A complete model of mouse embryogenesis through organogenesis enabled by chemically induced embryo founder cells.

Embryo models offer opportunities for understanding development and advancing medicine but rely on intricate procedures with limitations in efficiency and developmental fidelity. Here, we employ a small-molecule-only approach to induce mouse embryonic stem cells into 8- to 16-cell-like embryo founder cells, enabling the generation of a complete embryo model. These founder cells specify all blastocyst lineages, both embryonic and extraembryonic, in vivo and in vitro.

Protective Effects of Astaxanthin on Thioacetamide-Induced Hepatopancreatic Damage in : Insights from Biochemical, Histological, and Metabolomic Analyses.

The hepatopancreas of plays a crucial role in metabolism and immune response, encompassing vital physiological functions. In our study, we established a hepatopancreatic injury model using thioacetamide (TAA) and evaluated the therapeutic potential of a commercial astaxanthin-based product (AST-product) on hepatopancreatic health. The experimental framework included a control group (Con), an injury model group (M), and a treatment group (T), enabling a comprehensive analysis of the effects of treatments on hepatopancreatic biochemical markers, tissue architecture, gene expression, and metabolic pathways.

PRMT5 Maintains Homeostasis of the Intestinal Epithelium by Modulating Cell Proliferation and Survival.

Intestinal homeostasis is sustained by self-renewal of intestinal stem cells, which continuously divide and produce proliferative transit-amplifying (TA) and progenitor cells. Protein arginine methyltransferases 5 (PRMT5) plays a crucial role in regulating homeostasis of various mammalian tissues. However, its function in intestinal homeostasis remains elusive.

Kinetic Study on the H-Abstraction Reactions from 1-Nitropropane by H and OH Radicals.

To improve the comprehension of the combustion kinetics of 1-nitropropane (1-NP), the H-abstraction reactions from 1-NP by H and OH radicals are theoretically explored using the canonical variational transition-state theory combined with the multistructural torsional anharmonicity and small-curvature tunneling corrections (MS-CVT/SCT). The M08-HX/cc-pVTZ method is adopted for geometry optimizations and frequency calculations due to its effective performance in describing the current reaction systems with an average mean unsigned deviation of 0.95 kcal mol against the benchmark by the high-level DLPNO-CCSD(T)/CBS(T-Q) method.

Theoretical Investigation on Water-Free, Water- and Self-Assisted H-Abstraction Reactions from Dimethylamine by Hydroxy Radicals.

Accurate branching ratios of the H-abstraction reactions from dimethylamine (DMA) by OH radicals are important in understanding the atmospheric fate of DMA. In this work, the reaction kinetics of the water-free, water-assisted, and self-assisted H-abstraction reactions between DMA and OH radicals are accurately determined using the multipath canonical variational theory with the small-curvature tunneling correction, to explore the catalytic effects of the reactant (DMA) and product (water). To choose a suitable method that well describes the current reaction systems, various combinations with seven DFT methods and six basis sets are first evaluated, and the M08-HX/ma-TZVP method is identified as the most appropriate, with a mean unsigned deviation of 0.

CNV-FB: A Feature bagging strategy-based approach to detect copy number variants from NGS data.

Copy number variation (CNV), as a type of genomic structural variation, accounts for a large proportion of structural variation and is related to the pathogenesis and susceptibility to some human diseases, playing an important role in the development and change of human diseases. The development of next-generation sequencing technology (NGS) provides strong support for the design of CNV detection algorithms. Although a large number of methods have been developed to detect CNVs using NGS data, it is still considered a difficult problem to detect CNVs with low purity and coverage.

Spatial distribution and influencing factors analysis of national key rural tourism villages in the Yangtze River Delta region based on geographically weighted regression.

National key rural tourism villages (NKRTVs) can lead to the high-quality development of rural tourism, and their spatial distribution is influenced by a variety of factors. However, existing studies have neglected the fact that influencing factors can have different directions and effects in different geographic spaces. This study investigates 156 NKRTVs in the Yangtze River Delta region of China as the research object and employs ArcGIS spatial analysis technology to examine their spatial distribution characteristics.

Genetic Mapping and QTL Analysis of Fruit Traits in Melon ( L.).

Melon ( L.) is an important horticultural cash crop and its quality traits directly affect consumer choice and market price. These traits are controlled by genetic as well as environmental factors.

svBreak: A New Approach for the Detection of Structural Variant Breakpoints Based on Convolutional Neural Network.

Structural variation (SV) is an important type of genome variation and confers susceptibility to human cancer diseases. Systematic analysis of SVs has become a crucial step for the exploration of mechanisms and precision diagnosis of cancers. The central point is how to accurately detect SV breakpoints by using next-generation sequencing (NGS) data.

CIRCNV: Detection of CNVs Based on a Circular Profile of Read Depth from Sequencing Data.

Copy number variation (CNV) is a common type of structural variation in the human genome. Accurate detection of CNVs from tumor genomes can provide crucial information for the study of tumor genesis and cancer precision diagnosis. However, the contamination of normal genomes in tumor genomes and the crude profiles of the read depth make such a task difficult.

A comprehensive evaluation of the potential of semiterrestrial isopods, Ligia exotica, as a new animal food.

The semiterrestrial isopod, Ligia exotica represents one of the oldest documented species introductions of marine organisms and is known as an intermediate form between marine and strictly terrestrial isopods. In order to explore the potential value of Ligia as an animal food source, this study focused on the growth rate under laboratory rearing conditions and conducted a detailed analysis of the overall nutrient content of the species in comparison to two other marine food media (krill and fish meal). Evaluation of the growth rate of juveniles suggests it is a relatively fast-growing species of the Ligiidae family.

