bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel functional gene delivery platform based on a commensal human anellovirus demonstrates transduction in multiple tissue types
Authors: Prince Cato , Bounoutas George , Zhou Bolu , Raja Waseem , Gold Isabella , Pozsgai Rianna , Thakker Parmi , Boisvert Nicole , Reardon Christopher , Thurmond Stephanie , Ozturk Erin , Boggavarapu Rajendra , Springer Simeon , Chahal Lovepreet , Nogalski Maciej , Ong Tuyen , Nawandar Dhananjay , Wright Christopher , Mackey Ashley , Parsons Geoffrey , Cabral Joseph 
Published: March 2024

ABSTRACTAnelloviridaeis a family of non-enveloped viruses with negative-sense, circular, single-stranded deoxyribonucleic acid (ssDNA) genomes that infect vertebrates and are a ubiquitous component of the human virome. Human anelloviruses evade induction of humoral immune responses and appear to be non-pathogenic. These properties, in conjunction with their enormous genomic diversity and wide tissue distribution, make anelloviruses compelling candidates as vectors for next-generation genetic medicines. Here we report the first gene delivery vector system based on a human commensal virus. This Anellovector is based on a virus of theBetatorquevirusgenus. Production is enabled by the development of the Self-Amplifying Trans-complementation of a Universal Recombinant aNellovector (SATURN) system, which relies on a self-replicating plasmid to provide viral proteins in trans that drive replication and capsid-dependent packaging of vector genomes. The SATURN system also utilizes a Cre-lox-based recombination mechanism to generate single unit-sized circular genomes inside the MOLT-4 production cell line. We demonstrate that the SATURN system can package a vector genome from a single betatorquevirus with capsids from multiple betatorquevirus species, supporting the feasibility of establishing a novel vector platform that takes advantage of the remarkable diversity of anelloviruses. The Anellovector demonstrated functionin vitroin retinal pigment epithelial (RPE) cells. The Anellovector also demonstrated durablein vivofunction in the mouse eye for 9 months after subretinal administration, and achieved comparable gene expression to dose-matched adeno-associated virus 9 (AAV9) when transduced by the intracerebroventricular (ICV) route of administration. To our knowledge, this is the first report of a functional anellovirus-based gene therapy vector. Anellovectors have great potential to deliver safe, redosable, and potent therapeutics, helping to expand the reach of programmable medicines.
Circadian control of a sex-specific behaviour in Drosophila
Authors: Riva Sabrina , Ceriani M. Fernanda , Risau-Gusman Sebastián , Franco D. Lorena 
Published: March 2024

ABSTRACTAn endogenous circadian clock controls many of the behavioral traits ofDrosophila melanogaster. This “clock” relies on the activity of interconnected clusters of neurons that harbor the clock machinery. The hierarchy among clusters involved in the control of rest-activity cycles has been extensively studied. Sexually dimorphic behaviors, on the other hand, have received less attention. Even though egg-laying, a female characteristic behavior, has been shown to be rhythmic, it remains largely unexplored possibly due to metholodological constraints. The current study provides the first steps towards determining the neural substrates underlying the circadian control of egg-laying. We show that, whereas the lateral ventral neurons (LNvs) and the dorsal neurons (DNs) are dispensable, the lateral dorsal neurons (LNds) are necessary for rhythmic egg-laying. Systematically probing theDrosophilaconnectome for contacts between circadian clusters and oviposition-related neurons, we found no evidence of direct connections between LNvs or DNs and neurons recruited during oviposition. Conversely, we did find bidirectional connections between Cryptochrome (Cry) expressing LNd (Cry+ LNds) and oviposition related neurons. Taken together, these results reveal that Cry+ LNd neurons have a leading role in the control of the egg-laying rhythm inDrosophilafemales.
CORONATINE INSENSITIVE 1-mediated repression of immunity-related genes in Arabidopsis roots is overcome upon infection withVerticillium longisporum
Authors: Ulrich Louisa , Schmitz Johanna , Thurow Corinna , Gatz Christiane 
Published: March 2024

