bluuebunny/crossref_metadata_2025 huggingface dataset:
Oxytocin enhances acquisition in a social trust task in mice, whereas both oxytocin and its antagonist block trust violation learning
Authors: Budniok Samuel , Callaerts-Vegh Zsuzsanna , Bakermans-Kranenburg Marian , Bosmans Guy , D’Hooge Rudi
Published: January 2025

The complex effects of the neurohormone oxytocin (OT) on socio-cognitive phenomena have recently been proposed to be complementary with safety learning, where a stimulus acquires safety-predicting properties when it predicts non-occurrence of an aversive event. OT may enhance saliency of safety stimuli and promote positive social behavior, such as trust, by reducing anxiety and stress. Complementary, OT may reduce the ability to modulate previously learned behaviors based on new, contradicting information. This occurs through its attenuation of prediction error (PE)—the discrepancy between expectations and actual outcomes. In the current study, we stimulated or inhibited (with antagonist cligosiban, CL) the OT system and subjected male and female mice to our social transmission of food preference (STFP) protocol to assess social safety learning. STFP is based on the observation that food neophobia of rodents is attenuated when a conspecific signals the safety of the food. We used safe food preference as putative murine homologue of human trust acquisition, and modeled trust violation (PE) using lithium chloride (LiCl)-induced food aversion after social interaction. In males, results revealed that OT enhanced trust acquisition, whereas both OT and its antagonist CL similarly blocked trust violation learning. None of the manipulations affected female behavior. Our findings highlight the complexities of OT’s role in social behavior, emphasizing caution in therapeutic manipulations of this system.
Fecal Metabolite Quantitation for Rapid Assessment of the Gut Microbiome
Authors: Mullowney Michael W. , Moran Angelica , Hernandez Antonio , McMillin Mary , Rose Amber , Moran David , Little Jessica , Nguyen Ann B. , Patel Bhakti K. , Lehmann Christopher J. , Odenwald Matthew A. , Pamer Eric G. , Yeo Kiang-Teck J. , Sidebottom Ashley M.
Published: January 2025

The intestinal microbiome is composed of myriad microbial species that produce metabolites that impact host health. While loss of bacterial species and beneficial metabolites from the fecal microbiome is associated with development of a range of diseases and medical complications, there are currently no diagnostic tests that rapidly identify individuals with microbiome deficiencies. Reduced concentrations of fecal butyrate and deoxycholic acid are associated with adverse clinical outcomes and result from the loss of a subset of health-associated bacterial species. We present a rapid diagnostic test based on 3-nitrophenylhydrazine derivatization and ultrahigh-performance liquid chromatography-mass spectrometry that measures fecal butyrate and deoxycholic acid concentrations as markers of microbiome function. A matrix-matched calibration curve was developed using a simulated fecal mixture to optimize accuracy and facilitate adherence to clinical laboratory regulations. The assay showed an analytical measurement range from 4.3–3030.1 µM (LLOQ = 9.75 µM) for butyrate and from 0.9– 64.9 µM (LLOQ = 0.9 µM) for deoxycholic acid. Precision demonstrated a coefficient of variation <15% at all QC levels tested. The assay can be performed in under an hour from extraction to provision of quantitative results, enabling the rapid identification of patients with defective microbiome function.
Na+/Ca2+exchanger triggers transient disruption of axon initial segments in hippocampal granule cells after brief ischemia
Authors: Serra Carol , Martínez-Alonso Emma , Ayuso María I , Padmashri Ragunathan , Henneberger Christian , Rusakov Dmitri A. , Alcázar Alberto , Scott Ricardo
Published: January 2025

The axon initial segment (AIS) is the site of action potential initiation in many cell types. The large density of Na+channels and the small intraluminal volume of the AIS underlie the largest spike-dependent Na+raise along the neuron. Our Na+and Ca2+imaging experiments in dentate granule cells reveal that the Na+/Ca2+exchanger contributes to fast Na+clearance at the expense of Ca2+entry specifically at the AIS during short bursts of action potentials. The AIS is thought to be irreversibly disrupted during brain ischemia by the Ca2+- dependent protease calpain, as an early step leading to neuronal death. We find here that brief transitory ischemia produces a similar calpain-dependent disruption of the AIS in the dentate gyrus. However, this is not an irreversible process: a few days following the brief ischemic stress, intact initial segments re-appear, and calpain activity in the dentate gyrus returns to normal. Moreover, pharmacological blockade of Ca2+entry through the Na+/Ca2+exchanger prevents AIS disruptionin vivoand in slice preparations. Our results unveil a highly dynamic anoxia driven disruption-reconstruction of AIS, which is mediated by a previously unnoticed Ca2+entry through the Na+/Ca2+exchanger in the axon initial segment of hippocampal granule cells.
SurFlex Microscopy: Measuring Flexibility of Surface-Tethered Biomolecules
Authors: Chorlay Aymeric , Agarwal Siddhansh , Blackmon Lena , Fletcher Daniel A.
Published: January 2025

