bluuebunny/crossref_metadata_2025 huggingface dataset:
The spatial organization of ascending auditory pathway microstructural maturation from infancy through adolescence using a novel fiber tracking approach
Authors: Lynch Kirsten M. , Bodison Stefanie C. , Cabeen Ryan P. , Toga Arthur W. , Voelker Courtney C.J.
Published: June 2024

Auditory perception is established through experience-dependent stimuli exposure during sensitive developmental periods; however, little is known regarding the structural development of the central auditory pathway in humans. The present study characterized the regional developmental trajectories of the ascending auditory pathway from the brainstem to the auditory cortex from infancy through adolescence using a novel diffusion MRI-based tractography approach and along-tract analyses. We used diffusion tensor imaging (DTI) and neurite orientation dispersion and density imaging (NODDI) to quantify the magnitude and timing of auditory pathway microstructural maturation. We found spatially varying patterns of white matter maturation along the length of the tract, with inferior brainstem regions developing earlier than thalamocortical projections and left hemisphere tracts developing earlier than the right. These results help to characterize the processes that give rise to functional auditory processing and may provide a baseline for detecting abnormal development.

Highlights

We characterize the microstructural maturation of the auditory pathway

We show structural development of the auditory pathway is dynamic and heterogeneous

Diffusion metrics AD, RD and MD reach adult-like levels earlier than FA and NDI

Brainstem microstructure matures earlier than the subcortical white matter

Maturation of the right auditory pathway continues later than the left
Maternal Immunoglobulin A regulates the development of the neonatal microbiota and intestinal microbiota-specific CD4+ T cell responses
Authors: Abbott Darryl A. , Rai Ali T. , Yang Aaron , Cai Yixuan , Fabre Shelcie , Frazer Austin J. , Deschepper Jacob D. , Poholek Amanda C. , Hand Timothy W.
Published: June 2024

Breast milk is a complex mixture of nutrients and bioactives that promote infant development and decrease the incidence of chronic inflammatory disease. We investigated the role of one milk-derived bioactive, Immunoglobulin A (IgA) on the developing small intestinal microbiota and immune system. We demonstrate that early in life, milk-derived IgA suppressed colonization of the small intestine byEnterobacteriaceaeand regulated the maturation of the small intestinal epithelium and the development of intestinal IL-17-producing CD4+T cells.Enterobacteriaceae- specific CD4+T cells, induced in the first weeks of life in the absence of milk-derived IgA, persisted in the intestine as memory T cells that can contribute to inflammatory disease later in life. Our study suggests that milk-derived IgA shapes mucosal immunity by regulating the neonatal microbiota thus preventing the development of long-lived intestinal microbiota-specific T cells.
Genetically diverse Mycobacterium tuberculosis isolates manipulate inflammasome activation and IL-1β secretion independently of macrophage metabolic rewiring
Authors: Fernandes Ana Isabel , Pinto Alexandre Jorge , Silvério Diogo , Zedler Ulrike , Ferreira Carolina , Duarte Iola F. , Silvestre Ricardo , Dorhoi Anca , Saraiva Margarida
Published: June 2024

The natural diversity ofMycobacterium tuberculosisis gaining relevance in dictating the outcome of tuberculosis (TB). We previously revealed a link between TB severity andM. tuberculosis-driven evasion of the macrophage cytosolic surveillance systems, with isolates from severe TB cases reducing inflammasome activation and interleukin (IL)-1β production by infected cells. IL-1β production and inflammasome activation are commonly associated with the metabolic reprogramming of stimulated macrophages. Thus, we questioned whether the differential modulation of the inflammasome and IL-1β byM. tuberculosisisolates depended on distinct macrophage metabolic reprogramming. Using metabolic inhibitors, mice deficient for key metabolic regulators, and a metabolomics approach, we found that the macrophage metabolic landscape was similar regardless of the infectingM. tuberculosisisolate. Paralleling single-TLR activated macrophages, inhibition of glycolysis during infection impaired IL-1β secretion. However, departing from TLR based models, inM. tuberculosis-infected macrophages IL-1β secretion was independent of macrophage mitochondrial metabolic changes and the transcription factor hypoxia-inducible factor (HIF)-1α. Additionally, we found a previously unappreciated impact of host metabolic inhibitors on the pathogen, and show that inhibition of the mycobacteria metabolism dampened both inflammasome activation and IL-1β production. Collectively, our study raises awareness of the potential confounding effect of host metabolic inhibitors acting on the pathogen itself and demonstrates that the modulation of the inflammasome byM. tuberculosismay be uncoupled from the host metabolic reprogramming.

Author Summary

Mycobacterium tuberculosisis the causative agent of tuberculosis and one of the top infectious killers in the world, with around 1.3 million deaths reported annually. The genetic variability of this pathogen can shape its interaction with the host and modulate disease outcomes. We previously found thatM. tuberculosisclinical isolates from patients with severe forms of tuberculosis evade cytosolic surveillance systems in macrophages. Here, we explored whether this evasion tactic was linked to metabolic alterations in the infected macrophages. We found that differentM. tuberculosisisolates induced similar metabolic changes in infected macrophages. Additionally, we demonstrate that both host glycolysis and pathogen’s metabolism were pivotal for maximum IL-1β production. These findings highlight the complexity of macrophage-pathogen interactions and emphasize that bacterial metabolism should be considered in metabolic studies and may be amenable to therapeutic intervention against tuberculosis.
A Mechanistic Approach to Optimize Combination Antibiotic Therapy
Authors: Clarelli F. , Ankomah P. O. , Weiss H. , Conway J. M. , Forsdahl G. , Wiesch P. Abel zur
Published: June 2024

