bluuebunny/crossref_metadata_2025 huggingface dataset:
MYB transcription factor, NtMYB308, regulates anthocyanin and lignin content, and fungal tolerance in tobacco
Authors: Singh Nivedita , Dwivedi Shambhavi , Singh Deeksha , Pathak Pranshu Kumar , Trivedi Prabodh Kumar
Published: June 2024

Anthocyanins are secondary metabolites synthesized through the phenylpropanoid pathway. They attract pollinators, possess antioxidant properties that scavenge free radicals during environmental stress, and provide protection against various stress conditions. Lignin, another secondary metabolite, plays crucial roles in providing mechanical support, facilitating water and solute transport, and protecting against pathogens. MYB transcription factors, particularly R2R3 MYBs, are key regulators of secondary metabolism, especially within the phenylpropanoid pathway. These factors act as both activators and repressors. The N-terminal region of R2R3-MYB repressors contains a conserved bHLH-binding domain, while the C-terminal domain is divergent and includes an EAR repressor domain. R2R3-MYB proteins notably target sequences such as the MYB-response element and AC elements. In this study, we identified and characterized the Nicotiana MYB transcription factor, NtMYB308, and explored its regulatory function in anthocyanin and lignin biosynthesis in tobacco. Our Virus Induced Gene Silencing (VIGS) and Protein-DNA interaction studies suggest that NtMYB308 is a negative regulator of anthocyanin and lignin biosynthesis by binding to the promoters of genes involved in these pathways. To validate our findings, we developed CRISPR/Cas9-based knockout mutant plants of tobacco,NtMYB308CR, which showed up-regulation of anthocyanin and lignin biosynthesis. Conversely, NtMYB308 overexpression (NtMYB308OX) plants exhibited the opposite effect. Enhanced anthocyanin and lignin levels inNtMYB308CRplants provided tolerance against the fungusAlternaria solani, while NtMYB308OX lines were susceptible. This study advances our understanding of the regulatory mechanisms governing anthocyanin and lignin biosynthesis and their role in biotic stress in tobacco.

One Sentence Summary

A R2R3 MYB transcription factor, NtMYB308, negatively regulates anthocyanin and lignin content, and fungal tolerance in tobacco.
Sequential estimation of nonstationary oscillator states and stimulus responses
Authors: Nelson Joseph N. , Widge Alik S. , Netoff Théoden I.
Published: June 2024

Neural oscillations have been linked to multiple behaviors and neuropsychiatric disorders. The individual contributions to behavior from both oscillations and non-oscillatory activity are still unclear, complicating efforts to link neurophysiology to cognition, hindering the discovery of novel biomarkers, and preventing the development of effective therapeutics. To overcome these hurdles, it will be critical to investigate the biological origins of neural oscillations by characterizing the dynamic properties of different brain regions. The dynamical regime for a population of neurons generating oscillations in neural recordings can be discovered by stimulating the population and recording its subsequent response to stimulation. There are different dynamical regimes that can produce population-level neural oscillations. For certain dynamical regimes, like that of a nonlinear oscillator, the phase response curve (PRC) can help differentiate the dynamic state of the population. The PRC can be measured by stimulating the population across different phases of its oscillatory state. However, neural dynamics are non-stationary, so neural oscillations will vary in frequency and amplitude across a recording and the PRC can change over time. This non-stationarity could bias a PRC estimated from an electrophysiological experiment, preventing accurate characterization of a neural population’s dynamics. This necessitates tools that can operate online to trigger stimulation and update PRC estimates. To that end, we develop online methods for tracking non-stationary oscillations and recovering PRCs corrupted by estimation errors. We validate the performance of our non-stationary oscillation estimator compared to both a known ground truth model and an alternative phase estimation approach. We demonstrate that a PRC can be recovered online underdifferent random error conditionsin silicoand that a similar amplitude response curve (ARC) can be estimated from physiologic data using online methods compared to offline approaches.
Binocular Listing’s Law For Human Eyes’ Misaligned Optical Components
Authors: Turski Jacek
Published: June 2024

Human eyes’ optical components are misaligned. This study presents the geometric construction of ocular torsion in the binocular system, in which the eye model incorporates the fovea that is not located on and the lens that is tilted away from the eye’s optical axis. The ocular torsion computation involves Euler’s rotation theorem in the framework of Rodrigue’s vector. When the eyes’ binocular posture changes, each eye’s torsional orientation transformations are visualized inGeoGebra’sdynamic geometry environment. Listing’s law, which originally restricts single-eye torsional positions and has imprecise binocular extensions, is formulatedab initiofor binocular fixations using Euler’s rotation theorem. It replaces Listing’s plane and related perpendicular primary direction with the empirical horopter’s abathic distance fixation, which has a straight frontal line configuration at this fixation. Notably, it corresponds to the eye muscles’ natural tonus resting position, which serves as a zero-reference level for convergence effort, providing the missing neurophysiological significance of Listing’s plane. Thus, Listing’s law use in clinical diagnosis and management of strabismus should be updated.
Discovery of functional NLRs using expression level, high-throughput transformation, and large-scale phenotyping
Authors: Brabham Helen J. , Hernández-Pinzón Inmaculada , Yanagihara Chizu , Ishikawa Noriko , Komori Toshiyuki , Matny Oadi N. , Hubbard Amelia , Witek Kamil , Feist Alexis , Numazawa Hironobu , Green Phon , Dreiseitl Antonín , Takemori Naoki , Komari Toshihiko , Freedman Roger P. , Steffenson Brian , van Esse H. Peter , Moscou Matthew J.
Published: June 2024

