bluuebunny/crossref_metadata_2025 huggingface dataset:
Biogenesis, engineering and function of membranes in the CO2-fixing pyrenoid
Authors: Hennacy Jessica H. , Atkinson Nicky , Kayser-Browne Angelo , Ergun Sabrina L. , Franklin Eric , Wang Lianyong , Kafri Moshe , Fauser Friedrich , Vilarrasa-Blasi Josep , Jinkerson Robert E. , McCormick Alistair J. , Jonikas Martin C.
Published: August 2024

Summary Paragraph

Approximately one-third of global CO2assimilation is performed by the pyrenoid1, a liquid-like organelle found in most algae and some plants2. Specialized membranes are hypothesized to drive CO2assimilation in the pyrenoid by delivering concentrated CO23,4, but their biogenesis and function have not been experimentally characterized. Here, we show that homologous proteins SAGA1 and MITH1 mediate the biogenesis of the pyrenoid membrane tubules in the model algaChlamydomonas reinhardtiiand are sufficient to reconstitute pyrenoid-traversing membranes in a heterologous system, the plantArabidopsis thaliana. SAGA1 localizes to the regions where thylakoid membranes transition into tubules and is necessary to initiate tubule formation. MITH1 localizes to the tubules and is necessary for their extension through the pyrenoid. Tubule-deficient mutants exhibit growth defects under CO2-limiting conditions, providing evidence for the function of membrane tubules in CO2delivery to the pyrenoid. Furthermore, these mutants form multiple aberrant condensates of pyrenoid matrix, indicating that a normal tubule network promotes the coalescence of a single pyrenoid. The reconstitution of pyrenoid-traversing membranes in a plant represents a key milestone toward engineering a functional pyrenoid into crops for improving crop yields. More broadly, our study demonstrates the functional importance of pyrenoid membranes, identifies key biogenesis factors, and paves the way for the molecular characterization of pyrenoid membranes across the tree of life.
Examining Fetal Sex-Specific Placental DNA Methylation Intensities and Variability PostIn VitroFertilization
Authors: Lemaire Melanie , Smith Keaton Warrick , Wilson Samantha L
Published: August 2024

Infertility impacts up to 17.5% of reproductive-aged couples worldwide. To aid in conception, many couples turn to assisted reproductive technology, such asin vitrofertilization (IVF). IVF can introduce both physical and environmental stressors that may alter DNA methylation regulation, an important and dynamic process during early fetal development. This meta-analysis aims to assess the differences in the placental DNA methylome between spontaneous and IVF pregnancies. We identified three studies from NCBI GEO that measured DNA methylation with an Illumina Infinium Microarray in post-delivery placental tissue from both IVF and spontaneous pregnancies with a total of 575 samples for analysis (n = 96 IVF, n = 479 spontaneous). While there were no significant or differentially methylated CpGs in mixed or female stratified populations, we identified 9 CpGs that reached statistical significance (FDR <0.05) between IVF (n = 56) and spontaneous (n = 238) placentae. 7 autosomal CpGs and 1 X chromosome CpG was hypermethylated and 2 autosomal CpGs were hypomethylated in the IVF placentae compared to spontaneous. Autosomal CpGs closest toLIPJ,EEF1A2, andFBRSL1also met our criteria to be classified as biologically differentially methylated CpGs (FDR <0.05, |Δβ|>0.05). When analyzing variability differences in Δβvalues between IVF females, IVF males, spontaneous females and spontaneous males, we found a significant shift to greater variability in the both IVF males and females compared to spontaneous (p <2.2e-16, p <2.2e-16). Trends of variability were further analyzed in the biologically differentially methylated autosomal CpGs nearLIPJ EEF1A2, andFBRSL1, and while these regions were statistically significant in males, the female Δβs and ΔCoVs followed a similar trend that differed in magnitude. In males and females there was a statistically significant difference in proportions of endothelial cells, hofbauer cells, stromal cells and syncytiotrophoblasts between spontaneous andin vitroFertilization (IVF) populations. We also observed significant differences between sex within reproduction type in syncytiotrophoblasts and trophoblasts. The results of this study are critical to further understand the impact of IVF on tissue epigenetics which may help to investigate the connections between IVF and negative pregnancy outcomes. Additionally, our study supports sex specific differences in placental DNA methylation and cell composition should be considered as factors for future placental DNA methylation analyses.
Commensal Yeast PromotesSalmonellaTyphimurium Virulence
Authors: Jaswal Kanchan , Todd Olivia A , Flores Audelo Roberto C , Santus William , Paul Saikat , Singh Manmeet , Miao Jian , Underhill David M , Peters Brian M , Behnsen Judith
Published: August 2024

