bluuebunny/crossref_metadata_2025 huggingface dataset:
First isolate ofOrientia tsutsugamushifrom Vellore, South India
Authors: Kumaraswamy Janaki , Kirubanandan Agilandeeswari , Nagarajan Lakshmi Surya , Gunasekaran Karthik , Abhilash KPP , Jude Prakash John Antony
Published: November 2023

Background

Scrub typhus a common cause of acute febrile illness in India caused byOrientia tsutsugamushian obligate intracellular bacterium requiring cell culture for isolation. Cell lines like Vero and L929 are most suitable for isolating and maintaining this organism. This study was undertaken to isolate and characterize ofOrientia tsutsugamushifrom whole blood samples at a tertiary care centre in Southern India.

Methods

The PBMCs (peripheral blood mononuclear cells) collected from scrub typhus positive (47kDa qPCR positive) patients were inoculated into Vero and L929 cell line at 80% confluence for primary isolation. The inoculated flasks were incubated at 37°C with 5% CO2for 30 days and examined for presence ofOrientia tsutsugamushion the day 10, 15, 20 post-inoculation and everyday thereafter for a maximum of 30 days post inoculation. The scrapings were subjected to Giemsa staining, IFA, 47kDa qPCR and transmission electron microscopy (TEM). The isolates were passaged 3-4 times to ensure viability and then stored in DMEM with 10% FBS (-80°C). Genotyping of the isolates was performed by amplifying a 650 bp segment of the TSA 56 (type specific antigen 56) gene.

Results

Amongst the 50 samples inoculated, three were culture positive as confirmed by 47 kDa qPCR at 24thday of inoculation. This was further confirmed by Giemsa, IFA staining and TEM. The 650bp amplicons showed 99.5 to 100% homology withOrientia tsutsugamushiMW604716, MH003839, MW604718, MW604717, MH922787 and MH003838 strains. Phylogenetic analysis revealed that 2 isolates belong to TA763 genotype and one belongs to Gilliam genotype.

Conclusions

We have successfully isolated and characterised theOrientia tsutsugamushifor the first time at our centre from PBMCs. Based on the partial TSA56 gene sequence our isolates belongs to TA763 and Gilliam genotype. More number of samples are being processed for identifying further isolates followed by genomic analysis.
Contrasting and Combining Transcriptome Complexity Captured by Short and Long RNA Sequencing Reads
Authors: Han Seong Woo , Jewell San , Thomas-Tikhonenko Andrei , Barash Yoseph
Published: November 2023

Mapping transcriptomic variations using either short or long reads RNA sequencing is a staple of genomic research. Long reads are able to capture entire isoforms and overcome repetitive regions, while short reads still provides improved coverage and error rates. Yet how to quantitatively compare the technologies, can we combine those, and what may be the benefit of such a combined view remain open questions. We tackle these questions by first creating a pipeline to assess matched long and short reads data using a variety of transcriptome statistics. We find that across datasets, algorithms and technologies, matched short reads data detects roughly 50% more splice junctions, with 10-30% of the splice junctions included at 20% or more are missed by long reads. In contrast, long reads detect many more intron retention events, pointing to the benefit of combining the technologies. We introduce MAJIQ-L, an extension of the MAJIQ software to enable a unified view of transcriptome variations from both technologies and demonstrate its benefits. Our software can be used to assess any future long reads technology or algorithm, and combine it with short reads data for improved transcriptome analysis.
Host-derived oxidized phospholipids initiate effector-triggered immunity fostering lethality upon microbial encounter
Authors: Di Gioia Marco , Poli Valentina , Tan Piao J , Spreafico Roberto , Chu Anne , Cuenca Alex G , Gordts Philip LSM , Pandolfi Laura , Meloni Federica , Witztum Joseph L , Chou Janet , Springstead James R , Zanoni Ivan
Published: November 2023

Macrophages detect invading microorganisms via pattern recognition receptors that recognize pathogen-associated molecular patterns, or via sensing the activity of virulence factors that initiates effector-triggered immunity (ETI). Tissue damage that follows pathogen encounter leads to the release of host-derived factors that participate to inflammation. How theseself-derived molecules are sensed by macrophages and their impact on immunity remain poorly understood. Here we demonstrate that, in mice and humans, host-derived oxidized phospholipids (oxPLs) are formed upon microbial encounter. oxPL blockade restricts inflammation and prevents the death of the host, without affecting pathogen burden. Mechanistically, oxPLs bind and inhibit AKT, a master regulator of immunity and metabolism. AKT inhibition potentiates the methionine cycle, and epigenetically dampensIl10, a pluripotent anti-inflammatory cytokine. Overall, we found that host-derived inflammatory cues act as “self” virulence factors that initiate ETI and that their activity can be targeted to protect the host against excessive inflammation upon microbial encounter.
Neuroinfectiology of an atypical anthrax-causing pathogen in wild chimpanzees
Authors: Gräßle Tobias , Jäger Carsten , Kirilina Evgeniya , Jaffe Jenny E. , Carlier Penelope , Pizarro Andrea , Jauch Anna , Reimann Katja , Lipp Ilona ,   EBC consortium, Wittig Roman M. , Crockford Catherine , Weiskopf Nikolaus , Leendertz Fabian H. , Morawski Markus
Published: November 2023

Bacillus cereusbiovaranthracis(Bcbva) is an atypical anthrax-causing bacterium, inflicting wildlife fatalities across African rainforest ecosystems. The pathogen’s virulence in one of our closest living relatives, the chimpanzee, together with human serological evidence, suggestsBcbvais zoonotic. While classicalB. anthracis-induced anthrax has been described to affect the central nervous system at a progressive disease-state, the neuroinfectiology ofBcbvais yet unknown. Here we characterised the pathogen’s neuro-invasiveness via gross pathological assessment, ultra-high resolution quantitative Magnetic Resonance Imaging and histological analysis on four brains, which were extracted from naturally deceased wild chimpanzees in Taï National Park, Côte d’Ivoire.