Antimicrobial resistance is one of the most significant healthcare challenges of our times. Multidrug or combination therapies are sometimes required to treat severe infections; for example, the current protocols to treat pulmonary tuberculosis combine four antibiotics. However, combination therapy is usually based on lengthy empirical trials and it is difficult to predict its efficacy. We propose a new tool to identify antibiotic synergy or antagonism and optimize combination therapies. Our model explicitly incorporates the mechanisms of individual drug action and estimates their combined effect using a mechanistic approach. By quantifying the impact on growth and death of a bacterial population, we can identify optimal combinations of multiple drugs. Our approach also allows for the investigation of the drugs’ actions and the testing of theoretical hypotheses.

We demonstrate the utility of this tool with in vitroEscherichia colidata using a combination of ampicillin and ciprofloxacin. In contrast to previous interpretations, our model finds a slight synergy between the antibiotics. Our mechanistic model allows investigating possible causes of the synergy.
Sensitive tumor detection, accurate quantification, and cancer subtype classification using low-pass whole methylome sequencing of plasma DNA
Authors: Paoli Marta , Galardi Francesca , Nardone Agostina , Biagioni Chiara , Romagnoli Dario , Donato Samantha Di , Franceschini Gian Marco , Livraghi Luca , Pestrin Marta , Sanna Giuseppina , Risi Emanuela , Migliaccio Ilenia , Moretti Erica , Malorni Luca , Biganzoli Laura , Demichelis Francesca , Benelli Matteo
Published: June 2024

The analysis of circulating tumor DNA (ctDNA) is increasingly used for monitoring disease in patients with metastatic cancer. Here, we introduce a robust and reproducible strategy combining low-pass whole methylome sequencing of plasma DNA with METER, a novel computational tool. Engaging prediction models trained on independent available datasets, METER enables the detection and quantification of tumor content (TC) and performs molecular cancer subtyping. Applied to plasma methylomes from early metastatic breast cancer patients, our method demonstrated reliable quantification, sensitive tumor detection below 3% of TC, and the ability to perform accurate Estrogen Receptor (ER) subtyping. METER provided clinically relevant predictions, underscored by associations with relevant prognostic factors, robust correlation with matched circulating tumor cells, and highly correlated with patients’ outcomes in challenging scenarios as TC<3%. Our strategy provides comprehensive and sensitive analysis of plasma samples, serving as a valuable yet cost-effective precision oncology tool.
IsoBayes: a Bayesian approach for single-isoform proteomics inference
Authors: Bollon Jordy , Shortreed Michael R , Jordan Ben T , Miller Rachel , Jeffery Erin , Cavalli Andrea , Smith Lloyd M , Dewey Colin , Sheynkman Gloria M , Tiberi Simone
Published: June 2024

Studying protein isoforms is an essential step in biomedical research; at present, the main approach for analyzing proteins is via bottom-up mass spectrometry proteomics, which return peptide identifications, that are indirectly used to infer the presence of protein isoforms. However, the detection and quantification processes are noisy; in particular, peptides may be erroneously detected, and most peptides, known as shared peptides, are associated to multiple protein isoforms. As a consequence, studying individual protein isoforms is challenging, and inferred protein results are often abstracted to the gene-level or to groups of protein isoforms. Here, we introduceIsoBayes, a novel statistical method to perform inference at the isoform level. Our method enhances the information available, by integrating mass spectrometry proteomics and transcriptomics data in a Bayesian probabilistic framework. To account for the uncertainty in the measurement process, we propose a two-layer latent variable approach: first, we sample if a peptide has been correctly detected (or, alternatively filter peptides); second, we allocate the abundance of such selected peptides across the protein(s) they are compatible with. This enables us, starting from peptide-level data, to recover protein-level data; in particular, we: i) infer the presence/absence of each protein isoform (via a posterior probability), ii) estimate its abundance (and credible interval), and iii) target isoforms where transcript and protein relative abundances significantly differ. We benchmarked our approach in simulations, and in two multi-protease real datasets: our method displays good sensitivity and specificity when detecting protein isoforms, its estimated abundances highly correlate with the ground truth, and can detect changes between protein and transcript relative abundances.IsoBayesis freely distributed as a Bioconductor R package, and is accompanied by an example usage vignette.
Benchmarking second-generation methods for cell-type deconvolution of transcriptomic data
Authors: Dietrich Alexander , Merotto Lorenzo , Pelz Konstantin , Eder Bernhard , Zackl Constantin , Reinisch Katharina , Edenhofer Frank , Marini Federico , Sturm Gregor , List Markus , Finotello Francesca
Published: June 2024

In silico cell-type deconvolution from bulk transcriptomics data is a powerful technique to gain insights into the cellular composition of complex tissues. While first-generation methods used precomputed expression signatures covering limited cell types and tissues, second-generation tools use single-cell RNA sequencing data to build custom signatures for deconvoluting arbitrary cell types, tissues, and organisms. This flexibility poses significant challenges in assessing their deconvolution performance. Here, we comprehensively benchmark second-generation tools, disentangling different sources of variation and bias using a diverse panel of real and simulated data. Our study highlights the strengths, limitations, and complementarity of state-of-the-art tools shedding light on how different data characteristics and confounders impact deconvolution performance. We provide the scientific community with an ecosystem of tools and resources,omnideconv, simplifying the application, benchmarking, and optimization of deconvolution methods.
Where is the boundary of the human pseudoautosomal region?
Authors: Bellott Daniel W , Hughes Jennifer W , Skaletsky Helen , Owen Erik C , Page David C
Published: June 2024