Protecting crops from pests and diseases is vital for the sustainable agricultural systems needed for food security. Introducing functional resistance genes to enhance the plant immune system is an effective method of disease control, but identifying new immune receptors is time-consuming and resource intensive. We observed that functional immune receptors of the NLR class show a signature of high expression in uninfected plants across both monocot and dicot species. Here we show that this signature, combined with high throughput crop transformation, can be used to rapidly identify candidate NLRs from diverse plant species and validate pathogen resistance directly in crop plants. As a proof of concept, we generated a wheat transgenic library carrying 995 NLRs from 18 grass species. Screening the collection with the stem rust pathogenPuccinia graminis, which is a major threat to wheat production, we confirm 19 new resistance genes. This pipeline facilitates resistance gene discovery, unlocking a large gene pool of diverse and non-domesticated plant species and providingin-plantagene validation of disease resistance directly in crops.
Faster and more accurate assessment of differential transcript expression with Gibbs sampling and edgeR v4
Authors: Baldoni Pedro L. , Chen Lizhong , Smyth Gordon K.
Published: June 2024

Differential transcript expression analysis of RNA-seq data is an increasingly popular tool to assess changes in expression of individual transcripts between biological conditions. Software designed for transcript-level differential expression analyses account for the uncertainty of transcript quantification, the read-to-transcript ambiguity (RTA), in statistical analyses via resampling methods. Bootstrap sampling is a popular resampling method that is implemented in the RNA-seq quantification tools kallisto and Salmon. However, bootstrapping is computationally intensive and provides replicate counts with low resolution when the number of sequence reads originating from a gene is low. For lowly expressed genes, bootstrap sampling results in noisy replicate counts for the associated transcripts, which in turn leads to non reproducible and unrealistically high RTA-dispersion for those transcripts. Gibbs sampling is a more efficient and high resolution algorithm implemented in Salmon. Here we leverage the developments of edgeR v4 to present an improved differential transcript expression analysis pipeline with Salmon’s Gibbs sampling algorithm. The new bias-corrected quasi-likelihood method with adjusted deviances for small counts from edgeR, combined with the efficient Gibbs sampling algorithm from Salmon, provides faster and more accurate DTE analyses of RNA-seq data. Comprehensive simulations and test data show that the presented analysis pipeline is more powerful and efficient than previous differential transcript expression pipelines while providing correct control of the false discovery rate.
Fast-scBatch: Batch Effect Correction Using Neural Network-Driven Distance Matrix Adjustment
Authors: Chen Fu , Tian Leqi , Fei Teng , Yu Tianwei
Published: June 2024

Batch effect is a frequent challenge in deep sequencing data analysis that can lead to misleading conclusions. Existing methods do not correct batch effects satisfactorily, especially with single-cell RNA sequencing (scRNA-seq) data. To address this challenge, we introduce fast-scBatch, a novel and efficient two-phase algorithm for batch-effect correction in scRNA-seq data, designed to handle non-linear and complex batch effects. Specifically, this method utilizes the inherent correlation structure of the data for batch effect correction and employs a neural network to expedite the process. It outputs a corrected expression matrix, facilitating downstream analyses. We validated fast-scBatch through simulation studies and on two scRNA-seq datasets, demonstrating its superior performance in batch-effect correction compared to current methods, as evidenced by visualization using UMAP plots, and metrics including Adjusted Rand Index (ARI) and Adjusted Mutual Information (AMI).
Acute aerobic exercise does not modulate pain potentially due to differences in fitness levels and sex effects – results from a pharmacological fMRI study
Authors: Nold Janne I. , Fadai Tahmine , Büchel Christian
Published: June 2024

Exercise might lead to a release of endogenous opioids, potentially resulting in pain relief. However, the neurobiological underpinnings of this effect remain unclear. Using a pharmacological within-subject fMRI study with the opioid antagonist naloxone and different levels of aerobic exercise and pain we investigated exercise-induced hypoalgesia (N= 39, 21 female). Overall, we were unable to detect reduced pain after high-intensity aerobic exercise as compared to low-intensity aerobic exercise. Accordingly, we observed no significant changes in the descending pain modulatory system. The µ-opioid antagonist naloxone significantly increased overall pain ratings but showed no interaction with exercise intensity. An exploratory analysis suggested an influence of fitness level and sex where males showed greater hypoalgesia after high-intensity exercise with increasing fitness levels. This effect was attenuated by naloxone and mirrored by fMRI signal changes in the medial frontal cortex, where activation also varied with fitness level and sex, and was reversed by naloxone. These results indicate that aerobic exercise has no overall effect on pain in a mixed population sample, but individual factors such as fitness level and sex might play a role.
Vancomycin impairs macrophage fungal killing by disrupting mitochondrial morphology and function
Authors: Bojang Ebrima , Sheriff Lozan , Fu Man Shun , Wellings Chloe , Abdissa Ketema , Stavrou Victoria , Clark Callum , Southam Andrew D. , Dunn Warwick B. , Bending David , Hombrebueno Jose R. , Jacobsen Ilse , Dimeloe Sarah , Hall Rebecca A. , Drummond Rebecca A.
Published: June 2024

