bluuebunny/crossref_metadata_2025 huggingface dataset:
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

The 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.
The haplotype-resolved Prymnesium parvum (type B) microalga genome reveals the genetic basis of its fish-killing toxins
Authors: Kuhl Heiner , Strassert Jürgen F.H. , Čertnerova Dora , Varga Elisabeth , Kreuz Eva , Lamatsch Dunja K. , Wuertz Sven , Köhler Jan , Monaghan Michael T. , Stöck Matthias
Published: March 2024

The catastrophic loss of aquatic life in the Central European Oder River in 2022, caused by a toxic bloom of the haptophyte microalga Prymnesium parvum (in a wide sense, s.l.), underscores the need to improve our understanding of the genomic basis of the toxin. Previous morphological, phylogenetic, and genomic studies have revealed cryptic diversity within P. parvum s.l. and uncovered three clade-specific (types A, B, C) prymnesin toxins. Here, we used state-of-the-art long-read sequencing and assembled the first haplotype-resolved diploid genome of a P. parvum type B, the strain responsible for the Oder disaster. Comparative analyses with type A genomes uncovered a genome-size expansion driven by repetitive elements in type B. We also found conserved chromosomal synteny but divergent evolution in several polyketide synthase (PKS) genes, which are known to underlie toxin production in combination with environmental cues. We identified a specific, approximately 20 kilobase pair comprising deletion in the largest PKS gene of type B that we link to differences of the chemical structure of types A and B prymnesins. Electron-microscopy and flow cytometry confirmed diploidy in the Oder River strain and differences to closely related strains in morphology and ploidy. Our results provide unprecedented resolution of strain diversity in P. parvum and a better understanding of the genomic basis of toxin variability in haptophytes. The reference-quality genome will help to understand changes to microbial diversity in the face of increasing environmental pressures, and provides a basis for strain-level monitoring of invasive Prymnesium in the future.
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

Background

Correct 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.

Results

The 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.

Conclusions

The 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

Background

The 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.

Results

We 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.

Conclusions

Our 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

Mediation 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.

IMPORTANCE

Microbiome 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

The 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

Here, 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

In 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 Statement

How 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

Glycosylation 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
Epigenomic landscape of the human dorsal root ganglion: sex differences and transcriptional regulation of nociceptive genes
Authors: Franco-Enzástiga Úrzula , Inturi Nikhil N. , Natarajan Keerthana , Mwirigi Juliet M. , Mazhar Khadija , Schlachetzki Johannes C.M. , Schumacher Mark , Price Theodore J.
Published: March 2024

Gene expression is influenced by chromatin architecture via controlled access of regulatory factors to DNA. To better understand gene regulation in the human dorsal root ganglion (hDRG) we used bulk and spatial transposase-accessible chromatin technology followed by sequencing (ATAC-seq). Using bulk ATAC-seq, we detected that in females diverse differentially accessible chromatin regions (DARs) mapped to the X chromosome and in males to autosomal genes. EGR1/3 and SP1/4 transcription factor binding motifs were abundant within DARs in females, and JUN, FOS and other AP-1 factors in males. To dissect the open chromatin profile in hDRG neurons, we used spatial ATAC-seq. The neuron cluster showed higher chromatin accessibility in GABAergic, glutamatergic, and interferon-related genes in females, and in Ca2+-signaling-related genes in males. Sex differences in transcription factor binding sites in neuron-proximal barcodes were consistent with the trends observed in bulk ATAC-seq data. We validated thatEGR1expression is biased to female hDRG compared to male. Strikingly,XIST, the long-noncoding RNA responsible for X inactivation, hybridization signal was found to be highly dispersed in the female neuronal but not non-neuronal nuclei suggesting weak X inactivation in female hDRG neurons. Our findings point to baseline epigenomic sex differences in the hDRG that likely underlie divergent transcriptional responses that determine mechanistic sex differences in pain.
CARPDM: cost-effective antibiotic resistome profiling of metagenomic samples using targeted enrichment
Authors: Hackenberger Dirk , Imtiaz Hamna , Raphenya Amogelang R. , Alcock Brian P. , Poinar Hendrik N. , Wright Gerard D. , McArthur Andrew G.
Published: March 2024

