bluuebunny/crossref_metadata_2025_split huggingface dataset:
PRISM: A Python Package for Interactive and Integrated Analysis of Multiplexed Tissue Microarrays
Authors: Tubelleza Rafael , Kilgallon Aaron , Tan Chin Wee , Monkman James , Fraser John , Kulasinghe Arutha 
Published: December 2024

AbstractTissue microarrays (TMAs) enable researchers to analyse hundreds of tissue samples simultaneously by embedding multiple samples into single arrays, enabling conservation of valuable tissue samples and experimental reagents. Moreover, profiling TMAs allows efficient screening of tissue samples for translational and clinical applications. Multiplexed imaging technologies allow for spatial profiling of proteins at single cell resolution, providing insights into tumour microenvironments (TMEs) and disease mechanisms. High-plex spatial single cell protein profiling is a powerful tool for biomarker discovery and translational cancer research, however, there remain limited options for end-to-end computational analysis of this type of data. Here, we introduce PRISM, a Python package for interactive, end-to-end analyses of TMAs with a focus on translational and clinical research using multiplexed proteomic data from the CODEX, Phenocycler Fusion (Akoya Biosciences), Comet (Lunaphore), MACSima (Miltenyi Biotec), CosMx and Cellscape (Bruker Spatial Biology) platforms. PRISM leverages the SpatialData framework to standardise data storage and ensure interoperability with single cell and spatial analysis tools. It consists of two main components: TMA Image Analysis for marker-based tissue masking, TMA dearraying, cell segmentation, and single cell feature extraction; and AnnData Analysis for quality control, clustering, iterative cell-type annotation, and spatial analysis. Integrated as a plugin within napari, PRISM provides an intuitive and purely interactive graphical interface for real-time and human-in-the-loop analyses. PRISM supports efficient multi-resolution image processing and accelerates bioinformatics workflows using efficient scalable data structures, parallelisation and GPU acceleration. By combining modular flexibility, computational efficiency, and a completely interactive interface, PRISM simplifies the translation of raw multiplexed images to actionable clinical insights, empowering researchers to explore and interact effectively with spatial omics data.
Decoding transcriptional identity during Neuron-Astroglia Cell Fate driven by RAR-specific agonists
Authors: Galindo-Albarrán Ariel , Koshy Aysis , Mendoza-Ferri Maria Grazia , Mendoza-Parra Marco Antonio 
Published: December 2024

AbstractHow cells respond to different signals leading to defined lineages is an open question to understand physiological differentiation leading to the formation of organs and tissues. Among the various morphogens, retinoic acid signaling, via the RXR/RAR nuclear receptors activation, is a key morphogen of nervous system development and brain homeostasis. Here we analyze gene expression in ∼80,000 cells covering 16 days of monolayer mouse stem cell differentiation driven by the pan-RAR agonist all-trans retinoic acid, the RARα agonist BMS753 or the activation of both RARβ and RARγ receptors (BMS641+BMS961). Furthermore, we have elucidated the role of these retinoids for driving nervous tissue formation within 90 days of brain organoid cultures, by analyzing > 8,000 distinct spatial regions over 28 brain organoids.Despite a delayed progression in BMS641+BMS961, RAR-specific agonists led to a variety of neuronal subtypes, astrocytes and oligodendrocyte precursors. Spatially-resolved transcriptomics performed in organoids revealed spatially distinct RAR isotype expression leading to specialization signatures associated to matured tissues, including a variety of neuronal subtypes, retina-like tissue structure signatures and even the presence of microglia.
TRF1 and TRF2 form distinct shelterin subcomplexes at telomeres
Authors: Janovič Tomáš , Perez Gloria I. , Schmidt Jens C. 
Published: December 2024