Vancomycin is a widely prescribed antibiotic used in the treatment of Gram-positive bacterial infections. We recently showed that this antibiotic disrupted protective anti-fungal immune responses via microbiome dysbiosis, enhancing susceptibility to invasive candidiasis. Antibiotics are an independent risk factor for developing this life-threatening fungal infection, but whether microbiota-independent mechanisms also drive this association is not clear. Here, we show that vancomycin directly impairs macrophage responses toCandida albicans, the main causative agent of invasive candidiasis. Vancomycin-treated macrophages were less able to killC. albicansdespite normal phagocytosis rates and were hyper-inflammatory and more likely to die during infection. We found that vancomycin bound to macrophage mitochondria, leading to depolarisation, reduced respiratory capacity and a hyper-fragmented morphology associated with increased ROS production. Taken together, this work demonstrates direct effects of vancomycin on mammalian immune cells, helping us to understand pro-inflammatory effects of this drug and how it promotes susceptibility to life-threatening fungal infection.
Role of individual and population heterogeneity in shaping dynamics of multi-pathogen excretion in an island endemic bat
Authors: Aguillon Samantha , Turpin Magali , Le Minter Gildas , Lebarbenchon Camille , Hoarau Axel O. G. , Toty Céline , Duchet Avril , Joffrin Léa , Ramanantsalama Riana V. , Tortosa Pablo , Mavingui Patrick , Dietrich Muriel
Published: June 2024

Understanding processes driving pathogen transmission in bats is critical to prevent spillovers and emergence events. However, it requires fine-scale ecological investigations, which are rare because of the complexity and heterogeneity of bat populations. Here, based on the monitoring of 5,949 Reunion free-tailed bats (Mormopterus francoismoutoui) in 17 roosts over 24 months, we studied the simultaneous excretion of paramyxovirus andLeptospirabacteria in urine, and herpesvirus in saliva. We analysed the influence of individual and roost-level factors on co-excretion dynamics. We evidenced all year long excretion with high prevalence (37% - 87%), with low levels of temporal synchrony among roosts and no signal of density- dependent transmission. Recapture data support persistent infections for all infectious agents, alongside with clearance followed by reinfection for paramyxovirus andLeptospira. Our results suggest that sex-specific social behaviour or physiological adaptations drive herpesvirus excretion, while paramyxovirus andLeptospiraexcretion reactivate during reproduction. Our data also suggest the protection of juveniles by maternal antibodies, but different waning dynamics, much shorter for HSV infection, that could lead to a pathogen-dependent role of juveniles in the spread of infection. Interestingly, the excretion of one infectious agent was positively correlated to the excretion of a second one. However, the probability of excreting a third one was reduced for individuals already bi-excreting, suggesting negative interactions for cumulative infections. Connecting such spatio-temporal data with ecosystem alterations in Reunion Island could further contribute to our understanding of the links between human-mediated changes in the ecology of bats and infectious diseases emergence processes.

Significance Statement

Understanding risks of bat-borne pathogen spillover is challenging because of the difficulty in studying excretion dynamics in wild bat populations. Here, we used an original island-endemic model to build up a fine-scale spatio-temporal analysis of the excretion of two viruses (paramyxovirus and herpesvirus) and a bacterium (Leptospira) at both population- (roost) and individual- (through recaptured bats) levels. Excretion patterns are specific to each infectious agent and driven by the age and the reproduction of both females and males. Results also suggest that a combination of viral persistence and clearance, as well as interactions between infectious agents, are important within-host processes that contribute to the transmission of infections in bat populations. This information is crucial to better predict shedding pulses and prevent potential future spillovers.
Seasonal and hourly diversity patterns of anthropophagous female mosquito species in a semi-conserved area at the southern Mexico
Authors: Canales-Delgadillo Julio César , Vázquez-Pérez Nallely , Viveros-Santos Vicente , Pérez-Ceballos Rosela , Cardoso-Mohedano José Gilberto , Zaldívar-Jiménez Arturo , Celis-Hernández Omar , Gómez-Ponce Alejandro , Merino-Ibarra Martín
Published: June 2024

Mosquitoes are the most dangerous organisms on Earth because they spread causal agents of diseases. However, mosquito populations need to be better known in coastal areas of the Yucatan Peninsula to understand and prevent the spread of diseases effectively. To increase the knowledge about the mosquito community in the southern Gulf of Mexico region, we determined the diversity of mosquito species in Isla del Carmen Campeche. We trapped adult mosquitoes using buccal aspirators on monthly surveys (September 2019 to December 2020) in mangrove and low-semideciduous forest patches in three climate seasons. The sampling sessions consisted of 60 minutes of trapping performed every four hours (at 09, 13, 17, 21, 01, and 05 hrs) until a 24-hour cycle was completed. The trapped individuals were identified at the species level. We calculated Hill numbers using incidence data for each season and sampling hour. Abundances were compared through Kruskal-Wallis tests. A literature review determined the diseases associated with the species found. We collected 21,424 mosquito individuals from 11 genera, 26 species and four morphospecies. Seasonally, greater mosquito abundance and richness (n= 26) occurred during the norte season (χ2= 7.23, df = 2,p= 0.026) and between the 09:00 and 13:00 hrs (χ2= 15.25, df = 5,p= 0.009). Many species in this study are reported as disease vectors of medical and veterinary relevance.Conclusions:Isla del Carmen contributes to the Yucatan Peninsula’s mosquito diversity, and several of its species are vectors of pathogens to humans and wildlife.
Altered thymic niche synergistically drives the massive proliferation of malignant thymocytes
Authors: Tsingos Erika , Dick Advaita M. , Bajoghli Baubak
Published: June 2024

