Long-distance Interactions Research Articles

Dynamic O-GlcNAcylation governs long-range chromatin interactions in V(D)J recombination during early B-cell development.

V(D)J recombination secures the production of functional immunoglobulin (Ig) genes and antibody diversity during the early stages of B-cell development through long-distance interactions mediated by cis-regulatory elements and trans-acting factors. O-GlcNAcylation is a dynamic and reversible posttranslational modification of nuclear and cytoplasmic proteins that regulates various protein functions, including DNA-binding affinity and protein-protein interactions. However, the effects of O-GlcNAcylation on proteins involved in V(D)J recombination remain largely unknown. To elucidate this relationship, we downregulated O-GlcNAcylation in a mouse model by administering an O-GlcNAc inhibitor or restricting the consumption of a regular diet. Interestingly, the inhibition of O-GlcNAcylation in mice severely impaired Ig heavy-chain (IgH) gene rearrangement. We identified several factors crucial for V(D)J recombination, including YY1, CTCF, SMC1, and SMC3, as direct targets of O-GlcNAc modification. Importantly, O-GlcNAcylation regulates the physical interaction between SMC1 and SMC3 and the DNA-binding patterns of YY1 at the IgH gene locus. Moreover, O-GlcNAc inhibition downregulated DDX5 protein expression, affecting the functional association of CTCF with its DNA-binding sites at the IgH locus. Our results showed that locus contraction and long-range interactions throughout the IgH locus are disrupted in a manner dependent on the cellular O-GlcNAc level. In this study, we established that V(D)J recombination relies on the O-GlcNAc status of stage-specific proteins during early B-cell development and identified O-GlcNAc-dependent mechanisms as new regulatory components for the development of a diverse antibody repertoire.

Level splitting induced by collective interaction in a waveguide QED system

In waveguide quantum electrodynamics (QED) systems, noninteracting quantum entities can be coupled through the vacuum field of the waveguide, leading to both coherent and dissipative interactions. We systematically demonstrate that the reflection spectrum is clear and direct in representing the collective interaction using the mirror reflection properties of semi-infinite waveguides. Due to the destructive interference with its mirror image, the emitter is decoupled from the waveguide, suppressing the decay so that the reflection spectrum shows an anticrossing phenomenon induced by coherent interaction. Moreover, the reflection spectrum of an anti-parity-time symmetric Hamiltonian caused by dissipative coupling exhibits an unconventional splitting characterized by level attraction transitioning at exceptional points. Our findings highlight the significance of exploring non-Hermitian effects in waveguide quantum systems, offering potential applications in quantum networks reliant on long-distance interactions. Published by the American Physical Society 2024

Role of the short-distance interaction in e+e−→γX(3872)

In this study, we analyze the cross-section data from the e+e−→γJ/ψω process to explore both short-distance and long-distance interactions for the radiative transition Y(4200)→γX(3872). We investigate the short-distance effects through the E1 transition among the cc¯ components, and the long-distance effects via hadronic loop diagrams. Our numerical analysis reveals that short-distance interactions play a significantly larger role in the radiative transition than that of the long-distance interactions. This finding underscores the importance of the compact cc¯ components in both the initial and the final states for accurately understanding the cross-section σ[e+e−→γJ/ψω]. Furthermore, with the help of relative branch ratio R we estimate the Γ[Y(4200)→γX(3872)] implied in the experimental study. Finally, we also discuss the possible existence of the ψ(4040) signal within the cross-section data. Published by the American Physical Society 2024

Study of the interference fringes-caustic region interaction in a topological Young's interferometer.