AbstractVerticillium longisporumis a soil-borne fungal pathogen causing vascular disease predominantly inBrassicaceae. We have reported previously that the receptor of the plant defense hormone jasmonoyl-isoleucine (JA-Ile), CORONATINE INSENSITIVE 1 (COI1), is required in roots for efficient proliferation of the fungus in the shoot implicating a mobile root-borne signal that influences the outcome of the disease in shoots. To explore the underlying mechanism we compared the root transcriptome ofcoi1with the transcriptomes of three susceptible genotypes (wild-type, mutants deficient in JA-Ile and salicylic acid (SA) synthesis). At 10 days after infection, genes related to either xylem formation or plant immunity were induced independently of JA-Ile and SA. The biggest difference between the transcriptomes was due to 316 immunity-related genes that were pre-induced incoi1. Interfering with the expression of a subgroup of these genes partially suppressed thecoi1phenotype. We therefore hypothesize that mobile defense compounds secreted into the xylem and being transported with the transpiration stream confer tolerance to the shoot. We furthermore report that 149 of the COI1-repressed genes are induced in WT upon infection reaching similar levels as in mock-treatedcoi1. The majority of these were not further induced incoi1, indicating that COI1 is required for infection-induced expression.
Synchronization of Circadian Clock Gene Expression inArabidopsisandHyaloperonospora arabidopsidisand its Impact on Host-Pathogen Interactions
Authors: Telli Osman , Göl Deniz , Jin Weibo , Cevher-Keskin Birsen , Hong Yiguo , McDowell John M. , Studholme David J. , Tör Mahmut 
Published: March 2024

AbstractOrganisms across all kingdoms have an internal circadian clock running in 24h cycles. This clock affects a variety of processes, including innate immunity in plants. However, the role of pathogen circadian clocks had not been extensively explored. We previously showed that light can influence infection of the oomyceteHyaloperonospora arabidopsidis(Hpa, downy mildew disease) on its natural hostArabidopsis thaliana. Here, we identifiedHpaorthologs of known circadian clock genes (CCGs)Drosophila TIMELESS (TIM)andArabidopsis Sensitive to Red Light Reduced 1 (AtSRR1)genes. Expression of bothHpaTIMandHpaSRR1showed a circadian rhythm whenHpawas exposed to constant light. Contrastingly, these two genes were negatively regulated by constant dark exposure. Furthermore, the expression patterns ofHpaTIMandHpaSRR1correlate with those ofAtCCA1andAtLHY, indicating a synchronisation of biological clock genes between the host and the pathogen. In addition, screening mutants ofArabidopsisClock Regulated Genes (AtCRGs) with three virulentHpaisolates revealed that mutations inAtCRGsinfluencedHpaTIMandHpaSRR1expression andHpadevelopment, indicating a functional link between the plant biological clock and virulence. Moreover, sporulation ofHpawas reduced by targetingHpaTIMandHpaSRR1with short synthesized small interfering RNAs, indicating that the pathogen clock is also relevant to virulence. We propose that plant and pathogen clocks are synchronized during infection and that proper regulation of both clocks are genetically necessary for pathogen virulence.
The fMRI global signal and its association with the signal from cranial bone
Authors: Huber Daniel , Rabl Luna , Orsini Chiara , Labek Karin , Viviani Roberto 
Published: March 2024

AbstractThe nature of the global signal, i.e. the average signal from sequential functional imaging scans of the brain or the cortex, is not well understood, but is thought to include vascular and neural components. Using resting state data, we report on the strong association between the global signal and the average signal from the part of the volume that includes the cranial bone and subdural vessels and venous collectors, separated from each other and the subdural space by multispectral segmentation procedures. While subdural vessels carried a signal with a phase delay relative to the cortex, the association with the cortical signal was strongest in the parts of the scan corresponding to the laminae of the cranial bone, reaching 80% shared variance in some individuals. These findings suggest that in resting state data vascular components may play a prominent role in the genesis of fluctuations of the global signal. Evidence from other studies on the existence of neural sources of the global signal suggests that it may reflect the action of multiple mechanisms (including cerebrovascular reactivity and autonomic control) concurrently acting to regulate global cerebral perfusion.
EDSpliCE, a CRISPR-Cas9 gene editing platform to rescue splicing, effectively corrects inherited retinal dystrophy-associated splicing defects
Authors: Angeli Pietro De , Shliaga Stefanida , Flores-Tufiño Arturo , Roschi Eleonora , Spaag Salome , Stingl Katarina , Kühlewein Laura , Wissinger Bernd , Kohl Susanne 
Published: March 2024

