bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patient-derived organoids to study glycosylation dynamics during gastric disease
Authors: Santos-Ferreira Liliana , Duarte Henrique O. , Moia Eva , Costa Ana F. , Martins Álvaro M. , Faria-Ramos Isabel , Matos Rita , Barros Rita , Silva Marta , Pedrosa Sofia , Batista Diana A. , Gomes Joana , Borén Thomas , Sousa Fabiana , Casanova-Gonçalves Frederica , Barbosa José , Magalhães Ana , Gomes Catarina , Santos-Sousa Hugo , Bartfeld Sina , Carneiro Fátima , Reis Celso A. , Pinto Filipe 
Published: February 2025

ABSTRACTBACKGROUND AND AIMSAberrant cellular glycosylation remains a key event that accompanies and actively sustains gastric neoplastic transformation. Patient-derived organoids (PDOs) have recently emerged as a promisingex vivomodel to study human gastric disorders. Since the PDOs glycosylation landscape remains unknown, this study aims to evaluate PDOs as potentialavatarsofin vivotissue glycosylation profiles in the gastric context.METHODSFresh gastric mucosa samples derived from non-tumoral obese patients (n=11), adjacent tumor mucosa samples (n=29), and tumor tissue samples derived from gastric cancer (GC) patients (n=30) were used to establish a biobank of gastric PDOs (n=56). TheN- andO-glycophenotypes of normal, adjacent, and tumor PDOs and respectivein vivotissues were thoroughly characterized by immunostaining. Additionally, a comparative glycan analysis was performed over time, upon PDO biobanking and xenografting in mice. The binding of twoHelicobacter pylori(H. pylori) isogenic strains with distinct glycan-binding affinities was assessed in parental gastric mucosa tissues and compared with the respective PDOs before and after modulation of their glycan landscape.RESULTSOur results show that PDOs mimic different phenotypes of the carcinogenic cascade and recapitulate parental gastric tissues’ glycosylation profile. Tumor PDOs recapitulate the inter- and intra-heterogeneity features observed in GC, which is maintained over time, upon biobanking and xenografting. We demonstrated that the expression of type I and type II Lewis antigens is dynamically controlled by PDOs differentiation status, which results in differential binding toH. pyloristrains displaying distinct glycan-binding adhesins, mirroring the gastric epithelium tissue interactions.CONCLUSIONSThis study established PDOs as invaluableex vivotools to study the complex glycan dynamics in both gastric physiological and pathological settings.
Spatial mapping of DNA synthesis reveals dynamics and geometry of human replication nanostructures
Authors: Hawgood Micheal , Urién González Bruno , Agostinho Ana , Thiagarajan Praghadhesh , Yang Yiqiu , Zhang Xue , Giglio Giovanni , Quijada Gemma , Fonseca Matilde , Bartek Jiri , Blom Hans , Lemmens Bennie 
Published: February 2025

AbstractDNA replication is essential to life and ensures the accurate transmission of genetic information, which is significantly disturbed during cancer development and chemotherapy. While DNA replication is tightly controlled in time and space, methods to visualise and quantify replication dynamics within 3D human cells are lacking. Here, we introduce 3D-Spatial Assay for Replication Kinetics (3D-SPARK), an approach enabling nanoscale analysis of DNA synthesis dynamicsin situ. 3D-SPARK integrates optimised nucleotide analogue pulse labelling with super-resolution microscopy to detect, classify, and quantify replication nanostructures in single cells. By combining immunofluorescence techniques with click chemistry-based nascent DNA labelling and transfection of fluorescent nucleotide derivatives, we map multi-colour DNA synthesis events in relation to established replication proteins, local RNA-protein condensates or large subnuclear domains. We demonstrate quantitative changes in size, relative abundance and spatial arrangement of nanoscale DNA synthesis events upon chemotherapeutic treatment, CDC6 oncogene expression and loss of chromatin organiser RIF1. The flexibility, precision and modular design of 3D-SPARK helps bridging the gap between spatial cell biology, genomics, and 2D fibre-based replication studies in health and disease.
Central amygdalar PKCδ neurons mediate fentanyl withdrawal
Authors: Wooldridge Lisa M. , Wu Jacqueline W.K. , Jo Adrienne Y. , Zinn Morgan , Lee Angela M. , Mahmood Malaika , Cohen Savanna A. , Corder Gregory 
Published: February 2025