A recent publication describing the assembly of the Y chromosomes of 43 males was remarkable not only for its ambitious technical scope, but also for the startling suggestion that the boundary of the pseudoautosomal region 1 (PAR1), where the human X and Y chromosomes engage in crossing-over during male meiosis, lies 500 kb distal to its previously reported location. Where is the boundary of the human PAR1? We first review the evidence that mapped the PAR boundary, or PAB, before the human genome draft sequence was produced, then examine post-genomic datasets for evidence of crossing-over between the X and Y, and lastly re-examine the sequence assemblies presented by Hallast and colleagues to see whether they support a more distal PAB. We find ample evidence of X-Y crossovers throughout the 500 kb in question, some as close as 246 bp to the previously reported PAB. Our new analyses, combined with previous studies over the past 40 years, provide overwhelming evidence to support the original position, and narrow the probable location of the PAB to a 201-bp window.
Single-Cell and Spatial Transcriptomic Analyses Reveals the Dynamic Transcript Profiles of Myocardial Lymphangiogenesis post Myocardial Infarction
Authors: He Jiaqi , Zhang Dali , Song Haixu , Liu Ziqi , Liu Dan , Zhang Xiaolin , Zhao Xiaojie , Zhang Yan , Liu Jing , Xu Jiaxin , Yan Chenghui , Han Yaling
Published: June 2024

Cardiac lymphatics play an important role in myocardial edema and inflammation. This study integrated single-cell sequencing data and spatial transcriptome data from mouse heart tissue at different time points post-myocardial infarction (MI), and identified four transcriptionally distinct subtypes of lymphatic endothelial cells (LECs) and localized them in space. Interestingly, LECs subgroups was found to be localized in different zones of infarcted heart related to different functions. Additionally, LEC capillary III(LEC ca III) may be involved in the direct regulation of myocardial injuries in infarcted zone from the perspective of metabolic stress, while LEC ca II may be related to the rapid immune inflammatory responses of the border zone in the early stage of MI. LEC ca I, as well as LEC collection mainly participate in the regulation of myocardial tissue edema resolution in the middle and late stages post-MI. Cell trajectory and Cell-Chat analyses further identified that LECs may regulate myocardial edema through Aqp1, and might affect the infiltration of macrophages through the Galectin9-CD44 pathway. Collectively, our study revealed the dynamic transcriptional heterogeneity distribution of LECs in different regions of the infarcted heart, in detail; these LECs formed different functional subgroups, that might exhibit different bioeffects in myocardial tissue post-MI.
Morphometrics as a conservation tool for rapid in-situ distinction of native and introduced iguanas: comparingIguana delicatissimaandIguana iguana
Authors: van den Burg Matthijs P. , Kappelhof Jeroen , Mitchell Adam , Debrot Adolphe O.
Published: June 2024

Invasive alien species severely impact native and endemic species, disproportionately affecting insular species, and this is especially true for Caribbean reptiles. The Lesser Antillean iguana (Iguana delicatissima) experienced a drastic range decline strongly driven by hybridization with non-native green iguanas (NNGI,Iguana iguanaspecies complex). With numerous NNGI populations within the Lesser Antilles, it is a matter of time before these arrive on the lastI. delicatisismainhabited islands, whereupon rapid in-situ identification of non-native and hybrid animals is essential. However, only a few scale and coloration characters allow in-situ identification of NNGI, which are compromised by introgression. Here we assessed the differentiating power of an additional 20 scale and length-dependent characteristics between theI. delicatissimapopulation on St. Eustatius and the established NNGI population on St. Maarten, the main source of arriving stowaway iguanas on St. Eustatius. We identified 14 length-dependent characteristics that significantly differ betweenI. delicatissimaand NNGI’s, with multi-variate analysis showing clear morphospace separation and high assignment accuracy of predictive models (>91%). Additionally, the number of femorals and supra digital scales significantly differs between these iguanas. Morphospace knowledge of St. Eustatius’I. delicatissimanow allows rapid identification of any divergent iguanas using easy to obtain measurements and meristics. Given intraspecific variation inI. delicatissimaand green iguanas, we recommend that these characteristics are assessed and validated for other populations, including hybrid individuals. Our work demonstrates the urgent need to invest in baseline morphometric datasets to aid rapid in-situ conservation efforts once NNGI arrive and start to hybridize withI. delicatissima.
Daphnia-associated bacterial communities are influenced by infection status, environmental conditions and diet quantity across natural epidemics
Authors: Rajarajan Amruta , Wolinska Justyna , Walser Jean-Claude , Tardent Nadine , Käser Silvana , Keller Esther , Spaak Piet
Published: June 2024

