bluuebunny/crossref_metadata_2025 huggingface dataset:
AlphaRING: Missense Variant Classification via Protein Modelling and Residue Interaction Network Analysis
Authors: Logsdon Aaron , Safari Roghaiyeh , Barnard Anna , Maertens Goedele , Bellos Evangelos
Published: November 2024

Recent advancements in protein modelling, particularly with AlphaFold, have opened new avenues for assessing the structural impacts of missense variants on protein function. Tools like AlphaMissense leverage AlphaFold2 to predict missense variant pathogenicity with state-of-the-art performance. However, AlphaMissense is deep learning-based, and its process to predict pathogenicity is opaque and does not explicitly predict the impact of missense variants based on additional biophysical properties. Additionally, AlphaMissense is not publicly available, limiting accessibility. Here, we present AlphaRING, a publicly available tool that leverages AlphaFold2 and captures real physico-chemical properties of variant residues to predict the pathogenicity of both characterised and uncharacterised missense variants. AlphaRING models wild-type and variant proteins using AlphaFold2 and identifies atomic-level non-covalent interactions via residue interaction network analysis using RING4. Unlike deep learning models, our scoring captures real physico-chemical properties of mutated residues, providing interpretable insights into mutation effects. We developed novel formulas for each non-covalent bond type (hydrogen, ionic, π-cation, π-π stacking, and π-hydrogen), incorporating bond-specific energy and geometry values to calculate unique weighting scores per residue. The absolute log2fold change between wild-type and variant residue scores yields a non-negative AlphaRING score—the higher the score, the greater the predicted pathogenicity. Evaluating AlphaRING on over 1,300 human gold-standard missense variants curated by ClinVar expert panels, our results show effective distinction between benign and pathogenic variants, with a receiver operating characteristic area under the curve of 0.79. This strong performance suggests that AlphaRING is a reliable, open-source tool suitable for high-throughput structural predictions and large-scale variant characterisation, accessible to non-experts. By enabling detailed exploration of the relationship between genetic variation and protein structure, AlphaRING addresses key limitations of previous models and paves the way for broader applications in genetic research and precision medicine.
Chemogenetic Breakdown of the Dentate Gate Causes Seizures and Spatial Memory Deficits
Authors: Adam Christopher D. , Schellinger Emily D. , White Alicia , Joksimovic Srdjan M. , Takano Hajime , Coulter Douglas A.
Published: November 2024

The dentate gyrus has often been posited to act as a gate that dampens highly active afferent input into the hippocampus. Effective gating is thought to prevent seizure initiation and propagation in the hippocampus and support learning and memory processes. Pathological changes to DG circuitry that occur in temporal lobe epilepsy (TLE) can increase DG excitability and impair its gating ability which can contribute to seizures and cognitive deficits. There is evidence that TLE pathologies and seizures may independently contribute to learning and memory deficits in TLE through distinct mechanisms. These two factors are difficult to untangle since TLE pathologies can drive seizures, and seizures can worsen TLE pathologies. Here we assessed whether chemogenetically increasing dentate granule cell (DGC) excitability was enough to break down the dentate gate in the absence of TLE pathologies. We found that increasing excitability specifically in DGCs caused seizures in non-epileptic mice. Importantly, due to the modulatory nature of DREADD effects, seizures were driven by intrinsic circuit activity rather than direct activation of DGCs. These seizures resulted in a spatial memory deficit when induced after training in the spatial object recognition task and showed stereotypical patterns of activity in miniscope calcium recordings. Our results provide direct support for the dentate gate hypothesis since seizures could be induced in non-epileptic animals by artificially degrading the dentate gate with chemogenetics in the absence of epilepsy pathologies.
DreaM: A Computational Pipeline for Enhanced Short-Read Sequence Analysis in Repetitive Genomic Regions
Authors: Kumar Santosh , Esashi Fumiko
Published: November 2024

Mapping short sequencing reads to repetitive genomic regions, such as centromeres, presents significant challenges, primarily due to PCR duplicates, which can be erroneously mapped multiple times within these regions. Conventional bioinformatics pipelines often overlook this issue, potentially leading to misinterpretation as signal enrichment. To address this, we developedDreaM(Deduplication of Reads for Enhanced and Accurate Mapping), a computational pipeline that prioritises the preprocessing of raw sequencing data. DreaM firstly identifies and removes PCR duplicates, which is followed by read trimming to reduce noise from multiply mapped reads. When applied to ChIP-Seq and CUT&RUN datasets targeting CENP-A, a key marker of centromeres, DreaM demonstrated improved peak detection within centromeres. Overall, DreaM provides a robust solution for enhancing the analysis of DNA-protein binding sites in repetitive genomic regions using short-read sequencing.
Sox9 and Nfi transcription factors regulate the timing of neurogenesis and ependymal maturation in dopamine progenitors
Authors: Lahti Laura , Volakakis Nikolaos , Gillberg Linda , Salmani Behzad Yaghmaeian , Tiklová Katarína , Kee Nigel , Lundén-Miguel Hilda , Piper Michael , Gronostajski Richard , Perlmann Thomas
Published: November 2024