Enteric pathogens engage in complex interactions with the host and the resident microbiota to establish gut colonization. Although mechanistic interactions between enteric pathogens and bacterial commensals have been extensively studied, whether and how commensal fungi affect pathogenesis of enteric infections remains largely unknown. Here we show that colonization with the common human gut commensal fungusCandida albicansworsened infections with the enteric pathogenSalmonella entericaserovar Typhimurium. Presence ofC. albicansin the mouse gut increasedSalmonellacecum colonization and systemic dissemination. We investigated the underlying mechanism and found thatSalmonellabinds toC. albicansvia Type 1 fimbriae and uses its Type 3 Secretion System (T3SS) to deliver effector proteins intoC. albicans. A specific effector, SopB, was sufficient to manipulateC. albicansmetabolism, triggering increased arginine biosynthesis inC. albicansand the release of millimolar amounts of arginine into the extracellular environment. The released arginine, in turn, induced T3SS expression inSalmonella, increasing its invasion of epithelial cells.C. albicansdeficient in arginine production was unable to increaseSalmonellavirulencein vitroorin vivo. In addition to modulating pathogen invasion, arginine also directly influenced the host response to infection. Arginine-producingC. albicansdampened the inflammatory response duringSalmonellainfection, whereasC. albicansdeficient in arginine production did not. Arginine supplementation in the absence ofC. albicansincreased the systemic spread ofSalmonellaand decreased the inflammatory response, phenocopying the presence ofC. albicans. In summary, we identifiedC. albicanscolonization as a susceptibility factor for disseminatedSalmonellainfection, and arginine as a central metabolite in the cross-kingdom interaction between fungi, bacteria, and host.
Organ Chips with integrated multifunctional sensors enable continuous metabolic monitoring at controlled oxygen levels
Authors: Izadifar Zohreh , Charrez Berenice , Almeida Micaela , Robben Stijn , Pilobello Kanoelani , van der Graaf-Mas Janet , Benz Max , Marquez Susan L. , Ferrante Thomas C. , Shcherbina Kostyantyn , Gould Russell , LoGrande Nina T. , Sesay Adama M. , Ingber Donald E.
Published: August 2024

Despite remarkable advances in Organ-on-a-chip (Organ Chip) microfluidic culture technology, recreating tissue-relevant physiological conditions, such as the region-specific oxygen concentrations, remains a formidable technical challenge, and analysis of tissue functions is commonly carried out using one analytical technique at a time. Here, we describe two-channel Organ Chip microfluidic devices fabricated from polydimethylsiloxane and gas impermeable polycarbonate materials that are integrated with multiple sensors, mounted on a printed circuit board and operated using a commercially available Organ Chip culture instrument. The novelty of this system is that it enables the recreation of physiologically relevant tissue-tissue interfaces and oxygen tension as well as non-invasive continuous measurement of transepithelial electrical resistance, oxygen concentration and pH, combined with simultaneous analysis of cellular metabolic activity (ATP/ADP ratio), cell morphology, and tissue phenotype. We demonstrate the reliable and reproducible functionality of this system in living human Gut and Liver Chip cultures. Changes in tissue barrier function and oxygen tension along with their functional and metabolic responses to chemical stimuli (e.g., calcium chelation, oligomycin) were continuously and noninvasively monitored on-chip for up to 23 days. A physiologically relevant microaerobic microenvironment that supports co-culture of human intestinal cells with livingLactococcus lactisbacteria also was demonstrated in the Gut Chip. The integration of multi-functional sensors into Organ Chips provides a robust and scalable platform for the simultaneous, continuous, and non-invasive monitoring of multiple physiological functions that can significantly enhance the comprehensive and reliable evaluation of engineered tissues in Organ Chip models in basic research, preclinical modeling, and drug development.
Aperiodic neural activity distinguishes between phasic and tonic REM sleep
Authors: Rosenblum Yevgenia , Bogdány Tamás , Nádasy Lili Benedikta , Kovács Ilona , Gombos Ferenc , Ujma Péter , Bódizs Róbert , Adelhöfer Nico , Simor Péter , Dresler Martin
Published: August 2024

Introduction

Traditionally categorized as a uniform sleep phase, rapid eye movement (REM) sleep exhibits substantial heterogeneity with its phasic and tonic constituents showing marked differences regarding neuronal network activity, environmental alertness and information processing. Here, we investigate how tonic and phasic states differ with respect to aperiodic neural activity, a marker of arousal levels, sleep stages, depth of sleep and sleep intensity. We also attempt to challenge the binary categorisation of REM sleep states by introducing graduality into their definition. Specifically, we quantify the intensity of phasic oculomotor events and investigate their temporal relationships with aperiodic activity.

Method

We analyzed 57 polysomnographic recordings from three open-access datasets of healthy young volunteers aged 21.7±1.4 years. REM sleep heterogeneity was assessed using either binary phasic-tonic categorization or quantification of eye movement (EM) amplitudes detected by electrooculography with the YASA algorithm. Slopes of the aperiodic power component measured by electroencephalography in the low (2–30Hz) and high (30–48Hz) frequency bands were calculated using the Irregularly Resampled Auto-Spectral Analysis. For statistical analyses, we used ANOVA, Spearman correlations and cross-correlations.

Results

The binary approach revealed that the phasic state is characterized by steeper low-band aperiodic slopes compared to the tonic state with the strongest effect observed over the frontal area. The phasic state also showed flatter high-band slopes with the strongest effect over central and parietal areas. The gradual approach confirmed this result further showing that higher EM amplitudes are linked to steeper low-band and flatter high-band aperiodic slopes. The temporal analysis within REM episodes revealed that aperiodic activity preceding or following EM events did not cross-correlate with EM amplitudes.

