bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of recurrence of illness and adverse childhood experiences on effector, cytotoxic, and regulatory T cells, and cannabinoid receptor-bearing B cells in major depression, an autoimmune disorder
Authors: Maes Michael , Rachayon Muanpetch , Jirakran Ketsupar , Sughondhabirom Atapol , Sodsai Pimpayao 
Published: June 2023

AbstractBackgroundMajor depressive disorder (MDD) is characterized by increased T helper (Th)1 polarization, T cell activation (e.g., CD71+ and CD40L+), and cannabinoid receptor type 2 bearing CD20+ B cells; and lower T regulatory (Treg) numbers.AimsTo delineate the effects of adverse childhood experiences (ACEs) and recurrence of illness (ROI) on activated T and CB2-bearing B populations, and Tregs, including FoxP3+CD152+, FoxP3+GARP+, and FoxP3+CB1+ cells.MethodsWe measured ROI, ACEs, the number of activated T cells, Tregs, and CD20+CB2+ B cells, in 30 MDD patients and 20 healthy controls.ResultsA larger part of the variance in the depression phenome (40.8%) was explained by increased CD20+CB2+ and activated T cells, and lowered Tregs. ROI and lifetime suicidal behaviors were significantly and positively associated with CD20+CB2+, CD3+CD71+, CD3+CD40L+, CD4+CD71+, CD4+CD40L+, and CD4HLADR+ numbers. ROI was significantly correlated with CD8+CD40L+ numbers. The sum of ACEs was significantly associated with CD20+CB2+, CD3+CD40L+, CD4+40L+ numbers, T cell activation (positively) and Treg (inversely) indices. One replicable latent vector could be extracted from activated T cells, lifetime and current suicidal behaviors, number of depressive episodes, and severity of depression, and 48.8% of its variance was explained by ACEs.ConclusionsACE-induced activation of T effector and cytotoxic cells and B cells with autoimmune potential, coupled with lowered Treg numbers are a key component of depression. The findings indicate that increasing ROI, the phenome of depression and suicidal behaviors, are caused by autoimmune processes, which are the consequence of ACEs and increasing sensitization of immune responses.
Novel autoantibody targets identified in patients with autoimmune hepatitis (AIH) by PhIP-Seq reveals pathogenic insights
Authors: Klepper Arielle , Asaki James , Kung Andrew F. , Vazquez Sara E. , Bodansky Aaron , Mitchell Anthea , Mann Sabrina A. , Zorn Kelsey , Avila-Vargas Isaac , Kari Swathi , Tekeste Melawit , Castro Javier , Lee Briton , Duarte Maria , Khalili Mandana , Yang Monica , Wolters Paul , Price Jennifer , Perito Emily , Feng Sandy , Maher Jacquelyn J. , Lai Jennifer C. , Weiler-Normann Christina , Lohse Ansgar W. , DeRisi Joseph , Tana Michele 
Published: June 2023

AbstractBackground and AimsAutoimmune hepatitis (AIH) is a severe disease characterized by elevated immunoglobin levels. However, the role of autoantibodies in the pathophysiology of AIH remains uncertain.MethodsPhage Immunoprecipitation-Sequencing (PhIP-seq) was employed to identify autoantibodies in the serum of patients with AIH (n= 115), compared to patients with other liver diseases (metabolic associated steatotic liver disease (MASH)n= 178, primary biliary cholangitis (PBC),n= 26, or healthy controls,n= 94).ResultsLogistic regression using PhIP-seq enriched peptides as inputs yielded a classification AUC of 0.81, indicating the presence of a predictive humoral immune signature for AIH. Embedded within this signature were disease relevant targets, including SLA/LP, the target of a well-recognized autoantibody in AIH, disco interacting protein 2 homolog A (DIP2A), and the relaxin family peptide receptor 1 (RXFP1). The autoreactive fragment of DIP2A was a 9-amino acid stretch nearly identical to the U27 protein of human herpes virus 6 (HHV-6). Fine mapping of this epitope suggests the HHV-6 U27 sequence is preferentially enriched relative to the corresponding DIP2A sequence. Antibodies against RXFP1, a receptor involved in anti-fibrotic signaling, were also highly specific to AIH. The enriched peptides are within a motif adjacent to the receptor binding domain, required for signaling and serum from AIH patients positive for anti-RFXP1 antibody was able to significantly inhibit relaxin-2 singling. Depletion of IgG from anti-RXFP1 positive serum abrogated this effect.ConclusionsThese data provide evidence for a novel serological profile in AIH, including a possible functional role for anti-RXFP1, and antibodies that cross react with HHV6 U27 protein.
Choroid plexus defects in Down syndrome brain organoids enhance neurotropism of SARS-CoV-2
Authors: Shaker Mohammed R. , Slonchak Andrii , Al-mhanawi Bahaa , Morrison Sean D. , Sng Julian D. J. , Cooper-White Justin , Khromykh Alexander A. , Wolvetang Ernst J. 
Published: June 2023

