bluuebunny/crossref_metadata_2025_split huggingface dataset:
The regulatory grammar of human promoters uncovered by MPRA-trained deep learning
Authors: Barbadilla-Martínez Lucía , Klaassen Noud , Franceschini-Santos Vinícius H. , Breda Jérémie , Hernandez-Quiles Miguel , van Lieshout Tijs , Urzua Traslaviña Carlos G. , Yücel Hatice , Luong Boi Minh Chau , Hermana-Garcia-Agullo Celia , Gregoricchio Sebastian , Zwart Wilbert , Voest Emile , Franke Lude , Vermeulen Michiel , de Ridder Jeroen , van Steensel Bas 
Published: July 2024

AbstractOne of the major challenges in genomics is to build computational models that accurately predict genome-wide gene expression from the sequences of regulatory elements. At the heart of gene regulation are promoters, yet their regulatory logic is still incompletely understood. Here, we report PARM, a cell-type specific deep learning model trained on specially designed massively parallel reporter assays that query human promoter sequences. PARM requires ∼1,000 times less computational power than state-of-the-art technology, and reliably predicts autonomous promoter activity throughout the genome from DNA sequence alone, in multiple cell types. PARM can even design purely synthetic strong promoters. We leveraged PARM to systematically identify binding sites of transcription factors (TFs) that are likely to contribute to the activity of each natural human promoter. We uncovered and experimentally confirmed striking positional preferences of TFs that differ between activating and repressive regulatory functions, as well as a complex grammar of motif-motif interactions. For example, many, but not all, TFs act as repressors when their binding motif is located near or just downstream of the transcription start site. Our approach lays the foundation towards a deep understanding of the regulation of human promoters by TFs.HighlightsCausality-trained deep learning model PARM captures regulatory grammar of human promotersPARM is highly economical, both experimentally and computationallyTranscription factors have different preferred positions for their regulatory activityMany (but not all) transcription factors act as repressors when binding downstream of transcription start sites
Visual analysis of spatial transcriptomics data with RedeViz
Authors: Wang Dehe , Ren Xianwen 
Published: July 2024

AbstractSpatial transcriptomics (ST) technologies are powerful tools to illustrate the spatial hierarchy and heterogeneity of tissues with the lens of multiplexed gene readouts. However, ST technologies generate sequence data rather than images, preventing intuitive examination of the cellular contexture of tissues. Moreover, the inherent sparsity of ST data caused by molecular crowdedness and sequencing dropouts poses great challenges to accurate and clear visualization. In this study, we introduce RedeViz, a toolkit crafted for enhancing and visualizing subcellular-resolution ST data. RedeViz applies a pixel-level enhancement strategy, visualizes ST data in automatic or customized manners, and can display the cellular and genic spatial patterns with effects akin to HE staining. Strict evaluations confirm that RedeViz fits a wide range of ST platforms, including Xenium, Visium HD, MERFISH, CosMx, Stereoseq, as well as spatial proteomic platforms like CODEX. The impressive performance of RedeViz across various scales from cell-, tissue-, organ-, to organism-levels brings us a universal “What You See Is What You Get” framework for visual analysis of ST data.
A latitudinal gradient of reference genomes
Authors: Linck Ethan B. , Cadena Carlos Daniel 
Published: July 2024

AbstractGlobal inequality rooted in legacies of colonialism and uneven development can lead to systematic biases in scientific knowledge. In ecology and evolutionary biology, findings, funding and research effort are disproportionately concentrated at high latitudes while biological diversity is concentrated at low latitudes. This discrepancy may have a particular influence in fields like phylogeography, molecular ecology and conservation genetics, where the rise of genomics has increased the cost and technical expertise required to apply state-of-the-art methods. Here we ask whether a fundamental biogeographic pattern—the latitudinal gradient of species richness in tetrapods—is reflected in available reference genomes, an important data resource for various applications of molecular tools for biodiversity research and conservation. We also ask whether sequencing approaches differ between the Global South and Global North, reviewing the last five years of conservation genetics research in four leading journals. We find that extant reference genomes are scarce relative to species richness at low latitudes, and that reduced-representation and whole-genome sequencing are disproportionately applied to taxa in the Global North. We conclude with recommendations to close this gap and improve international collaborations in biodiversity genomics.
Changes in the functional diversity and abundance of ectomycorrhizal fungi are decoupled from water uptake patterns in European beech forests
Authors: Rodríguez-Uña Asun , Moreno-Mateos David , Matesanz Silvia , Wingate Lisa , Barbeta Adrià , Porras Javier , Gimeno Teresa E. 
Published: July 2024