Conclusion

This study demonstrates that aperiodic slopes can serve as a reliable objective marker able to differentiate between phasic and tonic constituents of REM sleep and reflect the intensity of phasic oculomotor events for instantaneous measurements. However, EM events could not be predicted by preceding aperiodic activity and vice versa, at least not with scalp electroencephalography.
Discrete Ollivier-Ricci Flow Finds Distinct Subpopulations of Patients Treated with PD-1 Inhibition
Authors: Bannon James J , Cantor Charles R , Mishra Bud
Published: August 2024

In recent years immune checkpoint inhibitors (ICIs), also called immune checkpoint blockers, have revolutionized the standard of care for patients with cancers of many types. Researchers across many disciplines have endeavored to find biomarkers of response to ICI therapy but so far little consensus has been reached. In this paper we attempt to cluster patients in an unsupervised manner using discrete Ollivier-Ricci Flow (ORF). Our method surfaces populations with distinct survival curves which in turn allows us to find many potential biomarkers, including gene expression modules. We believe the algorithm may be of independent interest for clustering other datasets in a diverse set of research areas.
Deletion of endocannabinoid synthesizing enzyme DAGLα from cerebellar Purkinje cells decreases social preference and elevates anxiety
Authors: Smith Gabriella , McCoy Kathleen , Di Prisco Gonzalo Viana , Kuklish Alexander , Grant Emma , Bhat Mayil , Patel Sachin , Mackie Ken , Atwood Brady , Kalinovsky Anna
Published: August 2024

The endocannabinoid (eCB) signaling system is robustly expressed in the cerebellum starting from the embryonic developmental stages to adulthood. There it plays a key role in regulating cerebellar synaptic plasticity and excitability, suggesting that impaired eCB signaling will lead to deficits in cerebellar adjustments of ongoing behaviors and cerebellar learning. Indeed, human mutations inDAGLαare associated with neurodevelopmental disorders. In this study, we show that selective deletion of the eCB synthesizing enzyme diacylglycerol lipase alpha (Daglα) from mouse cerebellar Purkinje cells (PCs) alters motor and social behaviors, disrupts short-term synaptic plasticity in both excitatory and inhibitory synapses, and reduces Purkinje cell activity during social exploration. Our results provide the first evidence for cerebellar-specific eCB regulation of social behaviors and implicate eCB regulation of synaptic plasticity and PC activity as the neural substrates contributing to these deficits.

Abstract Figure

Graphical abstract.

Cerebellar anatomy, morphology of Purkinje cells, localization, density, and spontaneous activity of excitatory and inhibitory synapses are normal in cerebellar-Purkinje-cell-specific Daglα KOs. However, endocannabinoid-dependent short-term synaptic plasticity (DSE and DSI) and activity of Purkinje cells in lobe VI during social exploration are dramatically reduced, and the KO mice exhibit alterations in sensorimotor coordination, deceased social preference, and increased anxiety.
A site selection decision framework for effective kelp restoration
Authors: Giraldo-Ospina Anita , Bell Tom , Carr Mark H. , Caselle Jennifer E.
Published: August 2024

Highlights

Site selection is one of the most important factors for ecosystem restoration success

A spatial prioritization framework for application to kelp restoration in California

The framework merges kelp metrics derived fromin-situsurveys and satellite imagery

Site prioritization classification for every kelp forest site in California

This framework can be applied to other species and regions with similar datasets

We present a decision support framework in the form of a spatially explicit site classification scheme to prioritize locations for conducting kelp restoration. The framework was created for the entire coast of California, where kelp has been lost and restoration projects are increasingly proposed, but the framework is broadly applicable to other coastal habitats or species that are being considered for restoration. We first created spatial distribution models using almost two decades ofin situkelp forest monitoring data and a comprehensive suite of environmental and biological variables, and used the outputs to evaluate the historical stability of kelp forests prior to a marine heatwave (MHW). We then used kelp canopy abundance data derived from satellite imagery to measure the impact of the MHW (i.e. extent of forest loss) and the recent state of kelp forests, including the trend of increase or decrease following the MHW. Finally, we integrated these site-specific kelp metrics to construct a classification tree for prioritizing restoration sites. Outputs of site prioritization are mapped across the study region, readily usable for managers and restoration practitioners with site-specific recommendations for restoration approaches. The framework can be updated due to knowledge of the important predictors of kelp and with new satellite imagery. Further, the framework can be adapted to other species and regions with similar data sets. This regional site selection framework is intended to be used in addition to socio-ecological, socio-economic, and administrative considerations.
Coralline companions: Exploring microbes in coral ecosystems
Authors: Bharti Daizy , Ghosh Arnab , Kumar Santosh
Published: August 2024

Coral reefs exhibit remarkable resilience to natural disturbances but face challenges due to global changes and emerging diseases. In the present study, we recorded a total of 51 ciliates and over 400 bacteria associated with healthy and diseased corals from the Ramsar site Gulf of Mannar Marine National Park, India, based on morphology, silver staining, and Next Generation Sequencing. Our study contributes to the growing understanding of ciliate diversity and provides insights into the dynamics of ciliate-associated coral diseases, towards developing effective biocontrol agents for coral bleaching and conservation strategies to safeguard coral reef ecosystems.
Overcoming cryo-EM map anisotropy reveals ALK-cytokine assemblies with distinct stoichiometries
Authors: Felix Jan , De Munck Steven , Bazan J. Fernando , Savvides Savvas N.
Published: August 2024

