bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evolutionary Dynamics of G-Quadruplexes in Human and Other Great Ape Telomere-to-Telomere Genomes
Authors: Mohanty Saswat K. , Chiaromonte Francesca , Makova Kateryna D. 
Published: November 2024

ABSTRACTG-quadruplexes (G4s) are non-canonical DNA structures that can form at approximately 1% of the human genome. G4s contribute to point mutations and structural variation and thus facilitate genomic instability. They play important roles in regulating replication, transcription, and telomere maintenance, and some of them evolve under purifying selection. Nevertheless, the evolutionary dynamics of G4s has remained underexplored. Here we conducted a comprehensive analysis of predicted G4s (pG4s) in the recently released, telomere-to-telomere (T2T) genomes of human and other great apes—bonobo, chimpanzee, gorilla, Bornean orangutan, and Sumatran orangutan. We annotated tens of thousands of new pG4s in T2T compared to previous ape genome assemblies, including 41,236 in the human genome. Analyzing species alignments, we found approximately one-third of pG4s shared by all apes studied and identified thousands of species– and genus-specific pG4s. pG4s accumulated and diverged at rates consistent with divergence times between the studied species. We observed a significant enrichment and hypomethylation of pG4 shared across species at regulatory regions, including promoters, 5’ and 3’UTRs, and origins of replication, strongly suggesting their formation and functional role in these regions. pG4s shared among great apes displayed lower methylation levels compared to species-specific pG4s, suggesting evolutionary conservation of functional roles of the former. Many species-specific pG4s were located in the repetitive and satellite regions deciphered in the T2T genomes. Our findings illuminate the evolutionary dynamics of G4s, their role in gene regulation, and their potential contribution to species-specific adaptations in great apes, emphasizing the utility of high-resolution T2T genomes in uncovering previously elusive genomic features.
Manipulation of alternative splicing ofIKZF1elicits distinct gene regulatory responses in T cells
Authors: Pastor Lucia , Newman Jeremy R.B. , Callahan Colin M. , Pickin Rebecca R. , Atkinson Mark A. , Onengut-Gumuscu Suna , Concannon Patrick 
Published: November 2024

AbstractGenome-wide studies have identified significant allelic associations between genetic variants in or near theIKZF1gene and multiple autoimmune disorders.IKZF1, encoding the transcription factor IKAROS, produces at least 10 distinct transcripts. To explore the impact of alternative splicing ofIKZF1on the function of mature T cells, we generated a panel of human T-cell clones with truncating mutations inIKZF1exons 4, 6 or both. Differences in gene expression, chromatin accessibility, and protein abundance among clones were assessed by RNA-seq, ATAC-seq and immunoblotting. Clones with single targeting events clustered separately from double-targeted clones on multiple parameters, but overall, clone responses were highly heterogeneous. Perturbation ofIKZF1splicing resulted in significant differences in expression and chromatin accessibility of other autoimmunity-associated genes and elicited compensatory expression changes in other IKAROS family members. Our results suggest that even modest alterations ofIKZF1splicing can have significant effects on gene expression and function in mature T cells, potentially contributing to autoimmunity in susceptible individuals.Author SummaryRNA sequencing has revealed an unexpectedly large population of alternative transcripts produced by most human genes, but the functional significance of such transcripts has been debated, with some authors arguing that they represent non-functional “noise” and others arguing that they are largely functional and greatly expand the potential human proteome. Here, we explore these issues for the transcription factorIKZF1, which produces numerous alternative transcripts in human T cells and is significantly associated with risk for type 1 diabetes and other autoimmune disorders. We introduce stop codons at multiple sites in alternatively spliced exons and evaluate transcript levels and chromatin accessibility in individually targeted clones, allowing us to assay the broad impact of alternative splicing ofIKZF1in human T cells. Our studies reveal that perturbation ofIKZF1splicing results in significant differences in gene expression, chromatin accessibility and protein production of other autoimmunity-associated genes and elicits compensatory expression changes in other IKAROS family members. Even modest alterations inIKZF1splicing had significant effects on gene expression and function in mature T cells, potentially contributing to autoimmunity in susceptible individuals and suggesting that transcript isoforms produced by alternative splicing can and do have functional impacts.
Efficient mRNA DeliveryIn VitroandIn VivoUsing a Polycharged Biodegradable Nanomaterial
Authors: Yang Xuejin , Xiao Jingya , Staveness Daryl , Zang Xiaoyu 
Published: November 2024

