bluuebunny/crossref_metadata_2025 huggingface dataset:
Male gonad-enriched microRNAs function to control sperm production inC. elegans
Authors: Lu Lu , Abbott Allison L.
Published: October 2023

Germ cell development and gamete production in animals require small RNA pathways. While studies indicate that microRNAs (miRNAs) are necessary for normal sperm production and function, the specific roles for individual miRNAs are largely unknown. Here, we use small RNA sequencing of dissected gonads and functional analysis of new loss of function alleles to identify functions for miRNAs in the control of fecundity and sperm production inCaenorhabditis elegansmales and hermaphrodites. We describe a set of 29 male gonad-enriched miRNAs and identify a set of 3 individual miRNAs (mir-58.1, mir-83,andmir-235)and a miRNA cluster (mir-4807-4810.1)that are required for optimal sperm production at 20°C and 5 additional miRNAs (mir-49, mir-57, mir-261,andmir-357/358) that are required for sperm production at 25°C. We observed defects in meiotic progression inmir-58.1, mir-83, mir-235,andmir-4807-4810.1mutants that may contribute to the reduced number of sperm. Further, analysis of multiple mutants of these miRNAs suggested complex genetic interactions between these miRNAs for sperm production. This study provides insights on the regulatory roles of miRNAs that promote optimal sperm production and fecundity in males and hermaphrodites.

Article Summary

MicroRNAs are small non-coding RNAs that are required for the normal production of sperm but the roles of individual microRNAs in the process of spermatogenesis are not well understood. Here, we use the nematodeCaenorhabditis elegansto identify microRNAs that are enriched in the male gonad to identify specific microRNAs that regulate male fertility. We generated new loss of function mutants for functional analysis to identify a set of microRNAs that are necessary for optimal fertility and fecundity in males.
HetMM: A Michaelis-Menten model for non-homogeneous enzyme mixtures
Authors: Douglas Jordan , Carter Charles W. , Wills Peter R.
Published: October 2023

The Michaelis-Menten model requires its reaction velocities to be measured from a preparation of homogeneous enzymes, with identical or near-identical catalytic activities. However, there are many cases where enzyme preparations do not satisfy this condition, or where one may wish to test the validity of this assumption. We introduce a kinetic model that relaxes this requirement, by assuming there are an unknown number of enzyme species drawn from an unknown probability distribution. This model features one additional parameter over the Michaelis-Menten model, describing the standard deviation of this distribution. We show that the assumption of homogeneity is usually sufficient even in non-homogeneous solutions, and only fails under extreme conditions where Km spans orders of magnitude. We validate this method through simulation studies, demonstrating the method does not overfit to random noise, despite its increase in dimensionality. The two models can be accurately discriminated between even with moderate levels of experimental error. We applied this model to three homogeneous and three heterogeneous biological systems, showing that the standard and heterogeneous models outperform in either case, respectively. Lastly, we show that heterogeneity is not readily distinguished from negatively-cooperative binding under the Hill model. These two fundamentally distinct properties - inequality in catalytic ability and interference between binding sites - give similar Michaelis-Menten curves that are not readily resolved without further experimentation. Our method allows testing for homogeneity and performing parameter inference in a Bayesian framework, and is available online in the user-friendly HetMM package athttps://github.com/jordandouglas/HetMM.
Oligodendroglial precursors orchestrate immune network instigating early demyelination in experimental autoimmune encephalomyelitis
Authors: Wang Qi , Huang Taida , Zheng Zihan , Su Yixun , Wu Zhonghao , Yu Guangdan , Liu Yang , Wang Xiaorui , Li Hui , Chen Xiaoying , Jiang Zhuoxu , Zhang Jinyu , Zhuang Yuan , Tian Yi , Yang Qingwu , Verkhratsky Alexei , Wan Ying , Yi Chenju , Niu Jianqin
Published: October 2023

The immunomodulatory cellular network that triggers early inflammation and demyelination, the key steps in multiple sclerosis (MS) pathogenesis remains poorly characterized. Here, we demonstrate that overactivation of Wnt pathway promotes pathological transformation of oligodendrocyte precursor cells (OPCs) to replicate pathological OPCs in human MS. In mouse experimental autoimmune encephalomyelitis (EAE), pathological OPCs attract CD4+T-helper 1 (Th1) cells into the spinal cord and brain through CC-chemokine ligand 4 (CCL4), whilst OPCs cooperate with Th1 cells inducing transformation of cytotoxic macrophages that execute early demyelination. Simultaneously, Th1 cells and cytotoxic macrophages upregulate Wnt signaling and CCL4 expression in OPCs, thus exerting positive feedback onto the OPC-immune cascade and establishing a vicious cycle propagating EAE pathogenesis. Breaking this cascade by targeting CCL4 reduces immune cell infiltration, alleviates demyelination, and attenuates EAE severity. Our findings demonstrate a closely coordinated network of OPCs and immune cells therefore providing an alternative insight into MS pathophysiology.
WDR23 mediates NRF2 proteostasis and cytoprotective capacity in the hippocampus
Authors: Liu Jiahui , Duangjan Chatrawee , Irwin Ronald W. , Curran Sean P.
Published: October 2023