Microbiomes associated with zooplankton play an important role for host health and contribute to ecosystem functions, such as nutrient cycling. Yet, few studies have assessed how environmental gradients and biotic interactions, such as parasitism and diet, shape the microbiome composition of wild zooplankton. Here, we used 16S rRNA gene sequencing and a long-term field dataset to investigate the microbiomes of water fleas belonging to theDaphnia longispinaspecies complex, across six sampling events spanning 13 years. Sampling coincided with epidemics of the virulent eukaryotic gut parasiteCaullerya mesnili.We further surveyed phytoplankton and zooplankton communities in the lake to explore associations betweenDaphniamicrobiome composition and diet (phytoplankton density), as well as zooplankton density and community composition. We observed temporal variation and infection-dependent shifts inDaphniamicrobiome composition. Importantly, host microbiome compositions co-varied with infection prevalence, indicating a correlation between host microbiome composition and epidemic size. Furthermore, environmental factors including temperature, dissolved oxygen and cyanobacterial abundance, previously found to driveCaulleryaepidemics, were associated with distinct host microbiome compositions. Dominant bacterial taxa in theDaphniamicrobiome correlated withDaphniadensity, whereas the phylogenetic composition of rare bacterial taxa correlated with total zooplankton density. Lastly,Daphniamicrobiome composition correlated with the density of green algae, protists and cyanobacteria in lake water, but not with their community composition. Our findings show the dynamic nature ofDaphnia-associated microbiomes and suggest potential mechanisms through which they may mediate host disease dynamics, including associations with temperature, host density and diet quantity.
Senescent fibroblasts support tumor growth by inducing immune cell death in humanized models
Authors: Cruz Monica , Dulong Joshua , Sonn Anthony , Moquin-Beaudry Gaël , Benabdallah Basma , Le Oanh , Beauséjour Christian
Published: June 2024

Syngeneic mouse models revealed that senescence influences the tumor immune response in many ways by, for example, inducing an immunosuppressive microenvironment or by favoring immune cell recruitment. Yet, the impact of senescence on the tumor immune response in a humanized setting is mostly unknown. Here, using tumor spheroids and humanized mice bearing tumors immunogenic to autologous human immune cells, we show that senescent fibroblasts exert a dual impact on the tumor immune response by attracting more immune cells but also by inducing the death of T and NK cells. Mechanistically, we demonstrate that this was mostly the result of increased Fas ligand (FasL) expression at the surface of senescent fibroblasts and that the deletion of FasL was sufficient to prevent immune cell death and increase tumor cell killing. Our results highlight the importance of evaluating the impact of therapy-induced senescence in humanized models to better understand and predict the outcome of cancer treatments.
Genetic and Environmental Contributions to Epigenetic Aging Across Adolescence and Young Adulthood
Authors: Kuznetsov Dmitry V. , Liu Yixuan , Schowe Alicia M. , Czamara Darina , Instinske Jana , Pahnke Charlotte K. L. , Noethen Markus M. , Spinath Frank M. , Binder Elisabeth B. , Diewald Martin , Forstner Andreas J. , Kandler Christian , Moenkediek Bastian
Published: June 2024

Background Epigenetic aging estimators commonly track chronological and biological aging, quantifying its accumulation (i.e., epigenetic age acceleration) or speed (i.e., epigenetic aging pace). Their scores reflect a combination of inherent biological programming and the impact of environmental factors, which are suggested to vary at different life stages. The transition from adolescence to adulthood is an important period in this regard, marked by an increasing and, then, stabilizing epigenetic aging variance. Whether this pattern arises from environmental influences or genetic factors is still uncertain. This study delves into understanding the genetic and environmental contributions to variance in epigenetic aging across these developmental stages. Using twin modeling, we analyzed four estimators of epigenetic aging, namely Horvath Acceleration, PedBE Acceleration, GrimAge Acceleration, and DunedinPACE, based on saliva samples collected at two timepoints approximately 2.5 years apart from 976 twins of four birth cohorts (aged about 9.5, 15.5, 21.5, and 27.5 years at first and 12, 18, 24, and 30 years at second measurement occasion). Results Half to two-thirds (50-68%) of the differences in epigenetic aging were due to unique environmental factors, indicating the role of life experiences and epigenetic drift, besides measurement error. The remaining variance was explained by genetic (Horvath Acceleration: 24%; GrimAge Acceleration: 32%; DunedinPACE: 47%) and shared environmental factors (Horvath Acceleration: 26%; PedBE Acceleration: 47%). The genetic and shared environmental factors represented the primary sources of stable differences in corresponding epigenetic aging estimators over 2.5 years. Age moderation analyses revealed that the variance due to individually-unique environmental sources was smaller in younger than in older cohorts in epigenetic aging estimators trained on chronological age (Horvath Acceleration: 47% to 49%; PedBE Acceleration: 33% to 68%). The variance due to genetic contributions, in turn, potentially increased across age groups for epigenetic aging estimators trained in adult samples (Horvath Acceleration: 18% to 39%; GrimAge Acceleration: 24% to 43%; DunedinPACE: 42% to 57%). Conclusions Transition to adulthood is a period of the increasing variance in epigenetic aging. Both environmental and genetic factors contribute to this trend. The degree of environmental and genetic contributions can be partially explained by the design of epigenetic aging estimators.
Autophagy repression by antigen and cytokines shapes mitochondrial, migration and effector machinery in CD8 T cells
Authors: Sinclair Linda V. , Youdale Tom , Spinelli Laura , Gakovic Milica , Langlands Alistair J. , Pathak Shalini , Howden Andrew J.M. , Ganley Ian G. , Cantrell Doreen A.
Published: June 2024

