bluuebunny/crossref_metadata_2025_split huggingface dataset:
The scaffold protein CasL regulates T cell migration by restricting membrane blebbing
Authors: Kurtz Liz A , Shearer Hope E , Trevail Rosanne , Symeonides Menelaos , Karimi Mobin , Roy Nathan H 
Published: January 2025

AbstractT cell migration into inflamed tissue is a key control point in the inflammatory response and relies on integrin interactions with their endothelial ligands. Here, we identify the signaling scaffold CasL (Hef1, NEDD9) as a central regulator of integrin-dependent migration in primary T cells. We found CasL is specifically needed for efficient migration on ICAM-1, but not VCAM-1 coated surfaces. While WT T cells migrating on ICAM-1 form an actin-rich cell front and move smoothly, T cells lacking CasL instead form numerous, aberrant membrane blebs. The abnormal blebbing observed in CasL KO T cells likely stems from diminished F-actin in the cell front coupled with increased contractile forces behind the nucleus, suggesting CasL regulates the cytoskeletal architecture in migrating T cells. Importantly, using anin vivoallogeneic hematopoietic transplant model we found that CasL promotes T cell migration into inflamed peripheral tissue, but was dispensable for trafficking to secondary lymphoid organs. Together, these results indicate CasL functions to control the balance of cytoskeletal components during integrin-dependent migration and highlight the importance of integrin signaling for proper migration into inflamed tissue.
Preclinical Proof of Concept for SNAPTM-TIL: a personalized, next-generation tumor-infiltrating lymphocyte therapy platform
Authors: Halder Tithi Ghosh , Kelley Erin , Soria-Bustos Jorge , Thode Trason , Ng Serina , Bargenquast Taylor , Weston Alexis , Rodriguez del Villar Ryan , Kaadige Mohan , Borazanci Erkut , Gordon Michael , Moser Justin , Tsai Frank , Priceman Saul J. , Forman Stephen J. , Xing Yan , Altin John A. , Soldi Raffaella , Sharma Sunil 
Published: January 2025

ABSTRACTTumor-infiltrating lymphocyte (TIL) therapy, which involves extracting, expanding, and reinfusing immune cells to target cancer cells, has shown promise in melanoma treatment, but requires optimization for broader efficacy. The success of TIL therapy depends on the recognition of tumor-associated antigens, but neoantigen-reactive T-cells are often rare and exhausted in less immunogenic malignancies. Isolating T cells enriched in neoantigen reactivity prior toin vitroexpansion and reinfusion may improve the response rates. To this end, our proprietary Specific Neo-Antigen Peptides (SNAP™) technology platform improves the accuracy of neoantigen prediction and validation by combining advanced computational modeling and PepSeq, a high-throughput screen for the physical credentialing of putative neoantigens based on their affinity to bind patient-specific HLA class II proteins. This approach allows for the education and enrichment of TILs (SNAP-TILs) with personalized, predefined, highly immunogenic neoantigens prior to expansion. Using the SNAP platform, we consistently achieved, on average, an SNAP-TIL product comprising 96% CD3+ cells, with a mixture of 75% effector and 23% central memory cells. SNAP-TILs exhibited greater efficacy and selectivity in immune infiltration than TIL, which was expanded by the rapid expansion protocol alone usingex vivomodels. SNAP-TIL was also reactive in highly and poorly immunogenic tumors, with 70% and 50% tumor growth inhibition in melanoma and pancreatic patient-derived xenograft models, respectively. This study demonstrates the novel benefit of our Personalized Neoantigen Pipeline approach, potentially providing a durable antitumor immune response for a larger proportion of cancer patients.
Intraflagellar Transport Selectivity Occurs with the Proximal Portion of the Trypanosome Flagellum
Authors: Alves Aline Araujo , Jung Jamin , Moneron Gaël , Vaucelle Humbeline , Fort Cécile , Buisson Johanna , Schietroma Cataldo , Bastin Philippe 
Published: January 2025