Correct timing of neurogenesis is critical for both generating the correct number and subtypes of glia and neurons in the embryo, as well as preventing tumours and the depletion of stem cell pools in the adults. Here we analyse how the midbrain dopamine neuron (mDA) progenitors transition into cell cycle arrest (G0) and begin to mature into ependymal cells. The comparison of mDA progenitors from different embryonic stages revealed the upregulation ofNfiandSox9transcription factors during development. Their conditional inactivation in the early embryonic midbrain leads to delayed G0 entry and ependymal maturation, reduced gliogenesis, and increased generation of neurons, including mDA neurons. In contrast, their inactivation in late embryogenesis does not result in mitotic re-entry, suggesting that these factors are necessary for the G0 induction, but not for its maintenance. Our characterisation of mDA-progenitor-derived adult ependymal cells by single-cell RNA sequencing and histology show that they both retain several progenitor features but also secrete neuropeptides and contact neighbouring cells and blood vessels, indicating that these cells may form a novel part of the circumventricular organ system.
Multimodal investigation of the neurocognitive deficits underlying dyslexia in adulthood
Authors: Cristina Cara , Giulia Zantonello , Marta Ghio , Marco Tettamanti
Published: November 2024

Dyslexia is a neurobiological disorder characterised by reading difficulties, yet its underlying causes remain unclear. Neuroimaging and behavioural studies found anomalous responses in tasks requiring phonological processing, motion perception, and implicit learning, and showed gray and white matter abnormalities in several brain regions of dyslexics compared to controls, indicating that dyslexia is a heterogeneous condition and promoting a multifactorial approach. In order to evaluate whether the combination of behavioural and multimodal MRI can have greater sensitivity in identifying neurocognitive traits of dyslexia compared to monocomponential approaches, in 19 dyslexic and 19 control subjects we acquired behavioural cognitive assessments, multiple (phonological, visual motion, rhythmic) mismatch-response functional MRI tasks, structural diffusion-weighted and T1-weighted images. To examine between-group differences in the multimodal neurocognitive measures, we applied univariate and multivariate approaches. Results showed that dyslexics performed worse than controls in behavioural phonological tasks. Neuroimaging analyses revealed that individuals with dyslexia present reduced cerebellar responses to mismatching rhythmic stimuli, as well as structural disorganization in several white matter tracts and cortical regions previously implicated in dyslexia. Most importantly, in line with the view of dyslexia as a multifactorial phenomenon, a machine learning model trained with features from all three MRI modalities (functional, diffusion, and T1-weighted) discriminated between dyslexics and controls with greater accuracy than models including just one modality. The individual classification scores in the multimodal machine learning model correlated with behavioural reading accuracy. These results confirm that dyslexia should be approached as a composite condition characterised by multiple distinctive cognitive and brain features.
Transferrin receptor-mediated transport at the blood-brain barrier is elevated during early development but maintained across adult aging
Authors: Torres Vanessa O. , Pizzo Michelle E. , Chan Darren , Dugas Jason C. , Huynh David , Joy David , Liang Eric K. , Sarrafha Lily , Becerra Isabel , Chau Roni , Chew Kylie S. , Chow Johann , Earr Timothy K. , Khoury Nathalie , Lechtenberg Kendra J. , Leung Amy W. , Nguyen Hoang N. , Ojo Emmanuel S. , Roche Elysia , Solanoy Hilda , Tong Mabel , Tong Raymond K. , Henne Kirk , Lewcock Joseph W. , Watts Ryan J. , Calvert Meredith E. , Thorne Robert G. , Zuchero Y. Joy Yu
Published: November 2024

Transferrin receptor (TfR)-mediated transcytosis across the blood-brain barrier (BBB) is a promising strategy to improve delivery of biologics to the central nervous system (CNS). However, it remains unclear whether age and aging-related diseases impact TfR expression and/or BBB transport capacity. Here, we used the TfR-targeted antibody transport vehicle (ATVTfR) to enhance CNS delivery in healthy mice and in the 5xFAD mouse model of Alzheimer’s disease (AD). Healthy neonates exhibited the highest vascular TfR expression and ATVTfRbrain exposure, whereas BBB transport capacity remained stable across adulthood. Additionally, neither TfR expression nor ATVTfRbrain uptake changed significantly in 5xFAD mice. Further, vascular TfR expression in AD patient brains was similar to age-matched controls, suggesting that TfR transport may be conserved for AD in humans. The elevated TfR-mediated brain delivery observed in early mouse development suggests the potential of added efficacy in utilizing TfR platforms for the treatment of early childhood diseases. Preservation of ATVTfRtransport in adult mice across healthy aging and in an AD model supports continued application of TfR platforms in age-related diseases.
Deep Neural Networks Explain Spiking Activity in Auditory Cortex
Authors: Ahmed Bilal , Downer Joshua D. , Malone Brian J. , Makin Joseph G.
Published: November 2024