The flexibility of tethered molecules, such as those bound to biological membranes, is an important property that can influence molecular height, mobility, and accessibility. However, quantifying the flexibility of surface-tethered biomolecules in aqueous environments has been difficult due to a lack of experimental tools. Here we introduce SurFlex microscopy, a method based on fluorescence anisotropy that exploits the relationship between the conformational dynamics of a tethered molecule and the rotational diffusion of an attached fluorophore to extract information about molecular flexibility. By analyzing the polarization state of photons emitted after polarized excitation, we quantify apparent molecular flexibilities that include effects of tethering, self-interactions and buffer conditions. We first demonstrate the capabilities of SurFlex microscopy by measuring the flexibility of bilayer-tethered single-stranded DNA (ssDNA) of different lengths and nucleotide sequences. We find that sequence significantly impacts ssDNA flexibility, consistent with theoretical estimates, with weak intramolecular interactions in random sequences leading to higher apparent stiffness. Interestingly, we show that a pathological DNA sequence linked to Huntington’s disease exhibits unusual flexibility despite intramolecular interactions. We next extend SurFlex microscopy to live cells by measuring surface glycoprotein flexibility on red blood cells using fluorescent lectins. We show that trypsinization decreases glycan fluctuations, demonstrating that modifications to the cell surface can alter the flexibility of remaining surface molecules. SurFlex microscopy provides a new tool for quantifying molecular flexibility that can be used to study the role of tethered surface molecules in fundamental biological processes.

Significance statement

Biomolecules immobilized on one end play crucial roles in diverse cellular processes, from cell-cell signaling through surface receptors to the formation of DNA secondary structures. However, measuring biomolecular flexibility on surfaces has remained challenging. Here we present SurFlex microscopy, a technique that uses fluorescence anisotropy to quantify the flexibility of surface-anchored molecules. By analyzing the rotational dynamics of fluorophores attached to the ends of fluctuating biomolecules, SurFlex microscopy can be used to quantify persistence length. We demonstrate its capabilities by measuring sequence-dependent flexibility of DNA and crowding-dependent changes in glycan flexibility on native cell surfaces. This method opens new avenues for understanding how biomolecular flexibility influences key biological processes, such as those at cell surfaces during cell-cell contact formation and subsequent signaling.
Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance
Authors: DenAdel Alan , Hughes Madeline , Thoutam Akshaya , Gupta Anay , Navia Andrew W. , Fusi Nicolo , Raghavan Srivatsan , Winter Peter S. , Amini Ava P. , Crawford Lorin
Published: January 2025

The success of transformer-based foundation models on natural language and images has motivated their use in single-cell biology. Single-cell foundation models have been trained on increasingly larger transcriptomic datasets, scaling from initial studies with 1 million cells to newer atlases with over 100 million cells. This study investigates the role of pre-training dataset size and diversity on the performance of single-cell foundation models on both zero-shot and fine-tuned tasks. Using a large corpus of 22.2 million cells, we pre-train a total of 375 models which we evaluate by conducting 3,750 experiments. Our results show that current methods tend to plateau in performance with pre-training datasets that are only a fraction of the size.
AlphaFold 3 proteomic modelling reveals multiple photosystem structural homologs in freshwater cyanophages
Authors: Meza-Padilla Isaac , Doxey Andrew C. , Nissimov Jozef I.
Published: January 2025

Accurate protein structure prediction followed by structural homology detection enable the functional annotation of large numbers of otherwise obscure viral protein-coding genes. Here we employ AlphaFold 3 modeling and DALI structural homology search to predict the structures and functions of all 219 cryptic open reading frames in two representative freshwater cyanophages. We discover 28 previously unknown structural homologs, including three putative PsaD proteins in the same cyanophage, several viral structural proteins, and (to our knowledge) the first reported virus-encoded cyanobacteriochrome (DALI Z-score > 4.2 in all cases). Our results suggest that photosystem proteins may be more widespread in freshwater cyanophages than previously thought and emphasize the importance of applying structural homology detection methods when annotating viral genomes.
Tau accumulation patterns in PSP constrain mechanisms and quantify cell-to-cell and cell-autonomous aggregation rates
Authors: Huang Shih-Huan , Quaegebeur Annelies , Pansuwan Tanrada , Rittman Timothy , Wang Ruiyan , Knowles Tuomas PJ , Rowe James B , Klenerman David , Meisl Georg
Published: January 2025

Protein aggregates are a hallmark of neurodegenerative disease, yet the molecular processes that control their appearance are still poorly understood. In particular, it is unknown to what degree the development of aggregates in one cell is triggered by nearby aggregated cells, as opposed to cell-autonomous processes. Here we develop a cell-level computational model to test alternative hypotheses of disease progression from human data and demonstrate its applicability in the primary tauopathy Progressive Supranuclear Palsy. From brain slices stained for aggregated tau, we quantify the contribution of cell-to-cell and cell-autonomous processes to the proliferation of aggregates across different brain regions and disease stages. We find that the triggering of aggregation by nearby aggregated cells, over distances in the order of 100µm, is the major driver of disease progression. Our computational model can then simulate interventions to evaluate potential therapeutic strategies in a virtual reconstruction of a human primary neurodegenerative tauopathy.

Highlights

A minimal mathematical model can reproduce tissue-level aggregate accumulation patternsin silicoat cellular resolution.

Cell-to-cell interactions determine aggregate patterns in progressive supranuclear palsy (PSP).

Cell-to-cell interactions are not limited to nearest neighbours, but act over a millimetre-scale.

