bluuebunny/crossref_metadata_2025_split huggingface dataset:
MLL3/MLL4 enzymatic activity shapes DNA replication timing
Authors: Gökbuget Deniz , Boileau Ryan M. , Lenshoek Kayla , Blelloch Robert 
Published: December 2023

SUMMARYMammalian genomes are replicated in a precise order during S phase, which is cell-type-specific1–3and correlates with local transcriptional activity2,4–8, chromatin modifications9and chromatin architecture1,10,11,12. However, the causal relationships between these features and the key regulators of DNA replication timing (RT) are largely unknown. Here, machine learning was applied to quantify chromatin features, including epigenetic marks, histone variants and chromatin architectural factors, best predicting local RT under steady-state and RT changes during early embryonic stem (ES) cell differentiation. About one-third of genome exhibited RT changes during the differentiation. Combined, chromatin features predicted steady-state RT and RT changes with high accuracy. Of these features, histone H3 lysine 4 monomethylation (H3K4me1) catalyzed by MLL3/4 (also known as KMT2C/D) emerged as a top predictor. Loss ofMll3/4(but notMll3 alone) or their enzymatic activity resulted in erasure of genome-wide RT dynamics during ES cell differentiation. Sites that normally gain H3K4me1 in a MLL3/4-dependent fashion during the transition failed to transition towards earlier RT, often with transcriptional activation unaffected. Further analysis revealed a requirement for MLL3/4 in promoting DNA replication initiation zones through MCM2 recruitment, providing a direct link for its role in regulating RT. Our results uncover MLL3/4-dependent H3K4me1 as a functional regulator of RT and highlight a causal relationship between the epigenome and RT that is largely uncoupled from transcription. These findings uncover a previously unknown role for MLL3/4-dependent chromatin functions which is likely relevant to the numerous diseases associated with MLL3/4 mutations.
Hypoxia alters the effects of hypomethylating agents in acute myeloid leukaemia cells
Authors: Humphries Sam , Burnard Sean M. , Keely Simon , Bond Danielle R. , Lee Heather J. 
Published: December 2023

AbstractBackgroundAcute myeloid leukaemia (AML) is a deadly haematological malignancy that originates from mutated myeloid progenitor cells that lie quiescent in the hypoxic bone marrow. Elderly patients who cannot tolerate standard chemotherapies are administered low-dose hypomethylating agents (HMA) which act in a replication-dependent manner to reprogram the epigenome. Relapse is common following HMA treatment and may arise from quiescent leukaemia cells in the hypoxic bone marrow. Therefore, the effects of hypoxia on HMA efficacy may influence AML progression.ResultsAML cell lines (MOLM-13, MV-4-11, HL-60) were treated with decitabine (100nM) or azacitidine (500-2000nM) in normoxic (21% O2) and hypoxic (1% O2) conditions. Exposure to hypoxia significantly reduced AML cell growth across all cell lines, with no additional effects observed upon HMA treatment. This was associated with distinct effects on DNA methylation. The extent of hypomethylation induced by AZA treatment was reduced in hypoxia, whereas DAC-induced hypomethylation was maintained in low oxygen conditions. Transcriptional response to HMA treatment were also altered in hypoxia, with HMAs failing to up-regulate antigen presentation pathways in hypoxia. In particular, human leukocyte antigens (HLAs) such as HLA-DR were increased upon HMA treatment in normoxia, but not hypoxia.ConclusionOur results suggest that HMA-induced antigen presentation may be impaired in hypoxic tissues such as the bone marrow. This study highlights the need to consider microenvironmental factors when designing co-treatment strategies to improve HMA therapeutic efficacy.
DNA-terminus-dependent transcription by T7 RNA polymerase and its C-helix mutants
Authors: Yu Bingbing , Chen Yifan , Yan Yan , Zhu Bin 
Published: December 2023

ABSTRACTThe remarkable success of mRNA-based vaccines has underscored their potential as a novel biotechnology platform for vaccine development and therapeutic protein delivery. However, the single-subunit RNA polymerase from bacteriophage T7 widely used for in vitro transcription is well known to generate double-stranded RNA (dsRNA) byproducts that strongly stimulate the mammalian innate immune response. The dsRNA was reported to be originated from self-templated RNA extension or promoter-independent transcription. Here, we identified that the primary source of the full-length dsRNA during in vitro transcription is the DNA-terminus-initiated transcription by T7 RNA polymerase. Guanosines or cytosines at the end of DNA templates enhance the DNA-terminus-initiated transcription. Moreover, we found that aromatic residues located at position 47 in the C-helix interfere with the binding of T7 RNA polymerase to DNA termini, leading to a significant reduction in the production of full-length dsRNA. As a result, the mRNA synthesized using the T7 RNA polymerase G47W mutant exhibits higher expression efficiency and lower immunogenicity compared to the mRNA produced using the wild-type T7 RNA polymerase.
Improved mRNA electroporation into immature oocytes to examine protein dynamics during development
Authors: Satouh Yuhkoh , Suzuki Emiko , Sasaki Keisuke , Sato Ken 
Published: December 2023