For static stimuli or at gross (∼1-s) time scales, artificial neural networks (ANNs) that have been trained on challenging en gineering tasks, like image classification and automatic speech recognition, are now the best predictors of neural responses in primate visual and auditory cortex. It is, however, unknown whether this success can be extended to spiking activity at fine time scales, which are particularly relevant to audition. Here we address this question with ANNs trained on speech audio, and acute multi-electrode recordings from the auditory cortex of squirrel monkeys. We show that layers of trained ANNs can predict the spike counts of neurons responding to speech audio and to monkey vocalizations at bin widths of 50 ms and below. For some neurons, the ANNs explain close to all of the explain able variance—much more than traditional spectrotemporal– receptive-field models, and more than untrained networks. Non-primary neurons tend to be more predictable by deeper layers of the ANNs, but there is much variation by neuron, which would be invisible to coarser recording modalities.
The Glutamatergic Projection from the Substantia Nigra Pars Reticulata to the Dorsal Raphe Nucleus Facilitates Social Hierarchy in Mice
Authors: Fan Yanzhu , Ge Shaoxiang , Lu Lidi , Niu Wenjun , Wang Zhiyue , Jiao Xiaoguo , Fang Guangzhan
Published: November 2024

Social hierarchy constitutes a fundamental organizational characteristic among various social species, significantly influencing individual survival, health, and reproductive success within these societies. Neurons in the substantia nigra pars reticulata (SNr) exhibit extensive connectivity with the dorsal raphe nucleus (DRN), a critical structure implicated in social interaction, reward processing, and the establishment of social rank. However, the specific neuronal types within the SNr, as well as the associated neural circuits that regulate social dominance, remain inadequately characterized. This study aims to elucidate the crucial role of SNr glutamatergic neurons in the establishment and maintenance of social hierarchy in mice. Employing fiber photometry, we observed that the activation of SNr glutamatergic neurons increased during the initiation of effortful behaviors in the tube test. Further investigations revealed that optogenetic activation or chemogenetic inhibition of the glutamatergic neural circuit connecting the SNr to the DRN induced upward or downward shifts in social ranks, respectively. Additionally, our findings indicate that the activation of SNr glutamatergic terminals in the DRN reduces anxiety levels in mice. Collectively, these results underscore the critical role of the glutamatergic pathway from the SNr to the DRN in regulating social hierarchy. This work enhances our understanding of the functions of SNr glutamatergic neurons in both physiological contexts and neurological disorders.
Risk factors for invasive Group A Streptococcal infection in children aged 6 months to 5 years, a case-control study, the Netherlands, February-May 2023
Authors: Hazelhorst Elizabeth I , van Ewijk Catharina E , Wielders Cornelia CH , te Wierik Margreet JM , Hahné Susan JM , de Melker Hester E , Knol Mirjam J , de Gier Brechje
Published: November 2024

In 2022, an increase in invasive Group A Streptococcal infections (iGAS) was observed in the Netherlands. A particular increase was seen among children, therefore we aimed to assess risk factors for iGAS in children aged 6 months to 5 years. A prospective case-control study was conducted between February and May 2023. We approached parents of notified iGAS cases to complete a questionnaire on exposures during 4 weeks prior to disease onset. Controls were recruited via social media and matched to cases (10:1) on sex and birthyear. Conditional logistic regression was performed to estimate odds ratios (OR) of exposures. For the analysis we included 18 cases and 103 controls. Varicella prior to onset of iGAS disease was reported in 2 (11%) cases and 1 (1%) control (OR: 12.0, 95% CI: 1.1-139.0). Exposure to GAS-like illnesses impetigo, pharyngitis and scarlet fever was reported in 8 (44%) cases and 15 (15%) controls (OR: 7.1, 95% CI: 1.8-29.0). Our findings are in line with previous studies by identifying varicella as a risk factor for iGAS among young children and highlight the association with non-invasive GAS infections in the community as a possible source of transmission.
Reducing phytate, an antinutritional factor, in sorghum dough using phytase-expressingSaccharomyces cerevisiae
Authors: Kale Tanaya , Kamble Rutuja , Pawar Aditi , Dawankar Sahil , Reshamwala Shamlan M. S.
Published: November 2024

Phytate, a major antinutritional factor present in millets and legumes, chelates minerals like calcium, iron and zinc leading to their poor bioavailability. Phytase fromAspergillus japonicuswas expressed extracellularly inSaccharomyces cerevisiaeand its ability to reduce phytate in sorghum flour was determined. When theA. japonicusphytase-expressing strain was used to ferment sorghum dough, phytate reduction increased by 43% as compared to control strain. This approach of simultaneous proofing and phytate reduction can be used to increase micronutrient availability of non-wheat food products.
Interactions established by isoform-specific TrkB-T1 sequences govern inflammatory response and neurotoxicity in stroke
Authors: Ugalde-Triviño Lola , Tejeda Gonzalo S. , Esteban-Ortega Gema M. , Díaz-Guerra Margarita
Published: November 2024

Ugalde-Triviño et al. develop cell-penetrating peptides derived from neurotrophin receptor TrkB-T1 to identify isoform-specific protein interactions and demonstrate protective effects on neuroinflammation and neurotoxicity reducing brain damage in a mice model of ischemic stroke, of relevance to human therapy.

