bluuebunny/crossref_metadata_2025 huggingface dataset:
Human P2X4 receptor gating is modulated by a stable cytoplasmic cap and a unique allosteric pocket
Authors: Shi Haoyuan , Ditter Ismayn A. , Oken Adam C. , Mansoor Steven E.
Published: July 2024

P2X receptors (P2XRs) are a family of ATP-gated ion channels comprising homomeric and heteromeric trimers of seven subunits (P2X1– P2X7) that confer different rates of desensitization. The helical recoil model of P2XR desensitization proposes the stability of the cytoplasmic cap sets the rate of desensitization, but timing of its formation is unclear for slow-desensitizing P2XRs. We report cryo-EM structures of full-length, wild-type human P2X4receptor in apo, antagonist-bound, and desensitized states. Because the apo and antagonist-bound structures of this slow-desensitizing P2XR include an intact cytoplasmic cap while the desensitized state structure does not, the cytoplasmic cap forms before agonist binding. Furthermore, structural and functional data suggests the cytoplasmic cap is stabilized by lipids to slow desensitization and that P2X4is further modified by glycosylation and palmitoylation. Finally, our antagonist-bound inhibited state structure reveals features specific to the allosteric ligand-binding pocket in human receptors that empower the development of small-molecule modulators.
A systematic review quantifying host feeding patterns ofCulicoidesspecies responsible for pathogen transmission
Authors: Fairbanks Emma L , Tildesley Michael J , Daly Janet M
Published: July 2024

Culicoidesbiting midges are significant vectors of various pathogens, impacting both human and animal health globally. Understanding their host feeding patterns is crucial for deepening our understanding of disease transmission dynamics and developing effective control strategies. While several studies have identified the sources of blood meals inCulicoides, a quantitative synthesis of their host preferences and the factors influencing these behaviours is lacking. A systematic literature search focused on gathering data on (1) host selection and (2) host preference. For reviewing host selection we focused on studies reporting the identification of blood meal sources in individualCulicoides. When reviewing host preference we focused on studies comparing the number ofCulicoidescaught on or nearby different host species at the same location. Analysis revealed that someCulicoidesspecies exhibit fixed host preferences, consistently feeding on specific hosts such as cattle and horses, while others display more opportunistic feeding behaviours. Notable variations were observed across different geographic regions. The findings indicate that host availability significantly influencesCulicoidesfeeding patterns. This study highlights the complexity of host selection inCulicoidesbiting midges, which has implications for disease transmission. The variability in feeding behaviours underscores the need for regional assessments to inform targeted vector control strategies.
Altering rRNA 2’O-methylation pattern during neuronal differentiation is regulated by FMRP
Authors: D’Souza Michelle Ninochka , Gowda Naveen Kumar Chandappa , Hariharan Nivedita , Qadri Syed Wasifa , Palakodeti Dasaradhi , Muddashetty Ravi S
Published: July 2024

The Fragile X Messenger Ribonucleoprotein (FMRP) is a selective RNA-binding protein that localizes to the cytoplasm and the nucleus. The loss of FMRP results in Fragile X Syndrome (FXS), an Autism Spectrum Disorder. FMRP interacts with ribosomes and regulates the translation of mRNAs essential for neuronal development and synaptic plasticity. However, the biochemical nature of this translation regulation is unknown. Here we report that a key feature of FMRP-mediated translation regulation during neuronal differentiation is modulating the 2’O-methylation of ribosomal RNA. 2’O-methylation, facilitated by C/D box snoRNAs in the nucleus, is a major epitranscriptome mark on rRNA, essential for ribosome assembly and function. We found that FMRP influences a distinct rRNA 2’O-Methylation pattern across neuronal differentiation. We show that in H9 ESCs, FMRP interacts with a selected set of C/D box snoRNA in the nucleus resulting in the generation of ribosomes with a distinct pattern of rRNA 2’O-Methylation. This epitranscriptome pattern on rRNA undergoes a significant change during the differentiation of ESCs to neuronal precursors and cortical neurons. ESCs display maximum hypomethylated residues on rRNA, which is eventually reduced in neuronal precursors and post-mitotic cortical neurons and this is correlated to the change in global protein synthesis among the states of differentiation. Importantly, this gradual change in the 2’O-methylation pattern during neuronal differentiation is altered in the absence of FMRP, which could impact neuronal development and contribute to dysregulated protein synthesis observed in Fragile X Syndrome. This also suggests the need for diversity in functional ribosomes during the early stages of development.
The rich evolutionary history of the ROS metabolic arsenal shapes its mechanistic plasticity at the onset of metazoan regeneration
Authors: Vullien Aurore , Amiel Aldine , Baduel Loeiza , Diken Dilara , Renaud Cécile , Vervoort Michel , Röttinger Eric , Gazave Eve
Published: July 2024

Regeneration, the ability to restore body parts after injury, is widespread in metazoans; however, the underlying molecular and cellular mechanisms involved in this process remain largely unknown, and its evolutionary history is consequently unresolved. In the last decade, ROS have emerged as shared actors that trigger apoptosis and cell proliferation to drive regenerative success in a few metazoan models. However, it is not known whether the contribution of ROS to regeneration relies on conserved mechanisms in animals.