The discovery of genetic alterations in patient samples over the last 20 years has promoted a cell-autonomous view of proliferative expansion during T-cell acute lymphoblastic leukemia (T-ALL) development in the thymus. However, the potential contribution of non-cell-autonomous factors, particularly the impact of thymic epithelial cells (TECs) within the thymic niche during the initiation phase, remains unexplored. In this study, we employ a unique combination of a cell-based computational model of the thymus andin vivoexperiments. We systematically analyze the impact of 12 cell-autonomous and non-autonomous factors, either alone or in combinations, on the proliferation of normal and malignant thymocytes with interleukin-7 receptor (IL7R) gain-of-function mutations or elevated IL7R levels, as observed in T-ALL patients. By simulating over 1500 scenarios, we show that while a dense TEC network favored the proliferation of normal thymocytes, it inhibited the proliferation of malignant lineages, which achieved their maximal proliferative capacity when TECs were sparsely distributed. Ourin silicomodel predicts that certain mutations could accelerate proliferative expansion within a few days. This was experimentally validated, revealing rapid onset of thymus lymphoma and infiltration of malignant T-cells into other organs within 8 days of medaka (Oryzias latipes) embryonic development, thus revealing that modifications in the thymic niche and oncogenes in thymocytes together accelerate the disease development. Our results also suggest that negative feedback from the proliferative state inhibits differentiation of thymocytes, thereby prolonging the proliferative state and further fueling malignant expansion. Overall, this work reveals the critical impact of TEC-thymocyte interactions in both the initiation and progression of disease.
My friend MIROSLAV: A Hackable Open-Source Hardware and Software Platform for High-Throughput Rodent Activity Monitoring in the Home Cage
Authors: Virag Davor , Homolak Jan , Kodvanj Ivan , Vargantolić Ana-Marija , Babić Perhoč Ana , Meglić Patrik , Šoštarić Mužić Petra , Knezović Ana , Osmanović Barilar Jelena , Cifrek Mario , Trkulja Vladimir , Šalković-Petrišić Melita
Published: June 2024

While conventional behavioural tests offer valuable insight into rodent behaviour in specific paradigms, rodents spend most of their time in a safe, undisturbed environment – their home cage. However, home cage monitoring (HCM) is often impractical at scale over prolonged periods of time without significant loss of data.

To achieve this, we developed MIROSLAV, the Multicage InfraRed Open Source Locomotor Activity eValuator, a home cage activity and environmental monitoring device designed to be open, adaptable, and robust. Its transparent and modular design allows the device to be tailored to varying experimental requirements and environmental conditions, while its wireless operation and multiple redundancies minimise loss of data and animal disturbance. Data quality is maintained by a modular software workflow for data preparation (Prepare-a-SLAV) and cleaning (TidySLAV), followed by exploratory (MIROSine – MIRO The Explorer) and statistical (MIROSine – StatistiSLAV) analysis of circadian periodicity.

Here, using MIROSLAV, we demonstrate circadian dysrhythmia and a disrupted response to regular stimuli (e.g. behavioural testing, bedding change) in a rat model of sporadic Alzheimer’s disease, showcasing MIROSLAV’s utility in a typical animal study of disease.

In accordance with the 3Rs, every rodent study and laboratory performing them can benefit from HCM, provided the existence of transparent and customisable tools which allow robust deployment to tens or hundreds of cages in various conditions. MIROSLAV provides this opportunity to researchers in a cost-effective manner.
Dissecting the temporal phenomics and genomics of maize canopy cover using UAV mediated image capture
Authors: Cooper Julian , Sweet Dorothy D. , Tirado Sara B. , Springer Nathan M. , Hirsch Candice N. , Hirsch Cory D.
Published: June 2024

Canopy cover is an important agronomic trait influencing photosynthesis, weed suppression, biomass accumulation, and yield. Conventional methods to quantify canopy cover are time and labor-intensive. As such, little is known about how canopy cover develops over time, the stability of canopy cover across environments, or the genetic architecture of canopy cover. We used unoccupied aerial vehicle-mediated image capture to quantify plot-level canopy coverage in maize throughout the growing season. Images of 501 diverse inbred lines were acquired between 300 and 1300 growing degree days in the 2018-2021 growing seasons. We observed that the maize canopy developed following a logistic curve. Phenotypic variation in percent canopy coverage and canopy growth rate was explained by genetic and environmental factors and genotype-by-environment interactions, however the percent of variance explained by each factor varied throughout the growing season. Environmental factors explained the largest portion of trait variance during the adult vegetative growth stage and had a larger impact on canopy growth rates than percent canopy coverage. We conducted multiple genome wide association studies and found that canopy cover is a complex, polygenic trait with a diverse range of marker trait associations throughout development. The change in associations indicated that single time point phenotyping was insufficient to capture the full phenomic and genetic diversity of canopy cover in maize.
Plant height defined growth curves during vegetative development have the potential to predict end of season maize yield and assist with mid-season management decisions
Authors: Sweet Dorothy D. , Cooper Julian , Hirsch Cory D. , Hirsch Candice N.
Published: June 2024

