bluuebunny/crossref_metadata_2025 huggingface dataset:
Murine gut microbiota dysbiosis via enteric infection modulates the foreign body response to a distal biomaterial implant
Authors: Yang Brenda , Rutkowski Natalie , Ruta Anna , Gray-Gaillard Elise , Maestas David R. , Kelly Sean H. , Krishnan Kavita , Wu Xinqun , Wu Shaoguang , Chen Allen , Amelung Connor D. , Mejías Joscelyn C. , Hooks Joshua S. T. , Vanderzee Isabel , Mensah Patricia , Celik Nazmiye , Eric Marie , Abraham Peter , Tam Ada , Gerecht Sharon , Housseau Franck , Pardoll Drew M. , Sears Cynthia L. , Elisseeff Jennifer H.
Published: January 2025

The gut microbiota influences systemic immunity and the function of distal tissues, including the brain, liver, skin, lung, and muscle. However, the role of the gut microbiota in the foreign body response (FBR) and fibrosis around medical implants is largely unexplored. To investigate this connection, we perturbed the homeostasis of the murine gut microbiota via enterotoxigenicBacteroides fragilis(ETBF) infection and implanted the synthetic polymer polycaprolactone (PCL) into a distal muscle injury. ETBF infection in mice led to increased neutrophil and γδ T cell infiltration into the PCL implant site. ETBF infection alone promoted systemic inflammation and increased levels of neutrophils in the blood, spleen, and bone marrow. At the PCL implant site, we found significant changes in the transcriptome of sorted fibroblasts but did not observe gross ETBF- induced differences in the fibrosis levels after 6 weeks. These results demonstrate the ability of the gut microbiota to mediate long-distance effects such as immune and stromal responses to a distal biomaterial implant.

Significance Statement

The foreign body response to implants leads to chronic inflammation and fibrosis that can be highly variable in the general patient population. Here, we demonstrate that gut dysbiosis via enteric infection promoted systemic inflammation and increased immune cell recruitment to an anatomically distant implant site. These results implicate the gut microbiota as a potential source of variability in the clinical biomaterial response and illustrate that the local tissue environment can be influenced by host factors that modulate systemic interactions.
Charge-based fingerprinting of unlabeled full-length proteins using an aerolysin nanopore
Authors: Rukes Verena , Norkute Evita , Barnikol Georges , Duan Jingze , Gao Jiajie , Cao Chan
Published: January 2025

Proteins play essential roles in cellular processes and are involved in numerous diseases, driving the need for efficient proteoform identification. While nanopore technology was highly successful for DNA sequencing, this approach has not yet delivered its full potential in protein identification. Here, we demonstrate the capabilities of an aerolysin nanopore for direct identification of a range of unlabeled full-length proteins. Combining low pH and guanidinium chloride, we generate a strong electroosmotic flow that enables an efficient capture and translocation, resulting in distinct fingerprints from single-protein translocations. Using machine learning classifier, we achieve 80% accuracy in distinguishing seven related proteins with 38%–70% pairwise sequence identities. Differences in fingerprints largely reflect the distribution of positive charges in the protein sequences, providing a rational basis for the observed sensitivity. With further development, fingerprint-predictions could allow to inferde novoprotein sequence information from single-molecule data, offering a powerful tool for proteomics.
3D Multiphoton Nanolithography with Bioresorbable Amino Acid-Based Resins
Authors: Naderer Christoph , Sivun Dmitry , Haudum Stefan , Teasdale Ian , Jacak Jaroslaw
Published: January 2025

We demonstrate that the newly designed amino acid phosphordiamidate-resins (APdA), containing vinyl reactive groups for polymerization, can be utilized to fabricate sub – 100 nm features through 3D multiphoton lithography. We have quantitatively analyzed the feature size, Young’s modulus, and functionalization of the nanostructures using atomic force and single-molecule fluorescence microscopy. Our results indicate that the polymer backbone, composed of either valine or alanine, imparts hydrophobic properties to the monomer, restricting the swelling of the polymeric nanostructure to 8% in aqueous environments. Despite minimal swelling, experiments revealed an up to 10-fold change of Young’s modulus for dry versus wet conditions. To enhance the versatility of the APdA-based structures, we incorporated biotin functionalization and utilized it for the immobilization of extracellular vesicles. Hence, these findings highlight the potential of APdA-based nanolithography photoresists for biomedicine and nanotechnology applications.
Support for the deuterostome clade comes from systematic errors
Authors: Silva Ana Serra , Natsidis Paschalis , Piovani Laura , Kapli Paschalia , Telford Maximilian J.
Published: January 2025

There is a long-standing consensus that the animal phyla closest to our own phylum of Chordata are the Echinodermata and Hemichordata. These three phyla constitute the major clade of Deuterostomia. Recent analyses have questioned the support for the monophyly of Deuterostomia, however, showing that the branch leading to deuterostomes is very short and may be influenced by systematic error. Here we use a site-by-site approach to explore multiple sources of error. Under conditions that promote long-branch attraction (LBA) – especially branch-length heterogeneity and sites constrained in their amino acid composition – we find that deuterostome monophyly is strongly supported. When we make efforts to mitigate these sources of error, we cannot distinguish between monophyletic and paraphyletic Deuterostomia. Our findings have implications for the interpretation of putative deuterostome fossils, for the reconstruction of a bilaterian ancestor and, more generally, for how datasets for deep-time phylogenetic analyses are assembled and analyzed.