Reducing cell-to-cell interactions or cell vulnerability, rather than targeting cell-autonomous processes, is a potential disease-modifying therapeutic strategy.
Sex differences in pant-hoot vocalizations in wild Eastern chimpanzees
Authors: Holden Eve , Grund Charlotte , Eguma Robert , Samuni Liran , Zuberbühler Klaus , Soldati Adrian , Hobaiter Catherine
Published: January 2025

Chimpanzee pant-hoots are frequently produced long-distance vocalisations that serve a number of social functions, such as to indicate coordinate travelling, food discovery, or social status. Calling often triggers replies by others, offering potential for some form of group-level decision-making through vocal exchanges. However, despite important physiological and social differences between male and female chimpanzees, pant-hoot research has traditionally focused on males, with very little known about female use. To address this gap, we collected all-occurrence behavioural data from wild adult female and male Eastern chimpanzees (Pan troglodytes schweinfurthii) in two communities in the Budongo Forest Reserve, Uganda. We show that females pant-hooted regularly, but less frequently than males and, when they did so, mostly in response to others. Response pant- hoots were more common than initiating pant-hoots in both sexes (females: 90.1%; males: 69.5%), and male and female chimpanzees responded to pant-hoots heard at a similar rate (females: 14.1%, males excluding alpha: 15.8%). Both sexes were more likely to respond to pant-hoots from within their own party, but this effect was stronger for females. The likelihood of male chimpanzees pant-hooting in response was inhibited in larger party sizes, while females’ response pant-hoots were not. Finally, female response pant-hoots were less common during periods of maximal oestrous as compared to other stages of their reproductive cycle. Overall, our findings demonstrate that response pant-hoots are subject to social factors, such as within-sex social competition and between-sex reproductive strategies, which affect male and female chimpanzees in different ways, a further demonstration of the high degree of audience awareness in this primate species.

Highlights

Chimpanzees use pant-hoots in both sex-specific and sex-non-specific ways

Individual and social factors impact likelihood of pant-hoot production

Our findings suggest pant-hoots are important flexible elements of vocal behaviour for male and female chimpanzees.
Clinical Immunoprofiling Reveals that High Numbers of CD8+and PD-1+Cells Predict Superior Patient Survival Across Major Cancer Types Independent of Major Risk Factors
Authors: Alessi Joao V , Lindsay James R , Giobbie-Hurder Anita , Sharma Bijaya , Felt Kristen , Kumari Priti , Mazor Tali , Cerami Ethan , Lotter William , Altreuter Jennifer , Weirather Jason , Dryg Ian , Hoebel Katharina , Manos Michael , Adib Elio , Curtis Jennifer D. , Ricciuti Biagio , Di Federico Alessandro , Ghandour Fatme , Saad Eddy , Wang Xin-an , Pecci Federica , Holovatska Marta , Gandhi Malini M. , Hughes Melissa E. , O’Meara Tess A. , Chan Sabrina J. , Pfaff Kathleen , Konstantinopoulos Panagiotis A. , Hodi F. Stephan , Shipp Margaret A. , Signoretti Sabina , Choueiri Toni , Wei Xiao X. , Santagata Sandro , Hanna Glenn J. , Lin Nancy U. , Tolaney Sara M. , Liu Joyce , Sorger Peter K. , Lindeman Neal , Sholl Lynette M. , Nowak Jonathan A. , Barbie David , Awad Mark M. , Johnson Bruce E. , Rodig Scott J.
Published: January 2025

Background

Numerous retrospective studies have shown associations between the number of intratumoral immune cells and patient outcomes for individual cancers treated with specific therapies. However, the clinical value of using a digital pathology platform to enumerate intratumoral immune biomarkers prospectively in the pan-cancer setting has not been established.

Methods

We developed ImmunoProfile, a clinical workflow combining automated multiplex immunofluorescence tissue staining, digital slide imaging, and machine learning-assisted scoring to quantify intratumoral CD8+, PD-1+, CD8+PD-1+, and FOXP3+immune cells and PD-L1 expression in formalin-fixed, paraffin-embedded tissue samples in a standardized and reproducible manner. Over three years, we prospectively applied ImmunoProfile to biopsies collected from 2,023 unselected cancer patients in the clinical laboratory. We correlated the results with patient survival.

Results

In the pan-cancer cohort, patients with intratumoral CD8+or PD-1+cells in the top or middle tertiles had significantly lower risks of death than those in the bottom (CD8+: (high vs. low) HR 0.62 [95% CI 0.48 – 0.81], (middle vs. low) HR 0.82 [95% CI 0.67 - 0.99], Wald p=0.002]; PD-1+: (high vs. low) HR 0.65 [95% CI 0.51 - 0.83], (middle vs. low) HR 0.74 [95% CI: 0.60 - 0.90], p=0.0009) after controlling for risk factors, including cancer type. In subset analyses, patients with high intratumoral CD8+, PD-1+, and/or CD8+PD-1+cells had lower risks of death from non-small cell lung, colorectal, breast, esophagogastric, head and neck, pancreatic, and ovarian cancers after controlling for clinical risk factors, including stage, and despite distinct therapies (all p<0.05).