Precision farming has been developing with the intention of identifying within field variability to adjust management strategies and maximize end of season yield and profitability and minimize negative environmental impacts. The development of quick, easy, and low cost methods to quantify field level variation is essential to successful implementation of precision agriculture at scale. Temporal plant height and growth rates collected with unoccupied aerial vehicles mounted with red, green, blue sensors have the potential to predict end of season grain yield, which could facilitate mid-season management decisions. Image-based plant height data was collected weekly from commercial maize fields in three growing seasons to assess variation within fields and the relationship with grain yield variation. Plant height, growth rate, and grain yield had variable relationships depending on the time point and growth environment. Models developed using temporal traits predicted grain yield variation within a commercial field up to r = 0.7, though insufficient water affected the prediction accuracy in one field due to the limited representation of drought environments in the model development. In the future, with more data from stress environments, such as drought, this method has potential for high accuracy grain yield prediction across a range of environmental conditions. This study demonstrates the potential of using unoccupied aerial vehicles to derive vegetative growth patterns and model within field variations, and has application in making mid-season management decisions.
PhyloFusion- Fast and easy fusion of rooted phylogenetic trees into rooted phylogenetic networks
Authors: Zhang Louxin , Cetinkaya Banu , Huson Daniel H.
Published: June 2024

Unrooted phylogenetic networks are often used to represent evolutionary data when incompatibilities are present. Although rooted phylogenetic networks are better suited for explicitly depicting evolutionary histories that involve reticulate events, they have been rarely used in practice, due to a lack of appropriate methods for their calculation. Here we present PhyloFusion, a fast and easily-applicable method for calculating rooted phylogenetic networks on sets of rooted phylogenetic trees. The algorithm can handle trees with unresolved nodes (which arise when edges with low support are contracted) and missing taxa. We illustrate how to use the algorithm to explore different groups of functionally-related genes and report that the algorithm can be applied to datasets containing tens of trees and hundreds of taxa.

Availability

An open source implementation of PhyloFusion is available in SplitsTree,https://www.github.com/husonlab/splitstree6(GPLv3 license)
Challenges and Progress in RNA Velocity: Comparative Analysis Across Multiple Biological Contexts
Authors: Ancheta Sarah , Dorman Leah , Le Treut Guillaume , Gurung Abel , Royer Loïc A. , Granados Alejandro , Lange Merlin
Published: June 2024

Single-cell RNA sequencing is revolutionizing our understanding of cell state dynamics, allowing researchers to observe the progression of individual cells’ transcriptomic profiles over time. Among the computational techniques used to predict future cellular states, RNA velocity has emerged as a predominant tool for modeling transcriptional dynamics. RNA velocity leverages the mRNA maturation process to generate velocity vectors that predict the likely future state of a cell, offering insights into cellular differentiation, aging, and disease progression. Although this technique has shown promise across biological fields, the performance accuracy varies depending on the RNA velocity method and dataset. We established a comparative pipeline and analyzed the performance of five RNA velocity methods on three datasets based on local consistency, method agreement, identification of driver genes, and robustness to sequencing depth. This benchmark provides a resource for scientists to understand the strengths and limitations of different RNA velocity methods.
Neuropathologically-directed profiling ofPRNPsomatic and germline variants in sporadic human prion disease
Authors: McDonough Gannon A. , Cheng Yuchen , Morillo Katherine , Doan Ryan N. , Kenny Connor J. , Foutz Aaron , Kim Chae , Cohen Mark L. , Appleby Brian S. , Walsh Christopher A. , Safar Jiri G. , Huang August Yue , Miller Michael B.
Published: June 2024

Creutzfeldt-Jakob Disease (CJD), the most common human prion disease, is associated with pathologic misfolding of the prion protein (PrP), encoded by thePRNPgene. Of human prion disease cases, ∼1% were transmitted by misfolded PrP, ∼15% are inherited, and ∼85% are sporadic (sCJD). While familial cases are inherited through germline mutations inPRNP, the cause of sCJD is unknown. Somatic mutations have been hypothesized as a cause of sCJD, and recent studies have revealed that somatic mutations accumulate in neurons during aging. To investigate the hypothesis that somatic mutations inPRNPmay underlie sCJD, we performed deep DNA sequencing ofPRNPin 205 sCJD cases and 170 age-matched non-disease controls. We included 5 cases of Heidenhain variant sporadic CJD (H-sCJD), where visual symptomatology and neuropathology implicate focal initiation of prion formation, and examined multiple regions across the brain including in the affected occipital cortex. We employed Multiple Independent Primer PCR Sequencing (MIPP-Seq) with a median depth of >5,000X across thePRNPcoding region and analyzed for variants using MosaicHunter. An allele mixing experiment showed positive detection of variants in bulk DNA at a variant allele fraction (VAF) as low as 0.2%. We observed multiple polymorphic germline variants among individuals in our cohort. However, we did not identify bona fide somatic variants in sCJD, including across multiple affected regions in H-sCJD, nor in control individuals. Beyond our stringent variant-identification pipeline, we also analyzed VAFs from raw sequencing data, and observed no evidence of prion disease enrichment for the known germline pathogenic variants P102L, D178N, and E200K. The lack ofPRNPpathogenic somatic mutations in H-sCJD or the broader cohort of sCJD suggests that clonal somatic mutations may not play a major role in sporadic prion disease. With H-sCJD representing a focal presentation of neurodegeneration, this serves as a test of the potential role of clonal somatic mutations in genes known to cause familial neurodegeneration.
Dual roles of histone H3 lysine-4 in antagonizing Polycomb group function and promoting target gene expression
Authors: Anyetei-Anum Cyril S. , Leatham-Jensen Mary P. , Fox Geoffrey C. , Smith B. Rutledge , Krajewski Krzysztof , Strahl Brian D. , Dowen Jill M. , Matera A. Gregory , Duronio Robert J. , McKay Daniel J.
Published: June 2024