Glia reactivity, neuroinflammation and excitotoxic neuronal death are central processes to ischemic stroke and neurodegenerative diseases, altogether a leading cause of death, disability, and dementia. Due to the high incidence of these pathologies and the lack of efficient treatments, it is a priority developing brain protective therapies impacting both neurons and glial cells. Truncated neurotrophin receptor TrkB-T1, a protein produced by all these cells, plays relevant roles in excitotoxicity and ischemia. We have hypothesized that interactions established by isoform-specific TrkB-T1 sequences might be relevant to neurotoxicity and/or reactive gliosis and, therefore, constitute a therapeutic target. We identify here the TrkB-T1-specific interactome, poorly described to date, and demonstrate that interference of these protein-protein interactions using brain-accessible TrkB-T1-derived peptides can prevent reactive gliosis and decrease excitotoxicity-induced damage in cellular and mouse models of stroke. The pivotal role played by TrkB-T1 on microglia and astrocyte reactivity suggests that isoform-derived peptides could become important in development of therapies for human stroke and other excitotoxicity-associated pathologies.
Conservation ofcis-regulatory codes over half a billion years of evolution
Authors: Ogawa Yohey , Liu Yu , Myers Connie A. , Morshedian Ala , Fain Gordon L. , Sampath Alapakkam P. , Corbo Joseph C.
Published: November 2024

The identification of homologous cell types across species represents a crucial step in understanding cell type evolution. The retina is particularly amenable to comparative analysis because the basic morphology, connectivity, and function of its six major cell classes have remained largely invariant since the earliest stages of vertebrate evolution. Here, we show that the retina’s highly conserved cellular architecture is mirrored by deep conservation of the underlyingcis-regulatory codes that control gene expression. We use comparative single-cell chromatin accessibility analysis of lamprey, fish, bird, and mammalian retinas— representing over half a billion years of evolutionary divergence—to demonstrate cross-species conservation ofcis-regulatory codes in all six retinal cell classes. This conservation persists despite extensive turnover ofcis-regulatory regions between distant species. Conservation manifests as the clustering of multiple distinct high-affinity transcription factor (TF) binding sites toward the center of cell-class-specific open chromatin regions with little cross-species preservation of higher-order syntax. Hierarchical clustering of machine-learning models of retinalcis-regulatory codes from diverse species recovers six clusters corresponding to the six retinal cell classes. Thus, the retina’s cellularBauplanis controlled bycis-regulatory codes which predate the divergence of extant vertebrates and persist despite nearly complete enhancer turnover.
Smc5/6 association with microtubules controls dynamic pericentromeric chromatin folding
Authors: Carré-Simon Ànnia , Batrin Renaud , Isler Sarah , Dahl Pinholt Henrik , Földes Timothy , Laflamme Guillaume , Barbi Maria , Mirny Leonid , D’Amours Damien , Fabre Emmanuelle
Published: November 2024

Centromeres and pericentromeres are specialized chromatin regions whose organization is critical for proper chromosome segregation through dynamic microtubule attachment. Smc5/6, highly enriched in pericentromeres, associates with microtubules. However, whether Smc5/6 contributes to chromatin folding and dynamics in these regions remains unclear. Here, we dissect Smc5/6 function at budding yeast centromeres by constructingsmc5-2KE,a separation-of-function mutant that reduces microtubule binding by replacing two lysines (K624 and K631) at the Smc5 hinge with glutamic acid. After demonstrating reduced microtubule binding bysmc5-2KE in vitro, we use high temporal resolution imaging in living cells and polymer modeling to show that Smc5/6 and microtubule binding restricts chromatin dynamics along chromosome arms, thus contributing to pericentromeric chromatin folding. Thesmc5-2KEmutant shows a strong pericentromere-specific reduction in homologous recombination repair, as well as defects in mitotic spindle length, centromere clustering and cytokinesis. Overall, our results reveal that Smc5/6-microtubule association ensures robust pericentromeric chromatin folding, contributing to genome integrity in the face of mitotic forces.
Upstream open reading frames buffer translational variability duringDrosophilaevolution and development
Authors: Sun Yuanqiang , Duan Yuange , Gao Peixiang , Liu Chenlu , Jin Kaichun , Dou Shengqian , Tang Wenxiong , Zhang Hong , Lu Jian
Published: November 2024

Protein abundance tends to be more evolutionarily conserved than mRNA levels both within and between species, yet the mechanisms underlying this phenomenon remain largely unknown. Upstream open reading frames (uORFs) are widespreadcis-regulatory elements in eukaryotic genomes that regulate translation, but it remains unclear whether and how uORFs contribute to stabilizing protein levels. In this study, we performed ribosome translation simulations on mRNA to quantitatively assess the extent to which uORF translation influences the translational variability of downstream coding sequences (CDS) across varying contexts. Our simulations revealed that uORF translation dampens CDS translational variability, with buffering capacity increasing in proportion to uORF efficiency, length, and number. We then compared the translatomes at different developmental stages of twoDrosophilaspecies, demonstrating that uORFs buffer mRNA translation fluctuations during both evolution and development. Experimentally, deleting a uORF in thebcdgene—a prominent example of translational buffering—resulted in extensive changes in gene expression and phenotypes inDrosophila melanogaster. Additionally, we observed uORF-mediated buffering between primates and within human populations. Together, our results reveal a novel regulatory mechanism by which uORFs stabilize gene translation during development and across evolutionary time.
ABA increases fatty acids levels in apple roots to boost colonization by arbuscular mycorrhizal fungi
Authors: Jing Shan , Li Mingjun , Zhu Lingcheng , Li Chunhui , Li Yuchao , Du Lijun , Wei Xiaoyu , Zhang Manrang , Ma Baiquan , Ruan Yongling , Ma Fengwang
Published: November 2024

