bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ethosuximide: subunit- and Gβγ-dependent blocker and reporter of allosteric changes in GIRK channels
Authors: Shalomov Boris , Friesacher Theres , Yakubovich Daniel , Combista J. Carlo , Reddy Haritha P. , Dabbah Shoham , Bernsteiner Harald , Zangerl-Plessl Eva-Maria , Stary-Weinzinger Anna , Dascal Nathan 
Published: June 2024

AbstractThe antiepileptic drug ethosuximide (ETX) suppresses epileptiform activity in a mouse model ofGNB1syndrome, caused by mutations in Gβ1protein, likely through the inhibition of G-protein gated K+(GIRK) channels. Here we show that ETX is a subunit-selective, allosteric blocker of GIRKs. The potency of ETX block is increased by the G protein subunit dimer Gβγ, the physiological activator of GIRKs. Molecular dynamics (MD) simulations and mutagenesis locate the ETX binding site in GIRK2 to a region associated with phosphatidylinositol-4,5-bisphosphate (PIP2) regulation, and suggest that ETX acts by closing the HBC gate and altering channel’s interaction with PIP2. The apparent affinity of ETX block is highly sensitive to changes in channel gating caused by mutations in Gβ1or GIRK subunits. Our findings pose GIRK as a potential therapeutic target for ETX, and ETX as a potent allosteric GIRK blocker and a tool for probing gating-related conformational changes in GIRK.
Uncovering nitroxoline activity spectrum, mode of action and resistance across Gram-negative bacteria
Authors: Cacace Elisabetta , Tietgen Manuela , Steinhauer Meike , Mateus André , Schultze Tilman G. , Eckermann Marina , Galardini Marco , Varik Vallo , Koumoutsi Alexandra , Parzeller Jordan J. , Corona Federico , Orakov Askarbek , Knopp Michael , Brauer-Nikonow Amber , Bork Peer , Romao Celia V. , Zimmermann Michael , Cloetens Peter , Savitski Mikhail M. , Typas Athanasios , Göttig Stephan 
Published: June 2024

AbstractNitroxoline is a bacteriostatic quinoline antibiotic, considered a metal chelator inhibiting the activity of RNA-polymerase1. Its clinical indications are limited to uncomplicated urinary tract infections (UTIs), with a clinical susceptibility breakpoint only available forEscherichia coli2. By testing > 1,000 clinical isolates, here we demonstrate a much broader activity spectrum and species-specific bactericidal activity, including multidrug-resistant Gram-negative bacteria for which therapeutic options are limited due to resistance. By combining systematic genetic and proteomic approaches with direct measurement of intracellular metals, we dissect nitroxoline perturbation of metal homeostasis and unveil additional effects on bacterial physiology. We show that nitroxoline affects outer membrane integrity, synergizing with large-scaffold antibiotics and resensitizing colistin-resistant Enterobacteriaceaein vitroandin vivo. We further characterise resistance mechanisms acrossE. coli,Acinetobacter baumanniiandKlebsiella pneumoniae, recapitulating knownE. coliresistance determinants and uncovering novel and conserved mechanisms across species, demonstrating their common effect on nitroxoline efflux.
Wound closure after brain injury relies on force generation by microglia in zebrafish
Authors: El-Daher Francois , Drake Louisa K. , Enos Stephen J. , Wehner Daniel , Westphal Markus , Porter Nicola J. , Becker Catherina G. , Becker Thomas 
Published: June 2024

Wound closure after a brain injury is critical for tissue restoration but this process is still not well characterised at the tissue level. We use live observation of wound closure in larval zebrafish after inflicting a stab wound to the brain. We demonstrate that the wound closes in the first 24 hours after injury by global tissue contraction. Microglia accumulation at the point of tissue convergence precedes wound closure and computational modelling of this process indicates that physical traction by microglia could lead to wound closure. Indeed, genetically or pharmacologically depleting microglia leads to defective tissue repair. Live observations indicate centripetal deformation of astrocytic processes contacted by migrating microglia. Severing such contacts leads to retraction of cellular processes, indicating tension. Weakening tension by disrupting the F-actin stabilising gene lcp1 in microglial cells, leads to failure of wound closure. Therefore, we propose a previously unidentified mechanism of brain repair in which microglia has an essential role in contracting spared tissue. Understanding the mechanical role of microglia will support advances in traumatic brain injury therapiesGraphical Abstract
Sampling bias corrections for accurate neural measures of redundant, unique, and synergistic information
Authors: Koçillari Loren , Lorenz Gabriel Matías , Engel Nicola Marie , Celotto Marco , Curreli Sebastiano , Blanco Malerba Simone , Engel Andreas K. , Fellin Tommaso , Panzeri Stefano 
Published: June 2024

