bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative essentiality in a reduced genome: a functional, regulatory and structural fitness map
Authors: Miravet-Verde Samuel , Burgos Raul , Garcia-Ramallo Eva , Weber Marc , Serrano Luis
Published: February 2025

Essentiality studies have traditionally focused on coding regions, often overlooking other small genetic regulatory elements. To address this, we obtained a high-resolution essentiality map at near-single-nucleotide precision of the genome-reduced bacteriumMycoplasma pneumoniae, combining transposon libraries containing promoter or terminator sequences. By integrating temporal transposon-sequencing data, we developed a novel method of essentiality assessment based on k-means unsupervised clustering, which provides dynamic and quantitative information on the fitness contribution of different genomic regions. We compared the insertion tolerance and persistence of the two engineered libraries, assessing the local impact of transcription and termination on cell fitness. Essentiality assessment at the local base-level revealed essential protein domains and small genomic regions that are either essential or inaccessible to transposon insertion. We also identified structural regions within essential genes that tolerate transposon disruptions, resulting in functionally split proteins. Overall, this study presents a nuanced view of gene essentiality, shifting from static and binary models to a more accurate perspective. Additionally, it provides valuable insights for genome engineering and enhances our understanding of the biology of genome-reduced cells.
Butterfly body size shrinkage: the impact of ecological traits across varied environments
Authors: Zografou Konstantina , Knop Eva , Sewall Brent J , Schweiger Oliver , De Moraes Consuelo M , Whitaker Melissa RL , Kati Vassiliki
Published: February 2025

Because of its close ties to numerous ecological and life history characteristics, body size is regarded as one of an organism's most important characteristics and is frequently considered a significant indicator of fitness. According to recent studies, ectotherms in particular, may see a reduction in body size with rising temperatures. How life history and ecological traits influence, however, shifts in butterfly body size in response to environmental changes, particularly focusing on the effects of temperature and land use is poorly studied. Using Generalized Additive Models (GAM), we analyzed forewing length data alongside various life history (phenology, overwintering developmental stage, voltinism, diet breadth, gender) and ecological traits (mobility, thermal tolerance) as well as environmental parameters for a period that lasts 110 years. Smaller body sizes were linked to early-season emergence and increasing forest cover, while larger sizes were linked to longer flight durations and later seasonal appearance. Males exhibited a pronounced decline in body size while females showed an opposite trend, suggesting sex-specific vulnerabilities to climate change. This research highlights the complex interplay between climate change, habitat fragmentation, and butterfly morphology, emphasizing the need for further investigation into sexual size dimorphism as anthropogenic influences continue to reshape butterfly populations.
LIMD1 Loss as an Early Driver of PD-L1 Upregulation and Immune Evasion in Lung Cancer
Authors: Shah Kunal M. , Kennedy Paul T. , Black James R. M. , Litchfield Kevin , Thakkar Krupa , Contreras-Gerenas Maria F. , Brooksbank Kirsten , Yuan Oliver , Grevitt Paul , Charrot Sarah , Davies Jeff , Dahal Lekh N. , Lagos Dimitris , McGranahan Nicholas , Sharp Tyson V.
Published: February 2025

LIMD1is a tumour suppressor gene frequently lost in non-small cell lung cancer (NSCLC), but its role in cancer-immune cell interactions remains unexplored. Here, we demonstrate that LIMD1 loss results in upregulation of the key immune checkpoint protein PD-L1. Using multi-region sequencing from the TRACERx dataset, we identify that LIMD1 loss is clonal in over 80% of squamous cell carcinoma (LUSC) and 40% of lung adenocarcinoma (LUAD) cases, correlating with increased PD-L1 expression. LIMD1 deficiency results in upregulation of basal and IFNγ-induced PD-L1 expression in NSCLC cells and, consistent with its early loss during oncogenesis, in primary human small airway epithelial cells. Mechanistically, we demonstrate that LIMD1 interacts with the E3 ubiquitin ligase ARIH1 to mediate efficient PD-L1 ubiquitination and degradation, a process that is significantly impaired in LIMD1-deficient cells, resulting in increased PD-L1 stability. As a consequence, LIMD1-deficient tumour cells suppressed CD8+ T cell activationin vitro, and blockade of PD-L1 reversed this suppression. Clinically, we show that LIMD1 loss is associated with enhanced response to immune checkpoint inhibitors (ICIs) in NSCLC patient cohorts, revealing a novel cancer cell-intrinsic correlation of ICI efficacy. Our results uncover a tumour suppressor-mediated mechanism of PD-L1 expression and pave the way for stratified immunotherapy approaches inLIMD1-/-NSCLC.
Soil protist diversity enhances prokaryotic diversity, and regulates dominant prokaryotes and the abundance of key nitrogen cycling genes
Authors: Perez-Villanueva Marta E. , Jurburg Stephanie D. , Malandain Cedric , Ghanem Nawras , Chatzinotas Antonis
Published: February 2025