The roots of most land plants are in symbiosis with arbuscular mycorrhizal (AM) fungi. The fungus promotes nutrient uptake from the soil while receiving plant photosynthate as lipids and sugars. Nutrient exchange must be regulated by both partners, but the mechanisms underlying the regulation of lipid supplement from the plant to the AM fungus remain elusive. Here, we conducted a molecular study on the role of increased abscisic acid (ABA) levels during AM fungus infection in the roots of apple (Malusspp.). AM fungus induced the expression of two ABA synthesis genes,MdNCED3.1and3.2, in apple roots and increased the ABA content, which promoted the growth of the AM fungus. The effect of ABA on symbiosis was confirmed in transgenic apple roots either overexpressing or silencingMdNCED3.1orMdNCED3.2. Transcriptome analysis and transgenic manipulation revealed that the transcription factor MdABF2 played a key role in the ABA-mediated formation of symbiosis during AM infection and that MdABF2 could regulate the expression levels of genes related to fatty acid (FA) synthesis (e.g.,MdKASIII) and translocation (such asMdSTR2) in apple roots. Activation of these genes boosted the levels of available fatty acids in the roots and increased the AM fungal colonization and arbuscule development in the roots. These results revealed a molecular pathway in which positive regulation of FA synthesis and transport by the ABA signaling pathway increases supplementation to AM fungi and promotes AM symbiosis.
Regulatory plasticity of the human genome
Authors: Srivastava Jaya , Ovcharenko Ivan
Published: November 2024

Evolutionary turnover in non-coding regions has driven phenotypic divergence during past speciation events and continues to facilitate environmental adaptation through variants. We used a deep learning model to identify the substrates of regulatory turnover using genome wide mutations mimicking three evolutionary pathways: recent history (human-chimp substitutions), modern population (human population variation), and mutational susceptibility (random mutations). We observed enhancer turnover in approximately 6% of the whole genome, with more than 80% of the novel activity arising from repurposing of enhancers between cell-types. Frequency of turnover in a cell-type is remarkably similar across the three pathways, despite only ∼19% overlap in the source regions. The enhancers predisposed to turnover display reduced evolutionary constraints and are depleted in GWAS variants. Most of these occur within 100kb of a gene, with the highest turnover occurring near neurodevelopmental genes including CNTNAP2, NPAS3, and AUTS2. Flanking enhancers of these genes undergo high turnover irrespective of the mutational model pathway, suggesting a high plasticity in neurocognitive evolution. Based on susceptibility to random mutations, these enhancers were identified as vulnerable by nature and feature a higher abundance of cell type-specific transcription factor binding sites (TFBSs). Our findings suggest that enhancer repurposing within vulnerable loci drives regulatory innovation while keeping the core regulatory networks intact.
Older is Order: Entropy reduction in cortical spontaneous activity marks healthy aging
Authors: Chang Da , Wang Xiu , Chen Yaojing , Han Zhuo , Liu Bing , Zhang Zhanjun , Zuo Xi-Nian
Published: November 2024

Entropy trajectories remain unclear for the aging process of human brain system due to the lacking of longitudinal neuroimaging resource. We used open data from an accelerated longitudinal cohort (PREVENT-AD) that included 24 healthy aging participants followed by 4 years with 5 visits per participant to establish cortical entropy aging curves and distinguish with the effects of age and cohort. This reveals that global cortical entropy decreased with aging, while a significant cohort effect was detectable that people who were born earlier showed higher cortical entropy. Such entropy reductions were also evident for large-scale cortical networks, although with different rates of reduction for different networks. Specifically, the primary and intermediate networks reduce their entropy faster than the higher-order association networks. We conclude two specific characteristics of the entropy of the human cortex with aging: the shift of the complexity hierarchy and the diversity of complexity strengthen.
Calcium signalling is required for anterior patterning in the mouse embryo
Authors: Stower Matthew J. , Tyser Richard C. V. , Thowfeequ Shifaan , Zhou Felix , Portela Marta , Miti Konstantinos , Sugnaseelan Jacintha , Lu Xin , Srinivas Shankar
Published: November 2024

Anterior-Posterior axis formation in the mouse embryo requires the active migration of the DVE cell population at E5.5. While intracellular Ca2+signalling has been shown to control cell migration in multiple cell contexts, it is unknown whether it is required for DVE migration. The pattern of Ca2+activity in the mouse embryo at early peri-implantation stages is also unknown. Using the GCaMP6f Ca2+reporter line we performed a detailed assessment of Ca2+dynamics between E0.5 – E5.5 using live imaging. We find that prior to implantation, Ca2+transients are rare, but at E5.5 widespread, periodic, Ca2+transients in extra-embryonic tissues can be observed, including in the VE and ExE. In contrast, cells of the E5.5 epiblast remain relatively quiescent but show sporadic large-scale multi-cellular waves. Inhibition of SERCA at E5.5 abolishes Ca2+transients and leads to DVE arrest, indicative that these transients are required for axial patterning. Together these results reveal the pattern of Ca2+handling in the early mouse embryo and a novel requirement in anterior-posterior axis formation.
AGAPE (computAtional G-quadruplex Affinitiy PrEdiction): The first AI In-silico workflow for G-quadruplex binding affinity prediction
Authors: D’anna Luisa , Perricone Ugo , De Simone Giada , Monari Antonio , Barone Giampaolo , Terenzi Alessio
Published: November 2024