Based on macroscopically evident pial vessel congestion and haemorrhages as well as cortical siderosis detected via MRI, we concluded thatBcbvainduced meningitis analogous toB. anthracis. Further, histological visualisation of bacteria and leukocytes in the subarachnoid space evidenced the bacterium’s capability to breach the arachnoid barrier.Bcbvawas detected in the brain parenchyma of all four cases. This indicates a higher ability to transgress the glia limitans and therefore exhibits a higher neuroinvasiveness compared toB. anthracisthat predominantly stays confined to the meninges. Heightened glial fibrillary acidic protein (GFAP) expression but little morphological gliosis suggest a rapid disease progression leading to host-death within hours to a few days after central nervous system invasion.

Overall our results revealBcbva’s ability to breach blood-brain barriers which results in a pronounced neuropathogenicity.Bcbvacauses extensive damage to the meninges and the brain parenchyma, as well as rapid and massive digestion of brain extracellular matrix in chimpanzees and potentially so in humans in case of zoonotic spillover.
Human leukocyte antigen HLA-DR-expressing fibroblast-like synoviocytes are inducible antigen presenting cells that present autoantigens in Lyme arthritis
Authors: Rouse Joseph R , Danner Rebecca , Wahhab Amanda , Pereckas Michaela , McClune Mecaila E , Steere Allen C , Strle Klemen , Jutras Brandon L , Lochhead Robert B
Published: November 2023

Background

HLA-DR-expressing fibroblast-like synoviocytes (FLS) are a prominent cell type in synovial tissue in chronic inflammatory forms of arthritis. We recently showed that peptides from several extracellular matrix (ECM) proteins, including fibronectin-1 (FN1), contained immunogenic CD4+ T cell epitopes in patients with postinfectious Lyme arthritis (LA). However, the role of FLS in presentation of these T cell epitopes remains uncertain.

Methods

Primary LA FLS and primary murine FLS stimulated with interferon gamma (IFNγ),Borrelia burgdorferi, and/orB. burgdorferipeptidoglycan (PG) were assessed for properties associated with antigen presentation. HLA-DR-presented peptides from stimulated LA FLS were identified by immunopeptidomics analysis. OT-II T cells were cocultured with stimulated murine FLS in the presence of cognate ovalbumin antigen to determine the potential of FLS to act as inducible antigen presenting cells (APC).

Results

FLS expressed HLA-DR molecules within inflamed synovial tissue and tendons from patients with post-infectious LA patientsin situ.MHC class II and costimulatory molecules were expressed by FLS followingin vitrostimulation with IFNγ andB. burgdorferiand presented both foreign and self MHC-II peptides, including T cell epitopes derived from two Lyme autoantigens fibronectin-1 (FN1) and endothelial cell growth factor (ECGF). Stimulated murine FLS induced proliferation of naïve OT-II CD4+ T cells, particularly when FLS were stimulated with both IFNγ and PG.

Conclusions

MHC-II+ FLS are inducible APCs that can induce CD4+ T cell activation and can present Lyme autoantigens derived from ECM proteins, thereby amplifying tissue-localized autoimmune CD4+ T cell responses in LA.

AUTHORS’ SUMMARY

This study demonstrates that IFNγ-activated MHC-II+ fibroblast-like synoviocytes (FLS) stimulated withBorrelia burgdorferipresent foreign and self MHC-II antigens, including Lyme autoantigens. Furthermore, IFNγ-activated MHC-II+ FLS stimulated withB. burgdorferipeptidoglycan can induce activation and proliferation of naïve CD4+ T cells in an MHC-II antigen-dependent manner, demonstrating that activated MHC-II+ FLS are inducible antigen presenting cells.
HAMLET, a human milk protein-lipid complex, modulates amoxicillin-induced changes in anex vivobiofilm model of the oral microbiome
Authors: Brar NK , Dhariwal A , Shekhar S , Junges R , Hakansson AP , Petersen FC
Published: November 2023

Challenges from infections caused by biofilms and antimicrobial resistance highlight the need for novel antimicrobials that work synergistically with antibiotics and minimize resistance risk. In this study we investigated the potential synergistic effect of HAMLET (human alpha-lactalbumin made lethal to tumor cells), a human milk protein-lipid complex and amoxicillin on microbial ecology using anex-vivooral biofilm model. HAMLET was chosen due to its multi-targeted antimicrobial mechanism, together with its synergistic effect with antibiotics on single species pathogens, and low risk of resistance development. The combination of HAMLET and amoxicillin significantly reduced biofilm viability, while each of them alone had little or no impact. Using a whole metagenomics approach, we found that the combination group promoted a most remarkable shift in overall microbial composition compared to the untreated samples. Up to 90% of the bacterial species in the combined treatment wereLactobacillus crispatus, a species with probiotic effects, whereas it was detected in minor fraction in untreated samples. Resistome analysis indicated no major shifts on alpha-diversity, while beta-diversity revealed distinct clustering patterns for each treatment group, signifying that each treatment group harbors a unique resistome. TEM beta-lactamase genes were detected in low proportions in all treated samples but absent in untreated samples. Our study highlights the potential of HAMLET to synergize with amoxicillin in anex-vivomodel of the oral microbiome and modulate the proportion of probiotic bacteria. The findings extend the knowledge on the synergistic effects of HAMLET and antibiotics from single-species studies to polymicrobial biofilms of human origin.