AbstractIntraflagellar transport (IFT) trains move bidirectionally along the doublet microtubules (DMTs) of the axoneme within the flagellum. InTrypanosoma brucei, IFT trains predominantly associate with four of the nine DMTs. Using high-resolution microscopy, we reveal how this selective association is put in place. IFT proteins form a ring surrounding the 9 DMTs on top of the transition fibres. Volume electron microscopy revealed densities along all DMTs in the proximal portion of the flagellum, exhibiting thinner, shorter profiles with branches absent in mature IFT trains. As the axoneme extends within the flagellar pocket, IFT trains are detected but are often positioned outside DMTs 3-4/7-8. After the axoneme exits the flagellar pocket, IFT trains localise exclusively to DMTs 3-4 and 7-8. Super-resolution and expansion microscopy demonstrated that IFT proteins follow the same distribution as the IFT-like densities. This suggests they represent IFT trains undergoing assembly and/or disassembly and reveals their unexpected ability to shift from one DMT to another.SummaryInTrypanosoma brucei, intraflagellar transport (IFT) trains selectively associate with specific axonemal microtubules. Using advanced microscopy, this study reveals how this restriction occurs at the proximal portion of the flagellum during the assembly and/or disassembly of IFT trains.
ggrain - a ggplot2 extension for raincloud plots
Authors: Judd Nicholas , van Langen Jordy , Poggiali Davide , Whitaker Kirstie , Rhys Marshall Tom , Allen Micah , Kievit Rogier 
Published: January 2025

AbstractClear data visualization isessentialto effectively communicate empirical findings across various research fields. Raincloud plots fill this need by offering a transparent and statistically robust approach to data visualization. This is achieved by combining three plots in an aesthetically pleasing fashion. First, a dot plot displays raw data with minimal distortion, allowing a fast glance at the sample size and outlier identification. Next, a box plot displays key distributional summary statistics such as the median and interquartile range. Lastly, a violin plot transparently displays the underlying distribution of the data. Despite the widespread use of raincloud plots, an R-package in alignment with the‘grammar of graphics’was lacking. ‘ggrain’ fills this need by offering one easy-to-use function (‘geom_rain’) allowing the quick and seamless plotting of rainclouds in the R ecosystem. Further, it enables more complex plotting features such as factorial grouping, mapping with a secondary (continuous) covariate, and connecting observations longitudinally across multiple waves.
Oxytocin enhances acquisition in a social trust task in mice, whereas both oxytocin and its antagonist block trust violation learning
Authors: Budniok Samuel , Callaerts-Vegh Zsuzsanna , Bakermans-Kranenburg Marian , Bosmans Guy , D’Hooge Rudi 
Published: January 2025