Tight control over cell identity gene expression is necessary for proper adult form and function. The opposing activities of Polycomb and trithorax complexes determine the ON/OFF state of targets like the Hox genes. Trithorax encodes a methyltransferase specific to histone H3 lysine-4 (H3K4). However, there is no direct evidence that H3K4 regulates Polycomb group target genesin vivo. Here, we demonstrate two key roles for replication-dependent histone H3.2K4 in target control. We find that H3.2K4 antagonizes Polycomb group catalytic activity and that it is required for proper target gene activation. We conclude that H3.2K4 directly regulates expression of Polycomb targets.
Pervasive conservation of intron number and other genetic elements revealed by a chromosome-level genomic assembly of the hyper-polymorphic nematode Caenorhabditis brenneri
Authors: Teterina Anastasia , Willis John H , Baer Charles F. , Phillips Patrick C
Published: June 2024

With within-species genetic diversity estimates that span the gambit of that seen across the entirety of animals, the Caenorhabditis genus of nematodes holds unique potential to provide insights into how population size and reproductive strategies influence gene and genome organization and evolution. Our study focuses on Caenorhabditis brenneri, currently known as one of the most genetically diverse nematodes within its genus and metazoan phyla. Here, we present a high-quality gapless genome assembly and annotation for C. brenneri, revealing a common nematode chromosome arrangement characterized by gene-dense central regions and repeat rich peripheral parts. Comparison of C. brenneri with other nematodes from the 'Elegans' group revealed conserved macrosynteny but a lack of microsynteny, characterized by frequent rearrangements and low correlation of orthogroup sizes, indicative of high rates of gene turnover. We also assessed genome organization within corresponding syntenic blocks in selfing and outcrossing species, affirming that selfing species predominantly experience loss of both genes and intergenic DNA. Comparison of gene structures revealed strikingly small number of shared introns across species, yet consistent distributions of intron number and length, regardless of population size or reproductive mode, suggesting that their evolutionary dynamics are primarily reflective of functional constraints. Our study provides valuable insights into genome evolution and expands the nematode genome resources with the highly genetically diverse C. brenneri, facilitating research into various aspects of nematode biology and evolutionary processes.
Polyommatine blue butterflies reveal unexpected integrity of the W sex chromosome amid extensive chromosome fragmentation
Authors: Hospodářská Monika , Chung Voleníková Anna , Koutecký Petr , Vila Roger , Talavera Gerard , Provazníková Irena , Dalíková Martina , Nguyen Petr
Published: June 2024

Chromosomal rearrangements are crucial in speciation, acting as barriers to gene flow. Holocentric chromosomes, such as those in Lepidoptera, can facilitate karyotype changes. Despite chromosome fusions being more common, speciation events are mostly linked to fissions. Notable karyotypic variation is observed in three clades of the subfamily Polyommatinae (Lycaenidae), with chromosome numbers ranging from n = 10 to n = 225. This study used flow cytometry and molecular cytogenetic analyses to investigate genome sizes and karyotypes in several species of the generaPolyommatusandLysandrawith derived and modal chromosome numbers. The findings show no support for polyploidy, supporting karyotypic diversification via fragmentation of chromosomes. Species with high chromosome numbers have larger genomes, which indicates a potential role of mobile elements but contradicts the hypothesis of holocentric drive. Telomeric signals were detected at the ends of fragmented chromosomes. No interstitial telomeric sequences were detected on autosomes. Interstitial telomeric signals on sex chromosomes, however, revealed multiple sex chromosome systems inPolyommatus dorylasandPolyommatus icarus, with two karyotype races differing in sex chromosome constitution in the latter. Pool-seq and coverage analyses indicated shared fusion of sex chromosomes with an autosome bearing the rDNA locus, followed by a fusion with chromosome 20 in the Czech population. Notably, the W chromosome resists fragmentation, likely due to epigenetic silencing protecting it from activity of mobile elements.
Matching Habitat Choice and the Evolution of a Species’ Range
Authors: Shirani Farshad , Miller Judith R.
Published: June 2024