Teaser

The apparently close relationship between Chordata and Ambulacraria (echinoderms and hemichordates) is boosted by a long-branch attraction artefact.
Novel Carbohydrate-substituted Indazole Derivatives Targeting SGLT1 Enhance the Efficacy of Receptor Tyrosine Kinase Inhibitors in Cancer Therapy
Authors: Sun Zhongjie , Qi Hailong
Published: January 2025

Receptor tyrosine kinase (RTK) inhibitors have demonstrated significant efficacy in treating malignant tumors. However, the development of drug resistance and limited efficacy in RTK inhibitor-insensitive patients pose challenges to their clinical application. To enhance the efficacy for RTK inhibitors-insensitive patients and overcome the resistance, beyond developing new RTK inhibitors, combination therapy has emerged as a promising approach. In this study, we discovered a novel compound,071, featuring an indazole core flanked by a carbohydrate moiety and two phenyl groups, which exhibits synergistic anti-tumor activity when combined with various RTK inhibitor. Several series of071analogues were synthesized through structure modification and evaluated the synergistic anti-tumor effects and the metabolic stability. Compound10d-02emerged as notably more potent in synergistic anti-tumor activity and demonstrated greater stability than compound071. Notably, the combination of compound10d-02and multiple RTK inhibitors significantly enhanced in vivo efficacy in both RTK inhibitor-sensitive and -insensitive tumor xenograft models without evident toxicity. Furthermore, compound10d-02exhibited an excellent pharmacokinetic profile with nearly 100% oral bioavailability. Using click chemistry technology combined with mass spectrometry analysis, we identified SGLT1 as a potential target for10d-02. SGLT1 has been previously proven to bind and stabilize EGFR, and we further discovered that SGLT1 also binds and stabilizes VEGFR2/3. While compound10d-02could partially block the interaction between SGLT1 and EGFR/VEGFRs, leading to the instability and degradation of EGFR and VEGFRs, potentially elucidating the mechanism of its synergistic effect with RTK inhibitors. Thus, compound10d-02holds substantial promise for use in combination therapies with RTK inhibitors in tumor clinical treatment.
Rare Variant Analyses in Ancestrally Diverse Cohorts Reveal Novel ADHD Risk Genes
Authors: Jung Seulgi , Caballero Madison , Olfson Emily , Newcorn Jeffrey H. , Fernandez Thomas V. , Mahjani Behrang
Published: January 2025

Attention-deficit/hyperactivity disorder (ADHD) is a highly heritable neurodevelopmental disorder, but its genetic architecture remains incompletely characterized. Rare coding variants, which can profoundly impact gene function, represent an underexplored dimension of ADHD risk. In this study, we analyzed large-scale DNA sequencing datasets from ancestrally diverse cohorts and observed significant enrichment of rare protein-truncating and deleterious missense variants in highly evolutionarily constrained genes. This analysis identified 15 high-confidence ADHD risk genes, including the previously implicatedKDM5B. Integrating these findings with genome-wide association study (GWAS) data revealed nine enriched pathways, with strong involvement in synapse organization, neuronal development, and chromatin regulation. Protein–protein interaction analyses identified chromatin regulators as central network hubs, and single-cell transcriptomic profiling confirmed their expression in neurons and glial cells, with distinct patterns in oligodendrocyte subtypes. These findings advance our understanding of the genetic architecture of ADHD, uncover core molecular mechanisms, and provide promising directions for future therapeutic development.
Time-resolved immune dynamics in rheumatoid arthritis under methotrexate therapy
Authors: Preglej Teresa , Tosevska Anela , Brinkmann Marie , Schatzlmaier Philipp , Simader Elisabeth , Sieghart Daniela , Hofer Philipp , Krausgruber Thomas , Dobnikar Lina , Bock Christoph , Karonitsch Thomas , Kain Renate , Stockinger Hannes , Ellmeier Wilfried , Aletaha Daniel , Göschl Lisa , Bonelli Michael
Published: January 2025

Rheumatoid arthritis (RA) is characterized by immune dysregulation, including alterations in peripheral blood mononuclear cell (PBMC) populations and aberrant cytokine signaling. Methotrexate (MTX) is the preferred first-line treatment for RA, yet its precise mechanisms of action remain incompletely understood. This study employed a multi-omics strategy—combining single-cell RNA sequencing (scRNA-seq) and immunophenotyping—to identify key effector peripheral immune cells and their cellular responses in RA patients over 12 weeks of MTX treatment.

In our study, MTX was associated with significant immune modulation, including the restoration of naïve T and B cells and reductions in T cell memory subsets with these effects detectable as early as three weeks post-treatment. Plasmablast levels also emerged as a potential biomarker for early therapeutic response, reflecting MTX’s impact on immune homeostasis. Transcriptional analysis revealed modulation of key pathways, including TNF-α signaling, B cell receptor signaling, and T cell receptor-mediated apoptosis. Network analysis identified critical regulatory hubs, such as EGR1, JAK2, and SOCS1, in monocytes and CD4 memory T cells, highlighting these cell types as key mediators of MTX’s effects.