AGAPE(computAtional G-quadruplex Affinitiy PrEdiction) is an innovative machine learning (ML)-based workflow developed to predict the potential stabilization of small molecules by G-quadruplex (G4) structures. G4s, especially prevalent in telomeres and oncogene promoters, represent promising therapeutic targets, yet designing selective binders remains challenging. This study, thus, addresses this gap by implementing an ML framework in KNIME, specifically designed for ease of use across the scientific community. TheAGAPEworkflow integrates 5666 classical and quantum chemical (QC) descriptors for G4 ligands, enabling a comprehensive representation of binding-relevant molecular features. Using data from G4LDB and in-house collections, we created a robust dataset of 1217 compounds categorized by Förster Resonance Energy Transfer (FRET) assays as ACTIVE or INACTIVE based on their G4 stabilization capacity. Feature selection algorithms and ML models, particularly XGBoost with Naïve Bayesian and Random Forest classifiers, were employed to achieve an optimized prediction model with an accuracy close to 90%. A consensus voting system among top-performing models further improved classification reliability.AGAPEefficiently predicts G4 stabilization, offers interpretability of key chemical interactions, and provides a scalable, accessible tool for G4-focused drug discovery. This workflow lays the foundation for targeted therapeutic development, enhancing ligand selectivity, and expanding the application of AI in chemoinformatics

GRAPHICAL ABSTRACT
Effect of endogenous earthworm’s extracts on “plant growth-promoting fungi”
Authors: Yakkou Lamia , Houida Sofia , Raouane Mohammed , Hatipoğlu Musa , Amghar Souad , El Harti Abdellatif , Jaber Mohammed
Published: November 2024

This study explores the in vitro effects of earthworm-derived crude extracts on the growth of key Plant Growth-Promoting Fungi (PGPF) strains, includingTrichodermasp.,Melanocarpussp., andAcaulosporasp. Crude extracts were prepared from freshly harvested earthworms (HE) and those that had been starved and devoid of soil for 10 days (FE), and their effects on fungal proliferation were assessed at varying concentrations. Results demonstrated that both HE and FE extracts significantly enhanced fungal growth rates compared to traditional growth media (PDA and SAB), even at lower concentrations. The enriched nutrient profile and growth factors present in these extracts suggest that earthworm decomposition contributes valuable bioactive compounds to the soil, promoting PGPF activity and soil fertility. Additionally, media derived from these extracts stimulated rapid spore germination, which is critical for fungal dissemination and ecological establishment. Notably, the study found that contents within the earthworm digestive tract did not influence fungal growth, affirming that the growth-promoting effects are inherent to the earthworm tissue structure itself. These findings underscore the potential of earthworm-based media as a natural and effective growth medium for enhancing PGPF propagation, with implications for sustainable agricultural practices and soil health improvement.
Interspecies Organoids Reveal Human-Specific Molecular Features of Dopaminergic Neuron Development and Vulnerability
Authors: Nolbrant Sara , Wallace Jenelle L. , Ding Jingwen , Zhu Tianjia , Sevetson Jess L. , Kajtez Janko , Baldacci Isabella A. , Corrigan Emily K. , Hoglin Kaylynn , McMullen Reed , Schmitz Matthew T. , Breevoort Arnar , Swope Dani , Wu Fengxia , Pavlovic Bryan J. , Salama Sofie R. , Kirkeby Agnete , Huang Hao , Schaefer Nathan K. , Pollen Alex A.
Published: November 2024

The disproportionate expansion of telencephalic structures during human evolution involved tradeoffs that imposed greater connectivity and metabolic demands on midbrain dopaminergic neurons. Despite the central role of dopaminergic neurons in human-enriched disorders, molecular specializations associated with human-specific features and vulnerabilities of the dopaminergic system remain unexplored. Here, we establish a phylogeny-in-a-dish approach to examine gene regulatory evolution by differentiating pools of human, chimpanzee, orangutan, and macaque pluripotent stem cells into ventral midbrain organoids capable of forming long-range projections, spontaneous activity, and dopamine release. We identify human-specific gene expression changes related to axonal transport of mitochondria and reactive oxygen species buffering and candidatecis-andtrans-regulatory mechanisms underlying gene expression divergence. Our findings are consistent with a model of evolved neuroprotection in response to tradeoffs related to brain expansion and could contribute to the discovery of therapeutic targets and strategies for treating disorders involving the dopaminergic system.
Soybean Cyst Nematode-Resistant Protein AATRhg1Affects Amino Acid Homeostasis and Betalain Accumulation
Authors: Du Yulin , Jung Soyoung , Maeda Hiroshi , Bent Andrew F.
Published: November 2024

