bluuebunny/crossref_metadata_2025_split huggingface dataset:
Distinct lung cell signatures define the temporal evolution of diffuse alveolar damage in fatal COVID-19
Authors: Milross Luke , Hunter Bethany , McDonald David , Merces George , Thompson Amanda , Hilkens Catharien M.U. , Wills John , Rees Paul , Jiwa Kasim , Cooper Nigel , Majo Joaquim , Ashwin Helen , Duncan Christopher J.A. , Kaye Paul M. , Bayraktar Omer Ali , Filby Andrew , Fisher Andrew J. 
Published: May 2023

AbstractBackgroundLung damage in severe COVID-19 is highly heterogeneous however studies with dedicated spatial distinction of discrete temporal phases of diffuse alveolar damage (DAD) and alternate lung injury patterns are lacking. Existing studies have also not accounted for progressive airspace obliteration in cellularity estimates. We used an imaging mass cytometry (IMC) analysis with a novel airspace correction step to more accurately identify the cellular immune response that underpins the heterogeneity of severe COVID-19 lung disease.MethodsLung tissue was obtained at post-mortem from severe COVID-19 deaths. Pathologist-selected regions of interest (ROIs) were chosen by light microscopy representing the patho-evolutionary spectrum of DAD and alternate disease phenotypes were selected for comparison. Architecturally normal SARS-CoV-2-positive lung tissue and tissue from SARS-CoV-2-negative donors served as controls. ROIs were stained for 40 cellular protein markers and ablated using IMC before segmented cells were classified. Cell populations corrected by ROI airspace and their spatial relationships were compared across lung injury patterns.ResultsForty patients (32M:8F, age:22-98), 345 ROIs and >900k single cells were analysed. DAD progression was marked by airspace obliteration and significant increases in mononuclear phagocytes (MnPs), T and B lymphocytes and significant decreases in alveolar epithelial and endothelial cells. Neutrophil populations proved stable overall although several interferon-responding subsets demonstrated expansion. Spatial analysis revealed immune cell interactions occur prior to microscopically appreciable tissue injury.ConclusionsThe immunopathogenesis of severe DAD in COVID-19 lung disease is characterised by sustained increases in MnPs and lymphocytes with key interactions occurring even prior to lung injury is established.
PiE: An open-source pipeline for home cage behavioral analysis
Authors: Benedict Jessie , Cudmore Robert H 
Published: May 2023

AbstractOver the last two decades a growing number of neuroscience labs are conducting behavioral assays in rodents. The equipment used to collect this behavioral data must effectively limit environmental and experimenter disruptions, to avoid confounding behavior data. Proprietary behavior boxes are expensive, offer limited compatible sensors, and constrain analysis with closed-source hardware and software. Here, we introduce PiE, an open-source, end-to-end, user-configurable, scalable, and inexpensive behavior assay system. The PiE system includes the custom-built behavior box to hold a home cage, as well as software enabling continuous video recording and individual behavior box environmental control. To limit experimental disruptions, the PiE system allows the control and monitoring of all aspects of a behavioral experiment using a remote web browser, including real-time video feeds. To allow experiments to scale up, the PiE system provides a web interface where any number of boxes can be controlled, and video data easily synchronized to a remote location. For the scoring of behavior video data, the PiE system includes a standalone desktop application that streamlines the blinded manual scoring of large datasets with a focus on quality control and assay flexibility. The PiE system is ideal for all types of behavior assays in which video is recorded. Users are free to use individual components of this setup independently, or to use the entire pipeline from data collection to analysis. Alpha testers have included scientists without prior coding experience. An example pipeline is demonstrated with the PiE system enabling the user to record home cage maternal behavior assays, synchronize the resulting data, conduct blinded scoring, and import the data into R for data visualization and analysis.
A disease-associated gene desert orchestrates macrophage inflammatory responses via ETS2
Authors: Stankey CT , Bourges C , Turner-Stokes T , Piedade AP , Palmer-Jones C , Papa I , Dos Silva dos Santos M , Randzavola LO , Speidel L , Parkes EC , Edwards W , Rochford AP , Murray CD , MacRae JI , Skoglund P , Wallace C , Cader MZ , Thomas DC , Lee JC 
Published: May 2023