Pathogenic brain aging and neurodegenerative diseases such as Alzheimer’s disease and Parkinson’s disease are characterized by chronic neuroinflammation and the accumulation of dysfunctional or misfolded proteins that lead to progressive neuronal cell death. Here we demonstrate that a murine model with global loss of the CUL4-DDB1 substrate receptor WDR23 (Wdr23KO) results in changes in multiple age-related hippocampal-dependent behaviors. The behavioral differences observed inWdr23KOanimals accompany the stabilization of the NRF2/NFE2L2 protein, an increase in RNA transcripts regulated by this cytoprotective transcription factor, and an increase in the steady state level of antioxidant defense proteins. Taken together, these findings reveal a role for WDR23-proteostasis in mediating cytoprotective capacity in the hippocampus and reveal the potential for targeting WDR23-NRF2 signaling interactions for development of therapies for neurodegenerative disorders.

HIGHLIGHTS

WDR23 regulates NRF2/NFE2L2 stability in the mouse hippocampus

Loss ofWdr23significantly increases the expression of NFE2L2/NRF2 target genes

Global loss of WDR23 influences age-related behaviors differentially in males and females
Causal effect of serum 25 hydroxyvitamin D concentration on cardioembolic stroke: Evidence from Two-sample Mendelian randomization
Authors: Habibi Danial , Teymoori Farshad , Ebrahimi Navid , Tehrani Fateh Sahand , Najd-Hassan-Bonab Leila , Saeidian Amir Hossein , Soleymani Taloubaghi Alireza , Asgarian Sara , Hosseinpanah Farhad , Hakonarson Hakon , Azizi Fereidoun , Hedayati Mehdi , Daneshpour Maryam Sadat , Akbarzadeh Mahdi , Mansourian Marjan
Published: October 2023

Background/Aim

The putative association between serum 25 hydroxyvitamin D concentration 25(OH)D and the risk of cardioembolic stroke (CES) has been examined in observational studies, which indicate controversial findings. We performed Mendelian randomization (MR) analysis to determine the causal relationship of serum 25(OH)D with the risk of CES.

Method

The summary statistics dataset on the genetic variants related to 25(OH)D was used from the published GWAS of European descent participants in the UK Biobank, including 417,580 subjects, yielding 143 independent loci in 112 1-Mb regions. GWAS summary data of CES was obtained from GIGASTROKE Consortium, which included European individuals (10,804 cases, 1,234,808 controls).

Results

Our results unveiled 99 SNPs contributing a causal relationship between 25(OH)D and CES using IVW [OR□=□0.82, 95% CI: 0.67-0.98, p□=□0.037]. Horizontal pleiotropy was not seen by the MR-Egger intercept-based test [MR-Egger intercept□=□0.001; p□=□0.792], suggesting an absence of horizontal pleiotropy. Cochrane’s Q value [Q=78.71, p-value□=□0.924], Rucker’s Q [Q=78.64, p-value=0.913], and I2=0.0% (95% CI: 0.0%, 24.6%) statistic suggested no heterogeneity in the connection between 25(OH)D and CES. This result remained consistent using different MR method and sensitivity analyses, including Maximum likelihood [OR=0.82, 95%CI: 0.67-0.98, p-value=0.036], Constrained maximum likelihood method [OR=0.76, 95%CI: 0.64-0.90, p-value=0.002], Debiased inverse-variance weighted method [OR=0.82, 95%CI: 0.68-0.99, p-value=0.002], MR-PRESSO [OR=0.82, 95%CI 0.77-0.87, p-value=0.022], RAPS [OR=0.82, 95%CI 0.67-0.98, p-value=0.038], MR-Lasso [OR=0.82, 95%CI 0.68-0.99, p-value=0.037].

Conclusion

Our MR analysis provides suggestive evidence that increased 25(OH)D levels may play a causally protective role in the development of cardioembolic stroke. Determining the role of 25(OH)D in stroke subtypes has important clinical and public health implications.
Transdiagnostic failure to adapt interoceptive precision estimates across affective, substance use, and eating disorders: A replication study
Authors: Lavalley Claire A. , Hakimi Navid , Taylor Samuel , Kuplicki Rayus , Forthman Katherine L. , Stewart Jennifer L. , Paulus Martin P. , Khalsa Sahib S. , Smith Ryan
Published: October 2023

Recent computational theories of interoception suggest that perception of bodily states rests upon an expected reliability- or precision-weighted integration of afferent signals and prior beliefs. The computational psychiatry framework further suggests that aberrant precision-weighting may lead to misestimation of bodily states, potentially hindering effective visceral regulation and promoting psychopathology. In a previous study, we fit a Bayesian computational model of perception to behavior on a heartbeat tapping task to test whether aberrant precision-weighting was associated with misestimation of bodily states. We found that, during an interoceptive perturbation designed to amplify afferent signal precision (inspiratory breath-holding), healthy individuals increased the precision-weighting assigned to ascending cardiac signals (relative to resting conditions), while individuals with symptoms of anxiety, depression, substance use disorders, and/or eating disorders did not. A second study also replicated the pattern observed in healthy participants. In this pre-registered study, we aimed to replicate our prior findings in a new transdiagnostic patient sample (N=285) similar to the one in the original study. These new results successfully replicated those found in our previous study, indicating that, transdiagnostically, patients were unable to adjust beliefs about the reliability of interoceptive signals – preventing the ability to accurately perceive changes in their bodily state. Follow-up analyses combining samples from the previous and current study (N=719) also afforded the power to identify group differences within narrower diagnostic groups and to examine predictive accuracy when logistic regression models were trained on one sample and tested on the other. Given the increased confidence in the generalizability of these effects, future studies should examine the utility of interceptive precision measures in predicting treatment outcomes or identify whether these computational mechanisms might represent novel therapeutic targets for improving visceral regulation.
Daughter circumcision and maternal life satisfaction: A cultural moderation effect revealed across two studies
Authors: Strand Paul S. , Maxwell Providence , Trang Justin
Published: October 2023