AbstractShannon Information theory has long been a tool of choice to measure empirically how populations of neurons in the brain encode information about cognitive variables. Recently, Partial Information Decomposition (PID) has emerged as principled way to break down this information into components identifying not only the unique information carried by each neuron, but also whether relationships between neurons generate synergistic or redundant information. While it has been long recognized that Shannon information measures on neural activity suffer from a (mostly upward) limited sampling estimation bias, this issue has largely been ignored in the burgeoning field of PID analysis of neural activity. We used simulations to investigate the limited sampling bias of PID computed from discrete probabilities (suited to describe neural spiking activity). We found that PID suffers from a large bias that is uneven across components, with synergy by far the most biased. Using approximate analytical expansions, we found that the bias of synergy increases quadratically with the number of discrete responses of each neuron, whereas the bias of unique and redundant information increase only linearly or sub-linearly. Based on the understanding of the PID bias properties, we developed simple yet effective procedures that correct for the bias effectively, and that improve greatly the PID estimation with respect to current state-of-the-art procedures. We apply these PID bias correction procedures to datasets of 53117 pairs neurons in auditory cortex, posterior parietal cortex and hippocampus of mice performing cognitive tasks, deriving precise estimates and bounds of how synergy and redundancy vary across these brain regions.
Cadmium Disrupts Blood-Testis Barrier (BTB) via An Oxidative Stress-Dependent Autophagy in Prepubertal Rats
Authors: Man Yonghong , Du Bingxue , Huang Jiaolong , Sun Yu , Liu Yunhao , Zhang Ling 
Published: June 2024

ABSTRACTBlood testis barrier (BTB) is an important target of cadmium (Cd) toxicology, but the mechanism underlying the Cd-induced impairment of BTB function remains fully elucidated. The mammalian target of rapamycin (mTOR) complex 2 (mTOR2) regulates BTB function via its effects on cellular junctions and the cytoskeleton of Sertoli cells. In this study, we investigated whether mTOR2 was involved in the effects of Cd exposure on BTB integrity. A Cd exposure modelin vivowas established in prepubertal male rats using a single intraperitoneal injection of Cadmium Chloride (CdCl2). A Cd exposure model of Sertoli cell was established using a CdCl2-treated TM4 cell line. The Acute cadmium exposure decreased the activity of mTOR2 signaling and adhesin proteins which is linked to the induction of oxidative stress-induced autophagy. In the presence of CdCl2, mTOR, the catalytic subunit of the mTOR2 complex, exhibits a reduction in levels of phosphorylation, accompanied by decreased adhesin proteins and Rictor, the key component of the mTOR2 complex. CdCl2treatment also drives a process of oxidative stress-induced autophagy, evidenced by alterations in cellular markers for oxidative stress and autophagy. Pharmaceutical inhibition of oxidative stress and/or autophagy alleviates the alternations in mTOR2 signaling and adhesin proteins upon CdCl2treatment in TM4, a Sertoli cell line. This work is the first to examine the effects of cadmium exposure on rictor/mTOR2 signaling pathways. Our results suggest that Cadmium might exert testicular toxicology via the perturbation in mTOR2 signaling, which can be associated with the cellular stress-related protolysis in Sertoli cells.
Potency, dissociation kinetics and reversibility of fentanyls and nitazenes by naloxone at the μ opioid receptor
Authors: Alhosan Norah , Cavallo Damiana , Santiago Marina , Kelly Eamonn , Henderson Graeme 
Published: June 2024

