bluuebunny/crossref_metadata_2025 huggingface dataset:
CUT&Tag Identifies Repetitive Genomic Loci that are Excluded from ChIP Assays
Authors: Park Brandon J , Hua Shan , Casler Karli D , Cefaloni Eric , Ayers Michael C , Lake Rahiim F , Murphy Kristin E , Vertino Paula M , O’Connell Mitchell R. , Murphy Patrick J
Published: February 2025

Determining the genomic localization of chromatin features is an essential aspect of investigating gene expression control, and ChIP-Seq has long been the gold standard technique for interrogating chromatin landscapes. Recently, the development of alternative methods, such as CUT&Tag, have provided researchers with alternative strategies that eliminate the need for chromatin purification, and allow forin situinvestigation of histone modifications and chromatin bound factors. Mindful of technical differences, we set out to investigate whether distinct chromatin modifications were equally compatible with these different chromatin interrogation techniques. We found that ChIP-Seq and CUT&Tag performed similarly for modifications known to reside at gene regulatory regions, such as promoters and enhancers, but major differences were observed when we assessed enrichment over heterochromatin-associated loci. Unlike ChIP-Seq, CUT&Tag detects robust levels of H3K9me3 at a substantial number of repetitive elements, with especially high sensitivity over evolutionarily young retrotransposons. IAPEz-int elements for example, exhibited underrepresentation in mouse ChIP-Seq datasets but strong enrichment using CUT&Tag. Additionally, we identified several euchromatin-associated proteins that co-purify with repetitive loci and are similarly depleted when applying ChIP-based methods. This study reveals that our current knowledge of chromatin states across the heterochromatin portions of the mammalian genome is extensively incomplete, largely due to limitations of ChIP-Seq. We also demonstrate that newerin situchromatin fragmentation-based techniques, such as CUT&Tag and CUT&RUN, are more suitable for studying chromatin modifications over repetitive elements and retrotransposons.

Highlights

In situfragmentation overcomes biases produced by ChIP-Seq.

Heterochromatic regions of the genome are lost to the insoluble pellet during ChIP-Seq.

CUT&Tag allows for mapping chromatin features at young repetitive elements.

Euchromatin-associated regulatory factors co-purify with insoluble heterochromatin.
Mycobacterium intracellulareABSURDO is a novel clinical isolate with three colony morphotypes that vary in pathogenicity and sequence at thePKSandMtrAloci
Authors: Claeys Tiffany A. , Liu Yijing , Prigodich Anneka , Peck Emily , Gokul Emily , Reed-Mera Nine , Tuah Albright , Wirekoh Abena , Quinn Kylie , Rosas Mejia Oscar , Clary Gillian , Sasindran Smitha , Dellos-Nolan Sheri , Gloag Erin , Huppler Anna R. , Hull Natalie M. , Jude Brooke A. , Robinson Richard T.
Published: February 2025

Mycobacterium intracellulareis a nontuberculous mycobacteria (NTM) species which can cause serious and sometimes fatal disease in immunocompromised individuals. Other NTM species, includingM. aviumandM. abscessus, commonly exhibit two colony morphotypes (smooth and rough) which vary in appearance and liquid growth properties. Here we characterize a novel clinical isolate ofM. intracellularewhich exhibits three (not two) colony morphotypes which differ in appearance, liquid growth properties, acid-fastness andin vivosurvival following infection of mice via an inhalational exposure model. The genome of this isolate, which we have termed ABSURDO, as well as the genome of each morphotype components, aligns with that ofM. intracellulareyet contains ∼16% more protein coding sequences than theM. intracellularetype strain ATCC 13590T. Variation analysis of each morphotype genome revealed that across the three morphotypes there were only two mutations which had a high likelihood of causing a phenotype due to a genetic change: one in the gene encoding modular polyketide synthase (PKS), and another in the two component system response regulator MtrA. Neither of these genes have been previously implicated in the morphotype shifting of an NTM. In summary,M. intracellulareABSURDO is a novel pathogenic isolate with a genome that aligns with (but is nevertheless larger than) theM. intracellularetype strain and comprises three morphotype components which differ in two genes that have not been implicated in NTM appearance, acid-fastness,in vitroandin vivogrowth.
Identification of Antituberculars with Favorable Potency and Pharmacokinetics through Structure-Based and Ligand-Based Modeling
Authors: Warapande Vedang , Meng Fanwang , Bozan Alexandra , Graff David E. , Fromer Jenna C. , Mughal Khadija , Mohideen Faheem K. , Shivangi  , Paruchuri Sindhuja , Johnston Melanie L. , Sharma Pankaj , Crea Timothy R. , Rudraraju Reshma S. , George Amir , Folvar Camilla , Nelson Andrew M. , Neiditch Matthew B. , Zimmerman Matthew D. , Coley Connor W. , Freundlich Joel S.
Published: February 2025