Herein, an analysis of the optical field emerging from a topological Young's interferometer is conducted. The interferometer consists of two 3D-slit shape curves and is studied by projecting it onto a trihedral reference system. From the projection, Airy, Pearcey, and cusped-type beams emerge. The optical field of these beams is organized around its caustic region. The interference between these types of beams presents interesting physical properties, which can be derived from the interaction between the interference fringes and the caustic regions. One property of the interaction is the irradiance flow, which induces a long-distance interaction between the caustic regions. Another property is the bending of the interference fringes toward the caustic regions, which acts as a sink. Due to the adiabatic features of the caustic regions, the interaction between the fringes-caustic and caustic irradiance is studied using a predator-prey model, which leads to a logistic-type differential equation with nonlinear harvesting. The stability analysis of this equation is in good agreement with the theoretical and experimental results.

Appearance-posture fusion network for distracted driving behavior recognition

In recent years, detection techniques using computer vision and deep learning have shown promise in assessing driver distraction. This paper proposes a fusion network that combines a Spatial-Temporal Graph Convolutional Network (ST-GCN) and a hybrid convolutional network to integrate multimodal input data for recognizing distracted driver behavior. Specifically, to address the limitations of the ST-GCN method in modeling long-distance joint interaction features and inadequate temporal feature extraction, we design the Spatially Symmetric Configuration Partitioning Graph Convolutional Network (SSCP-GCN) to model relative motion information of symmetric relationships between limbs. Specifically, we utilize densely connected blocks for processing multi-scale temporal information between consecutive frames, thereby enhancing the reuse of bottom features. Furthermore, the expression of important temporal information is augmented by the introduction of the channel attention mechanism. To tackle the problem that the Mixed Convolution (MC) combining 3D convolution with 2D convolution cannot extract higher-order timing information and has limitations in modeling global dependency relationships, we compensate for its inability to capture higher-order temporal semantic information using the Time Shift Module (TSM) without consuming additional computational resources. Additionally, the 3D Multi-Head Self-Attention mechanism (3D MHSA) is employed to integrate global spatial–temporal information of high-level features, avoiding the issue of model complexity proliferation caused by the deep stacking design of Convolutional Neural Networks (CNN). Lastly, we introduce a multistream network framework that integrates driver posture and appearance features to harness complementary advantages, enabling us to combine multimodal input features to achieve better model performance. Experimental results indicate that the accuracy of the network designed in this paper reaches 95.6% and 94.3% on ASU dataset and NTU-RGB+D dataset, respectively. The small size of the model offers the possibility for practical application of the algorithm.

Potential Transcriptional Enhancers in Coronaviruses: From Infectious Bronchitis Virus to SARS-CoV-2.

Coronaviruses constitute a global threat to human and animal health. It is essential to investigate the long-distance RNA-RNA interactions that approximate remote regulatory elements in strategies, including genome circularization, discontinuous transcription, and transcriptional enhancers, aimed at the rapid replication of their large genomes, pathogenicity, and immune evasion. Based on the primary sequences and modeled RNA-RNA interactions of two experimentally defined coronaviral enhancers, we detected via an in silico primary and secondary structural analysis potential enhancers in various coronaviruses, from the phylogenetically ancient avian infectious bronchitis virus (IBV) to the recently emerged SARS-CoV-2. These potential enhancers possess a core duplex-forming region that could transition between closed and open states, as molecular switches directed by viral or host factors. The duplex open state would pair with remote sequences in the viral genome and modulate the expression of downstream crucial genes involved in viral replication and host immune evasion. Consistently, variations in the predicted IBV enhancer region or its distant targets coincide with cases of viral attenuation, possibly driven by decreased open reading frame (ORF)3a immune evasion protein expression. If validated experimentally, the annotated enhancer sequences could inform structural prediction tools and antiviral interventions.

Local and Global Context-Enhanced Lightweight CenterNet for PCB Surface Defect Detection.

