Simultaneous profiling of spatial gene expression and chromatin accessibility during mouse brain development.

The brain is a complex tissue whose function relies on coordinated anatomical and molecular features. However, the molecular annotation of the spatial organization of the brain is currently insufficient. Here, we describe microfluidic indexing-based spatial assay for transposase-accessible chromatin and RNA-sequencing (MISAR-seq), a method for spatially resolved joint profiling of chromatin accessibility and gene expression. By applying MISAR-seq to the developing mouse brain, we study tissue organization and spatiotemporal regulatory logics during mouse brain development.

Clinical characteristics of persistent or recurrent pneumonia combined with airway malacia in children.

OBJECTIVE: The aim of this study is to investigate the clinical characteristics and pathogens involved in persistent or recurrent pneumonia combined with airway malacia in children. METHODS: We retrospectively reviewed the information of children hospitalised with persistent or recurrent pneumonia, including clinical presentations, laboratory examination results and pathogens. RESULTS: A total of 554 patients were admitted, 285 (51.44%) of whom were found to have airway malacia. There were 78 (27.37%), 166 (58.25%) and 41 (14.39%) patients with mild, moderate and severe malacia, respectively. Patients with airway malacia were younger than those without malacia (6.0 vs. 12.0 months, p < 0.01) and were more likely to present with wheezing (75.07%), fever (34.39%), dyspnoea (28.77%), cyanosis (13.68%) and wheezing in the lungs (78.95%). The incidence of preterm delivery, oxygen therapy, paediatric intensive care unit (PICU) admission and mechanical ventilation was higher, and the hospital stay (11.0 vs. 10.0 days, p = 0.04) was longer in these patients than in those without malacia. Patients with severe airway malacia were more likely to undergo oxygen therapy, PICU admission, mechanical ventilation and have multiple malacia than were those with mild or moderate malacia. Mycoplasma pneumoniae (30.18%) was the most common pathogen. CONCLUSION: Severe airway malacia likely aggravates conditions combined with pneumonia. The proportion of multisite malacia was greater in severe airway malacia patients.

A spatiotemporal molecular atlas of mouse spinal cord injury identifies a distinct astrocyte subpopulation and therapeutic potential of IGFBP2.

Spinal cord injury (SCI) triggers a cascade of intricate molecular and cellular changes that determine the outcome. In this study, we resolve the spatiotemporal organization of the injured mouse spinal cord and quantitatively assess in situ cell-cell communication following SCI. By analyzing existing single-cell RNA sequencing datasets alongside our spatial data, we delineate a subpopulation of Igfbp2-expressing astrocytes that migrate from the white matter (WM) to gray matter (GM) and become reactive upon SCI, termed Astro-GMii. Further, Igfbp2 upregulation promotes astrocyte migration, proliferation, and reactivity, and the secreted IGFBP2 protein fosters neurite outgrowth. Finally, we show that IGFBP2 significantly reduces neuronal loss and remarkably improves the functional recovery in a mouse model of SCI in vivo. Together, this study not only provides a comprehensive molecular atlas of SCI but also exemplifies how this rich resource can be applied to endow cells and genes with functional insight and therapeutic potential.

Non-Gaussian fluctuations and non-Markovian effects in the nuclear fusion process: Langevin dynamics emerging from quantum molecular dynamics simulations.

Macroscopic parameters as well as precise information on the random force characterizing the Langevin-type description of the nuclear fusion process around the Coulomb barrier are extracted from the microscopic dynamics of individual nucleons by exploiting the numerical simulation of the improved quantum molecular dynamics. It turns out that the dissipation dynamics of the relative motion between two fusing nuclei is caused by a non-Gaussian distribution of the random force. We find that the friction coefficient as well as the time correlation function of the random force takes particularly large values in a region a little bit inside of the Coulomb barrier. A clear non-Markovian effect is observed in the time correlation function of the random force. It is further shown that an emergent dynamics of the fusion process can be described by the generalized Langevin equation with memory effects by appropriately incorporating the microscopic information of individual nucleons through the random force and its time correlation function.

Spatial transcriptomics: new dimension of understanding biological complexity.

Cells and tissues are exquisitely organized in a complex but ordered manner to form organs and bodies so that individuals can function properly. The spatial organization and tissue architecture represent a keynote property underneath all living organisms. Molecular architecture and cellular composition within intact tissues play a vital role in a variety of biological processes, such as forming the complicated tissue functionality, precise regulation of cell transition in all living activities, consolidation of central nervous system, cellular responses to immunological and pathological cues. To explore these biological events at a large scale and fine resolution, a genome-wide understanding of spatial cellular changes is essential. However, previous bulk RNA sequencing and single-cell RNA sequencing technologies could not obtain the important spatial information of tissues and cells, despite their ability to detect high content transcriptional changes. These limitations have prompted the development of numerous spatially resolved technologies which provide a new dimension to interrogate the regional gene expression, cellular microenvironment, anatomical heterogeneity and cell-cell interactions. Since the advent of spatial transcriptomics, related works that use these technologies have increased rapidly, and new methods with higher throughput and resolution have grown quickly, all of which hold great promise to accelerate new discoveries in understanding the biological complexity. In this review, we briefly discussed the historical evolution of spatially resolved transcriptome. We broadly surveyed the representative methods. Furthermore, we summarized the general computational analysis pipeline for the spatial gene expression data. Finally, we proposed perspectives for technological development of spatial multi-omics.

Constraints on the density dependence of the symmetry energy.

Collisions involving 112Sn and 124Sn nuclei have been simulated with the improved quantum molecular dynamics transport model. The results of the calculations reproduce isospin diffusion data from two different observables and the ratios of neutron and proton spectra. By comparing these data to calculations performed over a range of symmetry energies at saturation density and different representations of the density dependence of the symmetry energy, constraints on the density dependence of the symmetry energy at subnormal density are obtained. The results from the present work are compared to constraints put forward in other recent analyses.