Amino acid transporters play crucial roles in plant nitrogen metabolism but also defense responses. AATRhg1, an apparent amino acid transporter encoded byGlyma.18g022400(Rhg1-GmAAT) at the soybeanRhg1locus, contributes to resistance to soybean cyst nematode (SCN), although thein plantafunction of AATRhg1remains elusive. In this study we discovered that overexpression ofRhg1-GmAATin soybean roots enhances the betalain pigment synthesis driven by aRUBYtransgene cassette, potentially through its transporter activity affecting tyrosine level and amino acid homeostasis. SilencingRhg1-GmAATalso moderately increased betalain accumulation while co-overexpression ofRhg1-GmAATandGmRBOHG(encoding an AATRhg1-interacting NADPH oxidase) blocked the betalain phenotype, indicating a complex role of AATRhg1in regulating cellular metabolism. Soybean AATRhg1did not show a betalain accumulation phenotype when co-overexpressed withRUBYinNicotiana benthamianaleaves, suggesting that soybean AATRhg1functions differently inN. benthamiana. In soybean, the expression of AATRhg1proteins mutated at conserved residues D122A or Y268L mitigated or enhanced the betalain phenotypes, respectively, suggesting that these residues are important for AATRhg1function. This study advances our understanding of AATRhg1while presenting a novel strategy for enhancing betalain biosynthesis by modulating transport and homeostasis of amino acids.
Photoaffinity enabled transcriptome-wide identification of splice modulating small molecule-RNA binding events in native cells
Authors: Shah Raven , Yan Wanlin , Rigal Joyce , Mullin Steve , Fan Lin , McGregor Lynn M , Krueger Andrew , Renuad Nicole , Byrnes Andrea , Thomas Jason R.
Published: November 2024

Splice modulating small molecules have been developed to promote the U1 snRNP to engage with pre-mRNAs with strong and altered sequence preference. Transcriptomic profiling of bulk RNA from compound treated cells enables detection of RNAs impacted; however, it is difficult to delineate whether transcriptional changes are a consequence of direct compound treatment or trans-acting effects. To identify RNA targets that bind directly with splice modulating compounds, we deployed a photoaffinity labeling (PAL)-based Chem-CLIP approach. Through this workflow, we identify the telomerase lncRNA (TERC) as a previously unknown target of this class of clinically relevant small molecules. Using cellular ∆ SHAPE-MaP, we orthogonally validate and further define the compound binding site as likely to be the conserved CR4/5 domain. Additionally, a thorough analysis of the PAL-based Chem-CLIP data reveals that considering competed RNAs, irrespective of magnitude of enrichment, adds a rich dimension of hit calling.
Attentional failures after sleep deprivation represent moments of cerebrospinal fluid flow
Authors: Yang Zinong , Williams Stephanie , Beldzik Ewa , Anakwe Stephanie , Schimmelpfennig Emilia , Lewis Laura D.
Published: November 2024

Sleep deprivation rapidly disrupts cognitive function, and in the long term contributes to neurological disease. Why sleep deprivation has such profound effects on cognition is not well understood. Here, we use simultaneous fast fMRI-EEG to test how sleep deprivation modulates cognitive, neural, and fluid dynamics in the human brain. We demonstrate that after sleep deprivation, sleep-like pulsatile cerebrospinal fluid (CSF) flow events intrude into the awake state. CSF flow is coupled to attentional function, with high flow during attentional impairment. Furthermore, CSF flow is tightly orchestrated in a series of brain-body changes including broadband neuronal shifts, pupil constriction, and altered systemic physiology, pointing to a coupled system of fluid dynamics and neuromodulatory state. The timing of these dynamics is consistent with a vascular mechanism regulated by neuromodulatory state, in which CSF begins to flow outward when attention fails, and flow reverses when attention recovers. The attentional costs of sleep deprivation may thus reflect an irrepressible need for neuronal rest periods and widespread pulsatile fluid flow.
Needle in a haystack: culturing plant-beneficial Helotiales lineages from plant roots
Authors: Bruyant Pauline , Doré Jeanne , Vallon Laurent , Moënne-Loccoz Yvan , Almario Juliana
Published: November 2024

Root-associated Helotiales fungi are increasingly recognized as beneficial fungal partners promoting plant growth under nutrient-limited conditions, particularly in non-mycorrhizal hosts, lacking the ancestral arbuscular mycorrhizal symbiosis. However, the ecology of these fungi is still cryptic as relatively few lineages have been successfully cultivated from roots for further study. Here, we attempted the mass isolation of root endophytic fungi to evaluate the recovery of known plant-beneficial Helotiales lineages using a tailored culture-based approach. We sampled six wild non-mycorrhizal species from the Brassicaceae, Caryophyllaceae, and Cyperaceae, growing in nutrient-limited alpine soils. We isolated 602 root endophytes and compared this culturable diversity with the one observed via fungal ITS2 metabarcoding. Metabarcoding revealed that Helotiales taxa dominated the fungal communities, with 43% of these detected taxa also represented in our collection. Accordingly, most root endophytes in our collection (53%) were Helotiales. These isolates, some with P solubilisation potential, belonged primarily to three Helotialean clades and were phylogenetically related to plant growth-promoting or mycorrhizal-like strains. This analysis highlights that roots of alpine non-mycorrhizal plants are reservoirs of plant-beneficial root-endophytic Helotiales, and the isolates obtained are a promising resource to explore the plant-beneficial mechanisms and ecological traits of these fungi.
Oligogalacturonides, produced by enzymatic degradation of sugar beet by-products, confer partial protection against wheat powdery mildew
Authors: Carton Camille , Šafran Josip , Mohanaraj Sangeetha , Roulard Romain , Domon Jean-Marc , Bassard Solène , Facon Natacha , Tisserant Benoît , Mongelard Gaelle , Gutierrez Laurent , Randoux Béatrice , Magnin-Robert Maryline , Pelloux Jérôme , Pau-Roblot Corinne , Sahraoui Anissa Lounès-Hadj
Published: November 2024