Activation of Anaplastic lymphoma kinase (ALK) and leukocyte tyrosine kinase (LTK) by their cognate cytokines ALKAL2 and ALKAL1 play important roles in development, metabolism, and cancer. Recent structural studies revealed ALK/LTK-cytokine assemblies with distinct stoichiometries. Structures of ALK-ALKAL2 and LTK-ALKAL1 complexes with 2:1 stoichiometry determined by X-ray crystallography (De Muncket al.Nature, 2021) contrasted the 2:2 ALK-ALKAL2 complexes determined by cryo-EM (Reshetnyaket al.,Nature, 2021) and X-ray crystallography (Liet al., Nature, 2021). Here, we show based on reanalysis of the cryo-EM data deposited in EMPIAR- 10930 that over half of the ALK-ALKAL2 particles in the dataset are classified into 2D classes obeying a 2:1 stoichiometry besides the originally reported structure displaying 2:2 stoichiometry. Unlike particles representing the 2:2 ALK-ALKAL2 complex, particles for the 2:1 ALK-ALKAL2 complex suffer severely from preferred orientations that resulted in cryo-EM maps displaying strong anisotropy. Here, we show that extensive particle orientation rebalancing in cryoSPARC followed by 3D refinement with Blush regularization in RELION constitutes an effective strategy for avoiding map artefacts relating to preferred particle orientations and report a 3D reconstruction of the 2:1 ALK-ALKAL2 complex to 3.2 Å resolution from EMPIAR-10930. This new cryo-EM structure together with the crystal structures of ALK-ALKAL2 and LTK-ALKAL1 complexes with 2:1 stoichiometry reconciles a common receptor dimerization mode for ALK and LTK and provides direct evidence for the presence of an ALK-ALKAL2 complex with 2:1 stoichiometry next to the reported 2:2 stoichiometric assembly in the EMPIAR-10930 dataset. Finally, our analysis emphasizes the importance of public deposition of raw cryo-EM data to allow reanalysis and interpretation.
A variant centric analysis of allele sharing in dogs and wolves
Authors: Funk Matthew W. , Kidd Jeffrey M.
Published: August 2024

Canines are an important model system for genetics and evolution. Recent advances in sequencing technologies have enabled the creation of large databases of genetic variation in canines, but analysis of allele sharing among canine groups has been limited. We applied GeoVar, an approach originally developed to study the sharing of single nucleotide polymorphisms across human populations, to assess the sharing of genetic variation among groups of wolves, village dogs, and breed dogs. Our analysis shows that wolves differ from each other at an average of approximately 2.3 million sites while dogs from the same breed differ at nearly 1 million sites. We find that 22% of variants are common across wolves, village dogs, and breed dogs, that ∼16% of variable sites are common across breed dogs, and that nearly half of the differences between two dogs of different breeds are due to sites that are common in all clades. These analyses represent a succinct summary of allele sharing across canines and illustrate the effects of canine history on the apportionment of genetic variation.
Emergence of temporal noise hierarchy in co-regulated genes of multi-output feed-forward loop
Authors: Nandi Mintu
Published: August 2024

Natural variations in gene expression, called noise, are fundamental to biological systems. The expression noise can be beneficial or detrimental to cellular functions. While the impact of noise on individual genes is well-established, our understanding of how noise behaves when multiple genes are co-expressed by shared regulatory elements within transcription networks remains elusive. This lack of understanding extends to how the architecture and regulatory features of these networks influence noise. To address this gap, we study the multi-output feed-forward loop motif. The motif is prevalent in bacteria and yeast and influences co-expression of multiple genes by shared transcription factors. Focusing on a two-output variant of the motif, the present study explores the interplay between its architecture, co-expression patterns of the two genes (including symmetric and asymmetric expressions), and the associated noise dynamics. We employ a stochastic modeling approach to investigate how the binding affinities of the transcription factors influence symmetric and asymmetric expression patterns and the resulting noise dynamics in the co-expressed genes. This knowledge could guide the development of strategies for manipulating gene expression patterns through targeted modulation of transcription factor binding affinities.
Reassessing the Neural Correlates of Social Exclusion: A Replication Study of the Cyberball Paradigm Using Arterial Spin Labelling
Authors: Labek Karin , Viviani Roberto
Published: August 2024

Background/Objectives

The cyberball paradigm has been used in numerous neuroimaging studies to elicit activation in neural substrates of social exclusion, which have been interpreted in terms of activity associated with “social pain”. The objectives of the study were to assess not only the replicability but also the specificity of the areas activated by this paradigm.

Methods

Functional imaging with arterial spin labelling, an approach to image longer mental states.

Results

we replicated findings of previous meta-analyses of this paradigm in the inferior frontal gyrus and ventral cingular cortex. However, these areas were also active in a watch condition (in which participants were not excluded), although less so.

