bluuebunny/crossref_metadata_2025_split huggingface dataset:
E2A SUMOylation promotes HAdV mediated inhibition of the tumor suppressor p53 during infection
Authors: Stubbe Miona , Stubbe Hans Christian , Mai Julia , Plank Verena , Hofmann Samuel , Göttig Lilian , Günther Thomas , Grundhoff Adam , Krebs Stefan , Groitl Peter , Mayerle Julia , Hay Ron T. , Dobner Thomas , Schreiner Sabrina 
Published: February 2025

ABSTRACTHAdV express early viral genes to modulate the activity of the cellular tumor suppressor p53 and ensure efficient viral replication, through various processes, whilst some of them are not completely understood. HAdV oncoprotein E1B-55K interactions with SUMO, PML-IV/V and Sp100A are tightly connected to the transforming potential of the viral factor in non-lytic infections. SUMO modified HAdV DNA binding protein (DBP) E2A interacts with PML and Sp100A acting as a molecular bridge between viral replication centers (RCs) and PML tracks. Here, we show for the first time, that HAdV E2A is involved in the inhibition of p53 activity and apoptosis and thus identified a novel route of exhibiting virus induced oncogenic potential. We revealed an E1B-55K independent localization of p53 within HAdV replication centers marked by E2A. In the absence of any functional E1B-55K protein expression, p53 interacts with E2A. E2A SUMOylation promotes HAdV-mediated inhibition of p53/DNA binding and p53-dependent transactivation by supporting p53 degradation, E1B-55K interaction and colocalization with PML-V that leads to E1B-55K induced upregulation of p53 SUMOylation. In sum, we provide evidence for a novel mechanism by which the HAdV DBP E2A protein inhibits p53-mediated transcriptional activation and apoptotic host cell response. Intriguingly, these findings change the longstanding dogma of host DNA damage response (DDR) inactivation by HAdV infection and offer crucial insights to improve future p53 selective oncolytic virus therapies and adenoviral vectors.
Intraspecies associations from strain-rich metagenome samples
Authors: Qu Evan B. , Baker Jacob S. , Markey Laura , Khadka Veda , Mancuso Chris , Tripp Delphine , Lieberman Tami D. 
Published: February 2025

AbstractGenetically distinct strains of a species can vary widely in phenotype, reducing the utility of species-resolved microbiome measurements for detecting associations with health or disease. While metagenomics theoretically provides information on all strains in a sample, current strain-resolved analysis methods face a tradeoff:de novogenotyping approaches can detect novel strains but struggle when applied to strain-rich or low-coverage samples, while reference database methods work robustly across sample types but are insensitive to novel diversity. We present PHLAME, a method that bridges this divide by combining the advantages of reference-based approaches with novelty awareness. PHLAME explicitly defines clades at multiple phylogenetic levels and introduces a probabilistic, mutation-based, framework to accurately quantify novelty from the nearest reference. By applying PHLAME to publicly available human skin and vaginal metagenomes, we uncover previously undetected clade associations with coexisting species, geography, and host age. The ability to characterize intraspecies associations and dynamics in previously inaccessible environments will propel new mechanistic insights from accumulating metagenomic data.
‘Trans-differentiation of neutrophils from plasmablast’ is an artefact caused by over-reliance on machine algorithms in single cell RNA sequencing analysis: Lesson learnt and steps ahead
Authors: Huang Jinghan , Yam Phillip S.C. , Tang Nelson L.S. 
Published: February 2025

AbstractSingle cell RNA sequencing (scRNA-seq) provides new opportunities to characterize gene expression for individual cells. However, the sparse nature of the scRNA-seq data with many zero counts or missing values presents a major challenge to its analysis. The presence of low-quality cells further complicates the analysis. Here, we showed that the trans-differentiation of plasmablasts (activated plasma cells) into neutrophils reported in COVID patients (Wilk et al., 2020 in Nature Medicine) was an artefact of trajectory analysis. It was caused by ∽30 low-quality cells linking the 2 cell populations that are of unrelated lineages in hematopoietic differentiation.Such artefacts are not readily spotted during the current practice of peer reviews as the current statistical guidelines of most journals are not catered for big data such as that of scRNA-seq. New standards of statistics and quality control measures for machine algorithms are not in place and they are urgently needed to safeguard against over-interpretation of high dimensional data. We propose a comprehensive framework to ensure reproducibility in high-dimensional data analysis, emphasizing quality checks, sensitivity analyses, alternative and multiple algorithms validation. Finally, and most importantly, a hypothesis-driven research approach should be upheld.
Chitosan gold nanoparticle-based dot-blot assay for sensitive visual detection of histidine-tagged recombinant proteins
Authors: Mahmoodi Sahar , Pourhassan-Moghaddam Mohammad , Majdi Hasan , Maleki Mohammad Jafar 
Published: February 2025

