Molecular adaptations in response to exercise training are associated with tissue-specific transcriptomic and epigenomic signatures.

Regular exercise has many physical and brain health benefits, yet the molecular mechanisms mediating exercise effects across tissues remain poorly understood. Here we analyzed 400 high-quality DNA methylation, ATAC-seq, and RNA-seq datasets from eight tissues from control and endurance exercise-trained (EET) rats. Integration of baseline datasets mapped the gene location dependence of epigenetic control features and identified differing regulatory landscapes in each tissue. The transcriptional responses to 8 weeks of EET showed little overlap across tissues and predominantly comprised tissue-type enriched genes. We identified sex differences in the transcriptomic and epigenomic changes induced by EET. However, the sex-biased gene responses were linked to shared signaling pathways. We found that many G protein-coupled receptor-encoding genes are regulated by EET, suggesting a role for these receptors in mediating the molecular adaptations to training across tissues. Our findings provide new insights into the mechanisms underlying EET-induced health benefits across organs.

The mitochondrial multi-omic response to exercise training across rat tissues.

Mitochondria have diverse functions critical to whole-body metabolic homeostasis. Endurance training alters mitochondrial activity, but systematic characterization of these adaptations is lacking. Here, the Molecular Transducers of Physical Activity Consortium mapped the temporal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats trained for 1, 2, 4, or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart, and skeletal muscle. The colon showed non-linear response dynamics, whereas mitochondrial pathways were downregulated in brown adipose and adrenal tissues. Protein acetylation increased in the liver, with a shift in lipid metabolism, whereas oxidative proteins increased in striated muscles. Exercise-upregulated networks were downregulated in human diabetes and cirrhosis. Knockdown of the central network protein 17-beta-hydroxysteroid dehydrogenase 10 (HSD17B10) elevated oxygen consumption, indicative of metabolic stress. We provide a multi-omic, multi-tissue, temporal atlas of the mitochondrial response to exercise training and identify candidates linked to mitochondrial dysfunction.

Spin disorder control of topological spin texture.

Stabilization of topological spin textures in layered magnets has the potential to drive the development of advanced low-dimensional spintronics devices. However, achieving reliable and flexible manipulation of the topological spin textures beyond skyrmion in a two-dimensional magnet system remains challenging. Here, we demonstrate the introduction of magnetic iron atoms between the van der Waals gap of a layered magnet, Fe3GaTe2, to modify local anisotropic magnetic interactions. Consequently, we present direct observations of the order-disorder skyrmion lattices transition. In addition, non-trivial topological solitons, such as skyrmioniums and skyrmion bags, are realized at room temperature. Our work highlights the influence of random spin control of non-trivial topological spin textures.

Protocol for high-throughput DNA methylation profiling in rat tissues using automated reduced representation bisulfite sequencing.

Although reduced representation bisulfite sequencing (RRBS) measures DNA methylation (DNAme) across CpG-rich genomic regions with high sensitivity, the assay can be time-consuming and prone to batch effects. Here, we present a high-throughput, automated RRBS protocol starting with DNA extraction from frozen rat tissues. We describe steps for RRBS library preparation, library quality control, and sequencing. We also detail an optimized pipeline for sequencing data processing. This protocol has been applied successfully to DNAme profiling across multiple rat tissues. For complete details on the use and execution of this protocol, please refer to Nair et al.1.

Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.

Rare structural variants (SVs) - insertions, deletions, and complex rearrangements - can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4x increase from short-reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals, and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that don't incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in FAM177A1 shared by two siblings, which were likely causal for a rare neurodevelopmental disorder. Our observations demonstrate the promise of integrating long-read sequencing with gene expression towards improving the prioritization of functional SVs and TREs in rare disease patients.

A substitutional quantum defect in WS2 discovered by high-throughput computational screening and fabricated by site-selective STM manipulation.

Point defects in two-dimensional materials are of key interest for quantum information science. However, the parameter space of possible defects is immense, making the identification of high-performance quantum defects very challenging. Here, we perform high-throughput (HT) first-principles computational screening to search for promising quantum defects within WS2, which present localized levels in the band gap that can lead to bright optical transitions in the visible or telecom regime. Our computed database spans more than 700 charged defects formed through substitution on the tungsten or sulfur site. We found that sulfur substitutions enable the most promising quantum defects. We computationally identify the neutral cobalt substitution to sulfur (Co S 0 ) and fabricate it with scanning tunneling microscopy (STM). The Co S 0 electronic structure measured by STM agrees with first principles and showcases an attractive quantum defect. Our work shows how HT computational screening and nanoscale synthesis routes can be combined to design promising quantum defects.

Interlayer Coupling Controlled Ordering and Phases in Polar Vortex Superlattices.