Better interrogation of antimicrobial resistance requires new approaches to detect the associated genes in metagenomic samples. Targeted enrichment is an ideal method for their sequencing and characterization. However, no open-source, up-to-date hybridization probe set targeting antimicrobial resistance genes exists. Here we describe CARPDM, a probe design software package made to run alongside all future Comprehensive Antibiotic Resistance Database releases. To test its efficacy, we have created and validated two separate probe sets: AllCARD, which enriches all genes encoded in the Comprehensive Antibiotic Resistance Database’s protein homolog models (n = 4,661), and clinicalCARD, which focuses on a clinically relevant subset of resistance genes (n = 323). We demonstrate that allCARD increases the number of reads mapping to resistance genes by up to 594-fold. ClinicalCARD performs similarly when clinically relevant genes are present, increasing the number of resistance-gene mapping reads by up to 598-fold. In parallel with this development, we have established a protocol to synthesize any probe set in-house, saving up to 350 dollars per reaction. Together, these probe sets, their associated design program CARPDM, and the protocol for in-house synthesis will democratize metagenomic resistome analyses, allowing researchers access to a cost-effective and efficient means to explore the antibiotic resistome.
Tracking of Lineage Mass via Quantitative Phase Imaging and Confinement in Low Refractive Index Microwells
Authors: Zhang Jingzhou , Griffin Justin , Roy Koushik , Hoffmann Alexander , Zangle Thomas A.
Published: March 2024

Measurements of cell lineages is central to a variety of fundamental biological questions, ranging from developmental to cancer biology. However, accurate lineage tracing requires nearly perfect cell tracking, which can be challenging due to cell motion during imaging. Here we demonstrate the integration of microfabrication, imaging, and image processing approaches to demonstrate a platform for cell lineage tracing. We use quantitative phase imaging (QPI) a label-free imaging approach that quantifies cell mass. This gives an additional parameter, cell mass, that can be used to improve tracking accuracy. We confine lineages within microwells fabricated to reduce cell adhesion to sidewalls made of a low refractive index polymer. This also allows the microwells themselves to serve as references for QPI, enabling measurement of cell mass even in confluent microwells. We demonstrate application of this approach to immortalized adherent and nonadherent cell lines as well as stimulated primary B cells culturedex vivo. Overall, our approach enables lineage tracking, or measurement of lineage mass, in a platform that can be customized to varied cell types.
Modeling cardiorespiratory coherence in exercise anticipation
Authors: Koppula Aditya , Sridharan Kousik Sarathy , Raghavan Mohan
Published: March 2024

Volitional motor activity is associated with a feedforward cardiorespiratory response to actual or impending movements. We have previously shown in the CRC study that the expectation of physical exercise causes a decrease in cardiorespiratory coherence that scales with the anticipated load. The present work uses a modeling approach to investigate the mechanisms that can cause a fall in cardiorespiratory coherence (CRC). We devised a Hodgkin-Huxley model of a cardiac pacemaker cell using the NEURON module. We simulated the effect of autonomic tone, sympathetic & respiratory-vagal modulation, and respiratory irregularity on pacemaker cell output by injecting efflux/influx current to model the parasympathetic/sympathetic effects, respectively. The vago-sympathetic tone was modeled by altering the direct current bias of the injected current and the respiratory-vagal effect by the periodic modulation of the injected current at a frequency of 0.2 Hz, corresponding to a respiratory rate of 12 breaths/min. Sympathetic modulation was simulated by injecting a low-frequency current close to Mayer wave frequency (0.08 Hz). We computed the coherence between the instantaneous pacemaker rate and respiratory-vagal modulation current as a model analog to experimental CRC. We found that sympathetic modulation, low vagal tone/high sympathetic tone, and respiratory irregularity can cause a decrease in CRC. We corroborated the model results with the actual data from the CRC study. In conclusion, we employ a novel approach combining insights from the experimental study and a physiologically plausible modeling framework to understand the mechanisms underlying the fall of cardiorespiratory coherence induced by the expectation of exercise.

NEW & NOTEWORTHY

Cardiorespiratory coherence is diminished in response to respiratory irregularity, low vagal/high sympathetic tone, and prominent low-frequency sympathetic modulation.