Drug discovery is inherently challenged by a multiple criteria decision making problem. The arduous path from hit discovery through lead optimization and preclinical candidate selection necessitates the evolution of a plethora of molecular properties. In this study, we focus on the hit discovery phase while beginning to address multiple criteria critical to the development of novel therapeutics to treatMycobacterium tuberculosisinfection. We develop a hybrid structure- and ligand-based pipeline for nominating diverse inhibitors targeting the β-ketoacyl synthase KasA by employing a Bayesian optimization-guided docking method and an ensemble model for compound nominations based on machine learning models forin vitroantibacterial efficacy, as characterized by minimum inhibitory concentration (MIC), and mouse pharmacokinetic (PK) plasma exposure. The application of our pipeline to the Enamine HTS library of 2.1M molecules resulted in the selection of 93 compounds, the experimental validation of which revealed exceptional PK (41%) and MIC (19%) success rates. Twelve compounds meet hit-like criteria in terms of MIC and PK profile and represent promising seeds for future drug discovery programs.
Quorum Sensing Regulators and Non-ribosomal Peptide Synthetases Govern Antibacterial Secretions inXenorhabdus szentirmaii
Authors: Dey Ritisha , Valle Domonique Olivia , Chakraborty Abhijit , Mayer Kimberly A , Uppala Jagadeesh , Chakraborty Anish , Mirza Shama , Forst Steven , Skwor Troy , Dey Madhusudan
Published: February 2025

The decades-long gap in antibiotic discovery has led to a significant health crisis due to antimicrobial resistance (AMR). The bacterial genusXenorhabdus, which forms symbiotic relationships with the soil nematodeSteinernema, are known to secrete a variety of antimicrobial compounds with potential effectiveness against AMR. These antimicrobial compounds are primarily bio-synthesized by non-ribosomal peptide synthetases (NRPS) and polyketide synthetase (PKS) genes. In this study, we report thatX. szentirmaiiproduces high levels of antibiotic activity during the stationary phase against diverse bacteria including known antibiotic resistant pathogens. It possesses 17 operons to encode predicted NRPS and PKS enzymes, designated asste1throughste17. Theste15-ste16andste17operons are predicted to produce the known antibiotics Pax peptide and Fabclavine, respectively. Additionally, the newly identified operonsste3,ste4,ste5,ste8, ste9, andste14consist of single genes, each containing two or moreNRPSgenes. Theste13operon harbors twoNRPSgenes, while the ste7 and ste12 operons contain threeNRPSgenes each. Further, RNA-seq analysis showed thatlsrFthat encodes a quorum sensing autoinducer-2 (AI-2) aldolase was expressed at high levels during stationary phase. These findings provide evidence thatX. szentirmaiiuses quorum sensing (QS) to synchronize the expression of multiple NRPS and PKS enzymes responsible for synthesizing various antimicrobial compounds. This study underscores the potential to leverage these regulatory insights for maximizing commercial applications of novel antibiotics combating AMR, as well as broader industrial uses.
Active surveillance of cats and dogs from households with human COVID-19 cases reveals over one quarter of pets infected with SARS-CoV-2 in 2020-2021 in Texas, United States
Authors: Pauvolid-Corrêa Alex , Davila Edward , Auckland Lisa D. , Zecca Italo B. , Busselman Rachel E. , Tang Wendy , Roundy Christopher M. , Killian Mary Lea , Torchett Mia K. , Jenkins-Moore Melinda , Austerman Suelee Robbe , Lantz Kris , Mozingo Katherine , Tell Rachel , Lim Ailam , Akpalu Yao , Fischer Rebecca S. B. , Ferreira Francisco C. , Hamer Gabriel L. , Hamer Sarah A.
Published: February 2025