Importance

Polymicrobial infections are challenging to treat and prevent, requiring the use of antibiotics that exhibit reduced efficacy due to biofilm formation. HAMLET has recently emerged as an antimicrobial agent that can synergize with antibiotics while limiting microbial resistance. We investigated the effects of HAMLET, alone and combined with low concentrations of amoxicillin, onex vivooral biofilms to simulate complex microbial interactions observed in the oral cavity. The combination of HAMLET and amoxicillin effectively targeted polymicrobial biofilms and led to an increase inLactobacillus crispatus. The potency of this combination appears to be due to the synergistic effect of HAMLET and amoxicillin. These findings underscore the potential of combining antimicrobials with different modes of action for the development of more effective strategies for preventing and treating polymicrobial infections.
Tumorigenesis driven by the BRAFV600Eoncoprotein requires secondary mutations that overcome its feedback inhibition of migration and invasion
Authors: Gadal Sunyana , Boyer Jacob A. , Roy Simon F. , Outmezguine Noah A. , Sharma Malvika , Li Hongyan , Fan Ning , Chan Eric , Romin Yevgeniy , Barlas Afsar , Chang Qing , Pancholi Priya , Timaul Neilawattie. Merna , Overholtzer Michael , Yaeger Rona , Manova-Todorova Katia , Stanchina Elisa de , Bosenberg Marcus , Rosen Neal
Published: November 2023

BRAFV600Emutation occurs in 46% of melanomas and drives high levels of ERK activity and ERK-dependent proliferation. However,BRAFV600Eis insufficient to drive melanoma in GEMM models, and 82% of human benign nevi harborBRAFV600Emutations. We show here that BRAFV600Einhibits mesenchymal migration by causing feedback inhibition of RAC1 activity. ERK pathway inhibition induces RAC1 activation and restores migration and invasion. In cells withBRAFV600E, mutant RAC1, overexpression of PREX1, PREX2, or PTEN inactivation restore RAC1 activity and cell motility. Together, these lesions occur in 48% of BRAFV600Emelanomas. Thus, although BRAFV600Eactivation of ERK deregulates cell proliferation, it prevents full malignant transformation by causing feedback inhibition of cell migration. Secondary mutations are, therefore, required for tumorigenesis. One mechanism underlying tumor evolution may be the selection of lesions that rescue the deleterious effects of oncogenic drivers.

Statement of significance

BRAFV600Eactivation of ERK causes feedback inhibition of cell migration and invasion and thus blocks tumorigenesis. Secondary genetic lesions are required to rescue these processes and enable tumor development. Thus, oncogenic feedback can shape the details of tumor progression and, in doing so, selects for new mutations that may be therapeutic targets.
High Frequency Longitudinal RNAseq Reveals Temporally Varying Genes and Recovery Trajectories in Rats
Authors: Chen Wei , Chai Yi , Jiang Qi , Miao Eva Y. , Gopinath Ashwin , Zhang David Yu
Published: November 2023

When living organisms are exposed to potentially toxic chemicals, they respond via changes in gene expression. Traditional differentially expressed gene analysis based on before/after blood samples does not reveal the response’s temporal dynamics, and often produces false positives and negatives. Here, we performed longitudinal daily RNA sequencing on rats dosed with tetracycline, isoniazid, carbon tetrachloride, or valproate. We identified 4,302 temporally variable genes (TVGs) with statistically strong change in expression following dosing. Projecting TVG expressions into a 3-dimensional principal component (PC) space reveals consistent trajectories for recovery following dosing, and enables separation of healthy from recovering states with 91% to 99% area under the receiver operator curve. Finally, we observed that Fast Recovery vs. Slow Recovery rats exhibited distinct temporal expression patterns in the TVGs, suggesting that individual variations could be potentially captured via longitudinal RNAseq analysis.
New genome reveals molecular signatures of adaptation to nocturnality in moth-like butterflies (Hedylidae)
Authors: Singh Rachit Pratap , Weng Yi-Ming , Sondhi Yash , Plotkin David , Frandsen Paul B. , Kawahara Akito Y.
Published: November 2023

Nearly all animals have a preferred period of daily activity (diel-niche), which is strongly influenced by the light environment. Sensory systems, particularly vision, are adapted to light, and evolutionary transitions to novel light environments, especially light limited ones, can impose strong constraints on eye evolution, color, and motion vision. The adaptive changes in sensory abilities of animals during these transitions, both at the genetic and neural levels, are largely unexplored. Butterflies and moths, with their diverse diel-niche shifts, are an ideal group for investigating the gene evolution linked to these transitions. While most butterflies are day-flying, hedylid butterflies are unique in being primarily nocturnal, and they represent an important evolutionary shift from diurnality to nocturnality in this clade. Here, we sequence the first high-quality Hedylidae genome and functionally annotate genes to understand genomic changes associated with shifts in diel niche. Comparing Hedylidae visual genes against day- and night-flying Lepidoptera species revealed that visual genes are highly conserved, with no major losses. However, hedylid butterfly opsins were more similar to nocturnal moths than their diurnal congeners. Tests on the evolutionary rates (dN/dS) confirmed that color vision opsins were under strong selection, similar to nocturnal moths. We propose that a convergent event of sequence evolution took place when these butterflies became nocturnal, approximately 98 million years ago.
Deep Learning Model Imputes Missing Stains in Multiplex Images
Authors: Shaban Muhammad , Lassoued Wiem , Canubas Kenneth , Bailey Shania , Liu Yanling , Allen Clint , Strauss Julius , Gulley James L , Jiang Sizun , Mahmood Faisal , Zaki George , Sater Houssein A
Published: November 2023