Natural selection is not the only mechanism that promotes adaptation of an organism to its environment. Another mechanism is matching habitat choice, in which individuals sense and disperse toward habitat best suited to their phenotype. This can in principle facilitate rapid adaptation, enhance range expansion, and promote genetic differentiation, reproductive isolation, and speciation. However, empirical evidence that confirms the evolution of matching habitat choice in nature is limited. Here we obtain theoretical evidence that phenotype-optimal dispersal, a particular form of matching habitat choice, is likely to evolve only in the presence of a steep environmental gradient. Such a gradient may be steeper than the gradient the majority of species typically experience in nature, adding to the collection of possible explanations for the scarcity of evidence for matching habitat choice. We draw this conclusion from numerical solutions of a system of deterministic partial differential equations for a population’s density along with the mean and variance of a fitness-related quantitative phenotypic trait such as body size. In steep gradients, we find that phenotype-optimal dispersal facilitates rapid adaptation on single-generation time scales, reduces within-population trait variation, increases range expansion speed, and enhances the chance of survival in rapidly changing environments. Moreover, it creates a directed gene flow that compensates for the maladaptive core-to-edge effects of random gene flow caused by random movements. These results suggest that adaptive gene flow to range margins, together with substantially reduced trait variation at central populations, may be hallmarks of phenotype-optimal dispersal in natural populations. Further, slowly-growing species under strong natural selection may particularly benefit from evolving phenotype-optimal dispersal.
A Tunable, Ultrasensitive Threshold in Enzymatic Activity Governs the DNA Methylation Landscape
Authors: Bonsu Kwadwo A. , Trinh Annie , Downing Timothy L. , Read Elizabeth L.
Published: June 2024

DNA methylation is a widely studied epigenetic mark, affecting gene expression and cellular function at multiple levels. DNA methylation in the mammalian genome occurs primarily at cytosine-phosphate-guanine (CpG) dinucleotides, and patterning of the methylation landscape (i.e., the presence or absence of CpG methylation at a given genomic location) exhibits a generally bimodal distribution. Although much is known about the enzymatic writers and erasers of CpG methylation, it is not fully understood how these enzymes, along with genetic, chromatin, and regulatory factors, control the genome wide methylation landscape. In this study, methylation is analyzed at annotated CpG Islands (CGIs) and independent CpGs as a function of their proximity to other CpG substrates. Analysis is aided by a computationally efficient stochastic mathematical model of methylation dynamics, enabling parameterization from data. We find that methylation exhibits a switch-like dependence on local CpG density. The threshold and steepness of the switch is modified in cell lines in which key enzymes are knocked out. Modeling further elucidates how enzymatic parameters, including catalytic rates and lengthscales of inter-CpG interaction, tune the properties of the switch. Together, the results support a model in which competition between opposing TET1-3 demethylating enzymes and DNA methyltransferases (DNMT3A/B) results in an ultrasensitive switch, analogous to the protein phosphorylation switch (termed ‘zero-order ultra-sensitivity’) proposed by Goldbeter and Koshland. Our study provides insight to the mechanisms underlying establishment and maintenance of bimodal DNA methylation landscapes, and further provides a flexible pipeline for gleaning molecular insights to the cellular methylation machinery across cell-specific, epigenomic datasets.
The Naïve Bayes Classifier++ for Metagenomic Taxonomic Classification – Query Evaluation
Authors: Duan Haozhe (Neil) , Hearne Gavin , Polikar Robi , Rosen Gail
Published: June 2024

This study examines the query performance of the NBC++ (Incremental Naive Bayes Classifier) program for variations in canonicality, kmer size, databases, and input sample data size. NBC++ can successfully assess a wide range of superkingdoms using a small training database. We demonstrate that NBC++ and Kraken2 are affected by database depth with macro measures increasing with depth but that the full diversity of life, especially viruses, is still a challenge for these classifiers. NBC++ spends less time training but at the cost of long querying time. The major enhancements are to accommodate canonicalkmer storage (with major storage savings), adaptable and optimized memory allocation that quickens the query analysis and allows the classifier to be run on almost any system, and enables output of the log-likelihood values against each training genome which provides users with valualbe confidence information.
Cytokinin-inducibleDIRIGENT13involved in lignan synthesis and ROS accumulation promotes root growth and abiotic stress tolerance inArabidopsis
Authors: Melnikava Alesia , Perreau François , Paniagua Candelas , Cheng Sy-Chyi , Huang Li-Min , Ubogoeva Elena , Zemlyanskaya Elena , Yang Yu-Liang , Mouille Grégory , Arnaud Dominique , Hejatko Jan
Published: June 2024

Dirigent (DIR) proteins mediate regio- and stereoselectivity of phenoxy radical coupling of monolignols for (neo)lignan or lignin synthesis. However, the role of DIR proteins and lignans in plant development and response to environmental stresses remains elusive. Here, we provide a functional characterization of the cytokinin-responsiveDIRIGENT13(DIR13) inArabidopsis thaliana. DIR13 was localized to the root endodermis and at the margins of lateral root primordia and lateral roots. While not necessary for Casparian strip formation, DIR13 promoted both main and lateral root growth. Untargeted metabolomics and imaging mass spectrometry analyses unveiled the role of DIR13 in facilitating (neo)lignan synthesis in primary and lateral roots. Interestingly, DIR13 activated the production of putative oxomatairesinol and matairesinol-cysteine which are oxidative derivatives of the lignan matairesinol. Our data also identified DIR13 as an enhancer of salt and drought tolerance. Particularly,DIR13attenuated salt stress-mediated inhibition of germination and root growth. Moreover, DIR13 activated reactive oxygen species (ROS) accumulation both under control and salt stress conditions, and cytokinin further enhanced the salt-induced ROS production specifically in theDIR13overexpressing line. Our results uncover a role for DIR13-produced lignans in the priming of ROS accumulation, mediating both abiotic stress tolerance and the control of root architecture.
APax3lineage gives rise to transient haematopoietic progenitors
Authors: Canu Giovanni , Correra Rosamaria , Díez Pinel Guillermo , Castellan Raphaël F. P. , Denti Laura , Fantin Alessandro , Ruhrberg Christiana
Published: June 2024