In conclusion, these findings advance our understanding of MTX’s effects on immune cell dynamics at different stages of treatment, showing for the first time the early cellular changes leading to immune modulation in RA. Altogether, our results provide the foundation for further mechanistic investigations into MTX.
Psychoacoustic Study of the Rock Art Sites of Cuevas de la Araña (Bicorp, Spain)
Authors: López Samantha , Lokki Tapio , Díaz-Andreu Margarita , Escera Carles
Published: January 2025

Acoustics play a crucial role in shaping our perception of sound and its emotional impact. The rock art site ofCuevas de la Arañain Bicorp, Spain, is an archaeological site where pre-historic communities gathered for social and ritual activities.Cuevas de la Arañaexhibits acoustical characteristics that could have enhanced the sensory and emotional impact during ceremonies performed with music. In the present study, a listening test was conducted to assess how the acoustics ofCuevas de la Arañaand other rock art sites influence modern-day listeners’ perception of sound. Listeners were asked to describe, using their own vocabulary, a series of auralizations created with the impulse responses collected inCuevas de la Arañaand other neighboring sites with and without rock art. The words written by participants underwent categorization through a hierarchical clustering approach. Significant results emerged indicating that listeners perceived auralizations from rock art sites as larger, wider, less direct, farther and more reverberant than the auralizations from sites lacking rock art. Notably, the most prominent disparities were observed in the categories of size, distance, and reverberation when contrasting the auralizations fromCuevas de la Arañawith those of non-painted sites. These findings align with the outcomes documented in prior literature that investigated the acoustic characteristics of the sites and offer valuable insights into the auditory experiences at rock art sites, shedding light on their unique acoustic properties.
Uncertainty during visual search: Insights from a computational model and behavioral experiment in natural stimuli
Authors: Bujia Gaston , Ruarte Gonzalo , Sclar Melanie , Solovey Guillermo , Kamienkowski Juan E.
Published: January 2025

Visual search, driven by bottom-up and top-down processes, offers a unique framework for investigating decision-making. This study examines individuals’ awareness of their own visual search by combining computational modeling with behavioral experiments. Fifty-seven participants performed a classical visual search task in which the goal was to find an object in a natural scene. Crucially, in some trials, the search was interrupted by clearing the screen before the gaze reached the target object. Participants had to report their best guess of the target’s location and the uncertainty on their response. We show that a modified version of the Entropy-Limit Minimization (ELM) model captures scanpaths and perceived target locations, while also revealing that uncertainty is influenced by scanpath length, the distance between the perceived and true target location, and the entropy of decision maps. These findings highlight the model’s capacity to reflect cognitive processes underlying response selection and uncertainty judgment.
Sequential visual stimuli increase high frequency power in the visual cortex
Authors: Keil Julian , Hernandez-Urbina Victor , Vassiliou Chrystalleni , Dean Camin , Schmitz Dietmar , Kremkow Jens , Sibille Jérémie
Published: January 2025

Today, 40 Hz flickering full-field visual stimulation is used to entrain neuronal oscillations for a variety of therapeutic purposes. We here propose spatially organized sequential visual flickering stimulation as a newer tool to entrain the visual system. We show that sequential visual flickering can evoke increased power in high frequencies (100 to 190 Hz) in the visual cortex of mice. Consequently, sequential sensory stimulation should be regarded as a putative new way leading to power increases in high frequency domains.
Specific and redundant roles for Gli2 and Gli3 in establishing cell fate during hair follicle development
Authors: Gozum Gokcen , Wirtz Lisa , Damen Mareike , Reckert Viktoria , Schettina Peter , Nelles Melanie , Bazzi Hisham , Niemann Catherin
Published: January 2025

Ectodermal appendage formation requires hedgehog (HH) signal reception, its conduction through the primary cilium and activation of Gli transcription factors (TF). How HH signalling induces cell-type-specific responses through Gli TF in stem cells (SCs) and their cilia-dependence remain open questions. Here, we use conditional mouse mutants to genetically dissect the roles of Gli and cilia HH mediators in the skin epithelium. Upon Gli2 depletion, hair follicle (HF) morphogenesis is delayed whereas sebaceous gland (SG) formation is enhanced, suggesting a dual role for Gli2 during appendage formation. By controlling proliferation of SG SCs, Gli2 impacts on the number and size of individual SG lobes. Whereas ablation of Gli3 shows no detectable phenotypes, HF cell fate is blocked in Gli2/3 double knockouts. In addition, loss of cilia phenocopies the loss of Gli2 but not the Gli2/3 mutants. Our study reveals that Gli3 exerts activator and cilia-independent functions in the absence of Gli2.

Bullet points

Epidermal Gli2 and Gli3 together mediate Hedgehog signalling and are essential for proper appendage formation

Gli3 activator function compensates for the loss of Gli2 during HF morphogenesis

Gli2 controls HF stem cell sub-compartments and SG formation

Cilia mediate epidermal Gli2 but not Gli3 signalling in the skin epithelium
An amygdala-cortical circuit for encoding generalized fear memories
Authors: Vincent Carly J. , Aguilar-Alvarez Ricardo , Vanderhoof Samantha O. , Mott David D. , Jasnow Aaron M.
Published: January 2025

