bluuebunny/crossref_metadata_2025_split huggingface dataset:
Construction and representation of human pangenome graphs
Authors: Andreace Francesco , Lechat Pierre , Dufresne Yoann , Chikhi Rayan 
Published: June 2023

AbstractAs a single reference genome cannot possibly represent all the variation present across human individuals, pangenome graphs have been introduced to incorporate population diversity within a wide range of genomic analyses. Several data structures have been proposed for representing collections of genomes as pangenomes, in particular graphs. In this work we collect all publicly available high-quality human haplotypes and constructed the largest human pangenome graphs to date, incorporating 52 individuals in addition to two synthetic references (CHM13 and GRCh38). We build variation graphs and de Bruijn graphs of this collection using five of the state-of-the-art tools:Bifrost,mdbg,Minigraph,Minigraph-Cactusandpggb. We examine differences in the way each of these tools represents variations between input sequences, both in terms of overall graph structure and representation of specific genetic loci. This work sheds light on key differences between pangenome graph representations, informing end-users on how to select the most appropriate graph type for their application.
Brain cell-specific origin of circulating microRNA biomarkers in experimental temporal lobe epilepsy
Authors: Brindley Elizabeth , Heiland Mona , Mooney Catherine , Diviney Mairead , Mamad Omar , Hill Thomas D. M. , Yan Yan , Venø Morten T. , Reschke Cristina Ruedell , Batool Aasia , Langa Elena , Sanz-Rodriguez Amaya , Heller Janosch , Morris Gareth , Conboy Karen , Kjems Jørgen , Brennan Gary P. , Henshall David C. 
Published: June 2023

AbstractThe diagnosis of epilepsy is complex and challenging and would benefit from the availability of molecular biomarkers, ideally measurable in a biofluid such as blood. Experimental and human epilepsy are associated with altered brain and blood levels of various microRNAs (miRNAs). Evidence is lacking, however, as to whether any of the circulating pool of miRNAs originates from the brain. To explore the link between circulating miRNAs and the pathophysiology of epilepsy, we first sequenced argonaute 2 (Ago2)-bound miRNAs in plasma samples collected from mice subject to status epilepticus induced by intraamygdala microinjection of kainic acid. This identified time-dependent changes in plasma levels of miRNAs with known neuronal and microglial-cell origins. To explore whether the circulating miRNAs had originated from the brain, we generated mice expressing FLAG-Ago2 in neurons or microglia using tamoxifen-inducibleThy1orCx3cr1promoters, respectively. FLAG immunoprecipitates from the plasma of these mice after seizures contained miRNAs, including let-7i-5p and miR-19b-3p. Taken together, these studies confirm that a portion of the circulating pool of miRNAs in experimental epilepsy originates from the brain, increasing support for miRNAs as mechanistic biomarkers of epilepsy.
In Vivo Tissue Distribution of Microplastics and Systemic Metabolomic Alterations After Gastrointestinal Exposure
Authors: Garcia Marcus M. , Romero Aaron S. , Merkley Seth D. , Meyer-Hagen Jewel L. , Forbes Charles , Hayek Eliane El , Sciezka David P. , Templeton Rachel , Gonzalez-Estrella Jorge , Jin Yan , Gu Haiwei , Benavidez Angelica , Hunter Russell P. , Lucas Selita , Herbert Guy , Kim Kyle Joohyung , Cui Julia Yue , Gullapalli Rama , In Julie G. , Campen Matthew J. , Castillo Eliseo F. 
Published: June 2023