AbstractIncreasing global rates of autoimmune and inflammatory disease present a burgeoning threat to human health1. This is compounded by the limited efficacy of available treatments1and high failure rates during drug development2– underscoring an urgent need to better understand disease mechanisms. Here we show how genetics could address this challenge. By investigating an intergenic haplotype on chr21q22, independently linked to inflammatory bowel disease (IBD), ankylosing spondylitis, primary sclerosing cholangitis and Takayasu’s arteritis3–6, we discover that the causal gene,ETS2, is a master regulator of inflammatory responses in human macrophages and delineate how the risk haplotype increasesETS2expression. Genes regulated by ETS2 were prominently expressed in affected tissues from chr21q22-associated diseases and more enriched for IBD GWAS hits than almost all previously described pathways. OverexpressingETS2in resting macrophages produced an activated effector state that phenocopied intestinal macrophages from IBD7, with upregulation of multiple drug targets including TNFα and IL-23. Using a database of cellular signatures8, we identify drugs that could modulate this pathway and validate the potent anti-inflammatory activity of one class of small moleculesin vitroandex vivo. Together, this highlights the potential for common genetic associations to improve both the understanding and treatment of human disease.
Conserved cardiolipin-mitochondrial ADP/ATP carrier interactions assume distinct structural and functional roles that are clinically relevant
Authors: Senoo Nanami , Chinthapalli Dinesh K. , Baile Matthew G. , Golla Vinaya K. , Saha Bodhisattwa , Ogunbona Oluwaseun B. , Saba James A. , Munteanu Teona , Valdez Yllka , Whited Kevin , Chorev Dror , Alder Nathan N. , May Eric R. , Robinson Carol V. , Claypool Steven M. 
Published: May 2023

SummaryThe mitochondrial phospholipid cardiolipin (CL) promotes bioenergetics via oxidative phosphorylation (OXPHOS). Three tightly bound CLs are evolutionarily conserved in the ADP/ATP carrier (AAC in yeast; adenine nucleotide translocator, ANT in mammals) which resides in the inner mitochondrial membrane and exchanges ADP and ATP to enable OXPHOS. Here, we investigated the role of these buried CLs in the carrier using yeast Aac2 as a model. We introduced negatively charged mutations into each CL-binding site of Aac2 to disrupt the CL interactions via electrostatic repulsion. While all mutations disturbing the CL-protein interaction destabilized Aac2 monomeric structure, transport activity was impaired in a pocket-specific manner. Finally, we determined that a disease-associated missense mutation in one CL-binding site in ANT1 compromised its structure and transport activity, resulting in OXPHOS defects. Our findings highlight the conserved significance of CL in AAC/ANT structure and function, directly tied to specific lipid-protein interactions.
Elucidating the structural basis for ligand binding and translocation in conserved insect odorant receptor co-receptors
Authors: Pacalon Jody , Audic Guillaume , Magnat Justine , Philip Manon , Golebiowski Jérôme , Moreau Christophe J. , Topin Jérémie 
Published: May 2023

AbstractIn numerous insects, the olfactory receptor family forms a unique class of heteromeric cation channels. Recent progress in resolving the odorant receptor structures offers unprecedented opportunities for deciphering their molecular mechanisms of ligand recognition. Unexpectedly, these structures in apo or ligand-bound states did not reveal the pathway taken by the ligands between the extracellular space and the deep internal cavities. By combining molecular modeling with electrophysiological recordings, we identified amino acids involved in the dynamic entry pathway and the binding of VUAA1 toDrosophila melanogaster’s odorant receptor co-receptor (Orco). Our results provide new evidence for the exact location of the agonist binding site and a detailed and original mechanism of ligand translocation controlled by a network of conserved residues. These findings would explain the particularly high selectivity of Orcos for their ligands.
CRISPR/Cas9-mediated mutagenesis of the Asian Citrus Psyllid,Diaphorina citri
Authors: Chaverra-Rodriguez Duverney , Bui Michelle , Gilleland Cody L. , Rasgon Jason L. , Akbari Omar S. 
Published: May 2023