Generalized learning is a fundamental process observed across species, contexts, and sensory modalities that enables animals to use past experiences to adapt to changing conditions. Evidence suggests that the prefrontal cortex (PFC) extracts general features of an experience that can be used across multiple situations. The anterior cingulate cortex (ACC), a region of the PFC, is implicated in generalized fear responses to novel contexts. However, the ACC’s role in encoding contextual information is poorly understood, especially under increased threat intensity that promotes generalization. Here, we show that synaptic plasticity within the ACC and signaling from amygdala inputs during fear learning are necessary for generalized fear responses to novel encountered contexts. The ACC did not encode specific fear to the training context, suggesting this region extracts general features of a threatening experience rather than specific contextual information. Together with our previous work, our results demonstrate that generalized learning about threatening contexts is encoded, in part, within an ascending amygdala-cortical circuit, whereas descending ACC projections to the amygdala drive generalized fear responses during exposure to novel contexts. Our results further demonstrate that schematic learning can occur in the PFC after single-trial learning, a process typically attributed to learning over many repeated learning episodes.
GenVarLoader: An accelerated dataloader for applying deep learning to personalized genomics
Authors: Laub David , Ho Aaron , Jaureguy Jeff , Klie Adam , Salem Rany M. , McVicker Graham , Carter Hannah
Published: January 2025

Deep learning sequence models trained on personalized genomics can improve variant effect prediction, however, applications of these models are limited by computational requirements for storing and reading large datasets. We address this with GenVarLoader, which stores personalized genomic data in new memory-mapped formats with optimal data locality to achieve ∼1,000x faster throughput and ∼2,000x better compression compared to existing alternatives.
Unified Measures Quantifying Intensity and Similarity of Pain and Somatosensory Percepts
Authors: Earley Eric J. , Ramne Malin , Wessberg Johan
Published: January 2025

Across somatosensory and pain literature, there exist several methods of characterizing the location and extent of perceived sensations, and quantifying how these sensory maps may differ. However, these measures of somatosensory intensity and similarity can give non-unique results, creating challenges in literature review and meta-analysis across different methods. In this paper, we propose novel and unifying measures to quantify the similarity and intensity of pain maps and somatosensory percepts. These measures are generalizable and can be applied to any application of somatosensory maps, and are usable with both discretized and free-hand drawings in both 2D and 3D representations. Somatosensory Percept Intensity (SPI) is inspired by Piper’s Law, which describes the phenomenon of incomplete spatial summation wherein changes in pain area do not yield linearly proportional changes in perceived intensity. Somatosensory Percept Deviation (SPD) is derived from optimal transport theory, which quantifies differences between two probability distributions or somatosensory maps. Mathematical derivations for both measures are provided. The utility of these measures is demonstrated using data from two studies – one characterizing elicited somatosensory percepts, and one investigating neuropathic pain drawings. The proposed measures strongly agree with the validation studies, illustrating their potential as agnostic measures for characterizing somatosensory percepts in studies and meta-analyses. Ultimately, our work yields powerful unified measures for use in the fields of perception and pain, and may aid in improved pain characterization within healthcare, granting a better understanding of the needs and progression of patients experiencing pain.

NEW & NOTEWORTHY

We propose novel and unifying measures to quantify the similarity and intensity of pain maps and somatosensory percepts. These measures are generalizable and applicable to any application of somatosensory maps, resulting in improved pain characterization within healthcare and better understanding of the needs and progression of patients experiencing pain.
Activation Metrics for Structural Connectivity Recruitment in Deep Brain Stimulation
Authors: Butenko Konstantin , Roediger Jan , Al-Fatly Bassam , Li Ningfei , Dembek Till A. , Yifei Gan , Guan-Yu Zhu , Jianguo Zhang , Kühn Andrea A. , Horn Andreas
Published: January 2025

Comparatively high excitability of myelinated fibers suggests that they represent a major mediator of deep brain stimulation effects. Such effects can be modeled using different levels of abstraction, ranging from simple electric field estimates to complex multicompartment axon models. In this study, we explore three approaches to estimate axonal activation: electric field magnitudes, electric field projections and (probabilistic) pathway activation modeling. Our aim is to describe these approaches and also illustrate their relevance. For that, we apply them to a clinical dataset of 15 Parkinson’s disease patients, who were stimulated in the subthalamic nucleus in bipolar mode. To make these approaches accessible for the community, necessary modeling and statistical processing was implemented in the openly available Lead-DBS toolbox.
Acute Respiratory Distress Syndrome in Adults: A Retrospective Analysis of Temperature Trends, Demographic Factors, and Clinical Outcomes from the eICU Collaborative Research Database
Authors: Al Mahrizi Ahmed Dawood , Ezenwanne Charles , Mossolem Fatima , Valladares Carlos , Gill Harman , Boyle Matthew
Published: January 2025

Background

Acute Respiratory Distress Syndrome is characterized by the sudden onset of hypoxemia, reduced lung compliance, and bilateral pulmonary infiltrates. We investigated patient demographics and clinical predictors of outcomes in adult patients with ARDS.

Methods

We conducted a retrospective multi-center intensive care unit database study using the eICU Collaborative Research Database (eICU-CRD). The Analysis included 304 patients with ARDS who met all inclusion criteria, including key demographic variables. We Assessed associations between these variables and outcomes, including mortality and length of stay (LoS).

Results

For each year of increased age, odds of mortality decreased by 4.7% (OR = 0.953, p < 0.001). Higher temperatures were associated with reduced mortality (OR=0.470, p=0.003). Gender (p = 0.596) and BMI (p = 0.964) were not significant predictors of mortality. A multiple linear regression model for predicting ICU length of stay was statistically significant at explaining the variance compared to the null model. High temperatures (β = 0.981, p = 0.015) and low temperatures (β = -1.038, p = 0.006) were significant predictors of LoS, while gender and BMI were not. There was significant association between ethnicity and hospital discharge status (χ2(5) = 13.123, p = 0.022), which suggests disparities in outcomes across ethnic groups.