Expectation of physical activity induces respiratory irregularity and increased sigh frequency and that contributes to diminished cardiorespiratory coherence in expectation of exercise.

There is a greater fall of coherence with the non-linear (logistic) transformation of injected current, indicating the non-linear nature of cardiorespiratory interactions preceding the onset of exercise.
Mesolimbic dopamine ramps reflect environmental timescales
Authors: Floeder Joseph R , Jeong Huijeong , Mohebi Ali , Namboodiri Vijay Mohan K
Published: March 2024

Mesolimbic dopamine activity occasionally exhibits ramping dynamics, reigniting debate on theories of dopamine signaling. This debate is ongoing partly because the experimental conditions under which dopamine ramps emerge remain poorly understood. Here, we show that during Pavlovian and instrumental conditioning, mesolimbic dopamine ramps are only observed when the inter-trial interval is short relative to the trial period. These results constrain theories of dopamine signaling and identify a critical variable determining the emergence of dopamine ramps.
Activation of IP3R in atrial cardiomyocytes leads to generation of cytosolic cAMP
Authors: Akerman Emily C , Read Matthew J. , Bose Samuel J. , Koschinski Andreas , Capel Rebecca A. , Chao Ying-Chi , Folkmanaite Milda , Hester Svenja , Fischer Roman , Ayagama Thamali , Broadbent Steven D. , Ahamed Rufaida , Simon Jillian N. , Terrar Derek A. , Zaccolo Manuela , Burton Rebecca A. B.
Published: March 2024

Atrial fibrillation (AF) is the most common sustained cardiac arrhythmia. Excessive stimulation of the IP3 signaling pathway has been linked to AF through abnormal calcium handling. However, little is known about the mechanisms involved in this process. We expressed Fluorescence resonance energy transfer (FRET) based cytosolic cAMP sensor EPAC-SH187in neonatal rat atrial myocytes (NRAMs) and neonatal rat ventricular myocytes (NRVMs). In NRAMs, addition of the alpha (α)-1 agonist phenylephrine (PE, 3µM) resulted in a bi-phasic FRET change (R1) 21.20 ± 7.43% and (R2) 9.67 ± 4.23% and addition of membrane permeant IP3 derivative, 2,3,6-tri-O-Butyryl-myo-IP3(1,4,5)-hexakis(acetoxymethyl)ester (IP3-AM, 20μM) resulted in a peak of 20.31 ± 6.74%. These FRET changes imply an increase in cAMP. Prior application of IP3 receptor (IP3R) inhibitors 2-Aminoethyl diphenylborinate (2-APB, 2.5μM) or Xestospongin-C (0.3μM) significantly inhibited the change in FRET in NRAMs in response to PE. Xestospongin-C (0.3μM) significantly inhibited the change in FRET in NRAMs in response to IP3-AM. The FRET change in response to PE in NRVMs were not inhibited by 2-APB or Xestospongin-C. Finally, the localisation of cAMP signals was tested by expressing the FRET-based cAMP sensor, AKAP79-CUTie, which targets the intracellular surface of the plasmalemma. We found in NRAMs that PE led to FRET change corresponding to an increase in cAMP that was inhibited by 2-APB and Xestospongin C. This data support further investigation of the pro-arrhythmic nature and components of IP3 induced cAMP signalling to identify potential pharmacological targets.

NEW & NOTEWORTHY

This study shows that indirect activation of the IP3 pathway in atrial myocytes using phenylephrine and direct activation using IP3-AM leads to an increase in cAMP and is in-part localized to the cell membrane. These changes can be pharmacologically inhibited using IP3R inhibitors. However, the cAMP rise in ventricular myocytes is independent of IP3R calcium release. Our data support further investigation into the pro-arrhythmic nature of IP3-induced cAMP signaling.
From resonance to chaos: modulating spatiotemporal patterns through a synthetic optogenetic oscillator
Authors: Park Jung Hun , Holló Gábor , Schaerli Yolanda
Published: March 2024