Households where people have COVID-19 are high risk environments for companion animals that are susceptible to SARS-CoV-2. We sampled 579 pets from 281 households with one or more laboratory-confirmed person with COVID-19 in central Texas from June 2020 to May 2021. Nineteen out of 396 (4.8%) dogs and 21 out of 157 (13.4%) cats were positive for SARS-CoV-2 by RT-qPCR. Additionally, 95/382 (25%) dogs and 52/146 (36%) cats harbored SARS-CoV-2 neutralizing antibodies. Twenty-six companion animals of ten other species were negative. Overall, 164 (29%) pets were positive for SARS-CoV-2 by molecular and/or serological tests; a total of 110 (39%) out of 281 households had at least one animal with active or past SARS-CoV-2 infection. Cats were more likely to be infected by SARS-CoV-2 and had higher endpoint antibody titers than dogs. Through viral isolation from a subset of respiratory swabs, we documented 6 different lineages in dogs and cats, including the B.1.1 lineage in a cat one month prior to the first known human case in the country. We observed animal and human-pet interaction factors associated with higher risk of infection for dogs and cats, such as days after COVID-19 diagnosis and sharing food. Frequency of clinical signs of disease reported by owners of pets with active infections did not differ from uninfected ones, suggesting that not all reported signs are attributed to SARS-CoV-2 infection. Characterizing animal infections using active SARS-CoV-2 surveillance in pets at risk of infection may aid in One Health pandemic prevention, response, and management.
Genetic basis of partner choice
Authors: Zheng Qinwen , van Alten Sjoerd , Lyngstad Torkild Hovde , Ciscato Edoardo , Sun Zhongxuan , Miao Jiacheng , Wu Yuchang , Dorn Stephen , Zheng Boyan , Havdahl Alexandra , Corfield Elizabeth C. , Nivard Michel , Galama Titus J. , Turley Patrick , Chiappori Pierre-André , Fletcher Jason M. , Lu Qiongshi
Published: February 2025

Previous genetic studies of human assortative mating have primarily focused on searching for its genomic footprint but have revealed limited insights into its biological and social mechanisms. Combining insights from the economics of the marriage market with advanced tools in statistical genetics, we perform the first genome-wide association study (GWAS) on a latent index for partner choice. Using 206,617 individuals from four global cohorts, we uncover phenotypic characteristics and social processes underlying assortative mating. We identify a broadly robust genetic component of the partner choice index between sexes and several countries and identify its genetic correlates. We also provide solutions to reduce assortative mating-driven biases in genetic studies of complex traits by conditioning GWAS summary statistics on the genetic associations with the latent partner choice index.
Genome-wide association study of neuropathic pain phenotypes implicates loci involved in neural cell adhesion, channels, collagen matrix formation and immune regulation
Authors: Packer Richard , Coley Kayesha , Williams Alexander T , Shrine Nick , Izquierdo Abril G , Chen Jing , Batini Chiara , Marttila Mikko , Rao Balasubramanya S , Bratty Raymond , Dudbridge Frank , Hennah William , Tobin Martin D.
Published: February 2025

Background

Neuropathic pain is a common and debilitating symptom with limited treatment options. Genetic studies, which can provide vital evidence for drug development, have identified only five genome-wide significant signals for neuropathic pain traits. To address this, we performed the largest genome-wide association study (GWAS) to date of all-cause neuropathic pain and neuropathic pain subtypes.

Methods

We defined all-cause neuropathic pain and 33 neuropathic pain subtypes using DeepPheWAS software in the UK Biobank, taking advantage of the longitudinal drug prescription data alongside clinical and self-reported records. We performed a GWAS of all-cause neuropathic pain (33,278 cases, 140,134 controls) as our primary analysis and GWASs of neuropathic pain subtypes as secondary analyses. We used eight variant-to-gene criteria to identify putative causal genes.

Results

We identified seven independent novel genome-wide associations for neuropathic pain phenotypes which mapped to 22 novel putative causal genes.NCAM1was the only gene identified from the primary analysis of all-cause neuropathic pain and met the most variant-to-gene criteria (four) of any identified gene. Of the 21 other genes,ASCC1, CHST3, C4A/C4BandKCNN2had the most compelling evidence for mechanistic involvement in neuropathic pain.

Discussion

We have performed the largest GWAS to date of all-cause neuropathic pain and more than doubled the number of genome-wide significant associations for neuropathic pain traits, identifying putative causal genes. There is strong evidence for the involvement ofNCAM1in neuropathic pain which merits for further study for drug development.
Rapid water flow navigates long-distance migration of thermophilic bacteria
Authors: Uemura Naoki A. , Chiba Naoya , Morikawa Ryota , Tamakoshi Masatada , Nakane Daisuke
Published: February 2025