Conclusion

Our study suggests that increasing age and higher temperatures may serve as protective factors, contrary to the popular belief of age-increasing fragility. Analysis also found that gender and BMI do not affect patient LoS nor mortality. These findings suggest clinicians should consider a patient’s age and core body temperature when assessing risk of mortality and prognosis, placing less emphasis on BMI and gender.
Standardized Measurement of Type 1 Diabetes Polygenic Risk Across Multi-Ancestry Population Cohorts
Authors: Luckett Amber M. , Oram Richard A. , Deutsch Aaron J. , Ortega Hector I , Fraser Diane P. , Ashok Kaavya , Manning Alisa K. , Mercader Josep M. , Rivas Manuel , Udler Miriam S. , Weedon Michael N , Gloyn Anna L. , Sharp Seth A.
Published: January 2025

Type 1 diabetes (T1D) polygenic risk scores (PRS) are effective tools for discriminating T1D from other diabetes types and predicting T1D risk, with applications in screening and intervention trials. A previously published T1D Genetic Risk Score 2 (GRS2) is widely adopted, but challenges in standardization and accessibility have hindered broader clinical and research utility. To address this, we introduce GRS2x, a standardized and cross- compatible method for accurate T1D PRS calculation, demonstrating genotyping and reference panel independent performance across diverse datasets. GRS2x as a unified approach facilitates accessible and portable measurement of T1D polygenic risk.
Rad5 and Telomere Replication
Authors: Mattarocci Stefano
Published: January 2025

The DNA Damage Tolerance pathway (DDT) is one of the major mechanisms for resolving replication fork blocks. A central factor for DDT is the fork-associated clamp, PCNA, which can undergo to mono- or polyubiquitination, leading to error-free or error-prone modes of repair, respectively. The Rad5 protein in the yeastSaccharomyces cerevisiaeplays important roles in both pathways: promoting the error-free mode by PCNA polyubiquitination and interacting with specialized DNA polymerases involved in the error-prone pathway. Rad5 also associates with telomeres, the repetitive DNA regions present at the ends of chromosomes. Telomeric DNA, tightly bound by tandem proteins arrays, poses unique challenges to replication fork progression. Here, I review the current understanding of the link between Rad5 and telomeres and present evidence that Rad5 is associated with yeast telomeres, with notable enrichment during telomere replication. This data highlights a connection between telomeres and a key DDT factor in unperturbed wild-type cells, raising intriguing possibilities about the functional interplay between telomere replication and DNA damage tolerance mechanisms.
A multilamellar organelle for chemosymbiosis in an aplacophoran mollusc adapted to anoxic cold seep sediment
Authors: Li Yunlong , Chen Chong , Liu Xu , Li Menggong , Zhou Haiyun , Wang Hui , Zheng Xiaoshan , He Xing , Liu Shanshan , Qiu Jian-Wen , Qian Pei-Yuan , Sun Jin
Published: January 2025

Symbiosis with chemoautotrophic bacteria has evolved in many animal lineages inhabiting reducing habitats such as hydrothermal vents, allowing these holobionts to thrive in dark biospheres1. In certain instances, the symbionts have become intracellular, residing within specialised bacteriocytes2. The integration of microbial symbionts with eukaryotic cells vary across known animals; however, no specialised organelle dedicated to chemosynthesis has been identified yet2. Here, we report a mode of symbiosis where sulphur-oxidising bacteria cultured within spherical multilamellar compartments (~12 μm) in the cold-seep aplacophoran molluscChaetoderma shenloong. This organelle, which we name ‘dracosphera’, is ubiquitous within the hypertrophied and intricately reticulate digestive gland ofC. shenloong, which has otherwise lost most of its gut. Given that the symbionts are strictly anaerobic and the host resides in anoxic sediments tens of centimetres below the surface, the dracosphera may serve to minimise oxygen diffusion to the bacteria, akin to mechanisms observed in microbial diazotrophs3or termite hindguts4, as supported by our genomic and spatial transcriptomic analyses. Hypoxic conditions have been known to induce radical adaptations in meiofauna, exemplified by the acquisition of hydrogenosomes5. Our discovery of similarly exceptional adaptations inC. shenloongprovides new insights into the evolution of such organelles also in larger animals.
The role of lipoteichoic acid in Staphylococcus aureus cell wall integrity
Authors: Bae Taeok , Kanampalliwar Amol , Shah Majid Ali , Park Youngseon , Jeong Bohyun , LAWSON PAUL A , Bell Madeline , Fesko Elizabeth Margaret , Sainato Anthony , Sainato Dominic , Walker Suzanne
Published: January 2025

In Staphylococcus aureus, lipoteichoic acid (LTA) is crucial for growth, cell division, osmoprotection, and beta-lactam resistance, yet its molecular mechanisms remain unclear. This study reveals that LTA binds to multiple proteins involved in cell wall processes and preserves cell wall integrity by regulating one of the LTA-binding proteins, ScaH. ScaH is a peptidoglycan hydrolase predicted to have N-acetylglucosaminidase and amidase/peptidase activities. LTA inhibits ScaH's enzymatic activities by direct binding and represses scaH transcription by an unknown mechanism. During early growth, LTA is highly expressed and sequesters ScaH at the cell membrane, preventing ScaH activity in the cell wall. However, LTA expression decreases during the late growth phase, leading to ScaH translocation into the cell wall. This reduction in LTA coincides with increased wall teichoic acid (WTA) expression and cleavage of the LTA synthase LtaS. In the LTA-null mutant, ScaH inactivation restored peptidoglycan crosslinking, osmoresistance, and beta-lactam resistance both in vitro and in vivo. These findings suggest that LTA protects the cell wall by suppressing ScaH expression and activity while sequestering it during active growth. Additionally, the reciprocal expression patterns of LTA and WTA indicate an interconnected regulation of teichoic acids in S. aureus, with their roles likely depending on the growth phase.
Cleaner wrasse failed in early testing stages of both visual and spatial Working Memory paradigms
Authors: Bonin Leonore , Manrique Héctor M. , Bshary Redouan
Published: January 2025