Here we performed a comparative genomic analysis of ROS metabolism actors across metazoans, and carried out a comparative study for the deployment and roles of ROS during regeneration in two different research models: the annelid Platynereis dumerilii and the cnidarian Nematostella vectensis. We established that the vast majority of metazoans possess a core redox kit allowing for the production and detoxification of ROS, and overall regulation of ROS levels. However, the precise composition of the redox arsenal can vary drastically from species to species, suggesting that evolutionary constraints apply to ROS metabolism functions rather than precise actors. We found that ROS are produced during and are necessary for regeneration in both Platynereis and Nematostella. However, we also uncovered different enzymatic activities underlying ROS dynamics, as well as distinct effects of ROS signalling on injury-induced apoptosis and cell proliferation in the two species. We conclude that, while ROS are a robust feature of metazoan regeneration, their production and contribution to this phenomenon may depend on plastic molecular mechanisms.
Cell surface ribonucleoproteins cluster with heparan sulfate to regulate growth factor signaling
Authors: Chai Peiyuan , Perr Jonathan , Kageler Lauren , Lebedenko Charlotta G. , Dias Joao M.L. , Yankova Eliza , Esko Jeffrey D. , Tzelepis Konstantinos , Flynn Ryan A.
Published: July 2024

Receptor-ligand interactions govern a wide array of biological pathways, facilitating a cell’s ability to interrogate and integrate information from the extracellular space. Here, using an unbiased genome-wide knockout screen, we identify heparan sulfate proteoglycans (HSPGs) as a major component in the organizational mechanism of cell surface glycoRNA and cell surface RNA binding proteins (csRBPs). Cleavage of mature heparan sulfate chains, knockout ofN-and 6-O-sulfotransferases, overexpression of endo-6-O-sulfatases, or the addition of exogenous heparan sulfate chains with high 2-Osulfation result in marked loss in glycoRNA-csRBP clustering in U2OS cells. Functionally, we provide evidence that signal transduction by HS-dependent growth factors such as VEGF-A165is regulated by cell surface RNAs, and in vitro VEGF-A165, selectively interacts with glycoRNAs. Our findings uncover a new molecular mechanism of controlling signal transduction of specific growth factors across the plasma membrane by the regulated assembly of glycoRNAs, csRBPs, and heparan sulfate clusters.
Eco-Evolutionary Consequences of Selective Exploitation on Metapopulations Illustrated With Atlantic Salmon
Authors: Lamarins Amaïa , Carlson Stephanie M. , Prévost Etienne , Satterthwaite William H. , Buoro Mathieu
Published: July 2024

While the eco-evolutionary consequences of dispersal and exploitation are increasingly recognized, consideration of these effects and how they interact for management and conservation remains limited. We addressed this gap by examining population exploitation within a metapopulation framework, using Atlantic salmon as a case study. We compared eco-evolutionary consequences of alternative exploitation strategies by incorporating selective exploitation based on life history traits and spatial dimension of exploitation (i.e., whether populations were net exporter or importer of individuals). We used a demo-genetic agent-based model to examine demographic and evolutionary consequences of these strategies across a gradient of population-specific exploitation rates. At the metapopulation scale, we found both lower abundance and earlier sexual maturation with increasing exploitation, particularly when fishing was selective on larger individuals. The spatial selectivity of exploitation had an overall additional detrimental effect on metapopulation performance and fisheries yield, and induced stronger evolutionary changes than when exploitation was evenly spread over all populations. We discuss the implications of metapopulation functioning for species management and how considering dispersal patterns and intensity might change how we apply harvest. Nevertheless, our findings suggest that the safest approach remains to distribute exploitation efforts evenly across all populations, especially in the absence of variation in intrinsic productivity and with the dispersal rates and spatial configuration simulated. However, this strategy might not completely prevent negative consequences at the local scale. Therefore, we advise managers to critically assess the relevance of our results and dispersal assumptions in the specific cases they may have to deal with.
Direct RNA sequencing enables improved transcriptome assessment and tracking of RNA modifications for medical applications
Authors: Hewel Charlotte , Wierczeiko Anna , Miedema Johannes , Hofmann Felix , Weißbach Stephan , Dietrich Vincent , Friedrich Johannes , Holthöfer Laura , Haug Verena , Mündnich Stefan , Schartel Lukas , Jenson Kristi , Diederich Stefan , Sys Stanislav , Butto Tamer , Paul Norbert W , Koch Jonas , Lyko Frank , Kraft Florian , Schweiger Susann , Lemke Edward A , Helm Mark , Linke Matthias , Gerber Susanne
Published: July 2024

Direct RNA sequencing (DRS) is a nanopore-based technique for analyzing RNA in its native form, promising breakthroughs in diagnostics and biomarker development. Coupled to RNA002 sequencing chemistry, its clinical implementation has been challenging due to low throughput, low accuracy, and lack of large-scale RNA-modification models. In this study, we evaluate the improvements achieved by pairing the latest RNA004 chemistry with novel modified-base-calling models for pseudouridine andN6-methyladenosine using diverse RNA samples from cell lines, synthetic oligos, and human blood. Finally, we present the first clinical application of DRS by confirming the loss of RNA methylation in a patient carrying truncating mutations in the methyltransferaseMETTL5. Conclusively, the combined use of RNA004 chemistry with the base-calling models significantly improved the throughput, accuracy, and site-specific detection of modifications. From this perspective, we offer an outlook on the potential suitability of DRS for use in routine diagnostics and quality assessments of RNA therapeutics.
Exploring Mobile Genetic Elements in Vibrio cholerae
Authors: Drebes Dörr Natalia C. , Lemopoulos Alexandre , Blokesch Melanie
Published: July 2024

