severity ofC. parvuminfection in mice. Collectively, these findings indicate that microbiota metabolites contribute to colonization resistance toCryptosporidiuminfection.
Comparing sparse inertial sensor setups for sagittal-plane walking and running reconstructions
Authors: Dorschky Eva , Nitschke Marlies , Mayer Matthias , Weygers Ive , Gassner Heiko , Seel Thomas , Eskofier Bjoern M. , Koelewijn Anne D.
Published: May 2023

Estimating spatiotemporal, kinematic, and kinetic movement variables with little obtrusion to the user is critical for clinical and sports applications. Previously, we developed an approach to estimate these variables from measurements with seven lower-body inertial sensors, i.e., the full setup, using optimal control simulations. Here, we investigated if this approach is similarly accurate when using sparse sensor setups with less inertial sensors. To estimate the movement variables, we solved optimal control problems on sagittal plane lower-body musculoskeletal models, in which an objective was optimized that combined tracking of accelerometer and gyroscope data with minimizing muscular effort. We created simulations for 10 participants at three walking and three running speeds, using seven sensor setups with between two and seven sensors located at the feet, shank, thighs, and/or pelvis. We calculated the correlation and root mean square deviations (RMSDs) between the estimated movement variables and those from inverse analysis using optical motion capture (OMC) and force plate data. We found that correlations between IMU- and OMC-based variables were high for all sensor setups, while including all sensors did not necessarily lead to the smallest RMSDs. Setups without a pelvis sensor led to too much forward trunk lean and inaccurate spatiotemporal variables. RMSDs were highest for the setup with two foot-worn IMUs. The smallest setup that estimated joint angles as accurately as the full setup (<1 degree difference in RMSD) was the setup with IMUs at the feet and thighs. The mean correlations for joint angles, moments, and ground reaction forces were at least 0.8 for walking and 0.9 for running when either a pelvic sensor or thigh sensors were included. Therefore, we conclude that we can accurately perform a comprehensive sagittal-plane motion analysis with sparse sensor setups when sensors are placed on the feet and on either the pelvis or the thighs.
The mechanical response of vinculin
Authors: Liu Xuyao , Wang Yinan , Yao Mingxi , Baker Karen B. , Klapholz Benjamin , Brown Nicholas H. , Goult Benjamin T. , Yan Jie
Published: May 2023

Vinculin is a mechanosensitive adapter protein that links the actin network to cell-extracellular matrix adhesions and cell-cell adhesions. It is perhaps the best characterized mechanoeffector, as it is recruited to sites of adhesion in response to force on the mechanotransducers talin and alpha-catenin. Here we examined the mechanical properties of vinculin to assess its potential role as a mechanotransducer. We find that at physiological loading rates, the structural domains of vinculin unfold at forces in the 5-15 pN range and rapidly refold when forces are reduced back to 1 pN. Thus, vinculin domains also have the potential to act as force dependent molecular switches, akin to those in talin and alpha-catenin. As with the force dependent switches in talin, the unfolding of these domains in vinculin introduces large extension changes in the vinculin cytoskeletal linkage up to 150 nm with 20-30 nm steps of unfolding. Modelling of the tension-dependent interactions of the unstructured vinculin linker region with a model protein containing two SH3 domains indicated that even unstructured protein regions can mediate force-dependent interactions with ligands, where the binding of a dual-SH3 model protein is predicted to be significantly suppressed by forces greater than 10 pN. Together, these findings suggest that vinculin has a complex mechanical response with force-dependent interaction sites, suggesting it also acts as a mechanotransducer, recruiting partners in response to force.
Contrasting functions of ATP hydrolysis by MDA5 and LGP2 in viral RNA sensing
Authors: Singh Rahul , Wu Yuan , Herrero del Valle Alba , Leigh Kendra E. , Cheng Mark T. K. , Ferguson Brian J. , Modis Yorgo
Published: May 2023

Cytosolic long double-stranded RNA (dsRNA), among the most potent proinflammatory signals, is recognized by MDA5. MDA5 binds dsRNA cooperatively, forming helical filaments. ATP hydrolysis by MDA5 fulfills a proofreading function by promoting dissociation of shorter endogenous dsRNAs from MDA5 while allowing longer viral dsRNAs to remain bound leading to activation of interferon-β responses. Here, we show that adjacent MDA5 subunits in MDA5-dsRNA filaments hydrolyze ATP cooperatively, inducing cooperative filament disassembly. This amplifies the RNA footprint expansion that accompanies each round of ATP hydrolysis and allows MDA5 to displace tightly bound proteins from dsRNA. Our electron microscopy and biochemical assays show that LGP2 binds to dsRNA at internal binding sites through noncooperative ATP hydrolysis. Unlike MDA5, LGP2 has low nucleic acid selectivity and can hydrolyze GTP and CTP as well as ATP. Binding of LGP2 to dsRNA promotes nucleation of MDA5 filament assembly resulting in shorter filaments. Molecular modeling of the MDA5-LGP2 interface suggests that MDA5 interacts with dsRNA stem-bound rather than end-bound LGP2. We conclude that NTPase-dependent binding of LGP2 to internal sites on dsRNA increases the number and signaling output of MDA5-dsRNA complexes. Our work identifies novel molecular mechanisms contributing the selectivity and sensitivity of cytosolic dsRNA sensing.