Conclusions

Enumerating intratumoral CD8+and PD-1+cells with a clinically validated digital pathology platform predicts patient survival across cancer types independent of clinical stage and despite disparate therapies.
Integrated transcriptomic, metabolomic, and lipidomic analyses reveal a unique lipid profile of regulatory T cells upon activation
Authors: Sato Yohei , Yura Misa , Chandler Alana , Hanawa Yamato , Tsubota Akihito
Published: January 2025

Regulatory T cells (Tregs) exhibit stable FOXP3 expression and regulate the immune response through suppressive activity. Their unique metabolic properties include reduced glycolysis and increased oxidative phosphorylation. We combined transcriptomic, metabolomic, and lipidomic analyses to dissect the metabolic dynamics of Tregs upon activation. Combined metabolomic and lipidomic analyses showed that freshly isolated and activated Tregs had distinct metabolomic and lipidomic properties, respectively. Activated Tregs contained omega-3 long-chain polyunsaturated fatty acid (PUFA)-rich diglycerides and triglycerides. These were supported by transcriptomics data, showing upregulation of PPAR-alpha and PPAR-gamma. Activated Tregs exhibited increased ceramide production, consistent with the upregulation of ceramide synthase and sphingomyelin synthase. Confocal microscopy revealed that Tregs were enriched in lysosomes and peroxisomes compared with effector T cells upon activation. Our data confirm the unique metabolic properties of Tregs, especially those characterized by omega-3 long-chain PUFA-rich triglycerides and ceramides, together with enriched lysosomes and peroxisomes, which correspond to metabolic alterations.
scMusketeers: Addressing imbalanced cell type annotation and batch effect reduction with a modular autoencoder
Authors: Collin Antoine , Pelletier Simon J. , Fierville Morgane , Droit Arnaud , Precioso Frédéric , Bécavin Christophe , Barbry Pascal
Published: January 2025

The growing number of single-cell gene expression atlases available offers a conceptual framework for improving our understanding of physio-pathological processes. To take full advantage of this revolution, data integration and cell annotation strategies need to be improved, in particular to better detect rare cell types and by better controlling batch effects in experiments. scMusketeers is a deep learning model that optimises the representation of latent data and solves both challenges. scMusketeers features three modules: (1) an autoencoder for noise and dimensionality reductions; (2) a focal loss classifier to enhance rare cell type predictions; and (3) an adversarial domain adaptation (DANN) module for batch effect correction. Benchmarking against state-of-the-art tools, including the UCE foundation model, showed that scMusketeers performs on par or better, particularly in identifying rare cell types. It also allows to transfer cell labels from single-cell RNA sequencing to spatial transcriptomics. With its modular and adaptable design, scMusketeers offers a versatile framework that can be generalized to other large-scale biological projects requiring deep learning approaches, establishing itself as a valuable tool for single-cell data integration and analysis.
Pre-oviposition development of the brown anole (Anolis sagrei)
Authors: Weberling Antonia , Shylo Natalia A. , Kircher Bonnie K. , Wilson Hannah , McClain Melainia , Marchini Marta , Starr Katherine , Sanger Thomas J. , Hollfelder Florian , Trainor Paul
Published: January 2025

The brown anole,Anolis sagrei, has emerged as a representative squamate species during the past several decades. Novel functional tools have been established to manipulate embryogenesis through genome editing or the introduction of small molecule inhibitors, and their effective use requires a thorough understanding of early anole embryogenesis. To enable precise and reproducible staging of anole embryos, we need knowledge of the progression of anole embryogenesis and morphogenesis. While post-oviposition development has been described, the pre-oviposition period remains to be explored. Here, we provide the first staging series of pre-oviposition development for the brown anole. Analysing the follicles and embryos through brightfield imaging, SEM, STEM, histology, and DAPI staining, we define 26 distinct developmental stages. Our dataset reveals that peri-gastrulation morphogenesis up to the initiation of neurulation diverges significantly from chicken, the common representative model of reptile embryogenesis. Furthermore, we followed heart development, neural crest cell migration and central nervous system development through immunofluorescence analyses and provide new comparative insights into the morphogenesis of each of these organ systems over time. Our work establishes the brown anole as a squamate model organism for cross clade evolutionary studies of early embryogenesis.
Probing the structural heterogeneity of Pup ligase PafA using H/D exchange mass spectrometry
Authors: Plourde Alicia , Ogata-Bean Jacquelyn C. , Vahidi Siavash
Published: January 2025

The Pup-proteasome system (PPS) is a unique bacterial proteolytic pathway found in some bacterial species, including inMycobacterium tuberculosis, that plays a vital role in maintaining proteome integrity and survival during infection. Pupylation is the process of tagging substrates with Pup for degradation and is catalyzed by PafA, the sole Pup ligase in bacteria. However, how PafA interacts with diverse targets and its oligomeric state remain poorly understood. Although X-ray crystal structures have characterized PafA as a domain-swapped dimer, it is widely regarded as functionally active in its monomeric form. It remains to be established whether PafA dimerizes in solution, and how dimerization influences its function. In this study, we employed hydrogen-deuterium exchange mass spectrometry (HDX-MS) alongside complementary biophysical techniques to explore the oligomeric states and conformational dynamics of PafA. We show that recombinantly-produced PafA exists in a monomeric and a domain-swapped dimeric state in solution. While PafAdimeris stabilized by nucleotide, it predominately resides in a catalytically inactive conformation. Our HDX-MS highlighted regions throughout the N- and C-terminal domains that facilitate the PafA dimerization process. HDX-MS also revealed nucleotide binding induces global conformational changes on the PafAmonomer, underscoring the structural plasticity of this promiscuous enzyme. Our findings provide insight into the structure-function-dynamics relationship of PafA, shedding light on how its oligomeric states and conformational flexibility might influence its role in the PPS.
A novel SARS-CoV-2-derived infectious vector system
Authors: Elfayres Ghada , Xiao Yong , Pan Qinghua , Liang Chen , Barbeau Benoit , Berthoux Lionel
Published: January 2025