Members of the bacterial species Vibrio cholerae are known both as prominent constituents of marine environments and as the causative agents of cholera, a severe diarrheal disease. While strains responsible for cholera have been extensively studied over the past century, less is known about their environmental counterparts, despite their contributions to the species' pangenome. This study analyzed the genome compositions of 46 V. cholerae strains, encompassing both pandemic and non-pandemic, toxigenic, and environmental variants, to explore the diversity of mobile genetic elements (MGEs) and bacterial defense systems. Our findings include both conserved and novel MGEs across the strains, pointing to shared evolutionary pathways and ecological niches. The defensome analysis revealed a wide array of antiviral mechanisms, extending well beyond the traditional CRISPR-Cas and restriction-modification systems. This underscores the dynamic arms race between V. cholerae and MGEs and/or bacteriophages and suggests that non-pandemic strains may act as reservoirs for emerging defense strategies. Moreover, the study showed that MGEs are integrated into genomic hotspots, which may serve as critical platforms for the exchange of defense systems, thereby enhancing V. cholerae's adaptive capabilities against phage attacks and invading MGEs. Overall, this research offers foundational insights into V. cholerae's genetic complexity and adaptive strategies, with implications for understanding the differences between environmental strains and their pandemic relatives, and the potential evolutionary paths that led to the emergence of pandemic strains.
Nematode-Trapping Devices of Arthrobotrys oligospora is an Iron Storage Phenotype Adapted to Temperature Changes
Authors: Zhou Jiao , Wu Qunfu , Wu Li , Yan Junxian , Cheng Qianyi , Wang Donglou , Niu Xuemei
Published: July 2024

Under low-nutrient conditions, Arthrobotrys oligospora and other NTFs can differentiate their mycelia into specialized trapping devices for capturing prey as their nutritional source. Using energy-dispersive X-ray spectroscopy (EDX) in conjunction with transmission electron microscopy (TEM), we identified that the characteristic electron-dense bodies in trapping devices contained more iron than vacuoles and mitochondria. Meanwhile, fungal mycelial cells used effective desferriferrichromes for iron chelation and storage. Complex bioassays showed that electron-dense bodies represent a novel type of microbial iron storage particle and trapping devices in A. oligospora function as an unprecedented phenotypic system for iron storage. Unexpectedly, all NTFs lack a crucial Ccc1-mediated vacuolar iron detoxification mechanism, which is conserved in most fungi. Inserting the Ccc1 gene cloned from yeast into A. oligospora significantly reduced formation of trapping devices and inhibited nematicidal activity. Notably, Bayesian relaxed molecular clock analysis indicated that the loss of Ccc1-mediated vacuolar iron storage occurred during the Late Paleozoic Ice Age, while the origin of the trapping devices and the acquisition of desferriferrichrome biosynthesis were strongly associated with significantly elevated temperatures. Temperature bioassays demonstrated that the formation of trapping devices is highly temperature-dependent, with free iron content in mycelial cells being inversely proportional to temperature, consistent with that A. oligospora is sensitive to high temperatures and fails to grow above 30 degrees celsius. Our findings revealed that global temperature fluctuations are a crucial driver of the genetic evolution of NTFs, as a catalyst for the origin of trapping devices, which are a novel phenotypic indicator of eukaryotic iron overload.
The divergence of DHN-derived melanin pathways inMetarhizium robertsii
Authors: Xie Linan , Liu Yang , Zhang Yujie , Chen Kang , Yue Qun , Wang Chen , Dun Baoqing , Xu Yuquan , Zhang Liwen
Published: July 2024

The important role of dihydroxynaphthalene-(DHN) melanin in enhancing fungal stress resistance and its importance in fungal development and pathogenicity are well-established. This melanin also aids biocontrol fungi in surviving in the environment and effectively infecting insects. However, the biosynthetic origin of melanin in the biocontrol agents,Metarhiziumspp., has remained elusive due to the complexity resulting from the divergence of two DHN-like biosynthetic pathways. Through the heterologous expression of biosynthetic enzymes from these two pathways in baker’s yeastSaccharomyces cerevisiae, we have confirmed the presence of DHN biosynthesis inM. roberstii, and discovered a novel naphthopyrone intermediate that can produce a different type of pigment. These two pigment biosynthetic pathways differ in terms of polyketide intermediate structures and subsequent modification steps. Stress resistance studies using recombinant yeast cells have demonstrated that both DHN and its intermediates confer resistance against UV light prior to polymerization; a similar result was observed for its naphthopyrone counterpart. This study contributes to the understanding of the intricate and diverse biosynthetic mechanisms of fungal melanin and has the potential to enhance the application efficiency of biocontrol fungi such asMetarhiziumspp. in agriculture.
CRISPR screens reveal ZBTB17/MIZ1 as a peroxisome regulator
Authors: Liu Hongqin , Chen Xi , Wang Hanlin , Zhuang Guanglei , Zhu Zheng-Jiang , Zhuang Min
Published: July 2024