AbstractThere are various techniques for detecting recombinant proteins such as western blot, SDS-PAGE, ELISA and fluorescence microscopy. However, these methods are difficult to handle, time-consuming and need special tools. We developed a rapid, inexpensive, sensitive, and straightforward approach to address these problems using an Antihistidine biosensor. Colloidal gold nanoparticles (GNPs) were synthesized by chitosan as reducer and stabilizer via the green synthesis method. Then, anti-His tag antibody was immobilized on the Chitosan-gold nanoparticles (CS-GNPs) surface to visually detect spotted target protein on nitrocellulose (NC) membrane. Our results showed that the designed dot-blot immunoassay can detect histidine-tagged recombinant proteins with the limit of detection (LOD) of 1µg/ml without any signal enhancement directly from cell lysate within 5 minutes. In an extra step, we applied HAuCl4 and NH2OH\ HCl as a gold enhancement system and increased the detection sensitivity to 0.1 µg/ml. The results showed that the developed assay can rapidly detect production of recombinant proteins, and it can be used as a screening method in low-resource laboratories.
Mechanism Underlying Carvacrol-induced Alveolar Bone Repair via the Phosphatidylinositol 3-kinase Pathway in Periodontal Disease
Authors: Nian Teng , Zhaoxun Li , Tiantian Gao , Yanrui Xiang , Lulu Zhou , Xiang Gao 
Published: February 2025

AbstractBackgroundConventional antibiotic treatments do not restore the structure of periodontal tissues and can cause antibiotic resistance. This study describes the mechanism by which carvacrol regulates alveolar bone osteoblasts in periodontal disease.MethodsA rat model of periodontal disease (P group) was created by ligating the first molar and injecting lipopolysaccharide (LPS). Additionally, a control model (C group) was created. The treatment models received low (L group), medium (M group), and high (H group) doses of carvacrol hydrogel. In vitro, rat osteoblast cells were divided into the C, P, L, M, H, and carvacrol + LY294002 (Car+LY group) groups. Immunohistochemical staining analyzed collagen type I and runt-related transcription factor 2 expressions. Western blot analysis detected the phosphatidylinositol 3-kinase (PI3K)/protein kinase B (AKT)/glycogen synthase kinase 3 beta (GSK-3β) pathway-related and osteoblastic proteins. Quantitative reverse transcription polymerase chain reaction measured the expression of inflammatory factors and osteoblastic proteins. The alkaline phosphatase (ALP) colorimetric kit and Alizarin Red S staining kit assessed the osteogenic ability. Detect the expression of COL1 in osteoblasts by immunofluorescence (IF). Transmission electron microscopy detected cell apoptosis.ResultsCarvacrol hydrogel alleviated periodontal symptoms, upregulated PI3K/AKT/GSK-3β pathway-related and osteoblastic proteins, and increased ALP expression and calcified nodules. However, it decreased cell apoptosis and inflammatory factors. LY294002 inhibited the PI3K/AKT pathway and decreased osteoblastic protein expression, ALP coloration, and calcified nodules.ConclusionCarvacrol hydrogel promotes the proliferation and differentiation of alveolar bone osteoblasts by activating the PI3K pathway and inhibiting inflammation-induced bone resorption. This study emphasizes the potential of carvacrol for treating periodontal diseases.
Development of potent humanized TNFα inhibitory nanobodies for therapeutic applications in TNFα-mediated diseases
Authors: Yin Tao , Ramon Aubin , Greenig Matthew , Sormanni Pietro , D’Adamio Luciano 
Published: February 2025

