bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cathodoluminescent and Characteristic X-ray-emissive Rare-Earth-doped Core/Shell Immunolabels for Spectromicroscopic Analysis of Cell Surface Receptors
Authors: Habermann Sebastian , Gerken Lukas R. H. , Kociak Mathieu , Monachon Christian , Kissling Vera M. , Gogos Alexander , Herrmann Inge K. 
Published: March 2024

AbstractUnderstanding the localization and the interactions of biomolecules at the nanoscale and in the cellular context remains challenging. Electron microscopy (EM) as a non-Abbe limited technique gives access to the cellular ultra-structure yet results in grey-scale images and averts unambiguous (co-)localization of biomolecules. Multimodal nanoparticle-based immunolabels for correlative cathodoluminescence electron microscopy (CCLEM) and energy-dispersive X-ray spectromicroscopy (EDX-SM) are presented. The single-particle STEM-cathodoluminescence (CL) and characteristic X-ray emissivity of sub-20 nm lanthanide-doped nanoparticles were exploited as unique spectral fingerprints for precise localization and label identification. To maximize the nanoparticle brightness, lanthanides were incorporated in a low-phonon host lattice and separated from the environment using a passivating shell. The core/shell nanoparticles were then functionalized with either folic (terbium-doped) or caffeic acid (europium-doped). Their potential for immunolabeling was successfully demonstrated using HeLa cells expressing different surface receptors that bind to folic or caffeic acid, respectively. Both particle populations showed single-particle CL emission along with a distinctive energy-dispersive X-ray signal, with the latter enabling colour-based localization of receptors within swift imaging times well below 2 mins per µm2while offering high resolution with a pixel size of 2.78 nm. Taken together, these results open a route to color immunolabelling based on electron spectromicroscopy.Table of ContentsSmall (sub-20 nm) lanthanide-doped nanoparticles were successfully utilized in electron microscopy to label biological structures and contextualize them in the cell’s ultrastructure. Leveraging unique energy-dispersive X-ray signatures, the nanoparticles’ location and doping-identity was easily and fast retrieved, demonstrating the methods’ potential to (co)-localize labels while supplying a holistic impression of the underlying processes, as entire cells could be mapped.
Integrative Omics reveals changes in the cellular landscape of yeast without peroxisomes
Authors: Kosir Tjasa , Das Hirak , Pedersen Marc Pilegaard , Anteghini Marco , Oeljeklaus Silke , Martins dos Santos Vitor , van der Klei Ida J. , Warscheid Bettina 
Published: March 2024

AbstractPeroxisomes are organelles that are crucial for cellular metabolism. However, these organelles play also important roles in non-metabolic processes, such as signalling. To uncover the consequences of peroxisome deficiency, we compared two extremes, namelySaccharomyces cerevisiaewild-type andpex3cells, which lack functional peroxisomes, employing transcriptomics and quantitative proteomics technology. Cells were grown on acetate, a carbon source that involves peroxisomal enzymes of the glyoxylate cycle and does not repress peroxisomal proteins. Transcripts of peroxisomal β-oxidation genes and the corresponding proteins were enhanced inpex3cells. Peroxisome-deficiency also caused reduced levels of membrane bound peroxins, while the soluble receptors Pex5 and Pex7 were enhanced at the protein level. In addition, we observed alterations in non-peroxisomal transcripts and proteins, especially mitochondrial proteins involved in respiration or import processes. Our results not only reveal the impact of the absence of peroxisomes in yeast, but also represent a rich resource of candidate genes/proteins that are relevant in peroxisome biology.SummaryOmics comparison of wild-type and peroxisome-deficient (pex3) yeast cells uncovered processes that are affected by loss of peroxisomes. β-oxidation enzymes were upregulated, whereas most peroxins were decreased. Also, several non-peroxisomal transcripts/proteins were significantly altered. Our data represent a rich source of candidate genes connected to peroxisome biology.
Chaperone-Mediated Autophagy in Fish: A Key Function Amid a Changing Environment
Authors: Schnebert Simon , Vélez Emilio J , Goguet Maxime , Dias Karine , Véron Vincent , García-Pérez Isabel , Radler Lisa M , Cardona Emilie , Fontagné-Dicharry Stéphanie , Van Delft Pierre , Dittrich-Domergue Franziska , Bernard Amélie , Beaumatin Florian , Herpin Amaury , Cleveland Beth , Seiliez Iban 
Published: March 2024