Detection of Pathogenic Microbe Composition Using Next-Generation Sequencing Data.

Next-generation sequencing (NGS) technologies have provided great opportunities to analyze pathogenic microbes with high-resolution data. The main goal is to accurately detect microbial composition and abundances in a sample. However, high similarity among sequences from different species and the existence of sequencing errors pose various challenges.

Requisite Chromatin Remodeling for Myeloid and Erythroid Lineage Differentiation from Erythromyeloid Progenitors.

The mammalian SWitch/Sucrose Non-Fermentable (SWI/SNF) chromatin-remodeling BAF (BRG1/BRM-associated factor) complex plays an essential role in developmental and pathological processes. We show that the deletion of Baf155, which encodes a subunit of the BAF complex, in the Tie2(+) lineage (Baf155 (CKO) leads to defects in yolk sac myeloid and definitive erythroid (EryD) lineage differentiation from erythromyeloid progenitors (EMPs). The chromatin of myeloid gene loci in Baf155 CKO EMPs is mostly inaccessible and enriched mainly by the ETS binding motif.

MFCNV: A New Method to Detect Copy Number Variations From Next-Generation Sequencing Data.

Copy number variation (CNV) is a very important phenomenon in tumor genomes and plays a significant role in tumor genesis. Accurate detection of CNVs has become a routine and necessary procedure for a deep investigation of tumor cells and diagnosis of tumor patients. Next-generation sequencing (NGS) technique has provided a wealth of data for the detection of CNVs at base-pair resolution.

Accurate Inference of Tumor Purity and Absolute Copy Numbers From High-Throughput Sequencing Data.

Inference of absolute copy numbers in tumor genomes is one of the key points in the study of tumor genesis. However, the mixture of tumor and normal cells poses a big challenge to this task. Accurate estimation of tumor purity (i.

STIC: Predicting Single Nucleotide Variants and Tumor Purity in Cancer Genome.

Single nucleotide variant (SNV) plays an important role in cellular proliferation and tumorigenesis in various types of human cancer. Next-generation sequencing (NGS) has provided high-throughput data at an unprecedented resolution to predict SNVs. Currently, there exist many computational methods for either germline or somatic SNV discovery from NGS data, but very few of them are versatile enough to adapt to any situations.

ERINS: Novel Sequence Insertion Detection by Constructing an Extended Reference.

Next generation sequencing technology has led to the development of methods for the detection of novel sequence insertions (nsINS). Multiple signatures from short reads are usually extracted to improve nsINS detection performance. However, characterization of nsINSs larger than the mean insert size is still challenging.

Single cell transcriptome dynamics from pluripotency to FLK1 mesoderm.

Hemangiogenic progenitors generating blood and endothelial cells are specified from FLK1-expressing (FLK1) mesoderm by the transcription factor ETV2. FLK1 mesoderm also contributes to smooth muscle and cardiomyocytes. However, the developmental process of FLK1 mesoderm generation and its allocation to various cell fates remain obscure.

A CRISPR screen identifies genes controlling Etv2 threshold expression in murine hemangiogenic fate commitment.

The ETS transcription factor Etv2 is necessary and sufficient for the generation of hematopoietic and endothelial cells. However, upstream regulators of Etv2 in hemangiogenesis, generation of hematopoietic and endothelial cells, have not been clearly addressed. Here we track the developmental route of hemangiogenic progenitors from mouse embryonic stem cells, perform genome-wide CRISPR screening, and transcriptome analysis of en route cell populations by utilizing Brachyury, Etv2, or Scl reporter embryonic stem cell lines to further understand the mechanisms that control hemangiogenesis.

ETS transcription factor ETV2/ER71/Etsrp in hematopoietic and vascular development, injury, and regeneration.

The major goal in regenerative medicine is to repair and restore injured, diseased or aged tissue function, thereby promoting general health. As such, the field of regenerative medicine has great translational potential in undertaking many of the health concerns and needs that we currently face. In particular, hematopoietic and vascular systems supply oxygen and nutrients and thus play critical roles in tissue development and tissue regeneration.

An increase in the incidence of hip fractures in Tangshan, China.

Unlabelled: We determined the number and incidence of hip fractures in Tangshan, China, in 2010. Compared with data we reported in Tangshan from 1994, the crude and age-specific incidence increased significantly for both sexes, especially in women. Strategies are needed for effective fracture prevention in the future.

The impact of R213 mutation on p53-mediated p21 activity.

p53 is a transcriptional regulator in the nucleus that functions as a tumor suppressor and its mutations are frequently found in human tumors. It has been reported that p53 with R213Q mutation is exist in certain tumor cell lines and its methylation on R213 as well. However, the mechanisms and consequences of these modifications on p53 function are not fully understood.

H3.3 actively marks enhancers and primes gene transcription via opening higher-ordered chromatin.

The histone variants H3.3 and H2A.Z have recently emerged as two of the most important features in transcriptional regulation, the molecular mechanism of which still remains poorly understood.

Differential effects of AdOx on gene expression in P19 embryonal carcinoma cells.

Background: Pluripotent cells maintain a unique gene expression pattern and specific chromatin signature. In this study, we explored the effect of the methyltransferase inhibitor adenosine dialdehyde (AdOx) on pluripotency maintenance and gene expression in P19 embryonal carcinoma cells.

Results: After AdOx treatment, the pluripotency-related gene network became disordered, and the early developmental genes were released from the repression.