AbstractAs RNA rises as one of the most significant modalities for clinical applications and life science research, efficient tools for delivering and integrating RNA molecules into biological systems become essential. We hereby report a formulation using a polycharged biodegradable nano-carrier, N1-501, which demonstrates superior efficiency and versatility in mRNA encapsulation and delivery in both cell and animal models. N1-501 is a polymeric material designed to function through a one-step facile formulation process suitable for various research settings. Its capability for mRNA transfection is investigated across a wide range of mRNA doses and in different biological models, including 18 tested cell lines and mouse models. This study also comprehensively analyzes N1-501’s application for mRNA transfection by examining factors such as buffer composition and pH, incubation condition, and media type. Additionally, N1-501’s superiorin vivomRNA transfection capability ensures its potential as an efficient and consistent tool for advancing mRNA-based therapies and genetic research.
Potential spillover effects on diagnostic delay for cancer during the NHS-Galleri trial: a quasi-experimental difference-in-differences study
Authors: Mann Sean , Eagan Joshua , Griffin Beth Ann 
Published: November 2024

AbstractObjectiveTo examine whether regions participating in the NHS-Galleri trial of a multi-cancer early detection test experienced changes in cancer diagnostic delay rates that could indicate the presence of spillover due to constraints on care delivery.DesignQuasi-experimental difference-in-differences analysis.SettingNHS England, April 2021-September 2023.ParticipantsAll 21 cancer alliance regions in NHS England, 8 of which participated in the trial and 13 of which did not.Main outcomesRates of cancer diagnostic delays, defined as the percentage of patient referrals for investigation of possible cancer that resulted in diagnostic resolution within 28 days of initial referral. A difference-in-differences analysis was used to compare diagnostic delay rates in regions that participated in the NHS-Galleri trial to regions that did not participate, before and after the start of the trial. Three primary analyses were conducted: for all types of suspected cancer; for the most commonly referred cancers (breast, skin, lower gastrointestinal); and for less commonly referred cancers (all other types).ResultsWe observed no significant differences in rates of diagnostic delay for all cancers or for the most commonly referred cancers. For less commonly referred cancers, the percentage of patients experiencing diagnostic delays increased from 32.6% to 35.1% in regions participating in the NHS-Galleri trial from the 6 months before to the 6 months after trial start, compared with a small reduction from 32.7% to 31.7% in regions that did not participate (adjusted difference 3.4 percentage points, 95% confidence interval 1.2 to 5.7). These differences persisted from 6 to 12 months after trial start and receded the following year.ConclusionsRegional participation in the NHS-Galleri trial was associated with a statistically significant increase in diagnostic delay rates for less commonly referred cancers in the first year of the trial, but not for cancer overall or the most commonly referred cancers. Rollout of the trial intervention may have increased demand for downstream diagnostic services and, in a capacity constrained environment, led to region-wide increases in delayed diagnosis for less commonly referred cancers. If patients in the control group faced delayed diagnosis as a result, this would represent spillover due to constraints on care delivery during the first year and could affect measurement of the trial’s primary outcome, incidence of later stage cancer at time of diagnosis. This study underscores the importance of addressing spillover in clinical trials of interventions that affect availability of healthcare services.
“Around the clock”. Exploring health care professionals’ experience of discharge of older people during out of hours from the emergency department: a qualitative study
Authors: Dunnion Mary , Goode Debbie , Ryan Assumpta , McIlfatrick Sonja 
Published: November 2024