Oscillations are a recurrent phenomenon in biological systems across scales, including circadian clocks, metabolic oscillations and embryonic genetic oscillators. Despite their fundamental significance in biology, deciphering core principles of biological oscillators is very challenging due to the multiscale complexity of genetic networks and the difficulty in perturbing organismsin vivo. In this study, we tackle this challenge by re-designing the well-characterised synthetic oscillator, known as “repressilator”, inEscherichia coliand controlling it using optogenetics, thus introducing the “optoscillator”. When we apply periodic light pulses, the optoscillator behaves as a forced oscillator. Bacterial colonies harboring synthetic oscillators manifest oscillations as spatial ring patterns. Leveraging this feature, we systematically investigate the number, intensity and sharpness of the rings under different regimes of light exposure. By integrating experimental approaches with mathematical modeling, we show that this simple oscillatory circuit can generate complex dynamics that, depending on the external periodic forcing, are transformed into distinct spatial patterns. We report the observation of synchronisation, resonance, undertone and period doubling. Furthermore, we present evidence supporting the existence of a chaotic regime. This work highlights the intricate spatiotemporal patterns accessible by synthetic oscillators and underscores the potential of our approach in understanding the underlying principles governing biological oscillations.
Extended longevity of termite kings and queens is accompanied by extranuclear localization of telomerase in somatic organs and caste-specific expression of its isoforms
Authors: Pangrácová Marie , Křivánek Jan , Vrchotová Markéta , Sehadová Hana , Hadravová Romana , Hanus Robert , Lukšan Ondřej
Published: March 2024

Kings and queens of termites are endowed with an extraordinary longevity coupled with lifelong fecundity. We recently reported that termite kings and queens display a dramatically increased enzymatic activity and abundance of telomerase in their somatic organs when compared to short-lived workers and soldiers. We hypothesized that this telomerase activation may represent a non-canonical pro-longevity function, independent of its canonical role in telomere maintenance.

Here, we explore this avenue and investigate whether the presumed non-canonical role of telomerase may be due to alternative splicing of the catalytic telomerase subunit TERT and whether the subcellular localization of TERT isoforms differs among organs and castes in the termiteProrhinotermes simplex. We empirically confirm the expression of four in silico predicted splice variants (psTERT1-A,psTERT1-B,psTERT2-A,psTERT2-B), defined by N-terminal splicing implicating differential localizations, and C-terminal splicing giving rise to full-length and truncated isoforms. We show that the transcript proportions of thepsTERTare caste- and tissue-specific and that the extranuclear full-length isoformTERT1-Ais relatively enriched in the soma of neotenic kings and queens compared to their gonads and to the soma of workers. We also show that extranuclear TERT protein quantities are significantly higher in the soma of kings and queens compared to workers, namely due to the cytosolic TERT. Independently, we confirm by microscopy the extranuclear TERT localization in somatic organs. We conclude that the presumed pleiotropic action of telomerase combining the canonical nuclear role in telomere maintenance with extranuclear functions is driven by complex TERT splicing.
ThePIN2ortholog in barley modifies root gravitropism and architecture without impacting the shoot
Authors: Aldiss Zachary , Robinson Hannah , Lam Yasmine , Dixon Richard , Crisp Peter , Godwin Ian , Borrell Andrew , Hickey Lee , Massel Karen
Published: March 2024

Roots provide the critical interface where plants acquire nutrients and water, but our limited understanding of the genetic controls modulating root system architecture (RSA) in crop species constrains opportunities to develop future cultivars with improved root systems. However, there is vast knowledge of root developmental genes in model plant species, which has the potential to accelerate progress in crops with more complex genomes, particularly given that genome editing protocols are now available for most species.PIN-FORMED2(PIN2) encodes a root specific polar auxin transporter, where its absence resulted in roots being unable to orient themselves using gravity, producing a significantly wider root system. To explore the role ofPIN2in a cereal crop, we used CRISPR/Cas9 editing to knockout ofPIN2in barley (Hordeum vulgare). Like Arabidopsis, the roots of barleypin2loss-of-function mutants displayed an agravitropic response at seedling growth stages, resulting in a significantly shallower and wider root system at later growth stages. Notably, despite the significant change in RSA, there was no change in shoot architecture or total shoot biomass. We discuss the future challenges and opportunities to harness thePIN2pathway to optimise RSA in crops for a range of production scenarios without a shoot trade-off.
Wounding perception by jasmonate-mediated JAZ condensation in plants
Authors: Yan Zi-Wei , Liu Jie , Chen Hui-Cheng , Wang Mu-Yang , Cai Wen-Juan , Li Jian-Xu , Wang Jia-Wei , Mao Ying-Bo
Published: March 2024