ABSTRACTChaperone-Mediated Autophagy (CMA) is a major pathway of lysosomal proteolysis critical for cellular homeostasis and metabolism. While extensively studied in mammals, CMA’s existence in fish has only been confirmed recently, offering exciting insights into its role in species facing environmental stress. Here, we shed light on the existence of 2 genes encoding the CMA-limiting factor Lamp2A (lysosomal associated membrane protein 2A) in rainbow trout (RT,Oncorhynchus mykiss), revealing distinct expression patterns across various tissues. Notably, RT lacking the most expressed Lamp2A exhibit profound hepatic proteome disturbances during acute nutritional stress, underscoring its pivotal role as a guardian of hepatic proteostasis. Building upon these findings, we introduce and validate the CMA activation score as a reliable indicator of CMA status, providing a valuable tool for detecting cellular stress in fish under environmental threats. Overall, our study offers new perspectives into understanding CMA from evolutionary and environmental contexts.Abstract Figure
Measuring X inactivation skew for retinal diseases with adaptive nanopore sequencing
Authors: Gocuk Sena A , Lancaster James , Su Shian , Jolly Jasleen K , Edwards Thomas L , Hickey Doron G , Ritchie Matthew E , Blewitt Marnie E , Ayton Lauren N , Gouil Quentin 
Published: March 2024

X-linked genetic disorders typically affect females less severely than males due to the presence of a second X chromosome not carrying the deleterious variant. However, the phenotypic expression in females is highly variable, which may be explained by an allelic skew in X chromosome inactivation. Accurate measurement of X inactivation skew is crucial to understand and predict disease phenotype in carrier females, with prediction especially relevant for degenerative conditions.We propose a novel approach using nanopore sequencing to quantify skewed X inactivation accurately. By phasing sequence variants and methylation patterns, this single assay reveals the disease variant, X inactivation skew, its directionality, and is applicable to all patients and X-linked variants. Enrichment of X-chromosome reads through adaptive sampling enhances cost-efficiency. Our study includes a cohort of 16 X-linked variant carrier females affected by two X-linked inherited retinal diseases: choroideremia andRPGR-associated retinitis pigmen-tosa. As retinal DNA cannot be readily obtained, we instead determine the skew from peripheral samples (blood, saliva and buccal mucosa), and correlate it to phenotypic outcomes. This revealed a strong correlation between X inactivation skew and disease presentation, confirming the value in performing this assay and its potential as a way to prioritise patients for early intervention, such as gene therapy currently in clinical trials for these conditions.Our method of assessing skewed X inactivation is applicable to all long-read genomic datasets, providing insights into disease risk and severity and aiding in the development of individualised strategies for X-linked variant carrier females.
Single cell RNA sequencing of nc886, a non-coding RNA transcribed by RNA polymerase III, with a primer spike-in strategy
Authors: Shin Gyeong-Jin , Choi Byung-Han , Eum Hye Hyeon , Jo Areum , Kim Nayoung , Kang Huiram , Hong Dongwan , Jang Jiyoung Joan , Lee Hwi-Ho , Lee Yeon-Su , Lee Yong Sun , Lee Hae-Ock 
Published: March 2024