Conclusions

These findings relativize a simple and specific interpretation of these areas as the neural substrates of social exclusion and social pain, as in previous studies. In a broader experimental context, similar activations have been reported by neuroimaging studies when semantic disambiguation and evaluation of action goals are required, an interpretation that may apply also to the effects elicited by this paradigm.
Clostridioides difficileToxins Unhinged: Allosterically Switchable Network Orientsβ-flap
Authors: Finn Lauren M. , Cummer Rebecca , Castagner Bastien , Keller Bettina G.
Published: August 2024

Allosteric proteins exhibit a functional response upon substrate binding far from the active site.Clostridioides difficiletoxins use allosteric binding by an endogenous co-factor to orchestrate self-cleavage from within the target cell. This binding event induces a conformational shift, primarily effecting a lever-like “β-flap” region, with two known orientations. We uncovered a mechanism for this allosteric transition using extensive atomistic MD simulations and computational and experimental mutagenesis. The mechanism relies on a switchable interaction network. The most prominent interaction pair is K600–E743, with K600 interactions explaining ∼70 % of the allosteric effect. Rather than gradually morphing between two end states, the interaction network adopts two mutually exclusive configurations in the active and inactive state. Similar switchable networks may explain allostery more broadly. This mechanism in particular could aid in drug development targeting theClostridioides difficiletoxins autoproteolysis.
Spatial Transcriptomic Analysis Reveals HDAC Inhibition Modulates Microglial Dynamics to Protect Against Ischemic Stroke in Mice
Authors: Jayaraj Kevin , Kumar Ritesh , Shyamasundar Sukanya , Arumugam Thiruma V , Polepalli Jai S , Dheen S Thameem
Published: August 2024

Ischemic stroke significantly contributes to global morbidity and disability through a cascade of neurological responses. Microglia, the immune modulators within the brain, exhibit dual roles in exacerbating and ameliorating ischemic injury through neuroinflammatory and neuroprotective roles, respectively. Despite emerging insights into microglia’s role in neuronal support, the potential of epigenetic intervention to modulate microglial activity remains largely unexplored. We have previously shown that sodium butyrate, a histone deacetylase inhibitor (HDACi) epigenetically regulates inflammatory response of microglia after ischemic stroke and this study was aimed to characterize the transcriptomic profiles of microglia and their spatial distribution in the stroke brain followed by HDACi administration. We hypothesized that the administration of HDACi epigenetically modulates microglial activation and a region-specific microglial phenotype in the stroke brain, shifting their phenotype from neurotoxic to neuroprotective and facilitating neuronal repair and recovery in the ischemic penumbra. Utilizing a rodent model of middle cerebral artery occlusion (MCAo), spatial transcriptomics and 3D morphometric reconstruction techniques were employed to investigate microglial responses in critical penumbral regions, such as the hippocampus, thalamus, cortex and striatum following HDACi administration. We found that HDACi significantly altered the microglial transcriptomic landscape involving biological pathways of neuroinflammation, neuroprotection and phagocytosis as well as morphological phenotype, promoting a shift towards reparative, neurotrophic profiles within the ischemic penumbra. These changes were also associated with enhanced neuronal survival and reduced neuroinflammation in specific regions in the ischemic brain. By elucidating the mechanisms through which HDAC inhibition influences microglial function, our findings propose therapeutic avenues for neuroprotection and rehabilitation in ischemic stroke, and possibly other neurodegenerative conditions that involve microglia-mediated neuroinflammation.
Potent LILRB1 D1D2-containing antibodies inhibit RIFIN-mediated immune evasions
Authors: Wang Yizhuo , Tang Hengfang , Wang Wanxue , Li Ming , Zhu Chenchen , Dai Han , Zhao Hongxin , Wu Bo , Wang Junfeng
Published: August 2024

The spread of drug-resistant malaria parasites presents a major challenge to global efforts in malaria control, increasing the urgency for new treatments and vaccines. A promising approach involves developing antibodies that can counteract the parasite’s immune evasion mechanisms. In this study, we designed a receptor-containing antibody, targeting the D1D2 domain of the LILRB1 receptor, using a structure-based rational approach. We began with the MDB1 antibody as a scaffold and replaced the LILRB1-D3D4 insertion domain with D1D2.v, a high-affinity variant optimized through yeast surface display. The modified D1D2.v-IgG efficiently blocked the interaction between RIFIN#1 (from PF3D7_1254800) and LILRB1, thereby reversing the inhibition of NK cell activity caused by RIFIN#1. To further enhance this effect, we developed NK-biAb, a bispecific antibody based on D1D2.v-IgG that targets both RIFIN#1 and NKG2D receptors. NK-biAb exhibited superior biological performance compared to D1D2.v-IgG alone. These findings provide a clear framework for designing antibodies that target immune evasion in malaria, potentially guiding the development of more effective treatments and vaccines.
DNA methylation status classifies pleural mesothelioma cells according to their immune profile: implication for precision epigenetic therapy
Authors: Lofiego Maria Fortunata , Tufano Rossella , Bello Emma , Solmonese Laura , Marzani Francesco , Piazzini Francesca , Celesti Fabrizio , Caruso Francesca Pia , Rosaria Noviello Teresa Maria , Mortarini Roberta , Anichini Andrea , Ceccarelli Michele , Calabrò Luana , Maio Michele , Coral Sandra , Di Giacomo Anna Maria , Covre Alessia ,   the EPigenetic Immune-oncology Consortium Airc (EPICA) investigators
Published: August 2024

Background

co-targeting of immune checkpoint inhibitors (ICI) CTLA-4 and PD-1 has recently become the new first-line standard of care therapy of pleural mesothelioma (PM) patients, with a significant improvement of overall survival over conventional chemotherapy. The analysis by tumor histotype demonstrated a greater efficacy of ICI therapy in non-epithelioid (non-E)vsepithelioid (E) PM; although some E PM patients also benefit from treatment. This evidence suggests that molecular tumor features, beyond histotype, could be relevant to improve the efficacy of ICI therapy in PM. Among these, tumor DNA methylation emerges as a promising factor to explore, due to its potential role in driving the immune phenotype of cancer cells. Thus, we utilized a panel of cultured PM cells of different histotype, to provide preclinical evidence supporting the role of the tumor methylation landscape and of its pharmacologic modulation, to prospectively improve the efficacy of ICI therapy of PM patients.