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of COVID-19. The development of antiviral drugs for COVID-19 has been hampered by the requirement of a biosafety level 3 (BSL3) laboratory for experiments related to SARS-CoV-2, and by the lack of easy and precise methods for quantification of infection. Here, we developed a SARS-CoV-2 viral vector composed of all four SARS-CoV-2 structural proteins constitutively expressed in lentivirally transduced cells, combined with an RNA replicon deleted for SARS-CoV-2 structural protein genes S, M and E, and expressing a luciferase-GFP fusion protein. We show that, after concentrating viral stocks by ultracentrifugation, the SARS-CoV-2 viral vector is able to infect two human cell lines expressing receptors ACE2 and TMPRSS2. Both luciferase activity and GFP fluorescence were detected, and transduction was remdesivir-sensitive. We also show that this vector is inhibited by three type I interferons (IFN-I) subtypes. Although improvements are needed to increase infectious titers, this vector system may prove useful for antiviral drug screening and SARS-CoV-2-related investigations.
ParaSurf: A Surface-Based Deep Learning Approach for Paratope-Antigen Interaction Prediction
Authors: Papadopoulos Angelos-Michael , Axenopoulos Apostolos , Iatrou Anastasia , Stamatopoulos Kostas , Alvarez Federico , Daras Petros
Published: January 2025

Motivation

Identifying antibody binding sites, is crucial for developing vaccines and therapeutic antibodies, processes that are time-consuming and costly. Accurate prediction of the paratope’s binding site can speed up the development by improving our understanding of antibody-antigen interactions.

Results

We present ParaSurf, a deep learning model that significantly enhances paratope prediction by incorporating both surface geometric and non-geometric factors. Trained and tested on three prominent antibody-antigen benchmarks, ParaSurf achieves state-of-the-art results across nearly all metrics. Unlike models restricted to the variable region, ParaSurf demonstrates the ability to accurately predict binding scores across the entire Fab region of the antibody. Additionally, we conducted an extensive analysis using the largest of the three datasets employed, focusing on three key components: (1) a detailed evaluation of paratope prediction for each Complementarity-Determining Region loop, (2) the performance of models trained exclusively on the heavy chain, and (3) the results of training models solely on the light chain without incorporating data from the heavy chain.

Availability and Implementation

Source code for ParaSurf, along with the datasets used, preprocessing pipeline, and trained model weights, are freely available athttps://github.com/aggelos-michael-papadopoulos/ParaSurf.

Contact

angepapa@iti.gr,axenop@iti.gr

Supplementary information

Supplementary data are available atBioinformaticsonline.
The resource elasticity of control
Authors: Solomyak Levi , Emanuel Aviv , Eldar Eran
Published: January 2025

The ability to determine how much the environment can be controlled through our actions has long been viewed as fundamental to adaptive behavior. While traditional accounts treat controllability as a fixed property of the environment, we argue that real-world controllability often depends on the effort, time and money we are able and willing to invest. In such cases, controllability can be said to beelasticto invested resources. Here we propose that inferring this elasticity is essential for efficient resource allocation, and thus, elasticity misestimations result in maladaptive behavior. To test these hypotheses, we developed a novel treasure hunt game where participants encountered environments with varying degrees of controllability and elasticity. Across two pre-registered studies (N=514), we first demonstrate that people infer elasticity and adapt their resource allocation accordingly. We then present a computational model that explains how people make this inference, and identify individual elasticity biases that lead to suboptimal resource allocation. Finally, we show that overestimation of elasticity is associated with elevated psychopathology involving an impaired sense of control. These findings establish the elasticity of control as a distinct cognitive construct guiding adaptive behavior, and a computational marker for control-related maladaptive behavior.
Immuno-moodulin is Differentially Expressed in T Cells and Plasma in Obsessive-Compulsive Disorder Patients
Authors: Blacksell Isobel Alice , Vismara Matteo , Lim Christine Maria , Dell’Osso Bernardo , Pallanti Stefano , Hollander Eric , Vendruscolo Michele , D’Addario Claudio , Cooper Dianne , D’Acquisto Fulvio
Published: January 2025

Immuno-moodulin (Imood), a recently discovered protein expressed in T cells, is associated with anxiety-like behavior in mice. However, its mechanism of action in modulating neuroimmune interactions remains unclear. To investigate this problem, we characterized Imood in human blood and immune cells using neutralizing monoclonal antibodies, revealing its nature as an intrinsically disordered protein (IDP) with unique expression patterns. Our findings indicate that Imood is predominantly expressed intracellularly in peripheral blood mononuclear cells (PBMCs), particularly T lymphocytes, but is absent in polymorphonuclear cells. Upon T-cell activation, Imood exhibits distinct mobilization patterns with increased surface expression. Bioinformatics analysis identified a strong propensity for oligomerization and liquid-liquid phase separation. We also found that T cells from patients with Obsessive-Compulsive-Disorder (OCD) displayed significantly elevated surface Imood expression compared to healthy controls, as well as an altered level of Imood polymerization in the plasma. Taken together, these results elucidate the expression patterns and structural properties of Imood in human immune cells, which open new avenues for OCD diagnostics, and prompt further study for understanding the aetiology of OCD and related disorders.
USP1/UAF1 targets polyubiquitinated PCNA with an exo-cleavage mechanism that enriches for monoubiquitinated PCNA
Authors: Keijzer Niels , Sakoltchik Jan , Majumder Kaustav , van Lil Nina , El Oualid Farid , Fish Alexander , Sixma Titia K.
Published: January 2025