Wounding is a common stress experienced by plants, resulting in a quick elicitation of jasmonates (JAs). The widely accepted mechanism of COI1-JAZ coreceptor posits that COI1 directly interacts with the active ligand of JAs, whereas JAZs facilitate to trap the ligand in the binding pocket. Here we show that the multiple JAZs ofArabidopsisundergo phase separation in response to wounding. Taking JAZ1 as an example, we found it is an independent sensor of JA-Ile, the active ligand in most plants. Under basal condition, dispersed JAZ1 interacts with MYC2 to inhibit downstream gene expressions. Upon wounding, JAZ1 binds to JA-Ile and forms condensates, reducing its affinity with MYC2 and tending to recruit COI1 as well as other proteasome related components for quick degradation, thereby accelerating signaling output. Our investigation unveils the underlying mechanism by which JAZ1 regulates swift signaling transduction via phase separation upon the direct perception of JA-Ile.
Oscillatory dynamics of Rac1 activity inDictyostelium discoideumamoebae
Authors: Šoštar Marko , Marinović Maja , Filić Vedrana , Pavin Nenad , Weber Igor
Published: March 2024

Small GTPases of the Rho family play a central role in the regulation of cell motility by controlling the remodeling of the actin cytoskeleton. In the amoeboid cells ofDictyostelium discoideum, the active form of the Rho GTPase Rac1 regulates actin polymerases at the leading edge and actin filament bundling proteins at the posterior cortex of polarized cells. However, constitutive Rac1 dynamics inD. discoideumhave not yet been systematically investigated. Therefore, we monitored the spatiotemporal dynamics of Rac1 activity in vegetative amoebae using a specific fluorescent probe. We observed that plasma membrane domains enriched in active Rac1 not only exhibited stable polarization, but also showed rotations and oscillations. To simulate the observed dynamics, we developed a mass-conserving reaction-diffusion model based on the circulation of Rac1 between the membrane and the cytoplasm in conjunction with its activation by GEFs, deactivation by GAPs and interaction with the Rac1 effector DGAP1. Our theoretical model accurately reproduced the experimentally observed dynamic patterns, including the predominant anti-correlation between active Rac1 and DGAP1. Significantly, the model predicted a new colocalization regime of these two proteins in polarized cells, which we confirmed experimentally. In summary, our results improve the understanding of Rac1 dynamics and reveal how the occurrence and transitions between different regimes depend on biochemical reaction rates, protein levels and cell size. This study not only expands our knowledge of the behavior of small GTPases inD. discoideumamoebae, but also provides a simple modeling framework that can be adapted to study similar dynamics in other cell types.
Amulti-tracklandscape of haematopoiesis informed by cellular barcoding and agent-based modelling
Authors: Lin Dawn S. , Zhang Stephen , Schreuder Jaring , Tran Jessica , Sargeant Toby , Metcalf Don , Ng Ashley P. , Weber Tom S. , Naik Shalin H.
Published: March 2024

In classic ‘ball-and-stick’ models of haematopoiesis the implicit assumption is that all cells within each defined stem or progenitor cell population are equivalent in their fate. Instead, more recent models suggest a haematopoietic stem and progenitor cell (HSPC) ‘continuum’ of lineage bias and commitment, which is largely inferred through ‘snapshot’ analysis of single cell gene expression or clonal fate. However, the dynamic assessment of lineage commitment of specific HSPC populations and their clonal output over timein vivois still lacking but is essential to fully inform accurate models of haematopoiesis. Here, using cellular barcoding we compare the single cell output of long-term haematopoietic stem cells (LT-HSCs), short-term HSCs (ST-HSCs), multipotent progenitors (LMPPs), common myeloid progenitors (CMPs), common lymphoid progenitors (CLPs), and macrophage/dendritic cell progenitors (MDPs). Each population was assessed for their output to multiple haematopoietic cell types spanning a subset of time points from 9 to 112 days of haematopoiesis after transplantation. These analyses revealed a wide range of clonal fate patterns that were inconsistent with their eponymous labels, i.e. stem and multipotent progenitors were rarely multi- or equipotent, and ‘common’ progenitors were often highly restricted in their fate. To better describe how these clonal patterns integrate into a revised landscape, a novel agent-based mathematical modelling approach that explicitly accounts for haematopoiesis at a clonal level was developed to allow the simulation of growth, timing and branching of clonal trajectories that underlie the process. Rather than a continuum, the proposed model is suggestive of multiple tracks down which clonal trajectories progress, and where fate can branch to a track of lower potency at multiple points down the entire cascade of haematopoiesis.