AbstractBackgroundOlder adults constitute a considerable number of attendances at emergency departments (EDs). Whilst many require hospital admission, a greater focus now is on admission avoidance with older adults being subsequently discharged from EDs. Little is known, however, about the experiences out of hours (OOH) when specialist older person support services are unavailable.AimTo explore senior health care professionals’ experiences of discharging older people during out of hours from EDs.MethodA qualitative study involving individual semi-structured interviews was used to explore the experiences of healthcare professionals. Fourteen participants in total responded from a wide geographical spread. Data analysis was undertaken using Braun and Clarke’s (2022) six-step framework for Thematic Analysis.ResultsOne overarching theme was identified focusing on risks and safety for the older person whilst being discharged OOH from the ED. Three sub-themes included “Should they stay, or should they go?”, “Bright lights and noise”, and “New ways of working”, which included risks in discharging an older person OOH from the ED, risks in delaying discharge, and recommendations for future practice. Significant differences were reported between office hours and OOH discharge of older adults from the ED. Diversity in practice assessments, and resources available was also evident across EDs. Significant adverse consequences were identified for older adults having to stay for prolonged periods in the ED.ConclusionsThere have been many welcome developments in healthcare services for older people who attend and are subsequently discharged from the ED. However, further innovative practice and collaboration with senior decision makers is needed to meet the healthcare needs of a rapidly ageing population. Safe, equitable and effective discharge practice 24/7 should be a norm for all older people in every ED regardless of location. Gaps in care identified must be addressed taking cognisance of the relevant recommendations for future practice.
The Infraslow Fluctuation of Sigma Power During Sleep: Links to Markers of Arousal and Memory Reactivation Across Development
Authors: Dimitriades Maria E. , Osorio-Forero Alejandro , Fattinger Sara , von Arx Simone , Kurth Salome , Pugin Fiona , Jaramillo Valeria , Volk Carina , Krugliakova Elena , Furrer Melanie , Leach Sven , Achermann Peter , Gerstenberg Miriam , Huber Reto 
Published: November 2024

AbstractSleep is both a state of disconnection from the environment and a critical period for restoration. But how does sleep balance responsiveness with the protection of key functions? The infraslow fluctuation of sigma power (ISFS)—the clustering of sleep spindles over 10-100 seconds—is thought to regulate this trade-off in rodents. However, the organization of arousal and memory reactivation markers within the human ISFS and its conservation in younger ages remain unclear. This study characterizes the ISFS from childhood to young adulthood (N = 154; ages 8-26), examining its relationship with functional markers. Results indicate that the ISFS is present across all ages, with frequency, variability, and strength increasing from early to late adolescence. Notably, markers of arousal and memory reactivation are organized within the spindle-rich ISFS peak. The consistent presence and organization of the ISFS suggest it is intrinsic to sleep, with adolescence marking a dynamic window. These insights may guide interventions to promote healthier sleep across development.
Cocaine, via ΔFosB, remodels gene expression and excitability in ventral hippocampus
Authors: Eagle Andrew L. , Doyle Marie A. , Sugimoto Chiho , Dykstra Megan , Kuhn Hayley M. , Murray Brooklynn R. , Bastle Ryan M. , Jin He , Maze Ian , Mazei-Robison Michelle S. , Robison Alfred J. 
Published: November 2024

AbstractVentral hippocampus (vHPC) CA1 pyramidal neurons send glutamatergic projections to nucleus accumbens (NAc), and this vHPC-NAc circuit mediates cocaine seeking and reward, but it is unclear whether vHPC-NAc neuron properties are modulated by cocaine exposure to drive subsequent behavior. The immediate early gene transcription factor ΔFosB is induced throughout the brain by cocaine and is critical for cocaine seeking, but it’s function in vHPC-NAc neurons is not understood. We now show that circuit-specific knockout of ΔFosB in vHPC-NAc neurons impaired cocaine reward expression and forced abstinence-induced seeking. We also found that vHPC-NAc excitability was decreased by experimenter-administered repeated cocaine and cocaine self-administration, and this cocaine-induced excitability decrease was mediated by ΔFosB expression. To uncover the mechanism of this change in circuit function, we used circuit-specific translating ribosome affinity purification (TRAP) to assess cocaine-induced, ΔFosB-dependent changes in gene expression in vHPC-NAc. We found that cocaine causes a ΔFosB-dependent increase in the expression of calreticulin, an ER-resident calcium-buffering protein. Calreticulin expression mediated vHPC-NAc excitability and was necessary for cocaine reward. These findings uncover a novel, non-canonical mechanism by which cocaine increases calreticulin in vHPC leading to decreased vHPC-NAc excitability and drives cocaine seeking and reward.
Lignocellulose Degradation in Bacteria and Fungi for Biomass Conversion
Authors: Hsin Kuan-Ting , Lee HueyTyng , Lin Ying-Chung Jimmy , Chen Pao-Yang 
Published: November 2024