Soil protists play crucial roles in soil microbial food-webs by preying on bacteria and other microorganisms. However, the effect of protist diversity on soil prokaryotic communities remains poorly understood. This study aimed to elucidate how different protist diversity treatments affect the composition and functionality of soil prokaryotic communities. We established soil microcosms with increasingly complex protist communities, including a control without protists, a medium diversity treatment with three small bacterivorous protists, and a high diversity treatment with seven protists of diverse trophic styles and sizes. Over 21 days, we monitored changes in the prokaryotic community using 16S rRNA gene sequencing and assessed the effects on nitrifiers and denitrifiers by qPCR of nitrogen-cycling genes. Protist diversity explained 23 % of the observed prokaryotic community differentiation over time, with the high-diversity treatment causing the greatest divergence from the control. The most abundant prokaryotes were preferentially predated in all protist treatments. Unexpectedly, the absolute abundance of the nirK gene, which is widely distributed among bacterial taxa and thus associated with high functional redundancy, decreased. The differential response of genes with lower distribution and redundancy, such as the bacterial and archaeal amoA and the Nitrospira-associated nxrB genes, to protist diversity indicated selective predation on archaea. High protist diversity systematically enhanced these effects compared to the medium diversity treatment. Overall, protist diversity was positively associated with prokaryotic diversity, which is crucial for maintaining ecosystem stability. These findings highlight the critical role of protist diversity and likely complementary predation in shaping soil prokaryotic communities and their functioning.
From imaging to computational domains for physics-driven molecular biology simulations: Hindered diffusion in platelet masses
Authors: House Catherine , Huang Ziyi , Shankar Kaushik N. , Young Sandra J. , Roberts Meghan E. , Diamond Scott L. , Tomaiuolo Maurizio , Stalker Timothy J. , Lu Lu , Sinno Talid
Published: February 2025

When formed in vivo, murine hemostatic thrombi exhibit a heterogeneous architecture comprised of distinct regions of densely and sparsely packed platelets. In this study, we utilize high-resolution electron microscopy alongside machine learning and physics-based simulations to investigate how such clot microstructure impacts molecular diffusivity. We used Serial Block Face – Scanning Electron Microscopy (SBF-SEM) to image select volumes of hemostatic masses formed in a mouse jugular vein, producing large stacks of high-resolution 2D images. Images were segmented using machine learning software (Cellpose), whose training was augmented by manually segmented images. The segmented images were then utilized as a computational domain for Lattice Kinetic Monte-Carlo (LKMC) simulations. This process constitutes a computational pipeline that combines purely data-derived biological domains with physics-driven simulations to estimate how molecular movement is hindered in a hemostatic platelet mass. Using our pipeline, we estimated that the hindered diffusion rates of a globular protein range from 2% to 40% of the unhindered rate, with denser packing regions lending to lower molecular diffusivity. These data suggest that coagulation reactions rates, thrombin generation and activity, as well as platelet releasate activity may be drastically impacted by the internal geometry of a hemostatic thrombus.

Author Summary

Hemostasis and coagulation are two exquisitely complex, intertwined, and tightly regulated biological processes. Dysregulation of either process may lead to severe health consequences or death. Coagulation reactions have been extensively studied under static laboratory conditions, which are different fromin vivoconditions. It is therefore imperative to understand if and how the chemical reactions underlying coagulation are regulated by the environment where they occur.In vivoexperimentation enables us to image hemostasis, but not chemical reactions. Physics-driven molecular simulations of chemical reactions can bridge the gap, provided the physical environment is correctly represented computationally. The present work serves as a much-needed foundation for image-to-computation for physics based molecular simulations in biological domains.
Hidden in plain sight: Discovery of sand flies in Singapore and description of four species new to science
Authors: Ding Huicong , Torno Majhalia , Vongphayloth Khamsing , Ng Germaine , Tan Denise , Sng Wendy , Ho Kelvin , Randrianambinintsoa Fano José , Depaquit Jérôme , Tan Cheong Huat
Published: February 2025

Phlebotomine sand flies (Diptera: Psychodidae) are small, blood-sucking insects that are of significant public and veterinary health importance for their role in the transmission ofLeishmaniaparasites, bacteria and arboviruses. Although sand flies have been documented in most Southeast Asian countries, there are no published records confirming their presence in Singapore. Here, we provide the first documented evidence on the presence of sand flies in Singapore. Using an integrated taxonomic approach that combines morphological analysis with DNA barcoding of the mitochondrialcytochrome b(cytb) andcytochrome c oxidase subunit I(COI) genes, we identified eight sand fly species, including four newly described species –Phlebotomus seowpohin. sp.,Sergentomyia leechingaen. sp.,Sergentomyia gublerin. sp., andSergentomyia retrocalcaraen. sp.. Phylogenetic analyses suggest that the newPhlebotomusspecies, belonging to subgenusEuphlebotomus, is closely related toPhlebotomus argentipes, an important vector ofLeishmania donovanifrom the South Asian region. The discovery of phlebotomine sand flies in Singapore underscores the importance of biosurveillance of biting arthropods. Given Singapore’s status as a major travel hub, there is a potential risk of leishmaniasis being introduced either by residents returning, or visitors arriving from endemic regions. This risk is compounded by the recent detection of local canine leishmaniasis. Thus, continuous monitoring is essential to assess and manage the risk of disease transmission, support the development of an early warning system, and enable timely and targeted public health interventions. The findings from this study contributes to the global knowledge on sand fly and enhance our understanding of local sand fly diversity and distribution.