Methods

the methylome profile (EPIC array) of distinct E (#5) and non-E (#9) PM cell lines was analyzed, followed by integrated analysis with their associated transcriptomic profile (Clariom S array), before and afterin vitrotreatment with the DNA hypomethylating agent (DHA) guadecitabine. The most variable methylated probes were selected to calculate the methylation score (CIMP index) for each cell line at baseline. Genes that were differentially expressed and methylated were then selected for gene ontology analysis.

Results

the CIMP index stratified PM cell lines in two distinct classes, CIMP (hyper-methylated; #7) and LOW (hypo-methylated; #7), regardless of their E or non-E histotype. Integrated analyses of methylome and transcriptome data revealed that CIMP PM cells had a substantial number of hyper-methylated, silenced genes, which negatively impacted their immune phenotype compared to LOW PM cells.

Treatment with DHA reverted the methylation-driven immune-compromised profile of CIMP PM cells and enhanced the constitutive immune-favorable profile of LOW PM cells.

Conclusion

the study highlighted the relevance of DNA methylation in shaping the constitutive immune classification of PM cells, that is independent from their histological subtypes. The identified role of DHA in shifting the phenotype of PM cells towards an immune-favorable state supports its role in clinical trials of precision epigenetic therapy combined with ICI.
A genome-wide association study identifies markers and candidate genes affecting tolerance to the wheat pathogenZymoseptoria tritici
Authors: Mikaberidze Alexey , McDonald Bruce A. , Kronenberg Lukas
Published: August 2024

Plants defend themselves against pathogens using either resistance, measured as the host’s ability to limit pathogen multiplication, or tolerance, measured as the host’s ability to reduce the negative effects of infection. Tolerance is a promising trait for crop breeding, but its genetic basis has rarely been studied and remains poorly understood. Here, we reveal the genetic basis of leaf tolerance to the fungal pathogenZymoseptoria triticithat causes the globally important septoria tritici blotch disease on wheat. Leaf tolerance toZ. triticiis a quantitative trait that was recently discovered in wheat by using automated image analyses that quantified the symptomatic leaf area and counted the number of pycnidia found on the same leaf. A genome-wide association study including both tolerance and resistance to STB found a strong negative genetic correlation between these traits, indicative of a trade-off. We identified four chromosome intervals associated with tolerance and a separate chromosome interval associated with resistance. Within these intervals, we identified candidate genes, including wall-associated kinases similar toStb6, the first cloned STB resistance gene. A trade-off between tolerance and resistance would hinder breeding simultaneously for both traits, but our findings suggest a way forward using marker-assisted breeding. We expect that the methods described here can be used to characterize tolerance to other fungal diseases that produce visible fruiting bodies, such as speckled leaf blotch on barley, potentially unveiling conserved tolerance mechanisms shared among plant species.
Detection of genome structural variation in normal cells and tissues by single molecule sequencing
Authors: Heid Johanna , Huang Zhenqiu , Lee Moonsook , Makhortov Sergey , Pan Elizabeth , Montagna Cristina , Sun Shixiang , Vijg Jan , Maslov Alexander Y.
Published: August 2024

Detecting somatic mutations in normal cells and tissues is notoriously challenging due to their low abundance, orders of magnitude below the sequencing error rate. While several techniques, such as single-cell and single-molecule sequencing, have been developed to identify somatic mutations, they are insufficient for detecting genomic structural variants (SVs), which have a significantly greater impact than single-nucleotide variants (SNVs). We introduce Single-Molecule Mutation Sequencing for Structural Variants (SMM-SV-seq), a novel method combining Tn5-mediated, chimera-free library preparation with the precision of error-corrected next-generation sequencing (ecNGS). This approach enhances SV detection accuracy without relying on independent supporting sequencing reads.

Our validation studies on human primary fibroblasts treated with varying concentrations of the clastogen bleomycin demonstrated a significant, up to tenfold and dose-dependent, increase in deletions and translocations 24 hours post-treatment. Evaluating SMM-SV-seq’s performance against established computational tools for SV detection, such as Manta and DELLY, using a well-characterized human cell line, SMM-SV-seq showed precision and recall rates of 61.9% and 85.8%, respectively, significantly outperforming Manta (10% precision, 23% recall) and DELLY (15% precision, 32% recall). Using SMM-SV-seq, we documented clear, direct evidence of negative selection against structural variants over time. After a single 2 Gy dose of ionizing radiation, SVs in normal human primary fibroblasts peaked at 24 hours post-intervention and then declined to nearly background levels by day six, highlighting the cellular mechanisms that selectively disadvantage cells harboring these mutations. Additionally, SMM-SV-seq revealed that BRCA1-deficient human breast epithelial cells are more susceptible to the mutagenic effects of ionizing radiation compared to BRCA1-proficient isogenic control cells, suggesting a potential molecular mechanism for increased breast cancer risk in BRCA1 mutation carriers.