DNA damage tolerance (DDT) is an important pathway that allows our cells to bypass DNA lesions during replication. DDT is orchestrated by ubiquitination of PCNA: Monoubiquitination (PCNA-Ub) initiates recruitment of TLS polymerases but also serves as substrate for K63-linked polyubiquitination that leads to HR-mediated bypass mechanisms. Recent work on USP1/UAF1 inhibition revealed that K48-linked chains are also formed on PCNA, resulting in its proteasomal degradation. USP1/UAF1 is established as deubiquitinating enzyme (DUB) for PCNA-Ub, but little is known about deubiquitination of chains on PCNA.

Here we show that USP1/UAF1 cleaves both K48 and K63-linked ubiquitin chains on PCNA efficiently, using an exo-cleavage mechanism. Kinetic analysis reveals that USP1/UAF1 prefers cleaving the ubiquitin-ubiquitin bond over cleavage of the ubiquitin-PCNA isopeptide bond and therefore treats poly- and monoubiquitinated PCNA as different substrates. A cryo-EM structure of USP1/UAF1 with a K63-diubiquitin and structure-based mutagenesis reveals that its mechanistic preference is maintained in evolution. Its kinetic mechanism results in relative enrichment of monoubiquitinated PCNA that could initially promote TLS over HR-like bypass. Taken together, these results suggest that USP1/UAF1 could be important in temporary protection of PCNA against K48- and K63-linked polyubiquitination and highlight this DUB as a potential regulator of DDT pathway choice.
Prediction of Gene Regulatory Connections with Joint Single-Cell Foundation Models and Graph-Based Learning
Authors: Kommu Sindhura , Wang Yizhi , Wang Yue , Wang Xuan
Published: January 2025

Motivation

Single-cell RNA sequencing (scRNA-seq) data offers unprecedented opportunities to infer gene regulatory networks (GRNs) at a fine-grained resolution, shedding light on cellular phenotypes at the molecular level. However, the high sparsity, noise, and dropout events inherent in scRNA-seq data pose significant challenges for accurate and reliable GRN inference. The rapid growth in experimentally validated transcription factor-DNA binding data (e.g., ChIP-seq) has enabled supervised machine learning methods, which rely on known gene regulatory interactions to learn patterns, and achieve high accuracy in GRN inference by framing it as a gene regulatory link prediction task. This study addresses the gene regulatory link prediction problem by learning informative vectorized representations at the gene level to predict missing regulatory interactions. However, a higher performance of supervised learning methods requires a large amount of known TF-DNA binding data, which is often experimentally expensive and therefore limited in amount. Advances in large-scale pre-training and transfer learning provide a transformative opportunity to address this challenge. In this study, we leverage large-scale pre-trained models, trained on extensive scRNA-seq datasets and known as single-cell foundation models (scFMs). These models are combined with joint graph-based learning to establish a robust foundation for gene regulatory link prediction.

Results

We propose scRegNet, a novel and effective framework that leverages scFMs with joint graph-based learning for gene regulatory link prediction. scRegNet achieves state-of-the-art results in comparison with nine baseline methods on seven scRNA-seq benchmark datasets. In addition, scRegNet is more robust than the baseline methods on noisy training data.

Availability

The source code is available athttps://github.com/sindhura-cs/scRegNet.
IL-17A primes an early progenitor compartment to tune the erythropoietic feedback circuit
Authors: Wu Qiu C , Swaminathan Aishwarya , Winward Ashley , Lalonde Logan , Hwang Yung , Littman Noah , Socolovsky Merav , Klein Allon M
Published: January 2025

Feedback control of erythropoiesis exemplifies conflicting goals in tissue homeostasis: maintaining fast reactivity to stress while minimizing proliferative burden on progenitors in the steady state. Here we show that these conflicting goals are tuned through the combinatorial action of cytokines. We find that IL-17A, a pro-inflammatory cytokine, mediates striking synergism with the negative feedback signal erythropoietin (Epo) in vivo, accelerating the erythropoietic response to hypoxia. A model of erythropoietic control shows increased reactivity may occur through two cell circuit designs, with one having far lower constitutive progenitor burden in normoxia. IL-17A acts through this optimal design by sensitizing progenitors to Epo, a model supported by multiple experimental observations. We suggest that IL-17A signals impending hypoxia during infections, tuning erythropoiesis in favor of a faster stress response. Our study highlights IL-17A as a potential erythropoietic therapeutic agent and serves as a model of homeostatic tuning in stem and progenitor cell circuits.
Exploring The Formation And Permeability Of Plasmodesmata In The Liverwort,Marchantia polymorpha
Authors: Hsu Chia-Yun , Hsu Chia-Hsuan , Chang Hui-Yu , Lu Kuan-Ju
Published: January 2025