The recent discovery of polar topological structures has opened the door for exciting physics and emergent properties. There is, however, little methodology to engineer stability and ordering in these systems, properties of interest for engineering emergent functionalities. Notably, when the surface area is extended to arbitrary thicknesses, the topological polar texture becomes unstable. Here we show that this instability of the phase is due to electrical coupling between successive layers. We demonstrate that this electrical coupling is indicative of an effective screening length in the dielectric, similar to the conductor-ferroelectric interface. Controlling the electrostatics of the superlattice interfaces, the system can be tuned between a pure topological vortex state and a mixed classical-topological phase. This coupling also enables engineering coherency among the vortices, not only tuning the bulk phase diagram but also enabling the emergence of a 3D lattice of polar textures.

Non-local dielectric effects in nanoscience.

The physical properties of charges and excitations in nanoscale materials are influenced both by the dielectric properties of the material itself and the surrounding environment. This non-local dielectric effect was first discussed in the context of molecules in solvents over a century ago. In this perspective, we discuss non-local dielectric effects in zero-dimensional, one-dimensional, and two-dimensional nanoscale systems.

Near-Field Coupling with a Nanoimprinted Probe for Dark Exciton Nanoimaging in Monolayer WSe2.

Tip-enhanced photoluminescence (TRPL) is a powerful technique for spatially and spectrally probing local optical properties of 2-dimensional (2D) materials that are modulated by the local heterogeneities, revealing inaccessible dark states due to bright state overlap in conventional far-field microscopy at room temperature. While scattering-type near-field probes have shown the potential to selectively enhance and reveal dark exciton emission, their technical complexity and sensitivity can pose challenges under certain experimental conditions. Here, we present a highly reproducible and easy-to-fabricate near-field probe based on nanoimprint lithography and fiber-optic excitation and collection. The novel near-field measurement configuration provides an ∼3 orders of magnitude out-of-plane Purcell enhancement, diffraction-limited excitation spot, and subdiffraction hyperspectral imaging resolution (below 50 nm) of dark exciton emission. The effectiveness of this high spatial XD mapping technique was then demonstrated through reproducible hyperspectral mapping of oxidized sites and bubble areas.

Transferable nano-patterned ALD membrane.

We demonstrate fabrication of nano-patterned thin ALD (Atomic layer deposition) membrane (suspended/transferable) by using a bi-layer resist process where the bottom layer resist acts as a sacrificial layer. This method enables an all dry deterministic transfer of nano-patterned ALD membrane on desired substrate, allowing assembly of multitude of hetero-structures and functionalities that are not yet accessible. Unlike conventional ways of achieving patterned alumina membrane reported in literature our technique requires significantly less fabrication steps and paves the way for novel ALD membrane-based technology.

Rotational and dilational reconstruction in transition metal dichalcogenide moiré bilayers.

Lattice reconstruction and corresponding strain accumulation plays a key role in defining the electronic structure of two-dimensional moiré superlattices, including those of transition metal dichalcogenides (TMDs). Imaging of TMD moirés has so far provided a qualitative understanding of this relaxation process in terms of interlayer stacking energy, while models of the underlying deformation mechanisms have relied on simulations. Here, we use interferometric four-dimensional scanning transmission electron microscopy to quantitatively map the mechanical deformations through which reconstruction occurs in small-angle twisted bilayer MoS2 and WSe2/MoS2 heterobilayers. We provide direct evidence that local rotations govern relaxation for twisted homobilayers, while local dilations are prominent in heterobilayers possessing a sufficiently large lattice mismatch. Encapsulation of the moiré layers in hBN further localizes and enhances these in-plane reconstruction pathways by suppressing out-of-plane corrugation. We also find that extrinsic uniaxial heterostrain, which introduces a lattice constant difference in twisted homobilayers, leads to accumulation and redistribution of reconstruction strain, demonstrating another route to modify the moiré potential.

Size-Induced Ferroelectricity in Antiferroelectric Oxide Membranes.

Despite extensive studies on size effects in ferroelectrics, how structures and properties evolve in antiferroelectrics with reduced dimensions still remains elusive. Given the enormous potential of utilizing antiferroelectrics for high-energy-density storage applications, understanding their size effects will provide key information for optimizing device performances at small scales. Here, the fundamental intrinsic size dependence of antiferroelectricity in lead-free NaNbO3 membranes is investigated. Via a wide range of experimental and theoretical approaches, an intriguing antiferroelectric-to-ferroelectric transition upon reducing membrane thickness is probed. This size effect leads to a ferroelectric single-phase below 40 nm, as well as a mixed-phase state with ferroelectric and antiferroelectric orders coexisting above this critical thickness. Furthermore, it is shown that the antiferroelectric and ferroelectric orders are electrically switchable. First-principle calculations further reveal that the observed transition is driven by the structural distortion arising from the membrane surface. This work provides direct experimental evidence for intrinsic size-driven scaling in antiferroelectrics and demonstrates enormous potential of utilizing size effects to drive emergent properties in environmentally benign lead-free oxides with the membrane platform.

