bluuebunny/crossref_metadata_2025_split huggingface dataset:
A subset of CD4+ effector memory T cells limit immunity to pulmonary viral infection and prevent tissue pathology via activation of latent TGFβ
Authors: McEntee CP , Houston S , Finlay CM , Rossi S , Liu G , Shaw TN , Casulli J , Fife M , Smedley C , Griffith TS , Pepper M , Hussell T , Hansbro PM , Schwartz J-M , Paidassi H , Travis MA 
Published: March 2023

AbstractA rapid immune response to pathogen re-exposure underpins immunological memory, with protection against divergent pathogens such as heterologous or novel viral strains requiring cross­reactive memory T cells. Understanding the pathways that control memory T cell function is therefore important for the rational design of viral vaccines and will aid the discovery of therapies to boost anti-viral immunity. Here, we identify a sub-population of memory T cells that limit secondary immune responses to viral re-infection, which is crucial in preventing host tissue damage. We show that a population of CD4+effector memory T (TEM) cells activate the important immunoregulatory cytokine TGFβ, via expression of an integrin, αvβ8. Integrin αvβ8 expression marks a transcriptionally distinct sub-population of CD4+TEM, enriched for anti-inflammatory pathways. Loss of integrin αvβ8 on murine CD4+TEM, but not Foxp3+regulatory T cells (TREG), led to exacerbated virus-specific CD8+T cell responses following secondary influenza A virus (IAV) infection, which was associated with enhanced viral clearance. However, although accelerating clearance, loss of integrin αvβ8 expression on CD4+TEMresulted in enhanced lung pathology following secondary IAV infection, which was completely reversed by adoptive transfer of αvβ8+CD4+TEMcells. These data highlight a new pathway by which a distinct CD4+memory T cell subset restrains anti-viral immunity to prevent host tissue damage during secondary viral infection. Such pathways could be targeted therapeutically to either boost memory T-cell-mediated immunity or restrain host tissue damage during viral infection.
Hub taxa are keystone microbes during early succession
Authors: Rawstern Amanda H. , Hernandez Damian J. , Afkhami Michelle E. 
Published: March 2023

AbstractMicroorganisms underpin numerous ecosystem processes and support biodiversity globally, yet we understand surprisingly little about what structures environmental microbiomes themselves. Combining culturing, sequencing, and microbial networks, we identified ‘central’ (highly-connected, hub taxa), ‘intermediate’ (moderately-connected), and ‘peripheral’ (weakly/un-connected) microbes and experimentally evaluated their effects on soil microbiome assembly during early succession. Our results demonstrate central early colonizers significantly (1) enhanced biodiversity, (2) increased recruitment of additional influential, hub taxa, and (3) shaped microbiome assembly trajectories. This work elucidates fundamental principles of network theory in microbial ecology and demonstrates for the first time in nature that central, hub microbes are keystones.
Single-cell RNA-sequencing of bronchoscopy specimens: development of a rapid, minimal-handling protocol
Authors: Gerayeli Firoozeh V , Milne Stephen , Yang Chen Xi , Li Xuan , Guinto Elizabeth , Yang Julia Shun-Wei , Cheung Chung Yan , Stach Tara R , Shaipanich Tawimas , Leung Janice M , Sin Don D 
Published: March 2023

AbstractSingle-cell RNA-sequencing (scRNA-seq) is an important tool for understanding disease pathophysiology, including airways diseases. Currently, the majority of scRNA-seq studies in airways diseases have used invasive methods (airway biopsy, surgical resection) which carry inherent risks and thus present a major limitation to scRNA-seq investigation of airway pathology. Bronchial brushing, where the airway mucosa is sampled using a cytological brush, is a viable, less invasive method of obtaining airway cells for scRNA-seq. Here we are describing the development of a rapid and minimal-handling protocol for preparing single cell suspensions from bronchial brush specimens for scRNA-seq. Our optimized protocol maximises cell recovery and cell quality, and may facilitate large-scale profiling of the airway transcriptome at single cell resolution.Lay abstractSingle-cell RNA-sequencing (scRNA-seq) measures the gene expression of individual cells, and may be useful for understanding disease processes. scRNA-seq may be used to investigate lung diseases, but using invasive methods such as biopsy or surgery limits our ability to conduct large research studies. Bronchial brushing, where a soft brush is used to collect cells from inside the lungs, is a safer method but we need a better way to isolate individual cells from the brush specimens. We developed a method that is faster and involves less handling of the specimens compared to other published methods. Our method may therefore be useful for conducting large scRNA-seq studies in lung diseases.
Host selection has stronger impact on leaf microbiome assembly compared to land-management practices
Authors: Singh Pankaj K. , Egidi Eleonora , Macdonald Catriona A. , Singh Brajesh K. 
Published: March 2023