Introduction

The present paper explored the relationship between maternal life satisfaction and the intergenerational transmission of female genital cutting (FGC; female circumcision).

Methods

Across two studies with more than 85,000 participants in 15 countries, maternal surveys reveal that the association is positive and moderated by country-level FGC prevalence.

Results

Contrary to predictions, in countries in which FGC is uncommon, it is more positively associated with maternal life satisfaction; and in countries in which it is common, it is weakly or negatively associated with maternal life satisfaction.

Conclusion

Results suggest a diversity of social motives for FGM. Customized messaging to reduce its inter-generational transmission should be considered.

KEY MESSAGES

What is already known about this topic?

Female genital cutting (FGC) has negative implications for health and gender equality and is practiced to different degrees in countries in parts of Africa, Asia, the Middle East, and their diasporas.

What this study adds?

This study explored the intergenerational transmission of FGC—in particular, how daughter FGC relates to maternal life satisfaction. Contrary to expectations, life satisfaction ratings were higher for mothers of circumcised daughters, although this relationship was moderated by country-level FGC frequency. In countries in which it is more common, daughter FGC is less strongly or negatively associated with maternal life satisfaction.

How might this study affect research, practice, or policy?

Study findings may inform anti-FGC messaging. In countries in which FGC is common, messaging should highlight its association with relative maternal dissatisfaction. In countries in which it is uncommon, messaging should highlight alternatives to FGC as an expression of cultural identity.
Single-value fMRI scores reflect both stage and risk across the Alzheimer’s disease continuum
Authors: Soch Joram , Richter Anni , Kizilirmak Jasmin M. , Schütze Hartmut , Ziegler Gabriel , Altenstein Slawek , Brosseron Frederic , Dechent Peter , Fliessbach Klaus , Freiesleben Silka Dawn , Glanz Wenzel , Gref Daria , Heneka Michael T. , Hetzer Stefan , Incesoy Enise I. , Kilimann Ingo , Kimmich Okka , Kleineidam Luca , Kuhn Elizabeth , Laske Christoph , Lohse Andrea , Lüsebrink Falk , Munk Matthias H. , Peters Oliver , Preis Lukas , Priller Josef , Ramirez Alfredo , Roeske Sandra , Rostamzadeh Ayda , Roy-Kluth Nina , Scheffler Klaus , Schmid Matthias , Schneider Anja , Spottke Annika , Spruth Eike Jakob , Teipel Stefan , Wiltfang Jens , Jessen Frank , Wagner Michael , Düzel Emrah , Schott Björn H.
Published: October 2023

Single-value scores reflecting the deviation from (FADE score) or similarity with (SAME score) prototypical novelty-related and memory-related functional magnetic resonance imaging (fMRI) activation patterns in young adults have been proposed as imaging biomarkers of healthy neurocognitive aging. Here, we tested the utility of these scores as potential diagnostic and prognostic markers in Alzheimer’s disease (AD) and risk states like mild cognitive impairment (MCI) or subjective cognitive decline (SCD).

To this end, we analyzed subsequent memory fMRI data from individuals with SCD, MCI, and AD dementia as well as healthy controls (HC) and first-degree relatives of AD dementia patients (AD-rel) who participated in the multi-center DELCODE study (N = 468). Based on the individual participants’ whole-brain fMRI novelty and subsequent memory responses, we calculated the FADE and SAME scores and assessed their association with AD risk stage, neuropsychological test scores, CSF amyloid positivity, and ApoE genotype.

Memory-based FADE and SAME scores showed a considerably larger deviation from a reference sample of young adults in the MCI and AD dementia groups compared to HC, SCD and AD-rel. In addition, novelty-based scores significantly differed between the MCI and AD dementia groups. Across the entire sample, single-value scores correlated with neuropsychological test performance. The novelty-based SAME score further differed between Aβ-positive and Aβ-negative individuals in SCD and AD-rel, and between ApoE ε4 carriers and non-carriers in AD-rel.

Hence, FADE and SAME scores are associated with both cognitive performance and individual risk factors for AD. Their potential utility as diagnostic and prognostic biomarkers warrants further exploration, particularly in individuals with SCD and healthy relatives of AD dementia patients.
Time-Dependent ECG-AI Prediction of Fatal Coronary Heart Disease
Authors: Butler L. , Ivanov A. , Celik T. , Karabayir I. , Chinthala L. , Tootooni S. M. , Jaeger B. C , Doerr A. , McManus D. D. , Davis L. R. , Herrington D. , Akbilgic O.
Published: October 2023

Background

Sudden cardiac death (SCD) affects >4 million people globally, and ∽300,000 yearly in the US. Fatal coronary heart disease (FCHD) is used as a proxy to SCD when coronary disease is present and no other causes of death can be identified. Electrocardiographic (ECG) artificial intelligence (AI) models (ECG-AI) show promise in predicting adverse coronary events yet their application to FCHD is limited.