Author Summary

Phlebotomine sand flies are small, blood-sucking insects recognized as significant vectors for various diseases including leishmaniasis. This study provides the first evidence of their presence in Singapore. Using an integrated taxonomic approach combining morphological analysis with DNA barcoding, we identified eight sand fly species that include four new species:Phlebotomus seowpohin. sp.,Sergentomyia leechingaen. sp.,Sergentomyia gublerin. sp., andSergentomyia retrocalcaraen. sp. The presence of sand flies in Singapore highlights an important biosurveillance need, as the region’s status as a major travel hub increases the risk of leishmaniasis being introduced. Importantly, recent findings of canine leishmaniasis in local dogs amplify the threat of disease transmission. Continuous monitoring and understanding of sand fly diversity and ecology are essential for developing effective public health strategies and early warning systems to manage this risk.
Evaluating discrepancies in dimensionality reduction for time-series single-cell RNA-sequencing data
Authors: Hackenberg Maren , Guitart Laia Canal , Backofen Rolf , Binder Harald
Published: February 2025

There are various dimensionality reduction techniques for visually inspecting dynamical patterns in time-series single-cell RNA-sequencing (scRNA-seq) data. However, the lack of one-to-one correspondence between cells across time points makes it difficult to uniquely uncover temporal structure in a low-dimensional manifold. The use of different techniques may thus lead to discrepancies in the representation of dynamical patterns. However, The extent of these discrepancies remains unclear. To investigate this, we propose an approach for reasoning about such discrepancies based on synthetic time-series scRNA-seq data generated by variational autoencoders. The synthetic dynamical patterns induced in a low-dimensional manifold reflect biologically plausible temporal patterns, such as dividing cell clusters during a differentiation process. We consider manifolds from different dimensionality reduction techniques, such as principal component analysis (PCA), t-distributed stochastic neighbor embedding (t-SNE), uniform manifold approximation and projection (UMAP) and single-cell variational inference (scVI). We illustrate how the proposed approach allows for reasoning about to what extent low-dimensional manifolds, obtained from different techniques, can capture different dynamical patterns. The results indicate that these techniques may not reliably represent dynamics when used in isolation. Thus, the proposed synthetic dynamical pattern approach provides a foundation for guiding future methods development to detect complex patterns in time-series scRNA-seq data.
Delayed lubricin injection improves cartilage repair tissue quality in an in vivo rabbit osteochondral defect model
Authors: Yoon Donghwan , Vishwanath Karan , Dankert John , Butler James J. , Azam Mohammad T. , Gianakos Arianna L. , Colville Marshall J. , Lopez Serafina G. , Paszek Matthew J. , Reesink Heidi L. , Kennedy John G. , Bonassar Lawrence J. , Irwin Rebecca M.
Published: February 2025

Osteochondral lesions (OCL) are common among young patients and often require surgical interventions since cartilage has a poor capacity for self-repair. Bone marrow stimulation (BMS) has been used clinically for decades to treat OCLs, however a persisting challenge with BMS and other cartilage repair strategies is the inferior quality of the resulting fibrocartilaginous repair tissue. Lubrication-based therapies have the potential to improve the quality of cartilage repair tissue as joint lubrication is linked to local cartilage tissue strains and subsequent cellular responses including death and apoptosis. Recently, a full length recombinant human lubricin (rhLubricin) was developed and has been shown to lower friction in cartilage. This study investigated the effect of a single delayed injection of rhLubricin on cartilage repair in anin vivorabbit OCL model using gross macroscopic evaluation, surface profilometry, histology, and tribology. Moderate improvement in macroscopic scores for cartilage repair were observed. Notably, quantitative analysis of Safranin-O histology showed that rhLubricin treated joints had significantly higher glycosaminoglycan content compared to saline treated joints, and there were no differences in repair integration between groups. Furthermore, rhLubricin treated joints had significantly lower friction coefficients tested across three sliding speeds compared to saline treated joints (rhLubricin: 0.15 ± 0.03 at 0.1 mm/s to 0.12 ± 0.03 at 10 mm/s, Saline: 0.22 ± 0.06 at 0.1 mm/s to 0.19 ± 0.05 at 10 mm/s). Overall, a single delayed injection of rhLubricin improved the quality and lubricating ability of the repair cartilage tissue without inhibiting repair tissue integration.
WormAI: Artificial Intelligence Networks for Nematode Phenotyping
Authors: Lieu Maggie , Cao Qi , Meng Ruoqing , Zhang Dong , Chauhan Veeren M.
Published: February 2025

The nematodeCaenorhabditis elegansis a key model organism in biological research due to its genetic similarity to humans and its utility in studying complex processes. Traditional image analysis methods, such as those using ImageJ, are labour-intensive, which has led to the integration of AI. This study introduces an AI framework with three machine learning models: WormGAN, a Generative Adversarial Network for generating synthetic nematode images to enhance training data; WormDET, for precise movement tracking; and WormREG, for accurate anatomical measurements. Together, these tools significantly improve the efficiency and accuracy of phenotypic analysis. WormAI demonstrates substantial potential for high-throughput dataset analysis, advancing research in systems biology, drug discovery, and aging. This framework streamlines workflows, enabling faster and more precise discoveries inC. elegansstudies.
Production of HPV-16 L1 virus-like particles in Physcomitrella photobioreactors
Authors: Niederau Paul Alexander , Weilguny Maria Caroline , Chamas Sarah , Turney Caitlin Elizabeth , Parsons Juliana , Rodríguez-Franco Marta , Hoernstein Sebastian N.W. , Decker Eva L. , Simonsen Henrik Toft , Reski Ralf
Published: February 2025