AbstractBackgroundCorrect splicing of transcripts is essential to ensure the production of functional gene products in eukaryotic cells. Missplicing of transcripts has been identified as the underlying molecular mechanisms behind various disease-causing variants in a wide range of inherited genetic conditions. Achieving therapeutic splicing correction is possible through antisense oligonucleotide and CRISPR/Cas9 strategies. However, while antisense oligonucleotides offer effective modulation, they do not enable for permanent correction. On the other hand, current CRISPR/Cas9 approaches often rely on dual-gRNA-inducing deletion of larger pieces of DNA, containing the site(s) responsible for the splicing defect, particularly the elimination of pseudoexons, raising concerns about potential chromosomal instability.ResultsThe novel gene editing strategy, Enhanced-Deletion Splicing Correction Editing (EDSpliCE), just uses single gRNAs to effectively correct aberrant splicing caused by pseudoexon sequence inclusion into the mature mRNA. By employing Cas9 fused to a human exonuclease (TREX2), EDSpliCE achieves targeted enhanced deletions of sequences involved in pseudoexon recognition, thereby restoring correct splicing of the pre-mRNA. By addressing two isolated (ABCA4:c.5197-557G>T andUSH2A:c.7595-2144A>G) and two clustered (ABCA4:c.5196+1013A>G andABCA4:c.5196+1056A>G) pathogenic deep-intronic variants, we demonstrated effective splicing rescue in minigene assay employing distinct single gRNAs. Further validation in patient-derived fibroblasts for the commonUSH2A:c.7595-2144A>G variant confirmed consistent and high splicing correction. Additionally, the characterization of achieved gene editing affirmed the generation of enhanced deletions by EDSpliCE, revealed high directionality of editing events for all the single gRNAs tested in patient-derived fibroblasts and did not show higher off-target editing potential on selected loci.ConclusionsThe successful implementation of the EDSpliCE platform for splicing correction and modulation offers a promising and versatile gene editing approach to address splicing defects, potentially providing a safer option to existing gene editing strategies.
Transposable elements as evolutionary driving force to host shift in cactophilicDrosophilaspecies
Authors: Oliveira D. S. , Larue A. , Nunes W. V. B. , Sabot F. , Bodelón A. , García Guerreiro M. P. , Vieira C. , Carareto C. M. A. 
Published: March 2024

ABSTRACTBackgroundThe host shift in insects has been considered a key process with potential to collaborate with reproductive isolation and speciation. Both genomics and transcriptomics variation has been attributed to such process, in which gene families with functions for host location, acceptance and usage have been proposed to evolve. In this context, cactophilicDrosophilaspecies are an excellent model to study host shift evolution, since they use a wide-range of cacti as hosts, and many species have different preferences. Transposable elements are engines of genetic novelty between populations and species, driving rapid adaptive evolution. However, the extent of TEs’ contribution to host shift remains unexplored.ResultsWe performed genomic and transcriptomic analysis in seven genomes of cactophilic species/subspecies to investigate how TEs interact with genes associated with host shift. Our results revealed enrichment of TEs at promoter regions of host shift-related genes, withHelitronsrepresenting ∼60% of the cases, demonstrating an unprecedented putativecis- regulatory role ofHelitronsinDrosophila. Differential expression analysis between species with different preferred hosts demonstrated divergence on gene expression in head and larvae tissues. Although TEs’ presence does not affect overall gene expression, we observed 1.31% of genes generating gene-TE chimeric transcripts, including those with function affecting host preference.ConclusionsOur combined genomic and transcriptomic approaches provide evidence of TE-driven divergence between species, highlighting the evolutionary role of TEs in the context of host shift, a key adaptive process that can cause reproductive isolation.
multimedia: Multimodal Mediation Analysis of Microbiome Data
Authors: Jiang Hanying , Miao Xinran , Thairu Margaret W. , Beebe Mara , Grupe Dan W. , Davidson Richard J. , Handelsman Jo , Sankaran Kris 
Published: March 2024