AbstractPlant microbiome contribute directly to plant health and productivity but mechanisms that underpin plant microbiome assembly in different compartments (e.g. root, leaf) are not fully understood. Identifying environmental and management factors that affect plant microbiome assembly is important to advance understanding of fundamental ecological processes and harnessing microbiome for improved primary productivity and environmental sustainability. Irrigation and fertilization are two common management practices in Australian tree plantations, but little is known about the effects of these treatments on soil, plant host, and their microbiome. Here, we investigated the impact of a decade long irrigation, fertilization, and their combined application, on soil, plant traits and microbiome of aEucalyptus salignaplantation at the Hawkesbury Forest Experiment, Western Sydney University, Richmond, NSW. Microbial profiling of bulk soil, rhizosphere, root, and leaves was performed using amplicon sequencing 16S rDNA and ITS markers for bacteria and fungi, respectively, along with measurements of soil properties and plant traits. The results indicated that both management practices affected soil properties and soil and root microbiome significantly. Irrigation increased but fertilizer treatment reduced microbial alpha diversity. However, neither irrigation nor fertilizer treatment significantly impacted the leaf microbiome. Our findings imply that management practices impact soil edaphic factors, which in turn influence the below ground microbiome (soil and root). In addition, the leaf microbiome was distinct from soil and root microbiome, and a source tracker analysis suggested root and bulk soils only contributed to 53% and 10% OTUs of the leaf bacterial community, suggesting strong and sequential host selection of the leaf microbiome. In addition, management practices had limited impact on leaf traits and, consequently, the leaf microbiome maintained its distinct composition. These findings provide mechanistic evidence for ecological processes that drive plant microbiome assembly and indicate that host selection plays a more important role than management practices on leaf microbiome assembly.
Excitatory: inhibitory imbalance in Alzheimer’s disease is exacerbated by seizures with attenuation after rapamycin treatment in 5XFAD mice
Authors: Barbour AJ , Gourmaud S , Lancaster E , Li X , Stewart D , Irwin DJ , Talos DM , Jensen FE 
Published: March 2023

AbstractApproximately 22% of Alzheimer’s disease (AD) patients suffer from seizures, and the co-occurrence of seizures and epileptiform activity exacerbate AD pathology and related cognitive deficits. Hence seizures may be a targetable component of AD progression. As epileptogenesis is associated with changes in neuronal excitatory: inhibitory (E:I) balance, we hypothesized that decreased markers of inhibition relative to those of excitation would be present in AD patients and exacerbated further when seizures were a comorbidity. We similarly hypothesized that an E:I imbalance would be present in five times familial AD (5XFAD) mice and augmented following pentylenetetrazol (PTZ) seizure kindling. AD temporal cortical tissue from patients with or without seizure history and brain tissue from 5XFAD mice were examined for changes in several markers of E:I balance, including the inhibitory GABAAreceptor, the chloride cotransporters, sodium potassium chloride cotransporter 1 (NKCC1) and potassium chloride cotransporter 2 (KCC2), and the excitatory NMDA and AMPA type glutamate receptors. We found that AD patients had decreased GABAAreceptor subunits and those with comorbid seizures had worsened cognitive and functional scores, and increased in NKCC1/KCC2 ratios, indicative of depolarizing GABA responses. The E:I imbalance appears to occur early in the disease course, as patch clamp recordings from CA1 neurons in hippocampal slices from prodromal 5XFAD mice showed decreased GABAergic inhibitory transmission and increased intrinsic excitability. In addition, seizure induction in prodromal 5XFAD mice further dysregulated NKCC1/KCC2, and altered the excitatory AMPA glutamate receptor protein expression, with a reduction in GluA2 subunit, indicative of calcium permeable-receptors. Finally, we found that chronic treatment with the mTORC1 inhibitor, rapamycin, at doses we have previously shown to attenuate seizure-induced α-amyloid pathology and cognitive deficits, could reverse aspects of E:I imbalance in these mice. Our data demonstrate novel mechanisms of interaction between AD and epilepsy and indicate that FDA-approved mTOR inhibitors hold therapeutic promise for AD patients with a seizure history.
A novel qPCR-based technique for identifying avian sex: an illustration within embryonic craniofacial bone
Authors: Houchen Claire J. , Bergman-Gonzalez Maria , Bumann Erin E. 
Published: March 2023

