bluuebunny/crossref_metadata_2025_split huggingface dataset:
ERGA-BGE Reference Genome ofLoboptera subterranea: a cave adapted cockroach endemic to the Canary Islands
Authors: López Heriberto , Oromí Pedro , Belles Xavier , Ylla Guillem , Escudero Nuria , Fernández Rosa , Böhne Astrid , Gut Marta , Aguilera Laura , Alioto Tyler , Ferreira Francisco Câmara , Gómez-Garrido Jèssica , Cruz Fernando , Monteiro Rita 
Published: February 2025

AbstractSpecies of the genusLobopterafrom the Canary Islands are adapted to life in subterranean environments, exceptLoboptera canariensisandLoboptera decipienswhich inhabit epigean, often influenced by human activities. The genome ofLoboptera subterraneaprovides a valuable resource for understanding the genetic basis of how the CanarianLobopteraspecies evolved and thrived in subterranean environments.A total of 14 contiguous chromosomal pseudomolecules were assembled from the genome sequence. This chromosome-level assembly encompasses 2.7 Gb, composed of 486 contigs and 90 scaffolds, with contig and scaffold N50 values of 13.1 Mb and 202.7 Mb, respectively.
CD4+Mucosal-associated Invariant T (MAIT) cells express highly diverse T cell receptors
Authors: Kaur Rimanpreet , Mehanna Nezar , Pradhan Atul , Xie Danielle , Li Kelin , Aubѐ Jeffrey , Rosati Barbara , Carlson David , Vorkas Charles K. 
Published: February 2025

AbstractMucosal-associated invariant T cells are highly conserved innate-like T cells in mammals recognized for their high baseline frequency in human blood and cytotoxic effector functions during infectious diseases, autoimmunity, and cancer. While the majority of these cells express a conserved CD8αβ+ TRAV1-2 T cell receptor recognizing microbially-derived Vitamin B2 intermediates presented by the evolutionarily conserved major histocompatibility complex I-related molecule, MR1, there is an emerging appreciation for diverse subsets that may be selected for in humans with distinct functions, including subpopulations that co-express CD4. Prior work has not examined T cell receptor (TCR) heterogeneity in CD4+MAIT cells, largely due to bias of identifying human MAIT cells as CD8+TRAV1-2+cells. In this study, we adopted an unbiased single-cell TCR-sequencing approach of total MR1-5-OP-RU-tetramer-reactive T cells and discovered that CD4+MAIT cells express highly diverse TRAV1-2 negative TCRs. To specifically characterize this TCR repertoire, we analyzed VDJ sequences of single MR1-5-OP-RU tetramer+MAIT cells across two datasets and identified distinct TCR usage among CD4+MAIT cells including TRAV21, TRAV8 (TRAV8-1, TRAV8-2, TRAV8-3), and TRAV12 families (TRAV12-2, TRAV12-3), as well as more variable J chain and CDR3 sequences. Non-TRAV1-2 MAIT cell TCRs were also enriched after in vitro expansion, including withMycobacterial tuberculosis. These results indicate that mature human CD4+MAIT cells adopt distinct TCR usage from the canonical TRAV1-2+CD8+subset and suggest that alternative MR1 ligands in addition to riboflavin intermediates may select them.
Measuring morphogen transport over multiple spatial scales in live zebrafish embryos
Authors: Nelanuthala Ashwin V. S. , Saha Bitan , Sankaran Jagadish , Carney Tom J. , Sampath Karuna , Wohland Thorsten 
Published: February 2025

AbstractMorphogenesis is controlled by signalling morphogens that form gradients across the embryo. The gradient formation requires that the low molecular weight morphogens slow down their diffusion by at least one order of magnitude. However, the precise slow-down of diffusion across the relevant micrometre scales has not been directly observed. Here, we develop and employ Single-Plane Illumination Microscope based spatial Fluorescence Cross-Correlation Spectroscopy (SPIM-sFCCS) to directly measure the diffusion coefficient of the morphogen Squint in early zebrafish embryos as a function of topography and length scale. We show that Squint’s diffusion coefficient changes on length scales that are commensurate with the diameter of the intercellular spaces in the embryo and that the slow-down is regulated by receptor binding. The slowdown can be reduced by either the knockdown of Activin receptor 2b, a receptor for Squint, or the overexpression of Lefty2, an inhibitor of Squint. Based on our results and supporting simulations, we propose an interstitial space-dependent transient receptor binding and diffusing mechanism to explain this slowdown, which is crucial for gradient formation and embryonic patterning.
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

ABSTRACTEssentiality 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.
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

AbstractLIMD1is 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.
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

AbstractWhen 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 SummaryHemostasis 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

AbstractPhlebotomine 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 SummaryPhlebotomine 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

AbstractThere 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

AbstractOsteochondral 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

AbstractThe 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

AbstractHuman 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

SUMMARYThe 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.
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

ABSTRACTLocal 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.