AbstractTemperate forests on their warm and dry distribution limit are expected to be most vulnerable to reductions in water availability. This prediction is mostly based on studies assessing single forest functions, mainly growth. Water and nutrient cycling are functions that rely on tree roots and their symbiotic association with ectomycorrhizal (ECM) fungi. Trees can compensate for seasonal reductions in water availability by shifting root water-uptake (RWU) towards deeper soil layers, but ECM fungi dwell in the upper soil, thus suffering from desiccation and compromising nutrient uptake. We hypothesised that drier sites should depict larger seasonal shifts in RWU, but at the expense of lower diversity and colonization of fine roots by ECM fungi. We selected three beech (Fagus sylvatica) forests in their warm distribution limit with contrasting geographic locations and mean annual precipitation: northern Atlantic (2500mm), intermediate transitional (1150mm) and southern Mediterranean (780mm). We collected soil, stem and root samples in spring (wet) and summer (dry) to quantify fine-root density and colonization by ECM fungi, to infer RWU from isotopic composition of plant and soil water, and to characterize ECM fungal diversity through DNA-metabarcoding. High moisture in the upper soil benefited the ECM community, but higher diversity and fine-root colonization by ECM fungi in the upper soil did not imply larger contributions of this soil layer to RWU. The prevailing climate and local abiotic conditions determined how ECM communities structured, more than seasonal variability. Across sites, ECM communities differed in their functional diversity: ECM fungi with long hyphae, more vulnerable to water scarcity, dominated at the site with the highest water availability. Our results suggest that transient reductions in soil water availability might not compromise RWU but could be detrimental for maintaining ECM-mediated nutrient uptake in beech forests experiencing longer and more severe drought periods under current climate change.
Interleukin-33 from oligodendrocytes sustains effector differentiation of tissue-resident CD8+ T cells and is a druggable target in CNS autoimmune disease
Authors: Fonta Nicolas , Page Nicolas , Klimek Bogna , Piccinno Margot , Di Liberto Giovanni , Lemeille Sylvain , Kreutzfeldt Mario , Kastner Anna Lena , Ertuna Yusuf I. , Vincenti Ilena , Wagner Ingrid , Pinschewer Daniel D. , Merkler Doron 
Published: July 2024

AbstractIn chronic inflammatory disorders of the central nervous system (CNS), tissue-resident self-reactive T cells perpetuate disease. The specific tissue factors governing the persistence and continuous differentiation of these cells remain undefined but could represent attractive therapeutic targets.In a model of chronic CNS autoimmunity, we find that oligodendrocyte-derived interleukin-33 (IL-33), an alarmin, is key for locally regulating the pathogenicity of self-reactive CD8+ T cells. The selective ablation of IL-33 from neo-self-antigen-expressing oligodendrocytes mitigates CNS disease. In this context, fewer self-reactive CD8+ T cells persist in the inflamed CNS, and the remaining cells are largely locked into a stem-like precursor program, failing to form TCF-1loweffector progeny. Importantly, interventional IL-33 blockade by locally administered somatic gene therapy reduces T cell infiltrates and improves the disease course.Our study identifies oligodendrocyte-derived IL-33 as a druggable tissue factor regulating the differentiation and survival of self-reactive CD8+ T cell in the inflamed CNS. This finding introduces tissue factors as a novel category of immune targets for treating chronic CNS autoimmune diseases.
Spleen Tyrosine Kinase (SYK) negatively regulates ITAM-mediated human NK cell signaling and CD19-CAR NK cell efficacy
Authors: Millan Alberto J. , Allain Vincent , Nayak Indrani , Aguilar Oscar A. , Arakawa-Hoyt Janice S. , Ureno Gabriella , Rothrock Allison Grace , Shemesh Avishai , Eyquem Justin , Das Jayajit , Lanier Lewis L. 
Published: July 2024