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

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

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

AbstractThe flexibility of tethered molecules, such as those bound to biological membranes, is an important property that can influence molecular height, mobility, and accessibility. However, quantifying the flexibility of surface-tethered biomolecules in aqueous environments has been difficult due to a lack of experimental tools. Here we introduce SurFlex microscopy, a method based on fluorescence anisotropy that exploits the relationship between the conformational dynamics of a tethered molecule and the rotational diffusion of an attached fluorophore to extract information about molecular flexibility. By analyzing the polarization state of photons emitted after polarized excitation, we quantify apparent molecular flexibilities that include effects of tethering, self-interactions and buffer conditions. We first demonstrate the capabilities of SurFlex microscopy by measuring the flexibility of bilayer-tethered single-stranded DNA (ssDNA) of different lengths and nucleotide sequences. We find that sequence significantly impacts ssDNA flexibility, consistent with theoretical estimates, with weak intramolecular interactions in random sequences leading to higher apparent stiffness. Interestingly, we show that a pathological DNA sequence linked to Huntington’s disease exhibits unusual flexibility despite intramolecular interactions. We next extend SurFlex microscopy to live cells by measuring surface glycoprotein flexibility on red blood cells using fluorescent lectins. We show that trypsinization decreases glycan fluctuations, demonstrating that modifications to the cell surface can alter the flexibility of remaining surface molecules. SurFlex microscopy provides a new tool for quantifying molecular flexibility that can be used to study the role of tethered surface molecules in fundamental biological processes.Significance statementBiomolecules immobilized on one end play crucial roles in diverse cellular processes, from cell-cell signaling through surface receptors to the formation of DNA secondary structures. However, measuring biomolecular flexibility on surfaces has remained challenging. Here we present SurFlex microscopy, a technique that uses fluorescence anisotropy to quantify the flexibility of surface-anchored molecules. By analyzing the rotational dynamics of fluorophores attached to the ends of fluctuating biomolecules, SurFlex microscopy can be used to quantify persistence length. We demonstrate its capabilities by measuring sequence-dependent flexibility of DNA and crowding-dependent changes in glycan flexibility on native cell surfaces. This method opens new avenues for understanding how biomolecular flexibility influences key biological processes, such as those at cell surfaces during cell-cell contact formation and subsequent signaling.
Evaluating the role of pre-training dataset size and diversity on single-cell foundation model performance
Authors: DenAdel Alan , Hughes Madeline , Thoutam Akshaya , Gupta Anay , Navia Andrew W. , Fusi Nicolo , Raghavan Srivatsan , Winter Peter S. , Amini Ava P. , Crawford Lorin 
Published: January 2025

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

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

SUMMARYProtein aggregates are a hallmark of neurodegenerative disease, yet the molecular processes that control their appearance are still poorly understood. In particular, it is unknown to what degree the development of aggregates in one cell is triggered by nearby aggregated cells, as opposed to cell-autonomous processes. Here we develop a cell-level computational model to test alternative hypotheses of disease progression from human data and demonstrate its applicability in the primary tauopathy Progressive Supranuclear Palsy. From brain slices stained for aggregated tau, we quantify the contribution of cell-to-cell and cell-autonomous processes to the proliferation of aggregates across different brain regions and disease stages. We find that the triggering of aggregation by nearby aggregated cells, over distances in the order of 100µm, is the major driver of disease progression. Our computational model can then simulate interventions to evaluate potential therapeutic strategies in a virtual reconstruction of a human primary neurodegenerative tauopathy.HighlightsA minimal mathematical model can reproduce tissue-level aggregate accumulation patternsin silicoat cellular resolution.Cell-to-cell interactions determine aggregate patterns in progressive supranuclear palsy (PSP).Cell-to-cell interactions are not limited to nearest neighbours, but act over a millimetre-scale.Reducing cell-to-cell interactions or cell vulnerability, rather than targeting cell-autonomous processes, is a potential disease-modifying therapeutic strategy.
Sex differences in pant-hoot vocalizations in wild Eastern chimpanzees
Authors: Holden Eve , Grund Charlotte , Eguma Robert , Samuni Liran , Zuberbühler Klaus , Soldati Adrian , Hobaiter Catherine 
Published: January 2025