ABSTRACTThe shelterin complex protects chromosome ends from the DNA damage repair machinery and regulates telomerase access to telomeres. Shelterin is composed of six proteins (TRF1, TRF2, TIN2, TPP1, POT1 and RAP1) that can assemble into various subcomplexesin vitro. However, the stoichiometry of the shelterin complex and its dynamic association with telomeres in cells is poorly defined. To quantitatively analyze the shelterin function in living cells we generated a panel of cancer cell lines expressing HaloTagged shelterin proteins from their endogenous loci. We systematically determined the total cellular abundance and telomeric copy number of each shelterin subunit, demonstrating that the shelterin proteins are present at telomeres in equal numbers. In addition, we used single-molecule live-cell imaging to analyze the dynamics of shelterin protein association with telomeres. Our results demonstrate that TRF1-TIN2-TPP1-POT1 and TRF2-RAP1 form distinct subcomplexes that occupy non-overlapping binding sites on telomeric chromatin. TRF1-TIN2-TPP1-POT1 tightly associates with chromatin, while TRF2-RAP1 binding to telomeres is more dynamic, allowing it to recruit a variety of co-factors to chromatin to protect chromosome ends from DNA repair factors. In total, our work provides critical mechanistic insight into how the shelterin proteins carry out multiple essential functions in telomere maintenance and significantly advances our understanding of macromolecular structure of telomeric chromatin.
Accurate sequence-to-affinity models for SH2 domains from multi-round peptide binding assays coupled with free-energy regression
Authors: Gagoski Dejan , Rube H. Tomas , Rastogi Chaitanya , Melo Lucas A. N. , Li Xiaoting , Voleti Rashmi , Shah Neel H. , Bussemaker Harmen J. 
Published: December 2024

ABSTRACTShort linear peptide motifs play important roles in cell signaling. They can act as modification sites for enzymes and as recognition sites for peptide binding domains. SH2 domains bind specifically to tyrosine-phosphorylated proteins, with the affinity of the interaction depending strongly on the flanking sequence. Quantifying this sequence specificity is critical for deciphering phosphotyrosine-dependent signaling networks. In recent years, protein display technologies and deep sequencing have allowed researchers to profile SH2 domain binding across thousands of candidate ligands. Here, we present a concerted experimental and computational strategy that improves the predictive power of SH2 specificity profiling. Through multi-round affinity selection and deep sequencing with large randomized phosphopeptide libraries, we produce suitable data to train an additive binding free energy model that covers the full theoretical ligand sequence space. Our models can be used to predict signaling network connectivity and the impact of missense variants in phosphoproteins on SH2 binding.
Biochemical dissection of a fungal highly reducing polyketide synthase condensing region reveals basis for acyl group selection
Authors: Foran Mia E. , Auckloo Nazia B. , Ho Y. T. Candace , Liu Shaonan , Hai Yang , Jenner Matthew 
Published: December 2024

ABSTRACTFungal highly reducing polyketide synthases (hrPKSs) are remarkable multidomain enzymes that catalyse the biosynthesis of a diverse range of structurally complex compounds. During biosynthesis, the ketosynthase (KS) and acyltransferase (AT) domains of the condensing region are visited by the acyl carrier protein (ACP) domain during every cycle, catalysing chain priming and elongation reactions. Despite their significance, our comprehension of how these steps contribute to biosynthetic fidelity remains poorly understood. Herein, we report the fullin vitroreconstitution of each catalytic step carried out by a hrPKS condensing region. Application of intact protein mass spectrometry shows that the AT domain operates selective acyl transfer to the ACP domain, ensuring loading of the correct starter / extender units, which is governed by a substrate recycling mechanism and kinetic parameters towards each substrate. The KS domain is shown to select for the correct starter unit for transacylation and subsequent chain elongation, yet harbours flexibility towards the extender unit supplied. This work provides the first comprehensive interrogation of a fungal hrPKS condensing region, which both affirms and expands our understanding of how these systems function, and provides a framework for future bioengineering efforts.
Cerebral perfusion and metabolic response of astrocytes and neurons during locomotion
Authors: Tiaglik Alisa , Morozova Kseniia , Fedotova Anna , Brazhe Alexey , Li Li , Liu Dan , Zhu Ling-Qiang , Bilan Dmitry , Oleinikov Vladimir , Brazhe Nadezda , Semyanov Alexey 
Published: December 2024