Multiplex staining enables simultaneous detection of multiple protein markers within a tissue sample. However, the increased marker count increased the likelihood of staining and imaging failure, leading to higher resource usage in multiplex staining and imaging. We address this by proposing a deep learning-basedMArker imputation model for multipleXIMages (MAXIM) that accurately impute protein markers by leveraging latent biological relationships between markers. The model’s imputation ability is extensively evaluated at pixel and cell levels across various cancer types. Additionally, we present a comparison between imputed and actual marker images within the context of a downstream cell classification task. The MAXIM model’s interpretability is enhanced by gaining insights into the contribution of individual markers in the imputation process. In practice, MAXIM can reduce the cost and time of multiplex staining and image acquisition by accurately imputing protein markers affected by staining issues.
Tibetan terrestrial and aquatic ecosystems collapsed with cryosphere loss inferred from sedimentary ancient metagenomics
Authors: Liu Sisi , Stoof-Leichsenring Kathleen R. , Harms Lars , Schulte Luise , Mischke Steffen , Kruse Stefan , Zhang Chengjun , Herzschuh Ulrike
Published: November 2023

Glacier and permafrost shrinkage and land-use intensification threaten diverse mountain wildlife and affect nature conservation strategy. Our understanding of alpine ecological dynamics is, however, insufficient because time series portraying ecosystem complexity adequately are missing. Here, we present an ancient metagenomic record tracing 317 terrestrial and aquatic taxa, including mammals, fish, plants, and microorganisms retrieved from a lake sediment core from the southeastern Tibetan Plateau covering the last 18,000 years. We infer that steppe-meadow turned into woodland at 14 ka (cal BP) controlled by warming-induced cryosphere loss, further driving a change of herbivore dominance from wild yak to deer. Network analyses reveal that root hemiparasitic and cushion plants are keystone taxa, likely altering the terrestrial ecosystem via facilitation. These findings refute the hypothesis of top-down control by large herbivores in the alpine ecosystem. We also find that glacier mass loss significantly contributes to considerable turnover in the aquatic community at 14 ka, transitioning from glacier-related (blue-green) algae to abundant non-glacier-preferring picocyanobacteria, macrophytes, fish, and fish-eating otters. Human impact contributes little to shaping the alpine ecosystems. By applying network analysis, we provide the first sedaDNA-based assessment of the stress-gradient hypothesis. As cryosphere loss is ongoing due to climate warming, prioritizing the protection of habitats with rich nurse plants that aid neighbors in adapting to stressful conditions is likely to be a more beneficial conservation measure than livestock reduction in the Tibetan Plateau.

Significance statement

Merging ancient metagenomics and network analysis gives new insights into conserving the Tibetan alpine ecosystem under ongoing warming and human perturbations. We investigated the assembly of the Yak steppe-meadow ecosystem and an alpine lake system in response to cryosphere changes over the past ∼18,000 years on the Tibetan Plateau. Large herbivores cannot be a cost-effective natural climate solution to stabilize the Tibetan alpine ecosystem because they are not keystone taxa at the ecosystem scale. Furthermore, there is no support that land use considerably shapes the alpine communities and ecosystems. Protection policy should thus prioritize focus on alpine areas with intense land use and rich in root hemiparasitic and cushion plants because these taxa act as facilitators in the ecosystem.
Msc1 is a nuclear envelope protein that reinforces DNA repair in late mitosis
Authors: Medina-Suárez Sara , Ayra-Plasencia Jessel , Pérez-Martínez Lara , Butter Falk , Machín Félix
Published: November 2023

Precise double-strand break (DSB) repair is paramount for genome stability. Homologous recombination (HR) repairs DSBs when cyclin-dependent kinase (CDK) activity is high, which correlates with the availability of the sister chromatid as a template. However, anaphase and telophase are paradoxical scenarios since high CDK favors HR despite sister chromatids being no longer aligned. To identify factors specifically involved in DSB repair in late mitosis, we have undertaken comparative proteomics inSaccharomyces cerevisiaeand found that Msc1, a poorly characterized nuclear envelope protein, is significantly enriched upon both random and guided DSBs. We further show that Δmsc1is more sensitive to DSBs in late mitosis, and has a delayed repair of DBSs, as indicated by increased Rad53 hyperphosphorylation, fewer Rad52 repair factories, and slower HR completion. We discuss how Msc1 may favor the formation of Rad52 factories and the timely completion of HR before cytokinesis.
CPSign - Conformal Prediction for Cheminformatics Modeling
Authors: McShane Staffan Arvidsson , Norinder Ulf , Alvarsson Jonathan , Ahlberg Ernst , Carlsson Lars , Spjuth Ola
Published: November 2023