AbstractSex is a biological variable important to consider in all biomedical experiments. However, analyzing sex differences in avian models can be challenging as the sexes are morphologically indistinguishable in most avian embryos. Unlike humans, female birds are the heterogametic sex with a Z and W chromosome. The female-specific W chromosome has previously been identified using species-specific polymerase chain reaction (PCR) techniques. We developed a novel quantitative real-time PCR (RT-qPCR) technique which amplifies the W chromosome gene histidine triad nucleotide binding protein W (HINTW) in chick, quail, and duck. We confirmed the accuracy of the single set ofHINTWRT-qPCR primers in all three species using species-specific PCR. Bone development-related gene expression was then analyzed by sex in embryonic lower jaws of duck and quail, as duck beak size is known to be sexually dimorphic while quail beak size is not. Trends towards sexual dimorphism were found in duck gene expression but not in quail, as expected. Our novelHINTWRT-qPCR technique to identify the sex of avian embryos is a useful tool for including sex as a biological variable in analysis of a variety of tissues and cells used in developmental biology research.
Unveiling causal regulatory mechanisms through cell-state parallax
Authors: Wu Alexander Po-Yen , Singh Rohit , Walsh Christopher , Berger Bonnie 
Published: March 2023

AbstractGenome-wide association studies (GWAS) identify numerous disease-linked genetic variants at noncoding genomic loci, yet therapeutic progress is hampered by the challenge of deciphering the regulatory roles of these loci in tissue-specific contexts. Single-cell multimodal assays that simultaneously profile chromatin accessibility and gene expression could predict tissue-specific causal links between noncoding loci and the genes they affect. However, current computational strategies either neglect the causal relationship between chromatin accessibility and transcription or lack variant-level precision, aggregating data across genomic ranges due to data sparsity. To address this, we introduce GrID-Net, a graph neural network approach that generalizes Granger causal inference to detect new causal locus–gene associations in graph-structured systems such as single-cell trajectories. Inspired by the principles of optical parallax, which reveals object depth from static snapshots, we hypothesized that causal mechanisms could be inferred from static single-cell snapshots by exploiting the time lag between epigenetic and transcriptional cell states, a concept we term “cell-state parallax.” Applying GrID-Net to schizophrenia (SCZ) genetic variants, we increased variant coverage by 36% and uncovered noncoding mechanisms that dysregulate 132 genes, including key potassium transporters such as KCNG2 and SLC12A6. Furthermore, we discovered evidence for the prominent role of neural transcription-factor binding disruptions in SCZ etiology. Our work not only provides a strategy for elucidating the tissue-specific impact of noncoding variants but also underscores the breakthrough potential of cell-state parallax in single-cell multiomics for discovering tissue-specific gene regulatory mechanisms.
The unique three-dimensional arrangement of Macrophage Galactose Lectin enablesE. coliLipoPolySaccharides recognition through two distinct interfaces
Authors: Abbas Massilia , Maalej Meriem , Nieto-Fabregat Ferran , Thépaut Michel , Kleman Jean-Philippe , Ayala Isabel , Molinaro Antonio , Simorre Jean-Pierre , Marchetti Roberta , Fieschi Franck , Laguri Cedric 
Published: March 2023