AbstractNK cells express activating receptors that signal through ITAM-bearing adapter proteins. The phosphorylation of each ITAM creates binding sites for SYK and ZAP70 protein tyrosine kinases to propagate downstream signaling including the induction of Ca2+influx. While all immature and mature human NK cells co-express SYK and ZAP70, clonally driven memory or adaptive NK cells can methylateSYKgenes and signaling is mediated exclusively using ZAP70. Here, we examined the role of SYK and ZAP70 in a clonal human NK cell line KHYG1 by CRISPR-based deletion using a combination of experiments and mechanistic computational modeling. Elimination ofSYKresulted in more robust Ca++influx after cross-linking of the CD16 and NKp30 receptors and enhanced phosphorylation of downstream proteins, whereasZAP70deletion diminished these responses. By contrast,ZAP70depletion increased proliferation of the NK cells. As immature T cells express both SYK and ZAP70 but mature T cells often express only ZAP70, we transduced the human Jurkat cell line with SYK and found that expression of SYK increased proliferation but diminished TCR-induced Ca2+flux and activation. We performed transcriptional analysis of the matched sets of variant Jurkat and KHYG1 cells and observed profound alterations caused by SYK expression. As depletion ofSYKin NK cells increased their activation, primary human NK cells were transduced with a CD19-targeting CAR and were CRISPR edited to ablateSYKorZAP70. Deletion ofSYKresulted in more robust cytotoxic activity and cytokine production, providing a new therapeutic strategy of NK cell engineering for cancer immunotherapy.
A novel mechanism of microbial attachment: the flagellar pump ofGiardia lamblia
Authors: Picou Theodore J. , Luo Haibei , Polackwich Robert J. , Gabilondo Beatriz Burrola , McAllister Ryan G. , Gagnon David A. , Powers Thomas R. , Elmendorf Heidi G. , Urbach Jeffrey S. 
Published: July 2024

AbstractThe ability of microbes to attach to biological and inert substrates is a necessary prerequisite for colonization of new habitats. In contrast to well-characterized mechanisms that rely on specific or non-specific chemical interactions between microbe and substrate, we describe here an effective hydrodynamic mechanism of attachment that relies on fluid flow generated by the microbe. The microbeGiardia lamblia, a flagellated protozoan parasite, naturally attaches to the microvilliated surface of the small intestine but is also capable of attaching indiscriminately to a wide range of natural and artificial substrates. By tracking fluorescent quantum dots, we demonstrate a persistent flow between the parasite and substrate generated by a pair ofGiardiaflagella. Using both experimental measures and computational modeling, we show that the negative pressure generated by this fluid flow is sufficient to generate the previously measured force of attachment. We further show that this dynamically-generated negative pressure allowsGiardiato attach to both solid and porous surfaces, thereby meeting the real-world demands of attachment to the microvilliated surface of intestinal cells. These findings provide experimental support for a hydrodynamic model of attachment that may be shared by other ciliated and flagellated microbes.
Roles of P-body factors inCandida albicansfilamentation and stress response
Authors: Tosiano Melissa A. , Lanni Frederick , Mitchell Aaron P. , McManus C. Joel 
Published: July 2024