AbstractBackground and PurposeFentanyls and nitazenes are μ opioid receptor agonists responsible for a large number of opioid overdose deaths. Here, we compared the potency, dissociation kinetics and antagonism by naloxone at the μ receptor of several fentanyl and nitazene analogues and compared them to morphine and DAMGO.Experimental ApproachIn vitroassays of G protein activation and signalling and arrestin recruitment were performed. AtT20 cells expressing μ receptors were loaded with a membrane potential dye and changes in fluorescence used to determine agonist potency, dissociation kinetics and susceptibility to antagonism by naloxone. BRET experiments were undertaken in HEK293T cells expressing μ opioid receptors, to assess Gi protein activation and β-arrestin 2 recruitment.Key ResultsThe rate of agonist dissociation from the μ receptor varied, with morphine, DAMGO, alfentanil and fentanyl dissociating rapidly whereas isotonitazene, etonitazene, ohmefentanyl and carfentanil dissociated slowly. Slowly dissociating agonists were more resistant to antagonism by naloxone. For carfentanil, the slow rate of dissociation was not due to G protein receptor kinase-mediated arrestin recruitment as its rate of dissociation was not affected by inhibition of GRKs with Compound 101. Thein vitrorelative potencies of fentanyls and nitazenes compared to morphine were much lower than that previously observed inin vivoexperiments.Conclusions and ImplicationsWith fentanyls and nitazenes, that slowly dissociate from the μ opioid receptor, antagonism by naloxone is pseudo competitive. In overdoses involving fentanyls and nitazenes higher doses of naloxone may be required for reversal than those normally used to reverse heroin overdose.What is already known“Fentanyls” and “nitazenes” are potent agonists at the μ opioid receptor.What does this study addSome fentanyls and nitazenes dissociate slowly and are less sensitive to naloxone antagonismWhat is the clinical significanceMore naloxone may be required to reverse overdoses involving fentanyls and nitazenes
Reducing competition betweenmsdand genomic DNA significantly improved the editing efficiency of the retron editing system
Authors: Ni Yuyang , Wang Yifei , Shi Xinyu , Ruan Qingmin , Na Tian , He Jin , Wang Xun 
Published: June 2024

AbstractA retron is a distinct system encoding reverse transcriptase and a unique single-stranded DNA/RNA hybrid called multicopy single-stranded DNA (msDNA). The ability of msDNA to serve as a homologous recombination donor for gene editing has attracted great interest. However, the mechanism by which msDNA expression affects editing efficiency remains unclear. In this study, we show that an increase inmsdnumber increased msDNA yield but was not necessarily accompanied by an increase in editing efficiency. Mechanistic studies indicate thatmsdand genomic regions competed for msDNA during recombination. As the number ofmsdincreased, the amount of msDNA allocated to the genomic targets decreased, resulting in a decrease in editing efficiency. Finally, we reducedmsdediting by expressing msDNA corresponding to the plasmid replication leading strand sequence, thus constructing a retron-based gene editing system that achieved 100% editing efficiency in the shortest time reported to date. The above results reveal a completely different features between retron-based gene editing system and oligonucleotide-mediated gene editing system and will provide theoretical guidance for the design and application of the retron system.
Chromosome-level genome assembly of the sacoglossan sea slugElysia timida(Risso, 1818)
Authors: Männer Lisa , Schell Tilman , Spies Julia , Galià-Camps Carles , Baranski Damian , Ben Hamadou Alexander , Gerheim Charlotte , Neveling Kornelia , Helfrich Eric J. N. , Greve Carola 
Published: June 2024

AbstractBackgroundSequencing and annotating genomes of non-model organisms helps to understand genome architecture, the genetic processes underlying species traits, and how these genes have evolved in closely-related taxa, among many other biological processes. However, many metazoan groups, such as the extremely diverse molluscs, are still underrepresented in the number of sequenced and annotated genomes. Although sequencing techniques have recently improved in quality and quantity, molluscs are still neglected due to difficulties in applying standardized protocols for obtaining genomic data.ResultsIn this study, we present the chromosome-level genome assembly and annotation of the marine sacoglossan speciesElysia timida, known for its ability to store the chloroplasts of its food algae. In particular, by optimizing the Long-read and chromosome conformation capture library preparations, the genome assembly was performed using PacBio HiFi and Arima HiC data. The scaffold and contig N50s, at 41.8 Mb and 1.92 Mb, respectively, are 100-fold and 4-fold higher compared to other published sacoglossan genome assemblies. Structural annotation resulted in 19,904 protein-coding genes, which are more contiguous and complete compared to publicly available annotations of Sacoglossa. We detected genes encoding polyketide synthases inE. timida, indicating that polypropionates are produced. HPLC-MS/MS analysis confirmed the presence of a large number of polypropionates, including known and yet uncharacterised compounds.ConclusionsWe can show that our methodological approach helps to obtain a high-quality genome assembly even for a “difficult-to-sequence” organism, which may facilitate genome sequencing in molluscs. This will enable a better understanding of complex biological processes in molluscs, such as functional kleptoplasty in Sacoglossa, by significantly improving the quality of genome assemblies and annotations.
AARS2 ameliorates myocardial ischemiaviafine-tuning PKM2-mediated metabolism
Authors: Zhang Zongwang , Zheng Lixia , Chen Yang , Chen Yuanyuan , Hou Junjie , Xiao Chenglu , Zhu Xiaojun , Zhao Shi-Min , Xiong Jing-Wei 
Published: June 2024