ABSTRACTAversion to opioid withdrawal is a significant barrier to achieving lasting opioid abstinence. The central amygdala (CeA), a key brain region for pain, threat-detection, autonomic engagement, and valence assignment, is active during opioid withdrawal. However, the role of molecularly distinct CeA neural populations in withdrawal remains underexplored. Here, we investigated the activity dynamics, brain-wide connectivity, and functional contribution of Protein Kinase C-delta (PKCδ)-expressing neurons in the CeA lateral capsule (CeLCPKCδ) during fentanyl withdrawal in mice. Mapping activity-dependent gene expression in CeLCPKCδneurons revealed a highly withdrawal-active subregion in the anterior half of the CeA. Fiber photometry calcium imaging showed that opioid-naïve CeLCPKCδneurons respond to salient noxious and startling stimuli. In fentanyl-dependent mice, naloxone-precipitated withdrawal increased spontaneous neural activity and enhanced responses to noxious stimuli. Chronic inhibition of CeLCPKCδneurons throughout fentanyl exposure, via viral overexpression of the potassium channel Kir2.1, attenuated withdrawal signs in fentanyl-dependent mice. Lastly, we identified putative opioid-sensitive inputs to CeLCPKCδneurons using rabies-mediated monosynaptic circuit tracing and color-switching tracers to map mu-opioid receptor-expressing inputs to the CeLC. Collectively, these findings suggest that the hyperactivity of CeLCPKCδneurons underlies the somatic signs of fentanyl withdrawal, offering new insights into the amygdala cell-types and circuits involved in opioid dependence.
Co-expression of Bovine leukemia virus and Bovine foamy virus-derived miRNAs in naturally infected cattle
Authors: Petersen MI , Suarez Archilla G , Perez CV , Gonzalez DD , Trono KG , Mongini C , Jaworski JP , Carignano HA 
Published: February 2025

AbstractMicroRNAs (miRNAs) derived from viruses play a central role in modulating the expression of both viral and host gene, facilitating immune evasion, viral persistence, and pathogenesis. Among the viruses that encode miRNAs and infect cattle such as Bovine leukemia virus (BLV), Bovine foamy virus (BFV), Bovine herpesvirus type 1 (BoHV-1), and Bovine herpesvirus type 5 (BoHV-5), BLV has gained increasing attention due to the critical role that BLV-miRNAs may play in inducing leukemia and lymphoma in infected animals. BLV is highly prevalent in the Americas and has a negatively affects dairy herds, primarily due to restrictions on the commercialization of dairy products from infected animals and a decrease in milk production.Mixed infections involving BLV and BFV appear to be common in cattle. Considering the ability of foamy viruses to cross species barriers, preventing their presence within the food chain is essential. In this study, through small RNA sequencing, we identified the co-expression of seven BLV-derived miRNAs (blv-miR-B1-3p,blv-miR-B2-5p,blv-miR-B2-3p,blv-miR-B3-5p,blv-miR-B3-3p,blv-miR-B4-3p,andblv-miR-B5-5p) and three BFV-derived (bfv-miR-BF1-5p,bfv-miR-BF1-3p, andbfv-miR-BF2-5p) in naturally BLV-infected cattle, while no BoHV-1/5 miRNAs were detected. A differential expression analysis revealed seven bovine miRNAs (bta-miR-375,bta-miR-133a,bta-miR-677, bta-miR-1,bta-miR-3613a,bta-miR-9-5p, andbta-miR-95) with altered expression levels (fold change > |1.5| and q-value < 0.05) between cows with a high BLV proviral load (PVL) and uninfected counterparts. A comprehensive functional analysis of protein-protein interaction networks for genes targeted by both viral and host-derived miRNAs highlighted key pathways implicated in tumorigenesis and the regulation of the immune response. Notably,bta-miR-375, previously proposed as an early biomarker for the progression of enzootic bovine leukosis progression, exhibited differential expression in cows with elevated PVL, reinforcing its diagnostic potential. The functional interaction among miRNAs derived from BLV and BFV raises important concerns regarding their potential influence on disease severity and the increased dissemination of BFV. The findings derived from this study offer new perspectives for creating diagnostic and treatment approaches to manage viral persistence and tumor growth in cattle.
Behavioral profiling of hyperbaric oxygen as an intervention for chemotherapy-related functional impairments in male and female mice
Authors: Trinh Oanh T.P. , Ferns Andrew , Zachariah Bethany S. , Sumien Nathalie 
Published: February 2025