AbstractThe hemodynamic response links neural oxidative metabolism changes to increased cerebral blood flow during brain activity1. Although Roy and Sherrington introduced this concept over a century ago (1890), the exact cellular mechanisms remain unclear. This study demonstrates how local blood supply increases correlate with the metabolic response of individual brain cells during locomotion. Using Raman microspectroscopy, we observed an elevation in oxygen saturation levels (sO2) in cortical venules but not in arterioles, which were already near saturation. The increased sO2in the venules was accompanied by vasodilation, indicating blood oversupply in the local brain area, a phenomenon known as functional hyperemia. We then analyzed the metabolic response of individual neurons and astrocytes to locomotion. In neurons, the levels of reduced cytochromes ofcandbtypes [cytc,b(Fe2+)] rapidly decreased at the onset of locomotion. This suggests an increase in the activity of the mitochondrial respiratory chain (electron transport chain, ETC) in response to heightened energy demands in these cells2. In contrast, because astrocytes rely less on oxidative phosphorylation for their energy metabolism than neurons3, we did not observe an initial decrease in reduced cytochromes in these cells. However, as locomotion continued, the cytc,b(Fe2+) levels steadily increased in both cell types. In neurons, this led to a slow recovery from the initial drop, while in astrocytes, the increase exceeded baseline levels. Consequently, we observed an overload of electrons in the astrocytic ETC. The distinct responses of astrocytic and neuronal mitochondria to locomotion may reflect differences in the organization of the ETC in the two cell types4. Furthermore, astrocytes may shift to glycolysis under increased neuronal activity5,6. This difference also resulted in hydrogen peroxide (H202) production in astrocytic mitochondria but not neuronal mitochondria. Since H202is a signaling molecule critical for cognitive function in the brain7, we speculate that astrocytic mitochondria act as signaling hubs during exercise.
CNSistent integration and feature extraction from somatic copy number profiles
Authors: Streck Adam , Schwarz Roland F. 
Published: December 2024

AbstractThe vast majority of cancers exhibit Somatic Copy Number Alterations (SCNAs)—gains and losses of variable regions of DNA. SCNAs can shape the phenotype of cancer cells,e.g. by increasing their proliferation rates, removing tumor suppressor genes, or immortalizing cells. While many SCNAs are unique to a patient, certain recurring patterns emerge as a result of shared selectional constraints or common mutational processes. To discover such patterns in a robust way, the size of the dataset is essential, which necessitates combining SCNA profiles from different cohorts, a non-trivial task.To achieve this, we developed CNSistent, a Python package for imputation, filtering, consistent segmentation, feature extraction, and visualization of cancer copy number profiles from heterogeneous datasets. We demonstrate the utility of CNSistent by applying it to the publicly available TCGA, PCAWG, and TRACERx cohorts. We compare different segmentation and aggregation strategies on cancer type and subtype classification tasks using deep convolutional neural networks. We demonstrate an increase in accuracy over training on individual cohorts and efficient transfer learning between cohorts. Using integrated gradients we investigate lung cancer classification results, highlightingSOX2amplifications as the dominant copy number alteration in lung squamous cell carcinoma.
Injury-induced Neuregulin-ErbB signaling from muscle mobilizes stem cells for whole-body regeneration in Acoels
Authors: Stevens Brian , Popp Riley , Valera Heather , Krueger Kyle , Petersen Christian P. 
Published: December 2024

AbstractThe activation of progenitor cells near wound sites is a common feature of regeneration across species, but the conserved signaling mechanisms responsible for this step in whole-body regeneration are still incompletely understood. The acoelHofstenia miamiaundergoes whole-body regeneration using Piwi+ pluripotent adult stem cells (neoblasts) that accumulate at amputation sites early in the regeneration process. The EGFR signaling pathway has broad roles in controlling proliferation, migration, differentiation, and cell survival across metazoans. Using a candidate RNAi screening approach, we identify theHofsteniaEGFRerbB4-2and Neuregulinnrg-1genes as essential for blastema formation. Structure prediction of NRG-1 and ERBB4-2 proteins supports the likelihood of these factors interacting directly. After amputation injuries,nrg-1expression is induced in body-wall muscle cells at the wound site by 6 hours and localizes to the tip of the outgrowing blastema over the next several days, whileerbB4-2is broadly expressed, including in muscle and neoblasts. Undernrg-1(RNAi)anderbB4-2(RNAi)conditions that impair blastema formation, animals still undergo the earliest responses to injury to activate expression of the Early Growth Response transcription factoregr, indicating a crucial role for EGFR signaling downstream of initial wound activation.nrg-1(RNAi)anderbB4-2(RNAi)animals possess Piwi+ and H3P+ mitotic neoblasts which hyperproliferate normally after amputation, but these cells fail to accumulate at the wound site. Therefore, muscle provides a source for Neuregulin-ErbB signaling necessary for the mobilization of proliferative progenitors to enable blastema outgrowth for whole-body regeneration inHofstenia. These results indicate a shared functional requirement for muscle signaling to enable regeneration between planarians and acoels across 550 million years of evolution.
Targeted delivery of rhodopsin’s assembled core is required for outer segment extension in mouse rod photoreceptors
Authors: Martínez-Márquez Jorge Y. , Hua Sandy , Beu Andreea M. , Stein Christopher B. , Pearring Jillian N. 
Published: December 2024