Graphical abstract

In a multi-track model, while some HSPCs are multipotent and branch into daughters with committed fate (left trajectory), other HSPCs may already committed or biased to a certain lineage such that their daughters inherit and maintain it in subsequent divisions during haematopoiesis. However, this commitment/fate bias is not evident through current phenotypic definitions of HSPC subsets (background colour) but occurs through putative expression of transcription factors, epigenetic programming or other factor that is currently unresolved (as indicated by the coloured fate potential triangles inside cells).
Utilising citizen science data to rapidly assess potential wild bridging hosts and reservoirs of infection: avian influenza outbreaks in Great Britain
Authors: Vickers Stephen H. , Raghwani Jayna , Banyard Ashley C , Brown Ian H , Fournie Guillaume , Hill Sarah C.
Published: March 2024

High pathogenicity avian influenza virus (HPAIV) is a rapidly evolving orthomyxovirus causing significant economic and environmental harm. Wild birds are a key reservoir of infection and an important source of viral incursions into poultry populations. However, we lack thorough understanding of which wild species drive incursions and whether this changes over time. We explored associations between abundances of 152 avian species and cases of HPAI in poultry premises across Great Britain between October-2021 and January-2023. Spatial generalised additive models were used, with species abundance distributions sourced from eBird modelled predictions. Associations were investigated at the species-specific level and across aggregations of species. During autumn/winter, associations were generally strongest with waterbirds such as ducks and geese; however, we also found significant associations in other groups such as non-native gamebirds, and rapid change in species-specific associations over time. Our results demonstrate the value of citizen science in rapid exploration of wild reservoirs of infection as facilitators of disease incursion into domestic hosts, especially in regions where surveillance programmes in wild birds are absent. This can be a critical step towards improving species-specific biosecurity measures and targeted surveillance; particularly for HPAIV, which has undergone sudden shifts in host-range and continues to rapidly evolve.
Multi-Omics Analysis Reveals the Attenuation of the Interferon Pathway as a Driver of Chemo-Refractory Ovarian Cancer
Authors: Afenteva Daria , Yu Rong , Rajavuori Anna , Salvadores Marina , Launonen Inga-Maria , Lavikka Kari , Zhang Kaiyang , Marchi Giovanni , Jamalzadeh Sanaz , Isoviita Veli-Matti , Li Yilin , Micoli Giulia , Erkan Erdogan Pekcan , Falco Matias M. , Ungureanu Daniela , Lahtinen Alexandra , Oikkonen Jaana , Hietanen Sakari , Vähärautio Anna , Sur Inderpreet , Virtanen Anni , Färkkilä Anniina , Hynninen Johanna , Muranen Taru A. , Taipale Jussi , Hautaniemi Sampsa
Published: March 2024

Ovarian high-grade serous carcinoma (HGSC) represents the deadliest gynecological malignancy, with 10-15% of patients exhibiting primary resistance to first-line chemotherapy. These primarily chemo-refractory patients have particularly poor survival outcomes, emphasizing the urgent need for developing predictive biomarkers and novel therapeutic approaches. Here, we show that interferon type I (IFN-I) pathway activity in cancer cells is a crucial determinant of chemotherapy response in HGSC. Through a comprehensive multi-omics analysis within the DECIDER observational trial (ClinicalTrials.govidentifierNCT04846933) cohort, we identified that chemo-refractory HGSC is characterized by diminished IFN-I and enhanced hypoxia pathway activities. Importantly, IFN-I pathway activity was independently prognostic for patient survival, highlighting its potential as a biomarker. Our results elucidate the heterogeneity of treatment response at the molecular level and suggest that augmentation of IFN-I response could enhance chemosensitivity in refractory cases. This study underscores the potential of the IFN-I pathway as a therapeutic target and advocates for the initiation of clinical trials testing external modulators of the IFN-I response, promising a significant stride forward in the treatment of refractory HGSC.
Transcriptomic Changes in Oligodendrocyte Lineage Cells During the Juvenile to Adult Transition in the Mouse Corpus Callosum
Authors: Hoshino Tomonori , Takase Hajime , Hamanaka Gen , Kimura Shintaro , Fukuda Norito , Mandeville Emiri T , Lok Josephine , Lo Eng H , Arai Ken
Published: March 2024