Conformal prediction has seen many applications in pharmaceutical science, being able to calibrate outputs of machine learning models and producing valid prediction intervals. We here present the open source software CPSign that is a complete implementation of conformal prediction for cheminformatics modeling. CPSign implements inductive and transductive conformal prediction for classification and regression, and probabilistic prediction with the Venn-ABERS methodology. The main chemical representation is signatures but other types of descriptors are also supported. The main modeling methodology is support vector machines (SVMs), but additional modeling methods are supported via an extension mechanism, e.g. DeepLearning4j models. We also describe features for visualizing results from conformal models including calibration and efficiency plots, as well as features to publish predictive models as REST services. We compare CPSign against other common cheminformatics modeling approaches including random forest, and a directed message-passing neural network. The results show that CPSign produces robust predictive performance with comparative predictive efficiency, with superior runtime and lower hardware requirements compared to neural network based models. CPSign has been used in several studies and is in production-use in multiple organizations. The ability to work directly with chemical input files, perform descriptor calculation and modeling with SVM in the conformal prediction framework, with a single software package having a low footprint and fast execution time makes CPSign a convenient and yet flexible package for training, deploying, and predicting on chemical data.
A novel clinical metaproteomics workflow enables bioinformatic analysis of host-microbe dynamics in disease
Authors: Do Katherine , Mehta Subina , Wagner Reid , Bhuming Dechen , Rajczewski Andrew T. , Skubitz Amy P.N. , Johnson James E. , Griffin Timothy J. , Jagtap Pratik D.
Published: November 2023

Clinical metaproteomics has the potential to offer insights into the host-microbiome interactions underlying diseases. However, the field faces challenges in characterizing microbial proteins found in clinical samples, which are usually present at low abundance relative to the host proteins. As a solution, we have developed an integrated workflow coupling mass spectrometry-based analysis with customized bioinformatic identification, quantification and prioritization of microbial and host proteins, enabling targeted assay development to investigate host-microbe dynamics in disease. The bioinformatics tools are implemented in the Galaxy ecosystem, offering the development and dissemination of complex bioinformatic workflows. The modular workflow integrates MetaNovo (to generate a reduced protein database), SearchGUI/PeptideShaker and MaxQuant (to generate peptide-spectral matches (PSMs) and quantification), PepQuery2 (to verify the quality of PSMs), and Unipept and MSstatsTMT (for taxonomy and functional annotation). We have utilized this workflow in diverse clinical samples, from the characterization of nasopharyngeal swab samples to bronchoalveolar lavage fluid. Here, we demonstrate its effectiveness via analysis of residual fluid from cervical swabs. The complete workflow, including training data and documentation, is available via the Galaxy Training Network, empowering non-expert researchers to utilize these powerful tools in their clinical studies.
Development and validation of a reliable DNA copy-number-based machine learning algorithm (CopyClust) for breast cancer integrative cluster classification
Authors: Young Cameron C. , Eason Katherine , Garcia Raquel Manzano , Moulange Richard , Mukherjee Sach , Chin Suet-Feung , Caldas Carlos , Rueda Oscar M.
Published: November 2023

The Integrative Clusters (IntClusts) provide a framework for the classification of breast cancer tumors into 10 distinct genomic subtypes based on DNA copy number and gene expression. Current classifiers achieve only low accuracy without gene expression data, warranting the development of new approaches to copy-number-only-based IntClust classification. A novel XGBoost-driven classification algorithm,CopyClust, was trained using genomic features from METABRIC and validated on TCGA achieving a nine-percentage point or greater improvement in overall IntClust subtype classification accuracy.
Symbiosis modulates gene expression of symbionts, but not hosts, under thermal challenge
Authors: Aichelman Hannah E , Huzar Alexa K , Wuitchik Daniel M , Atherton Kathryn F , Wright Rachel M , Dixon Groves , Schlatter E , Haftel Nicole , Davies Sarah W
Published: November 2023

Increasing ocean temperatures are causing dysbiosis between coral hosts and their symbionts. Previous work suggests that coral host gene expression responds more strongly to environmental stress compared to their intracellular symbionts; however, the causes and consequences of this phenomenon remain untested. We hypothesized that symbionts are less responsive because hosts modulate symbiont environments to buffer stress. To test this hypothesis, we leveraged the facultative symbiosis between the scleractinian coralOculina arbusculaand its symbiontBreviolum psygmophilumto characterize gene expression responses of both symbiotic partnersinandex hospiteunder thermal challenges. To characterize host andin hospitesymbiont responses, symbiotic and aposymbioticO. arbusculawere exposed to three treatments: 1) control (18°C), 2) heat (32°C), and 3) cold (6°C). This experiment was replicated withB. psygmophilumcultured fromO. arbusculato characterizeex hospitesymbiont responses. Both thermal challenges elicited classic environmental stress responses (ESRs) inO. arbuscularegardless of symbiotic state, with hosts responding more strongly to cold challenge. Hosts also exhibited stronger responses thanin hospitesymbionts.Inandex hospite B. psygmophilumboth downregulated genes associated with photosynthesis under thermal challenge; however,ex hospitesymbionts exhibited greater gene expression plasticity and differential expression of genes associated with ESRs. Taken together, these findings suggest thatO. arbusculahosts may buffer environments ofB. psygmophilumsymbionts; however, we outline the future work needed to confirm this hypothesis.
A novel, wave-shaped profile of germline selection of pathogenic mtDNA mutations is discovered by bypassing a classical statistical bias.
Authors: Cote-LHeureux Auden , Fleischmann Zoe , Franco Melissa , Chen Zhibin , Khrapko Mark , Vyshedskiy Benjamin , Braverman Maxim , Popadin Konstantin , Pickett Sarah , Woods Dori C. , Tilly Jon , Turnbull Doug , Khrapko Konstantin
Published: November 2023