Human Papilloma Virus (HPV) infections are the main causal agent of cervical and other anogenital cancers. Modern HPV vaccines are based on virus-like particles (VLPs), which are self-assembling nanoparticles composed of viral structural proteins. VLPs mimic native virions but lack viral DNA, rendering these pseudovirions non-infectious while retaining high immunogenicity. Despite available vaccines, the majority of cervical cancer deaths are due to HPV infections, particularly in low– and middle-income countries where inequalities in access to vaccination, screening, and treatment persist. While current HPV vaccines are produced in yeast or insect cells, alternative production platforms are explored, focusing on cost-effectiveness and scalability. Here, we used the moss plant Physcomitrella (Physcomitrium patens) to produce HPV-16 VLPsviaexpression of the major structural protein L1. We characterized Physcomitrella chloroplast transit peptides, which we used for targeting of L1 to chloroplasts, leading to higher recombinant protein accumulation compared to nuclear or cytoplasmic localization. We confirmed subcellular localization with confocal laser scanning microscopy and found L1 to accumulate within the chloroplast stroma. Production in 5 L-photobioreactors yielded more than 0.3 mg L1 per g fresh weight. We established a purification protocol for moss-produced L1 using a combination of ammonium sulphate precipitation and cation exchange chromatography. Purified samples were subjected to a controlled dis– and reassembly, ultimately yielding fully assembled HPV-16 L1 VLPs. This is the first report of production, purification and assembly of pseudovirions in a non-vascular plant.
KHSRP-mediated Decay of Axonally Localized Prenyl-Cdc42 mRNA Slows Nerve Regeneration
Authors: Zdradzinski M.D. , Vaughn Lauren S. , Matoo Samaneh , Trumbull Kayleigh , Loomis Ashley , Thames Elizabeth , Lee Seung Joon , Perrone-Bizzozero Nora , Lu Qun , Larsen Jessica M. , Twiss J.L.
Published: February 2025

The small GTPase CDC42 promotes axon growth through actin filament polymerization and this growth is driven by axonal localization of the mRNA encoding the prenylated CDC42 isoform (Prenyl-Cdc42). Here, we show that axonalPrenyl-Cdc42mRNA transport and translation are decreased by growth-inhibiting stimulation and increased by growth-promoting stimulation. In contrast, axonalRhoAmRNA transport and translation are increased by growth inhibition but unaffected by growth promotion. Localized increase in KHSRP in response to growth inhibitory stimulation, through elevation of intracellular Ca2+, promotes decay of axonalPrenyl-Cdc42mRNA. Distinct 3’UTR motifs regulate transport and stability of axonalPrenyl-Cdc42mRNA. KHSRP protein binds to aPrenyl-Cdc42mRNA motif within nt 801-875 and the mRNA is remarkably increased in axons ofKhsrp-/-mice. Selective depletion ofPrenyl-Cdc42mRNA from axons reverses the accelerated axon regeneration seen inKhsrp-/-mice.
X-CRISP: Domain-Adaptable and Interpretable CRISPR Repair Outcome Prediction
Authors: Seale Colm , Gonçalves Joana P.
Published: February 2025

Motivation: Controlling the outcomes of CRISPR editing is crucial for the success of gene therapy. Since donor template-based editing is often inefficient, alternative strategies have emerged that leverage mutagenic end-joining repair instead. Existing machine learning models can accurately predict end-joining repair outcomes, however: generalisability beyond the specific cell line used for training remains a challenge, and interpretability is typically limited by suboptimal feature representation and model architecture. Results: We propose X-CRISP, a flexible and interpretable neural network for predicting repair outcome frequencies based on a minimal set of outcome and sequence features, including microhomologies (MH). Outperforming prior models on detailed and aggregate outcome predictions, X-CRISP prioritised MH location over MH sequence properties such as GC content for deletion outcomes. Through transfer learning, we adapted X-CRISP pre-trained on wild-type mESC data to target human cell lines K562, HAP1, U2OS, and mESC lines with altered DNA repair function. Adapted X-CRISP models improved over direct training on target data from as few as 50 samples, suggesting that this strategy could be leveraged to build models for new domains using a fraction of the data required to train models from scratch. Availability: An implementation of X-CRISP is available at \href{https://github.com/joanagoncalveslab/xcrisp}{github.com/joanagoncalveslab/xcrisp}.
Modeling cryo-EM structures in alternative states with generative AI and density-guided simulations
Authors: Shugaeva Tatiana , Howard Rebecca J , Haloi Nandan , Lindahl Erik
Published: February 2025

