Identification of feature genes in intestinal epithelial cell types.

The intestine, is responsible for food digestion, nutrient absorption, endocrine secretion, food residue excretion, and immune defense. These function performances are based on the intricate composition of intestinal epithelial cells, encompassing differentiated mature cells, rapidly proliferative cells, and intestinal stem cells. Although the characteristics of these cell types are well-documented, in-depth exploration of their representative markers and transcription factors is critical for comprehensive cell fate trajectory analysis.

Microfluidic fabrication of monodisperse microcapsules with gas cores.

A facile strategy for efficient and continuous fabrication of monodisperse gas-core microcapsules with controllable sizes and excellent ultrasound-induced burst performances is developed based on droplet microfluidics and interfacial polymerization. Monodisperse gas-in-oil-in-water (G/O/W) double emulsion droplets with a gas core and monomer-contained oil layer are fabricated in the upstream of a microfluidic device as templates, and then water-soluble monomers are added into the aqueous continuous phase in the downstream to initiate rapid interfacial polymerization at the O/W interfaces to prepare monodisperse gas-in-oil-in-solid (G/O/S) microcapsules with gas cores. The sizes of both microbubbles and G/O/W droplet templates can be precisely controlled by adjusting the gas supply pressure and the fluid flow rates.

Remote Charging and Degradation Suppression for the Quantum Battery.

The quantum battery (QB) makes use of quantum effects to store and supply energy, which may outperform its classical counterpart. However, there are two challenges in this field. One is that the environment-induced decoherence causes the energy loss and aging of the QB, the other is that the decreasing of the charger-QB coupling strength with increasing their distance makes the charging of the QB become inefficient.

The cyclooxygenase-expressing mesenchyme resists intestinal epithelial injury by paracrine signaling.

Paracrine signals play pivotal roles in organ homeostasis. Mesenchymal stromal cells (MSCs) play a key role in regulating epithelium homeostasis in the intestine while their paracrine effects are poorly characterized. Here, we identified prostaglandin E2 (PGE2) secreted by cyclooxygenase (COX)-expressing MSCs as a vital factor to maintain the intestinal mucosal barrier.

Intestinal cellular heterogeneity and disease development revealed by single-cell technology.

The intestinal epithelium is responsible for food digestion and nutrient absorption and plays a critical role in hormone secretion, microorganism defense, and immune response. These functions depend on the integral single-layered intestinal epithelium, which shows diversified cell constitution and rapid self-renewal and presents powerful regeneration plasticity after injury. Derailment of homeostasis of the intestine epithelium leads to the development of diseases, most commonly including enteritis and colorectal cancer.

Mesenchymal-epithelial interaction regulates gastrointestinal tract development in mouse embryos.

After gut tube patterning in early embryos, the cellular and molecular changes of developing stomach and intestine remain largely unknown. Here, combining single-cell RNA sequencing and spatial RNA sequencing, we construct a spatiotemporal transcriptomic landscape of the mouse stomach and intestine during embryonic days E9.5-E15.

Mutual dependency between lncRNA LETN and protein NPM1 in controlling the nucleolar structure and functions sustaining cell proliferation.

Fundamental processes such as ribosomal RNA synthesis and chromatin remodeling take place in the nucleolus, which is hyperactive in fast-proliferating cells. The sophisticated regulatory mechanism underlying the dynamic nucleolar structure and functions is yet to be fully explored. The present study uncovers the mutual functional dependency between a previously uncharacterized human long non-coding RNA, which we renamed LETN, and a key nucleolar protein, NPM1.

Single-cell transcriptome analysis reveals differential nutrient absorption functions in human intestine.

The intestine plays an important role in nutrient digestion and absorption, microbe defense, and hormone secretion. Although major cell types have been identified in the mouse intestinal epithelium, cell type-specific markers and functional assignments are largely unavailable for human intestine. Here, our single-cell RNA-seq analyses of 14,537 epithelial cells from human ileum, colon, and rectum reveal different nutrient absorption preferences in the small and large intestine, suggest the existence of Paneth-like cells in the large intestine, and identify potential new marker genes for human transient-amplifying cells and goblet cells.

Dependency of the Cancer-Specific Transcriptional Regulation Circuitry on the Promoter DNA Methylome.

Dynamic dysregulation of the promoter DNA methylome is a signature of cancer. However, comprehensive understandings about how the DNA methylome is incorporated in the transcriptional regulation circuitry and involved in regulating the gene expression abnormality in cancers are still missing. We introduce an integrative analysis pipeline based on mutual information theory and tailored for the multi-omics profiling data in The Cancer Genome Atlas (TCGA) to systematically find dependencies of transcriptional regulation circuits on promoter CpG methylation profiles for each of 21 cancer types.

Insights from multidimensional analyses of the pan-cancer DNA methylome heterogeneity and the uncanonical CpG-gene associations.

Although the DNA methylome profiles have been available in large cancer cohorts such as The Cancer Genome Atlas (TCGA), integrative analysis of the DNA methylome architectures in a pan-cancer manner remains limited. In the present study, we aimed to systematically dissect the insightful features related to the inter-tumoral DNA methylome heterogeneity in a pan-cancer context of 21 cancers in TCGA. First, pan-cancer clustering of the DNA methylomes revealed convergence of cancers and, meanwhile, new classifications of cancer subtypes, which are often associated to prognostic differences.