Peroxisomes are integral metabolic organelles involved in both catabolic and anabolic processes in humans, with defects often linked to diseases. The functions of peroxisomes are regulated at transcriptional, translational, and post-translational levels. In this study, we employed the CRISPR/Cas9-based genetic screening of a ubiquitin ligase library to identify regulators of human peroxisomes. We discovered that ZBTB17 (also referred as MIZ1) plays a role in regulating the import of proteins into peroxisomes. Independent of its ubiquitin ligase activity, ZBTB17/MIZ1 operates as a transcription factor to directly modulate the expression of key importer PEX13, thereby influencing the localization of peroxisomal enzymes. Furthermore, metabolomic profiling reveals that the knockdown ofZBTB17orPEX13results in similar metabolic alterations, characterized by downregulated purine synthesis, suggesting that ZBTB17’s role in metabolic regulation likely operates through peroxisomes. Collectively, we identify ZBTB17 as a key regulator of peroxisomal protein import, thereby affecting peroxisomal function and nucleotide metabolism. Our findings provide insights into the multifaceted regulation of peroxisomes in complex human cells and shed light on the molecular mechanisms underlying ZBTB17’s role as a transcriptional regulator.
ChromBERT: Uncovering Chromatin State Motifs in the Human Genome Using a BERT-based Approach
Authors: Lee Seohyun , Lin Che , Chen Chien-Yu , Nakato Ryuichiro
Published: July 2024

Chromatin states, fundamental to gene regulation and cellular identity, are defined by a unique combination of histone post-translational modifications. Despite their importance, comprehensive patterns within chromatin state sequences, which could provide insights into key biological functions, remain largely unexplored. In this study, we introduce ChromBERT, a BERT-based model specifically designed to detect distinct patterns of chromatin state annotation data sequences. Notably, ChromBERT was pre-trained on promoter regions across a diverse range of epigenomes and subsequently fine-tuned using a dataset from multiple cell lines where RNA-seq data were available, highlighting the model’s ability to discern conserved chromatin state patterns within these regions. In addition to its predictive powers across tasks, evidenced by high AUC scores, ChromBERT provides further analysis through the incorporation of motif clustering using Dynamic Time Warping (DTW). This method enhances the model’s ability to dissect chromatin state sequence motifs, typically involving transcription and enhancer sites. The introduction of motif clustering with DTW into ChromBERT’s workflow is poised to facilitate the discovery of genomic regions linked to novel biological functions, deepening our understanding of chromatin state dynamics.
New integrative vectors increaseAgrobacterium rhizogenestransformation and help characterise roles for soybeanGmTMLgene family members
Authors: Su Huanan , Zhang Mengbai , Grundy Estelle B. , Ferguson Brett J.
Published: July 2024

Hairy-root transformation is widely used to generate transgenic plant roots for genetic functional characterisation studies. However, transformation efficiency can be limited, largely due to the use of binary vectors. Here, we report on the development of novel integrative vectors that significantly increase the transformation efficiency of hairy roots. This includes pHGUS7, for promoter::reporter visualisation studies, and pHOG13, for genetic insertion and overexpression studies. These vectors have been designed to simplify cloning workflows, enhance the selection of positively transformedAgrobacteriumcolonies, and increase the transformation efficiency and ease of selection of genetically modified hairy roots. To demonstrate the efficacy of the new vectors, Too Much Love (TML) encoding genes acting in the Autoregulation Of Nodulation (AON) pathway of soybean were investigated. Both constructs provided significantly higher transformation rates than the binary vector control, often resulting in >70% of the roots being transformed. Overexpression of each individual TML encoding gene (GmTML1a,GmTML1bandGmTML2) using pHOG13 resulted in a significant reduction in nodule number, demonstrating the role of all three in inhibiting nodule organogenesis. Moreover, reporter-fusions with the promoter of each TML encoding gene using pHGUS7 revealed that each exhibits a unique pattern of expression in nodules, withGmTML1bdisplaying considerably stronger expression thanGmTML1aorGmTML2. Taken together, these results demonstrate the utility and efficiency of the new pHOG13 and pHGUS7 integrative vectors in hairy-root transformation, and improve our understanding of the criticalTML-encoding genes in soybean nodulation control.
Competitive modulation of Kv1.2 gating by LMAN2 and Slc7a5
Authors: Das Damayantee , Lamothe Shawn M. , Wong Anson , Baronas Victoria A. , Kurata Harley T.
Published: July 2024

Kv1.2 is a prominent ion channel in the CNS, where it regulates neuronal excitability. Kv1.2 structure and function are well understood, but there is less consensus on mechanisms of regulation of Kv1.2 and other potassium channels by auxiliary proteins. We identified novel regulators of Kv1.2 by a mass spectrometry approach. The neutral amino acid transporter Slc7a5 causes a dramatic hyperpolarizing shift of channel activation. In contrast, LMAN2 is a recently identified candidate regulator that has the opposite effect on gating: large depolarizing voltages are required to activate Kv1.2 channels co-expressed with LMAN2. In this study, we characterized the functional interaction between LMAN2 and Slc7a5 on Kv1.2 gating properties and identified key structural elements that underlie sensitivity to each regulator. When LMAN2 and Slc7a5 are expressed together, Kv1.2 activation exhibits a bi-modal voltage-dependence, suggesting two distinct populations of channels regulated either by LMAN2 or Slc7a5, but not both. Using a Kv1.2:1.5 chimeric approach, we identified specific regions between the S1 to S3 segments of the voltage sensing domain (VSD) that are distinct for either Slc7a5 or LMAN2 sensitivity. By replacing either segment with sequence from Kv1.5, modulation by the corresponding regulator was selectively abolished. These results suggest that Slc7a5 and LMAN2 compete for interaction with the Kv1.2 voltage sensor, leading to complex voltage-dependence of channel activity when both regulators are present in the cell.
Role of somatic HCN in epileptiform activity in subicular neurons
Authors: Alfred Monica , Sikdar Sujit K.
Published: July 2024