Printed circuit board (PCB) surface defect detection is an essential part of the PCB manufacturing process. Currently, advanced CCD or CMOS sensors can capture high-resolution PCB images. However, the existing computer vision approaches for PCB surface defect detection require high computing effort, leading to insufficient efficiency. To this end, this article proposes a local and global context-enhanced lightweight CenterNet (LGCL-CenterNet) to detect PCB surface defects in real time. Specifically, we propose a two-branch lightweight vision transformer module with local and global attention, named LGT, as a complement to extract high-dimension features and leverage context-aware local enhancement after the backbone network. In the local branch, we utilize coordinate attention to aggregate more powerful features of PCB defects with different shapes. In the global branch, Bi-Level Routing Attention with pooling is used to capture long-distance pixel interactions with limited computational cost. Furthermore, a Path Aggregation Network (PANet) feature fusion structure is incorporated to mitigate the loss of shallow features caused by the increase in model depth. Then, we design a lightweight prediction head by using depthwise separable convolutions, which further compresses the computational complexity and parameters while maintaining the detection capability of the model. In the experiment, the LGCL-CenterNet increased the mAP@0.5 by 2% and 1.4%, respectively, in comparison to CenterNet-ResNet18 and YOLOv8s. Meanwhile, our approach requires fewer model parameters (0.542M) than existing techniques. The results show that the proposed method improves both detection accuracy and inference speed and indicate that the LGCL-CenterNet has better real-time performance and robustness.

Self-Regulation of the Posterior-Frontal Brain Activity with Real-Time fMRI Neurofeedback to Influence Perceptual Discrimination.

The Global Neuronal Workspace (GNW) hypothesis states that the visual percept is available to conscious awareness only if recurrent long-distance interactions among distributed brain regions activate neural circuitry extending from the posterior areas to prefrontal regions above a certain excitation threshold. To directly test this hypothesis, we trained 14 human participants to increase blood oxygenation level-dependent (BOLD) signals with real-time functional magnetic resonance imaging (rtfMRI)-based neurofeedback simultaneously in four specific regions of the occipital, temporal, insular and prefrontal parts of the brain. Specifically, we hypothesized that the up-regulation of the mean BOLD activity in the posterior-frontal brain regions lowers the perceptual threshold for visual stimuli, while down-regulation raises the threshold. Our results showed that participants could perform up-regulation (Wilcoxon test, session 1: p = 0.022; session 4: p = 0.041) of the posterior-frontal brain activity, but not down-regulation. Furthermore, the up-regulation training led to a significant reduction in the visual perceptual threshold, but no substantial change in perceptual threshold was observed after the down-regulation training. These findings show that the up-regulation of the posterior-frontal regions improves the perceptual discrimination of the stimuli. However, further questions as to whether the posterior-frontal regions can be down-regulated at all, and whether down-regulation raises the perceptual threshold, remain unanswered.

Enhancement of alkaline water-oxidation activity for amorphous CoOx by the underlying remote-region atom seeding

Scaling up hydrogen production via large-current-density water electrolysis requires durable electrocatalysts of oxygen evolution reaction (OER) to reduce energy consumption. While amorphous metal oxides are promising OER catalysts, the surface-sites-electronic-orbital chance from the underlying remote-region atom seeding remains elusive. Herein, vanadium atom was controllable seated in the underlying remote region of the bulk materials as a typical coupling mode of amorphous-CoVOx-supported amorphous CoOx (CoVOx@CoOx), to study long-distance atoms correlation. XPS characterization for CoVOx@CoOx can't reveal the V signal due to the limited test depth of 5 nm, suggesting that V is existent in the internal region where it can be detected by EDS with 1 μm test depth. For surface-etched CoVOx@CoOx, V XPS signal appeared due to the exposure of CoVOx counterpart. The bionic flower structured, amorphous CoVOx@CoOx presents low overpotential of 338.5 mV at an extremely high current density of 1000 mA cm−2 in 1 M KOH and reserves 90.4% of the initial catalytical current after 24 h operation, significantly outperforming single amorphous CoOx. Density functional theory calculations evidence that the charge transfer from V atoms of CoVOx to surface active Co sites of CoOx part leads to the d-band center of Co-3d orbital shifted towards the Fermi level, which enhanced O adsorption effect thus promoting the OER activity. This research not only provides an ultrahigh-current-tolerance OER catalyst but also throws in-depth insight into the long-distance atoms charge interaction towards knowledge-guide catalyst construction for practical utilization.