Modeling atomic coordinates into a target cryo-electron microscopy map is a crucial step in structure determination. Despite recent advances, proteins with multiple functional states remain a challenge - particularly when suitable molecular templates are unavailable for certain states, and the map resolution is not high enough to build de novo models. This is a common scenario, for example, among pharmacologically relevant membrane-bound receptors and transporters. Here, we introduce a refinement approach in which i) several initial models are generated by stochastic subsampling of the multiple sequence alignment (MSA) space in AlphaFold2, ii) the resulting models are subjected to structure-based clustering, iii) density-guided molecular dynamics simulations are performed from the centroid structures, and iv) a final model is selected on the basis of both map fit and model quality. This results in improved fitting accuracy compared to single starting point scenarios for three membrane proteins (the calcitonin receptor-like receptor, L-type amino acid transporter and alanine-serine-cysteine transporter which undergo substantial conformational transitions between functional states. Our results indicate that ensemble construction using generative AI combined with simulation-based refinement facilitates building of alternative states in several families of membrane proteins.
Testing the Vogt-Bailey Index using task-based fMRI across pulse sequence protocols
Authors: Galea Kristian , Escudero Aitor Alberdi , Attard-Montalto Nina , Vella Nolan , Smith Robert E. , Farrugia Christine , Galdi Paola , Scerri Kenneth , Butler Liam , Bajada Claude J.
Published: February 2025

Local connectivity analyses in fMRI such as the Vogt-Bailey Index, investigate the prevalence of co-fluctuations in the time-series of adjacent voxels. While there have beenin silicoassessments of the VB Index, this technique has not yet been assessedin vivo. This study has two aims: first, to assess the VB Index using a task paradigm with well establisheda prioriexpectations on the brain region predominantly responsible for executing this task to determine whether the VB Index highlights this area. Second, we investigate if, and how, the spatial resolution of the sequence protocols employed, with their inherent effects on the signal-to-noise ratio, affect the resultant VB maps. A cohort of 10 research volunteers underwent fMRI acquisitions utilising a block design finger tapping experiment. Each volunteer was scanned with three sequence protocols, with all parameters equivalent except for the volume of the voxels. The resulting parametric maps derived using the VB Index were compared with those obtained from the conventional General Linear Model approach. Particular emphasis was placed on the identification of the hand portion of the motor homunculus. Across sequence protocols, the VB Index consistently identified elevated local connectivity in, qualitatively, the same portion of the motor cortex as that yielded by the General Linear Model based on the task paradigm. However, the VB Index also detected elevated local connectivity outside the motor cortex while the General Linear Model results were mostly restricted to the motor cortex. The consistently high VB Index, across sequence protocols, in the cortical region associated with an fMRI task paradigm, despite the approach’s agnosticism to that task, provides support for the biological relevance of such local connectivity measures.
Liquid-solid coexistence at single fibril resolution during tau condensate ageing
Authors: Sahu Mahaprasad S. R. , Wei Jiapeng , Weitz David A. , Knowles Tuomas P. J. , Garai Kanchan
Published: February 2025

Aggregated fibrillar tangles of the microtubule-associated protein tau are a hallmark of Alzheimer’s disease. It is becoming increasingly clear that a key process that can trigger the formation of such tau tangles is the aberrant ageing of biomolecular condensates of tau formed via liquid-liquid phase separation. This ageing process affects the overall mechanical and structural properties of the condensates, but the molecular-level mechanisms by which aggregation takes place in the condensates have remained elusive. Here, by tracking individual tau molecules inside the condensates by single molecule microscopy we show that the ageing process is characterized by the co-existence of a growing solid phase of tau within a dense liquid phase. The liquid phase is increasingly confined to the pores of the growing fibril gel network, but maintains its initial viscosity. These findings add a spatial dimension to the ageing of condensates and demonstrate that spatial heterogeneity is a key feature of the liquid-to-solid transition of tau.
Magnetite Nanoparticle Photothermal Therapy in a Pancreatic Tumor-on-Chip: A Dual-Action Approach Targeting Cancer Cells and their Microenvironment
Authors: Dubrova Anastasiia , Cavaniol Charles , Van de Walle Aurore , Mathieu Paul , Fusilier Zoé , Yaacoub Nader , Lalatonne Yoann , Descroix Stéphanie , Wilhelm Claire
Published: February 2025

The application of magnetite nanoparticles (MagNPs) for photothermal therapy (MagNP-PTT) has recently expanded in cancer treatment. This study introduces MagNP-PTT in a tumor-on-chip model to target highly aggressive pancreatic ductal adenocarcinoma (PDAC). A tumor-on-chip system was developed using PANC-1 PDAC cells embedded in a collagen type I extracellular matrix and cultured for one week to form tumor spheroids. This platform serves as the foundation for applying PTT in a model system that is aimed to mimic the native tumor microenvironment. MagNPs efficiently penetrate the tumor spheroids, achieving controlled heating via near-infrared (NIR) light. By adjusting nanoparticle concentration and laser power, temperature increments of 2°C between 38-48°C were established. Temperatures above 44°C significantly increased cell death, while lower temperatures allowed partial recovery. Beyond inducing cancer cell death, MagNP-PTT altered the extracellular matrix, and triggered a slight epithelial-mesenchymal transition marked by increased vimentin expression. These findings highlight MagNP-PTT as a dual-action therapy, targeting both tumor cells and their microenvironment, offering a novel approach for overcoming stromal barriers in pancreatic cancer treatment.
Spatio-temporal dynamics of M1and M2macrophages in a multiphase model of tumor growth
Authors: Lampropoulos Ioannis , Kevrekidis Panayotis , Zois Christos , Byrne Helen , Kavousanakis Michail
Published: February 2025