ABSTRACTGlobal plastic use has consistently increased over the past century with several different types of plastics now being produced. Much of these plastics end up in oceans or landfills leading to a substantial accumulation of plastics in the environment. Plastic debris slowly degrades into microplastics (MPs) that can ultimately be inhaled or ingested by both animals and humans. A growing body of evidence indicates that MPs can cross the gut barrier and enter into the lymphatic and systemic circulation leading to accumulation in tissues such as the lungs, liver, kidney, and brain. The impacts of mixed MPs exposure on tissue function through metabolism remains largely unexplored. To investigate the impact of ingested MPs on target metabolomic pathways, mice were subjected to either polystyrene microspheres or a mixed plastics (5 µm) exposure consisting of polystyrene, polyethylene and the biodegradability and biocompatible plastic, poly-(lactic-co-glycolic acid). Exposures were performed twice a week for four weeks at a dose of either 0, 2, or 4 mg/week via oral gastric gavage. Our findings demonstrate that, in mice, ingested MPs can pass through the gut barrier, be translocated through the systemic circulation, and accumulate in distant tissues including the brain, liver, and kidney. Additionally, we report on the metabolomic changes that occur in the colon, liver and brain which show differential responses that are dependent on dose and type of MPs exposure. Lastly, our study provides proof of concept for identifying metabolomic alterations associated with MPs exposure and adds insight into the potential health risks that mixed MPs contamination may pose to humans.
A solid beta-sheet structure is formed at the surface of FUS liquid droplets during aging
Authors: Emmanouilidis Leonidas , Bartalucci Ettore , Kan Yelena , Ijavi Mahdiye , Pérez Maria Escura , Afanasyev Pavel , Boehringer Daniel , Zehnder Johannes , Parekh Sapun H. , Bonn Mischa , Michaels Thomas C. T. , Wiegand Thomas , Allain Frédéric H.-T. 
Published: June 2023

AbstractInsights into liquid droplet formation via liquid-liquid phase separation and the subsequent liquid-to-solid phase transition are important for understanding cell dynamics, as well as a number of neurodegenerative disorders. We report here, using the example of the FUsed in Sarcoma (FUS) protein, an investigation of the liquid droplet maturation process combining solution- and solid-state NMR spectroscopy, Raman spectroscopy, and light and electron microscopies. Our study reveals that the surface of the droplets plays a critical role in this process. Indeed, when comparing a biphasic sample, in which liquid droplets are stabilized in an agarose matrix, with a pure monophasic condensed phase sample, we find that the liquid-droplet maturation kinetics is faster in the biphasic FUS sample, owing to the larger surface-to-volume ratio. In addition, using Raman spectroscopy, we observe structural differences upon liquid-droplet maturation between the inside and the surface of liquid droplets, which is of β-sheet content as revealed by solid-state NMR. This is detected very early on and increases over time. In agreement with these observations, a solid crust-like shell is visually seen by microaspiration experiments. After several months, electron microscopy reveals that the matured FUS droplets have converted into solid linear fibrils distinct from the fibril core of seeded fibrils reported previously, as arginine side-chains from the arginine-and-glycine-rich domain (RGG) motif are partially rigidified, highlighting the participation of this motif in the liquid-to-solid transition. In presence of RNA, this aging process is not taking place.
An efficient behavioral screening platform classifies natural products and other chemical cues according to their chemosensory valence inC. elegans
Authors: Fryer Emily , Guha Sujay , Rogel-Hernandez Lucero E. , Logan-Garbisch Theresa , Farah Hodan , Rezaei Ehsan , Mollhoff Iris N. , Nekimken Adam L. , Xu Angela , Seyahi Lara Selin , Fechner Sylvia , Druckmann Shaul , Clandinin Thomas R. , Rhee Seung Y. , Goodman Miriam B. 
Published: June 2023

AbstractThroughout history, humans have relied on plants as a source of medication, flavoring, and food. Plants synthesize large chemical libraries and release many of these compounds into the rhizosphere and atmosphere where they affect animal and microbe behavior. To survive, nematodes must have evolved the sensory capacity to distinguish plant-made small molecules (SMs) that are harmful and must be avoided from those that are beneficial and should be sought. This ability to classify chemical cues as a function of their value is fundamental to olfaction, and represents a capacity shared by many animals, including humans. Here, we present an efficient platform based on multi-well plates, liquid handling instrumentation, inexpensive optical scanners, and bespoke software that can efficiently determine the valence (attraction or repulsion) of single SMs in the model nematode,Caenorhabditis elegans. Using this integrated hardware-wetware-software platform, we screened 90 plant SMs and identified 37 that attracted or repelled wild-type animals, but had no effect on mutants defective in chemosensory transduction. Genetic dissection indicates that for at least 10 of these SMs, response valence emerges from the integration of opposing signals, arguing that olfactory valence is often determined by integrating chemosensory signals over multiple lines of information. This study establishes thatC. elegansis an effective discovery engine for determining chemotaxis valence and for identifying natural products detected by the chemosensory nervous system.
DNAJB1-PRKACA fusion protein-regulated LINC00473 promotes tumor growth and alters mitochondrial fitness in fibrolamellar carcinoma
Authors: Ma Rosanna K. , Tsai Pei-Yin , Farghli Alaa R. , Shumway Alexandria , Kanke Matt , Gordan John D. , Gujral Taranjit S. , Vakili Khashayar , Nukaya Manabu , Noetzli Leila , Ronnekleiv-Kelly Sean , Broom Wendy , Barrow Joeva , Sethupathy Praveen 
Published: June 2023