Spatial proximity and gene function: a new dimension in prokaryotic gene association network analysis with 3D-GeneNet.

Understanding the biological functions and processes of genes, particularly those not yet characterized, is crucial for advancing molecular biology and identifying therapeutic targets. The hypothesis guiding this study is that the 3D proximity of genes correlates with their functional interactions and relevance in prokaryotes. We introduced 3D-GeneNet, an innovative software tool that utilizes high-throughput sequencing data from chromosome conformation capture techniques and integrates topological metrics to construct gene association networks. Through a series of comparative analyses focused on spatial versus linear distances, we explored various dimensions such as topological structure, functional enrichment levels, distribution patterns of linear distances among gene pairs, and the area under the receiver operating characteristic curve by utilizing model organism Escherichia coli K-12. Furthermore, 3D-GeneNet was shown to maintain good accuracy compared to multiple algorithms (neighbourhood, co-occurrence, coexpression, and fusion) across multiple bacteria, including E. coli, Brucella abortus, and Vibrio cholerae. In addition, the accuracy of 3D-GeneNet's prediction of long-distance gene interactions was identified by bacterial two-hybrid assays on E. coli K-12 MG1655, where 3D-GeneNet not only increased the accuracy of linear genomic distance tripled but also achieved 60% accuracy by running alone. Finally, it can be concluded that the applicability of 3D-GeneNet will extend to various bacterial forms, including Gram-negative, Gram-positive, single-, and multi-chromosomal bacteria through Hi-C sequencing and analysis. Such findings highlight the broad applicability and significant promise of this method in the realm of gene association network. 3D-GeneNet is freely accessible at https://github.com/gaoyuanccc/3D-GeneNet.

DNA methylation-based high-resolution mapping of long-distance chromosomal interactions in nucleosome-depleted regions.

3C-based methods have significantly advanced our understanding of 3D genome organization. However, it remains a formidable task to precisely capture long-range chromosomal interactions between individual loci, such as those between promoters and distal enhancers. Here, we present Methyltransferase Targeting-based chromosome Architecture Capture (MTAC), a method that maps the contacts between a target site (viewpoint) and the rest of the genome in budding yeast with high resolution and sensitivity. MTAC detects hundreds of intra- and inter-chromosomal interactions within nucleosome-depleted regions (NDRs) that cannot be captured by 4C, Hi-C, or Micro-C. By applying MTAC to various viewpoints, we find that (1) most long-distance chromosomal interactions detected by MTAC reflect tethering by the nuclear pore complexes (NPCs), (2) genes co-regulated by methionine assemble into inter-chromosomal clusters near NPCs upon activation, (3) mediated by condensin, the mating locus forms a highly specific interaction with the recombination enhancer (RE) in a mating-type specific manner, and (4) correlation of MTAC signals among NDRs reveal spatial mixing and segregation of the genome. Overall, these results demonstrate MTAC as a powerful tool to resolve fine-scale long-distance chromosomal interactions and provide insights into the 3D genome organization.

Explaining the B+→K+νν¯\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$B^+\\rightarrow K^+ \ u \\bar{\ u }$$\\end{document} excess via a massless dark photon