ABSTRACTLignocellulose biomass is one of the most abundant resources for sustainable biofuels. However, scaling up the biomass-to-biofuels conversion process for widespread usage is still pending. Bottlenecks during the process of enzymatic hydrolysis are the high cost of enzymes and the labor-intensive need for substrate-dependent enzyme mixtures. Current research efforts are therefore targeted at searching for or engineering lignocellulolytic enzymes of high efficiency. One way is to engineer multi-enzyme complexes that mimic the bacterial cellulosomal system, known to increase degradation efficiency up to 50-fold when compared to freely-secreted enzymes. However, these designer cellulosomes are instable and less efficient than wild type cellulosomes. Fungi cellulosomes discovered in recent years have significant differences from bacterial counterparts and hold great potential for industrial applications, both as designer cellulosomes and as additions to the enzymatic repertoire. Up to date, they are only found in a few anaerobic fungi. In this review, we extensively compared the degradation mechanisms in bacteria and fungi, and highlighted the essential gaps in applying these mechanisms in industrial applications. To better understand cellulosomes in microorganisms, we examined their sequences in 66,252 bacterial species and 823 fungal species and identified several bacterial species that are potentially cellulosome-producing. These findings act as a valuable resource in the biomass community for further proteomic and genetic sequence analysis. We also collated the current strategies of bioengineering lignocellulose degradation to suggest concepts that could be favorable for industrial usage.
Inhibiting DPP4 activity protects hiPSC-derived steatotic HLCs by supporting fatty acid and purine metabolism and dampening inflammation
Authors: Loerch Christiane , Wruck Wasco , Julian Reiss , Adjaye James , Graffmann Nina 
Published: November 2024

AbstractBackground and AimMetabolic dysfunction-associated steatotic liver disease (MASLD/MAFLD) has a high prevalence and high co-morbidity for other diseases. Due to the complexity of this multifactorial disease, therapy options are still rather limited. We employed anin vitropluripotent stem cell-based model to decipher basic disease-associated molecular pathways and to study the mode of action of potential drugs.MethodsWe induced the steatosis phenotype in human induced pluripotent stem cell (iPSC) derived hepatocyte-like cells (HLCs) by oleic acid (OA)-feeding and confirmed regulation of clinically relevant pathways by NGS-based global transcriptomic analyses. Analysis of the secretome of steatotic HLCs revealed Dipeptidyl peptidase 4 (DPP4) as a potential key mediator of the disease. To further elucidate its role in the development of MAFLD, we inhibited DPP4 activity with Vildagliptin (VILDA) and analyzed the global transcriptome changes as well as specific gene and protein expression of steatosis-associated genes with and without DPP4 inhibition.ResultsMAFLD-associated pathways such as PPAR– and TNF signaling were differentially regulated in hiPSC-derived steatotic HLCs. We found increased hepatic DPP4 activity and secretion upon OA. Fatty acid and purine metabolism and inflammation response pathways were improved upon DPP4 inhibition.ConclusionOur HLC-model confirmed clinically-relevant association of DPP4 with metabolism and inflammation which foster the development of MAFLD. Inhibiting DPP4 with VILDA partially relieved the steatotic phenotype.Impact and implicationsGiven the difficulties of identifying suitable anti-MAFLD drugs, novel model systems are urgently needed. Ourin vitroHLC-model reproduced DPP4-dependent aspects of the disease and responded positively to Vildagliptin treatment. Further elucidation of the role of DPP4 in the etiology of MAFLD is warranted.
Correction of RBFOX1 deficit rescues Huntington’s disease mis-splicing and pathology
Authors: Lozano-Muñoz David , Elorza Ainara , Mayor Lucía , Santos-Galindo María , Lucas-Santamaría Miriam , Parras Alberto , Lucas José J. 
Published: November 2024