ABSTRACTWhy individuals with Down Syndrome (DS, trisomy 21) are particularly susceptible to SARS CoV-2 induced neuropathology remains largely unclear. Since the choroid plexus (CP) performs important barrier and immune-interface functions, secretes the cerebrospinal fluid and strongly expresses the ACE2 receptor and the chromosome 21 encoded TMPRSS2 protease, we hypothesized that the CP could play a role in establishing SARS-CoV-2 infection in the brain. To investigate the role of the choroid plexus in SARS-CoV-2 central nervous system infection in DS, we established a new type of brain organoid from DS and isogenic euploid control iPSC that consists of a core of appropriately patterned functional cortical neuronal cell types that is surrounded by a patent and functional choroid plexus (CPCOs). Remarkably, DS-CPCOs not only recapitulated abnormal features of DS cortical development but also revealed defects in ciliogenesis and epithelial cell polarity of the developing choroid plexus. We next demonstrate that the choroid plexus layer facilitates SARS-CoV-2 replication and infection of cortical neuronal cells, and that this is increased in DS-CPCOs. We further show that inhibition of TMPRSS2 and Furin activity inhibits SARS-CoV-2 replication in DS CPCOs to the level observed in euploid organoids. We conclude that CPCOs are a useful model for dissecting the role of the choroid plexus in euploid and DS forebrain development and enables screening for therapeutics that can inhibit SARS-CoV-2 induced neuro-pathogenesis.
Simultaneous LC-MS determination of glucose regulatory peptides secreted by stem cell-derived islet organoids
Authors: Olsen Christine , Wang Chencheng , Aizenshtadt Aleksandra , Abadpour Shadab , Lundanes Elsa , Skottvoll Frøydis Sved , Golovin Alexey , Busek Mathias , Krauss Stefan , Scholz Hanne , Wilson Steven Ray 
Published: June 2023

AbstractFor studying stem cell-derived islet organoids (SC-islets) in an organ-on-chip platform, we have developed a reversed phase liquid chromatography tandem mass spectrometry (RPLC-MS/MS) method allowing for simultaneous determination of insulin, somatostatin-14, and glucagon, with improved matrix robustness compared to earlier methodology. Combining phenyl/hexyl-C18 separations using 2.1 mm inner diameter LC columns and triple quadrupole mass spectrometry, identification and quantification were secured with negligible variance in retention time and quantifier/qualifier ratios, negligible levels of carry-over (< 2%), and sufficient precision (± 10% RSD) and accuracy (± 15% relative error) with and without use of internal standard. The here developed RPLC-MS/MS method showed that the SC-islets have an insulin response dependent on glucose concentration, and the SC-islets produce and release somatostatin-14 and glucagon. The RPLC-MS/MS method for these peptide hormones was compatible with an unfiltered off-line sample collection from SC-islets cultivated on a pump-less, recirculating organ-on-chip (rOoC) platform. The SC-islets background secretion of insulin was not significantly different on the rOoC device compared to a standard cell culture well-plate. Taken together, RPLC-MS/MS is well suited for multi-hormone measurements of SC-islets on an organ-on-chip platform.
The influence of social lifestyles on host-microbe symbioses in the bees
Authors: Mee Lauren , Barribeau Seth M 
Published: June 2023