The shift of the level of disease-causing mtDNA mutations (heteroplasmy) from mother to child is typically negatively correlated with the mother ′ s heteroplasmy (Hm). In other words, mothers with low Hm tend to have children with a higher mutation level (Hch) than their own. In contrast, mothers with high Hm typically see a decrease in heteroplasmy in their children. This peculiar trend has been commonly interpreted as a result of a descending germline selection profile, i.e., positive selection at low Hm, gradually turning negative at high Hm. Here we demonstrate, however, that the negative correlation is mostly driven by RTM, or ′ Regression To the Mean ′, a classical statistical bias. We further show that RTM can be nullified by using the average between the mother ′ s and child ′ s heteroplasmy, as a new variable, instead of the commonly used mother ′ s heteroplasmy in blood. Additionally, we demonstrate that mother/child average is a better proxy of the actual germline heteroplasmy. Moreover, the elimination of RTM revealed a previously hidden wave-shaped HS-profile (positive mother-to-child shift at intermediate average mother/child heteroplasmy, decreasing towards high and low average heteroplasmy). In confirmation of this finding, we show that simulations that involve both wave-shaped HS-profile and RTM, reproduce the observed patterns of inheritance of mtDNA mutations in unprecedented detail. From the health care perspective, the uncovering of the wave-shaped HS-profile (and the removal of the RTM bias) are crucial for millions of families affected by mtDNA disease. From the fundamental perspective, the wave-shaped profile offers a novel understanding of the germline dynamics of mtDNA and a novel potential mechanism that prevents the spread of detrimental mtDNA mutations in the population.
ANDES: a novel best-match approach for enhancing gene set analysis in embedding spaces
Authors: Li Lechuan , Dannenfelser Ruth , Cruz Charlie , Yao Vicky
Published: November 2023

Abstract

Embedding methods have emerged as a valuable class of approaches for distilling essential information from complex high-dimensional data into more accessible lower-dimensional spaces. Applications of embedding methods to biological data have demonstrated that gene embeddings can effectively capture physical, structural, and functional relationships between genes. However, this utility has been primarily realized by using gene embeddings for downstream machine learning tasks. Much less has been done to examine the embeddings directly, especially analyses of gene sets in embedding spaces. Here, we propose ANDES, a novel best-match approach that can be used with existing gene embeddings to compare gene sets while reconciling gene set diversity. This intuitive method has important downstream implications for improving the utility of embedding spaces for various tasks. Specifically, we show how ANDES, when applied to different gene embeddings encoding protein-protein interactions, can be used as a novel overrepresentation-based and rank-based gene set enrichment analysis method that achieves state-of-the-art performance. Additionally, ANDES can use multi-organism joint gene embeddings to facilitate functional knowledge transfer across organisms, allowing for phenotype mapping across model systems. Our flexible, straightforward best-match methodology can be extended to other embedding spaces with diverse community structures between set elements.
Multi-Step Control of Homologous Recombination by Mec1/ATR Ensures Robust Suppression of Gross Chromosomal Rearrangements
Authors: Xie Bokun , Sanford Ethan James , Hung Shih-Hsun , Wagner Mateusz Maciej , Heyer Wolf-Dietrich , Smolka Marcus B.
Published: November 2023

The Mec1/ATR kinase is crucial for genome stability, yet the mechanism by which it prevents gross chromosomal rearrangements (GCRs) remains unknown. Here we find that in cells with deficient Mec1 signaling, GCRs accumulate due to the deregulation of multiple steps in homologous recombination (HR). Mec1 primarily suppresses GCRs through its role in activating the canonical checkpoint kinase Rad53, which ensures the proper control of DNA end resection. Upon loss of Rad53 signaling and resection control, Mec1 becomes hyperactivated and triggers a salvage pathway in which the Sgs1 helicase is recruited to sites of DNA lesions via the 911-Dpb11 scaffolds to favor heteroduplex rejection and limit HR-driven GCR accumulation. Fusing an ssDNA recognition domain to Sgs1 bypasses the requirement of Mec1 signaling for GCR suppression and nearly eliminates D-loop formation, thus preventing non-allelic recombination events. We propose that Mec1 regulates multiple steps of HR to prevent GCRs while ensuring balanced HR usage when needed for promoting tolerance to replication stress.
Single-cell and spatial detection of senescent cells using DeepScence
Authors: Qu Yilong , Dong Runze , Gu Liangcai , Chan Cliburn , Xie Jichun , Glass Carolyn , Wang Xiao-Fan , Nixon Andrew , Ji Zhicheng
Published: November 2023

Accurately identifying senescent cells is essential for studying their spatial and molecular features. We developed DeepScence, a method based on deep neural networks, to identify senescent cells in single-cell and spatial transcriptomics data. DeepScence is based on CoreScence, a senescence-associated gene set we curated that incorporates information from multiple published gene sets. We demonstrate that DeepScence can accurately identify senescent cells in single-cell gene expression data collected both in vitro and in vivo, as well as in spatial transcriptomics data generated by different platforms, substantially outperforming existing methods.
Prokrustean Graph: A substring index for rapid k-mer size analysis
Authors: Park Adam , Koslicki David
Published: November 2023

Despite the widespread adoption ofk-mer-based methods in bioinformatics, understanding the influence ofk-mer sizes remains a persistent challenge. Selecting an optimalk-mer size or employing multiplek-mer sizes is often arbitrary, application-specific, and fraught with computational complexities. Typically, the influence ofk-mer size is obscured by the outputs of complex bioinformatics tasks, such as genome analysis, comparison, assembly, alignment, and error correction. However, it is frequently overlooked that every method is built above a well-definedk-mer-based object like Jaccard Similarity, de Bruijn graphs,k-mer spectra, and Bray-Curtis Dissimilarity. Despite these objects offering a clearer perspective on the role ofk-mer sizes, the dynamics ofk-mer-based objects with respect tok-mer sizes remain surprisingly elusive.