AbstractSingle cell RNA sequencing (scRNA-seq) has emerged as a versatile tool in biology, enabling comprehensive genomic-level characterization of individual cells. Currently, most scRNA-seq methods generate barcoded cDNAs by capturing polyA tails of mRNAs, which excludes many non-coding RNAs (ncRNAs), especially those transcribed by RNA polymerase III (Pol III). Although previously thought to be expressed constitutively, Pol III-transcribed ncRNAs are expressed variably in healthy and disease states and play important roles therein, necessitating their profiling at the single cell level. In this study, we have developed a measurement protocol for nc886 as a model case, as an initial step for scRNA-seq for Pol III-transcribed ncRNAs. Specifically, we spiked in an oligo-tagged nc886-specific primer during the polyA tail capture process for the 5’-reading in scRNA-seq. We then produced sequencing libraries for standard 5’ gene expression and oligo-tagged nc886 separately, to accommodate different cDNA sizes and ensure undisturbed transcriptome analysis. We applied this protocol in three cell lines which express high, low, and zero levels of nc886, respectively. Our results show that the identification of oligo tags exhibited limited target specificity, and sequencing reads of nc886 enabled the correction of non-specific priming. These findings suggest that gene-specific primers (GSPs) can be employed to capture RNAs lacking a polyA tail, with subsequent sequence verification ensuring accurate gene expression counting. Moreover, we embarked on an analysis of differentially expressed genes in cell line sub-clusters with differential nc886 expression, demonstrating variations in gene expression phenotypes. Collectively, the primer spike-in strategy allows us for a combined analysis of ncRNAs and gene expression phenotype.
Antigenic drift expands viral escape pathways from imprinted host humoral immunity
Authors: Maurer Daniel P. , Vu Mya , Schmidt Aaron G. 
Published: March 2024

ABSTRACTAn initial virus exposure can imprint antibodies such that future responses to antigenically drifted strains are dependent on the identity of the imprinting strain. Subsequent exposure to antigenically distinct strains followed by affinity maturation can guide immune responses toward generation of cross-reactive antibodies. How viruses evolve in turn to escape these imprinted broad antibody responses is unclear. Here, we used clonal antibody lineages from two human donors recognizing conserved influenza virus hemagglutinin (HA) epitopes to assess viral escape potential using deep mutational scanning. We show that even though antibody affinity maturation does restrict the number of potential escape routes in the imprinting strain through repositioning the antibody variable domains, escape is still readily observed in drifted strains and attributed to epistatic networks within HA. These data explain how influenza virus continues to evolve in the human population by escaping even broad antibody responses.
scDTL: single-cell RNA-seq imputation based on deep transfer learning using bulk cell information
Authors: Zhao Liuyang , Tian Jun , Xie Yufeng , Jiang Landu , Huang Jianhao , Xie Haoran , Zhang Dian 
Published: March 2024

AbstractMotivationThe growing amount of single-cell RNA sequencing (scRNA-seq) data allows researchers to investigate cellular heterogeneity and gene expression profiles, providing a high-resolution view of transcriptome at the single-cell level. However, dropout events, which are often present in scRNA-seq data, remain challenges for downstream analysis. Although a number of studies have been developed to recover single-cell expression profiles, their performance is sometimes limited by not fully utilizing the inherent relations between genes.ResultsTo address the issue, we propose a deep transfer learning based approach called scDTL for scRNA-seq data imputation by exploring the bulk RNA-sequencing information. scDTL firstly trains an imputation model for bulk RNA-seq data using a denoising autoencoder (DAE). We then apply a domain adaptation architecture that builds a mapping between bulk gene and single-cell gene domains, which transfers the knowledge learned by the bulk imputation model to scRNA-seq learning task. In addition, scDTL employs a parallel operation with a 1D U-Net denoising model to provide gene representations of varying granularity, capturing both coarse and fine features of the scRNA-seq data. At the final step, we use the cross-channel attention mechanism to fuse the features learned from the transferred bulk imputer and U-Net model. In the evaluation, we conduct extensive experiments to demonstrate that scDTL based approach could outperform other state-of-the-art methods in the quantitative comparison and downstream analyses.Contactzhangd@szu.edu.cnortianj@sustech.edu.cn
Seasonal genotypic and phenotypic differentiation of a cosmopolitan freshwater diatom
Authors: Cristini Domiziana , Kelly Joseph B. , Mahler Pia , Becks Lutz 
Published: March 2024