1AbstractMicrobiomes are increasingly recognised as critical for the health of an organism. In eusocial insect societies, frequent social interactions allow for high fidelity transmission of microbes across generations, leading to closer host-microbe coevolution. The microbial communities of bees with different social lifestyles are less well studied, and few comparisons have been made between taxa that vary in social structure. To address this gap, we leveraged a cloud-computing resource and publicly available transcriptomic data to conduct a survey of microbial diversity in bee samples from a variety of social lifestyles and taxa. We consistently recover the core microbes of well-studied corbiculates, supporting this method’s ability to accurately characterise microbial communities. We find that the bacterial communities of bees are influenced by host location, phylogeny, and social lifestyle, although no clear effect was found for fungal or viral microbial communities. Bee genera with more complex societies tend to harbour more diverse microbes, withWolbachiadetected more commonly in solitary tribes. We present the first description of the microbiota of Euglossine bees and find that they do not share the “corbiculate” core microbiome. Notably, we find that bacteria with known anti-pathogenic properties are present across social bee genera, suggesting that symbioses that enhance host immunity are important with higher sociality. Our approach provides an inexpensive means of exploring microbiomes of a given taxa and identifying avenues for further research. These findings contribute to our understanding of the relationships between bees and their associated microbial communities, highlighting the importance of considering microbiome dynamics in investigations of bee health.
Tetraspanins fromOpisthorchis viverrinistimulate cholangiocyte migration and inflammatory cytokine production
Authors: Ruangsuwast Apisit , Smout Michael J. , Brindley Paul J. , Loukas Alex , Laha Thewarach , Chaiyadet Sujittra 
Published: June 2023

AbstractThe liver flukeOpsithorchis viverrinisecretes extracellular vesicles (EVs) bearing CD63-like tetraspanins on their surface. Fluke EVs are actively internalized by host cholangiocytes in the bile ducts, where they drive pathology and promote neoplasia through induction of cellular proliferation and secretion of inflammatory cytokines. We investigated the effects of tetraspanins of the CD63 superfamily by co-culturing recombinant forms of the large extracellular loop (LEL) ofO. viverrinitetraspanin-2 (rLEL-Ov-TSP-2) and tetraspanin-3 (rLEL-Ov-TSP-3) with non-cancerous human bile duct (H69) and cholangiocarcinoma (CCA, M213) cell lines. The results showed that cell lines co-cultured with excretory/secretory products from adultO. viverrini(Ov-ES) underwent significantly increased cell proliferation at 48 hours but not 24 hours compared to untreated control cells (P<0.05), whereas rLEL-Ov-TSP-3 co-culture resulted in significantly increased cell proliferation at both 24 hr (P<0.05) and 48 hr (P<0.01) time points. In like fashion, H69 cholangiocytes co-cultured with bothOv-ES and rLEL-Ov-TSP-3 underwent significantly elevatedIl-6andIl-8gene expression for at least one of the time points assessed. Finally, both rLEL-Ov-TSP-and rLEL-Ov-TSP-3 significantly enhanced migration of both M213 and H69 cell lines. These findings indicated thatO. viverriniCD63 family tetraspanins can promote a cancerous microenvironment by enhancing innate immune responses and migration of biliary epithelial cells.
BERTrand - peptide:TCR binding prediction using Bidirectional Encoder Representations from Transformers augmented with random TCR pairing
Authors: Myronov Alexander , Mazzocco Giovanni , Król Paulina , Plewczynski Dariusz 
Published: June 2023

AbstractMotivationThe advent of T cell receptor (TCR) sequencing experiments allowed for a significant increase in the amount of peptide:TCR binding data available and a number of machine learning models appeared in recent years. High-quality prediction models for a fixed epitope sequence are feasible, provided enough known binding TCR sequences are available. However, their performance drops significantly for previously unseen peptides.ResultsWe prepare the dataset of known peptide:TCR binders and augment it with negative decoys created using healthy donors’ T-cell repertoires. We employ deep learning methods commonly applied in Natural Language Processing (NLP) to train part a peptide:TCR binding model with a degree of cross-peptide generalization (0.66 AUROC). We demonstrate that BERTrand outperforms the published methods when evaluated on peptide sequences not used during model training.AvailabilityThe datasets and the code for model training are available athttps://github.com/SFGLab/bertrandContactalexander.myronov@gmail.com,dariusz.plewczynski@pw.edu.plSupplementary informationSupplementary data are available atBioinformaticsonline.
ModularImageAnalysis (MIA): Assembly of modularised image and object analysis workflows in ImageJ
Authors: Cross Stephen J. , Fisher Jordan D. J. R. , Jepson Mark A. 
Published: June 2023