This paper introduces a computational framework that generalizes the transition ofk-mer-based objects acrossk-mer sizes, utilizing a novel substring index, the Prokrustean graph. The primary contribution of this framework is to compute quantities associated withk-mer-based objects for allk-mer sizes, where the computational complexity depends solely on the number of maximal repeats and is independent of the range ofk-mer sizes. For example, counting vertices of compacted de Bruijn graphs fork= 1, …, 100 can be accomplished in mere seconds with our substring index constructed on a gigabase-sized read set.

Additionally, we derive a space-efficient algorithm to extract the Prokrustean graph from the Burrows-Wheeler Transform. It becomes evident that modern substring indices, mostly based on longest common prefixes of suffix arrays, inherently face difficulties at exploring varyingk-mer sizes due to their limitations at grouping co-occurring substrings.

We have implemented four applications that utilize quantities critical in modern pangenomics and metagenomics. The code for these applications and the construction algorithm is available athttps://github.com/KoslickiLab/prokrustean.
Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome
Authors: Olm Matthew R. , Spencer Sean P. , Silva Evelyn Lemus , Sonnenburg Justin L.
Published: November 2023

IgA, the most highly produced human antibody, is continually secreted into the gut to shape the intestinal microbiota. Methodological limitations have critically hindered defining which microbial strains are targeted by IgA and why. Here, we develop a new technique, Metagenomic Immunoglobulin Sequencing (MIG-Seq), and use it to determine IgA coating levels for thousands of gut microbiome strains in healthy humans. We find that microbes associated with both health and disease have higher levels of coating, and that microbial genes are highly predictive of IgA binding levels, with mucus degradation genes especially correlated with high binding. We find a significant reduction in replication rates among microbes bound by IgA, and demonstrate that IgA binding is more correlated with host immune status than traditional microbial abundance measures. This study introduces a powerful technique for assessing strain-level IgA binding in human stool, paving the way for deeper understanding of IgA-based host microbe interactions.
Sex-dependent effects of angiotensin type 2 receptor expressing medial prefrontal cortex (mPFC) interneurons in fear extinction learning
Authors: Smith Hannah C. , Yu Zhe , Iyer Laxmi , Marvar Paul J.
Published: November 2023

Background

The renin-angiotensin system (RAS) has been identified as a potential therapeutic target for PTSD, though its mechanisms are not well understood. Brain angiotensin type 2 receptors (AT2Rs) are a subtype of angiotensin II receptors located in stress and anxiety-related regions, including the medial prefrontal cortex (mPFC), but their function and mechanism in the mPFC remain unexplored. We therefore used a combination of imaging, cre/lox, and behavioral methods to investigate mPFC-AT2R-expressing neuron involvement in fear learning.

Methods

To characterize mPFC-AT2R-expressing neurons in the mPFC, AT2R-Cre/td-Tomato male and female mice were used for immunohistochemistry (IHC). mPFC brain sections were stained with glutamatergic or interneuron markers, and density of AT2R+cells and colocalization with each marker was quantified. To assess fear-related behaviors in AT2R-flox mice, we selectively deleted AT2R from mPFC neurons using an AAV-Cre virus. Mice then underwent Pavlovian auditory fear conditioning, approach/avoidance, and locomotion testing.

Results

IHC results revealed that AT2R is densely expressed in the mPFC. Furthermore, AT2R is primarily expressed in somatostatin interneurons in females but not males. Following fear conditioning, mPFC-AT2R deletion impaired extinction in female but not male mice. Locomotion was unaltered by mPFC-AT2R deletion in males or females, while AT2R-deleted females had increased exploratory behavior.

Conclusion

These results lend support for mPFC-AT2R+ neurons as a novel subgroup of somatostatin interneurons that influence fear extinction in a sex-dependent manner. This furthers underscores the role of mPFC in top-down regulation and a unique role for peptidergic (ie., angiotensin) mPFC regulation of fear and sex differences.
Muscle cofilin alters neuromuscular junction postsynaptic development to strengthen functional neurotransmission
Authors: Christophers Briana , Leahy Shannon N. , Soffar David B. , von Saucken Victoria E. , Broadie Kendal , Baylies Mary K.
Published: November 2023

Cofilin, an actin severing protein, plays critical roles in muscle sarcomere addition and maintenance. Our previous work has shownDrosophilacofilin (DmCFL) knockdown causes progressive deterioration of muscle structure and function and produces features seen in nemaline myopathy (NM) caused by cofilin mutations. We hypothesized that disruption of actin cytoskeleton dynamics byDmCFLknockdown would impact other aspects of muscle development, and, thus, conducted an RNA sequencing analysis which unexpectedly revealed upregulated expression of numerous neuromuscular junction (NMJ) genes. We found that DmCFL is enriched in the muscle postsynaptic compartment and that DmCFL deficiency causes F-actin disorganization in this subcellular domain prior to the sarcomere defects observed later in development. Despite NMJ gene expression changes, we found no significant changes in gross presynaptic Bruchpilot active zones or total postsynaptic glutamate receptor levels. However,DmCFLknockdown results in mislocalization of glutamate receptors containing the GluRIIA subunit in more deteriorated muscles and neurotransmission strength is strongly impaired. These findings expand our understanding of cofilin’s roles in muscle to include NMJ structural development and suggest that NMJ defects may contribute to NM pathophysiology.