This study investigates the complex dynamics of vascular tumors and their interplay with macrophages, key agents of the innate immune response. We model the tumor microenvironment as a multiphase fluid, with each cellular population treated as a distinct, non-mixing phase. The framework also incorporates diffusible species that are critical for processes such as nutrient transport, angio-genesis, chemotaxis, and macrophage activation. Numerical simulations of our model show how phenotypic and spatial heterogeneity in the macrophage population arises and how such heterogeneity impacts a tumor’s growth dynamics. Finally, we propose an immunotherapeutic strategy based on the experimental agent vactosertib which promotes an anti-tumor macrophage phenotype. Our simulations demonstrate an increased density of anti-tumor macrophages over the period of a few months, followed by a relapse period where the tumor regains its original dynamics.
A self-assembling cross-protective antigen against multiple Gram-positive nosocomial pathogens
Authors: Kramarska Eliza , Romero-Saavedra Felipe , Squeglia Flavia , La Manna Sara , Sadones Oceane , Marasco Daniela , Berisio Rita , Huebner Johannes
Published: February 2025

ESKAPE pathogens are responsible for complicated nosocomial infections worldwide and are usually resistant to commonly used antibiotics in clinical settings. Among these bacteria, vancomycin-resistantEnterococcus faeciumand methicillin-resistantStaphylococcus aureusare the two most important Gram-positive pathogens for which alternative treatments and preventions are urgently needed. We previously designed a multi-presenting antigen, embedding the main epitope displayed by the AdcA protein ofE. faecium, that conferred protection against different Gram- positive pathogens both in passive and active immunization models. Here, we developed a new presentation strategy for this epitope, the EH-motif, based on a self-assembling peptide. Self- assembling peptides have been promising in the fields of material sciences, nanoscience, and medicine and have also potential in vaccine development, as they allow multiple presentations of the epitope and provide an ideal size for production and application. We show that this multi- presenting peptide, here Q11-EH, forms stable fibers of nanometric size. We also demonstrate that antibodies raised against Q11-EH mediate the opsonic killing of a wide-spectrum of Gram-positive pathogens, includingE. faecium,S. aureus,andE. faecalis. Our data indicate that multiple presentation strategies are a potent tool for vaccine antigen improvement and point to Q11-EH as a promising antigen for the development of novel cross-protective vaccines.
Targeting BRAF kinase fusions with pan-RAF and vertical MAPK inhibition
Authors: Turner Jacqueline A. , MacBeth Morgan , Bagby Stacey , Whitty Phaedra , Hartman Sarah , Simmons Dennis , Yacob Betelehem , Robinson William A. , Couts Kasey L.
Published: February 2025

BRAFkinase fusions are a form of structural variation in the genome and are recurrent events in driver-negative melanomas. WhileBRAFfusions reproducibly conserve the kinase domain, there is genetic variability with 5’ gene partners and specificBRAFbreakpoints. We investigated how genetic diversity ofBRAFkinase fusions affects dimeric signaling and ERK activation. We overexpressedBRAFfusions with 5’ gene partners includingAGK, ZKSCAN1, ARMC10, PPFIBP2, andTRIM24and found fusion dependent signaling and inhibitor sensitivity. Despite the development of next generation RAF inhibitors, there was paradoxical ERK phosphorylation with multiple pan-RAF inhibitors, which was ameliorated in certainBRAFfusions with vertical RAF/MEK inhibition using trametinib and LY3009120. Collectively, we observed some fusion-dependent effects but also tumor growth suppression and resolution of paradoxical activation with vertical pathway inhibition.
Climate-Driven Reshuffling of Butterfly Communities: Body Size Declines and Community Homogenization in a Rapidly Warming Switzerland
Authors: Zografou Konstantina , Kati Vassiliki , Knop Eva
Published: February 2025

Climate change has been reshaping natural communities by driving species to change their ranges in response to warming temperatures. In Switzerland, the rate of warming since 1950 has approached nearly double the global average, making these impacts important for community composition and ecosystem function. Using the Community Weighted Length Index (CWLI) as the body size estimator, previously extracted by museum specimens, we studied two decades of butterfly community data that have been inventoried by the Biodiversity Monitoring Switzerland program. We checked for deviations from the expectation of random trends in the CWLI using null models. We modeled the long-term patterns at each site and the overall long-term patterns through linear regression and mixed-effects models alongside the model of the relationship between wing length, elevation, and abundance. CWLI of Swiss butterfly assemblages dropped by 5.2% over two decades, suggesting that warmer temperatures are differentially affecting large-bodied species. While CWLI trends were significantly declining at most sites (73%), a subset of sites (27%) showed trends of increasing CWLI, sometimes associated with cooler microclimates either in forests or at higher elevation. Our results further indicate a progressive homogenization of butterfly communities, marked by smoother CWLI slopes and reduced CWLI range over time. These results underline complex relations of climate-driven range shifts with body-size dynamics and community restructuring, emphasizing the importance of understanding the processes to mitigate biodiversity loss in thermally sensitive ecosystems.
From Mechanistic Interpretability to Mechanistic Biology: Training, Evaluating, and Interpreting Sparse Autoencoders on Protein Language Models
Authors: Adams Etowah , Bai Liam , Lee Minji , Yu Yiyang , AlQuraishi Mohammed
Published: February 2025