Working memory (WM), an attention-based short-term storage system responsible for the manipulation and integration of past knowledge with present information for goal-directed behavior, is a key executive function and a principal predictor of general intelligence. As WM has not been a major research topic in animal behavior, we first summarize key ideas from the social sciences for interested colleagues. Given that past methodological inconsistencies have led to mixed results and conclusions across various species, we designed experiments that incorporate the critical components of WM, facilitating cross-species comparisons and accounting for potential ecological influences. We present such experiments on WM in an ectothermic vertebrate, the cleaner wrasse (Labroides dimidiatus), which faces environmental challenges potentially requiring complex cognitive adaptations. Overcoming several experimental challenges, we consistently obtained negative results across multiple experimental paradigms. Our negative results using experiments specifically designed to test WM call into question previous studies that used other experiments and reported positive WM findings in other fish species. If the negative results in specific WM tests were to be confirmed in other ectotherm vertebrates, the absence of WM may turn out to be a key factor underlying the significant encephalization gap between ectotherm and endotherm vertebrate species.
Investigation of Bile Salt Hydrolase Activity in Human Gut Bacteria Reveals Production of Conjugated Secondary Bile Acids
Authors: Lucas Lauren N. , Mallikarjun Jillella , Cattaneo Lea E. , Gangwar Bhavana , Zhang Qijun , Kerby Robert L. , Stevenson David , Rey Federico E. , Amador-Noguez Daniel
Published: January 2025

Through biochemical transformation of host-derived bile acids (BAs), gut bacteria mediate host-microbe crosstalk and sit at the interface of nutrition, the microbiome, and disease. BAs play a crucial role in human health by facilitating the absorption of dietary lipophilic nutrients, interacting with hormone receptors to regulate host physiology, and shaping gut microbiota composition through antimicrobial activity. Bile acid deconjugation by bacterial bile salt hydrolase (BSH) has long been recognized as the first necessary BA modification required before further transformations can occur. Here, we show that BSH activity is common among human gut bacterial isolates spanning seven major phyla. We observed variation in both the extent and the specificity of deconjugation of BAs among the tested taxa. Unexpectedly, we discovered that certain strains were capable of directly dehydrogenating conjugated BAs via hydroxysteroid dehydrogenases (HSD) to produce conjugated secondary BAs. These results challenge the prevailing notion that deconjugation is a prerequisite for further BA modifications and lay a foundation for new hypotheses regarding how bacteria act individually or in concert to diversify the BA pool and influence host physiology.
Validation of Structure Tensor Analysis for Orientation Estimation in Brain Tissue Microscopy
Authors: Gray Bryson , Smith Andrew , MacKenzie-Graham Allan , Shattuck David W. , Tward Daniel
Published: January 2025

Accurate localization of white matter pathways using diffusion MRI is critical to investigating brain connectivity, but the accuracy of current methods is not thoroughly understood. A fruitful approach to validating accuracy is to consider microscopy data that have been co-registered with MRI of post mortem samples. In this setting, structure tensor analysis is a standard approach to computing local orientations for validation. However, structure tensor analysis itself has not been well-validated and is subject to uncertainty in its angular resolution, and selectivity to specific spatial scales. In this work, we conducted a simulation study to investigate the accuracy of using structure tensors to estimate the orientations of fibers arranged in configurations with and without crossings. We examined a range of simulated conditions, with a focus on investigating the method’s behavior on images with anisotropic resolution, which is particularly common in microscopy data acquisition. We also analyzed 2D and 3D optical microscopy data. Our results show that parameter choice in structure tensor analysis has relatively little effect on accuracy for estimating single orientations, although accuracy decreases with anisotropy. On the other hand, when estimating the orientations of crossing fibers, the choice of parameters becomes critical, and poor choices result in orientation estimates that are essentially random. This work provides a set of recommendations for researchers seeking to apply structure tensor analysis effectively in the study of axonal orientations in brain imaging data and quantifies the method’s limitations, particularly in the case of anisotropic data.

Highlights

Structure tensor estimates of homogeneous orientations are robust to parameter choice

Accuracy in crossing-fiber regions is highly sensitive to parameter choice

Image anisotropy has a large effect on accuracy in 3D images

Simulations provide guidelines for choosing parameters based on image characteristics
Gaze dynamics prior to navigation support hierarchical planning
Authors: Gordon Jeremy , Chuang John , Pezzulo Giovanni
Published: January 2025