SMM-SV-seq represents a significant advancement in genomic analysis, enabling the accurate detection of somatic structural variants in normal cells and tissues for the first time. This method complements our previously published Single-Molecule Mutation sequencing (SMM-seq), effective for detecting single-nucleotide variants (SNVs) and small insertions and deletions (INDELs). By addressing challenges such as self-ligation in library preparation and leveraging a powerful ecNGS strategy, SMM-SV-seq enhances the robustness of our genomic analysis toolkit. This breakthrough paves the way for new research into genetic variability and mutation processes, offering deeper insights that could advance our understanding of aging, cancer, and other human diseases.
ProCogGraph: A Graph-Based Mapping of Cognate Ligand Domain Interactions
Authors: Crown Matthew , Bashton Matthew
Published: August 2024

Motivation

Mappings of domain-cognate ligand interactions can enhance our understanding of the core concepts of evolution and be used to aid docking and protein design. Since the last available cognate-ligand domain database was released, the PDB has grown significantly and new tools are available for measuring similarity and determining contacts.

Results

We present ProCogGraph, a graph database of cognate-ligand domain mappings in PDB structures. Building upon the work of the predecessor database, PROCOGNATE, we use data-driven approaches to develop thresholds and interaction modes. We explore new aspects of domain-cognate ligand interactions, including the chemical similarity of bound cognate ligands and how domain combinations influence cognate ligand binding. Finally, we use the graph to add specificity to partial EC IDs, showing that ProCogGraph can complete partial annotations systematically through assigned cognate ligands.

Availability and Implementation

The ProCogGraph pipeline, database and flat files are available athttps://github.com/bashton-lab/ProCogGraphandhttps://doi.org/10.5281/zenodo.13165851.

Contact

matthew.bashton@northumbria.ac.uk

Supplementary information

Supplementary data are available atBioinformaticsonline.
PyBootNet: A Python Package for Bootstrapping and Network Construction
Authors: Akhavan Shayan R. , Kelley Scott T.
Published: August 2024

PyBootNet is a user-friendly Python package that integrates bootstrapping analysis and correlation network construction. The package offers functions for generating bootstrapped network metrics, statistically comparing network metrics among datasets, and visualizing bootstrapped networks. PyBootNet is designed to be accessible and efficient, with minimal dependencies and straightforward input requirements. To demonstrate its functionality, we applied PyBootNet functions to compare networks within two disparate microbial community datasets: a mouse gut microbiome study and a microbiome study of a built environment. The PyBootNet functions applied include data preprocessing, bootstrapping, correlation matrix calculation, network statistics computation, and network visualization. In both datasets, we show that PyBootNet can generate robust bootstrapped network metrics and identify significant differences in one or more network metrics between pairs of networks. We also show that PyBootNet can create bootstrapped network graphs and identify clusters of nodes that are highly interconnected. We also confirmed its computational efficiency and scalability, which allows it to handle large and complex datasets. PyBootNet provides a powerful and extendible Python bioinformatics solution for bootstrapping analysis and network construction that can be applied to microbial, gene, metabolite and other biological data appropriate for network correlation comparison and analysis.
Cspg4 sculpts oligodendrocyte precursor cell morphology
Authors: Bromley-Coolidge Samantha , Iruegas Diego , Appel Bruce
Published: August 2024

The extracellular matrix (ECM) provides critical biochemical and structural cues that regulate neural development. Chondroitin sulfate proteoglycans (CSPGs), a major ECM component, have been implicated in modulating oligodendrocyte precursor cell (OPC) proliferation, migration, and maturation, but their specific roles in oligodendrocyte lineage cell (OLC) development and myelinationin vivoremain poorly understood. Here, we use zebrafish as a model system to investigate the spatiotemporal dynamics of ECM deposition and CSPG localization during central nervous system (CNS) development, with a focus on their relationship to OLCs. We demonstrate that ECM components, including CSPGs, are dynamically expressed in distinct spatiotemporal patterns coinciding with OLC development and myelination. We found that zebrafish lackingcspg4function produced normal numbers of OLCs, which appeared to undergo proper differentiation. However, OPC morphology in mutant larvae was aberrant. Nevertheless, the number and length of myelin sheaths produced by mature oligodendrocytes were unaffected. These data indicate that Cspg4 regulates OPC morphogenesisin vivo, supporting the role of the ECM in neural development.
Computational Prediction of Multiple Antigen Epitopes
Authors: Viswanathan R. , Carroll M. , Roffe A. , Fajardo J.E. , Fiser A.
Published: August 2024

Motivation

Identifying antigen epitopes is essential in medical applications, such as immunodiagnostic reagent discovery, vaccine design, and drug development. Computational approaches can complement low-throughput, time-consuming, and costly experimental determination of epitopes. Currently available prediction methods, however, have moderate success predicting epitopes, which limits their applicability. Epitope prediction is further complicated by the fact that multiple epitopes may be located on the same antigen and complete experimental data is often unavailable.