Autophagy is important for CD8 T-cells but autophagy timing, triggers and targets are poorly defined. Herein, we show naïve CD8-T cells have high autophagic flux and identify an autophagy checkpoint whereby antigen receptor engagement represses autophagy by regulating amino acid transporter expression and intracellular amino acid delivery. Effector cytotoxic T cells with high levels of amino acid transporters driven by proinflammatory cytokines have low autophagic flux but rapidly reinduce autophagy when amino acid restricted. A census of proteins degraded and fuelled by autophagy shows how autophagy shapes CD8-T cell proteomes. In cytotoxic T-cells, dominant autophagy substrates include cytolytic effector molecules, amino acid and glucose transporters. In naïve T-cells mitophagy dominates and selective mitochondrial pruning supports the expression of molecules that coordinate T-cell migration and survival. Autophagy thus differentially prunes naive and effector T-cell proteomes and is dynamically repressed by antigen receptors and inflammatory cytokines to shape T-cell differentiation.
Local increases in admixture with hunter-gatherers followed the initial expansion of Neolithic farmers across continental Europe
Authors: Tsoupas Alexandros , Reyna-Blanco Carlos S. , Quilodrán Claudio S. , Blöcher Jens , Brami Maxime , Wegmann Daniel , Burger Joachim , Currat Mathias
Published: June 2024

The replacement of hunter-gatherer lifestyles by agriculture represents a pivotal change in human history. The initial stage of this Neolithic transition in Europe was instigated by the migration of farmers from Anatolia and the Aegean basin. In this study, we modeled the expansion of Neolithic farmers into Central Europe from Anatolia, along the Continental route of dispersal. We employed spatially explicit simulations of palaeogenomic diversity and high-quality palaeogenomic data from 67 prehistoric individuals to assess how population dynamics between indigenous European hunter-gatherers and incoming farmers varied across space and time. Our results demonstrate that admixture between the two groups increased locally over time at each stage of the Neolithic expansion along the Continental route. We estimate that the effective population size of farmers was about five times that of the hunter-gatherers. Additionally, we infer that sporadic long distance migrations of early farmers contributed to their rapid dispersal, while competitive interactions with hunter-gatherers were limited.

Teaser

The first farmers of continental Europe increasingly admixed over time with indigenous hunter-gatherers.
Phosphorylation of disordered proteins tunes local and global intramolecular interactions
Authors: Usher Emery T. , Fossat Martin J. , Holehouse Alex S.
Published: June 2024

Protein post-translational modifications, such as phosphorylation, are important regulatory signals for diverse cellular functions. In particular, intrinsically disordered protein regions (IDRs) are subject to phosphorylation as a means to modulate their interactions and functions. Toward understanding the relationship between phosphorylation in IDRs and specific functional outcomes, we must consider how phosphorylation affects the IDR conformational ensemble. Various experimental techniques are suited to interrogate the features of IDR ensembles; molecular simulations can provide complementary insights and even illuminate ensemble features that may be experimentally inaccessible. Therefore, we sought to expand the tools available to study phosphorylated IDRs by all-atom Monte Carlo simulations. To this end, we implemented parameters for phosphoserine (pSer) and phosphothreonine (pThr) into the OPLS version of the continuum solvent model, ABSINTH, and assessed their performance in all-atom simulations compared to published findings. We simulated short (< 20 residues) and long (> 80 residues) phospho-IDRs that, collectively, survey both local and global phosphorylation-induced changes to the ensemble. Our simulations of four well-studied phospho-IDRs show near-quantitative agreement with published findings for these systems via metrics including changes to radius of gyration, transient helicity, and persistence length. We also leveraged the inherent advantage of sequence control in molecular simulations to explore the conformational effects of diverse combinations of phospho-sites in two multi-phosphorylated IDRs. Our results support and expand on prior observations that connect phosphorylation to changes in the IDR conformational ensemble. Herein, we describe phosphorylation as a means to alter sequence chemistry, net charge and charge patterning, and intramolecular interactions, which can collectively modulate the local and global IDR ensemble features.

SIGNIFICANCE

Spatially and temporally controlled phosphorylation in disordered protein regions is critical to many facets of protein function and broader cellular health. Intrinsically disordered protein regions (IDRs) are overrepresented as targets of phosphorylation, but the structural and functional consequences of such modifications remain elusive for many systems. Toward rigorous modeling of phosphorylated IDRs using all-atom simulations, we present new parameters for phosphoserine and phosphothreonine for the ABSINTH implicit solvent paradigm. Through the study of four example phospho-IDRs, we demonstrate excellent agreement between our phospho-IDR simulations and published datasets.
Increased pathogenicity and transmission of SARS-CoV-2 Omicron XBB.1.9 sublineage, including HK.3 and EG.5.1
Authors: Jin Qiushi , Liu Ruixue , Wang Wenqi , Xie Jichen , Wang Tiecheng , Xiang Haiyang , Xia Xianzhu , Li Jianmin , Wang Xuefeng , Gao Yuwei
Published: June 2024

With the SARS-CoV-2 Omicron XBB.1.9 sublineage circulating worldwide, two XBB.1.9 variants, EG.5.1 and HK.3 spread rapidly and became dominant from middle 2023. However, the spike features, pathogenicity, and transmissibility of HK.3 are largely unknown. Here, we performed multiscale investigations to reveal the virological features of XBB.1.9 subvariants, especially the newly emerging HK.3. HK.3 revealed high replication efficiency in vitro. The HK.3 spike exhibited enhanced processing, although its infectivity, fusogenicity, and hACE2 binding affinity were comparable to those of the EG.5 and XBB.1 spikes. All XBB.1.9.1, EG.5.1 and HK.3 strains demonstrated efficient transmission in hamsters, although XBB.1.9.1 exhibited stronger fitness in the upper airways. HK.3 and EG.5.1 exhibited greater pathogenicity than XBB.1.9.1 and BA.2 in H11-K18-hACE2 hamsters. Our studies provide insight into the newly emerging pathogens HK.3 and EG.5.1.