KEY POINTS

Cooperative ATP hydrolysis in MDA5 filaments confers selectivity for dsRNA and displaces other proteins from RNA

Noncooperative NTP hydrolysis by LGP2 induces binding to internal RNA sites with low selectivity

RNA stem-bound LGP2 nucleates assembly of MDA5 signaling complexes on a broader set of RNA ligands
Cerebellar granular neuron progenitors exit their germinative niche via Barhl1 mediated silencing of T-Cell Factor transcriptional activity
Authors: Bou-Rouphael Johnny , Doulazmi Mohammed , Eschstruth Alexis , Abdou Asna , Durand Béatrice C.
Published: May 2023

SUMMARY

T-Cell Factors (TCFs) are the main transcriptional effectors of Wnt/β-catenin signaling. TCF responsiveness is a hallmark of self-renewal in mouse embryonic, and adult, neural stem cells (NSC). However,in vivocontribution(s) of TCF activities in long-lived NSCs are poorly understood. Granule neuron progenitors (GNP) in the upper rhombic lip (URL) are long-lived NSCs which expressAtoh1and generate cerebellar granule neurons. Using functional and transcriptomic approaches in amphibian, we demonstrate that TCFs are active in the URL, and are strictly necessary for the emergence and maintenance of the GNP germinative zone. We identify BarH-like 1 (Barhl1), a direct target of Atoh1, as a gate keeper for GNP exit from the URL, through silencing of TCF transcriptional activity. Our transcriptomic andin silicoanalysis identifies Barhl1/TCF URL target genes, and confirms our functional data. Our study providesin vivoevidence that inhibition of TCF repressive activity is necessary for maintenance of the URL, a long-lived neural germinative niche.
Beclin1-Deficient Adipocytes Promote Tumor Progression by YAP/TAZ-dependent Adipocyte Transformation
Authors: Song Yaechan , Na Heeju , Lee Seung Eon , Moon Jihyun , Nam Tae Wook , Kim You Min , Ji Yul , Jin Young , Park Jae Hyung , Cho Seok Chan , Hwang Daehee , Ha Sang-Jun , Park Hyun Woo , Kim Jae Bum , Lee Han-Woong
Published: May 2023

Adipocytes are crucial components of the tumor microenvironment (TME) that play a prominent role in supporting tumor growth. However, the characteristics of cancer-associated adipocytes (CAAs) that contribute to the pro-tumorigenic niche remain to be fully established. Here, we used adipocyte-specificBeclin1 KO(BaKO) mice to investigate the role of maladaptive adipocytes in promoting tumor progression. BECN1-deficient adipocytes exhibited downregulation of adipogenic markers and activation of YAP/TAZ signaling, similar to the traits observed in CAAs. Thus, we generated adipocyte-specificBecn1/Yap1/Taz KOmice, which exhibit markedly restored phenotypes in adipose tissue, resulting in tumor regression compared to that in BaKO. Further, we observed dysregulation of the BECN1-YAP/TAZ axis in the adipose tissue of mice fed a high-fat diet (HFD). Treatment with the YAP/TAZ inhibitor, verteporfin, suppressed tumor progression in BaKO and HFD-fed mice, highlighting its efficacy against mice with metabolic dysregulation. Our findings provide insights into CAA formation and its significance in determining malignant TME, thereby suggesting a potential dual therapeutic strategy simultaneously targeting adipocyte homeostasis and cancer growth.
A deep learning solution for crystallographic structure determination
Authors: Pan Tom , Jin Shikai , Miller Mitchell D. , Kyrillidis Anastasios , Phillips George N.
Published: May 2023

The general de novo solution of the crystallographic phase problem is difficult and only possible under certain conditions. This paper develops an initial pathway to a deep learning neural network approach for the phase problem in protein crystallography, based on a synthetic dataset of small fragments derived from a large well curated subset of solved structures in the Protein Data Bank (PDB). In particular, electron-density estimates of simple artificial systems are produced directly from corresponding Patterson maps using a convolutional neural network architecture as a proof of concept.
Pyridin-4-ylmethanaminium perchlorate monohydrate
Authors: Seidel Rüdiger W. , Kolev Tsonko M.
Published: May 2023