The Belle II collaboration has recently observed the rare decay B+→K+νν¯\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$B^+\\rightarrow K^+ \ u \\bar{\ u }$$\\end{document}, finding an excess with respect to the Standard Model prediction. We explore the possibility that the data entails long-distance interactions induced by a massless dark photon, γD\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\gamma _{\\scriptscriptstyle {D}}$$\\end{document}. This couples at the tree-level to an invisible, dark sector and to the Standard Model via higher-dimensional operators, such as the chromomagnetic-dipole coupling that we use to explain the excess. As the process B+→K+γD\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$B^+\\rightarrow K^+ \\gamma _{\\scriptscriptstyle {D}}$$\\end{document} is forbidden by angular momentum conservation, the transition mediated by the off-shell dark photon yields a three-body final state comprising a pair of dark fermions that show as a missing energy continuum in the detector, faking the neutrino signature. We show that the Belle II data is explained for perturbative values of the parameters of the model. This scenario predicts new contributions to the neutral B meson decays B0→K∗γD\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$B^0\\rightarrow K^* \\gamma _{\\scriptscriptstyle {D}}$$\\end{document}, in which the emission of a on-shell dark photon is allowed, yielding a monochromatic missing energy signature. Analogously, an excess due to the emission of a dark photon is predicted for the Bs0→ϕ+Emiss\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$B^0_s\\rightarrow \\phi + E_\ extrm{miss}$$\\end{document} decay that could be scrutinized next at the LHCb experiments.

Development of a New Model System to Study Long-Distance Interactions Supported by Architectural Proteins.

Chromatin architecture is critical for the temporal and tissue-specific activation of genes that determine eukaryotic development. The functional interaction between enhancers and promoters is controlled by insulators and tethering elements that support specific long-distance interactions. However, the mechanisms of the formation and maintenance of long-range interactions between genome regulatory elements remain poorly understood, primarily due to the lack of convenient model systems. Drosophila became the first model organism in which architectural proteins that determine the activity of insulators were described. In Drosophila, one of the best-studied DNA-binding architectural proteins, Su(Hw), forms a complex with Mod(mdg4)-67.2 and CP190 proteins. Using a combination of CRISPR/Cas9 genome editing and attP-dependent integration technologies, we created a model system in which the promoters and enhancers of two reporter genes are separated by 28 kb. In this case, enhancers effectively stimulate reporter gene promoters in cis and trans only in the presence of artificial Su(Hw) binding sites (SBS), in both constructs. The expression of the mutant Su(Hw) protein, which cannot interact with CP190, and the mutation inactivating Mod(mdg4)-67.2, lead to the complete loss or significant weakening of enhancer-promoter interactions, respectively. The results indicate that the new model system effectively identifies the role of individual subunits of architectural protein complexes in forming and maintaining specific long-distance interactions in the D. melanogaster model.

CAT-Unet: An enhanced U-Net architecture with coordinate attention and skip-neighborhood attention transformer for medical image segmentation

With the rise of deep learning, the U-Net network, based on a U-shaped architecture and skip connections, has found widespread application in various medical image segmentation tasks. However, the receptive field of the standard convolution operation is limited, because it is difficult to achieve global and long-distance semantic information interaction. Inspired by the advantages of ConvNext and Neighborhood Attention (NA), we propose CAT-Unet in this study to address the aforementioned challenges. We effectively reduce the number of parameters by utilizing large kernels and depthwise separable convolutions. Meanwhile, we introduce a Coordinate Attention (CA) module, which enables the model to learn more comprehensive and contextual information from surrounding regions. Furthermore, we introduce Skip-NAT (Neighborhood Attention Transformer) as the main algorithmic framework, replacing U-Net's original skip-connection layers, to lessen the impact of shallow features on network efficiency. Experimental results show that CAT-Unet achieves better segmentation results. On the ISIC2018 dataset, the best results for Dice (Dice Coefficient), IoU (Intersection over Union), and HD (Hausdorff Distance) are 90.26%, 83.58%, and 4.259, respectively. For the PH2 dataset, the best Dice, IoU, and HD results are 96.49%, 91.81%, and 3.971, respectively. Finally, on the DSB2018 dataset, the best Dice, IoU, and HD results are 94.58%, 88.78%, and 3.749, respectively.