ABSTRACTVertebrate vision in dim-light environments is initiated by rod photoreceptor cells that express the photopigment rhodopsin, a G-protein coupled receptor (GPCR). To ensure efficient light capture, rhodopsin is densely packed into hundreds of membrane discs that are tightly stacked within the rod-shaped outer segment compartment. Along with its role in eliciting the visual response, rhodopsin serves as both a building block necessary for proper outer segment formation as well as a trafficking guide for a few outer segment resident membrane proteins. An interesting aspect of rod homeostasis is that mutations that affect the localization of rhodopsin to the outer segment result in photoreceptor degeneration. In this study, we focus on determining the necessary properties of rhodopsin’s cytosolic C-terminus required for either proper outer segment trafficking and/or the capacity to extend the rudimentary outer segment in rhodopsin knockout (RhoKO) rods. We find that the well-described C-terminal QVAPA outer segment targeting motif also plays a role in endoplasmic reticulum (ER) exit and is necessary for outer segment elongation. Even minor rhodopsin mislocalization prevents efficient outer segment elongation suggesting that QVAPA-targeted delivery of rhodopsin drives outer segment extension. We identify that rhodopsin’s core, helix-8, and accessible QVAPA targeting motif are the minimal requirements to extend the rudimentary outer segment in RhoKO rods. Our findings provide useful insights into rhodopsin’s molecular features needed for outer segment delivery and subsequent elongation of this membrane-rich compartment.
Mathematical Modeling of Estrogen-Mediated Inflammation in the Gut and Immune System
Authors: Lighty Ariel M. , Islam Mohammad Aminul , Smith Brenda J. , Ford Versypt Ashlee N. 
Published: December 2024

AbstractPostmenopausal osteoporosis is a chronic inflammatory disease characterized by decreased bone mass and increased bone fracture risk. Estrogen deficiency during menopause plays a major role in post-menopausal osteoporosis by influencing bone, immune, and gut cell activity. In the gut, estrogen loss decreases tight junction proteins that bind epithelial cells of the intestinal barrier together. This increases gut permeability and alters the balance of T cells, increasing inflammatory T helper (Th17) cells and decreasing anti-inflammatory regulatory T cells (Tregs). Prebiotic dietary fibers are a promising treatment modality for gut-mediated inflammation and bone loss associated with estrogen deficiency. In a previous study, we investigated the effect of butyrate (a prebiotic by-product) on Treg levels in the gut, blood, and bone starting with healthy conditions. However, a gap remains in our mechanistic understanding of how estrogen affects systemic inflammation separately and in combination with prebiotic fibers.We developed a two-compartment dynamic model of estrogen in the gut and immune system to investigate the mechanisms of gut-mediated inflammation induced by estrogen-deficient conditions. Our initial model contains ODEs for estrogen, naive T cells, Tregs, and Th17 cells in gut and blood compartments. Estrogen is modeled using physiological mass balance equations considering its production, migration, and elimination. We integrate our estrogen model with an adapted version of our previous butyrate model, adding a population balance for Th17 cells and terms for bidirectional migration of Tregs and Th17 cells. Estrogen interactions with cells are modeled using Hill-type activation and inhibition functions. Our mathematical model predicts changes in T cell dynamics associated with changes in endogenous estrogen levels. We compare our predictions to in vivo results of estrogen, Tregs, and Th17 levels in the gut and blood after surgical menopause in mice. In the future, we will leverage this model to investigate whether the effect of prebiotic fiber treatment on estrogen-deficient bone loss is significantly affected by gut-mediated inflammation. The emphasis in this preprint is on the methods, particularly those for literature-based model parameterization.
Metabolic tuning facilitates nociceptor resilience to excitotoxicity
Authors: Yuan Lin , Chandel Navdeep S. , Julius David 
Published: December 2024