Protein language models (pLMs) are powerful predictors of protein structure and function, learning through unsupervised training on millions of protein sequences. pLMs are thought to capture common motifs in protein sequences, but the specifics of pLM features are not well understood. Identifying these features would not only shed light on how pLMs work, but potentially uncover novel protein biology––studying the model to study the biology. Motivated by this, we train sparse autoencoders (SAEs) on the residual stream of a pLM, ESM-2. By characterizing SAE features, we determine that pLMs use a combination of generic features and family-specific features to represent a protein. In addition, we demonstrate how known sequence determinants of properties such as thermostability and subcellular localization can be identified by linear probing of SAE features. For predictive features without known functional associations, we hypothesize their role in unknown mechanisms and provide visualization tools to aid their interpretation. Our study gives a better understanding of the limitations of pLMs, and demonstrates how SAE features can be used to help generate hypotheses for biological mechanisms. We release our code, model weights and feature visualizer.1
Do camera light traps for moths provide similar data as conventional funnel light traps?
Authors: Holzhauer Vivian , Böttger Dennis , Bodesheim Paul , Brehm Gunnar
Published: February 2025

Insects are of crucial importance for terrestrial ecosystems but many populations decline rapidly. Conventional collecting methods are usually time-consuming, resulting in a low temporal, spatial and taxonomic resolution of data. Automated camera light traps (CLT) allow non-lethal monitoring of species-rich moths (Lepidoptera) and other nocturnal insects, but so far little is known about their performance compared to conventional collecting methods.

By observing the behaviour of moths in previous field work, we hypothesized that CLT perform well in moth groups in which species tend to sit down quietly after approaching the lamp (such as Geometridae) but worse in moth groups in which species are persistently active (such as Sphingidae).

We tested the performance of two CLTs, equipped with Sony alpha 7II (24 megapixel sensor) cameras that resulted in images with approx. 420 dpi resolution. The study was carried out in a forested area near Bielefeld in NW Germany for 196 nights in a row from April to September 2023, and photos were taken every two minutes during the night. All macromoths recognizable in the photos were identified and counted individually. We directly compared the data from the CLTs with moth samples obtained from conventional funnel light traps (FLTs) during 12 nights which were spread across the flight season.

The resulting 420 dpi images from the CLTs allowed reliable species identification of all observed macromoths with only few exceptions due to technical problems. In direct comparison during 12 nights, CLTs recorded 39 species exclusively, FLTs recorded 48 species exclusively, and 53 species were recorded by both methods equally. During the whole sampling period of 196 nights in a row, a total of 225 moth species were recorded by CLTs. CLTs tended to record Geometridae better than FLTs whereas Sphingidae tended to be undersampled by the new method. Familes differed in the length to which they remained on the screen of the CLTs.

Our study is the first to systematically compare the methods and it shows that CLTs perform overall very well. Results from CLTs differ to a certain extent from conventional trapping methods because they seem to perform worse in groups with highly active species and perform better in calmer groups like geometrid moths. CLTs are promising devices for insect monitoring since they deliver data with high resolution in time, space and taxonomy. The use of artificial intelligence (AI) for the analysis of images is intended as the next logic step.
Decoding the restriction of T cell receptors to human leukocyte antigen alleles using statistical learning
Authors: ElAbd Hesham , Mahdy Aya K.H. , Wacker Eike Matthias , Gretsova Maria , Ellinghaus David , Franke Andre
Published: February 2025

Conventional T cells recognize peptides presented by the human leukocyte antigen (HLA) proteins through their T cell receptors (TCRs). Given that thousands of HLA proteins have been discovered, each presenting thousands of different peptide antigens, decoding the cognate HLA protein of a TCR experimentally is a challenging task. To address this problem, we combined statistical learning methods with a unique dataset of paired T cell repertoires and HLA allele information for 6,794 individuals. This enabled us to discover 53,870 T cell receptor alpha (TRA) and 1,095,576 beta (TRB) clonotypes that were associated with 437 unique HLA alleles. The identified clonotypes were targeting prevalent infections,e.g.influenza, cytomegalovirus and Epstein-Barr virus. Utilizing these clonotypes, we developed statistical models that impute the carriership of common HLA alleles from the TRA- or TRB-repertoire. In conclusion, the identified allele-associated clonotypes encode the HLA fingerprints and the immune exposure history of individuals and populations.
TRPV1+ neurons promote cutaneous immunity againstSchistosoma mansoni
Authors: Inclan-Rico Juan M. , Stephenson Adriana , Napuri Camila M. , Rossi Heather L. , Hung Li-Yin , Pastore Christopher F. , Luo Wenqin , Herbert De’Broski R.
Published: February 2025

Immunity against skin-invasive pathogens requires mechanisms that rapidly detect, repel or immobilize the infectious agent. While bacteria often cause painful cutaneous reactions, host skin invasion by the human parasitic helminthSchistosoma mansonioften goes unnoticed. This study investigated the role of pain-sensing skin afferents that express the ion channel Transient Receptor Potential Vanilloid 1 (TRPV1) in the detection and initiation of skin immunity againstS. mansoni. Data show that mice infected withS. mansonihave reduced behavioral responses to painful stimuli and sensory neurons exposed from infected mice have significantly less calcium influx and neuropeptide release in response to the TRPV1 agonist capsaicin. Using both gain- and loss-of-function approaches, data show that TRPV1+ neurons are critical regulators ofS. mansonisurvival during migration from the skin into the pulmonary tract. Moreover, TRPV1+ neurons were both necessary and sufficient to promote proliferation and cytokine production from dermal γδ T cells as well as neutrophil and monocyte skin accumulation post-infection. These results suggest a model in whichS. mansonimay have evolved to inhibit TRPV1+ neuron activation as a countermeasure that limits IL-17-mediated inflammation, facilitating systemic dissemination and chronic parasitism.

