bluuebunny/crossref_metadata_2025_split huggingface dataset:
Female C57BL/6J mice perform distinctive urination behaviour accompanied by ultrasonic vocalisations sequences with a stereotypic temporal organisation
Authors: de Chaumont Fabrice , Yvenou Gaëlle , Perez Villalba Ana , Hérault Yann , Bourgeron Thomas , Ey Elodie 
Published: February 2025

AbstractUltrasonic vocalisations (USVs) are largely studied in mice as a marker of social communication. These USVs are usually recorded during short social encounters in unfamiliar test cages. In the present study, we explored how freely interacting pairs of C57BL/6J adult female mice spontaneously use USVs over long-term monitoring. In this situation, we discovered that these mice display a previously undescribed behaviour: they emit specific USV sequences while depositing a large quantity of urine in a corner of the cage. The most striking feature of USVs accompanying this vocalised urination behaviour was the stereotyped duration of the inter-USV intervals. The variability in the frequency of occurrence of this behaviour was important between pairs. Interestingly, when accompanied by the specific USV sequence, urination was correlated with a significant increase in locomotor activity in both the emitter and the cage mate, in contrast with urination without USVs. Altogether, the observation and description of this vocalised urination behaviour argue for exploring mouse vocalisations at the sequence level to understand the USV-behaviours interactions.
Specificity and Mechanism of tRNA cleavage by the AriB Toprim nuclease of the PARIS bacterial immune system
Authors: Belukhina Svetlana , Saudemont Baptiste , Depardieu Florence , Lorthios Tom , Maviza Tinashe P. , Livenskyi Alexei , Serebryakova Marina , Aleksandrova Maria , Ukholkina Elizaveta , Burmistrova Nadezhda , Sergiev Petr V. , Libiad Marouane , Dubrac Sarah , Barras Frederic , Motorin Yuri , Marchand Virginie , Hagelueken Gregor , Isaev Artem , Bikard David , Rouillon Christophe 
Published: February 2025

AbstractTransfer RNA molecules have been recently recognized as widespread targets of bacterial immune systems. Translation inhibition through tRNA cleavage or modification inhibits phage propagation, thereby protecting the bacterial population. To counteract this, some viruses encode their own tRNA molecules, allowing infection to take place. The AriB effector of the PARIS defence system is a Toprim nuclease previously shown to target theE. colitRNALys(UUU), but not a tRNALys(UUU)variant encoded by bacteriophage T5. We demonstrate here that the T5-tRNALys(UUU)is required but not sufficient to bypass PARIS immunity. Combining tRNA-sequencing, genetics, phage infection andin vitrobiochemical data, we reveal that theE. colitRNAThr(UGU), is another prime target of AriB and tRNAAsn(GUU)represents a secondary, yet biologically relevant, target of the PARIS effector. Activated AriB protein cleaves these targetsin vitro, and the cleavage reaction is not dependent on the presence of specific tRNA modifications. We show that the overexpression of phage T5 tRNALys(UUU), tRNAThr(UGU)and tRNAAsn(GUU)variants is sufficient to inhibit PARIS anti-viral defence. Finally, we propose a model for tRNA recognition by the AriB dimer and provide molecular details of its nuclease activity and specificity.
SAMHD1Knockout iPSC model enables high lenti-viral transduction in myeloid cell types
Authors: Li Huinan , Afroze Maliha , Arora Gunisha , Federman Scot , Shevade Kaivalya , Yang Yeqing Angela , Nguyen Phuong , Esanov Rustam , Przybyla Laralynne , Litterman Adam , Shafer Shawn 
Published: February 2025