The subiculum, owing to its bursting nature and recurrent connections, plays a critical role in Temporal Lobe Epilepsy (TLE). Studying neuronal subtypes in the subiculum can elucidate the mechanisms underlying the patterning of epileptiform firing. We observed that epileptogenic 4AP-0Mg induced different patterns of epileptiform discharges in burst firing neurons and interneurons. Hyperpolarization-activated cyclic nucleotide-gated (HCN) channels regulate the intrinsic excitability of the neurons by governing the neuronal firing properties and membrane potential. To study the role of Ih(HCN currents) in epileptiform activity in subicular neurons, we modeled subicular HCN currents in the dynamic clamp that mimicked downregulation and overexpression observed in epilepsy-associated pathophysiology. Our results indicated that the burst firing neurons contribute to the epileptic firing characteristics due to HCN in the subiculum. We subsequently investigated the homeostatic modulation of HCN during the epileptiform activity in subicular burster cells. Our study is the first report showing Ihin rat subicular neurons during 4AP 0Mg-induced epileptogenic activity undergoes modulation on a time scale of a few minutes. Additionally, we observed that the changes in sag and chirp responses were persistent after the wash-out of 4AP-0Mg; thus, the changes appear irreversible. Our studies further showed that the neuronal excitability changes paralleled the changes in the HCN conductance during epileptogenesis. We conclude that a very rapid decline in somatic HCN function during epileptiform activity represents a previously unidentified mechanism of homeostatic dysfunction over a very short period, impeding the neuron’s ability to reestablish its regulatory processes in the subicular burster cells.
A benchmark of muscle models to length changes great and small
Authors: Millard Matthew , Stutzig Norman , Fehr Jorg , Siebert Tobias
Published: July 2024

Digital human body models are used to simulate injuries that occur as a result of vehicle collisions, vibration, sports, and falls. Given enough time the body's musculature can generate force, affect the body's movements, and change the risk of some injuries. The finite-element code LS-DYNA is often used to simulate the movements and injuries sustained by the digital human body models as a result of an accident. In this work, we evaluate the accuracy of the three muscle models in LS-DYNA (MAT_156, EHTMM, and the VEXAT) when simulating a range of experiments performed on isolated muscle: force-length-velocity experiments on maximally and sub-maximally stimulated muscle, active-lengthening experiments, and vibration experiments. The force-length-velocity experiments are included because these conditions are typical of the muscle activity that precedes an accident, while the active-lengthening and vibration experiments mimic conditions that can cause injury. The three models perform similarly during the maximally and sub-maximally activated force-length-velocity experiments, but noticeably differ in response to the active-lengthening and vibration experiments. The VEXAT model is able to generate the enhanced forces of biological muscle during active lengthening, while both the MAT_156 and EHTMM produce too little force. In response to vibration, the stiffness and damping of the VEXAT model closely follows the experimental data while the MAT_156 and EHTMM models differ substantially. The accuracy of the VEXAT model comes from two additional mechanical structures that are missing in the MAT_156 and EHTMM models: viscoelastic cross-bridges, and an active titin filament. To help others build on our work we have made our simulation code publicly available.
Incomplete recombination suppression fuels extensive haplotype diversity in a butterfly color pattern supergene
Authors: De-Kayne Rishi , Gordon Ian J. , Terblanche Reinier F. , Collins Steve , Omufwoko Kennedy Saitoti , Martins Dino J. , Martin Simon H.
Published: July 2024

Supergenes can evolve when recombination-suppressing mechanisms like inversions promote co-inheritance of alleles at two or more polymorphic loci that affect a complex trait. Theory shows that such genetic architectures can be favoured under balancing selection or local adaptation in the face of gene flow, but they can also bring costs associated with reduced opportunities for recombination. These costs may in turn be offset by rare ‘gene flux’ between inverted and ancestral haplotypes, with a range of possible outcomes. We aimed to shed light on these processes by investigating the BC supergene, a large genomic region comprising multiple rearrangements associated with three distinct wing color morphs inDanaus chrysippus, a butterfly known as the African monarch, African queen and plain tiger. Using whole-genome resequencing data from 174 individuals, we first confirm the effects of BC on wing color pattern: background melanism is associated with SNPs in the promoter region ofyellow, within an inverted subregion of the supergene, while forewing tip pattern is most likely associated with copy number variation in a separate subregion of the supergene. We then show that haplotype diversity within the supergene is surprisingly extensive: there are at least six divergent haplotype groups that experience suppressed recombination with respect to each other. Despite high divergence between these haplotype groups, we identify an unexpectedly large number of natural recombinant haplotypes. Several of the inferred crossovers occurred between adjacent inversion ‘modules’, while others occurred within inversions. Furthermore, we show that new haplotype groups have arisen through recombination between two pre-existing ones. Specifically, an allele for dark coloration in the promoter ofyellowhas recombined into distinct haplotype backgrounds on at least two separate occasions. Overall, our findings paint a picture of dynamic evolution of supergene haplotypes, fuelled by incomplete recombination suppression.
Episodic rhythmicity is generated by a distributed neural network in the developing mammalian spinal cord
Authors: Milla-Cruz Jonathan J. , Lognon Adam P. , Tran Michelle A. , Di Vito Stephanie A. , Löer Carlotta , Shonak Anchita , Broadhead Matthew J. , Miles Gareth B. , Sharples Simon A. , Whelan Patrick J.
Published: July 2024