AbstractRNA mis-splicing correction therapies have been developed for neurological disorders like spinal muscular atrophy and neuronal ceroid lipofuscinosis. In Huntington’s disease (HD), pathogenic mis-splicing was initially observed in genes linked to neurodegeneration, such asHTTitself,MAPT, andTAF1. Later, genome-wide analyses identified a broader mis-splicing signature in HD brains, involving additional neurodegeneration-related genes. Correcting each mis-spliced gene individually would be unfeasible, highlighting the need to target upstream splicing factors altered in HD. Our previous motif-enrichment analyses of intronic sequences flanking the exons mis-spliced in HD identified RBFOX and U2AF2 as candidate splicing factors, both of which are reduced in HD brains. In this study, we tested their pathogenic relevance generating conditional transgenic mouse models that overexpress RBFOX1 or U2AF2 in forebrain neurons and combining them with HD mice. Our results show that moderate overexpression of RBFOX1, but not U2AF2, corrects multiple HD-associated mis-splicing events and alleviates HD mice neuropathology and motor symptoms. These findings demonstrate that RBFOX1 downregulation contributes to HD pathology and underscore the therapeutic potential of strategies aimed at increasing RBFOX1 levels.
Spinal cord phosphoproteome of a SCA2/ALS13 mouse model reveals alteration of ATXN2-N-term SH3-actin interactome and of autophagy via WNK1-MYO6-OPTN-SQSTM1
Authors: Almaguer-Mederos Luis-Enrique , Kandi Arvind Reddy , Sen Nesli-Ece , Canet-Pons Júlia , Berger Luca-Malena , Key Jana , Brunstein Melinda-Elaine , Münch Christian , Gispert Suzana , Auburger Georg 
Published: November 2024

AbstractToxic polyglutamine (polyQ) expansions in ATXN2 trigger neurodegenerative processes, causing Spinocerebellar Ataxia type 2 (SCA2), and enhancing TDP-43-dependent pathology in Amyotrophic Lateral Sclerosis (ALS) / Fronto-Temporal Dementia (FTD). Primary disease events can be compensated transiently, delaying disease manifestation. To define potential therapy targets, we documented how cells modify their phospho-signals and how the ATXN2 interactome changes, using preferentially affected nervous tissues from end-stageAtxn2-CAG100-KnockIn mice. The spinal cord phosphorylome revealed massive hyperphosphorylations flanking the polyQ expansion in ATXN2 and for SQSTM1, and moderate hyperphosphorylations also for ALS proteins OPTN, UBQLN2, TNIP1 and TBK1-targeted TAX1BP1, versus strong hypophosphorylations of WNK1, SPARCL1 and PSMD9. Significant enrichments of SH3-containing proteins, autophagy / endocytosis factors, and actin modulators could be explained by N-terminal, polyQ-adjacent, proline-rich motifs in ATXN2. Coimmunoprecipitation profiling in cerebellum documented known associations with RNA-binding proteins like PABPC1 and TDP-43 with its modifier PPIA to decrease upon expansion, contrasting with increased binding of SH3-proteins, like MYO6, RPL21 and DLG4. Validation of protein and mRNA levels in mouse spinal cord, and embryonic fibroblasts or patient fibroblasts after bafilomycin or arsenite treatment, observed polyQ-dependent OPTN deficiency and SQSTM1 induction impairment. Overall, this combined phosphoproteome / interactome study efficiently revealed key pathways and molecular events.