SummaryFibrolamellar carcinoma (FLC) is a rare liver cancer that disproportionately affects adolescents and young adults. Currently, no standard of care is available and there remains a dire need for new therapeutics. Most patients harbor the fusion oncogeneDNAJB1-PRKACA(DP fusion), but clinical inhibitors are not yet developed and it is critical to identify downstream mediators of FLC pathogenesis. Here, we identify long non-coding RNA LINC00473 among the most highly upregulated genes in FLC tumors and determine that it is strongly suppressed by RNAi-mediated inhibition of the DP fusion in FLC tumor epithelial cells. We show by loss- and gain-of-function studies that LINC00473 suppresses apoptosis, increases the expression of FLC marker genes, and promotes FLC growth in cell-based andin vivomodels of disease. Mechanistically, LINC00473 plays an important role in promoting glycolysis and altering mitochondrial activity. Specifically, LINC00473 knockdown leads to increased spare respiratory capacity, an indicator of mitochondrial fitness. Overall, we propose that LINC00473 could be a viable target for this devastating disease.HighlightsFibrolamellar carcinoma (FLC) is a lethal liver cancer lacking effective therapeutic options. Ma et al. demonstrate that primate-specific RNA LINC00473 is enriched in tumor epithelial cells and functions to promote FLC growth and dysregulate cellular energetics, unveiling an important mechanism downstream of the fusion oncogene, DNAJB1-PRKACA, in FLC pathogenesis.In BriefLINC00473 is consistently elevated in primary FLC tumor tissue from different patient cohorts and in multiple disease models.DP fusion, the signature oncoprotein of FLC, drives LINC00473 expression.LINC00473 promotes FLC growth via anti-apoptotic function.LINC00473 modulates FLC energetics by promoting glycolysis and altering mitochondrial fitness.Abstract Figure
A novel phenylpropanoid methyl esterase enables catabolism of aromatic compounds that inhibit biological nitrification
Authors: Wilson Andrew , Fossen Elise Van , Shrestha Ritu , Trotter Valentine , Poirier Brenton , Frank Andrew , Nelson William , Kim Young-Mo , Deutschbauer Adam , Egbert Robert , Elmore Joshua R. 
Published: June 2023

AbstractAgriculture is the largest source of greenhouse gases (GHG) production. Conversion of nitrogen fertilizers into more reduced forms by microbes through a process known as biological nitrification drives GHG production, enhances proliferation of toxic algal blooms, and increases cost of crop production. Some plants reduce biological nitrification in soils by exuding a diverse array of biological nitrification inhibitors (BNIs) that inhibit the ammonium oxidizing microbes responsible for nitrification. Applying synthetic biology to enhance and transfer BNI production into food and bioenergy crops is a promising approach to reduce nitrification but the success of this strategy is contingent upon improving our limited understanding of BNIs mechanisms-of-action and degradation in the soil. We addressed this gap by investigating the previously unknown metabolic route through which a prominent class of aromatic BNIs known as phenylpropanoid methyl esters (PPMEs) are catabolized. While neither transcriptomics (RNAseq) or high-throughput functional genomics (RB-TnSeq) methods reduced the genetic search space for pathway discovery into a tenable number of genes, the combination of narrowed the search space to a collection of 4 proteins of unknown function. Using genetic and biochemical analyses we found that two previously uncharacterized enzymes, including a novel phenylpropanoid methyl esterase, funnel PPMEs into an established phenylpropanoid catabolism pathway. Transfer of these two enzymes into bacteria capable of using other phenylpropanoids use of PPMEs as carbon sources. This work both provided insight into BNI catabolism and is the first step towards development of modelin vivoplant-microbe systems for studying BNI mechanisms under well controlled conditions.
Mapping the genomic landscape of multidrug resistance inPlasmodium falciparumand its impact on parasite fitness
Authors: Mok Sachel , Yeo Tomas , Hong Davin , Shears Melanie J. , Ross Leila S. , Ward Kurt E. , Dhingra Satish K. , Kanai Mariko , Bridgford Jessica L. , Tripathi Abhai K. , Mlambo Godfree , Burkhard Anna Y. , Fairhurst Kate J. , Gil-Iturbe Eva , Park Heekuk , Rozenberg Felix D. , Kim Jonathan , Mancia Filippo , Quick Matthias , Uhlemann Anne-Catrin , Sinnis Photini , Fidock David A. 
Published: June 2023