Spinal circuits produce diverse motor outputs that coordinate the rhythm and pattern of locomotor movements. Despite the episodic nature of these behaviours, the neural mechanisms encoding these episodes are not well understood. This study investigated mechanisms producing episodic rhythms evoked by dopamine in isolated neonatal mouse spinal cords. Dopamine-induced rhythms were primarily synchronous and propagated rostro-caudally across spinal segments, with occasional asynchronous episodes. Electrical stimulation of the L5 dorsal root could entrain episodes across segments, indicating afferent control of the rhythm generator and a distributed rostro-caudal network. Episodic activity was observed in isolated thoracic or sacral segments after full spinal transection or bilateral ventrolateral funiculus (VLF) lesions, suggesting a distributed network coupled via VLF projections. Rhythmicity was recorded from axons projecting through the VLF and dorsal roots, but not from cholinergic recurrent excitation via motoneurons or isolated dorsal inhibitory circuits. The data suggest episodic rhythmicity is generated by a flexibly coupled network of spinal interneurons distributed throughout the spinal cord.
Dose-related Mutagenic and Clastogenic Effects of Benzo[b]fluoranthene in Mouse Somatic Tissues Detected by Duplex Sequencing and the Micronucleus Assay
Authors: Schuster D. M. , LeBlanc D. P. M. , Zhou G. , Meier M. J. , Dodge A. E. , White P. A. , Long A. S. , Williams A. , Hobbs C. , Diesing A. , Smith-Roe S. L. , Salk J. J. , Marchetti F. , Yauk C. L.
Published: July 2024

Polycyclic aromatic hydrocarbons (PAHs) are common environmental pollutants that originate from the incomplete combustion of organic materials. We investigated the clastogenicity and mutagenicity of benzo[b]fluoranthene (BbF), one of 16 priority PAHs, in MutaMouse males after a 28-day oral exposure. BbF causes robust dose-dependent increases in micronucleus frequency in peripheral blood, indicative of chromosome damage. Duplex Sequencing (DS), an error-corrected sequencing technology, reveals that BbF induces dose-dependent increases in mutation frequencies in bone marrow (BM) and liver. Mutagenicity is increased in intergenic relative to genic regions, suggesting a role for transcription-coupled repair of BbF-induced DNA damage. At higher doses, the maximum mutagenic response to BbF is higher in liver, which has a lower mitotic index but higher metabolic capacity than BM; however, mutagenic potency is comparable between the two tissues. BbF induces primarily C:G>A:T mutations, followed by C:G>T:A and C:G>G:C, indicating that BbF metabolites mainly target guanines and cytosines. The mutation spectrum of BbF correlates with cancer mutational signatures associated with tobacco exposure, supporting its contribution to the carcinogenicity of combustion-derived PAHs in humans. Overall, BbF’s mutagenic effects are similar to benzo[a]pyrene, a well-studied mutagenic PAH. Our work showcases the utility of DS for effective mutagenicity assessment of environmental pollutants.

Synopsis

We used Duplex Sequencing to study the mutagenicity of benzo[b]fluoranthene across the mouse genome. Dose-dependent changes in mutation frequency and spectrum quantify its role in PAH-induced carcinogenicity.
Activating Cognitive Processes in Human Cortex at Multiple Frequency Bands
Authors: Gong Zhu-Qing , Zuo Xi-Nian
Published: July 2024

Neural oscillations are fundamental for brain function, governing various cognitive processes. While electrophysiological studies have characterized the frequency properties of these oscillations, their spatial resolution is limited. In contrast, functional magnetic resonance imaging (fMRI) provides high spatial resolution but was initially restricted to a narrow frequency range. This study aims to bridge the gap by investigating the role of blood-oxygen-level-dependent (BOLD) oscillations across multiple frequency bands in cognitive processes using high temporal resolution task-fMRI data. Our findings reveal that different frequency bands are associated with distinct functional processes. Specifically, the slow-1 to slow-3 bands primarily contribute to local sensory information processing, while the slow-4 band is crucial for various fundamental cognitive functions, including somatic motor function and social cognitive function. The slow-5 band is involved in cognitive processes requiring higher memory load, integrated cognitive processing, and attention maintenance. Through multiband activation analysis, this study underscores the importance of analyzing a broad frequency range to capture the full spectrum of brain function. These findings highlight the diverse roles of different frequency bands in brain activity, shedding light on the underlying mechanisms of cognitive processes. This research enhances our understanding of the neural mechanisms underlying cognitive processes and has significant implications for cognitive neuroscience and clinical applications.
Specific pre-plasma cell states and local proliferation at the dark zone - medulla interface characterize germinal center-derived plasma cell differentiation in lymph node
Authors: Binet Laurine , Dong Chuang , Attaf Noudjoud , Gil Laurine , Fallet Matthieu , Boudier Thomas , Escalière Bertrand , Chasson Lionel , Siret Carole , Van de Pavert Serge , Navarro Jean-Marc , Milpied Pierre
Published: July 2024