AbstractAARS2, an alanyl-tRNA synthase, is essential for protein translation, but its function in mouse hearts is not fully addressed. Here, we found that cardiomyocyte-specific deletion of mouse AARS2 exhibited evident cardiomyopathy with impaired cardiac function, notable cardiac fibrosis and cardiomyocyte apoptosis. Cardiomyocyte-specific AARS2 overexpression in mice improved cardiac function and reduced cardiac fibrosis after myocardial infarction (MI), without affecting cardiomyocyte proliferation and coronary angiogenesis. Mechanistically, AARS2 overexpression suppressed cardiomyocyte apoptosis and mitochondrial reactive oxide species production, and changed cellular metabolism from oxidative phosphorylation toward glycolysis in cardiomyocytes, thus leading to cardiomyocyte survival from ischemia and hypoxia stress. Ribo-Seq revealed that AARS2 overexpression increased pyruvate kinase M2 (PKM2) protein translation and the ratio of PKM2 dimers to tetramers that promote glycolysis. Additionally, PKM2 activator TEPP-46 reversed cardiomyocyte apoptosis and cardiac fibrosis caused by AARS2 deficiency. Thus, this study demonstrates that AARS2 plays an essential role in protecting cardiomyocytes from ischemic pressureviafine-tuning PKM2-mediated energy metabolism, and presents a novel cardiac protective AARS2-PKM2 signaling during the pathogenesis of MI.
The genetic architecture of floral trait divergence between hummingbird- and self-pollinated monkeyflower (Mimulus) species
Authors: Chen Hongfei , Berg Colette S. , Samuli Matthew , Sotola V. Alex , Sweigart Andrea L. , Yuan Yao-Wu , Fishman Lila 
Published: June 2024

SUMMARYPollination syndromes are a key component of flowering plant diversification, prompting questions about the architecture of single traits and genetic coordination among traits. Here, we investigate the genetics of extreme floral divergence between naturally hybridizing monkeyflowersMimulus parishii(self-pollinated) andM. cardinalis(hummingbird-pollinated).We mapped quantitative trait loci (QTLs) for 18 pigment, pollinator reward/handling, and dimensional traits in parallel sets of F2hybrids plus recombinant inbred lines and generated nearly isogenic lines (NILs) for two dimensional traits, pistil length and corolla size.Our multi-population approach revealed a highly polygenic basis (n = 190 QTLs total) for pollination syndrome divergence, capturing minor QTLs even for pigment traits with leading major loci. There was significant QTL overlap within pigment and dimensional categories. Nectar volume QTLs clustered with those for floral dimensions, suggesting a partially shared module. The NILs refined two pistil length QTLs, only one of which has tightly correlated effects on other dimensional traits.An overall polygenic architecture of floral divergence is partially coordinated by genetic modules formed by linkage (pigments) and likely pleiotropy (dimensions plus nectar). This work illuminates pollinator syndrome evolution in a model radiation and generates a robust framework for molecular and ecological genomics.
Extremely charged coral protein AGARP regulates calcium carbonate growth through liquid phase separation
Authors: Klepka Barbara P. , Michaś Agnieszka , Wojciechowski Tomasz , Niedźwiecka Anna 
Published: June 2024

AbstractBiomineralizationviathe non-classical crystallization pathway is postulated to involve a transient liquid phase of calcium carbonate formed in the presence of polymers. In the context of coral biocalcification, these polymers may include coral acid-rich proteins (CARPs), secreted into the skeletal organic matrix. However, direct evidence for the existence of this liquid phase with proteins is lacking. Here we report the properties of the intrinsically disordered aspartic and glutamic acid-rich protein (AGARP), which is the first CARP cloned from one of the most studied scleractinian coral of the Great Barrier Reef,Acropora millepora, a model species for biomineralization and ecological studies. We show that AGARP can significantly influence early stages of CaCO3nucleation and crystal growth through liquid-liquid phase separation. Consequently, we introduce the concept of a biologically relevant crystallization precursor, a liquid protein-calcium condensate composed of CARP molecules and Ca2+ions, that forms as a result of liquid phase separation in a viscous, crowded environment. Our work bridges the gap between the liquid phase separation and biomineralization research.
Human left ventricle circRNA-miRNA-mRNA network analyses reveals a novel proangiogenic role for circNPHP1 under ischemic conditions
Authors: Anwar Maryam , Sarkar Moumita , Ford Kerrie , Angelini Gianni D , Punjabi Prakash , Laftah Abas , Chamorro-Jorganes Aránzazu , Ji Jiahui , Srivastava Prashant K , Petretto Enrico , Emanueli Costanza 
Published: June 2024