Nowadays, it becomes urgent to use new alternative strategies for a more sustainable agriculture, by developing eco-friendly biocontrol compounds leading to an induction of plant resistance against pathogens. In recent years, oligogalacturonides (OGs), fragments of pectin resulting from the degradation of the plant cell wall, have been particularly under focus for their ability to induce plant defense, leading to plant protection against pathogens. In the current work, 2 mixtures of OGs, bio-sourced from sugar beet by-products, were produced and assessed for their protective efficacy on wheat againstBlumeria graminis f. sp. tritici(Bgt), responsible for powdery mildew. These OGs pools were obtained by hydrolysing pectins with twoA. thalianapolygalacturonases (PGs), ADPG2 and PGLR (EC 3.2.1.15), produced in heterologous systemPichia pastoris. No direct effect of OGs generated by either ADPG2, named OGs-ADPG2 (degree of polymerisation/DP 1-10 and degree of esterification/DE 41%) or PGLR, named OGs-PGLR (DP 1-16, DE 34 %), was observed onBgtspore germinationin vitro. After a preventive foliar spraying of wheat by OGs, only OGs-PGLR provided a 31 % partial protection againstBgt. Both pools of OGs triggered an increase in the expression of some plant defense-related genes (peroxidase or PR proteins encoding genes), before inoculation with the pathogen. However, only OGs-PGLR induced the expression of a gene encoding a lipoxygenase (LOX), which is the first enzyme involved in the octadecanoic pathway, leading to oxylipins production in plant defense. Taking together, these findings revealed that some OGs, produced from sugar beet by-products by enzymatic hydrolysis, could be used as an alternative of phytochemicals.
Moiré plane wave expansion model for scanning tunneling microscopy simulations of incommensurate two-dimensional materials
Authors: Le Ster M. , Dabrowski P. , Krukowski P. , Rogala M. , Lutsyk I. , Ryś W. , Märkl T. , Brown S. A. , Sławińska J. , Palotás K. , Kowalczyk P. J.
Published: November 2024

Incommensurate heterostructures of two-dimensional (2D) materials, despite their attractive electronic behavior, are challenging to simulate because of the absence of translation symmetry. Experimental investigations of these structures often employ scanning tunneling microscopy (STM); however, there is to date no comprehensive theory to simulate an STM image in such systems. In this paper, we present a geometry-based method to generate STM images in incommensurate van der Waals (vdW) heterostructures, which we call the moiré plane wave expansion model (MPWEM). We generate the STM images using a weighted sum of three image terms: the noninteracting STM images of (1) the substrate layer, (2) the adsorbate layer, and (3) a semi-empirical Fourier expansion of the moiré wave vectors obtained analytically which results from the interaction of (1) and (2). We illustrate and benchmark the model using selected vdW 2D systems composed of structurally and electronically distinct crystals, and show that the method reproduces experimental STM images down to angstrom-scale details. The MPWEM, thanks to its simplicity, can serve as an image generation tool prior to more computationally expensive calculations which are often limited by the number of atoms and the requirement of periodic supercells, and thus offers a promising class of computationally friendly STM simulations, of high relevance in the growing field of twistronics.

Published by the American Physical Society
2024
Strong
CP
problem in the quantum rotor
Authors: Albandea D. , Catumba G. , Ramos A.
Published: November 2024

Recent studies have claimed that the strong CP problem does not occur in QCD, proposing a new order of limits in volume and topological sectors when studying observables on the lattice. In order to shed light on this issue, we study the effect of the topological θ-term on a simple quantum mechanical rotor that allows a lattice description. The topological susceptibility and the θ-dependence of the energy spectrum are both computed using local lattice correlation functions. The sign problem is overcome by considering Taylor expansions in θ, exploiting automatic differentiation methods for Monte Carlo processes. Our findings confirm the conventional wisdom on the strong CP problem.

Published by the American Physical Society
2024
Probing effective operators in single top quark production in association with a lepton-neutrino pair
Authors: Goldouzian Reza , Hildreth Michael D.
Published: November 2024

We study single top quark production in association with a lepton-neutrino pair at the LHC within the framework of the Standard Model effective field theory (SMEFT). We focus on relevant two-quark-two-lepton operators (Olq3, Olequ1, and Olequ3). It is known that these operators have tiny effects on the inclusive cross section of standard model tW production and are thus typically ignored in the SMEFT searches. However, we show that by employing smart observables, such as mT2, the pp→tℓν process is significantly sensitive to these operators. We set the most stringent limit on the coupling strength of the Olq3 operator by reinterpreting the results of a search for new phenomena with two opposite-charge leptons, jets and missing transverse momentum at s=13  TeV performed by the ATLAS collaboration. The limits derived on the Olequ1 and Olequ3 operators are comparable to those obtained from probing EFT effects in pp→tt¯ℓν and pp→tt¯ℓℓ processes at the LHC. Consequently, we propose to include the effects of these three operators on the pp→tℓν process in future global SMEFT analyses to increase the sensitivity and to reduce possible degeneracies.

Published by the American Physical Society
2024