The task of planning future actions in the context of an uncertain world results in massive state spaces that preclude exhaustive search and other strategies explored in the domains of both human decision-making and computational agents. One plausible solution to this dimensionality explosion is to decompose the task into subgoals that match the information geometry of the task at hand. However, how individuals identify a productive hierarchy, and perceive and select subgoals suitable to planning, is not well understood. To investigate this topic, we designed a virtual-reality based behavioral experiment which collected eye movements during a pre-navigation planning phase. By capturing gaze dynamics correlated with the simulative processes used in planning, we were able to identify the spatiotemporal evolution of visual search under uncertainty. Our results highlight gaze dynamics indicative of a search process that exhibits hierarchical structure. These include a decreasing trend seen in gaze distance from origin and a broad to narrow shift (with reducing saccade distances and longer fixation durations) as plans are established. In line with prior work, critical tiles to which landscape connectivity is most sensitive were the strongest predictors of visual attention. We also find that deeper planning was correlated with success only on the most complex maps (e.g. those with a larger number of information-nodes, higher branching factor, and more forks, according to an info-graphical map analysis). This study highlights the role of embodied visual search during planning, and the skill-dependence of the specific subgoals and hierarchical decomposition used which unlocked successful performance.
Reactivation of an Embryonic Cardiac Neural Crest Transcriptional Subcircuit During Zebrafish Heart Regeneration
Authors: Dhillon-Richardson Rekha M. , Haugan Alexandra K. , Lyons Luke W. , McKenna Joseph K. , Bronner Marianne E. , Martik Megan L.
Published: January 2025

During vertebrate development, the heart primarily arises from mesoderm, with crucial contributions from cardiac neural crest cells that migrate to the heart and form a variety of cardiovascular derivatives. Here, by integrating bulk and single cell RNA-seq with ATAC-seq, we identify a gene regulatory subcircuit specific to migratory cardiac crest cells composed of key transcription factorsegr1, sox9a, tfap2aandets1. Notably, we show that cells expressing the canonical neural crest genesox10are essential for proper cardiac regeneration in adult zebrafish. Furthermore, expression of all transcription factors from the migratory cardiac crest gene subcircuit are reactivated after injury at the wound edge. Together, our results uncover a developmental gene regulatory network that is important for cardiac neural crest fate determination, with key factors reactivated during regeneration.

SIGNIFICANCE

Many common human congenital heart defects are linked to problems that arise during cardiac neural crest development. Here, we use the zebrafish, which has the remarkable ability to regenerate their adult heart, to understand the genetic programs that control cardiac development and adult repair. We discover a set of genes that control the development of the cardiac neural crest and find that these genes are reactivated after heart injury in the adult zebrafish. Unlike the zebrafish, human hearts have a very limited ability to regenerate after injury. Our findings in zebrafish can provide insight to potential clinical interventions for congenital heart defects and adult heart damage.
The medial prefrontal cortex encodes procedural rules as sequential neuronal activity dynamics
Authors: Ohno Shuntaro , Nomoto Masanori , Inokuchi Kaoru
Published: January 2025

The prefrontal cortex plays a crucial role in procedural rule learning; however, the specific neuronal mechanism through which it represents rules is unknown. We hypothesized that sequential neuronal activities in the prefrontal cortex encode these rules. To investigate this, we recorded neuronal activities in the medial prefrontal cortex of mice during rule learning using Ca2+imaging. We utilized a method based on convolutional negative matrix factorization, iSeq, to automatically detect temporal neuronal sequences in the recorded data. As rule learning advanced, these neuronal sequences began to encode critical information for rule execution. In mice that had mastered the rule, the dynamics of neuronal sequences could predict success and failure of reward acquisition. Furthermore, the composition of cell populations within the neuronal sequences was rearranged throughout the learning process. These findings suggest that as animals learn a rule, the medial prefrontal cortex continually updates its neuronal sequences to assign significance to behavioral actions crucial for reward acquisition.
Repopulation of the brain with microglia-like cells following intraperitoneal bone marrow cell transfer in microglia-deficient mice
Authors: Taylor Isis , Patkar Omkar L. , Liu Yajun , Jacquelin Sebastien , Ranpura Ginell , Carter-Cusack Dylan , Ewing Adam , Kurniawan Nyoman D. , Li Mosi , Vasoya Deepali , He Xin , Dando Owen R. , Kind Peter , Hardingham Giles E. , Bradford Barry M. , Mabbott Neil A. , LeFevre Lucas , Pridans Clare , Summers Kim M. , Irvine Katharine M. , Hume David A.
Published: January 2025

Germ-line deletion of a conserved enhancer (the Fms intrinsic regulatory element, FIRE) in the mouseCsf1rlocus causes congenital absence of microglia. Homozygous FIRE deletion on a C57BL/6J background leads to perinatal lethality and hydrocephalus (HC) in surviving pups. We developed a congenic C57BL/6J line with defined regions of non-C57BL/6J genomic DNA, increased postnatal viability and reduced incidence of HC. Both perinatal lethality and HC were eliminated in F2 mice following outcross of the congenic line to CBA/J or BALBc/J backgrounds. To assess the impacts of microglial deficiency in postnatal neurodevelopment we analyzed deep total RNA-seq data from multiple brain regions of wild-type andCsf1rΔFIRE/ΔFIREmice. Aside from the loss of microglial-specific transcripts, we found no significant alterations in relative abundance of any cell-type or region-specific transcriptomic signature. Transcripts associated with endosome/lysosome function, which are enriched in microglia, were not affected, suggesting compensatory expression by other cell types. On the C57BL/6J x CBA/J F2 background, congenital absence of microglia did not affect motor activity, behavior or myelination up to 7 months of age but was associated with astrocytosis and calcification in the thalamus. In the congenic C57BL/6JCsf1rΔFIRE/ΔFIREmouse line, intraperitoneal transfer of wild-type bone marrow cells (BMT) at weaning led to complete repopulation of the brain with microglia-like cells without giving rise to monocytic intermediates. Our results suggest novel strategies for treatment of microglial deficiency.
The ratio of Wnt signaling activity to Sox2 transcription factor levels predicts neuromesodermal fate potential
Authors: Morabito Robert D. , Tatarakis David , Swick Ryan , Stettnisch Samantha , Schilling Thomas F. , Horsfield Julia A. , Martin Benjamin L.
Published: January 2025