AbstractRecent advances in functional genomics tools have ushered in a new era of genetic editing to identify molecular pathways relevant to developmental and disease biology. However, limited model systems are available that adequately mimic cell states and phenotypes associated with human disease pathways. Here, we quantitatively analyzed the founder population bottleneck effect and demonstrated how the population changes from induced pluripotent stem cells (iPSCs) to hematopoietic stem cells and to the final induced macrophage population. We then engineeredSAMHD1knockout (KO) iPSC and characterized the iPSC line with RNA Seq, and induced macrophages from two distinct protocols with functional analysis. We then generatedSAMHD1KO CRISPR-dCAS9 KRAB iPSC through lenti-viral transduction aiming to increase the efficiency of lentiviral mediated gene transfer. We demonstrated increased lenti-viral transduction efficiency in induced macrophage, as well as microglia induced with two distinct protocols. This model allows for efficient gene knock down, as well as large-scale functional genomics screens in mature iPSC-derived macrophages or microglia with applications in innate immunity and chronic inflammatory disease biology. These experiments highlight the broad applicability of this platform for disease-relevant target identification and may improve our ability to run large-scale screens in iPSC-derived myeloid model systems.
Identification of actionable targeted protein degradation effector sites through Site-specific Ligand Incorporation-induced Proximity (SLIP)
Authors: Xiao Zhangping , Gavriil Efthymios Spyridon , Cao Fangyuan , Zhang Xinyue , Li Stan Xiaogang , Kotelnikov Sergei , Michalska Patrycja , Marte Friederike , Huang Chloe , Lu Yudi , Zhang Yunxuan , Bernardini Erika , Kozakov Dima , Tate Edward W. 
Published: February 2025

ABSTRACTTargeted protein degradation (TPD) is a rapidly emerging and potentially transformative therapeutic modality. However, the large majority of >600 known ubiquitin ligases have yet to be exploited as TPD effectors by proteolysis-targeting chimeras (PROTACs) or molecular glue degraders (MGDs). We report here a chemical–genetic platform, Site-specific Ligand Incorporation-induced Proximity (SLIP), to identify actionable (“PROTACable”) sites on any potential effector protein in intact cells. SLIP uses genetic code expansion (GCE) to encode copper-free “click” ligation at a specific effector site in intact cells, enablingin situformation of a covalent PROTAC-effector conjugate against a target protein of interest (POI). Modification at actionable effector sites drives degradation of the targeted protein, establishing the potential of these sites for TPD. Using SLIP, we systematically screened dozens of sites across E3 ligases and E2 enzymes from diverse classes, identifying multiple novel potentially PROTACable effector sites which are competent for TPD. SLIP adds a powerful approach to the proximity-induced pharmacology (PIP) toolbox, enabling future effector ligand discovery to fully enable TPD, and other emerging PIP modalities.
Directionality range in Emlen funnels
Authors: Patmanidis Ilias , Leberecht Bo , Fränzle Martin , Lentink David , Solov’yov Ilia A. , Mouritsen Henrik 
Published: February 2025

AbstractEmlen funnels can be used to study the birds’ ability to orient during the migratory seasons. Birds are so eager to migrate that they will jump in the direction in which they want to fly, even if they are placed in small cages during the night. Emlen funnels have therefore been used for decades to study the sensory capabilities and mechanisms that migratory birds use to find their way. A significant part of this research has focused on how night-migratory songbirds perceive the Earth’s magnetic field. Even though Emlen funnels have been proven quite successful in capturing the birds’ behavioural responses to different experimental conditions, the orientation behaviour of night-migratory songbirds in Emlen funnels is very noisy, i.e. tends to have a low signal to noise ratio. This noise makes Emlen funnel experiments very time consuming and limits the types of questions that can be studied to those which require very few different experimental conditions (permutations). Furthermore, the experimental design choices can be crucial, e.g. degree of blinding of the experimenters and data evaluators to the conditions tested, pre-testing of birds to make sure they are in a migratory state, and planning of the effective sample sizes. Hence, different traditions in experimental design choices can reduce reproducibility and comparability and render the interpretation of the results non-trivial. To better understand Emlen funnel data and the minimal requirements for good experimental design, we constructed and analyzed a large data set that we compiled by combining behavioural data from many previous Emlen funnel studies performed in Oldenburg. Our results provide realistic ranges for the expected orientation of the birds in Emlen funnels, which can be useful (and in some research crucial) for predicting the optimal sample sizes for future experiments. Our results thus offer concrete information for the design and analysis of statistically powerful future magnetic orientation experiments.
Ectopic head regeneration after nervous system ablation in a sea anemone
Authors: Mazloumi Gavgani Fatemeh , Kraus Johanna E.M. , November Joshua , Al-Shaer Layla , Seybold Anna Cosima , Lerstad Benjamin , Hausen Harald , Layden Michael J. , Rentzsch Fabian 
Published: February 2025