One sentence summary

The parasitic helminthSchistosoma mansoniaverts IL-17-dependent protective immunity by suppressing skin-innervating TRPV1+ neurons.
Genome Sequence of a Marine Threespine Stickleback (Gasterosteus aculeatus) from Rabbit Slough in the Cook Inlet
Authors: Au Eric H , Weaver Seth , Katikaneni Anushka , Wucherpfennig Julia I , Luo Yanting , Mangan Riley J , Wund Matthew A , Bell Michael A , Lowe Craig B
Published: February 2025

The Threespine Stickleback, Gasterosteus aculeatus, is an emerging model system for understanding the genomic basis of vertebrate adaptation. A strength of the system is that marine populations have repeatedly colonized freshwater environments, serving as natural biological replicates. These replicates have enabled researchers to efficiently identify phenotypes and genotypes under selection during this transition. While this repeated adaptation to freshwater has occurred throughout the northern hemisphere, the Cook Inlet in south-central Alaska has been an area of focus. The freshwater lakes in this area are being studied extensively and there is a high-quality freshwater reference assembly from a population in the region, Bear Paw Lake. Using a freshwater reference assembly is a potential limitation because genomic segments are repeatedly lost during freshwater adaptation. This scenario results in some of the key regions associated with marine-freshwater divergence being absent from freshwater genomes, and therefore absent from the reference assemblies. It may also be that isolated freshwater populations are more genetically diverged, potentially increasing reference biases. Here we present a highly-continuous marine assembly from Rabbit Slough in the Cook Inlet. All contigs are from long-read sequencing and have been ordered and oriented with Hi-C. The contigs are anchored to chromosomes and form a 454 Mbp assembly with an N50 of 1.3 Mbp, an L50 of 95, and a BUSCO score over 97%. The organization of the chromosomes in this marine individual is similar to existing freshwater assemblies, but with important structural differences, including the 3 previously known inversions that repeatedly separate marine and freshwater ecotypes. We anticipate that this high-quality marine assembly will more accurately reflect the ancestral population that founded the freshwater lakes in the area and will more closely match most other populations from around the world. This marine assembly, which includes the repeatedly deleted segments and offers a closer reference sequence for most populations, will enable more comprehensive and accurate computational and functional genomic investigations of Threespine Stickleback evolution.
Genome report: Genome sequence of the hibiscus mealybug,Nipaecoccus viridis(Newstead), an invasive pest of citrus
Authors: Liesenfelt Tracy , Markee Amanda , Demard Emilie P. , Diepenbrock Lauren M. , Mongue Andrew J.
Published: February 2025

Mealybugs are frequently known for being pest insects to both ornamental and large-scale agricultural crops. Yet despite their agricultural importance, the genomic resources for this group remain quite small. One such species is the hibiscus mealybug,Nipaecoccus viridis(Newstead) (Hemiptera: Coccomorpha: Pseudococcidae). This invasive mealybug species has recently expanded throughout Florida and has spread across the state. Genomic resources would provide a new means to better understand the invasive nature of this insect, and thus, we present the de novo genome assembly forNipaecoccus viridis. Our genome assembly is 289 Mb, in which 91.2% of this sequence assembled into 5 chromosomal scaffolds. We report 15,370 genes to be present within our genome. We found that repetitive elements in the genome accounted for 32.40% of the sequence. These statistics follow similar trends to other previously sequenced pseudococcid species.
A Dapl1+ subpopulation of naive CD8 T cells contains committed precursors of memory lineage.
Authors: Lynch Adam C. , Hioki Kaito A. , Liang Xueting , Thesmar Iris , Cernjul Julia , He Xinjian , Mager Jesse , Cui Wei , Alfandari Dominique , Pobezinskaya Elena E. , Pobezinsky Leonid A.
Published: February 2025

Memory CD8 T cells play a vital role in providing lasting immune protection, yet their origins remain incompletely understood. Contrary to classical models, emerging evidence suggests that heterogeneity within the naive T cell pool may influence fate decisions prior to antigen encounter. However, the markers of naive T cell heterogeneity have not yet been clearly defined. Here, we describe intraclonal heterogeneity within the naive T cell population marked by the protein Dapl1. Using novel monoclonal antibodies and a reporter-knockout mouse model, we found that Dapl1-positive naive CD8 T cells exhibit distinct phenotypes compared to their Dapl1-negative counterparts. Furthermore, this population includes a subset of pre-programmed precursors biased toward memory lineage fate. The differentiation of these precursors is independent of Dapl1 but relies on the transcription factor Bcl11b, resulting in the generation of Dapl1-positive central memory-like CD8 T cells in response to infection, and stem-like memory cells in response to cancer. Notably, naive Dapl1-positive T cells originate in the thymus among mature thymocytes and gradually appear in the periphery within several days after birth. Our findings suggest that committed memory precursors in the Dapl1-positive population may represent an alternative pathway for memory CD8 T cell generation, offering new avenues for therapeutic application.