AbstractModularImageAnalysis (MIA) is an ImageJ plugin providing a code-free graphical environment in which complex automated analysis workflows can be constructed and distributed. The near 200 included modules cover all stages of a typical analysis workflow, from image loading through image processing, object detection, extraction of measurements, measurement-based filtering, visualisation, and data exporting. MIA provides out-of-the-box compatibility with many advanced image processing plugins for ImageJ including Bio-Formats, DeepImageJ, MorphoLibJ and TrackMate, allowing these tools and their outputs to be directly incorporated into analysis workflows. By default, modules support spatially calibrated 5D images, meaning measurements can be acquired in both pixel and calibrated units. A hierarchical object relationship model allows for both parent-child (one-to-many) and partner (many-to-many) relationships to be established. These relationships underpin MIA’s ability to track objects through time, represent complex spatial relationships (e.g. skeletons) and measure object distributions (e.g. count puncta per cell). MIA features dual graphical interfaces: the “editing view” offers access to the full list of modules and parameters in the workflow, while the simplified “processing view” can be configured to display only a focused subset of controls. All workflows are batch-enabled by default, with image files within a specified folder being processed automatically and exported to a single spreadsheet. Beyond the included modules, functionality can be extended both internally, through integration with the ImageJ scripting interface, and externally, by developing third-party Java modules that extend the core MIA framework. Here we describe the design and functionality of MIA in the context of a series of real-world example analyses.
A hybrid RNA FISH immunofluorescence protocol onDrosophilapolytene chromosomes
Authors: Gilbonio Hannah E. , Puckett Gwyn L. , Nguyen Erica , Rieder Leila E. 
Published: June 2023

ABSTRACTObjectivesInvestigating protein-DNA interactions is imperative to understanding fundamental concepts such as cell growth, differentiation, and cell development in many systems. Sequencing techniques such as ChIP-seq can yield genome-wide DNA binding profiles of transcription factors; however this assay can be expensive, time-consuming, may not be informative for repetitive regions of the genome, and depend heavily upon antibody suitability. Combining DNA fluorescence in situ hybridization (FISH) with immunofluorescence (IF) is a quicker and inexpensive approach which has historically been used to investigate protein-DNA interactions in individual nuclei. However, these assays are sometimes incompatible due to the required denaturation step in DNA FISH that can alter protein epitopes, hindering primary antibody binding. Additionally, combining DNA FISH with IF may be challenging for less experienced trainees. Our goal was to develop an alternative technique to investigate protein-DNA interactions by combining RNA FISH with IF.ResultsWe developed a hybrid RNA FISH and IF protocol for use onDrosophila melanogasterpolytene chromosome spreads in order to visualize colocalization of proteins and DNA loci. We demonstrate that this assay is sensitive enough to determine if our protein of interest, Multi-sex combs (Mxc), localizes to single-copy target transgenes carrying histone genes. Overall, this study provides an alternative, accessible method for investigating protein-DNA interactions at the single gene level inDrosophila melanogasterpolytene chromosomes.
Combined direct/indirect detection allows identification of DNA termini in diverse sequencing datasets and supports a multiple-initiation-site model for HIV plus-strand synthesis
Authors: Wang William , Artiles Karen L. , Machida Shinichi , Benkirane Monsef , Jain Nimit , Fire Andrew Z. 
Published: June 2023

AbstractReplication of genetic material involves the creation of characteristic termini. Determining these termini is important to refine our understanding of the mechanisms involved in maintaining the genomes of cellular organisms and viruses. Here we describe a computational approach combining direct and indirect readouts to detect termini from next-generation short-read sequencing. While a direct inference of termini can come from mapping the most prominent start positions of captured DNA fragments, this approach is insufficient in cases where the DNA termini are not captured, whether for biological or technical reasons. Thus, a complementary (indirect) approach to terminus detection can be applied, taking advantage of the imbalance in coverage between forward and reverse sequence reads near termini. A resulting metric (“strand bias”) can be used to detect termini even where termini are naturally blocked from capture or ends are not captured during library preparation (e.g., in tagmentation-based protocols). Applying this analysis to datasets where known DNA termini are present, such as from linear double-stranded viral genomes, yielded distinct strand bias signals corresponding to these termini. To evaluate the potential to analyze a more complex situation, we applied the analysis to examine DNA termini present early after HIV infection in a cell culture model. We observed both the known termini expected based on standard models of HIV reverse transcription (the U5-right-end and U3-left-end termini) as well as a signal corresponding to a previously described additional initiation site for plus-strand synthesis (cPPT [central polypurine tract]). Interestingly, we also detected putative terminus signals at additional sites. The strongest of these are a set that share several characteristics with the previously characterized plus-strand initiation sites (the cPPT and 3’ PPT [polypurine tract] sites): (i) an observed spike in directly captured cDNA ends, an indirect terminus signal evident in localized strand bias, (iii) a preference for location on the plus-strand, (iv) an upstream purine-rich motif, and (v) a decrease in terminus signal at late time points after infection. These characteristics are consistent in duplicate samples in two different genotypes (wild type and integrase-lacking HIV). The observation of distinct internal termini associated with multiple purine-rich regions raises a possibility that multiple internal initiations of plus-strand synthesis might contribute to HIV replication.
Late-life Rapamycin Treatment Enhances Cardiomyocyte Relaxation Kinetics and Reduces Myocardial Stiffness
Authors: Chakraborty Akash D. , Kooiker Kristi , Kobak Kamil A. , Cheng Yuanhua , Lee Chi Fung , Razumova Maria , Granzier H Henk , Regnier Michael , Rabinovitch Peter S. , Moussavi-Harami Farid , Chiao Ying Ann 
Published: June 2023