SUMMARYSome animals are able to regenerate all missing cell types and large body parts after bisection, a phenomenon called whole-body regeneration. Many of these animals regenerate the correct tissues and structures with remarkable fidelity according to the original polarity of the body, reflecting positional information present in the remaining tissue. Understanding the cellular and molecular basis of this positional information is a central question in regeneration biology. In planarians and acoels, muscle cells have been shown to carry such positional information, but where this information originates and whether this function is conserved in other highly regenerative animals, is not well understood. Here we use the cnidarianNematostella vectensisto address the role of the nervous system in whole-body regeneration. We generated a transgenic line for conditional ablation of neurons and first showed thatNematostellacan repeatedly regenerate its nervous system. Bisection experiments following nervous system ablation showed that all head fragments regenerate a second head instead of a foot, whereas foot fragments correctly regenerate the missing head. We further found that regenerating head fragments of nervous system-ablated animals increase the expression of Wnt signaling genes that in wildtype animals are only upregulated in regenerating foot fragments. These molecular changes and the initiation of ectopic head regeneration precede the re-appearance of neurons, suggesting that the nervous system does not directly control whether a head or foot will be regenerated. Instead, we propose a model in which the nervous system provides positional information to the tissue of the body column, and that this information allows foot regeneration by suppressing a default program for head regeneration.
Reduced inter-subject functional connectivity during movies in autism: Replicability across cross-national fMRI datasets
Authors: Lin Feng , Albantakis Laura , Noppari Tuomo , Santavirta Severi , Brandi Marie-Luise , Sun Lihua , Lukkarinen Lasse , Tani Pekka , Salmi Juha , Nummenmaa Lauri , Dukart Juergen , Schilbach Leonhard , Lahnakoski Juha M. 
Published: February 2025

AbstractBackgroundAutism is a neurodevelopmental disorder characterized by repetitive behaviors and difficulties in social communication and interaction. Previous research has shown that these symptoms are linked to idiosyncratic behavioral and brain activity patterns while viewing natural social events in movies. This study aimed to investigate the replicability of brain activity idiosyncrasy in autistic individuals by comparing their inter-subject functional connectivity (ISFC) with that of neurotypical individuals.MethodsWe tested for ISFC differences between autism and neurotypical groups using functional magnetic resonance imaging (fMRI) data from two independent datasets from Germany (Nneurotypical= 25, 7 Males, 18 Females; Nautism= 22, 12 Males, 10 Females) and Finland (Nneurotypical= 19, Nautism= 18; All males). Participants watched short movie stimuli, and pairwise ISFCs were computed across 273 brain regions. Group differences were evaluated using subject-wise permutation tests for each dataset.ResultsIn both datasets, the autism group showed lower ISFCs compared to the neurotypical group, specifically between visual regions (e.g., occipital gyrus, cuneus) and parietal regions (e.g., superior and inferior parietal lobules), as well as between visual regions and frontal regions (e.g., inferior frontal gyrus, precentral gyrus). ISFC was higher in the Finnish autism group in temporal regions associated with sound and speech processing.ConclusionsThe study confirmed the replicability of reduced ISFCs in autistic individuals during naturalistic movie-watching, especially between visual and parietal/frontal brain regions. These findings reinforce the utility of ISFC and naturalistic movie-watching paradigm in studying neural connectivity alterations in autism.
Distinct Structural Connectivity Patterns Associated with Variations in Language Lateralisation
Authors: Andrulyte Ieva , Zago Laure , Jobard Gael , Lemaitre Herve , Rheault Francois , Keller Simon S , Petit Laurent 
Published: February 2025