Adornment deposits: a study of bead and jewellery remains from Late Antiquity tombs in the Red Sea port of Berenike

ABSTRACT Next to pottery, items of adornment comprise the most abundant material excavated in Northeast Africa, often being the only evidence for long-distance interactions. Interdisciplinary research has been developed to demonstrate that beads, particularly those of Indian origin from port sites on the Red Sea coast of Egypt, may attest to intense relations between North Africa and Asia. Parallels and provenance examination of recent bead and jewellery finds (four silver and coral earrings, eight silver rings and about eleven ivory bangles) from two Late Antiquity tombs of the fourth/fifth centuries AD at Berenike also suggest links between the Red Sea coast and the Nubian Nile Valley. Additionally, these ornaments raise questions as to their function in multiple burials. It is not possible to determine whether they were used as part of the funerary ritual or as offerings to the individuals buried, but several observations can be offered.

Yin Yang 1 regulates cohesin complex protein SMC3 in mouse hematopoietic stem cells

AbstractYin Yang 1 (YY1) and structural maintenance of chromosomes 3 (SMC3) are 2 critical chromatin structural factors that mediate long-distance enhancer-promoter interactions and promote developmentally regulated changes in chromatin architecture in hematopoietic stem/progenitor cells (HSPCs). Although YY1 has critical functions in promoting hematopoietic stem cell (HSC) self-renewal and maintaining HSC quiescence, SMC3 is required for proper myeloid lineage differentiation. However, many questions remain unanswered regarding how YY1 and SMC3 interact with each other and affect hematopoiesis. We found that YY1 physically interacts with SMC3 and cooccupies with SMC3 at a large cohort of promoters genome wide, and YY1 deficiency deregulates the genetic network governing cell metabolism. YY1 occupies the Smc3 promoter and represses SMC3 expression in HSPCs. Although deletion of 1 Smc3 allele partially restores HSC numbers and quiescence in YY1 knockout mice, Yy1−/−Smc3+/− HSCs fail to reconstitute blood after bone marrow transplant. YY1 regulates HSC metabolic pathways and maintains proper intracellular reactive oxygen species levels in HSCs, and this regulation is independent of the YY1–SMC3 axis. Our results establish a distinct YY1–SMC3 axis and its impact on HSC quiescence and metabolism.

Combined Study of Gene Expression and Chromosome Three-Dimensional Structure in Escherichia coli During Growth Process.

The chromosome structure of different bacteria has its unique organization pattern, which plays an important role in maintaining the spatial location relationship between genes and regulating gene expression. Conversely, transcription also plays a global role in regulating the three-dimensional structure of bacterial chromosomes. Therefore, we combine RNA-Seq and Hi-C technology to explore the relationship between chromosome structure changes and transcriptional regulation in E. coli at different growth stages. Transcriptome analysis indicates that E. coli synthesizes many ribosomes and peptidoglycan in the exponential phase. In contrast, E. coli undergoes more transcriptional regulation and catabolism during the stationary phase, reflecting its adaptability to changes in environmental conditions during growth. Analyzing the Hi-C data shows that E. coli has a higher frequency of global chromosomal interaction in the exponential phase and more defined chromosomal interaction domains (CIDs). Still, the long-distance interactions at the replication termination region are lower than in the stationary phase. Combining transcriptome and Hi-C data analysis, we conclude that highly expressed genes are more likely to be distributed in CID boundary regions during the exponential phase. At the same time, most high-expression genes distributed in the CID boundary regions are ribosomal gene clusters, forming clearer CID boundaries during the exponential phase. The three-dimensional structure of chromosome and expression pattern is altered during the growth of E. coli from the exponential phase to the stationary phase, clarifying the synergy between the two regulatory aspects.