Importance

In animal models, the ongoing attenuated pathogenicity and poor transmission of Omicron subvariants seems to reach a consensus. However, our results revealed that Omicron XBB.1.9 subvariants, including one of the key variants of interest, EG.5 with its another key subvariant HK.3, universally exhibited both increased pathogenicity and highly transmission. This study reemphasized the importance of surveillance in characteristics of epidemic Omicron subvariants.
Longitudinal sex-at-birth and age analyses of cortical structure in the ABCD Study®
Authors: Marshall Andrew T. , Adise Shana , Kan Eric C. , Sowell Elizabeth R.
Published: June 2024

While the brain continues to develop during adolescence, such development may depend on sex-at-birth. However, the elucidation of such differences may be hindered by analytical decisions (e.g., covariate selection to address body/brain-size differences) and the typical reporting of cross-sectional data. To further evaluate adolescent cortical development, we analyzed data from the Adolescent Brain Cognitive Development StudySM, whose cohort of 11,000+ youth participants with biannual neuroimaging data collection can facilitate understanding neuroanatomical change during a critical developmental window. Doubly considering individual differences in the context of group-level effects, we analyzed regional changes in cortical thickness, sulcal depth, surface area, and volume between two timepoints (∼2 years apart) in 9-to 12-year-olds assigned male or female sex-at-birth. First, we conducted linear mixed-effects models to gauge how controlling for intracranial volume, whole-brain volume (WBV), or a summary metric (e.g., mean cortical thickness) influenced interpretations of age-dependent cortical change. Next, we evaluated the relative changes in thickness and surface area as a function of sex-at-birth and age. Here, we showed that WBV (thickness, sulcal depth, volume) and total cortical surface area were more optimal covariates; controlling for different covariates would have substantially altered our interpretations of overall and sex-at-birth-specific neuroanatomical development. Further, we provided evidence to suggest that aggregate change in how cortical thickness is changing relative to surface area is generally comparable across those assigned male or female sex-at-birth, with corresponding change happening at slightly older ages in those assigned male sex-at-birth. Overall, these results help elucidate neuroanatomical developmental trajectories in early adolescence.

Significance Statement

While most of our brain’s development happens early in life, much of it still happens in adolescence. Because many factors can alter those developmental trajectories, it is important to evaluate the shape/timing of those trajectories (i.e., what generally constitutes typical brain development). Here, we showed that our understanding of those trajectories can be affected by how we choose to analyze them. First, we showed that the way researchers address differences in brain/body size affects how we interpret regional variation in brain change over time. Further, we showed that it is important to consider how similar patterns of development may simply be happening at different ages in different groups. These results support a relatively novel way of analyzing adolescent brain development.
Adjuvant Delivery Method and Nanoparticle Charge Influence Peptide Amphiphile Micelle Vaccine Bioactivity
Authors: Zhang Rui , Rygelski Brett T. , Kruse Luke E. , Smith Josiah D. , Wang Xiaofei , Allen Brittany N. , Kramer Jake S. , Seim Gracen F. , Faulkner Trent J. , Kuang Huihui , Kokkoli Efrosini , Schrum Adam G. , Ulery Bret D.
Published: June 2024

Vaccines are an indispensable public health measure that have enabled the eradication, near elimination, and prevention of a variety of pathogens. As research continues and our understanding of immunization strategies develops, subunit vaccines have emerged as exciting alternatives to existing whole vaccine approaches. Unfortunately, subunit vaccines often possess weak antigenicity, requiring delivery devices and adjuvant supplementation to improve their utility. Peptide amphiphile micelles have recently been shown to function as both delivery devices and self-adjuvanting systems that can be readily associated with molecular adjuvants to further improve vaccine-mediated host immunity. While promising, many “design rules” associated with the plethora of underlying adjustable parameters in the generation of a peptide amphiphile micelle vaccine have yet to be uncovered. This work explores the impact micellar adjuvant complexation method and incorporated antigen type have on their ability to activate dendritic cells and induce antigen specific responses. Interestingly, electrostatic complexation of CpG to micelles resulted in improvedin vitrodendritic cell activation over hydrophobic association and antigen|adjuvant co-localization influenced cell-mediated, but not antibody-mediated immune responses. These exciting results complement those previously published to build the framework of a micelle vaccine toolbox that can be leveraged for future disease-specific formulations.
Jagged-1+ Skin Tregs Modulate the Innate Immune Response to Wound Healing
Authors: Lui Prudence PokWai , Xu Jessie Z. , Aziz Hafsah , Sen Monica , Ali Niwa
Published: June 2024