Objectives

This research aimed to develop accurate ECG-AI models to predict risk for FCHD within the general population using waveform 12- and single-lead ECG data as well as assess time-dependent risk.

Methods

Standard 10-second 12-lead ECGs sampled at 250Hz, demographic and clinical data from University of Tennessee Health Science Center (UTHSC) were used to develop and validate models. Eight models were developed and tested: two classification models with convolutional neural networks (CNN) using 12- and single-lead ECGs as inputs (12-ECG-AI and 1-ECG-AI, respectively) and six time- dependent cox proportional hazard regression (CPHR) models using demographics, clinical data and ECG-AI outputs. The dataset was split into 80% for model derivation, with five-fold cross-validation, and 20% holdout test set. Models were evaluated using the AUC and C-Index. Correlation of predicted risks from the 12-lead (12-ECG-AI) and single-lead (1-ECG-AI) CNN models was assessed.

Results

A total of 50,132 patients were included in this study (29,093 controls and 21,039 cases) with a total of 167,662 ECGs with mean age of 62.50±14.80years, 53.4% males and 48.5% African-Americans. The 12- and 1-ECG-AI models resulted AUCs=0.77 and 0.76, respectively on the holdout data. The best performing model was C12-ECG-AI-Cox (demographics+clinical+ECG) with no time restriction AUC=0.85(0.84-0.86) and C-Index= 0.78(0.77-0.79). 2-year FCHD risk prediction reached AUC=0.91(0.90-0.92). The 12-/1-ECG-AI models’ predictions were highly correlated (R2= 0.72).

Conclusion

2-year risk for FCHD can be predicted with moderate accuracy from ECG data alone. When combined with other data, a very high accuracy was obtained. High correlation between single-lead and 12-lead ECG models infer opportunities for screening larger patient populations for FCHD risk.

Graphical Abstract
FSL-CP: A Benchmark for Small Molecule Activity Few-Shot Prediction using Cell Microscopy Images
Authors: Ha Son V. , Leuschner Lucas , Czodrowski Paul
Published: October 2023

Predicting small molecule activities using information from high-throughput microscopy images has been shown to tremendously increase hit rates and chemical diversity of the hits in previous drug discovery projects. However, due to high cost of acquiring data or ethical reasons, data sparsity remains a big challenge in drug discovery. This opens up the opportunity for few-shot prediction: fine-tuning a model on a low-data assay of interest after pretraining on other more populated assays. Previous efforts have been made to establish a benchmark for few-shot learning of molecules based on molecular structure. With cell images as a molecular representation, methods in the computer vision domain are also applicable for activity prediction. In this paper, we make two contributions: a) A public data set for few-shot learning with cell microscopy images for the scientific community, b) A range of baseline models encompassing different existing single-task, multi-task and meta-learning approaches.
Compensation of compromised PRC2 regulation by a miRNA ensures robustness of Arabidopsis leaf development
Authors: Maugarny Aude , Vialette Aurélie , Adroher Bernard , Mathy-Franchet Nathalie , Roudier François , Laufs Patrick
Published: October 2023

Robustness is pervasive throughout biological systems, enabling them to maintain persistent outputs despite perturbations in their components. Here, we reveal a novel mechanism contributing to leaf morphology robustness in the face of genetic perturbations. In Arabidopsis, leaf shape is established during early development through the quantitative action of theCUP-SHAPED COTYLEDON2(CUC2) gene that is negatively regulated by the co-expressedMICRORNA164A(MIR164A) gene. Compromised epigenetic regulation due to defective Polycomb Repressive Complex 2 (PRC2) function results in the transcriptional derepression ofCUC2but has no impact on CUC2 protein dynamics or early morphogenesis. We solve this apparent paradox by showing that compromised PRC2 function simultaneously activates a compensatory mechanism involving another member of theMIR164gene family, theMIR164Bgene. This mechanism dampens CUC2 protein levels, thereby compensating for compromised PRC2 function and canalizing early leaf morphogenesis. Furthermore, we show that this compensation mechanism is active under different environmental conditions. Our findings shed light on how the interplay between different types of transcriptional regulation can contribute to developmental robustness.
WITHDRAWN: Nitrogen sources enhance siderophore-mediated competition for iron between potato common scab and late blight causative agents
Authors: Stulanovic Nudzejma , Kerdel Yasmine , Rezende Lucas , Deflandre Benoit , Burguet Pierre , Belde Loic , Denoel Romane , Tellatin Deborah , Rigolet Augustin , Hanikenne Marc , Quinton Loic , Ongena Marc , Rigali Sebastien
Published: October 2023