AbstractMediation analysis has emerged as a versatile tool for answering mechanistic questions in microbiome research because it provides a statistical framework for attributing treatment effects to alternative causal pathways. Using a series of linked regressions, this analysis quantifies how complementary data relate to one another and respond to treatments. Despite these advances, existing software’s rigid assumptions often result in users viewing mediation analysis as a black box. We designed the multimedia R package to make advanced mediation analysis techniques accessible, ensuring that statistical components are interpretable and adaptable. The package provides a uniform interface to direct and indirect effect estimation, synthetic null hypothesis testing, bootstrap confidence interval construction, and sensitivity analysis, enabling experimentation with various mediator and outcome models while maintaining a simple overall workflow. The software includes modules for regularized linear, compositional, random forest, hierarchical, and hurdle modeling, making it well-suited to microbiome data. We illustrate the package through two case studies. The first re-analyzes a study of the microbiome and metabolome of Inflammatory Bowel Disease patients, uncovering potential mechanistic interactions between the microbiome and disease-associated metabolites, not found in the original study. The second analyzes new data about the influence of mindfulness practice on the microbiome. The mediation analysis highlights shifts in taxa previously associated with depression that cannot be explained indirectly by diet or sleep behaviors alone. A gallery of examples and further documentation can be found athttps://go.wisc.edu/830110.IMPORTANCEMicrobiome studies routinely gather complementary data to capture different aspects of a microbiome’s response to a change, such as the introduction of a therapeutic. Mediation analysis clarifies the extent to which responses occur sequentially via mediators, thereby supporting causal, rather than purely descriptive, interpretation. multimedia is a modular R package with close ties to the wider microbiome software ecosystem that makes statistically rigorous, flexible mediation analysis easily accessible, setting the stage for precise and causally informed microbiome engineering.
α-Synuclein Strain Propagation is Independent of Cellular Prion Protein Expression in Transgenic Mice
Authors: So Raphaella W.L. , Stuart Erica , Amini Aeen Ebrahim , Aguzzi Adriano , Collingridge Graham L. , Watts Joel C. 
Published: March 2024

AbstractThe cellular prion protein, PrPC, has been postulated to function as a receptor for α-synuclein, potentially facilitating cell-to-cell spreading and/or toxicity of α-synuclein aggregates in neurodegenerative disorders such as Parkinson’s disease. To test this hypothesis, we compared the propagation behavior of two different α-synuclein aggregate strains in M83 transgenic mice that either expressed or did not express PrPC. Following intracerebral inoculation with the S or NS strain, the presence of PrPChad minimal influence on α-synuclein strain-specified attributes such as the kinetics of disease progression, the extent of cerebral α-synuclein deposition, selective targeting of specific brain regions and cell types, the morphology of induced α-synuclein deposits, and the structural fingerprints of protease-resistant α-synuclein aggregates. Likewise, there were no appreciable differences in disease manifestation between PrPC-expressing and PrPC-lacking M83 mice following intraperitoneal inoculation of the S strain. Interestingly, intraperitoneal inoculation with the NS strain resulted in two distinct disease phenotypes, indicative of α-synuclein strain evolution, but this was also independent of PrPCexpression. Overall, these results suggest that PrPCplays at most a minor role in the propagation, neuroinvasion, and evolution of α-synuclein strains. Thus, other putative receptors or cell-to-cell propagation mechanisms may play a larger role in the spread of α-synuclein aggregates during disease.
Tissue-Specific Dynamics ofTCF4Triplet Repeat Instability Revealed by Optical Genome Mapping
Authors: Zarouchlioti Christina , Efthymiou Stephanie , Fracchini Stefano , Dominik Natalia , Bhattacharyya Nihar , Liu Siyin , Costa Marcos Abreu , Szabo Anita , Sadan Amanda N , Jun Albert S , Bugiardini Enrico , Houlden Henry , Cortese Andrea , Skalicka Pavlina , Dudakova Lubica , Muthusamy Kirithika , Cheetham Micheal E , Hardcastle Alison J , Liskova Petra , Tuft Stephen J , Davidson Alice E 
Published: March 2024