AbstractDrug-resistantPlasmodium falciparumparasites have swept across Southeast Asia and now threaten Africa. By implementing aP. falciparumgenetic cross using humanized mice, we report the identification of key determinants of resistance to artemisinin (ART) and piperaquine (PPQ) in the dominant Asian KEL1/PLA1 lineage. We mappedk13as the central mediator of ART resistance and identified secondary markers. Applying bulk segregant analysis, quantitative trait loci mapping and gene editing, our data reveal an epistatic interaction between mutant PfCRT and multicopy plasmepsins 2/3 in mediating high-grade PPQ resistance. Susceptibility and parasite fitness assays implicate PPQ as a driver of selection for KEL1/PLA1 parasites. Mutant PfCRT enhanced susceptibility to lumefantrine, the first-line partner drug in Africa, highlighting a potential benefit of opposing selective pressures with this drug and PPQ. We also identified that the ABCI3 transporter can operate in concert with PfCRT and plasmepsins 2/3 in mediating multigenic resistance to antimalarial agents.
Negative feedback on Retinoic Acid by Brachyury guides gastruloid symmetry-breaking
Authors: Hennessy Meagan J. , Fulton Timothy , Turner David A. , Steventon Ben 
Published: June 2023

AbstractEstablishment of the vertebrate body plan requires a combination of extra-embryonic signalling to establish morphogen gradients, and an underlying self-assembly mechanism that contributes to pattern regulation and robustness. Gastruloids are aggregates of mouse embryonic stem cells that break morphological symmetry and polariseBrachyury(Bra) expression in the absence of extra-embryonic signals. However, the mechanism by which symmetry breaking occurs is not yet known. During gastrulation and body axis elongation, retinoic acid (RA) andCyp26a1are polarised along the anteroposterior axis, and this is critical for balancing the decision of cells to self-renew or differentiate. We found that symmetry-breaking in gastruloids is coincident with the separation ofAldh1a2andCyp26a1expression, and that feedback fromBrais critical for maintaining polarisedCyp26a1gene expression in the gastruloid posterior region. Furthermore, we reveal a short temporal window where RA signalling can negatively influence bothBraandCyp26a1expression. These observations lead us to suggest a mechanism of how initial gastruloid patterning, subsequent elongation, and evolving network topologies can create defined boundaries of RA signalling that permits proper axial patterning and gastruloid growth.
Silk Road Revealed: Mechanism of silk fibre formation inBombyx mori
Authors: Moreno-Tortolero R.O. , Luo Y. , Parmeggiani F. , Skaer N. , Walker R. , Serpell L. , Holland C. , Davis S.A. 
Published: June 2023

AbstractThe transition of silk fibroin from liquid to solid is fundamental to silk-fibre production and key to the superior materials properties of native silks. Here we discover that the fibroin heavy chain from the silkworm mothBombyx morifolds into a novel β-solenoid structure, where the N-terminal domain (NTD) promotes higher-order oligomerization driven by pH reduction. These findings elucidate the complex rheological behaviour of silk and the liquid crystalline textures within the silk gland. We also find that NTD undergoes hydrolysis during standard regeneration, explaining differences between native and regenerated silk feedstocks. Overall, this study establishes a fibroin heavy chain fold, which could be relevant for other similar proteins, and explains mechanistically its liquid-to-solid transition, driven by pH reduction and stress.One sentence summaryThis study redefines the molecular structure of fibroin heavy chain and its role in the transition from solution to fibre.
Imaging membrane damage in ferroptosis and necrosis by wash-free fluorogenic chemical probes
Authors: Mauker Philipp , Beckmann Daniela , Kitowski Annabel , Heise Constanze , Wientjens Chantal , Davidson Andrew J. , Wood Will , Wilhelm Christoph , Thorn-Seshold Julia , Misgeld Thomas , Kerschensteiner Martin , Thorn-Seshold Oliver 
Published: June 2023