Neuromesodermal progenitors (NMPs) are a vertebrate cell type that contribute descendants to both the spinal cord and the mesoderm. The undifferentiated bipotential NMP state is maintained when both Wnt signaling is active and Sox2 is present. We used transgenic reporter lines to live-image both Wnt activity and Sox2 levels in NMPs and observed a unique cellular ratio in NMPs compared to NMP-derived mesoderm or neural tissue. We used this unique signature to identify the previously unknown anatomical position of a progenitor population that gives rise to the midline tissues of the floor plate of the spinal cord and the mesodermal notochord. Thus, quantification of the active Wnt signaling to Sox2 ratio can be used to predict and identify cells with neuromesodermal potential. We also developed the auxin inducible degron 2 system for use in zebrafish to test the temporal role that Sox2 plays during midline formation. We found ectopic Sox2 in the presence of Wnt activity holds cells in the undifferentiated floor plate/notochord progenitor state, and that degradation of the ectopic Sox2 is required for cells to adopt a notochord fate.
High Prevalence and Genotypic Diversity of PersistentChlamydia trachomatisInfections Among South African Adolescent Girls and Young Women: A Tale of Two Cities
Authors: Dabee Smritee , Barnabas Shaun , Versteeg Bart , Kullin Brian , Jaumdally Shameem Z. , Gamieldien Hoyam , Mkhize Nonhlanhla , Muller Etienne , Maseko Venessa , Gill Katherine , Martin Darren P. , Gray Glenda , Bekker Linda-Gail , Lewis David A. , Jaspan Heather B. , Bruisten Sylvia M. , Passmore Jo-Ann S.
Published: January 2025

Chlamydia trachomatis(CT) is the most common sexually transmitted bacterial infection globally, significantly affecting adolescent girls and young women (AGYW) in South Africa. This study investigated CT prevalence and genotypic diversity among 298 AGYW from Cape Town and Johannesburg, revealing an overall prevalence of 29.5%. Prevalence was higher in Cape Town (41.6%) compared to Johannesburg (17.4%; p<0.0001). Genetic analysis identified 34 sequence types, including 15 novel variants. Longitudinal data highlighted frequent reinfections or persistent infections despite treatment. These findings underscore the importance of addressing CT’s genetic diversity for improved reproductive health strategies and vaccine development.
LINE-1 retrotransposons regulate the exit of human pluripotency and early brain development
Authors: Adami Anita , Garza Raquel , Gerdes Patricia , Johansson Pia A. , Dorazehi Fereshteh , Koutounidou Symela , Castilla-Vallmanya Laura , Atacho Diahann A.M. , Sharma Yogita , Johansson Jenny G. , Tam Oliver , Kirkeby Agnete , Barker Roger A. , Gale-Hammell Molly , Douse Christopher H. , Jakobsson Johan
Published: January 2025

Long interspersed nuclear element 1 (L1) retrotransposons represent a vast source of divergent genetic information. However, mechanistic analysis of whether and how L1s contribute to human developmental programs is lacking, in part due to the challenges associated with specific profiling and manipulation of human L1 expression. Here we show that thousands of hominoid-specific L1 integrants are expressed in human induced pluripotent stem cells and cerebral organoids. The activity of individual L1 promoters is surprisingly divergent and correlates with an active epigenetic state. Efficient on-target CRISPRi silencing of L1s revealed nearly a hundred co-opted L1-derived chimeric transcripts and L1 silencing resulted in changes in neural differentiation programs and reduced cerebral organoid size. Together, these data implicate L1s and L1-derived transcripts in hominoid-specific CNS developmental processes.
A new statistical metric for robust target detection in cryo-EM using 2D template matching
Authors: Zhang Kexin , Cossio Pilar , Rangan Aaditya V. , Lucas Bronwyn A. , Grigorieff Nikolaus
Published: January 2025

2D template matching (2DTM) can be used to detect molecules and their assemblies in cellular cryo-EM images with high positional and orientational accuracy. While 2DTM successfully detects spherical targets such as large ribosomal subunits, challenges remain in detecting smaller and more aspherical targets in various environments. In this work, a novel 2DTM metric, referred to as the 2DTM p-value, is developed to extend the 2DTM framework to more complex applications. The 2DTM p-value combines information from two previously used 2DTM metrics, namely the 2DTM signal-to-noise ratio (SNR) and z-score, which are derived from the cross-correlation coefficient between the target and the template. The 2DTM p-value demonstrates robust detection accuracies under various imaging and sample conditions and outperforms the 2DTM SNR and z-score alone. Specifically, the 2DTM p-value improves the detection of aspherical targets such as a modified artificial tubulin patch particle (500 kDa) and a much smaller clathrin monomer (193 kDa) in simulated data. It also accurately recovers mature 60S ribosomes in yeast lamellae samples, even under conditions of increased Gaussian noise. The new metric will enable the detection of a wider variety of targets in both purified and cellular samples through 2DTM.