ABSTRACTBackgroundIschemic heart disease (IHD) is characterized by insufficient myocardial blood flow in the left ventricle and aggravated by diabetes mellitus. Endothelial resilience and reparative angiogenesis are tightly controlled processes. Gene expression is regulated by multimodal interactions between RNA species. Circular RNAs (circRNAs) can sponge microRNAs (miRNAs) to reduce the repressive effects of miRNAs on its messenger RNA (mRNAs) targets.MethodsLeft ventricle whole RNA-sequencing (circRNAs, mRNAs) and small RNA- sequencing (miRNAs) datasets were obtained from 3 patient groups: IHD with/out T2DM and controls (N=11 to 12/group) as part of a prospective observational cardiac surgery study.The interactions between differentially expressed (DE) circRNAs, miRNA and mRNAs were identified with a customized bioinformatics pipeline. The emerging networks were screened using endothelial-specific RNA-sequencing datasets from GEO resulting in EC-rich networks. CircRNAs from these networks were subsequently screened (RT-PCR) in endothelial cells (ECs) exposed to disease-mimicking conditions vs control. Afterwards, circRNA pulldown allowed to interrogate the circRNA-miRNAs interactome in ECs. EC biology assays using loss-of-function and gain-of-function approaches corroborated the study.ResultsWe identified novel circRNA-miRNA-mRNA interactions in the human diseased heart. CircNPHP1, which is upregulated in IHD with/out Type-2 diabetes mellitus (T2DM), sponges miR-221-3p to de-repress VEGF-A and BCL2, increasing the angiogenic capacity of ECs under disease and disease-mimicking conditions.ConclusionsThe interactions between individual members of different RNA species are affected by IHD. The therapeutic value of circNPHP1/miR-221-3p axis could be further investigated.Visual AbstractHighlightsWe found a novel circRNA-miRNA-mRNA network in IHD and Type 2 diabetes.CircNPHP1 regulates angiogenesis and proliferation in the cardiac ECs exposed to conditions mimicking IHD and Type 2 diabetes.We elucidated a novel pro-angiogenic subnetwork commanded by circNPHP1/miR-221-3p/BCL2/VEGFA.We identified circNPHP1 as a potential new target for therapeutic angiogenesis.
Distinct computational mechanisms of uncertainty processing explain opposing exploratory behaviors in anxiety and apathy
Authors: Yan Xinyuan , Ebitz R. Becket , Grissom Nicola , Darrow David P. , Herman Alexander B. 
Published: June 2024

AbstractDecision-making in uncertain environments often leads to varied outcomes. Understanding how individuals interpret the causes of unexpected feedback is crucial for adaptive behavior and mental well-being. Uncertainty can be broadly categorized into two components: volatility and stochasticity. Volatility is about how quickly conditions change, impacting results. Stochasticity, on the other hand, refers to outcomes affected by random chance or “luck”. Understanding these factors enables individuals to have more effective environmental analysis and strategy implementation (explore or exploit) for future decisions. This study investigates how anxiety and apathy, two prevalent affective states, influence the perceptions of uncertainty and exploratory behavior. Participants (N = 1001) completed a restless three-armed bandit task that was analyzed using latent state models. Anxious individuals perceived uncertainty as more volatile, leading toincreasedexploration and learning rates, especially after reward omission. Conversely, apathetic individuals viewed uncertainty as more stochastic, resulting indecreasedexploration and learning rates. The perceived volatility-to-stochasticity ratio mediated the anxiety-exploration relationship post-adverse outcomes. Dimensionality reduction showed exploration and uncertainty estimation to be distinct but related latent factors shaping a manifold of adaptive behavior that is modulated by anxiety and apathy. These findings reveal distinct computational mechanisms for how anxiety and apathy influence decision-making, providing a framework for understanding cognitive and affective processes in neuropsychiatric disorders.