bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractGene 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

AbstractBetter 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

AbstractMeasurements 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

ABSTRACTVolitional 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 & NOTEWORTHYCardiorespiratory 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.
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

ABSTRACTAtrial 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 & NOTEWORTHYThis 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

AbstractOscillations 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

AbstractKings 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

SUMMARYRoots 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

AbstractWounding 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

AbstractSmall 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

AbstractIn 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 abstractIn 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

AbstractHigh 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.