High affinity antibody-producing plasma cells (PC) generated in germinal centers (GC) are crucial for durable immunity after vaccination or infection. The selection of high affinity B cells in the GC light zone instructs PC differentiation in a subset of cells, but the cellular transitions and spatial organization of GC-to-PC differentiation remain poorly understood. Here, we have used a mouse model to track GC-derived B cells with integrative single-cell and spatial analyses in draining lymph node after immunization. We first identified putative PrePC cells in scRNA-seq datasets, then enriched those cells through their specific surface phenotype for further analysis of their gene expression trajectories and BCR repertoire. We found a continuum of actively proliferating transitional states bridging selected LZ GC B cells and recently exported PCs, with gradually increasing levels of endoplasmic reticulum stress-associated genes and Ig transcripts. Spatial analyses revealed that recently differentiated PC continued their maturation and affinity-restricted proliferation at a previously uncharacterized interface between the DZ and extensions of the lymph node medulla. Our findings provide insights into the intermediate stages and microenvironmental factors involved in the differentiation of GC B cells into PC, with implications for vaccine development and understanding antibody responses.
Identification of a novel myosin antigen activating CD8+T cells in C57BL/6 mice
Authors: Richter Leon , Bauer Michelle , Bernsen Chiara , Vogel Elena , Mahmud Zabed , Saliba Antoine-Emmanuel , Schulz Richard , Frantz Stefan , Ashour DiyaaElDin , Ramos Gustavo Campos
Published: July 2024

Heart-specific T cells play important roles in myocardial diseases, including myocarditis, myocardial infarction, and heart failure. However, only few cardiac antigens and their respective specific T cell receptors (TCRs) have been validated so far. Therefore, we sought to identify new cardiac T cell epitopes in C57BL/6 mice and to characterize the specific TCRs. Antigen mapping of myosin heavy chain alpha (MYHCA) led to the identification of a 9-mer epitope (MYHCA724-732) recognized by CD8+T cells. Single-cell TCR sequencing (scTCR-seq) analysis of MYHCA-stimulated CD8+T cells enabled the identification of distinct TCRs enriched on specific T cells. Selected TCRs inferred from scTCR-seq data were then expressed on reporter cell lines and functionally validated. Our study expands the toolkit required to study heart-directed immune responses by revealing a new cardiac antigen and specific TCRs. These tools will enablein vivocharacterization of myosin-specific CD8+T cells in murine models of myocardial diseases.
Interindividual vocal tract diversity influences the phonetic diversification of spoken languages
Authors: Moran Steven , Danner Tiena , Ponce de León Marcia , Zollikofer Christoph
Published: July 2024

Vocal tracts, like other physical traits, exhibit extensive interindividual variation. However, little is known about how this variation translates into phonetic diversity between speakers, and ultimately, across languages. We demonstrate that different vocal tract shapes and associated articulatory strategies leave consistent acoustic signatures, which show congruent patterns of phonetic variation both within and across speech communities. Recalling a central tenet of evolutionary biology - that within-group variation feeds processes of between-group diversification - our findings suggest that the sounds of language evolve according to a neutral-like evolutionary process. Our “neutral-like evolution model” serves as a null hypothesis for disentangling the biological versus cultural mechanisms at play in phonetic diversification, where deviations from the neutral expectation indicate culturally mediated processes of language change at work.
Different CMV-specific effector T cell subtypes are associated with age, CMV serostatus, and increased systolic blood pressure
Authors: Roesner LM , Traidl S , Bošnjak B , Huehn J , Förster R , Werfel T
Published: July 2024

Cytomegalovirus (CMV) infection is one of the most common infections in humans, and CMV antigens are the major drivers of repetitive T-cell stimulation as a part of a well-adapted immune response in immunocompetent individuals. With higher age, the recurrent clonal expansion of CMV-specific T cells results in high frequencies of CMV-specific effector T cells. CMV seropositivity has also been linked to arterial stiffness and an increased risk of developing cardiovascular diseases (CVD). The RESIST Senior Individuals (SI) cohort is a population-based cohort with focus on the elderly, established to shed light on the age-related changes of the immune system and the accompanied reduced capability to fight infectious diseases.

Here we investigated the frequency and phenotype of CMVpp65-specific CD8+T cells in the circulation of individuals of different age groups by means of MHC-I tetramer staining and their associations with age and associated factors such as serostatus and blood pressure.