Withdrawal Statement

The authors have withdrawn their manuscript owing to the fact that theP.infestansstrain received from third parties is not the one referred in the manuscript despite having the certificate from the providing collection. All the experiments and data are correct but not included into a proper research context. A new version of this work will be published in near future. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.
Biodistribution Analysis of Peptide-Coated Magnetic Iron Nanoparticles: A Simple and Quantitative Method
Authors: Natarajan Pavithra , Horak Katherine , Rowe Jennifer , Lingo Joshua , Tomich John M , Fleming Sherry D
Published: October 2023

Biodistribution is the tracking of compounds or molecules of interest in the subject which is integral to understanding their anticipated efficacy and safety. Nanoparticles are highly desirable delivery systems which have the ability to deliver higher nucleic acid and drug payloads and they have enhanced tumor permeability due to their unique properties such as high surface area to volume ratio. Studying the biodistribution of nanoparticles is crucial to understand their effectiveness and safety in vivo, facilitate a more application driven approach for nanoparticle development which will lead to their successful translation into clinical use. In this study, we present a relatively simple method to determine the biodistribution of magnetic iron nanoparticles in mice. Branched Amphiphilic Peptide coated Magnetic Nanobeads BAPc-MNBs like their counterpart i.e., Branched Amphiphilic Peptide capsules (BAPCs) with a hollow water-filled core, are readily taken up by cells in vitro and have widespread application as a nanodelivery systems. We evaluated the BAPc-MNBs tissue distribution in wildtype mice injected intravenously (i.v.), intraperitoneally (i.p.) or orally gavaged to understand the biological interactions of the peptide nanoparticles and to further the development of branched amphiphilic peptides-based nanoparticles. BAPc-MNBs were distributed widely to various organs when injected i.v. and were eliminated from the system via the intestines in feces. The spleen was found to accumulate the highest amount of BAPc-MNBs in mice administered the NPs i.v. and i.p. while they were not absorbed into the system via oral gavage. This study not only presents a relatively simple quantification method to determine in vivo biodistribution of magnetic iron nanoparticles that can be widely applied but also demonstrates the potential of Branched Amphiphilic Peptides in the form of BAPCs or BAPc-MNBs as a delivery system.
DNA methylation is linked to the monoallelic expression ofMRP3, a diatom mating type determining gene
Authors: Ruggiero Antonella , Mager Svenja , Manfellotto Francesco , Tuccio Viviana Di , Nishimura Tomohiro , Pan Leslie , Russo Monia T. , Sanges Remo , Ferrante Maria I.
Published: October 2023

Diatoms are unicellular microalgae widely distributed in aquatic ecosystems. In diatoms, sexual reproduction is needed to counteract cell miniaturization imposed by the rigid silica shell, and only small cells, below a species-specific size threshold, are competent for sex.

We performed a genome-wide Enzymatic Methyl-seq analysis in the heterothallic diatomPseudo-nitzschia multistriatacomparing cells of different size and opposite mating type (MT) to investigate potential epigenetic controls in life cycle transitions. We found an imprinting-like pattern of methylation at the sex locus: alleles of the gene responsible for the specification of the MT+,MRP3, are hypermethylated in MT- and differentially methylated in MT+, with transcription occurring only on the MT+ hypomethylated variant. The methylation pattern is overall stable over theP. multistriatalife cycle. Absence of methylation inMRP3is necessary for its expression but not sufficient, since large non-sexual cells have the same methylation profile of small sexual cells but do not expressMRP3, suggesting that additional controls are involved in the mechanism of sex determination.

The methylation profile of the mating type determining geneMRP3of the diatomPseudo-nitzschia multistriatais different between opposite mating types. Lack of methylation is necessary but not sufficient forMRP3expression in the sexually competent MT+ strains.

Highlights

- The mating type locus is differentially methylated in MT+ and MT-

- DNA methylation is linked to MRP3 expression

- DNA methylation does not play a role in the acquisition of sexual competence
Microbiota may affect the tumor type but not overall tumor development in two models of heritable cancer
Authors: Spring Jessica , Gurbuxani Sandeep , Golovkina Tatyana
Published: October 2023

Microbial impact on tumorigenesis of heritable cancers proximal to the gut is well documented. Whether the microbiota influences cancers arising from inborn mutations at sites distal to the gut is undetermined. Using two models of heritable cancer, we found the microbiota to be inconsequential for tumor development. However, the type of tumor that develops may be influenced by the microbiota. This work furthers our understanding of the microbial impact on tumor development.
Structural basis for CFTR inhibition by CFTRinh-172
Authors: Young Paul , Levring Jesper , Fiedorczuk Karol , Blanchard Scott C. , Chen Jue
Published: October 2023

The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel that regulates electrolyte and fluid balance in epithelial tissues. Whereas activation of CFTR is vital to treating cystic fibrosis, selective inhibition of CFTR is a potential therapeutic strategy for secretory diarrhea and autosomal dominant polycystic kidney disease (ADPKD). Although several CFTR inhibitors have been developed by high-throughput screening, their modes of action remain elusive. In this study, we determined the structure of CFTR in complex with the inhibitor CFTRinh- 172 to 2.7 Å resolution by cryogenic electron microscopy (cryo-EM). We observe that CFTRinh- 172 binds inside the pore near transmembrane helix 8 (TM8), a critical structural element that links ATP hydrolysis with channel gating. Binding of CFTRinh-172 stabilizes a conformation in which the chloride selectivity filter is collapsed and the pore is blocked from the extracellular side of the membrane. Single molecule fluorescence resonance energy transfer (smFRET) experiments indicate that CFTRinh-172 inhibits channel gating without compromising nucleotide-binding domain (NBD) dimerization. Together, these data show that CFTRinh-172 acts as both a pore blocker and a gating modulator, setting it apart from typical ion channel inhibitors. The dual functionality of CFTRinh-172 reconciles previous biophysical observations and provides a molecular basis for its activity.