AbstractMost ecosystems are characterized by seasonality, which, through biotic and abiotic changes, influences species biomass dynamics. Recent studies have shown that ecologically important traits can evolve rapidly in response to environmental changes, resulting in eco-evolutionary dynamics with consequences for population and community dynamics. Evidence for seasonal effects on intraspecific variation is still scarce and understanding eco-evolutionary dynamics in the presence of seasonal fluctuations remains a major challenge. Following the phytoplankton spring bloom in Lake Constance, we investigated how seasonal changes influence the intraspecific diversity ofAsterionella formosaboth at genotypic and phenotypic levels. We found a high degree of genetic and phenotypic differentiation characterizingAsterionellapopulation, explained by a clustering of the isolates into early and late spring according to lake thermal stratification. Yet, most traits related to environmental parameters as well as fitness in different seasonal environments did not show a clear response to seasonality (i.e., temperature and nutrients), indicating that seasonal changes in biotic interactions (i.e., parasitic chytrids) were the major drivers of the observed seasonal shift inAsterionellagenotypes. Our results highlight the importance of studying eco-evolutionary processes for understanding variations in population and community dynamics in response to seasonal environmental fluctuations.
EXPLANA: A user-friendly workflow for EXPLoratory ANAlysis and feature selection in cross-sectional and longitudinal microbiome studies
Authors: Fouquier Jennifer , Stanislawski Maggie , O’Connor John , Scadden Ashley , Lozupone Catherine 
Published: March 2024

AbstractMotivationLongitudinal microbiome studies (LMS) are increasingly common but have analytic challenges including non-independent data requiring mixed-effects models and large amounts of data that motivate exploratory analysis to identify factors related to outcome variables. Although change analysis (i.e. calculating deltas between values at different timepoints) can be powerful, how to best conduct these analyses is not always clear. For example, observational LMS measurements show natural fluctuations, so baseline might not be a reference of primary interest; whereas, for interventional LMS, baseline is a key reference point, often indicating the start of treatment.ResultsTo address these challenges, we developed a feature selection workflow for cross-sectional and LMS that supports numerical and categorical data called EXPLANA (EXPLoratory ANAlysis). Machine-learning methods were combined with different types of change calculations and downstream interpretation methods to identify statistically meaningful variables and explain their relationship to outcomes. EXPLANA generates an interactive report that textually and graphically summarizes methods and results. EXPLANA had good performance on simulated data, with an average area under the curve (AUC) of 0.91 (range: 0.79-1.0, SD = 0.05), outperformed an existing tool (AUC: 0.95 vs. 0.56), and identified novel order-dependent categorical feature changes. EXPLANA is broadly applicable and simplifies analytics for identifying features related to outcomes of interest.
Development of a high-throughput, quantitative platform using human cerebral organoids to study virus-induced neuroinflammation in Alzheimer’s disease
Authors: Olson Meagan N. , Dawes Pepper , Murray Liam F. , Barton Nathaniel J. , Sundstrom Jonathan , Orszulak Adrian R. , Chigas Samantha M. , Tran Khanh , Aylward Aimee J. , Caliandro Michele F. , Riechers Sean-Patrick H. , Afshari Khashayar , Wang Qi , Garber Manuel , Humphries Fiachra , Orzalli Megan H. , Golenbock Douglas T. , Heneka Michael T. , Oh Hyung Suk , Church George M. , Young-Pearse Tracy L. , Knipe David M. , Readhead Benjamin , Chan Yingleong , Lim Elaine T. 
Published: March 2024

ABSTRACTNeuroinflammation is a central process in the pathogenesis of several neurodegenerative diseases such as Alzheimer’s disease (AD), and there are active efforts to target pathways involved in neuroinflammation for molecular biomarker discovery and therapeutic development in neurodegenerative diseases. It was also proposed that there may be an infectious etiology in AD that is associated with viruses such as herpes simplex virus (HSV-1) and influenza A virus (IAV), leading to neuroinflammation-induced AD pathogenesis or disease progression. We sought to develop high-throughput, quantitative molecular biomarker assays using dissociated cells from human cerebral organoids (dcOrgs), that can used for screening compounds to reverse AD-associated neuroinflammation. We found that HSV-1 infection, but not IAV infection, in dcOrgs led to increased intracellular Aβ42 and phosphorylated Tau-Thr212 (pTau-212) expression, lower ratios of secreted Aβ42/40, as well as neuronal loss, and increased proportions of astrocytes and microglia, which are hallmarks of AD. Among the glia cell-type markers, Iba1 (microglia) and GFAP (astrocyte) expression were most strongly correlated with HSV-1 expression, which further supported that these biomarkers are perturbed by glia-mediated neuroinflammation. By performing large-scale RNA sequencing, we observed that differentially expressed transcripts in HSV-1 infected dcOrgs were specifically enriched for AD-associated GWAS genes, but not for genes associated with other common neurodegenerative, neuropsychiatric or autoimmune diseases. Immediate treatment of HSV-1 infected dcOrgs with anti-herpetic drug acyclovir (ACV) rescued most of the cellular and transcriptomic biomarkers in a dosage-dependent manner, indicating that it is possible to use our high-throughput platform to identify compounds or target genes that can reverse these neuroinflammation-induced biomarkers associated with AD.
Constant companions: Wild zebra finch pairs display extreme spatial cohesion
Authors: Tyson Chris , Loning Hugo , Griffith Simon C. , Naguib Marc 
Published: March 2024