Skin-resident regulatory T cells (Tregs) play an irreplaceable role in orchestrating cutaneous immune homeostasis and repair, including the promotion of hair regeneration via the Notch signaling ligand Jagged-1 (Jag1). While skin Tregs are indispensable for facilitating tissue repair post-wounding, it remains unknown if Jag1-expressing skin Tregs impact wound healing. Using a tamoxifen inducible Foxp3creERT2Jag1fl/flmodel, we show that loss of functional Jag1 in Tregs significantly delays the rate of full-thickness wound closure. Unlike in hair regeneration, skin Tregs do not utilize Jag1 to impact epithelial stem cells during wound healing. Instead, mice with Treg-specific Jag1 ablation exhibit a significant reduction in Ly6G+ neutrophil accumulation at the wound site. However, during both homeostasis and wound healing, the loss of Jag1 in Tregs does not impact the overall abundance or activation profile of immune cell targets in the skin, such as CD4+ and CD8+ T cells, or pro-inflammatory macrophages. This collectively suggests that skin Tregs may utilize Jag1-Notch signalling to co-ordinate innate cell recruitment under conditions of injury but not homeostasis. Overall, our study demonstrates the importance of Jag1 expression in Tregs to facilitate adequate wound repair in the skin.
Novel genomic features in entomopathogenic fungusBeauveria bassiana: supernumerary chromosomes and putative virulence genes involved in the infection process of soybean pestPiezodorus guildinii
Authors: Oberti H. , Sessa L. , Oliveira-Rizzo C. , Di Paolo A. , Sanchez-Vallet A. , Seidl M.F. , Abreo E.
Published: June 2024

Biological control methods involving entomopathogenic fungi likeBeauveria bassianahave shown to be a valuable approach in integrated pest management as an environmentally friendly alternative to control pests and pathogens. Identifying genetic determinants of pathogenicity inB. bassianais instrumental for enhancing its virulence against insects like the resistant soybean pestPiezodorus guildinii. This study focused on comparative genomics of differentB. bassianastrains and gene expression analyses to identify virulence genes in the hypervirulent strain ILB308, especially in response to infection ofP. guildniiiand growth on hydrocarbon HC15, a known virulence enhancer. Strain ILB308 showed the highest number of virulence-related features, such as candidate virulence proteins, effectors, small secreted proteins, and biosynthetic gene clusters. ILB308 also had a high percentage of unique DNA sequences, including six putative supernumerary scaffolds. Gene expression analysis at 4 days post-inoculation revealed upregulation of known virulence factors, including Tudor domain proteins, LysM motif-containing proteins, and subtilisin-like proteases, and novel genes like secreted effectors and heat-labile enterotoxins. Growth on HC15 led to the upregulation of genes associated with oxidoreductase activity related to cuticular alkane degradation and fermentation metabolism/antioxidant responses in the hemolymph. The presence of supernumerary chromosomes and unique virulence genes in ILB308 may contribute to its higher virulence and could be considered as potential targets for enhancing fungal virulence through genetic manipulation.

Author Summary

Understanding mechanisms of virulence and virulence enhancement inBeauveria bassianacan lay the basis for the development of improved biocontrol agents. Here we used genomic and transcriptomic approaches to study the infection process of ILB308 -an hypervirulent strain- against insect pestPiezodorus guildinii. We found that this strain has putative supernumerary chromosomes and an enriched set of presumed virulence proteins like secreted effectors. We infer that the particular assortment of strain specific genes and supernumerary chromosome/s play a role in the degree of virulence exhibited by ILB308 and could be used for future strain improvement strategies.
Dysregulated STAT3 signaling and T cell immunometabolic dysfunction define a targetable, high mortality subphenotype of critically ill children
Authors: Lindell Robert B. , Sayed Samir , Campos Jose S. , Knight Montana , Mauracher Andrea A. , Hay Ceire A. , Conrey Peyton E. , Fitzgerald Julie C. , Yehya Nadir , Famularo Stephen T. , Arroyo Teresa , Tustin Richard , Fazelinia Hossein , Behrens Edward M. , Teachey David T. , Freeman Alexandra F. , Bergerson Jenna R. E. , Holland Steven M. , Leiding Jennifer W. , Weiss Scott L. , Hall Mark W. , Zuppa Athena F. , Taylor Deanne M. , Feng Rui , Wherry E. John , Meyer Nuala J. , Henrickson Sarah E.
Published: June 2024

Sepsis is the leading cause of death of hospitalized children worldwide. Despite the established link between immune dysregulation and mortality in pediatric sepsis, it remains unclear which host immune factors contribute causally to adverse sepsis outcomes. Identifying modifiable pathobiology is an essential first step to successful translation of biologic insights into precision therapeutics. We designed a prospective, longitudinal cohort study of 88 critically ill pediatric patients with multiple organ dysfunction syndrome (MODS), including patients with and without sepsis, to define subphenotypes associated with targetable mechanisms of immune dysregulation. We first assessed plasma proteomic profiles and identified shared features of immune dysregulation in MODS patients with and without sepsis. We then employed consensus clustering to define three subphenotypes based on protein expression at disease onset and identified a strong association between subphenotype and clinical outcome. We next identified differences in immune cell frequency and activation state by MODS subphenotype and determined the association between hyperinflammatory pathway activation and cellular immunophenotype. Using single cell transcriptomics, we demonstrated STAT3 hyperactivation in lymphocytes from the sickest MODS subgroup and then identified an association between STAT3 hyperactivation and T cell immunometabolic dysregulation. Finally, we compared proteomics findings between patients with MODS and patients with inborn errors of immunity that amplify cytokine signaling pathways to further assess the impact of STAT3 hyperactivation in the most severe patients with MODS. Overall, these results identify a potentially pathologic and targetable role for STAT3 hyperactivation in a subset of pediatric patients with MODS who have high severity of illness and poor prognosis.
Effects of temperature settings on information quality of ChatGPT-3.5 responses: A prospective, single-blind, observational cohort study
Authors: Akamine Akihiko , Hayashi Daisuke , Tomizawa Atsushi , Nagasaki Yuya , Akamine Chikae , Fukawa Takahiro , Hirosawa Iori , Saigo Orie , Hayashi Misa , Nanaoya Mitsuru , Odate Yuka
Published: June 2024

Objective

The effect of temperature settings on the quality of ChatGPT version 3.5 (OpenAI) responses related to drug information remains unclear. We investigated ChatGPT-3.5’s response quality on apixaban information with and without the temperature being set to 0.