Significance statement

The pathogenesis of secretory diarrhea and autosomal dominant polycystic kidney disease involves hyperactivation of the CFTR ion channel. CFTR inhibitors, including the small-molecule CFTRinh-172, have been developed as therapeutic candidates to treat these diseases. This study offers a structural understanding of CFTRinh-172’s mode of action, clarifying its dual inhibitory role as both a pore blocker and gating modulator. The molecular description of how CFTRinh-172 interacts with CFTR provides a structural foundation to its specificity and efficacy. Furthermore, the observation that CFTR inhibitors and potentiators both interact with TM8 strengthens the notion that this helix serves as an allosteric link between the ATPase site and the channel gate, and is therefore a hotspot for pharmacological modulation.
Computational mechanisms underlying motivation to earn symbolic reinforcers
Authors: Burk Diana C. , Taswell Craig , Tang Hua , Averbeck Bruno B.
Published: October 2023

Reinforcement learning (RL) is a theoretical framework that describes how agents learn to select options that maximize rewards and minimize punishments over time. We often make choices, however, to obtain symbolic reinforcers (e.g. money, points) that can later be exchanged for primary reinforcers (e.g. food, drink). Although symbolic reinforcers are motivating, little is understood about the neural or computational mechanisms underlying the motivation to earn them. In the present study, we examined how monkeys learn to make choices that maximize fluid rewards through reinforcement with tokens. The question addressed here is how the value of a state, which is a function of multiple task features (e.g. current number of accumulated tokens, choice options, task epoch, trials since last delivery of primary reinforcer, etc.), drives value and affects motivation. We constructed a Markov decision process model that computes the value of task states given task features to capture the motivational state of the animal. Fixation times, choice reaction times, and abort frequency were all significantly related to values of task states during the tokens task (n=5 monkeys). Furthermore, the model makes predictions for how neural responses could change on a moment-by-moment basis relative to changes in state value. Together, this task and model allow us to capture learning and behavior related to symbolic reinforcement.

Significance statement

Symbolic reinforcers, like money and points, play a critical role in our lives. Like rewards, symbolic reinforcers can be motivating and can even lead to compulsive behaviors like gambling addiction. However, we lack an understanding of how symbolic reinforcement can drive fluctuations in motivation. Here we investigated the effect of symbolic reinforcers on behaviors related to motivation during a token reinforcement learning task, using a novel reinforcement learning model and data from five monkeys. Our findings suggest that the value of a task state can affect willingness to initiate a trial, speed to choose, and persistence to complete a trial. Our model makes testable predictions for within trial fluctuations of neural activity related to values of task states.
Rapid generation of single-insertion transgenics by Tol2 transposition in zebrafish
Authors: Kalvaitytė Miglė , Gabrilavičiūtė Sofija , Balciunas Darius
Published: October 2023

The Tol2 transposable element is the most widely used transgenesis tool in zebrafish. However, its high activity almost always leads to multiple unlinked integrations of the transgenic cassette in F1fish. Each of these transgenes is susceptible to position effects from surrounding regulatory landscape, which can lead to altered expression and, consequently, activity. Scientists therefore must strike a balance between the need to maximize reproducibility by establishing single-insertion transgenic lines and the need to complete experiments within a reasonable timeframe. In this article, we introduce a simple competitive dilution strategy for rapid generation of single-insertion transgenics. By usingcry:BFPreporter plasmid as a competitor, we achieved a nearly fourfold reduction in the number of the transgene of interest(TgOI) integrations while simultaneously increasing the proportion of single-insertion F1generation transgenics to over 50%. We also observed variations inTgOIexpression among independent single-insertion transgenics, highlighting that the commonly used ubiquitousubbpromoter is susceptible to position effects. Wide application of our competitive dilution strategy will save time, reduce animal usage, and improve reproducibility of zebrafish research.

Competitive dilution of Tol2 transgenesis vectors facilitates isolation of single-insertion transgenic zebrafish lines in the F1generation, reducing animal usage, improving reproducibility, and saving time.
ECM-Focused Proteomic Analysis of Ear Punch Regeneration inAcomys Cahirinus
Authors: McCabe Maxwell C. , Okamura Daryl M. , Erickson Christopher B. , Perry Blair W. , Brewer Chris M. , Nguyen Elizabeth D. , Saviola Anthony J. , Majesky Mark W. , Hansen Kirk C.
Published: October 2023