AbstractOne of the major cause of oocyte quality deterioration along with aging, chromosome segregation abnormalities occur mainly during meiosis I. However, currently, there is a technical limitation in the introduction of mRNA into premature oocytes without impairing embryonic developmental ability. In this study, we established a low-invasive electroporation (EP) method to introduce mRNA into pre-ovulatory, germinal vesicle (GV) mouse oocytes in an easier manner than the traditional microinjection method. The EP method with an optimized impedance value resulted in the efficient introduction of mRNAs encoding enhanced green fluorescent protein (EGFP) into the GV oocytes surrounded by cumulus cells at a survival rate of 95.0%. Furthermore, the introduction of histone H2B-EGFP mRNA into the GV oocytes labeled most of the oocytes without affecting the blastocyst development rate, indicating the feasibility of the visualization of oocyte chromosomal dynamics that enable us to assay chromosomal integrity in oocyte maturation and cell count in embryonic development. The establishment of this EP method offers extensive assays to select pre-implantation embryos and enables the surveying of essential factors for mammalian oocyte quality determination.Summary blurbThis study introduces a low-invasive electroporation method with high survival rate and developmental ability, offering a potential breakthrough in preimplantation embryo treatment and assessment.
Evidence based Unification of poTato gene models with UniTato collaborative genome browser
Authors: Zagorščak Maja , Zrimec Jan , Bleker Carissa , Nolte Nadja , Ramšak Živa , Gruden Kristina , Petek Marko 
Published: December 2023

AbstractPotato (Solanum tuberosum) is the most popular tuber crop and model organism. Though its gene models are frequently updated, they are not unified, leading to missing or wrongly annotated genes. Here, we thus unify the recent potato double monoploid v4 and v6 gene models by automatic merging. We established an Apollo web server that enables access to the Unified poTato genome annotation database (UniTato) as well as further community-based manual curation atunitato.nib.si. We demonstrate how the web server interface can help to resolve problems with missing or misplaced genes and can be used to further update them or consolidate a wider set of gene models or genome information. Genome annotation files and a comprehensive translation table are provided atgithub.com/NIB-SI/unitato.
GeneMAP: A discovery platform for metabolic gene function
Authors: Khan Artem , Unlu Gokhan , Lin Phillip , Liu Yuyang , Kilic Ece , Kenny Timothy C. , Birsoy Kıvanç , Gamazon Eric R. 
Published: December 2023

AbstractOrganisms maintain metabolic homeostasis through the combined functions of small molecule transporters and enzymes. While many of the metabolic components have been well-established, a substantial number remains without identified physiological substrates. To bridge this gap, we have leveraged large-scale plasma metabolome genome-wide association studies (GWAS) to develop a multiomic Gene-Metabolite Associations Prediction (GeneMAP) discovery platform. GeneMAP can generate accurate predictions, even pinpointing genes that are distant from the variants implicated by GWAS. In particular, our work identifiedSLC25A48as a genetic determinant of plasma choline levels. Mechanistically, SLC25A48 loss strongly impairs mitochondrial choline import and synthesis of its downstream metabolite, betaine. Rare variant testing and polygenic risk score analyses have elucidated choline-relevant phenomic consequences of SLC25A48 dysfunction. Altogether, our study proposes SLC25A48 as a mitochondrial choline transporter and provides a discovery platform for metabolic gene function.
Maintenance and evolution of individual differences in a prey defence trait examined with a dynamic predator-prey model
Authors: Eigentler L. , Reinhold K. 
Published: December 2023

AbstractPredator-prey systems often feature periodic population cycles. In an empirical system with a heritable prey defence trait, ecological oscillations were previously shown to cause evolution of prey defence on the timescale of the population cycles. In this paper, we develop an eco-evolutionary mathematical model comprising partial differential equations to investigate the evolutionary dynamics of prey defence during population cycles. We reveal that ecological population cycles induce evolutionary oscillations of the mean prey defence trait. In contrast to existing continuum modelling frameworks, our model allows for the evolution of individual variability. We show that eco-evolutionary oscillations select for increased individual variability close to the transition from stable to oscillatory states. We also reveal that evolution of prey defence requires both high efficiency and low cost of prey defence and highlight that more information on trade-offs between cost and efficiency is required.
Structural connectivity predicts individual perceived stress
Authors: Amos Toluwani Joan , Bamisile Olusola , Jin Zhenlan , Zhang JunJun , Ling Li 
Published: December 2023