AbstractMany animals maintain long-term monogamous partnerships, but the extent to which partners associate varies substantially and has implications for the scope of cooperation between pair members. Zebra finches (Taeniopygia castanosis) are monogamously paired for life and maintain continuous partnerships, raising questions as to if and how they maintain pair cohesion despite being nonterritorial and having only short-range acoustic signals. While zebra finches are the best studied songbird in captivity, their social and spatial behaviour in the wild is poorly understood. Determining pair cohesion in songbirds to date has almost exclusively been studied at specific locations where pairs would be expected to meet, such as nesting or feeding sites, without quantifying broader movements. Here, we used solar-powered automated tracking to simultaneously monitor the movements of radio-tagged zebra finch pairs during periods with breeding activity. We reveal extremely high spatial cohesion with pairs using nearly identical home ranges and maintaining close spatial proximity across large areas. This characterisation of extremely high spatio-temporal coordination of zebra finch pairs provides important insights into the operation and benefits of monogamous relationships in highly mobile taxa, such as birds.
Reproductive modes in populations of late-acting self-incompatible and self-compatible polyploidLudwigia grandiflorasubsp.hexapetalain western Europe
Authors: Stoeckel Solenn , Becheler Ronan , Portillo-Lemus Luis , Harang Marilyne , Besnard Anne-Laure , Lassalle Gilles , Causse-Védrines Romain , Michon-Coudouel Sophie , Park Daniel J. , Pope Bernard J. , Petit Eric J. , Barloy Dominique 
Published: March 2024

AbstractReproductive mode,i.e.,the proportion of individuals produced by clonality, selfing and outcrossing in populations, determines how hereditary material is transmitted through generations. It shapes genetic diversity and its structure over time and space, which can be used to infer reproductive modes.Ludwigia grandiflorasubsp.hexapetala(Lgh) is a partially clonal, polyploid, hermaphroditic, and heteromorphic plant that recently colonized multiple countries worldwide. In western Europe, individuals are either self-incompatible caused by a late-acting self-incompatibility (LSI) system developing long-styled flowers, or self-compatible (SC), with short-styled flowers.In this study, we genotyped 53 long- and short-styled populations newly colonizing France and northern Spain using SNPs to estimate rates of clonality, selfing and outcrossing. We found that populations reproduced mainly clonally but with a high diversity of genotypes along with rates of sexuality ranging from 10% up to 40%. We also found evidence for local admixture between long- and short-styled populations in a background of genetic structure between floral morphs that was twice the level found within morphs. Long- and short-styled populations showed similar rates of clonality but short-styled populations presented significantly higher rates of selfing, as expected considering their breeding system, and despite the small rates of failure of the LSI system. Within the 53 studied populations, the 13 short-styled populations had fewer effective alleles, lower observed heterozygosity, and higher inbreeding coefficients, linkage disequilibrium and estimates of selfing than what was found in long-styled populations. These results emphasize the necessity to consider the variation of reproductive modes when managing invasive plant species. The overall maintenance of higher genetic diversity with the possibility of maintaining populations clonally in the absence of compatible partners may explain why long-styled individuals seem to be more prevalent in all newly expanding populations worldwide. BeyondLgh, our methodological approach may inspire future studies to assess the reproductive modes in other autopolyploid populations.