AbstractThe capsaicin receptor, TRPV1, mediates the detection of harmful chemical and thermal stimuli. Overactivation of TRPV1 can lead to cellular damage or death through excitotoxicity, a phenomenon associated with painful neuropathy and the paradoxical use of capsaicin as an analgesic. We exploited capsaicin-evoked death to conduct a systematic analysis of excitotoxicity through a genome-wide CRISPRi screen, thereby revealing a comprehensive network of regulatory pathways. We show that decreased expression of mitochondrial electron transport chain (ETC) components protects against capsaicin-induced toxicity by mitigating calcium imbalance and mitochondrial reactive oxygen species production via distinct pathways. Interestingly, TRPV1+sensory neurons in adult mice maintain lower expression of ETC components and can better tolerate excitotoxicity and oxidative stress compared to other sensory neuron subtypes. We further confirm the regulatory roles of the ETC in sensory neurons through gain-of-function and loss-of-function experiments. These findings implicate ETC tuning as a cellular protective strategy against sensory excitotoxicity.
The Restoration of Social Defects in Schizophrenic Mice by Plant Exposure
Authors: Li Mingxuan , Li Mingda , Zhou Kai , Zhang Xiangyu , Liu Shanshan , Wu Yuyu , Li Xinjian 
Published: December 2024

AbstractSchizophrenia is a serious psychotic disorder caused by both individuals’ genetic background and their living environment. However, how the cognitive and negative symptoms can be treated is still a challenge since most anti-psychotic drugs are only effective for positive symptoms. Previous epidemic studies have demonstrated that plant exposure could decrease the risk of schizophrenia and shorten the length of psychiatric hospital admissions for patients. However, it is still unknown whether plant exposure could improve cognition-related defects in schizophrenia, with no related animal studies. In the present study, we first induced a schizophrenia mice model by giving mice long-term (2 weeks) injections of the antagonist of the NMDA receptor: MK801. We then raised the animals in environments containing plants (4 weeks) including Epipremnumaureumand rosemary, and tested their locomotive, anxious and social behaviors. We found that plant exposure did not change the locomotion behaviors of wild-type animals, but significantly reduced the schizophrenia-related social and anxious behaviors in the schizophrenic animals. In addition, we tested the expression of c-Fos in animals exposed to plants after social behavioral testing and found that the deficits in c-Fos expression in both the hippocampus and prefrontal cortex were partially rescued after plant exposure. These results indicate plant exposure will be a new tool to improve the clinical deficits of schizophrenia.
Histone H4 limits transcription of the histone locus in Drosophila
Authors: Ahmad Kami , Wooten Matt , Takushi Brittany N , Vidaurre Velinda , Chen Xin , Henikoff Steven 
Published: December 2024

AbstractThe expression of core histone genes is coupled to DNA replication of the genome to support chromatin packaging. In Drosophila, core histone genes are repeated in one locus as a 100-copy array and forms the Histone Locus Body; these multiple copies support varying rates of cell proliferation in different developmental stages and various tissues of the animal. We show here that the Drosophila Histone Locus Body contains a mix of active and silenced units. In the male germline reporter histone repeat units are strongly silenced, and we used this setting to test the dependence of expression on chromatin factors and histones. We find that silenced histone genes are induced in response to demand for histones, and from a selected survey we identify that only the H4 histone is required for reporter silencing. Further, histone H4 protein localizes to the Histone Locus Body and is most enriched immediately after S phase of the cell cycle. This argues for a role of histone H4 in coupling the demand for histones for chromatin packaging to histone gene expression. Binding patterns of the NPAT regulatory factor and RNA Polymerase II in K562 cells suggests that this regulatory principle also operates in human cells.Author SummaryCell proliferation in eukaryotes requires the coordination of DNA replication to duplicate the genome and synthesis of new histones to package that DNA.Drosophila melanogasterhas a single array of histone genes, where some are actively transcribed and others are silenced. Here, we present evidence that the number of activated genes responds to the demand for histones during DNA replication. We identify one histone protein as a factor that localizes to the histone gene array, and that reduced levels of this histone induce the expression of otherwise silenced histone genes. In human cells, the gene encoding this same histone is the predominant target for activating transcription proteins, and is expressed more highly than other histones. The amount of this one histone may serve to sense the demand for histones during DNA replication, so that increased levels of this histone when DNA replication is complete represses histone gene expression.