AbstractTumor necrosis factor-alpha (TNFα) is a key pro-inflammatory cytokine implicated in the pathogenesis of numerous inflammatory and autoimmune diseases, including rheumatoid arthritis, inflammatory bowel disease, and neurodegenerative disorders such as Alzheimer’s Disease. Effective inhibition of TNFα is essential for mitigating disease progression and improving patient outcomes. In this study, we present the development and comprehensive characterization of potent humanized TNFα inhibitory nanobodies (TNFINbs) derived from camelid single-domain antibodies. In silico analysis of the original camelid nanobodies revealed low immunogenicity, which was further reduced through machine-learning-guided humanization and developability optimization. The two humanized TNFI-Nb variants we developed demonstrated exceptional anti-TNFα activity, achieving IC50values in the picomolar range. Binding assays confirmed their high affinity for TNFα, underscoring robust neutralization capabilities. These TNFI-Nbs present valid alternatives to conventional monoclonal antibodies currently used in human therapy, offering potential advantages in potency, specificity, and reduced immunogenicity. Our findings establish a solid foundation for further preclinical development and clinical translation of TNFα-targeted nanobody therapies in TNFα-mediated diseases.
Driving factors for beta-lactam resistance gene amplification duringde novoresistance evolution inE. coli
Authors: Nong Luyuan , Liu Xinwei , Wang Xinyu , de Leeuw Wim , Jonker Martijs , Brul Stanley , ter Kuile Benno 
Published: February 2025

AbstractLong-term exposure ofE. colito non-lethal step-wise increasing concentrations of beta-lactam antibiotics induces high levels of resistance that can be accompanied by amplification of a chromosomal fragment around theampCgene. We compared the amplification of theampCfragment in the wildtype, anampCknockout mutant, a mutant in which theampCgene was replaced by a tetracycline resistance genetet(B)and a strain in which theampChas been translocated. WhenampCwas removed, no amplification occurred at the originalampClocation, but DNA fragments were amplified around the genes coding for efflux pump AcrAB and the multiple antibiotic resistance operon MarRAB. Whentet(B)replacedampC, exposure to tetracycline induced amplification of comparable fragments, while exposure to amoxicillin induced duplication of a larger fragment elsewhere. WhenampCwas translocated, a fragment around it at the new location was amplified. The importance of the presence but not of the location within the chromosome of the resistance genes for the amplification process indicates that the mechanisms are neither gene nor location specific. Without the relatively efficient resistance geneampC, duplication and amplification occur aroundacrABandmarRABthat code for amoxicillin and tetracycline resistance factors. These duplications and amplifications are prevented byampCamplification.
Dimethyl sulfoxide primes induced pluripotent stem cells for more efficient nephron progenitor and kidney organoid differentiation
Authors: Kearney Helen , Rak-Raszewska Aleksandra , Seijas-Gamardo Adrián , Escarda-Castro Enrique , Wieringa Paul , Moroni Lorenzo , Mota Carlos 
Published: February 2025

AbstractThe field of human induced pluripotent stem cells (hiPSCs) has seen significant progress since the discovery of reprogramming somatic cells using the transcription factors Oct4, Sox2, Klf4, and c-Myc. hiPSCs are similar to embryonic stem cells in a primed state of pluripotency and has the potential to differentiate into any adult human cell type, offering a versatile tool for research and potential therapeutic applications. However, the efficiency of differentiation protocols for generating complex structures with multiple cell types, like kidney organoids, remains a challenge. This study investigates the impact of treating hiPSCs with a low-dose dimethyl sulfoxide to enhance kidney organoid differentiation using a well-established protocol from literature. We found that treating hiPSCs with 1-2% DMSO affects gene expression of pluripotent transcription factors, hiPSC colony morphology, and enhances the expression of key metanephric mesenchyme nephron progenitor marker, SIX2 after 9 days of kidney organoid differentiation. Our findings also suggest that DMSO treatment helps improve hiPSC differentiation protocol efficiency toward the development of tubular kidney organoids. Further research is needed to elucidate the mechanisms underlying these effects and to refine the differentiation process for potentialin vitroresearch applications in biomedical research and drug development.
Insect wings arose with a genetic circuit that extends the useful range of a BMP morphogen
Authors: Huang Anqi , Cocconi Luca , Nicholls-Mindlin Ben , Alexandre Cyrille , Salbreux Guillaume , Vincent Jean-Paul 
Published: February 2025