AbstractThe most devastating disease affecting the global citrus industry is Huanglongbing (HLB), caused by the pathogenCandidatus Liberibacter asiaticus. HLB is primarily spread by the insect vectorDiaphorina citri(Asian Citrus Psyllid). To counteract the rapid spread of HLB byD. citri, traditional vector control strategies such as insecticide sprays, the release of natural predators, and mass introductions of natural parasitoids are used. However, these methods alone have not managed to contain the spread of disease. To further expand the available tools forD. citricontrol via generating specific modifications of theD. citrigenome, we have developed protocols for CRISPR/Cas9-based genetic modification. Until now, genome editing inD. citrihas been challenging due to the general fragility and size ofD.citrieggs. Here we present optimized methods for collecting and preparing eggs to introduce the Cas9 ribonucleoprotein (RNP) into early embryos and alternative methods (ReMOT Control) for injecting RNP into the hemocoel of adult females for ovarian transduction. Using these methods, we have generated visible somatic mutations, indicating their suitability for gene editing inD. citri. These methods represent the first steps towards advancingD. citriresearch in preparation for future genetic-based systems for controlling HLB.
B. subtilisMutS2 splits stalled ribosomes into subunits without mRNA cleavage
Authors: Park Esther , Mackens-Kiani Timur , Berhane Rebekah , Esser Hanna , Erdenebat Chimeg , Burroughs A. Maxwell , Berninghausen Otto , Aravind L. , Beckmann Roland , Green Rachel , Buskirk Allen R. 
Published: May 2023

AbstractStalled ribosomes are rescued by pathways that recycle the ribosome and target the nascent polypeptide for degradation. InE. coli, these pathways are triggered by ribosome collisions through recruitment of SmrB, a nuclease that cleaves the mRNA. InB. subtilis, the related protein MutS2 was recently implicated in ribosome rescue. Here we show that MutS2 is recruited to collisions by its SMR and KOW domains and reveal the interaction of these domains with collided ribosomes by cryo-EM. Using a combination ofin vivoandin vitroapproaches, we show that MutS2 uses its ABC ATPase activity to split ribosomes, targeting the nascent peptide for degradation by the ribosome quality control pathway. Notably, we see no evidence of mRNA cleavage by MutS2, nor does it promote ribosome rescue by tmRNA as SmrB cleavage does inE. coli. These findings clarify the biochemical and cellular roles of MutS2 in ribosome rescue inB. subtilisand raise questions about how these pathways function differently in various bacteria.
Structural basis ofγ-chain family receptor sharing at the membrane level
Authors: Cai Tiantian , Lenoir Capello Rachel , Pi Xiong , Wu Hao , Chou James J. 
Published: May 2023

AbstractThe common γ-chain (γc) family of cytokine receptors, including interleukin (IL)-2, IL-4, IL-7, IL-9, IL-15, and IL-21 receptors, are activated upon engagement with the common γc receptor in ligand dependent manner. Sharing of γc by the IL receptors (ILRs) is thought to be achieved by concomitant binding of γc and ILR ectodomains to a cytokine. Here, we found that direct interactions between the transmembrane domain (TMD) of γc and those of the ILRs are also required for receptor activation, and remarkably, the same γc TMD can specifically recognize multiple ILR TMDs of diverse sequences. Heterodimer structures of γc TMD bound to the TMDs of IL-7R and IL-9R, determined in near lipid bilayer environment, reveal a conserved knob-into-hole mechanism of recognition that mediates receptor sharing within the membrane. Functional mutagenesis data indicate the requirement of the heterotypic interactions of TMDs in signaling, which could explain disease mutations within the receptor TMDs.One-Sentence SummaryThe transmembrane anchors of interleukin receptors of the gamma-chain family are critical for receptor sharing and activation.
Lipid modification of DNA nanocages enhances cellular uptake, migration, andin vivouptake
Authors: Kansara Krupa , Singh Ramesh , Yadav Pankaj , Kumar Ashutosh , Bhatia Dhiraj 
Published: May 2023