AbstractHemispheric asymmetries in white matter tracts are proposed key determinants of language lateralisation, yet evidence in healthy individuals remains inconsistent. This suggests that simple tractography techniques might not be sensitive enough to identify language dominance. Significant insights into the functional organization of the human brain may be achieved by considering networks and brain connectivity, providing more information about discrepancies in people with different hemispheric language dominance. In this study, we examined 285 healthy participants compare their structural connectomes at the whole-brain level and determine the networks responsible for the three different functional language lateralisation groups (typical, atypical and strongly atypical). Probabilistic tractography generated whole-brain tractograms, and white matter fibres were filtered according to anatomical Boolean guidelines. Connectivity matrices with nodes corresponding to supramodal sentence areas in the language atlas and edges weighted by fractional anisotropy (FA) were generated to compare the groups using graph theory and network-based statistic (NBS) approaches. We demonstrated that both atypical (bilateral) and strongly atypical (right-lateralised) lateralisation are characterised by heightened interhemispheric temporal connectivity. Post-hoc analyses showed that strongly atypical individuals exhibited increased temporo-frontal connectivity, while atypical individuals had enhanced temporal and frontal connectivity but lacked temporo-frontal connections. These connectivity patterns diverge from traditional models of hemispheric dominance, suggesting a reliance on integrated bilateral networks in atypically lateralised individuals. This reflects distinct neural mechanisms underlying atypical language organisation, departing from developmental trajectory of typical lateralisation and offering insights into cognitive flexibility and clinical applications.
Coordinated representational drift supports stable place coding in hippocampal CA1
Authors: Sylte Ole Christian , Kilias Antje , Bartos Marlene , Sauer Jonas-Frederic 
Published: February 2025

SummaryThe phenomenon of representational drift (i.e., changing neuronal tuning during repeated exposure to the same stimuli), is a fundamental paradox in neuroscience that raises the question how stable behaviour can emerge from unstable neural representations. Place cells in CA1 of the hippocampus are crucial for spatial navigation and memories1but show gradual changes in their preferred firing location over time when exposed to the same environment2–9. This drift occurs despite the fact that the animal maintains the ability to navigate and to perform spatial tasks, suggesting a complex relationship between neural activity and behaviour. Here, we show that while the spatial tuning functions of individual CA1 neurons drift over time, stable space coding prevails at the population level: Representational drift is not random but can be described as a translation and rotation in population state space, which preserves the internal geometry of population activity over time. Compensating for the coordinated translation and rotation allows for drift correction and a recovery of spatial tuning on future days. Moreover, the preserved internal geometry stabilises downstream readout under noisy conditions. We propose that the conserved population geometry might serve as a mechanism by which downstream reader networks achieve effective drift correction and, thus, ameliorate the readout of stable information.
Characterization ofMycobacterium tuberculosisrhodanese-like sulfurtransferase SseA and its newly identified activator Rv3284: A new pathway to exploit as a drug target?
Authors: Napoli Giulia Di , Fissore Alex , Salladini Edoardo , Raccuia Eleonora , Oliaro-Bosso Simonetta , Ruggiero Alessia , Berisio Rita , Medina Milagros , Velazquez-Campoy Adrian , Adinolfi Salvatore , Marengo Mauro 
Published: February 2025

AbstractTuberculosis (TB) remains a critical global health challenge, withMycobacterium tuberculosis(Mtb) causing 10.8 million cases and 1.25 million deaths in 2023. Key issues include the dormant state of Mtb, resistant to drugs and immune responses, and the emergence of multi-drug-resistant strains. This underscores the need for new therapeutic targets and deeper research into Mtb pathogenesis and immunology.A potential drug target is the enzyme thiosulfate-sulfurtransferase SseA, which plays a role in macrophage infection by Mtb and its resistance to oxidative stress. SseA belongs to the rhodanese-like enzyme family, which catalyzes sulfur transfer reactions essential for Mtb survival.In our research, we identified a new protein (Rv3284), hereinafter referred to as SufEMtbdue to its high homology withE. coliSufE, that interacts with SseA and modulates its activity. Sequence analysis and AI molecular modelling revealed detailed insights into their interaction that can contribute to the modulation of SseA activity. This research provides a mechanistic explanation to the need of a partner for SseA activation. Indeed, we propose that SufEMtbenhances SseA enzymatic function by binding to its non-catalytic N-terminal domain and bringing the active sites of the two proteins in close proximity, thus preparing for the activation-enhancing conformational change in a regulatory loop of SseA. This interaction is crucial for the effective enzyme activity and the maintenance of redox homeostasis in Mtb, making the SseA-SufEMtbprotein complex a potential target for new TB therapies.
Spatial coding supports auditory conceptual navigation
Authors: Jasmin Kyle , Bullock Max , Dick Frederic , Atkins Roger , Bottini Roberto , Sigismondi Federica , Tierney Adam 
Published: February 2025