In mammals, significant injury is generally followed by the formation of a fibrotic scar which provides structural integrity but fails to functionally restore damaged tissue. Spiny mice of the genusAcomysrepresent the first example of full skin autotomy in mammals.Acomys cahirinushas evolved extremely weak skin as a strategy to avoid predation and is able to repeatedly regenerate healthy tissue without scar after severe skin injury or full-thickness ear punches. Extracellular matrix (ECM) composition is a critical regulator of wound repair and scar formation and previous studies have suggested that alterations in its expression may be responsible for the differences in regenerative capacity observed betweenMus musculusandA. cahirinus, yet analysis of this critical tissue component has been limited in previous studies by its insolubility and resistance to extraction. Here, we utilize a 2-step ECM-optimized extraction to perform proteomic analysis of tissue composition during wound repair after full-thickness ear punches inA. cahirinusandM. musculusfrom weeks 1 to 4 post-injury. We observe changes in a wide range of ECM proteins which have been previously implicated in wound regeneration and scar formation, including collagens, coagulation and provisional matrix proteins, and matricryptic signaling peptides. We additionally report differences in crosslinking enzyme activity and ECM protein solubility betweenMusandAcomys.Furthermore, we observed rapid and sustained increases in CD206, a marker of pro-regenerative M2 macrophages, inAcomys,whereas little or no increase in CD206 was detected inMus.Together, these findings contribute to a comprehensive understanding of tissue cues which drive the regenerative capacity ofAcomysand identify a number of potential targets for future pro-regenerative therapies.
Uncovering DUB Selectivity Through Ion-Mobility-Based Assessment of Ubiquitin Chain Isomers
Authors: Shestoperova Elizaveta I. , Strieter Eric R.
Published: October 2023

Ubiquitination is a reversible posttranslational modification that maintains cellular homeostasis and regulates protein turnover. Deubiquitinases (DUBs) are a large family of proteases that catalyze the removal of ubiquitin (Ub) along with the dismantling and editing of Ub chains. Assessing the activity and selectivity of DUBs is critical for defining physiological function. Despite numerous methods for evaluating DUB activity, none are capable of assessing activity and selectivity in the context of multicomponent mixtures of native, unlabeled ubiquitin conjugates. Here we report on an ion mobility (IM)-based approach for measuring DUB selectivity in the context of unlabeled mixtures of Ub chains. We show that IM-MS can be used to assess the selectivity of DUBs in a time-dependent manner. Moreover, using the branched Ub chain selective DUB UCH37/UCHL5 along with a mixture of Ub trimers, a strong preference for branched Ub trimers bearing K6 and K48 linkages is revealed. Our results demonstrate that IM coupled with mass spectrometry (IM-MS) is a powerful method for evaluating DUB selectivity under conditions more physiologically relevant than single component mixtures.
AI-predicted protein deformation encodes energy landscape perturbation
Authors: McBride John M. , Tlusty Tsvi
Published: October 2023

AI algorithms have proven to be excellent predictors of protein structure, but whether and how much these algorithms can capture the underlying physics remains an open question. Here, we aim to test this question using the Alphafold2 (AF) algorithm: We use AF to predict the subtle structural deformation induced by single mutations, quantified by strain, and compare with experimental datasets of corresponding perturbations in folding free energy ΔΔG. Unexpectedly, we find that physical strain alone – without any additional data or computation – correlates almost as well with ΔΔGas state-of-the-art energy-based and machine-learning predictors. This indicates that the AF-predicted structures alone encode fine details about the energy landscape. In particular, the structures encode significant information on stability, enough to estimate (de-)stabilizing effects of mutations, thus paving the way for the development of novel, structure-based stability predictors for protein design and evolution.
Tunneling nanotubes enable intercellular transfer in zebrafish embryos
Authors: Korenkova Olga , Liu Shiyu , Prlesi Inès , Pepe Anna , Albadri Shahad , Bene Filippo Del , Zurzolo Chiara
Published: October 2023

Tunneling nanotubes (TNTs) are thin intercellular connections facilitating the transport of diverse cargoes, ranging from ions to organelles. While TNT studies have predominantly been conducted in cell cultures, the existence of open-ended TNTs within live organisms remains unverified. Despite the observation of intercellular connections during embryonic development across various species, their functional role has not been confirmed. In this study, we performed mosaic labeling of gastrula cells in zebrafish embryos to demonstrate the coexistence of TNT-like structures alongside other cellular protrusions. These embryonic TNT-like connections exhibited similar morphology to TNTs described in cell culture, appeared to have similar formation mechanisms and could be induced by Eps8 overexpression and CK666 treatment. Most notably, to classify them as TNTs, we demonstrated their capability to transfer both soluble cargoes and organelles, which is a defining feature of open-ended TNTs. This study marks the first demonstration of functional TNTs in a living embryo.
ESICCC as a systematic computational framework for evaluation, selection, and integration of cell-cell communication inference methods
Authors: Luo Jiaxin , Deng Minghua , Zhang Xuegong , Sun Xiaoqiang
Published: October 2023