AbstractThe extraordinary self-assembling nature of DNA nanostructures and high functionality enables the formulation of DNA nanostructures with multiple chemical and biological molecules. How the whole organisms in native as well as modified; and how stable they are inside take up exactly these modified DNA nanostructures the organisms still remains to be explored. Here we report the fabrication and evaluation of a new conjugate of a cationic lipid, N-[one-(two, 3-dioleyloxy) propyl]-N, N, N-trimethylammonium chloride (DOTMA) and DNA tetrahedron nanostructure (TdN) for the enhanced uptake, stability, bioimaging, and biotherapeutics in cells and zebrafish (Danio rerio) eleuthero embryos as a model organism. We summarise the enhanced uptake potential of TdN-DOTMA conjugate for futuristic biomedical applications such as drug delivery, bioimaging, biosensing, and therapeutics.
Autoacetylation-mediated phase separation of TIP60 is critical for its functions
Authors: Dubey Shraddha , Gupta Himanshu , Gupta Ashish 
Published: May 2023

ABSTRACTTIP60 is an important lysine acetyl transferase protein that participates in various essential cellular activities by catalyzing the post-translational acetylation of lysine residues on histones and various non-histone protein substrates. TIP60 typically localizes to the nucleus in a punctate foci pattern, although defining factors and mechanisms regulating the assembly of TIP60 foci and their spatial distribution inside the nucleus are not understood. In the present study, we report that TIP60 can undergo phase separation to form liquid like droplets in the nuclear compartment, which is facilitated by the presence of an intrinsically disordered region (IDR) located between its chromodomain and catalytic domain. Importantly, we identified that autoacetylation on lysine 187, located within the IDR region of TIP60, is important for nuclear localization, oligomer formation and phase separation. Finally, we observed that the phase separation of TIP60 promotes its interaction with its partner proteins and actively contribute to its cellular functions.
Combinatorial quantification of 5mC and 5hmC at individual CpG dyads and the transcriptome in single cells reveals modulators of DNA methylation maintenance fidelity
Authors: Chialastri Alex , Sarkar Saumya , Schauer Elizabeth E. , Lamba Shyl , Dey Siddharth S. 
Published: May 2023

AbstractTransmission of 5-methylcytosine (5mC) from one cell generation to the next plays a key role in regulating cellular identity in mammalian development and diseases. While recent work has shown that the activity of DNMT1, the protein responsible for the stable inheritance of 5mC from mother to daughter cells, is imprecise; it remains unclear how the fidelity of DNMT1 is tuned in different genomic and cell state contexts. Here we describe Dyad-seq, a method that combines enzymatic detection of modified cytosines with nucleobase conversion techniques to quantify the genome-wide methylation status of cytosines at the resolution of individual CpG dinucleotides. We find that the fidelity of DNMT1-mediated maintenance methylation is directly related to the local density of DNA methylation, and for genomic regions that are lowly methylated, histone modifications can dramatically alter the maintenance methylation activity. Further, to gain deeper insights into the methylation and demethylation turnover dynamics, we extended Dyad-seq to quantify all combinations of 5mC and 5-hydroxymethylcytosine (5hmC) at individual CpG dyads to show that TET proteins preferentially hydroxymethylate only one of the two 5mC sites in a symmetrically methylated CpG dyad rather than sequentially convert both 5mC to 5hmC. To understand how cell state transitions impact DNMT1-mediated maintenance methylation, we scaled the method down and combined it with the measurement of mRNA to simultaneously quantify genome-wide methylation levels, maintenance methylation fidelity and the transcriptome from the same cell (scDyad&T-seq). Applying scDyad&T-seq to mouse embryonic stem cells transitioning from serum to 2i conditions, we observe dramatic and heterogenous demethylation and the emergence of transcriptionally distinct subpopulations that are closely linked to the cell-to-cell variability in loss of DNMT1-mediated maintenance methylation activity, with regions of the genome that escape 5mC reprogramming retaining high levels of maintenance methylation fidelity. Overall, our results demonstrate that while distinct cell states can substantially impact the genome-wide activity of the DNA methylation maintenance machinery, locally there exists an intrinsic relationship between DNA methylation density, histone modifications and DNMT1-mediated maintenance methylation fidelity that is independent of cell state.
Humanized nucleosomes reshape replication initiation and rDNA/nucleolar integrity in yeast
Authors: Lazar-Stefanita Luciana , Haase Max A. B. , Boeke Jef D. 
Published: May 2023