Abstract‘Chemobrain’ or chemotherapy-related cognitive impairment (CRCI) affects up to 75% of cancer patients and survivors following chemotherapy treatments. Chemotherapy typically affects multiple domains including learning, memory, attention, executive function, and mood regulation, persisting for decades after treatment cessation and significantly diminishing cancer survivors’ quality of life. Despite its prevalence and long-term impact, effective interventions for CRCI remain limited. This study investigated the behavioral effects of HBO on mice exposed to chemotherapy drugs methotrexate (MTX) and 5-fluorouracil (5-FU). Adult male and female C57BL/6 mice received intraperitoneal injections of either saline or chemotherapy (Low-dose: MTX 37.5 mg/kg and 5-FU 50 mg/kg; High-dose: MTX 70 mg/kg and 5-FU 100 mg/kg) once a week for three weeks. Concurrently, subsets of mice underwent daily HBO (2.4 ATA, 90 minutes) five days a week for three weeks. Animals’ health was evaluated weekly, and behavioral assessment of cognitive, motor, and affective functions was conducted post-treatment. Our results showed that chemotherapy, especially at high-dose, impaired spatial memory and navigation, avoidance learning, fear discrimination, and anxiety regulation differently between males and females. HBO significantly alleviated chemotherapy-induced avoidance learning impairment in both sexes and improved coordinated running capacity in high-dose treated males. However, chemotherapy-HBO cotreatment increased spatial memory deficit in males and increased anxiety-like behaviors in females. In conclusion, even though HBO had some nuanced effects on the various domains, some reversal of CRCI effects were observed. Therefore, HBO should be further studied and considered as a potential treatment for ‘chemobrain’.
The Myo2 adaptor Ldm1 and its receptor Ldo16 mediate actin-dependent lipid droplet motility
Authors: Zhao Xue-Tong , Vien Diep Duy Trong , Percifull Louis , Fausten Rebecca Martina , Hugenroth Marie , Höhne Pascal , Esch Bianca Marie , Collado Javier , Keller Jenny , Wilmes Stephan , Wälte Mike , Kümmel Daniel , Schuberth Christian , Fernández-Busnadiego Rubén , Fröhlich Florian , Wedlich-Söldner Roland , Bohnert Maria 
Published: February 2025

SUMMARYOrganelle motility enables strategic cellular reorganizations. In yeast, this process depends on the actin cytoskeleton, type V myosin motor proteins, and organelle-specific myosin adaptor proteins. While the myosin adaptors for most organelles are known, the coupling of myosin to lipid droplets (LDs), the cellular lipid storage organelles, remained enigmatic. Using genome-wide screening, we identified Ldm1 (Lipid Droplet Motility 1/Yer085c) as a myosin adaptor. Ldm1 binds to the globular tail domain of the myosin Myo2 and to the LD surface protein Ldo16 to enable actin-dependent LD motility. Ldo16 has additional roles in LD contact sites to the vacuole and the ER, suggesting a coordination of LD motility and organelle tethering. Ldm1 has a second role in mitochondrial transport and elevated Ldm1 levels rescue defects of the mitochondrial Myo2-adaptors Mmr1/Ypt11. Our work identifies the molecular machinery for LD motility and contributes to a comprehensive understanding of acto-myosin-based cellular reorganization.
Understanding barriers to effective injury care in low-income contexts: a mixed methods analysis of insights from medical trainees and traffic law enforcement first responders in Uganda
Authors: Lule Herman , Oguttu Benson , Mugerwa Micheal , Wilson Michael Lowery , Posti Jussi P. 
Published: February 2025