Results

Here, we introduce the antigen epitope prediction program ISPIPab that combines information from two feature-based methods and a docking-based method. We demonstrate that ISPIPab outperforms each of its individual classifiers as well as other state-of-the-art methods, including those designed specifically for epitope prediction. By combining the prediction algorithm with hierarchical clustering, we show that we can effectively capture epitopes that align with available experimental data while also revealing additional novel targets for future experimental investigations.

Contact

raji@yu.edu

Supplementary information

Supplementary data are available atBioinformaticsonline.
Tunturi virus isolates and metagenome-assembled viral genomes provide insights into the virome of Acidobacteriota in Arctic tundra soils
Authors: Demina Tatiana , Marttila Heli , Pessi Igor S , Mannisto Minna K , Dutilh Bas E , Roux Simon , Hultman Jenni
Published: August 2024

Background: Arctic soils are climate-critical areas, where microorganisms play crucial roles in nutrient cycling processes. Acidobacteriota are phylogenetically and physiologically diverse bacteria that are abundant and active in Arctic tundra soils. Still, surprisingly little is known about acidobacterial viruses in general and those residing in the Arctic in particular. Here, we applied both culture-dependent and -independent methods to study the virome of Acidobacteriota in Arctic soils. Results: Five virus isolates, Tunturi 1-5, were obtained from Arctic tundra soils, Kilpisjarvi, Finland (69 N), using Tunturibacter spp. strains originating from the same area as hosts. The new virus isolates have tailed particles with podo- (Tunturi 1, 2, 3), sipho- (Tunturi 4), or myovirus-like (Tunturi 5) morphologies. The dsDNA genomes of the viral isolates are 63-98 kbp long, except Tunturi 5, which is a jumbo phage with a 309-kbp genome. Tunturi 1 and Tunturi 2 share 88% overall nucleotide identity, while the other three are not related to one another. For over half of the open reading frames in Tunturi genomes, no functions could be predicted. To further assess the Acidobacteriota-associated viral diversity in Kilpisjarvi soils, bulk metagenomes from the same soils were explored and a total of 1881 viral operational taxonomic units (vOTUs) were bioinformatically predicted. Almost all vOTUs (98%) were assigned to the class Caudoviricetes. For 125 vOTUs, including five (near-)complete ones, Acidobacteriota hosts were predicted. Acidobacteriota-linked vOTUs were abundant across sites, especially in fens. Terriglobia-associated proviruses were observed in Kilpisjarvi soils, being related to proviruses from distant soils and other biomes. Approximately genus- or higher-level similarities were found between Tunturi viruses, Kilpisjarvi vOTUs, and other soil vOTUs, suggesting some shared groups of Acidobacteriota viruses across soils. Conclusions: This study provides acidobacterial virus isolates as laboratory models for future research and adds insights into the diversity of viral communities associated with Acidobacteriota in tundra soils. Predicted virus-host links and viral gene functions suggest various interactions between viruses and their host microorganisms. Largely unknown sequences in the isolates and metagenome-assembled viral genomes highlight a need for more extensive sampling of Arctic soils to better understand viral functions and contributions to ecosystem-wide cycling processes in the Arctic.
An extension of the Benefit Risk Assessment of VaccinEs (BRAVE) Toolkit to evaluate Comirnaty and Spikevax vaccination in the European Union
Authors: Loedy Neilshan , Dorta Hector G , Abrams Steven , Crèvecoeur Jonas , Morales Daniel R. , Cohet Catherine , Willem Lander , Molenberghs Geert , Hens Niel , Kurz Xavier , Quinten Chantal , Verbeeck Johan
Published: August 2024

Introduction

Amid the global COVID-19 pandemic, vaccines were conditionally authorised for human use to protect against severe infection. The BRAVE toolkit, a user-friendly R Shiny application, was developed retrospectively together with the European Medicine Agency (EMA) with the aim of fulfilling the need for flexible tools to assess vaccine benefits and risks during and outside a pandemic situation.

Method

This study employed BRAVE to evaluate the impact of COVID-19 mRNA vaccines across 30 EU/EEA countries by quantifying the number of prevented clinical events (i.e., confirmed infections, hospitalisations, intensive care unit (ICU) admissions, and deaths), using a probabilistic model informed by real-time incidence data and vaccine effectiveness estimates. The analysis assumes fixed population dynamics and behaviour. Additionally, BRAVE assesses risks associated with mRNA-based vaccines (myocarditis or pericarditis) by comparing observed incidence rates in vaccinated individuals with background incidence rates.

Results

mRNA vaccines were estimated to directly prevent 11.150 million (95% Confidence Interval (CI): 10.876 – 11.345) confirmed COVID-19 infections, 0.739 million (95% CI: 0.727 – 0.744) COVID-19 hospitalisations, 0.107 million (95% CI: 0.104 – 0.109) ICU admissions, and 0.187 million (95% CI: 0.182 – 0.189) COVID-19-related deaths in the EU/EEA between 13 December 2020 and 31 December 2021. Despite increased vaccination-associated myocarditis or pericarditis observed in younger men, the benefits of vaccination still outweigh these risks.

Conclusion

Our study supports the benefit/risk profile of COVID-19 vaccines and emphasises the utility of employing a flexible toolkit to assess risks and benefits of vaccination. This user-friendly and adaptable toolkit can serve as a blueprint for similar tools, enhancing preparedness for future public health crises.