Plasmodesmata are cell-wall-embedded channels that evolved in the common ancestor of land plants to increase cell-to-cell communication. Whether all the fundamental properties of plasmodesmata emerged and were inherited in all land plants at the same time is unknown. Here we show that the bryophyteMarchantia polymorpha(a non-vascular plant) forms mostly simple plasmodesmata in early-developing gemmae. The complexity of plasmodesmata increases during gemma maturation, and complex plasmodesmata with enlarged cavities are majorly observed in thalli. In contrast to vascular plants, whose simple plasmodesmata can transport monomeric fluorescent proteins, plasmodesmata inMarchantia polymorphalimited their permeability before the juvenile-to-adult transition. In support, callose, a known polysaccharide regulating plasmodesmata permeability in vascular plants, accumulated in most of theMarchantia polymorphatissues examined. Furthermore, we found that in the apical meristematic region, plasmodesmata allowed the transport of monomeric fluorescent proteins, and this relaxation might correlate with the lower accumulation of callose. Taken together, our study suggests that certain plasmodesmata properties, such as complexity progression and callose accumulation, may have evolved before the divergence between vascular and non-vascular plants.
Age and sex effects on blood retrotransposable element expression levels: Findings from the population-based Rhineland Study
Authors: Talevi Valentina , Lee Hang-Mao , Liu Dan , Beyer Marc D. , Salomoni Paolo , Breteler Monique M.B. , Aziz N. Ahmad
Published: January 2025

Retrotransposable elements (RTEs) have been implicated in the pathogenesis of several age-associated diseases. Although model systems indicate that age- and sex-dependent loss of heterochromatin increases RTE expression, data from large human studies are lacking. Here we assessed the expression levels of 795 blood RTE subfamilies in 2467 participants of the population-based Rhineland Study. We found that the expression of more than 98% of RTE subfamilies increased with both chronological and biological age. Moreover, the expression of heterochromatin regulators involved in RTE silencing were negatively related to the expression of 690 RTE subfamilies. Finally, we observed sex differences in 42 RTE subfamilies, with higher expression in men. The genes mapped to sex-related RTEs were enriched in immune response-related pathways. Importantly, we validated our key findings in an independent population-based cohort. Our findings indicate that RTEs and their repressors are markers of aging, and that their dysregulation is linked to inflammation, especially in men.

Graphical abstract
Task-Optimized Machine Learning for High-Accuracy Alzheimer’s Diagnosis from Handwriting Data
Authors: Seyedi HosseiniNian Zahra , Tajari Ahmadreza , Barati B Behrouz , Baharlouei Sina
Published: January 2025

Training complex models on Alzheimer’s Disease (AD) datasets is challenging due to the costly process of extracting features from a wide range of patient tasks. Developing high-performance AD detection models that rely on a small number of tasks can help reduce dataset acquisition costs and improve the interpretability of the AD detection model. To address this, we propose a two-stage forward-backward feature selection approach to identify the most relevant tasks and features for predicting AD with high accuracy. We evaluate a range of machine learning methods, including Extreme Gradient Boosting (XGBoost), Random Forest, K-Nearest Neighbors, Support Vector Machine, Multi-Layer Perceptron, and Logistic Regression, to determine the best classification model for feature selection and downstream prediction tasks. Given the limited sample size, we assess model performance using Leave-One-Out-Cross-Validation (LOOCV) to ensure robust results. Our method was compared with multiple state-of-the-art approaches for feature selection. The results of our analysis indicate that combining our proposed methods for feature selection with the XGBoost classifier, using only four tasks, produces a model that is both more interpretable and high-performing compared to other approaches. This suggests focusing on these four tasks, rather than collecting extensive task data from patients, can yield a reliable predictor for diagnosis of AD with an accuracy of 91.37%, 93.94% recall, 89.77% precision, and 91.32% F1 score - surpassing other classification methods. This research represents a significant advancement in the efficiency and reliability of AD diagnosis, improving patient prognosis and offering potential benefits to healthcare systems.
Deuterium-reinforced polyunsaturated fatty acids protect against muscle atrophy induced by type 1 diabetes in mice
Authors: Eshima Hiroaki , Tomoaki Ishihara , Tabuchi Ayaka , Kano Yutaka , Kurokawa Kenji , Shchepinov Mikhail S.
Published: January 2025

HIGHLIGHTS

D-PUFA diet prevents muscle atrophy in STZ-induced diabetic mice.

D-PUFA diet prevents muscle weakness depending on increased calcium release in STZ-induced diabetic mice.

D-PUFA diet may show a trend to decrease blood glucose in STZ-induced diabetic mice.

D-PUFA diet does not alter ferroptosis-related protein profiles including ACSL4, LPCAT3, ALOX12, and Gpx4.