AbstractMany previous studies have investigated the neural mechanisms of perceived stress using either task or resting-state functional connectomes. However, to date, the structural connectivity predictors of individual perceived stress remain unknown. In this study, using connectome-based predictive modeling with a leave-one-out cross-validation framework in a sample of 100 unrelated healthy young adults, we show that individual differences in perceived stress can be reliably predicted from their structural connectivity. The obtained results show that perceived stress could be predicted from the interaction of visual association, and motor and sub-cortical networks. This present work highlights that structural connectivity can be used to investigate the neural mechanism of PS in healthy populations.
The Ptk2-Pma1 pathway enhances tolerance to terbinafine inTrichophyton rubrum
Authors: Ishii Masaki , Yamada Tsuyoshi , Monod Michel , Ohata Shinya 
Published: December 2023

AbstractThe increasing prevalence of dermatophyte resistance to terbinafine, a key drug in the treatment of dermatophytosis, represents a significant obstacle to treatment.Trichophyton rubrumis the most commonly isolated fungus in dermatophytosis. InT. rubrum, we identified TERG_07844, a gene encoding a previously uncharacterized putative protein kinase, as an ortholog of budding yeastSaccharomyces cerevisiaepolyamine transport kinase 2 (Ptk2) and found thatT. rubrumPtk2 (TrPtk2) is involved in terbinafine tolerance. In bothT. rubrumandS. cerevisiae, Ptk2 knockout strains were more sensitive to terbinafine compared to the wild types, suggesting that promotion of terbinafine tolerance is a conserved function of fungal Ptk2. TheT. rubrumPtk2 knockout strain (ΔTrPtk2) was sensitive to omeprazole, an inhibitor of plasma membrane proton pump Pma1, which is activated through phosphorylation by Ptk2 inS. cerevisiae. Overexpression ofT. rubrumPma1 (TrPma1) in ΔTrPtk2 suppressed terbinafine sensitivity, suggesting that the induction of terbinafine tolerance by TrPtk2 is mediated by TrPma1. Furthermore, omeprazole increased the terbinafine sensitivity of clinically isolated terbinafine-resistant strains. These findings suggest that, in dermatophytes, the TrPtk2-TrPma1 pathway plays a key role in promoting intrinsic terbinafine tolerance and may serve as a potential target for combinational antifungal therapy against terbinafine- resistant dermatophytes.
Estimating butterfly population trends from sparse monitoring data using Generalized Additive Models
Authors: Edwards Collin , Schultz Cheryl , Sinclair David , Marschalek Daniel , Crone Elizabeth 
Published: December 2023

AbstractConcerns of declines in insects and population level responses to climate change have highlighted the importance of estimating trends in abundance and phenology from existing monitoring data. As the taxa with the most systematic monitoring data, butterflies are a frequent focus for understanding trends in insects. Even so, ecologists often have only sparse monitoring data for at-risk butterfly populations. As existing statistical techniques are typically poorly suited to such data, these at-risk populations are frequently excluded from analyses of butterfly trends. Here we present guidelines for estimating population trends from sparse butterfly monitoring data using generalized additive models (GAMs), based on extensive simulations and our experiences fitting hundreds of butterfly species. These recommendations include pre-processing steps, model structure choices, and post-hoc analysis decisions that reduce bias and prevent or mitigate biologically implausible model fits. We also present the ButterflyGamSim package for the programming language R, available athttps://github.com/cbedwards/butterflyGamSims. This open source software provides tools for ecologists and applied statisticians to simulate realistic butterfly monitoring data and test the efficacy of different GAM model choices or monitoring schemes.
Temporal dynamics and representational consequences of the control of processing conflict between visual working memory and visual perception
Authors: Teng Chunyue , Fulvio Jacqueline M. , Pietrelli Mattia , Jiang Jiefeng , Postle Bradley R. 
Published: December 2023