Multi-omic identification of key transcriptional regulatory programs during endurance exercise training.

Transcription factors (TFs) play a key role in regulating gene expression and responses to stimuli. We conducted an integrated analysis of chromatin accessibility, DNA methylation, and RNA expression across eight rat tissues following endurance exercise training (EET) to map epigenomic changes to transcriptional changes and determine key TFs involved. We uncovered tissue-specific changes and TF motif enrichment across all omic layers, differentially accessible regions (DARs), differentially methylated regions (DMRs), and differentially expressed genes (DEGs). We discovered distinct routes of EET-induced regulation through either epigenomic alterations providing better access for TFs to affect target genes, or via changes in TF expression or activity enabling target gene response. We identified TF motifs enriched among correlated epigenomic and transcriptomic alterations, DEGs correlated with exercise-related phenotypic changes, and EET-induced activity changes of TFs enriched for DEGs among their gene targets. This analysis elucidates the unique transcriptional regulatory mechanisms mediating diverse organ effects of EET.

The mitochondrial multi-omic response to exercise training across tissues.

Mitochondria are adaptable organelles with diverse cellular functions critical to whole-body metabolic homeostasis. While chronic endurance exercise training is known to alter mitochondrial activity, these adaptations have not yet been systematically characterized. Here, the Molecular Transducers of Physical Activity Consortium (MoTrPAC) mapped the longitudinal, multi-omic changes in mitochondrial analytes across 19 tissues in male and female rats endurance trained for 1, 2, 4 or 8 weeks. Training elicited substantial changes in the adrenal gland, brown adipose, colon, heart and skeletal muscle, while we detected mild responses in the brain, lung, small intestine and testes. The colon response was characterized by non-linear dynamics that resulted in upregulation of mitochondrial function that was more prominent in females. Brown adipose and adrenal tissues were characterized by substantial downregulation of mitochondrial pathways. Training induced a previously unrecognized robust upregulation of mitochondrial protein abundance and acetylation in the liver, and a concomitant shift in lipid metabolism. The striated muscles demonstrated a highly coordinated response to increase oxidative capacity, with the majority of changes occurring in protein abundance and post-translational modifications. We identified exercise upregulated networks that are downregulated in human type 2 diabetes and liver cirrhosis. In both cases HSD17B10, a central dehydrogenase in multiple metabolic pathways and mitochondrial tRNA maturation, was the main hub. In summary, we provide a multi-omic, cross-tissue atlas of the mitochondrial response to training and identify candidates for prevention of disease-associated mitochondrial dysfunction.

Non-volatile electric-field control of inversion symmetry.

Competition between ground states at phase boundaries can lead to significant changes in properties under stimuli, particularly when these ground states have different crystal symmetries. A key challenge is to stabilize and control the coexistence of symmetry-distinct phases. Using BiFeO3 layers confined between layers of dielectric TbScO3 as a model system, we stabilize the mixed-phase coexistence of centrosymmetric and non-centrosymmetric BiFeO3 phases at room temperature with antipolar, insulating and polar semiconducting behaviour, respectively. Application of orthogonal in-plane electric (polar) fields results in reversible non-volatile interconversion between the two phases, hence removing and introducing centrosymmetry. Counterintuitively, we find that an electric field 'erases' polarization, resulting from the anisotropy in octahedral tilts introduced by the interweaving TbScO3 layers. Consequently, this interconversion between centrosymmetric and non-centrosymmetric phases generates changes in the non-linear optical response of over three orders of magnitude, resistivity of over five orders of magnitude and control of microscopic polar order. Our work establishes a platform for cross-functional devices that take advantage of changes in optical, electrical and ferroic responses, and demonstrates octahedral tilts as an important order parameter in materials interface design.

Bidirectional phonon emission in two-dimensional heterostructures triggered by ultrafast charge transfer.

Photoinduced charge transfer in van der Waals heterostructures occurs on the 100 fs timescale despite weak interlayer coupling and momentum mismatch. However, little is understood about the microscopic mechanism behind this ultrafast process and the role of the lattice in mediating it. Here, using femtosecond electron diffraction, we directly visualize lattice dynamics in photoexcited heterostructures of WSe2/WS2 monolayers. Following the selective excitation of WSe2, we measure the concurrent heating of both WSe2 and WS2 on a picosecond timescale-an observation that is not explained by phonon transport across the interface. Using first-principles calculations, we identify a fast channel involving an electronic state hybridized across the heterostructure, enabling phonon-assisted interlayer transfer of photoexcited electrons. Phonons are emitted in both layers on the femtosecond timescale via this channel, consistent with the simultaneous lattice heating observed experimentally. Taken together, our work indicates strong electron-phonon coupling via layer-hybridized electronic states-a novel route to control energy transport across atomic junctions.