AbstractHere, we demonstrate the utility of optical genome mapping (OGM) to interrogate the Fuchs endothelial corneal dystrophy (FECD)-associated intronic TCF4 triplet repeat (termed CTG18.1) and gain novel insights into the tissue-specific nature of the disease. Genomic DNA (gDNA) samples derived from peripheral blood leukocytes and primary corneal endothelial cells (CECs) were analysed by OGM. Concurrently, all samples were genotyped by standard PCR-based methods to classify their expansion status. Individuals with one or more CTG18.1-expanded alleles (≥50 CTG repeats) detected in their leukocyte-derived gDNA were classified as expansion-positive. A customised bioinformatics pipeline was developed to perform CTG18.1-targeted OGM analysis. All linearised gDNA molecules containing labels flanking CTG18.1 were extracted, corrected for the repeats on the reference human genome and sized. Analysis of paired bio-samples revealed that expanded CTG18.1 alleles behave dynamically, regardless of cell-type origin, but displayed significantly higher levels of instability within the diseased corneal endothelium. Clusters of CTG18.1 molecules of approximately 1,800-11,900 repeats, beyond the ranges observed in individual-matched leukocyte samples, were detected in all CEC gDNA samples from expansion-positive cases. In conclusion, OGM is a powerful method to analyse the somatically unstable CTG18.1 locus. More generally, this work exemplifies the broader utility of OGM in exploring somatically unstable short tandem repeat loci. Furthermore, this study has highlighted the extreme levels of tissue-specific CTG18.1 somatic instability occurring within the diseased corneal endothelium, which we hypothesise plays a pivotal role in driving downstream pathogenic mechanisms of CTG18.1-mediated FECD.
Neurophysiology of effortful listening: Decoupling motivational modulation from task demands
Authors: Kraus Frauke , Ross Bernhard , Herrmann Björn , Obleser Jonas 
Published: March 2024

AbstractIn demanding listening situations, a listener’s motivational state may affect their cognitive investment. Here, we aim to delineate how domain-specific sensory processing, domain-general neural alpha power, and pupil size as a proxy for cognitive investment encode influences of motivational state under demanding listening. Participants performed an auditory gap-detection task while pupil size and the magnetoencephalogram (MEG) were simultaneously recorded. Task demand and a listener’s motivational state were orthogonally manipulated through changes in gap duration and monetary-reward prospect, respectively. Whereas task difficulty impaired performance, reward prospect enhanced it. Pupil size reliably indicated the modulatory impact of an individual’s motivational state. At the neural level, the motivational state did not affect auditory sensory processing directly but impacted attentional post-processing of an auditory event as reflected in the late evoked-response field and alpha power change. Both pre-gap pupil dilation and higher parietal alpha power predicted better performance at the single-trial level. The current data support a framework wherein the motivational state acts as an attentional top-down neural means of post-processing the auditory input in challenging listening situations.Significance StatementHow does an individual’s motivational state affect cognitive investment during effortful listening? In this simultaneous pupillometry and MEG study, participants performed an auditory gap-detection task while their motivational state was manipulated through varying prospect of a monetary reward. The pupil size directly mirrored this motivational modulation of the listening demand. The individual’s motivational state also enhanced top-down attentional post-processing of the auditory event but did neither change auditory sensory processing nor pre-gap parietal alpha power. These data suggest that a listener’s motivational state acts as a late attentional top-down effect on auditory neural processes in challenging listening situations.
LeGenD: determining N-glycoprofiles using an explainable AI-leveraged model with lectin profiling
Authors: Li Haining , Peralta Angelo G. , Schoffelen Sanne , Hansen Anders Holmgaard , Arnsdorf Johnny , Schinn Song-Min , Skidmore Jonathan , Choudhury Biswa , Paulchakrabarti Mousumi , Voldborg Bjorn G. , Chiang Austin W.T. , Lewis Nathan E. 
Published: March 2024

AbstractGlycosylation affects many vital functions of organisms. Therefore, its surveillance is critical from basic science to biotechnology, including biopharmaceutical development and clinical diagnostics. However, conventional glycan structure analysis faces challenges with throughput and cost. Lectins offer an alternative approach for analyzing glycans, but they only provide glycan epitopes and not full glycan structure information. To overcome these limitations, we developed LeGenD, a lectin and AI-based approach to predictN-glycan structures and determine their relative abundance in purified proteins based on lectin-binding patterns. We trained the LeGenD model using 309 glycoprofiles from 10 recombinant proteins, produced in 30 glycoengineered CHO cell lines. Our approach accurately reconstructed experimentally-measuredN-glycoprofiles of bovine Fetuin B and IgG from human sera. Explanatory AI analysis with SHapley Additive exPlanations (SHAP) helped identify the critical lectins for glycoprofile predictions. Our LeGenD approach thus presents an alternative approach forN-glycan analysis.Graphical Abstract