bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

ABSTRACTHairy-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

ABSTRACTKv1.2 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

ABSTRACTThe 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.
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

AbstractSupergenes 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

SummarySpinal 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

AbstractPolycyclic 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.SynopsisWe 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

AbstractNeural 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

ABSTRACTHigh 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

SummaryHeart-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

ABSTRACTVocal 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

AbstractCytomegalovirus (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.
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

AbstractProgrammed 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

AbstractGenome-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

AbstractBacterial 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.