ABSTRACTBackgroundInjury-related mortality exhibits a significant social gradient, particularly in low-middle-income countries (LMICs), with approximately 4.5 million premature deaths annually.ObjectiveThis study explores prehospital and in-hospital barriers to timely injury care as perceived by frontline healthcare personnel in Uganda.MethodsWe utilized a mixed methods approach, gathering qualitative data from five hundred frontline workers including surgical residents, interns, and law enforcement professionals, alongside quantitative data from 1,003 trauma patients. Barriers were categorized into pre- and in-hospital trauma team-related, patient-related, and systemic healthcare challenges.ResultsFrom frontline workers, prehospital barriers included delays in emergency medical services activation (21.2%), ambulance arrival (19.3%), and transportation to hospitals (15.2%) whereas in-hospital barriers primarily involved supply shortages (28.3%), delays in identifying life-threatening injuries (27.3%), and insufficient critical care services (26.3%). Among the 1003 audited trauma patients, 41.5% (n=416) faced barriers during treatment. The most common barriers were delays in treatment decisions (n=232, 23.1%) and securing necessary supplies (n=180, 17.9%). Presence of a barrier correlated with higher odds of unfavourable Glasgow Outcome Scale scores compared to those without barriers [OR 1.750, 95% CI (1.497-2.047) vs. OR 0.556, 95% CI (0.436-0.708), p<0.001]. Moreover, the odds of mortality were higher for those whom a barrier was encountered compared to those where there was no barrier [OR 1.901, 95% CI (1.057-3.420) vs. OR 0.588, 95% CI (0.397-0.869), p<0.001].ConclusionsOur findings highlight the need for multifaceted targeted interventions, integrating frontline healthcare perspectives to improve trauma care delivery in LMICs which face both prehospital and in-hospital disparities to accessing injury care.
Trans-ancestry Genome-Wide Analyses in UK Biobank Yield Novel Risk Loci for Major Depression
Authors: Singh Madhurbain , Chatzinakos Chris , Barr Peter B. , Gentry Amanda Elswick , Bigdeli Tim B. , Webb Bradley T. , Peterson Roseann E. 
Published: February 2025

AbstractMost genome-wide association studies (GWASs) of depression focus on broad, heterogeneous outcomes, limiting the discovery of genomic risk loci specific to major depressive disorder (MDD). Previous UK Biobank (UKB) studies had limited ability to pinpoint MDD-associated loci due to a smaller sample with strictly defined MDD outcomes and further exclusion of many participants based on ancestry or relatedness, significantly underutilizing this resource’s potential for elucidating the genetic architecture of MDD. Here, we present novel genomic insights into MDD by fully utilizing existing UKB data through (1) a trans-ancestry GWAS pipeline using two complementary approaches controlling for population structure and relatedness and (2) an increased sample with MDD symptom-level data across two mental health assessments. We identified strict MDD outcomes among 211,535 participants, representing a 38% increase in eligible participants from prior studies with only one assessment. Ancestrally inclusive analyses yielded 61 genomic risk loci across depression phenotypes, compared to 47 in the analyses restricted to participants genetically similar to European ancestry. Fourteen of these loci, including five novel, were associated with strict MDD phenotypes, whereas only one locus has been previously reported in UKB. MDD-associated genomic loci and predicted gene expression levels showed little overlap with broad depression, indicating higher specificity. Notably, polygenic scores based on these results were significantly associated with depression diagnoses across ancestry groups in theAll of UsResearch Program, highlighting the shared genetic architecture across populations. While the trans-ancestry analyses, which included non-European participants, increased the number of associated loci, the discovery of non-European ancestry-specific loci was limited, underscoring the need for larger, globally representative studies of MDD. Importantly, beyond these results, our GWAS pipeline will facilitate inclusive analyses of other traits and disorders, helping improve statistical power, representation, and generalizability in genomic studies.
ERM proteins support perinuclear actin rim formation
Authors: Fracchia Andrea , Hadad Yuval , Babele Dagmawit , Gerlitz Gabi 
Published: February 2025

AbstractThe interaction of actin filaments with the nuclear envelope is essential for diverse cellular processes, including cell migration, nuclear positioning, and transcriptional control. The main studied mechanism that links F-actin to the nucleus is the Linker of Nucleoskeleton and Cytoskeleton (LINC) complex. Recently, the formation of a perinuclear actin rim has been identified in various cell types in response to external force or migration signals. This rim depends on the activation of the actin nucleator Inverted formin 2 (INF2) by calcium influx. However, it is not clear how the rim is coupled with the nuclear envelope. Here we show that the nuclear membrane protein Emerin, which has an actin-binding domain, is not required for the perinuclear actin rim formation. Interestingly, we found that the Ezrin-Radixin-Moesin (ERM) proteins, known to link actin filaments to the cell membrane, are also localized to the nuclear envelope in melanoma cells. Overexpression of ERM proteins increased the perinuclear actin rim levels, while knockdown of ERM proteins led to a reduction in the rim levels. Thus, the ERM proteins appear as part of the mechanism that links actin filaments to the nuclear envelope.
Convergence in amino acid outsourcing between animals and predatory bacteria
Authors: Kasalo Niko , Domazet-Lošo Mirjana , Domazet-Lošo Tomislav 
Published: February 2025