Bacteria thrive in nearly all environments on Earth, demonstrating remarkable adaptability to physical stimuli, as well as chemicals and light. However, the mechanisms by which bacteria locate and settle in ecological niches optimal for their growth remains poorly understood. Here, we show thatThermus thermophilus, a highly thermophilic non-flagellated species of bacteria, exhibits positive rheotaxis, navigating upstream in unidirectional rapid water flow. Mimicking their natural habitat at 70°C with a water current under optical microscopy, cells traveled distances up to 1 mm in 30 min, with infrequent directional changes. This long-distance surface migration is driven by type IV pili, facilitating vertical attachment at the cell pole, and shear-induced tilting of the cell body, resulting in alignment of the leading pole toward the direction of water flow. Direct visualization of T4P filaments and their dynamics revealed that rheotaxis is triggered by weakened attachment at the cell pole, regulated by ATPase activity, which was further validated by a mathematical modeling. Flow experiments on 16 bacterial strains and species in theDeinococcus-Thermusphylum revealed that positive rheotaxis is highly conserved among rod-shapedThermaceae, whereas no rheotactic behavior was observed in spherical-shapedDeinococcus. Our findings suggest that thermophilic bacteria reach their ecological niches by responding to the physical stimulus of rapid water flow, a ubiquitous feature in hot spring environments. This study highlights unforeseen survival strategies, showcasing an evolutionary adaptation to a surface-associated lifestyle where swimming bacteria would otherwise be swept away.
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

Ultrasonic 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

Transfer 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

Recent 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

Targeted 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

Emlen 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

Some 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

Background

Autism 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.

Methods

We 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.

Results

In 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.

Conclusions

The 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

Hemispheric 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

The 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

Tuberculosis (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

Grid 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

The 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

Risk, 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.
Critical Evaluation of Sphingolipids Detection by MALDI-MSI
Authors: Chen Bo , Pathak Ranjana , Subekti Albar , Cheng Xiaolu , Singh Sukhjit , Ostermeyer-Fay Anne G. , Hannun Yusuf A. , Luberto Chiara , Canals Daniel
Published: February 2025

The increasing interest in the role of sphingolipids in (patho)physiology has led to the demand for visualization of these lipids within tissue samples (both from animal models and patient specimens) using techniques such as matrix-assisted laser desorption/ionization mass spectrometry imaging (MALDI-MSI). While increasingly adopted, detection of sphingolipids with MALDI-MSI is challenging due to: i) the significant structural variations of sphingolipid molecules, ii) the potential breakdown of the more complex molecules into structurally simpler species which may confound the analysis, and iii) the great difference in levels among sphingolipid classes and subspecies, with the low-abundant ones often being close to the detection limit. In this study, we adopted a multi-pronged approach to establish a robust pipeline for the detection of sphingolipids by MALDI-MSI and to establish best practices and limitations of this technology. First, we evaluated the more commonly adopted methods [2,5-Dihydroxyacetophenon (DHA) or 2,5-Dihydroxybenzoic acid (DHB) matrix in positive ion mode and 1,5-Diaminonaphthalene (DAN) matrix in negative ion mode] using MALDI-MS on reference standards. These standards were used at ratios similar to their relative levels in biological samples to evaluate signal artifacts originating from fragmentation of more complex sphingolipids and impacting low level species. Next, by applying the most appropriate protocol for each sphingolipid class, MALDI-MSI signals were validated in cell culture by modulating specific sphingolipid species using sphingolipid enzymes and inhibitors. Finally, the optimized parameters were utilized on breast cancer tissue from the PyMT mouse model.

We report the optimal signal for sphingomyelin (SM) and, for the first time, Sph in DHB positive ion mode (in cells and PyMT tissue), and the validated detection of ceramides and glycosphingolipids in DAN negative ion mode. We document the extensive fragmentation of SM into sphingosine-1-phosphate (S1P) and even more so into ceramide-1-phosphate (C1P) using DAN in negative ion mode and its effect in generating an artifactual C1P tissue signal; we also report the lack of detectable signal for S1P and C1P in biological samples (cells and tissue) using the more suitable DHB positive ion mode protocol.
CryoEM-enabled visual proteomics revealsde novostructures of oligomeric protein complexes fromAzotobacter vinelandii
Authors: Warmack Rebeccah A. , Maggiolo Ailiena O. , Shen Yuanbo , Zhang Tianzheng
Published: February 2025