Pyridin-4-ylmethanaminium perchlorate monohydrate (synonym: 4-picolylammonium perchlorate monohydrate), C6H9N2
+·ClO4
−·H2O, crystallizes in the monoclinic system (space group P21/n) with the asymmetric unit comprising two formula units (Z′ = 2). All molecular entities are located on general positions. The two crystallographically distinct 4-picolylammonium cations exhibit different conformations. The two unique perchlorate anions are non-disordered, showing an r.m.s. deviation of 0.011 Å from molecular T
d symmetry. The supramolecular structure in the solid state features an intricate tri-periodic network of N—H...O, O—H...N and O—H...O hydrogen bonds.
Do small- and medium-sized companies intend to use the Metaverse as part of their strategy? A behavioral intention analysis
Authors: Gil-Cordero Eloy , Maldonado-López Belén , Ledesma-Chaves Pablo , García-Guzmán Ana
Published: May 2023

Purpose

The purpose of the research is to analyze the factors that determine the intention of small- and medium-sized enterprises (SMEs) to adopt the Metaverse. For this purpose, the analysis of the effort expectancy and performance expectancy of the constructs in relation to business satisfaction is proposed.

Design/methodology/approach

The analysis was performed on a sample of 182 Spanish SMEs in the technology sector, using a PLS-SEM approach for development. For the confirmation of the model and its results, an analysis with PLSpredict was performed, obtaining a high predictive capacity of the model.

Findings

After the analysis of the model proposed in this research, it is recorded that the valuation of the effort to be made and the possible performance expected by the companies does not directly determine the intention to use immersive technology in their strategic behavior. Instead, the results obtained indicate that business satisfaction will involve obtaining information, reducing uncertainty and analyzing the competition necessary for approaching this new virtual environment.

Originality/value

The study represents one of the first approaches to the intention of business behavior in the development of performance strategies within Metaverse systems. So far, the literature has approached immersive systems from perspectives close to consumer behavior, but the study of strategic business behavior has been left aside due to the high degree of experimentalism of this field of study and its scientific approach. The present study aims to contribute to the knowledge of the factors involved in the intention to use the Metaverse by SMEs interested in this field.
Omnichannel retailing: exploring future research avenues in retail marketing and distribution management
Authors: Sharma Neha , Dutta Nirankush
Published: May 2023

Purpose

This study explores the present state of research related to omnichannel retail, investigates retail's different sub-areas and suggests future research directions.

Design/methodology/approach

The subdomains of omnichannel retail have been identified using a keyword co-occurrence network (KCN) map and content analysis. The 5W1H method assisted in finding the bibliographies of 258 SCOPUS-indexed and ABDC-ranked journal articles and showcasing the omnichannel retail landscape.

Findings

Most research on omnichannel retail is concentrated on five subdomains: customer behaviour, channel integration, technological innovation, supply chain and operations and strategy. The study's conceptual framework illustrates the omnichannel retailing environment and the variables that must be considered whilst establishing an omnichannel strategic vision. Besides, future researchers have been urged to concentrate on interdisciplinary research, as a seamless experience is unachievable if focussed on a single subdomain.

Research limitations/implications

There is a slight probability of missing out on some good articles as this study considered only those articles that have been published in SCOPUS and ranked by the ABDC quality list.

Practical implications

This study emphasises that for businesses to capitalise on the omnichannel model, the businesses must undergo a transformation involving technology convergence, customer-centricity and internal process reorganisation that integrates consumer feedback to co-create value. When a business adopts an omnichannel model, the business's priorities shift. Rather than depending solely on technology, faster delivery and channel integration, an omnichannel strategy requires strong leadership, a clear vision, training for all stakeholders and an understanding of customer pain points to reach the full potential.

Originality/value

The illustration of the omnichannel retail landscape using the 5W1H methodology and antecedents-decisions-outcomes (ADO) framework.
The coping strategies in fitness apps: a three-stage analysis with findings from SEM and FsQCA
Authors: Xu XiaoYu , Tayyab Syed Muhammad Usman , Jia Qingdan , Wu Kuang
Published: May 2023

Purpose

Combining the coping theory and social support theory, this study aims to reveal users' coping strategies for mobile fitness app (MFA) engagement and fitness intentions with a rigorous and comprehensive hybrid research approach.

Design/methodology/approach

A three-stage hybrid research design was employed in this study. In the first stage, this study utilized structural equation modeling (SEM) to investigate the associations between coping resources and coping outcomes. A post hoc analysis was conducted in the second stage to unveil the reasons behind the insignificant or weak linkages. In the third stage, the fuzzy-set qualitative comparative analysis (fsQCA) technique was applied to explore the various configurations of coping resources that lead to the coping outcomes.

Findings

The results in the three stages verify and compensate each other. The SEM results confirm the presence of two coping strategies in MFA, highlighting the importance of the intertwining of the strategies, and the post hoc analysis unveils the mediating role of positive affect. Moreover, the fsQCA results reinforce and complement the SEM findings by revealing eight alternative configurations that are sufficient for leading to users' MFA engagement and fitness intention.

Originality/value

This study offers a prominent methodological paradigm by demonstrating the application of multi-analysis in exploring users' coping strategies. In addition, the study also advances the understanding of the complexity of the mechanism that determines users' behavioral decisions by presenting a comprehensive interpretation.