AbstractHyphal growth is strongly associated with virulence in the human fungal pathogenCandida albicans. While hyphal transcriptional networks have been the subject of intense study, relatively little is known about post-transcriptional regulation. Previous work reported that P-Body (PB) factors Dhh1 and Edc3 were required forC. albicansvirulence and filamentation, suggesting an essential role for post-transcriptional regulation of these processes. However, the molecular roles of these factors have not been determined. To further study the function of PB factors in filamentation, we generated homozygous deletions ofDHH1andEDC3in diverse prototrophic clinical strains using transient CRISPR-Cas9. HomozygousDHH1deletion strongly impaired growth, altered filamentation, and exhibited unusual colony morphology in response to heat stress in five strain backgrounds. Using RNA-seq, we foundDHH1deletion disrupts the regulation of thousands of genes under both yeast and hyphal growth conditions in SC5314 and P57055. This included upregulation of many stress response genes in the absence of external stress, similar to deletion of theS. cerevisiae DHH1homolog. In contrast, we foundEDC3was not required for heat tolerance or filamentation in diverse strains. These results support a model in whichDHH1, but notEDC3, represses hyphal stress response transcripts in yeast and remodels the transcriptome during filamentation. Our work supports distinct requirements for specific mRNA decay factors, bolstering evidence for post-transcriptional regulation of filamentation inC. albicans.Author summaryIn the dimorphic fungal pathogenC. albicans, the hyphal phenotype strongly correlates with pathogenicity. While transcriptional control of hyphal growth has been extensively studied, comparatively little is known about post-transcriptional regulation of this significant morphological shift. PB factors are associated with mRNA decay and translational repression. Here we investigate the roles of two PB factors in growth, filamentation, and gene expression. Although deletion of PB factorEDC3did not impact growth or filamentation,dhh1Δ/Δhad greatly impaired growth and heat tolerance as well as unusual hyphal phenotypes in multiple clinical isolate strains. Additionally, we found that the transcriptomes of SC5314 and P57055dhh1Δ/Δyeast and hyphae were highly dysregulated. The extensive transcriptomic impacts of the absence of Dhh1 correlated with our phenotypic findings. Stress-associated genes were induced under non-stress conditions and the filamentation response was blunted under physiologically relevantin vitroconditions. We demonstrate that mRNA decay factors play distinct roles in regulatingC. albicansmorphology and that Dhh1 contributes to environmentally appropriate expression of the stress response and hyphal growth.
Cytokinin acts as a systemic signal coordinating reproductive effort in Arabidopsis
Authors: Volkava Darya , Bukovcakova Sona Valuchova , Mikulkova Pavlina , Pecinkova Jana , Skalak Jan , Hejatko Jan , Riha Karel 
Published: July 2024

AbstractThe duration of the flowering phase is a key adaptive trait related to reproductive effort and plant longevity. In plants with indeterminate inflorescences, the number of flowers produced is determined by the activity of the inflorescence meristem. However, the integration of inflorescence meristem activity with the physiological and developmental status of a plant is not well understood. We combined quantitative imaging of the inflorescence meristem with the manipulation of cytokinin levels and distribution to investigate how meristem activity is regulated. Our data support the hypothesis that emerging fruits drain the acropetal flow of cytokinin away from the meristem inducing its proliferative arrest. We further show that the duration of flowering and cytokinin signaling in the inflorescence meristem is influenced by nitrate availability. Taken together, these data suggest that cytokinin functions as a systemic signal that integrates information about ongoing reproductive effort and plant nutrient status to control flower production.
The impact of physical activity on physical performance, mitochondrial bioenergetics, ROS production and calcium handling across the human adult lifespan
Authors: Cefis Marina , Marcangeli Vincent , Hammad Rami , Granet Jordan , Leduc-Gaudet Jean-Philippe , Gaudreau Pierrette , Trumpff Caroline , Huang Hannah , Picard Martin , Aubertin-Leheudre Mylène , Bélanger Marc , Robitaille Richard , Morais José A. , Gouspillou Gilles 
Published: July 2024

AbstractAging-related muscle atrophy and weakness contribute to loss of mobility, falls and disability. Mitochondrial dysfunction is widely considered a key contributing mechanism to muscle aging. However, mounting evidence position physical activity as a confounding factor, making unclear whether muscle mitochondria accumulate bona fide defects with aging. To disentangle aging from physical activity-related mitochondrial adaptations, we functionally profiled skeletal muscle mitochondria in 51 inactive and 88 active men aged 20-93. Physical activity status conferred partial protection against age-related decline in physical performance. A trend for reduced muscle mitochondrial respiration with aging was observed in inactive but not in active participants, indicating that agingper sedoes not alter mitochondrial respiratory capacity. Mitochondrial reactive oxygen species (ROS) production was unaffected by aging and active participants displayed higher ROS production. In contrast, mitochondrial calcium retention capacity decreased with aging regardless of physical activity status and correlated with muscle mass, performance and the stress-responsive metabokine GDF15. Targeting mitochondrial calcium handling may hold promise for treating aging-related muscle impairments.
Regulation of Kv1.2 redox-sensitive gating by the transmembrane lectin LMAN2
Authors: Lamothe Shawn M. , Das Damayantee , Wong Anson A. , Hao Yubin , Maguire Aislinn D. , Kerr Bradley J. , Baronas Victoria A. , Kurata Harley T. 
Published: July 2024