Single particle cryoelectron microscopy (cryoEM) and cryoelectron tomography (cryoET) are powerful methods for unveiling unique and functionally relevant structural states. Aided by mass spectrometry and machine learning, they promise to facilitate the visual exploration of proteomes. Leveraging visual proteomics, we interrogate structures isolated from a complex cellular milieu by cryoEM to identify and classify molecular structures and complexesde novo. That approach determines the identity of six distinct oligomeric protein complexes from partially purified extracts ofAzotobacter vinelandiiusing both anaerobic and aerobic cryoEM. Identification of the first unknown species, phosphoglucoisomerase (Pgi1), is achieved by comparing three automated model building programs: CryoID, DeepTracer, and ModelAngelo with or withouta prioriproteomics data. All three programs identify the Pgi1 protein, revealed to be in a new decameric state, as well as additional globular structures identified as glutamine synthetase (GlnA) and bacterioferritin (Bfr). Large filamentous assemblies are observed in tomograms reconstructed from cryoFIB milled lamellae of nitrogen-fixingA. vinelandii. Enrichment of these species from the cells by centrifugation allows for structure determination of three distinct filament types by helical reconstruction methods: the Type 6 Secretion System non-contractile sheath tube (TssC), a novel filamentous form of the soluble pyridine transhydrogenase (SthA), and the flagellar filament (FliC). The multimeric states of Pgi1 and SthA stand out in contrast to known crystallographic structures and offer a new structural framework from which to evaluate their activities. Overall, by allowing the study of near-native oligomeric protein states, cryoEM-enabled visual proteomics reveals novel structures that correspond to relevant species observedin situ.

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Systematic Investigation of Double Emulsion Dewetting Dynamics for the Droplet Microfluidic Production of Giant Unilamellar Vesicles (GUVs) under Biocompatible Conditions
Authors: Jing Wenyang , Noh Heewon , Tan Timothy J. C. , Wu Nicholas C. , Han Hee-Sun
Published: February 2025

Giant unilamellar vesicles (GUVs) embody biomimetic membranes with compartmentalization that serve not only as simplified models to better understand complex biochemical and biophysical processes, but also as a chassis for the bottom-up assembly of synthetic cells. Recently, double emulsion droplet microfluidics has proven to be a promising platform for their production, offering greater throughput, control, and reproducibility over traditional methods. However, the interplay of parameters—particularly under biocompatible conditions—that influence the complex multiphase fluid dynamics of the dewetting process underlying GUV production has not been thoroughly studied, limiting the democratization of the approach. In this study, we systematically investigate how lipid composition and concentration, aqueous phase conditions, droplet confinement, and fluid dynamics effects promote or impede the dewetting process. We show that the prevalent use of high concentrations of glycerol and P188 are unnecessary, and the altered dewetting dynamics with restricted surfactant usage can be tuned by adjusting chip dimensions and multi-phase compositions. Guided by these findings, we achieved robust, high throughput production of monodisperse GUVs using 0.1% P188 and no glycerol with salts. Our results improve the reliability and accessibility of droplet-microfluidics GUV platforms to catalyze advances in biophysics, synthetic biology, and drug discovery.
Structural variation, selection, and diversification of theNPIPgene family from the human pangenome
Authors: Dishuck Philip C. , Munson Katherine M. , Lewis Alexandra P. , Dougherty Max L. , Underwood Jason G. , Harvey William T. , Hsieh PingHsun , Pastinen Tomi , Eichler Evan E.
Published: February 2025

TheNPIP(nuclear pore interacting protein) gene family has expanded to high copy number in humans and African apes where it has been subject to an excess of amino acid replacement consistent with positive selection (1). Due to the limitations of short-read sequencing,NPIPhuman genetic diversity has been poorly understood. Using highly accurate assemblies generated from long-read sequencing as part of the human pangenome, we completely characterize 169 human haplotypes (4,665NPIPparalogs and alleles). Of the 28NPIPparalogs, just three (NPIPB2,B11, andB14) are fixed at a single copy, and only a single locus,B2, shows no structural variation. FourNPIPparalogs map to large segmental duplication blocks that mediate polymorphic inversions (355 kbp–1.6 Mbp) corresponding to microdeletions associated with developmental delay and autism. Haplotype-based tests of positive selection and selective sweeps identify two paralogs,B9andB15, within the top percentile for both tests. Using full-length cDNA data from 101 tissue/cell types, we construct paralog-specific gene models and show that 56% (31/55 most abundant isoforms) have not been previously described in RefSeq. We define six distinct translation start sites and other protein structural features that distinguish paralogs, including a variable number tandem repeat that encodes a beta helix of variable size that emerged ∼3.1 million years ago in human evolution. Among the 28NPIPparalogs, we identify distinct tissue and developmental patterns of expression with only a few maintaining the ancestral testis-enriched expression. A subset of paralogs (NPIPA1,A5,A6-9,B3-5, andB12/B13) show increased brain expression. Our results suggest ongoing positive selection in the human population and rapid diversification ofNPIPgene models.