SummaryEukaryotic DNA wraps around histone octamers forming nucleosomes, which modulate genome function by defining chromatin environments with distinct accessibility. These well-conserved properties allowed “humanization” of the nucleosome core particle (NCP) inSaccharomyces cerevisiaeat high fitness costs. Here we studied nucleosome-humanized yeast-genomes to understand how species-specific chromatin affects nuclear organization and function. We found a size increase in human-NCP, linked to shorter free linker DNA, supporting decreased chromatin accessibility. 3-D humanized-genome maps showed increased chromatin compaction and defective centromere clustering, correlated with high chromosomal aneuploidy rate. Site-specific chromatin alterations were associated with lack of initiation of early origins of replication and dysregulation of the ribosomal (rDNA and rRNA) metabolism. This latter led to nucleolar fragmentation and rDNA-array instability, through a non-coding RNA dependent mechanism, leading to its extraordinary, but entirely reversible, intra-chromosomal expansion. Overall, our results reveal species-specific properties of the NCP that define epigenome function across vast evolutionary distances.HighlightsHumanized nucleosomes wrap 10 additional nucleotides, shortening free linker lengthHistone-humanized nucleosomes have increased occupancy for DNAHumanized nucleosomes potentially decrease chromatin accessibility by blocking-out free linker DNANucleosome humanization impedes DNA replication by affecting chromatin structure at originsHumanized nucleosomes reversibly destabilize the ribosomal DNA array and leads to massive intrachromosomal rDNA locus expansionHistone humanization disrupts rDNA silencing and leads to nucleolar fragmentation
A murine commensal protozoan relievesClostridium difficileinfection through regulating the arginine metabolism and the host intestinal immune response
Authors: Yang Huan , Wu Xiaoxiao , Zang Wanqing , Zhou Yuan , Li Xiao , Wang Liang , Cui Wenwen , Kou Yanbo , Wang Yugang , Gu Bing 
Published: May 2023

AbstractAntibiotic-induced dysbiosis is a key predisposing factor forClostridium difficileinfection (CDI), fecal microbiota transplantation (FMT) is recommended for treating CDI. However, the mechanisms remain unclear. Here, we uncover that one integral member of the murine gut microbiota, a commensal protozoan from mice,Tritrichomonas musculis(T. mu), that reduced intestinal damage by inhibiting the recruitment of neutrophil and secretion of IL-1β, and increased Th1 cell differentiation and secretion of IFN-γ, which increased the goblet cell and secretion of mucin to protect the intestinal mucosa. TheT. muupregulated the key enzymes of arginine metabolism iNOS, ASS, OTC and down-regulated ARG1 in CDI mice, resulting in an increase in arginine, citrulline and a decrease in ornithine, which worked together to regulate the host intestinal immune response and alleviate CDI. This work reveals the interaction mechanism between intestinal commensal eukaryotes and pathogenic bacteria, and also provide new ideas for treating CDI.
Distinct functional roles and connectivity rules for lower and higher order intracortical and pulvinar thalamocortical pathways in mouse visual cortex
Authors: Han Xu , Bonin Vincent 
Published: May 2023

SUMMARYFunctional specialization of cortical areas is a fundamental feature of brain organization and is critical for perception and behavior. Such an organization must depend on specialized connectivity between areas, yet the underlying wiring rules remain unclear. We characterized intracortical and thalamocortical pathways in the mouse visual cortex using neural tracing and functional imaging. We uncovered multiple structural-functional connectivity rules underlying the functional specialization of higher visual cortical areas (HVAs). Individual higher visual areas integrate specific cortical and thalamic inputs with distinct functional biases. Higher order Layer 2/3 and thalamocortical pathways show higher target specificity than feedforward intracortical pathways and might impart specific functional preferences to the recipient HVAs. In contrast, higher order Layer 5 pathways lacking specificity may contribute to the tuning diversity in the recipient HVAs. Altogether, this study reveals fundamental organization rules of long-range interareal connectivity that underlie the parallel modular organization of the visual cortex.HIGHLIGHTSHVAs AL, PM and A receive diverse and specific inputs from V1, HVA and LP pathwaysDensity of intracortical inputs correlates with similarity of tuning between visual areasTuning of HVA inputs correlates with HVA’s preferences and functional heterogeneityHVA output pathways differ in tuning homogeneity and target specificity