Methods

On 6 September 2023, 37 questions regarding apixaban, derived from the frequently asked questions on the Bristol–Myers Squibb’s website, were entered into ChatGPT in Japanese. The primary endpoint was the effect of temperature settings on ChatGPT-3.5’s responses to apixaban-related questions. The response accuracy, clarity, detail, and adequacy were rated on a 5-point Likert scale by 10 pharmacists, with higher scores indicating higher response quality. Cumulative score means were analyzed using the Mann–Whitney U test. In the subgroup analysis, evaluators were limited to pharmacists at university hospitals. Welch’s t-test was employed in sensitivity analysis to validate primary endpoint findings.

Results

The mean scores for ChatGPT-3.5’s apixaban-related responses with (13.08) and without (14.40) the temperature being set to 0 were not significantly different (p = 0.064). Accuracy differed significantly (3.15 vs. 3.54, p = 0.045), whereas clarity, detail, and appropriateness were similar. Subgroup analysis (13.30 vs. 14.21, p = 0.394) and sensitivity analysis confirmed similar results (13.45 vs. 14.52, p = 0.105).

Conclusions

ChatGPT-3.5 temperature setting does not significantly affect overall responses to apixaban-related inquiries. However, the variance in accuracy suggests that ChatGPT-3.5 is unable to consistently provide precise responses. Hence, it is more suitable as a supplementary tool rather than a primary medical resource.
Estimation of Sexual and Gender Minorities in the adult population of Japan: Descriptive Epidemiological Study utilizing a Nationwide Cross-Sectional Internet Survey
Authors: Minami Tetsuji , Inoue Manami , Matsushima Midori , Yoshioka Takashi , Tabuchi Takahiro
Published: June 2024

Background

Descriptive study of Japanese sexual and gender minority (SGM) population with national representativeness have not been conducted. We sought to estimate the proportion of the Japanese SGM, and to describe those demographic, socioeconomic, and health-related variables.

Methods

Utilizing data on a nationwide cross-sectional internet survey from September 12th to October 19th, 2022, we conducted a comprehensive descriptive study by applying inverse probable weighting method for national representativeness. Participants self-reported as heterosexual, homosexual, bisexual, or gender minority (GM) and responded to questions on various demographic, socioeconomic, and health-related concerns.

Findings

Among Japanese adults, 4.8% identified as homosexuals, 1.3% as bisexuals, and 3.8% as GMs. SGMs were less likely to be married/partnered compared to heterosexuals, though a certain proportion were in opposite-sex marriages/partnerships. SGMs had lower household equivalent income, insurance coverage, home ownership, current smoking rates, good self-rated health, and full COVID-19 vaccination rates. They also exhibited higher rates of substance use, severe psychological distress, feelings of loneliness, and fear of COVID-19 compared to heterosexuals. When divided by assigned sex at birth, SGM males had poorer employment status, lower academic attainment, and higher body mass index compared to their heterosexual counterparts, while SGM females showed opposite trends.

Interpretation

Differences in demographic, socioeconomic, and health status between heterosexuals and SGMs underscore the need for targeted health policies and interventions to address health disparities among Japanese SGMs. Additionally, these results suggest that directly applying Western health policies to the Japanese context may not always be appropriate.

Funding

Funded by the Japan Society for the Promotion of Science, the Research Support Program to Apply the Wisdom of the University to tackle COVID-19 Related Emergency Problems, University of Tsukuba, and Health Labour Sciences Research Grantand the Japan Agency for Medical Research and Development.
Structures of Native Doublet Microtubules fromTrichomonas vaginalisReveal Parasite-Specific Proteins as Potential Drug Targets
Authors: Stevens Alexander , Kashyap Saarang , Crofut Ethan H. , Wang Shuqi E. , Muratore Katherine A. , Johnson Patricia J. , Zhou Z. Hong
Published: June 2024

Doublet microtubules (DMTs) are flagellar components required for the protistTrichomonas vaginalis(Tv) to swim through the human genitourinary tract to cause trichomoniasis, the most common non-viral sexually transmitted disease. Lack of DMT structures has prevented structure-guided drug design to manageTvinfection. Here, we determined the cryo-EM structure of nativeTv-DMTs, identifying 29 unique proteins, including 18 microtubule inner proteins and 9 microtubule outer proteins. While the A-tubule is simplistic compared to DMTs of other organisms, the B-tubule features specialized, parasite-specific proteins, likeTvFAP40 andTvFAP35 that form filaments near the inner and outer junctions, respectively, to stabilize DMTs and enableTvlocomotion. Notably, a small molecule, assigned as IP6, is coordinated within a pocket ofTvFAP40 and has characteristics of a drug molecule. This first atomic model of theTv-DMT highlights the diversity of eukaryotic motility machinery and provides a structural framework to inform the rational design of therapeutics.