The first investigation of an Iron Age shell midden in Oman: The Nafūn complex

The Nafūn shell midden complex is a cluster of eight shell mounds in al-Wusṭā Governorate (south-central Oman). Located 40 km north of Duqm, the shell midden is part of a unique cultural landscape encompassing a variety of archaeological features. With a total of 207 recorded archaeological sites, the Nafūn area emerges as a significant site for studying the Early and Late Iron Age communities in south-central Oman. The first investigations of the shell midden were conducted between 2019 and 2022. Radiocarbon dating of charcoal samples from the site provided a date range of 1012–536 BCE (cal. 2σ), aligning with the Iron Age II (1000–600 BCE) material culture. Together with stratigraphic observations, this indicates that the midden was intermittently occupied for at least 500 years. Additional evidence indicates that there was also activity in the area during the Late Iron Age, evidenced by the presence of a large rock art site, circular stone burial mounds and numerous clusters of trilith stone monuments along the wadi Nafūn route, with a source of drinking water 3 km from the coast. Such findings underscore the importance of Nafūn as a significant site for enduring socio-economic and cultural contacts, strategically located at the mouth of the wadi that connects with the Indian Ocean. The effective utilisation of marine resources by the local communities not only supported their economic and subsistence needs but also fostered strong economic, social and cultural connections with the inland regions. Furthermore, it facilitated their active engagement in long-distance trade and interactions along the coastal areas. The unique combination of sites and the fusion of elements from both northern Oman and Dhofar make Nafūn an intriguing and, so far, undocumented intersection along the long-distance routes connecting the northern and southern cultural circles.

Astronomy, Architecture, and Landscape in the Olmec Area and Western Maya Lowlands: Implications for Understanding Regional Variability and Evolution of Orientation Patterns in Mesoamerica

AbstractIn the area along the southern Gulf Coast in Mexico, a large number of previously unrecorded archaeological sites have recently been detected with the aid of lidar data, which also allowed us to determine the orientations of hundreds of structures and architectural assemblages, including many standardized complexes dated to the Early-to-Middle Formative transition. As revealed by our analyses, most orientations were based on astronomical and calendrical principles, occasionally combined with certain concepts of sacred geography. While the results of these analyses were presented in a recently published article, here we explore the potential of alignment data for addressing other questions of archaeological relevance. The distribution of particular building types and regional variations in alignment patterns in the study area suggest the existence of two somehow different cultural spheres, loosely corresponding to the areas conventionally called the Gulf Olmec region and the western Maya Lowlands. Examining pertinent evidence, we argue that it was in this area where some of the most prominent orientation groups materialized in later Mesoamerican architecture originated. We also attempt to reconstruct the paths of their diffusion, which are expected to contribute to understanding the dynamics of long-distance cultural interaction in Mesoamerica.

Increased long-distance and homo-trans interactions related to H3K27me3 in Arabidopsis hybrids.

In plants, the genome structure of hybrids changes compared with their parents, but the effects of these changes in hybrids remain elusive. Comparing reciprocal crosses between Col × C24 and C24 × Col in Arabidopsis using high-throughput chromosome conformation capture assay (Hi-C) analysis, we found that hybrid three-dimensional (3D) chromatin organization had more long-distance interactions relative to parents, and this was mainly located in promoter regions and enriched in genes with heterosis-related pathways. The interactions between euchromatin and heterochromatin were increased, and the compartment strength decreased in hybrids. In compartment domain (CD) boundaries, the distal interactions were more in hybrids than their parents. In the hybrids of CURLY LEAF (clf) mutants clfCol × clfC24 and clfC24 × clfCol , the heterosis phenotype was damaged, and the long-distance interactions in hybrids were fewer than in their parents with lower H3K27me3. ChIP-seq data revealed higher levels of H3K27me3 in the region adjacent to the CD boundary and the same interactional homo-trans sites in the wild-type (WT) hybrids, which may have led to more long-distance interactions. In addition, the differentially expressed genes (DEGs) located in the boundaries of CDs and loop regions changed obviously in WT, and the functional enrichment for DEGs was different between WT and clf in the long-distance interactions and loop regions. Our findings may therefore propose a new epigenetic explanation of heterosis in the Arabidopsis hybrids and provide new insights into crop breeding and yield increase.