Summary statement

Cofilin regulates muscle postsynaptic actin organization, structural maintenance, glutamate receptor composition, and neuromuscular junction function in aDrosophilanemaline myopathy disease model.
Versatile toolkit for highly-efficient and scarless overexpression of circular RNAs
Authors: Stringer Brett W. , Gabryelska Marta , Marri Shashikanth , Clark Letitia , Lin He , Gantley Laura , Liu Ryan , Wilusz Jeremy E. , Conn Vanessa M. , Conn Simon J.
Published: November 2023

Circular RNAs (circRNAs) are a class of single-stranded, covalently closed RNA that contain a unique back-splice junction (bsj) sequence created by the ligation of their 5’ and 3’ ends via spliceosome-catalyzed back-splicing. A key step in illuminating the cellular roles of specific circRNAs is via increasing their expression. This is frequently done by transfecting cells with plasmid DNA containing cloned exons from which the circRNA is transcribed, flanked by sequences that promote back-splicing. We observed that commonly used plasmids lead to the production of circRNAs with molecular scars at the circRNA bsj. Stepwise redesign of the cloning vector corrected this problem, ensuringbona fidecircRNAs are produced with their natural bsj at high efficiency. The fidelity of circRNAs produced from this new construct was validated by RNA sequencing and also functionally validated. To increase the utility of this modified resource for expressing circRNA, we developed an expanded set of vectors incorporating this design that (i) enables selection with a variety of antibiotics and fluorescent proteins, (ii) employs a range of promoters varying in promoter strength and (iii) generated a complementary set of lentiviral plasmids for difficult-to-transfect cells. These resources provide a novel and versatile toolkit for high-efficiency and scarless overexpression of circular RNAs that fulfill a critical need for the investigation of circRNA function.
Solving the time-dependent protein distributions for autoregulated bursty gene expression using spectral decomposition
Authors: Wu Bingjie , Holehouse James , Grima Ramon , Jia Chen
Published: November 2023

In this study, we obtain an exact time-dependent solution of the chemical master equation (CME) of an extension of the two-state telegraph model describing bursty or non-bursty protein expression in the presence of positive or negative autoregulation. Using the method of spectral decomposition, we show that the eigenfunctions of the generating function solution of the CME are Heun functions, while the eigenvalues can be determined by solving a continued fraction equation. Our solution generalizes and corrects a previous time-dependent solution for the CME of a gene circuit describing non-bursty protein expression in the presence of negative autoregulation [“Exact time-dependent solutions for a self-regulating gene.” Phys. Rev. E 83: 062902 (2011)]. In particular, we clarify that the eigenvalues are generally not real as previously claimed. We also investigate the relationship between different types of dynamic behavior and the type of feedback, the protein burst size, and the gene switching rate.
Nationwide SARS-CoV-2 Seroprevalence Trends in the Netherlands in the Variant of Concern Era, 2021-2022: an Ongoing Prospective Cohort Study
Authors: Vos Eric R.A. , van Hagen Cheyenne C.E. , Wong Denise , Smits Gaby , Kuijer Marjan , Wijmenga-Monsuur Alienke J. , Kaczorowska Joanna , van Binnendijk Robert S. , van der Klis Fiona R.M. , den Hartog Gerco , de Melker Hester E.
Published: November 2023

Background

Repeated population-based SARS-CoV-2 serosurveillance is key in complementing other surveillance tools.

Aim

Assessing trends in infection- and/or vaccine-induced immunity, including breakthrough infections, among (sub)groups and regions in the Dutch population during the Variant of Concern (VOC)-era whilst varying levels of stringency, to evaluate population immunity dynamics and inform future pandemic response planning.

Methods

In this prospective population-based cohort, randomly-selected participants (n=9,985) aged 1-92 years (recruited since early-2020) donated home-collected fingerstick blood samples at six timepoints in 2021-2022, covering waves dominated by Alpha, Delta, and Omicron (BA.1, BA.2, BA.5). IgG antibody assessments against Spike-S1 and Nucleoprotein were combined with vaccination- and testing data to estimate infection-induced (inf) and total (infection- and vaccination-induced) seroprevalence.

Results

In 2021, nationwide inf-seroprevalence rose modestly from 12% since Alpha to 26% amidst Delta, while total seroprevalence increased rapidly to nearly 90%, particularly fast in vulnerable groups (i.e., elderly and those with comorbidities). Highest infection rates were noticeable in adolescents and young adults, low/middle educated elderly, non-Western, contact professions (other than healthcare), and low-vaccination coverage regions. In 2022, following Omicron emergence, inf-seroprevalence elevated sharply to 62% and further to 86%, with frequent breakthrough infections and reduction of seroprevalence dissimilarities between most groups. Whereas >90% of <60-year-olds had been infected, 30% of vaccinated vulnerable individuals had not acquired hybrid immunity.

Conclusion

Although total SARS-CoV-2 seroprevalence had increased rapidly, infection rates were unequally distributed within the Dutch population. Ongoing tailored vaccination efforts and (sero-)monitoring of vulnerable groups remain important given their lowest rate of hybrid immunity and highest susceptibility to severe disease.