In the SI cohort, the frequency of CMV-specific T cells within the CD8+T cell fraction was increased with age, as previously reported. We add to previous knowledge by showing that this frequency is associated with the total percentage and absolute counts of CD8+and CD4+CD8+double-positive T cells within leukocytes. Systolic blood pressure (SBP) and history of CVD correlated with the frequency of CMV-specific CD8+T cells. Focusing on CMV-specific T cell subtypes, we show here that the frequencies of TEMand CD27-expressing TEMRAcells were associated with higher age. TEMand CD27-TEMRAcell frequencies were increased in donors with high CMV-IgG titers. Furthermore, SBP significantly correlated with CMV-specific effector CD8+T cells, which was mostly reflected by CD27-TEMRAcells.

In conclusion, different effector T-cell subtypes were associated with age, serostatus and SBP, suggesting that it is not ageper sethat renders elderly CMV-positive individuals susceptible to CVD, but the immune response to CMV. Our study suggests that detailed immunophenotyping may identify individuals whose immune systems are strongly influenced by the response to CMV, leading to health consequences and impairing healthy aging.
ConsensuSV-ONT - a modern method for accurate structural variant calling
Authors: Pietryga Antoni , Chilinski Mateusz , Gadakh Sachin , Plewczynski Dariusz
Published: July 2024

The improvements in sequencing technology make the development of new tools for the detection of structural variance more and more common. However, the tools available for the long-read Oxford Nanopore sequencing are limited, and it is hard to choose one, which is the best. That is why there is a need to create a tool based on consensus that combines existing work in order to discover a set of high-quality, reliable structural variants that can be used for further downstream analysis. The field has also been subject to revolution in machine learning techniques, especially deep learning. In the spirit of the aforementioned need and developments, we propose a novel, fully automated ConsensuSV-ONT algorithm. The method uses six independent, state-of-the-art structural variant callers for long-read sequencing along with a convolutional neural network for filtering high-quality variants. We provide a runtime environment in the form of a docker image, wrapping a nextflow pipeline for efficient processing using parallel computing. The solution is complete in its form and is ready to use not only by computer scientists but accessible and easy to use for everyone working with Oxford Nanopore long-read sequencing data.
PD-1 negatively regulates helper T cell differentiation into Th2
Authors: Tajima Masaki , Ikuta Naoko , Nakajima Yuka , Suzuki Kensuke , Tokumaru Yosuke , Li Peng , Kiyonari Hiroshi , Honjo Tasuku , Ohta Akio
Published: July 2024

Programmed Cell Death Protein-1 (PD-1) represents endogenous mechanisms of negative immunoregulation. While the modulation of effector functions has been the major focus of PD-1 research, quick PD-1 upregulation in naïve T cells starting 1 h after priming raised a possibility that PD-1 also affects the development of effector T cells. The role of PD-1 in functional differentiation into Th1 and Th2 has been unclear. In murine naïve CD4+T cell activation, we found that PD-1 stimulation during the early stage of T cell activation strongly impaired Th2 cell development, while Th1 cell induction was relatively resistant to this immunosuppressive signaling. The steep decline in Th2 cell induction suggested the significance of PD-1 in allergic inflammation. Treatment with anti-human PD-1 agonist antibody inhibited allergic inflammation in human PD-1-knock-in mice as shown by the reduction of Th2 cells, IgE levels and eosinophilic infiltration. This study shows that PD-1 regulates not only the intensity but also the quality of immune response by deviating Th differentiation. PD-1 stimulators are projected to be valuable in suppressing various forms of inflammatory activities, but the efficacy against Th2-dominant immune response may be particularly high.
GW: ultra-fast chromosome-scale visualisation of genomics data
Authors: Cleal Kez , Kearsey Alexander , Baird Duncan M.
Published: July 2024

Genome-Wide (GW) is an interactive genome browser that expedites analysis of aligned sequencing reads and data tracks, and introduces novel interfaces for exploring, annotating and quantifying data. GW’s high-performance design enables rapid rendering of data at speeds approaching the file reading rate, in addition to removing the memory constraints of visualizing large regions. We report substantial gains in performance and demonstrate GW’s utility in exploring massive genomic regions or chromosomes without requiring additional processing.
Avian-specificSalmonellatransition to endemicity is accompanied by localized resistome and mobilome interaction
Authors: Jia Chenghao , Huang Chenghu , Zhou Haiyang , Zhou Xiao , Wang Zining , Siddique Abubakar , Kang Xiamei , Cao Qianzhe , Huang Yingying , He Fang , Li Yan , Yue Min
Published: July 2024

Bacterial regional demonstration after global dissemination is an essential pathway for selecting distinct finesses. However, the evolution of the resistome during the transition to endemicity remains unaddressed. Using the most comprehensive whole-genome sequencing dataset ofSalmonella entericaserovar Gallinarum (S. Gallinarum) collected from 15 countries, including 45 newly recovered samples from two related local regions, we established the relationship among avian-specific pathogen genetic profiles and localization patterns. Initially, we revealed the international transmission and evolutionary history ofS. Gallinarum to recent endemicity through phylogenetic analysis conducted using a spatiotemporal Bayesian framework. Our findings indicate that the independent acquisition of the resistome via the mobilome, primarily through plasmids and transposons shapes a unique antimicrobial resistance profile among different lineages. Notably, the mobilome-resistome combination among distinct lineages exhibits a geographical-specific manner, further supporting a localized endemic mobilome-driven process. Collectively, this study elucidates resistome adaptation in the endemic transition of an avian-specific pathogen, likely driven by the localized farming style, and provides valuable insights for targeted interventions.