The corpus callosum, a major white matter tract in the brain, undergoes age-related functional changes. To extend our investigation of age-related gene expression dynamics in the mouse corpus callosum, we compared RNA-seq data from 2-week-old and 12-week-old wild-type C57BL/6J mice and identified the differentially expressed genes (e.g.,Serpinb1a, Ndrg1, Dnmt3a, etc.) between these ages. Interestingly, we found that genes highly expressed in myelinating oligodendrocytes were upregulated in 12-week-old mice compared to 2-week-old mice, while genes highly expressed in oligodendrocyte precursor cells (OPCs) and newly formed oligodendrocytes were downregulated. Furthermore, by comparing these genes with the datasets from 20-week-old and 96-week-old mice, we identified novel sets of genes with age-dependent variations in the corpus callosum. These gene expression changes potentially affect key biological pathways and may be closely linked to age-related neurological disorders, including dementia and stroke. Therefore, our results provide an additional dataset to explore age-dependent gene expression dynamics of oligodendrocyte lineage cells in the corpus callosum.
Elucidating the link between binding statistics and Shannon information in biological cooperative networks
Authors: Banerjee Kinshuk , Das Biswajit
Published: March 2024

Cooperative response is ubiquitous and vital for regulatory control and ultra-sensitivity in various cellular biophysical processes. Ligands, acting as signaling molecules, carry information which is transmitted through the elements of the biochemical network during binding processes. In this work, we address a fundamental issue regarding the link between the information content of the various states of the binding network and the observable binding statistics. Two seminal models of cooperativity,viz., the Koshland-Nemethy-Filmer (KNF) network and the Monod-Wyman-Changeux (MWC) network are considered for this purpsoe which are solved using the chemical master equation approach. Our results establish that the variation of Shannon information associated with the network states has a generic form related to the average binding number. Further, the logarithmic sensitivity of the slope of Shannon information is shown to be related to the Hill slope in terms of the variance of the binding number distributions.

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Remodeling Ca2+dynamics by targeting a promising E-box containing G-quadruplex atORAI1promoter in triple-negative breast cancer
Authors: Chatterjee Oishika , Jana Jagannath , Panda Suman , Dutta Anindya , Sharma Akshay , Saurav Suman , Motiani Rajender K. , Weisz Klaus , Chatterjee Subhrangsu
Published: March 2024

ORAI1 is an intrinsic component of store-operated calcium entry (SOCE) that strictly regulates Ca2+influx in most non-excitable cells. ORAI1 has been extensively studied to have been overexpressed in various cancer phenotypes, and its signal transduction has been associated with oncotherapy resistance. There is extensive proteomic interaction of ORAI1 with other channels and effectors, resulting in various altered phenotypes. However, the transcription regulation of this gene is not well understood. We have found a putative G-quadruplex (G4) motif,ORAI1-Pu, in the upstream promoter region of the gene, having regulatory functions. High-resolution 3-D NMR structure elucidation suggests thatORAI1-Puis a stable parallel-stranded G4, having an unusual 8-nt loop imparting dynamics without affecting the structural stability. The protruded loop further houses an E-box motif that provides a docking site for transcription factors like Zeb1. The G4 structure was also endogenously observed using Chromatin Immunoprecipitation (ChIP) with anti-G4 antibody (BG4) in the MDA-MB-231 cell line overexpressingORAI1. Ligand-mediated stabilization suggested that the stabilized G4 represses transcription in cancer cell line MDA-MB-231. Downregulation of transcription further cascaded down to a decrease in Ca2+entry by the SOCE pathway, as observed by Fura-2 confocal Ca2+imaging.