AbstractDiastolic dysfunction is a key feature of the aging heart. We have shown that late-life treatment with mTOR inhibitor, rapamycin, reverses age-related diastolic dysfunction in mice but the molecular mechanisms of the reversal remain unclear. To dissect the mechanisms by which rapamycin improves diastolic function in old mice, we examined the effects of rapamycin treatment at the levels of single cardiomyocyte, myofibril and multicellular cardiac muscle. Compared to young cardiomyocytes, isolated cardiomyocytes from old control mice exhibited prolonged time to 90% relaxation (RT90) and time to 90% Ca2+transient decay (DT90), indicating slower relaxation kinetics and calcium reuptake with age. Late-life rapamycin treatment for 10 weeks completely normalized RT90and partially normalized DT90, suggesting improved Ca2+handling contributes partially to the rapamycin-induced improved cardiomyocyte relaxation. In addition, rapamycin treatment in old mice enhanced the kinetics of sarcomere shortening and Ca2+transient increase in old control cardiomyocytes. Myofibrils from old rapamycin-treated mice displayed increased rate of the fast, exponential decay phase of relaxation compared to old controls. The improved myofibrillar kinetics were accompanied by an increase in MyBP-C phosphorylation at S282 following rapamycin treatment. We also showed that late-life rapamycin treatment normalized the age-related increase in passive stiffness of demembranated cardiac trabeculae through a mechanism independent of titin isoform shift. In summary, our results showed that rapamycin treatment normalizes the age-related impairments in cardiomyocyte relaxation, which works conjointly with reduced myocardial stiffness to reverse age-related diastolic dysfunction.
Cytoplasmic Male Sterility and Abortive Seed Traits Generated through Mitochondrial Genome Editing Coupled with Allotopic Expression ofatp1in Tobacco
Authors: Dewey Ralph E. , Selote Devarshi , Griffin H. Carol , Dickey Allison N. , Jantz Derek , Smith J. Jeff , Matthiadis Anna , Strable Josh , Kestell Caitlin , Smith William A. 
Published: June 2023

ABSTRACTAllotopic expression is the term given for the deliberate relocation of gene function from an organellar genome to the nuclear genome. We hypothesized that the allotopic expression of an essential mitochondrial gene using a promoter that expressed efficiently in all cell types except those responsible for male reproduction would yield a cytoplasmic male sterility (CMS) phenotype once the endogenous mitochondrial gene was inactivated via genome editing. To test this, we repurposed the mitochondrially encodedatp1gene of tobacco to function in the nucleus under the transcriptional control of a CaMV 35S promoter (construct 35S:nATP1), a promoter that has been shown to be minimally expressed in early stages of anther development. The endogenousatp1gene was eliminated (Δatp1) from 35S:nATP1 tobacco plants using custom-designed meganucleases directed to the mitochondria. Vegetative growth of most 35S:nATP1/Δatp1plants appeared normal, but upon flowering produced malformed anthers that failed to shed pollen. When 35S:nATP1/Δatp1plants were cross-pollinated, ovary/capsule development appeared normal, but the vast majority of the resultant seeds were small, largely hollow and failed to germinate, a phenotype akin to the seedless trait known as stenospermocarpy. Characterization of the mitochondrial genomes from three independent Δatp1events suggested that spontaneous recombination over regions of microhomology and substoichiometric shifting were the mechanisms responsible foratp1elimination and genome rearrangement in response to exposure to theatp1-targeting meganucleases. Should the results reported here in tobacco prove to be translatable to other crop species, then multiple applications of allotopic expression of an essential mitochondrial gene followed by its elimination through genome editing can be envisaged. Depending on the promoter(s) used to drive the allotopic gene, this technology may have potential application in the areas of: (1) CMS trait development for use in hybrid seed production; (2) seedless fruit production; and (3) transgene containment.