Cell-cell communication (CCC) is critical for determining cell fates and functions in multicellular organisms. With the advent of single-cell RNA-sequencing (scRNA-seq) and spatial transcriptomics (ST), an increasing number of CCC inference methods have been developed. Nevertheless, a thorough comparison of their performances is yet to be conducted. To fill this gap, we developed a systematic benchmark framework called ESICCC to evaluate 18 ligand-receptor (LR) inference methods and five ligand/receptor-target inference methods using a total of 116 data sets, including 15 ST data sets, 15 sets of cell line perturbation data, two sets of cell type–specific expression/proteomics data, and 84 sets of sampled or unsampled scRNA-seq data. We evaluated and compared the agreement, accuracy, robustness, and usability of these methods. Regarding accuracy evaluation, RNAMagnet, CellChat, and scSeqComm emerge as the three best-performing methods for intercellular ligand-receptor inference based on scRNA-seq data, whereas stMLnet and HoloNet are the best methods for predicting ligand/receptor-target regulation using ST data. To facilitate the practical applications, we provide a decision-tree-style guideline for users to easily choose best tools for their specific research concerns in CCC inference, and develop an ensemble pipeline CCCbank that enables versatile combinations of methods and databases. Moreover, our comparative results also uncover several critical influential factors for CCC inference, such as prior interaction information, ligand-receptor scoring algorithm, intracellular signaling complexity, and spatial relationship, which may be considered in the future studies to advance the development of new methodologies.
Light-load performance optimization for LLC resonant converter
Authors: Yao Xuliang , Han Xiao , Liao Yuefeng , Wang Jingfang
Published: October 2023

Purpose

This study aims to solve the problem that under light-load conditions, the output voltage regulation capability is lost due to the fact that the voltage gain of the LLC resonant converter does not decrease with the increase of the switching frequency.

Design/methodology/approach

In this paper, the impedance model considering the parasitic parameters of the primary and secondary sides is calculated under light-load conditions, the limitations of the previous method are explained and a new circuit improvement is proposed.

Findings

In this paper, an improved circuit is proposed, and the impedance Bode plot is used to verify that the circuit can effectively improve the voltage gain problem under light-load conditions. Finally, the experimental results verify the effectiveness of the proposed circuit through comparison with traditional solutions and circuits.

Originality/value

In this paper, the impedance model considering the parasitic parameters of the primary and secondary sides is calculated, the limitations of the previous method are explained and a new circuit improvement is proposed. When compared with the previous method, the proposed circuit improvement can suppress the voltage gain increase that occurs when the switching frequency increases to a certain level.
Mirroring digital content marketing framework: capturing providers’ perspectives through stimuli assessment and behavioural engagement response
Authors: Filipovic Jelena , Arslanagic-Kalajdzic Maja
Published: October 2023

Purpose

This study aims to propose a novel mirroring digital content marketing (MDCM) framework that extends the current consumer-based digital content marketing (DCM) framework to encompass the provider’s perspective. Relying on the stimulus–organism–response theory, the authors posit that content stimuli influence behavioural engagement responses that, respectively, mirror the motives and self-reported engagement from the consumer-based DCM.

Design/methodology/approach

To empirically verify the provider side of the MDCM framework, the authors used one newsletter and one matching website with corresponding 117 weekly data points. Data were drawn from three sources for six countries: newsletter content stimuli, newsletter performance indicators and Google Analytics metrics on matching website performance. OLS and panel regressions were used to analyse the data and generate results.

Findings

The results show that content stimuli do explain the behavioural engagement responses of consumers recorded by the provider. However, the effects of the different stimuli are inconsistent: functional stimuli have both positive and negative effects, while social stimuli positively impact the behavioural engagement response. The authors further show that the newsletter engagement response influences subsequent engagement responses across channels (e.g. via the linked news media website).

Research limitations/implications

Further research definitely needs to empirically verify the connection between two sides of the MDCM framework. As proposed by authors, provider-based stimuli are corresponding to the consumer-based motivations, however, which stimuli are triggering which motivations and how they can consequently be translated to both consumer- and provider-based behavioural engagement is still an open question. Different theoretical lenses could be taken in the usage of MDCM framework.

Practical implications

Our observations are relevant for marketers that want to use certain stimuli in their digital content, in particular a content introduced in the newsletter and the website. The authors show that stimuli are indeed related to the behavioural engagement response of consumers and that various stimuli impact engagement differently. Furthermore, the recommendations for the marketing managers of news media are to use priming across the platforms in their Web communication strategies.

Originality/value

This study proposes and empirically tests the provider side of the MDCM framework across two news media channels, focusing on behavioural engagement responses.
Speak up to speed up innovation: servant leadership triggered innovative work behavior mediated through voice behavior
Authors: Khan Muhammad Mumtaz , Mubarik Muhammad Shujaat , Ahmed Syed Saad , Islam Tahir
Published: October 2023

Purpose

This study aims to unfurl the mediating role of facets of voice behavior. The study also unearths the relationship between servant leadership and voice behavior.

Design/methodology/approach

The data were collected from follower manager dyads in two waves of data collection initiated after the completion of the preceding wave. The final sample size obtained was 312.

Findings

The study found servant leadership to be related to innovative work behavior and facets of voice behavior. The study also found promotive voice behavior and preventive voice behavior to be related to the innovative work behavior of employees. The study found promotive voice behavior and prohibitive voice behavior work as parallel mediators linking servant leadership to the innovative work behavior of employees.

Originality/value

To the best of the authors’ knowledge, this study is the first to unearth mediation linking servant leadership to innovative work behavior through both facets of voice behavior.