Oncogenic Properties of NEAT1 in Prostate Cancer Cells Depend on the CDC5L-AGRN Transcriptional Regulation Circuit.

The long noncoding RNA nuclear-enriched abundant transcript 1 (NEAT1) has been shown to regulate multiple cancer-related cellular activities including cell proliferation, apoptosis, and migration. In this study, we confirm that repression of NEAT1 induces DNA damage, disturbs the cell cycle, and arrests the proliferation of prostate cancer cells. By taking advantage of the prostate cancer tumor transcriptome profiles from The Cancer Genome Atlas, our data-mining pipeline identified a series of transcription factors (TF) whose regulatory activities on target genes depended on the level of NEAT1.

Dissipation-assisted spin squeezing of nitrogen-vacancy centers coupled to a rectangular hollow metallic waveguide.

Spin squeezing has received much attention due to the interesting physics and important applications such as quantum metrology and quantum information processing. We here present a scheme to engineer stable spin squeezing in an array of nitrogen vacancy centers (NVCs) coupled to a rectangular hollow metallic waveguide. The remarkable feature of the waveguide as the common environment media is that one can switch on/off either the waveguide induced dipole-dipole interactions or correlated spontaneous emissions among the NVCs by designing their spatial separation.

Controllable quantum dynamics of inhomogeneous nitrogen-vacancy center ensembles coupled to superconducting resonators.

We explore controllable quantum dynamics of a hybrid system, which consists of an array of mutually coupled superconducting resonators (SRs) with each containing a nitrogen-vacancy center spin ensemble (NVE) in the presence of inhomogeneous broadening. We focus on a three-site model, which compared with the two-site case, shows more complicated and richer dynamical behavior, and displays a series of damped oscillations under various experimental situations, reflecting the intricate balance and competition between the NVE-SR collective coupling and the adjacent-site photon hopping. Particularly, we find that the inhomogeneous broadening of the spin ensemble can suppress the population transfer between the SR and the local NVE.

The divergence and positive selection of the plant-specific BURP-containing protein family.

BURP domain-containing proteins belong to a plant-specific protein family and have diverse roles in plant development and stress responses. However, our understanding about the genetic divergence patterns and evolutionary rates of these proteins remain inadequate. In this study, 15 plant genomes were explored to elucidate the genetic origins, divergence, and functions of these proteins.

Entanglement dynamics for three nitrogen-vacancy centers coupled to a whispering-gallery-mode microcavity.

The solid-state qubits based on diamond nitrogen-vacancy centers (NVC) are promising for future quantum information processing. We investigate the dynamics of entanglement among three NVCs coupled to a microtoroidal cavity supporting two counter-propagating whispering-gallery-modes (WGMs) in the presence of Rayleigh scattering. Our results indicate that the maximal entanglement among all the NVCs could be achieved through adjusting several key parameters, such as the scattering-induced coupling between the WGMs, the distance between the NVCs, and the NVC-WGM coupling strengths, as well as the frequency detuning between the NVC and cavity.

One-step generation of multipartite entanglement among nitrogen-vacancy center ensembles.

We describe a one-step, deterministic and scalable scheme for creating macroscopic arbitrary entangled coherent states (ECSs) of separate nitrogen-vacancy center ensembles (NVEs) that couple to a superconducting flux qubit. We discuss how to generate the entangled states between the flux qubit and two NVEs by the resonant driving. Then the ECSs of the NVEs can be obtained by projecting the flux qubit, and the entanglement detection can be realized by transferring the quantum state from the NVEs to the flux qubit.

Unusual tandem expansion and positive selection in subgroups of the plant GRAS transcription factor superfamily.

Background: GRAS proteins belong to a plant transcription factor family that is involved with multifarious roles in plants. Although previous studies of this protein family have been reported for Arabidopsis, rice, Chinese cabbage and other species, investigation of expansion patterns and evolutionary rate on the basis of comparative genomics in different species remains inadequate.

Results: A total of 289 GRAS genes were identified in Arabidopsis, B.

Delineation of plant caleosin residues critical for functional divergence, positive selection and coevolution.

Background: The caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. These proteins may be involved in many cellular and biological processes coupled closely to the synthesis, degradation, or stability of oil bodies. Although previous studies of this protein family have been reported for Arabidopsis and other species, understanding of the evolution of the caleosin gene family in plants remains inadequate.

Soybean (Glycine max) expansin gene superfamily origins: segmental and tandem duplication events followed by divergent selection among subfamilies.

Background: Expansins are plant cell wall loosening proteins that are involved in cell enlargement and a variety of other developmental processes. The expansin superfamily contains four subfamilies; namely, α-expansin (EXPA), β-expansin (EXPB), expansin-like A (EXLA), and expansin-like B (EXLB). Although the genome sequencing of soybeans is complete, our knowledge about the pattern of expansion and evolutionary history of soybean expansin genes remains limited.