During embryonic development, muscle tissues, skin, and a subset of vascular endothelial cells arise fromPax3-expressing embryonic progenitors defined as paraxial mesoderm. By contrast, haemogenic potential is well established for extra-embryonic mesoderm and intra-embryonic lateral plate mesoderm which do not expressPax3. To date, it is not known whether the haematopoietic system also containsPax3lineage cells. Here, we show that the mouse foetal liver and foetal circulation contain a transient population ofPax3lineage cells with hallmarks of haematopoietic progenitors and the potential to generate both myeloid and erythroid cells. We propose thatPax3lineage haematopoietic cells should be investigated to better understand normal haematopoietic development from different mesodermal derivatives. Further, genetic alterations ofPax3lineage haematopoietic cells should be investigated for their potential to cause haematopoietic malignancies.
Transient inhibition of type I interferon enhances CD8+T cell stemness and vaccine protection
Authors: Broomfield Benjamin J. , Tan Chin Wee , Qin Raymond Z. , Duckworth Brigette C. , Alvarado Carolina , Dalit Lennard , Chen Jinjin , Mackiewicz Liana , Muramatsu Hiromi , Pellegrini Marc , Rogers Kelly L. , Moon Woohyun J. , Nutt Stephen L. , Davis Melissa J. , Pardi Norbert , Wimmer Verena C. , Groom Joanna R.
Published: June 2024

Developing vaccines that promote CD8+T cell memory is a challenge for infectious disease and cancer immunotherapy. TCF-1+stem cell-like memory T (TSCM) cells are important determinants of long-lived memory. Yet, the developmental requirements for TSCMformation are unclear. Here, we identify the temporal window for type I interferon (IFN-I) receptor (IFNAR) blockade to drive TSCMcell generation. TSCMcells were transcriptionally distinct and emerged from a transitional precursor of exhausted (TPEX) cellular state concomitant with viral clearance. TSCMdifferentiation correlated with T cell retention within the lymph node paracortex, due to increased CXCR3 chemokine abundance which disrupted gradient formation. These affects were due a counterintuitive increase in IFNψ, which controlled cell location. Combining IFNAR inhibition with mRNA-LNP vaccination promoted specific TSCMdifferentiation and enhanced protection against chronic infection. These finding propose a new approach to vaccine design whereby modulation of inflammation promotes memory formation and function.

HIGHLIGHTS

Early, transient inhibition of the type I interferon (IFN) receptor (IFNAR) during acute viral infection promotes stem cell-like memory T (TSCM) cell differentiation without establishing chronic infection.

TSCMand precursor of exhausted (TPEX) cellular states are distinguished transcriptionally and by cell surface markers.

Developmentally, TSCMcell differentiation occurs via a transition from a TPEXstate coinciding with viral clearance.

Transient IFNAR blockade increases IFNψ production to modulate the ligands of CXCR3 and couple TSCMdifferentiation to cell retention within the T cell paracortex of the lymph node.

Specific promotion of TSCMcell differentiation with nucleoside-modified mRNA-LNP vaccination elicits enhanced protection against chronic viral challenge.
Identification of a mimotope of a complex gp41 Human Immunodeficiency VIrus epitope related to a non-structural protein ofHepaciviruspreviously implicated in Kawasaki disease
Authors: Sojar Hakimuddin , Baron Sarah , Hicar Mark D
Published: June 2024

Background

We have previously isolated a highly mutated VH1-02 antibody termed group C 76-Q13-6F5 (6F5) that targets a conformational epitope on gp41. 6F5 has the capacity to mediate Ab dependent cell cytotoxicity (ADCC). When the VH1-02 group C 76 antibodies variable chain sequence was reverted to germline (76Canc), this still retained ADCC activity. Due to this ability for the 76Canc germline antibody to functionally target this epitope, we sought to identify a protein target for vaccine development.

Methods

Initially, we interrogated peptide targeting by screening a microarray containing 29,127 linear peptides. Western blot and ELISAs were used to confirm binding and explore human serum targeting. Autoimmune targeting was further interrogated on a yeast-displayed human protein microarray.

Results

76Canc specifically recognized a number of acidic peptides. Meme analysis identified a peptide sequence similar to a non-structural protein ofHepaciviruspreviously implicated in Kawasaki disease (KD). Binding was confirmed to top peptides, including theHepacivirus-related and KD-related peptide. On serum competitions studies using samples from children with KD compared to controls, targeting of this epitope showed no specific correlation to having KD. Human protein autoantigen screening was also reassuring.

Conclusions

This study identifies a peptide that can mimic the gp41 epitope targeted by 76C group antibodies (i.e.a mimotope). We show little risk of autoimmune targeting including any inflammation similar to KD, implying non-specific targeting of this peptide during KD. Development of such peptides as the basis for vaccination should proceed cautiously.