AbstractAll animals have outsourced about half of the 20 proteinogenic amino acids (AAs). We recently demonstrated that the loss of biosynthetic pathways for these outsourced AAs is driven by energy-saving selection. Paradoxically, these metabolic simplifications enabled animals to use costly AAs more frequently in their proteomes, allowing them to explore sequence space more freely. Based on these findings, we proposed that environmental AA availability and cellular respiration mode are the two primary factors determining the evolution of AA auxotrophies in animals. Remarkably, our recent analysis showed that bacterial AA auxotrophies are also governed by energy-related selection, thereby roughly converging with animals. However, bacterial AA auxotrophies are highly heterogeneous and scattered across the bacterial phylogeny, making direct ecological and physiological comparisons with the animal AA outsourcing model challenging. To better test the universality of our model, we focused on Bdellovibrionota and Myxococcota—two closely related bacterial phyla that, through aerobic respiration and a predatory lifestyle, best parallel animals. Here, we show that Bdellovibrionota, driven by energy-related selection, outsourced a highly similar set of AAs to those in animals. This sharply contrasts with Myxococcota, which exhibit far fewer AA auxotrophies and rarely show signatures of energy-driven selection. These differences are also reflected in Bdellovibrionota proteomes, which are substantially more expensive than those of Myxococcota. Finally, we found evidence that the expression of costly proteins plays a crucial role in the predatory phase of the Bdellovibrio life cycle. Together, our findings suggest that Bdellovibrionota, through their obligate predatory lifestyle, exhibit the closest analogy to the AA auxotrophy phenotype observed in animals. In contrast, facultative predation, as seen in Myxococcota, appears to substantially limit the evolution of AA auxotrophies. These cross-domain convergences strongly support the general validity of our AA outsourcing model.
Arrayed CRISPR/Cas9 Loss-Of-Function Screen in a Neuronal Model of Adaptor Protein Complex 4 Deficiency Identifies Modulators of ATG9A Trafficking
Authors: Ziegler Marvin , Böger Cedric , Alecu Julian E. , Kim Hyo-Min , Saffari Afshin , Davies Alexandra K. , Sahin Mustafa , Ebrahimi-Fakhari Darius 
Published: February 2025

SUMMARYBiallelic loss-of-function variants in the adaptor protein complex 4 (AP-4) disrupt trafficking of transmembrane proteins at thetrans-Golgi network, including the autophagy-related protein 9A (ATG9A), leading to childhood-onset hereditary spastic paraplegia (AP-4-HSP). AP-4-HSP is characterized by features of both a neurodevelopmental and degenerative neurological disease. To investigate the molecular mechanisms underlying AP-4-HSP and identify potential therapeutic targets, we conducted an arrayed CRISPR/Cas9 loss-of-function screen of 8,478 genes, targeting the ‘druggable genome’, in a human neuronal model of AP-4 deficiency. Through this phenotypic screen and subsequent experiments, key modulators of ATG9A trafficking were identified, and complementary pathway analyses provided insights into the regulatory landscape of ATG9A transport. Knockdown ofANPEPandNPM1enhanced ATG9A availability outside thetrans-Golgi network, suggesting they regulate ATG9A localization. These findings deepen our understanding of ATG9A trafficking in the context of AP-4 deficiency and offer a framework for the development of targeted interventions for AP-4-HSP.
Long-term development of a motor memory
Authors: Franklin David W. , Nietschmann Pascal , Papadopoulou Thalia , Franklin Sae 
Published: February 2025

AbstractHuman behavior is developed through continuous adaptation to our environment over a range of timescales. Extensive studies have investigated the mechanisms and computations underlying this process of sensorimotor adaptation using several hundred trials. However, most of our motor skills have had countless hours of practice. Here we study a simple motor adaptation task using thousands of training trials over multiple weeks to study the long-term development of a motor memory, and examine changes in adaptation, retention, inter-limb transfer, decay, spontaneous recovery and generalization. Unlike previous studies, participants showed complete compensation to the novel dynamics, along with long-term increases in retention and spontaneous recovery. Moreover, we find narrowing in the angular generalization, suggesting continual tuning of the motor memory to the task. This demonstrates the extensive changes occurring with longer training of motor tasks, highlighting their importance in studies of sensorimotor control, rehabilitation and training.