AbstractMorphogens are produced by a subset of cells to trigger a signalling gradient that provides positional information to surrounding tissues. At increasing distances from the source, the dwindling number of morphogen molecules is expected to constrain the useful range of morphogen gradients. We have identified a genetic circuit that counteracts this limitation in developing wings ofDrosophilaby boosting BMP signalling at the distal end of the gradient without amplifying the signal near the source. This circuit involves Brinker, a transcription factor that represses BMP target genes while itself being repressed by BMP signalling. We suggest that temporal averaging inherent to the production of the inverse Brk gradient contributes to the enhancement of the positional information far from the Dpp source. Despite being a core component of BMP signalling in flies, Brinker is exclusively found in insects, likely in all insect species. Genomic analysis across a wide range of insects and gene expression analysis in limb primordia of the apterygoteThermobia domesticasuggests that Brinker is an insect-specific innovation that was subsequently wired into the BMP signalling network in pterygotes, perhaps to enable wing development.
The CST complex mediates a post-resection non-homologous end-joining repair pathway and promotes local deletions
Authors: Ilioaia Oana , Dudragne Liébaut , Brocas Clémentine , Meneu Léa , Koszul Romain , Dubrana Karine , Xu Zhou 
Published: February 2025

AbstractRepair of a DNA double-strand break (DSB) by non-homologous end-joining (NHEJ) generally leaves an intact or minimally modified DNA sequence. Resection initiation exposes single-stranded DNA and directs repair towards homology-dependent pathways and away from NHEJ. Therefore, NHEJ is not thought to be an available repair pathway once the DSB is resected. Here, we report that the Cdc13/Stn1/Ten1 (CST) complex, well characterized for its telomere-associated functions, acts after resection initiation to mediate a backup NHEJ repair. We found a CST-specific mutation signature after DSB repair, characterized by deletions of 5-85 bp, mostly dependent on NHEJ. In contrast, NHEJ-mediated small deletions of 1-4 bp and insertions are not affected in CST mutants. The interaction between CST and Polα-primase is critical for these intermediate size deletions, suggesting a role for fill-in synthesis. Consistently, instn1Δand Polα-primase mutant deficient for interaction with CST, resection is increased, leading to larger deletions of several kilobases mediated by microhomologies. Collectively, these results depict a more complex picture of repair pathway choice where CST allows a post-resection NHEJ repair, promoting local deletions but guarding against much larger and potentially more deleterious deletions and rearrangements.
Dissociable effects of LSD and MDMA on striato-cortical connectivity in healthy subjects
Authors: Ertl Natalie , Ashraf Imran , Azizi Lisa , Roseman Leor , Erritzoe David , Nutt David J , Carhart-Harris Robin L , Wall Matthew B 
Published: February 2025

AbstractIntroductionLysergic acid diethylamide (LSD) and 3,4-Methylenedioxymethamphetamine (MDMA) are widely used psychoactive drugs and their potential use in psychiatric medicine is currently generating interest. The mechanism by which these drugs may assist recovery in addiction, mood disorders and post-traumatic stress disorder (PTSD) is still not well understood. Most investigations of the effects of these drugs on brain activity have focussed on cortical resting-state networks, however the striatum is a key reward and motivation hub of the brain and aberrant striatal processing may be part of the pathophysiology of these disorders. Consequently, we investigated striatal connectivity following acute MDMA and LSD administration.MethodResting-state fMRI (rs-fMRI) data were acquired, and seed-voxel functional connectivity analyses were used with the striatum subdivided into three seed regions: the associative, limbic, and sensorimotor striatum. Within-network connectivity was measured using group mean network maps and whole-brain connectivity (seed-to-voxel) was also examined.ResultsNeither MDMA nor LSD significantly changed within-network connectivity of any of the three striatal seed regions. However, striatal connectivity with other brain regions was significantly altered with both MDMA and LSD. Most notably, MDMA reduced connectivity between the limbic striatum and the amygdala, while LSD increased connectivity between the associative striatum and the frontal, sensorimotor, and visual cortices.ConclusionChanges in connectivity were mostly observed outside the standard striatal networks, consistent with previous findings that psychedelics reduce network modularity or between-network segregation and increase connectivity across standard networks.
Experimentally mimicking 30 years ofMagallana gigasinfections with the OsHV-1 virus reveals evolution through positive selection
Authors: Pelletier Camille , Faury Nicole , Mege Mickaël , Dégremont Lionel , Hattinguais Maelle , Vidal-Dupiol Jeremie , Chevignon Germain , Jacquot Maude , Morga Benjamin 
Published: February 2025