ABSTRACTLipoPolySaccharides are a hallmark of Gram-negative bacteria and their presence at the cell surface is key for bacterial integrity. As surface exposed components, they are recognized by immunity C-type lectin receptors present on Antigen Presenting Cells. Human Macrophage Galactose Lectin bindsE. colisurface that presents a specific glycan motif. Nevertheless, this high affinity interaction occurs regardless of the integrity of its canonical calcium-dependent glycan binding site. Nuclear Magnetic Resonance of MGL carbohydrate recognition domain and complete extracellular domain revealed a new glycan binding site opposite to the canonical site. A model of trimeric Macrophage Galactose Lectin was determined based on a combination of Small Angle X-ray scattering and Alphafold. A disulphide bond positions the Carbohydrate Recognition Domain perpendicular to the coiled-coil domain. This unique configuration for a C-type lectin orients the six glycan sites of MGL in an ideal position to bind LipoPolySaccharides at the bacterial surface with high avidity.
Systematic analyses of the resistance potential of drugs targeting SARS-CoV-2 main protease
Authors: Flynn Julia M. , Huang Qiu Yu J. , Zvornicanin Sarah N. , Schneider-Nachum Gily , Shaqra Ala M. , Yilmaz Nese Kurt , Moquin Stephanie A. , Dovala Dustin , Schiffer Celia A. , Bolon Daniel N.A. 
Published: March 2023

AbstractDrugs that target the main protease (Mpro) of SARS-CoV-2 are effective therapeutics that have entered clinical use. Wide-scale use of these drugs will apply selection pressure for the evolution of resistance mutations. To understand resistance potential in Mpro, we performed comprehensive surveys of amino acid changes that can cause resistance in a yeast screen to nirmatrelvir (contained in the drug Paxlovid), and ensitrelvir (Xocova) that is currently in phase III trials. The most impactful resistance mutation (E166V) recently reported in multiple viral passaging studies with nirmatrelvir showed the strongest drug resistance score for nirmatrelvir, while P168R had the strongest resistance score for ensitrelvir. Using a systematic approach to assess potential drug resistance, we identified 142 resistance mutations for nirmatrelvir and 177 for ensitrelvir. Among these mutations, 99 caused apparent resistance to both inhibitors, suggesting a strong likelihood for the evolution of cross-resistance. Many mutations that exhibited inhibitor-specific resistance were consistent with distinct ways that each inhibitor protrudes beyond the substrate envelope. In addition, mutations with strong drug resistance scores tended to have reduced function. Our results indicate that strong pressure from nirmatrelvir or ensitrelvir will select for multiple distinct resistant lineages that will include both primary resistance mutations that weaken interactions with drug while decreasing enzyme function and secondary mutations that increase enzyme activity. The comprehensive identification of resistance mutations enables the design of inhibitors with reduced potential of developing resistance and aids in the surveillance of drug resistance in circulating viral populations.
Genome-resolved metagenomics reveals abundant nitrate reducers and partitioning of nitrite usage within global oxygen deficient zones
Authors: Zhang Irene H. , Sun Xin , Jayakumar Amal , Fortin Samantha G. , Ward Bess B. , Babbin Andrew R. 
Published: March 2023

AbstractOxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially-mediated pathway proceeding stepwise from NO3−to N2. This process may be performed entirely by complete denitrifiers capable of all four steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes are primarily carried by complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. From 56 metagenomes spanning all three major ODZs, we use genome-resolved metagenomics to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 metagenome-assembled genomes presents the largest collection of pelagic ODZ microbes and reveals a clearer picture of the nitrogen cycling community within this environment.
No isolate, no problem: Using a novel insertion sequence PCR to link rats to human shigellosis cases in an underserved urban community
Authors: Ritchie Gordon , Leung Victor , Himsworth Chelsea G. , Byers Kaylee A. , Lee Lisa K.F. , Chorlton Samuel D. , Stefanovic Aleksandra , Romney Marc G. , Matic Nancy , Lowe Christopher F. 
Published: March 2023

