Catálogo de publicaciones - revistas

<jats:p> The oxygen concentrations of oceanic deep-water and atmospheric carbon dioxide ( <jats:italic>p</jats:italic> CO <jats:sub>2</jats:sub> ) are intrinsically linked through organic carbon remineralization and storage as dissolved inorganic carbon in the deep sea. We present a high-resolution reconstruction of relative changes in oxygen concentration in the deep North Atlantic for the past 1.5 million years using the carbon isotope gradient between epifaunal and infaunal benthic foraminifera species as a proxy for paleo-oxygen. We report a significant (&gt;40 micromole per kilogram) reduction in glacial Atlantic deep-water oxygenation at ~960 thousand to 900 thousand years ago that coincided with increased continental ice volume and a major change in ocean thermohaline circulation. Paleo-oxygen results support a scenario of decreasing deep-water oxygen concentrations, increased respired carbon storage, and a reduction in glacial <jats:italic>p</jats:italic> CO <jats:sub>2</jats:sub> across the Middle Pleistocene Transition. </jats:p>

<jats:p> The microbiome contributes to the development and maturation of the immune system. In response to commensal bacteria, intestinal CD4 <jats:sup>+</jats:sup> T lymphocytes differentiate into functional subtypes with regulatory or effector functions. The development of small intestine intraepithelial lymphocytes that coexpress CD4 and CD8αα homodimers (CD4IELs) depends on the microbiota. However, the identity of the microbial antigens recognized by CD4 <jats:sup>+</jats:sup> T cells that can differentiate into CD4IELs remains unknown. We identified β-hexosaminidase, a conserved enzyme across commensals of the Bacteroidetes phylum, as a driver of CD4IEL differentiation. In a mouse model of colitis, β-hexosaminidase–specific lymphocytes protected against intestinal inflammation. Thus, T cells of a single specificity can recognize a variety of abundant commensals and elicit a regulatory immune response at the intestinal mucosa. </jats:p>

<jats:p> Muscle stem cells (MuSCs) reside in a specialized niche that ensures their regenerative capacity. Although we know that innate immune cells infiltrate the niche in response to injury, it remains unclear how MuSCs adapt to this altered environment for initiating repair. Here, we demonstrate that inflammatory cytokine signaling from the regenerative niche impairs the ability of quiescent MuSCs to reenter the cell cycle. The histone H3 lysine 27 (H3K27) demethylase JMJD3, but not UTX, allowed MuSCs to overcome inhibitory inflammation signaling by removing trimethylated H3K27 (H3K27me3) marks at the <jats:italic>Has2</jats:italic> locus to initiate production of hyaluronic acid, which in turn established an extracellular matrix competent for integrating signals that direct MuSCs to exit quiescence. Thus, JMJD3-driven hyaluronic acid synthesis plays a proregenerative role that allows MuSC adaptation to inflammation and the initiation of muscle repair. </jats:p>

<jats:p>Time crystals are classified as discrete or continuous depending on whether they spontaneously break discrete or continuous time translation symmetry. Although discrete time crystals have been extensively studied in periodically driven systems, the experimental realization of a continuous time crystal is still pending. We report the observation of a limit cycle phase in a continuously pumped dissipative atom-cavity system that is characterized by emergent oscillations in the intracavity photon number. The phase of the oscillation was found to be random for different realizations, and hence, this dynamical many-body state breaks continuous time translation symmetry spontaneously. Furthermore, the observed limit cycles are robust against temporal perturbations and therefore demonstrate the realization of a continuous time crystal.</jats:p>

<jats:p>Skeletal or concave polyhedral crystals appear in a variety of synthetic processes and natural environments. However, their morphology, size, and orientation are difficult to control because of their highly kinetic growth character. We report a methodology to achieve synchronous, uniaxial, and stepwise growth of micrometer-scale skeletal single crystals from planar-chiral double-decker molecules. Upon drop-casting of a heated ethanol solution onto a quartz substrate, the molecules spontaneously assemble into standing vessel-shaped single crystals uniaxially and synchronously over the wide area of the substrate, with small size polydispersity. The crystal edge is active even after consumption of the molecules and resumes stereoselective growth with successive feeding. The resultant morphology can be packed into polycyclic aromatic hydrocarbon–like microarchitectures and behaves as a microscopic container.</jats:p>

<jats:p>Mammalian genomes possess multiple enhancers spanning an ultralong distance (&gt;megabases) to modulate important genes, yet it is unclear how these enhancers coordinate to achieve this task. Here, we combine multiplexed CRISPRi screening with machine learning to define quantitative enhancer-enhancer interactions. We find that the ultralong distance enhancer network possesses a nested multi-layer architecture that confers functional robustness of gene expression. Experimental characterization reveals that enhancer epistasis is maintained by three-dimensional chromosomal interactions and BRD4 condensation. Machine learning prediction of synergistic enhancers provides an effective strategy to identify non-coding variant pairs associated with pathogenic genes in diseases beyond Genome-Wide Association Studies (GWAS) analysis. Our work unveils nested epistasis enhancer networks, which can better explain enhancer functions within cells and in diseases.</jats:p>

<jats:p> Postmeiotic spermatids use a unique strategy to coordinate gene expression with morphological transformation, in which transcription and translation take place at separate developmental stages, but how mRNAs stored as translationally inert messenger ribonucleoproteins in developing spermatids become activated remains largely unknown. Here, we report that the RNA binding protein FXR1, a member of the fragile X–related (FXR) family, is highly expressed in late spermatids and undergoes liquid-liquid phase separation (LLPS) to merge messenger ribonucleoprotein granules with the translation machinery to convert stored mRNAs into a translationally activated state. Germline-specific <jats:italic>Fxr1</jats:italic> ablation in mice impaired the translation of target mRNAs and caused defective spermatid development and male infertility, and a phase separation–deficient FXR1 <jats:sup>L351P</jats:sup> mutation in <jats:italic>Fxr1</jats:italic> knock-in mice produced the same developmental defect. These findings uncover a mechanism for translational reprogramming with LLPS as a key driver in spermiogenesis. </jats:p>

<jats:p>Seismic waves from earthquakes and other sources are used to infer the structure and properties of Earth’s interior. The availability of large-scale seismic datasets and the suitability of deep-learning techniques for seismic data processing have pushed deep learning to the forefront of fundamental, long-standing research investigations in seismology. However, some aspects of applying deep learning to seismology are likely to prove instructive for the geosciences, and perhaps other research areas more broadly. Deep learning is a powerful approach, but there are subtleties and nuances in its application. We present a systematic overview of trends, challenges, and opportunities in applications of deep-learning methods in seismology.</jats:p>

<jats:p>Many organisms have evolved specialized immune pattern-recognition receptors, including nucleotide-binding oligomerization domain–like receptors (NLRs) of the STAND superfamily that are ubiquitous in plants, animals, and fungi. Although the roles of NLRs in eukaryotic immunity are well established, it is unknown whether prokaryotes use similar defense mechanisms. Here, we show that antiviral STAND (Avs) homologs in bacteria and archaea detect hallmark viral proteins, triggering Avs tetramerization and the activation of diverse N-terminal effector domains, including DNA endonucleases, to abrogate infection. Cryo–electron microscopy reveals that Avs sensor domains recognize conserved folds, active-site residues, and enzyme ligands, allowing a single Avs receptor to detect a wide variety of viruses. These findings extend the paradigm of pattern recognition of pathogen-specific proteins across all three domains of life.</jats:p>