AbstractChimpanzee pant-hoots are frequently produced long-distance vocalisations that serve a number of social functions, such as to indicate coordinate travelling, food discovery, or social status. Calling often triggers replies by others, offering potential for some form of group-level decision-making through vocal exchanges. However, despite important physiological and social differences between male and female chimpanzees, pant-hoot research has traditionally focused on males, with very little known about female use. To address this gap, we collected all-occurrence behavioural data from wild adult female and male Eastern chimpanzees (Pan troglodytes schweinfurthii) in two communities in the Budongo Forest Reserve, Uganda. We show that females pant-hooted regularly, but less frequently than males and, when they did so, mostly in response to others. Response pant- hoots were more common than initiating pant-hoots in both sexes (females: 90.1%; males: 69.5%), and male and female chimpanzees responded to pant-hoots heard at a similar rate (females: 14.1%, males excluding alpha: 15.8%). Both sexes were more likely to respond to pant-hoots from within their own party, but this effect was stronger for females. The likelihood of male chimpanzees pant-hooting in response was inhibited in larger party sizes, while females’ response pant-hoots were not. Finally, female response pant-hoots were less common during periods of maximal oestrous as compared to other stages of their reproductive cycle. Overall, our findings demonstrate that response pant-hoots are subject to social factors, such as within-sex social competition and between-sex reproductive strategies, which affect male and female chimpanzees in different ways, a further demonstration of the high degree of audience awareness in this primate species.HighlightsChimpanzees use pant-hoots in both sex-specific and sex-non-specific waysIndividual and social factors impact likelihood of pant-hoot productionOur findings suggest pant-hoots are important flexible elements of vocal behaviour for male and female chimpanzees.
Clinical Immunoprofiling Reveals that High Numbers of CD8+and PD-1+Cells Predict Superior Patient Survival Across Major Cancer Types Independent of Major Risk Factors
Authors: Alessi Joao V , Lindsay James R , Giobbie-Hurder Anita , Sharma Bijaya , Felt Kristen , Kumari Priti , Mazor Tali , Cerami Ethan , Lotter William , Altreuter Jennifer , Weirather Jason , Dryg Ian , Hoebel Katharina , Manos Michael , Adib Elio , Curtis Jennifer D. , Ricciuti Biagio , Di Federico Alessandro , Ghandour Fatme , Saad Eddy , Wang Xin-an , Pecci Federica , Holovatska Marta , Gandhi Malini M. , Hughes Melissa E. , O’Meara Tess A. , Chan Sabrina J. , Pfaff Kathleen , Konstantinopoulos Panagiotis A. , Hodi F. Stephan , Shipp Margaret A. , Signoretti Sabina , Choueiri Toni , Wei Xiao X. , Santagata Sandro , Hanna Glenn J. , Lin Nancy U. , Tolaney Sara M. , Liu Joyce , Sorger Peter K. , Lindeman Neal , Sholl Lynette M. , Nowak Jonathan A. , Barbie David , Awad Mark M. , Johnson Bruce E. , Rodig Scott J. 
Published: January 2025

ABSTRACTBackgroundNumerous retrospective studies have shown associations between the number of intratumoral immune cells and patient outcomes for individual cancers treated with specific therapies. However, the clinical value of using a digital pathology platform to enumerate intratumoral immune biomarkers prospectively in the pan-cancer setting has not been established.MethodsWe developed ImmunoProfile, a clinical workflow combining automated multiplex immunofluorescence tissue staining, digital slide imaging, and machine learning-assisted scoring to quantify intratumoral CD8+, PD-1+, CD8+PD-1+, and FOXP3+immune cells and PD-L1 expression in formalin-fixed, paraffin-embedded tissue samples in a standardized and reproducible manner. Over three years, we prospectively applied ImmunoProfile to biopsies collected from 2,023 unselected cancer patients in the clinical laboratory. We correlated the results with patient survival.ResultsIn the pan-cancer cohort, patients with intratumoral CD8+or PD-1+cells in the top or middle tertiles had significantly lower risks of death than those in the bottom (CD8+: (high vs. low) HR 0.62 [95% CI 0.48 – 0.81], (middle vs. low) HR 0.82 [95% CI 0.67 - 0.99], Wald p=0.002]; PD-1+: (high vs. low) HR 0.65 [95% CI 0.51 - 0.83], (middle vs. low) HR 0.74 [95% CI: 0.60 - 0.90], p=0.0009) after controlling for risk factors, including cancer type. In subset analyses, patients with high intratumoral CD8+, PD-1+, and/or CD8+PD-1+cells had lower risks of death from non-small cell lung, colorectal, breast, esophagogastric, head and neck, pancreatic, and ovarian cancers after controlling for clinical risk factors, including stage, and despite distinct therapies (all p<0.05).ConclusionsEnumerating intratumoral CD8+and PD-1+cells with a clinically validated digital pathology platform predicts patient survival across cancer types independent of clinical stage and despite disparate therapies.