AbstractIntroductionDuring an investigation into a cluster ofShigella flexneriserotype 2a cases in an underserved community, we assessed the relatedness of human and ratS. flexneriisolates utilizing a novel PCR targeting insertion sites (IS-PCR) of mobile elements in theShigellagenome characteristic of the cluster strain.MethodsWhole genome sequences ofS. flexneri(n=50) associated with the cluster were analyzed.de novogenome assemblies were analyzed by a Geneious V10.2.6 motif search, and 2 unique IS were identified in all humanShigellasequences of the local cluster. Hydrolysis probe PCR assays were designed to detect these sequences consisting of forward and reverse primers to amplify across each insertion site, and a hydrolysis probe spanning the insertion site. IS-PCR was performed for threeShigellaPCR-positive culture-negative rat intestine specimens from this community.ResultsBoth insertion sites were detected in thede novogenome assemblies of all clinicalS. flexneriisolates (n=50). Two of the three PCR-positive culture-negative rat samples were positive for both unique IS identified in the humanS. flexneriisolates, suggesting that the ratShigellaspp. strains were closely related to the human strains in the cluster. The cycle threshold (Ct) values were >35, indicating that the bacterial load was very low in the rat samples.ConclusionsTwo unique IS were identified in clinical isolates from a communityS. flexnericluster. Both IS targets were identified in PCR-positive (Shigellaspp.), culture-negative rat tissue and clinical isolates from humans, indicating relatedness.
3D Confinement-enabled Priming of Synaptic Activation Promotes Primary T Cell Expansion
Authors: Jiang Ruoyu , Chen Yu-Hsi , Parajuli Ritesh , Agrawal Anshu , Lee Abraham P. 
Published: March 2023

AbstractThe success of autologous cell therapy, which depends highly on T lymphocyte expansion efficiency, is often hindered by suboptimal interactions between T-cell receptors and peptide-MHC molecules. Here, we demonstrate 3D confinement-enabled priming of T cell–MHC immune synapse junctions based on cytoskeletal forces within minutes, which is 200-fold faster than conventional 24 h bulk shaking method. Using T cell–Dynabead binding skeletons in the starting culture, two- to six-fold greater T cell expansion was achieved over the conventional T cell expansion approach without inducing excessive cell exhaustion. Under 3D force-confinement, T-cell division (G1, S, and G2 phases) was increased to be twice as fast. Creating 3D T cell–Dynabead skeletons as the “booster” material enables highly efficient T cell expansion, without requiring complex surface modification of antigen-presenting cells. This method can be modularly adapted to existing T cell expansion processes for a wide range of applications including adoptive cell therapies.Teaser3D confinement-enabled priming of synaptic activation enables radically faster autologous cell production.
The Human Mitochondrial Genome Encodes for an Interferon-Responsive Host Defense Peptide
Authors: Rice MC , Imun M , Jung SW , Park CY , Kim JS , Lai RW , Barr CR , Son JM , Tor K , Kim E , Lu RJ , Cohen I , Benayoun BA , Lee C 
Published: March 2023

AbstractThe mitochondrial DNA (mtDNA) can trigger immune responses and directly entrap pathogens, but it is not known to encode for active immune factors. The immune system is traditionally thought to be exclusively nuclear-encoded. Here, we report the identification of a mitochondrial-encoded host defense peptide (HDP) that presumably derives from the primordial proto-mitochondrial bacteria. We demonstrate that MOTS-c (mitochondrial open reading frame from the twelve S rRNA type-c) is a mitochondrial-encoded amphipathic and cationic peptide with direct antibacterial and immunomodulatory functions, consistent with the peptide chemistry and functions of known HDPs. MOTS-c targetedE. coliand methicillin-resistantS. aureus(MRSA), in part, by targeting their membranes using its hydrophobic and cationic domains. In monocytes, IFNγ, LPS, and differentiation signals each induced the expression of endogenous MOTS-c. Notably, MOTS-c translocated to the nucleus to regulate gene expression during monocyte differentiation and programmed them into macrophages with unique transcriptomic signatures related to antigen presentation and IFN signaling. MOTS-c-programmed macrophages exhibited enhanced bacterial clearance and shifted metabolism. Our findings support MOTS-c as a first-in-class mitochondrial-encoded HDP and indicates that our immune system is not only encoded by the nuclear genome, but also by the co-evolved mitochondrial genome.