AbstractOstreid herpesvirus 1 (OsHV-1) poses a significant threat to the global oyster farming industry, causing substantial economic losses due to mortality outbreaks. While OsHV-1 primarily affects the Pacific oysterMagallana gigas, it has been linked to mortality events in various host species. Despite advancements in understanding OsHV-1 epidemiology, knowledge gaps persist regarding its evolutionary mechanisms and adaptation to host genetic backgrounds. This study employs experimental evolution and extensive genomic analysis to unravel the dynamics of OsHV-1 evolution in response to oyster host genetic variation. Our results show that genetic mutations, particularly transitions and transversions, played a significant role in shaping the viral population, leading to a trend toward genetic homogenization. Stronger positive selection signals were observed in the oyster population with higher susceptibility, suggesting adaptation of viral genotypes to specific host genetic backgrounds. These findings shed light on the complex evolutionary dynamics of OsHV-1 and its interactions with oyster hosts. Understanding how this virus adapts to host genetic diversity is crucial for developing strategies to mitigate its impact on the oyster farming industry and provides valuable insights into the broader mechanisms of viral evolution in response to host variation.
Using single-cell perturbation screens to decode the regulatory architecture of splicing factor programs
Authors: Anglada-Girotto Miquel , Miravet-Verde Samuel , Serrano Luis 
Published: February 2025

SUMMARYSplicing factors shape the isoform pool of most transcribed genes, playing a critical role in cellular physiology. Their dysregulation is a hallmark of diseases like cancer, where aberrant splicing contributes to progression. While exon inclusion signatures accurately assess changes in splicing factor activity, systematically mapping disease-driver regulatory interactions at scale remains challenging. Perturb-seq, which combines CRISPR-based perturbations with single-cell RNA sequencing, enables high-throughput measurement of perturbed gene expression signatures but lacks exon-level resolution, limiting its application for splicing factor activity analysis. Here, we show that shallow artificial neural networks (ANNs) can estimate splicing factor activity from gene expression signatures, bypassing the need for exon-level data. As a case study, we map the genetic interactions regulating splicing factors during carcinogenesis, using the shift in splicing program activity –where oncogenic-like splicing factors become more active than tumor suppressor-like factors– as a molecular reporter of a Perturb-seq screen. Our analysis reveals a cross-regulatory loop among splicing factors, involving protein-protein and splicing-mediated interactions, with MYC linking cancer driver mutations to splicing regulation. This network recapitulates splicing factor modulation during development. Altogether, we establish a versatile framework for studying splicing factor regulation and demonstrate its utility for uncovering disease mechanisms.GRAPHICAL ABSTRACT
Bronze AgeYersinia pestisgenome from sheep sheds light on hosts and evolution of a prehistoric plague lineage
Authors: Light-Maka Ian , Hermes Taylor R. , Bianco Raffaela Angelina , Semerau Lena , Kosintsev Pavel , Alekseeva Valeriia , Kim Donghee , Hanage William P. , Herbig Alexander , Jeong Choongwon , Warinner Christina , Key Felix M. 
Published: February 2025

SummaryMost human pathogens are of zoonotic origin. Many emerged during prehistory, coinciding with domestication providing more opportunities for spillover from original host species. However, we lack direct evidence linking past animal reservoirs and human infections. Here we present aYersinia pestisgenome recovered from a 3rd millennium BCE domesticated sheep from the Eurasian Steppe belonging to the Late Neolithic Bronze Age (LNBA) lineage, until now exclusively identified in ancient humans across Eurasia. We show that this ancient lineage underwent ancestral gene decay paralleling extant lineages, but evolved under distinct selective pressures contributing to its lack of geographic differentiation. We collect evidence supporting a scenario where the LNBA lineage, unable to efficiently transmit via fleas, spread from an unidentified reservoir to humans via sheep and likely other domesticates. Collectively, our results connect prehistoric livestock with infectious disease in humans and showcase the power of moving paleomicrobiology into the zooarcheological record.