ABSTRACTSelectively labelling cells with damaged membranes is needed in contexts as simple as identifying dead cells in culture, or as complex as imaging membrane barrier functionalityin vivo. The commonly used dyes are permanently coloured/fluorescent dyes that are simply excluded by intact membranes, but to achieve good image contrast therefore requires removing their extracellular signal by washing or background subtraction, which are not possiblein vivo. Here, we develop fluorogenic probes which sensitively and selectively reveal damaged cells, without needing washing steps since their fluorescence turns on from near-zero background. From a set of novel fluorogenic probes impermeabilised by sulfonations along different vectors, we identify a specific disulfonated fluorogenic scaffold that enters cells only upon membrane damage, where it is enzymatically activated to mark them. The esterase probeiPS-FS2is a reliable tool to reveal live cells that have been permeabilised by biological, biochemical, or physical membrane damage; and it can be used in multicolour microscopy. We confirm the modularity of this approach by also adapting it for redox-unmasked cell-excluded probes with improved hydrolytic stability. This scaffold-based design thus provides tools for wash-freein vivoimaging of membrane damage, which is relevant across many pathologies. The insightss gained from these probes should also be translatable to damage-targeted prodrugs, for selective therapy of membrane-compromised cells.Abstract Figure
De novo design of modular protein hydrogels with programmable intra- and extracellular viscoelasticity
Authors: Mout Rubul , Bretherton Ross C. , Decarreau Justin , Lee Sangmin , Edman Natasha I. , Ahlrichs Maggie , Hsia Yang , Sahtoe Danny D. , Ueda George , Gregorio Nicole , Sharma Alee , Schulman Rebecca , DeForest Cole A. , Baker David 
Published: June 2023

AbstractRelating the macroscopic properties of protein-based materials to their underlying component microstructure is an outstanding challenge. Here, we exploit computational design to specify the size, flexibility, and valency ofde novoprotein building blocks, as well as the interaction dynamics between them, to investigate how molecular parameters govern the macroscopic viscoelasticity of the resultant protein hydrogels. We construct gel systems from pairs of symmetric protein homo-oligomers, each comprising 2, 5, 24, or 120 individual protein components, that are crosslinked either physically or covalently into idealized step-growth biopolymer networks. Through rheological assessment and molecular dynamics (MD) simulation, we find that the covalent linkage of multifunctional precursors yields hydrogels whose viscoelasticity depends on the crosslink length between the constituent building blocks. In contrast, reversibly crosslinking the homo-oligomeric components with a computationally designed heterodimer results in non-Newtonian biomaterials exhibiting fluid-like properties under rest and low shear, but shear-stiffening solid-like behavior at higher frequencies. Exploiting the unique genetic encodability of these materials, we demonstrate the assembly of protein networks within living mammalian cells and showviafluorescence recovery after photobleaching (FRAP) that mechanical properties can be tuned intracellularly, in correlation with matching formulations formed extracellularly. We anticipate that the ability to modularly construct and systematically program the viscoelastic properties of designer protein-based materials could have broad utility in biomedicine, with applications in tissue engineering, therapeutic delivery, and synthetic biology.SignificanceProtein-based hydrogels have many applications in cellular engineering and medicine. Most genetically encodable protein hydrogels are made from naturally harvested proteins or protein-polymer hybrid constructs. Here we describede novoprotein hydrogels and systematically investigate the impact of microscopic properties of the building blocks (e.g., supramolecular interaction, valencies, geometries, flexibility) on the resultant macroscopic gel mechanics, both intra-and extracellularly. Thesede novosupramolecular protein assemblies, whose properties can be tuned from solid gels to non-Newtonian fluids, provide expanded opportunities for applications in synthetic biology and medicine.
Gel-assisted mass spectrometry imaging
Authors: Chan Yat Ho , Pathmasiri Koralege C. , Pierre-Jacques Dominick , Cologna Stephanie M. , Gao Ruixuan 
Published: June 2023

AbstractCompatible with label-free detection and quantification, mass spectrometry imaging (MSI) is a powerful tool for spatial investigation of biomolecules in intact specimens. Yet, the spatial resolution of MSI is limited by the method’s physical and instrumental constraints, which often preclude it from single-cell and subcellular applications. By taking advantage of the reversible interaction of analytes with superabsorbent hydrogels, we developed a sample preparation and imaging workflow named Gel-Assisted Mass Spectrometry Imaging (GAMSI) to overcome these limits. With GAMSI, the spatial resolution of lipid and protein MALDI-MSI can be enhanced severalfold without changing the existing mass spectrometry hardware and analysis pipeline. This approach will further enhance the accessibility to (sub)cellular-scale MALDI-MSI-based spatial omics.