ABSTRACTKv1.2 potassium channels influence excitability and action potential propagation in the nervous system. Unlike closely-related Kv1 channels, Kv1.2 exhibits highly variable voltage-dependence of gating, attributed to regulation by unidentified extrinsic factors. Variable Kv1.2 gating is strongly influenced by the extracellular redox potential, and we demonstrate that Kv1.2 currents in dorsal root ganglion sensory neurons exhibit similar variability and redox sensitivity as observed when the channel is heterologously expressed in cell lines. We used a functional screening approach to test the effects of candidate regulatory proteins on Kv1.2 gating, using patch clamp electrophysiology. Among 52 candidate genes tested, we observed that co-expression with the transmembrane lectin LMAN2 led to a pronounced gating shift of Kv1.2 activation to depolarized voltages in CHO and L(tk-) cell lines, caused by deceleration of activation kinetics. Overexpression of LMAN2 promoted a slow gating mode of Kv1.2 that mimics the functional outcomes of extracellular reducing conditions, and enhanced sensitivity to extracellular reducing agents. In contrast, shRNA-mediated knockdown of endogenous LMAN2 in cell lines reduced Kv1.2 redox sensitivity and gating variability. Kv1.2 sensitivity to LMAN2 is abolished by mutation of neighboring residues F251 and T252 in the intracellular S2-S3 linker, and these also abolish redox-dependent modulation of Kv1.2, suggesting that LMAN2 is an important contributor to the mechanism of redox sensitivity. In conclusion, we identified LMAN2 as a candidate regulatory protein that influences redox-dependent modulation of Kv1.2, and clarified the structural elements of the channel that are required for sensitivity.
AGEing of Collagen: The Effects of Glycation on Collagen’s Stability, Mechanics and Assembly
Authors: Sloseris Daniel , Forde Nancy R. 
Published: July 2024

ABSTRACTAdvanced Glycation End Products (AGEs) are the end result of the irreversible, non-enzymatic glycation of proteins by reducing sugars. These chemical modifications accumulate with age and have been associated with various age-related and diabetic complications. AGEs predominantly accumulate on proteins with slow turnover rates, of which collagen is a prime example. Glycation has been associated with tissue stiffening and reduced collagen fibril remodelling. In this study, we investigate the effects of glycation on the stability of type I collagen, its molecular-level mechanics and its ability to perform its physiological role of self-assembly. Collagen AGEing is inducedin vitroby incubation with ribose. We confirm and assess glycation using fluorescence measurements and changes in collagen’s electrophoretic mobility. Susceptibility to trypsin digestion and circular dichroism (CD) spectroscopy are used to probe changes in collagen’s triple helical stability, revealing decreased stability due to glycation. Atomic Force Microscopy (AFM) imaging is used to quantify how AGEing affects collagen flexibility, where we find molecular-scale stiffening. Finally we use microscopy to show that glycated collagen molecules are unable to self-assemble into fibrils. These findings shed light on the molecular mechanisms underlying AGE-induced tissue changes, offering insight into how glycation modifies protein structure and stability.
TPM4 condensates glycolytic enzymes to fuel actin reorganization under hyperosmotic stress
Authors: Yang Wenzhong , Wang Yuan , Liu Geyao , Wang Yan , Wu Congying 
Published: July 2024

AbstractActin homeostasis is fundamental for cell structure and consumes a large portion of cellular ATP. It has been documented in the literature that certain glycolytic enzymes can interact with actin, indicating an intricate interplay between the cytoskeleton and cellular metabolism. Here we report that hyperosmotic stress triggers actin severing and subsequent phase separation of the actin-binding protein TPM4. TPM4 condensates glycolytic enzymes such as HK2, PFKM, and PKM2, and adhere to and wrap around actin filaments. Notably, the condensates of TPM4 and glycolytic enzymes are enriched of NADH and ATP, suggestive of their functional importance in cell metabolism. At cellular level, actin filaments assembly is enhanced upon hyperosmotic stress and TPM4 condensation, while depletion of TPM4 impaired osmolarity-induced actin reorganization. At tissue level, co-localized condensates of TPM4 and glycolytic enzymes are observed in renal tissues subjected to hyperosmotic stress. Together, our findings suggest that stress-induced actin perturbation may act on TPM4 to organize glycolytic hubs that tether energy production to cytoskeletal reorganization.Graphical Abstract