AbstractVisual working memory (WM) extensively interacts with visual perception. When information between the two processes is in conflict, cognitive control can be recruited to effectively mitigate the resultant interference. The current study investigated the neural bases of the control of conflict between visual WM and visual perception. We recorded the electroencephalogram (EEG) from 25 human subjects (13 male) performing a dual task combining visual WM and tilt discrimination, the latter occurring during the WM delay. The congruity in orientation between the memorandum and the discriminandum was manipulated. Behavioral data were fitted to a reinforcement-learning model of cognitive control to derive trial-wise estimates of demand for proactive and reactive control, which were then used for EEG analyses. The level of proactive control was associated with sustained frontal-midline theta activity preceding trial onset, as well as with the strength of the neural representation of the memorandum. Subsequently, discriminandum onset triggered a control prediction error signal that was reflected in a left frontal positivity. On trials when an incongruent discriminandum was not expected, reactive control that scaled with the prediction error acted to suppress the neural representation of the discriminandum, producing below-baseline decoding of the discriminandum that, in turn, exerted a repulsive serial bias on WM recall on the subsequent trial. These results illustrate the flexible recruitment of two modes of control and how their dynamic interplay acts to mitigate interference between simultaneously processed perceptual and mnemonic representations.Significance StatementOne hallmark of human cognition is the context dependent, flexible control of behavior. Here we studied the “mental juggling” required when, while holding information in mind, we have to respond to something that “pops up in front of us” before returning to the interrupted task. Using parameter estimates from a reinforcement-learning model, we analyzed EEG data to identify neural correlates of two discrete modes of cognitive control that act to minimize interference between perception and WM. Proactive control, indexed by frontal midline theta power, increased prior to trial onset when a high level of conflict was expected. Reactive control acted to suppress the representation of items likely to interfere with performance, a processing step with consequences for the subsequent trial.
The dysregulated IL-23/TH17 axis in endometriosis pathophysiology
Authors: Sisnett Danielle J. , Zutautas Katherine B. , Miller Jessica E. , Lingegowda Harshavardhan , Ahn Soo Hyun , McCallion Alison , Bougie Olga , Lessey Bruce A. , Tayade Chandrakant 
Published: December 2023

AbstractEndometriosis is a chronic inflammatory disease where endometrial-like tissue grows ectopically, resulting in pelvic pain and infertility. Interleukin (IL)-23 is established as a key contributor in the development and differentiation of a subset of T cells known as T-helper 17 (TH17) cells, driving TH17 cells towards a pathogenic profile. In a variety of inflammatory and autoimmune disorders, such as psoriasis and rheumatoid arthritis, TH17 cells secrete proinflammatory cytokines including IL-17, contributing to the disease pathophysiology. Our studies and others have implicated IL-17 and TH17 cell dysregulation in endometriosis, which is associated with disease severity. Here we address whether IL-23 driven TH17 cells contribute to the cardinal features of lesion proliferation, vascularization, and inflammation in endometriosis using patient samples, representative cell lines, and our established mouse model of endometriosis. Our results indicate significantly dysregulated expression of key genes in the IL-23/TH17 axis in patient ectopic and eutopic endometrial samples and increased IL-23 protein in patient plasma compared to healthy controls.In-vitrostudies using primary human THcells determined that IL-23 cocktail treatment significantly increased the frequency of pathogenic TH17 cells. Similarly, treatment with recombinant human (rh)IL-23 on cell lines (12Z, EECC, HUVEC, and hESC) representative of the endometriotic lesion microenvironment led to a significant increase in cytokines and growth factors known to play a role in lesion establishment and maintenance. In a syngeneic mouse model of endometriosis, treatment with recombinant mouse (rm)IL-23 led to significant alterations in numbers of myeloid and T cell subsets in peritoneal fluid and significantly increased numbers of giant cells within the lesion. Endometriotic lesions from rmIL-23 mice did not reveal significant alterations in proliferation and vascularization, although trends of increased proliferation and vascularization were observed. Collectively, these findings provide insights into the impact of the IL-23/TH17 axis on local immune dysfunction and broadly on the pathophysiology of endometriosis.
Adapting to changing methodology in a long-term experiment
Authors: Manning Katherine McNamara , Perrone Julia , Petrycki Stephanie , Landis Douglas A. , Bahlai Christie A. 
Published: December 2023

AbstractLong-term experiments are critical for understanding ecological processes, but their management comes with unique challenges. As time passes, projects may encounter unavoidable changes due to external factors, like availability of materials, affecting aspects of their research methodology. At the Kellogg Biological Station Long-Term Ecological Research Site, one of many National Science Foundation-funded long-term research stations, a three-decade project recently experienced a supply-chain-induced change in insect sampling methodology in their lady beetle observation study. Since 1989, lady beetles (Coleoptera: Coccinellidae) have been sampled weekly over the growing season using yellow sticky cards. In 2021, the original sticky traps were discontinued by the manufacturer and replaced with a similar, but not identical trap. We conducted a 3-year study while the new traps were phased in to examine how the trap change would impact the observed biodiversity patterns at the site. We examined community metrics and individual taxa captures to examine within year and between year differences in performance between the card types. Overall, we noted several small but statistically detectable differences in capture patterns between the two trap types. After accounting for other sources of variation, we observed a difference in Shannon diversity of insects captured on the two card types, but not richness or abundance, in the overall insect community. Yet, these differences were dwarfed by the magnitude of difference observed between years within card types. For individual taxa, similar patterns held: between trap differences could be detected statistically, but the number of differences between capture rates of traps was less than the number of differences observed for the same trap, between years. Thus, we conclude that while subtle changes in methodology could impact data produced in long-term experiments, in this case the magnitude of this change is smaller than other factors such as time and plant treatment. However, if sustained changes in the capture rates of focal taxa are observed, future data users may use our observations to specifically quantify and correct for these shifting patterns related to the protocol change.