AbstractGrid cells in human entorhinal cortex encode spatial layouts for real-world navigation, yet their role in conceptual navigation remains unclear. Here we show that mentally transforming tones within a purely auditory pitch-duration space engages spatial circuits, and that such resources are causally necessary. In Experiment 1, participants trained for five days to navigate through a purely conceptual pitch-duration auditory space, then underwent fMRI on Day 6. We observed a six-fold modulation of entorhinal BOLD signals aligned to each participant’s trajectory angles, similar to grid-cell firing in physical space. Stronger grid-like coding predicted larger training-related gains. In Experiment 2, a new cohort performed the same task under either a spatial or non-spatial interference load. Only the spatial condition selectively disrupted performance on trials requiring mental “movement,” indicating a causal reliance on spatial resources. These findings provide evidence that auditory conceptual transformations recruit—and depend on—spatial grid-like computations in the entorhinal-hippocampal system, pointing to a domain-general role for spatial coding in organizing new knowledge along continuous dimensions.
Commercially Relevant Species in the Mediterranean Sea: A Perspective from Late Pleistocene to the Industrial Revolution
Authors: Leal Daniela , Agiadi Konstantina , Bas Maria 
Published: February 2025

ABSTRACTThe Mediterranean Sea is the world’s second-largest biodiversity hotspot and has been impacted by several environmental changes and human activities since pre-historic times. We present the results of a systematic review of the published literature on the nature and extent of these impacts on the ancient–historic Mediterranean marine ecosystems. We aim to provide an overview of the current state of knowledge and identify research gaps about climate and human-activity impacts on commercially relevant species of marine mammals, fishes, and molluscs in the Mediterranean Sea over the last 130 thousand years until the Industrial Revolution (the year 1850). In most of the reviewed publications, species were used as indicators of past climatic conditions or human subsistence strategies. A research gap remains, however, in quantifying their effects on marine ecosystems. Based on our results, we identify data trends in time and space and by functional group. Data are available primarily from the Holocene rather than the Late Pleistocene, reflecting a heterogeneous availability of records. The Adriatic Sea is underrepresented among subregions, which may indicate variability of accessible data between subregions, rather than an actual lack of information. Marine mammals were less studied than fishes and molluscs in the three subregions. Despite the lack of standardised guidelines to conduct studies and subsequent variability in information, this work provides novel insights into the importance of studying the evolution of research focused on past environmental and anthropogenic impacts in the Mediterranean Sea. Research efforts need to be balanced to examine both economically and ecologically valuable species in the marine ecosystem. We also reinforce the need for uniform approaches to gather data in a usable format for posterior research.
Risk preferences depend on environmental richness in rats performing a patch-foraging task
Authors: Garcia Marissa , Wikenheiser Andrew M. 
Published: February 2025

AbstractRisk, or variance over outcomes, features prominently in many decisions, but the factors that determine when and how risk modulates decision making remain unclear. We tested how risk affected rats’ strategies for exploiting a diminishing food source as the overall richness of the environment was manipulated. Long-Evans rats earned food by sequentially visiting two foraging patches with different reward schedules—a low-variance standard option and a high-variance risky option—that provided the same average rate of reward. When rats switched between options, they encountered either a long or short delay during which no food was available to simulate the cost of travelling between patches. When the travel delay was short rats allocated more time to the low-variance standard reward schedule than the high-variance risky option. When the travel time was long rats spent the same amount of time in risky and standard patches. Consistent with previous work, rats “overharvested” patches, remaining for longer than the optimal patch residence duration. Overharvesting was prevalent in both risky and standard patches, and the magnitude of overharvesting increased with successive visits to the same patch, suggesting that overharvesting was not driven by uncertainty about the reward statistics of patches.