Oxidative stress and reactive oxygen species (ROS) have been linked to muscle atrophy and weakness. Diabetes increases the oxidative status of lipoproteins in nearly all tissues, including muscle tissues, but the role of lipid ROS on diabetes-induced muscle atrophy is not fully understood. Deuterium reinforced polyunsaturated fatty acids (D-PUFA) are more resistant to ROS-initiated chain reaction of lipid peroxidation than regular hydrogenated PUFA (H-PUFA). In this study, we tested the hypothesis that D-PUFA would protect muscle atrophy induced by diabetes driven by an accumulation of lipid hydroperoxides (LOOH). C57BL/6J mice were dosed with H-PUFA or D-PUFA for four weeks through dietary supplementation and then injected with streptozotocin (STZ) to induce insulin-deficient diabetes. After two weeks, muscles tissues were analyzed for individual muscle mass, force generating capacity and cross-sectional area. Skeletal muscle fibers from diabetic mice exhibited increased total ROS and LOOH. This was abolished by the D-PUFA supplementation regardless of accumulated iron. D-PUFA were found to be protective against muscle atrophy and weakness from STZ-induced diabetes. Prevention of muscle atrophy and weakness by D-PUFA might be independent of ACSL4/LPCAT3/15-LOX pathway. These findings provide novel insights into the role of LOOH in the mechanistic link between oxidative stress and diabetic myopathy and suggest a novel therapeutic approach to diabetes-associated muscle weakness.
The RING-finger domain ofArabidopsisRMR functions as an E3 ligase essential for post-Golgi trafficking
Authors: Chen Shuai , Zeng Yonglun , Wong Hiu Yan , Chen Yihong , Yang Lei , Luo Fang , Gao Caiji , Jiang Liwen , Wong Kam-Bo
Published: January 2025

Receptor-homology-transmembrane-RING-H2 (RMR) sorting receptors are essential for directing soluble cargo proteins to protein storage vacuoles in plants. These type I integral membrane proteins comprise a single transmembrane domain, an N-terminal lumenal region containing a protease-associated domain for cargo recognition, and a C-terminal cytoplasmic region (CT) with a Really-Interesting-New-Gene-H2 (RING-H2) domain. Here, we determined the crystal structure of the RING-H2 domain ofArabidopsisRMR isoform-1 (AtRMR1-RING), where the conserved C3H2C3 motif coordinates two Zn ions, a feature typical of RING-type E3 ligases. AtRMR1-RING was shown to interact withArabidopsisE2 ubiquitin-conjugating enzyme, and exhibits E3 ligase activity in an in vitro ubiquitination assay. Biochemical analysis reveals that I234Y substitution disrupted the E2/E3 interaction and greatly reduced E3 ligase activity. Furthermore, we showed that the conserved RING-H2 domains of AtRMR isoform 2, 3 and 4 are also E3 ligases. Inactivation of E3 ligase activity by the I234Y mutation resulted in Golgi retention of AtRMR1-CT and AtRMR2. These findings suggest that the E3 ligase activity is essential for post-Golgi trafficking of RMR receptors, providing new insights into receptor-mediated protein sorting in plants.
Structural and Mechanistic Insights into Symmetry Conversion in Plant GORK K+Channel Regulation
Authors: Li Qi-yu , Qin Li , Tang Ling-hui , Zhang Chun-rui , Huang Shouguang , Wang Ke , Zhang Gao-hua , Hao Ning-jie , Su Min , Hedrich Rainer , Chen Yu-hang
Published: January 2025

GORK is a shaker-like potassium channel in plants that contains ankyrin (ANK) repeats. In guard cells, activation of GORK causes K+efflux, reducing turgor pressure and closing stomata. However, how GORK is regulated remains largely elusive. Here, we solved the cryo-EM structure ofArabidopsisGORK, revealing an unusual symmetry reduction (from C4 to C2) feature within its tetrameric assembly. This symmetry reduction in GORK channel is driven by ANK dimerization, which disrupts the coupling between transmembrane helices and cytoplasmic domains, thus maintaining GORK in an autoinhibited state. Electrophysiological and structural analyses further confirmed that ANK dimerization inhibits GORK, and its removal restores C4 symmetry, converting GORK to an activatable state. This dynamic switching between C2 and C4 symmetry, mediated by ANK dimerization, presents a GORK target site that guard cells regulate to switch the plant K+channel between inhibited and activatable states, thus controlling stomatal movement in response to environmental stimuli.
On the evolution of dispersal strategies under the costs of acquisition of private and social information
Authors: Sion Antoine , Marcantonio Matteo , Masier Stefano , Tuci Elio
Published: January 2025

Dispersal between patches of suitable habitat is a key behaviour for the survival of animal populations and is impacted by rapid environmental changes. Animals must cope with several costs related to the dispersal process, such as expenses in energy for acquiring information or increased mortality risks. There is a growing interest in studying how the costs of acquisition of information influence the dispersal be- haviour of species, and particularly how the use of social and private information can shape this behaviour over multiple generations. Current models of dispersal rarely incorporate both sources of information, and there is specifically a lack of modelling studies taking into account costs of acquisition for private and social information. We develop an agent-based model simulating a population of butterflies with genetic factors linked to the acquisition of both types of information and their associated reproductive costs. We show that different costs, environmental variability conditions and sensory abilities result in various dispersal behaviours and have an impact on the fitness of the population. In stable environments, low-cost information is used by a varying proportion of agents to disperse, but when the cost rises lightly, all agents stay uninformed. In highly variable environments, the same trend is observed, but agents rely on information even if the cost of acquisition increases up to twice compared to stable environments as it provides an evolutionary advantage. Agents with a limited perceptual range use both information sources equally in variable environments, and those with a bigger perceptual range rely exclusively on private information to take dispersal decisions, except at free cost of acquisition. Globally, the use of information induces a higher fitness for the population in stable environments if costs of acquisition are free or very low. In variable environmental conditions, the highest fitness is maintained with a limited perceptual range when the total cost rises up to twice the value found for stable environments. With a bigger perceptual range, the highest fitness is maintained for the whole range of total costs studied.