A novel interpretable deep learning-based computational framework designed synthetic enhancers with broad cross-species activity.

Enhancers play a critical role in dynamically regulating spatial-temporal gene expression and establishing cell identity, underscoring the significance of designing them with specific properties for applications in biosynthetic engineering and gene therapy. Despite numerous high-throughput methods facilitating genome-wide enhancer identification, deciphering the sequence determinants of their activity remains challenging. Here, we present the DREAM (DNA cis-Regulatory Elements with controllable Activity design platforM) framework, a novel deep learning-based approach for synthetic enhancer design.

Chemoproteomics of Marine Natural Product Naamidine J Unveils CSE1L as a Therapeutic Target in Acute Lung Injury.

Acute lung injury is a devastating illness characterized by severe inflammation mediated by aberrant activation of macrophages, resulting in significant morbidity and mortality, highlighting the urgent need for novel pharmacological targets and drug candidates. In this study, we identified a novel target for regulating inflammation in macrophages and acute lung injury via chemical proteomics and genetics based on a marine alkaloid, naamidine J (NJ). The structures of NJ-related naamidine alkaloids were first confirmed or revised by a combination of quantum chemical calculations and X-ray diffraction analysis.

The Mitogenomic Landscape of Hexacorallia Corals: Insight into Their Slow Evolution.

The utility of the mitochondrial genomes (mitogenomes) in analyzing the evolutionary history of animals has been proven. Five deep-sea corals ( sp.1, sp.

CRISPR/dCas9-Mediated DNA Methylation Editing on in Chinese Tongue Sole () Testis Cells.

DNA methylation is a key epigenetic mechanism orchestrating gene expression networks in many biological processes. Nonetheless, studying the role of specific gene methylation events in fish faces challenges. In this study, we validate the regulation of DNA methylation on empty spiracles homeobox 2 () expression with decitabine treatment in Chinese tongue sole testis cells.

The Role of Z Chromosome Localization Gene in Spermatogenesis of .

Proteasome 26S Subunit, Non-ATPase 9 () plays an important role in the balance of protamine and the stability of the nucleolar structure during spermatogenesis. In this study, we cloned the of and analyzed its expression pattern. was identified on the Z chromosome of , which is considered an interesting candidate gene for spermatogenesis.

Molecular and Physiological Effects of 17α-methyltestosterone on Sex Differentiation of Black Rockfish, .

It is widely known that all-female fish production holds economic value for aquaculture. , a preeminent economic species, exhibits a sex dimorphism, with females surpassing males in growth. In this regard, achieving all-female black rockfish production could significantly enhance breeding profitability.

Unveiling Gene Expression Dynamics during Early Embryogenesis in : A Transcriptomic Perspective.

Commencing with sperm-egg fusion, the early stages of metazoan development include the cleavage and formation of blastula and gastrula. These early embryonic events play a crucial role in ontogeny and are accompanied by a dramatic remodeling of the gene network, particularly encompassing the maternal-to-zygotic transition. Nonetheless, the gene expression dynamics governing early embryogenesis remain unclear in most metazoan lineages.

Examining the Impact of Phased Nursing within the Chronic Disease Trajectory Model on Glioma Patient Outcomes.

Background: Glioma ‎(GL)‎, a primary brain tumor, presents significant challenges in patient care due to its complex disease trajectory and psychological impact. Phased nursing interventions, grounded in the Chronic Illness Trajectory Model (CITM), offer a holistic approach to addressing these multifaceted needs.

Objective: The objective of this study was to assess the impact of phased nursing within the CITM on the psychological well-being, quality of life, and cancer-related fatigue (CRF) of glioma patients.

Telomere-to-telomere gapless genome assembly of the Chinese sea bass (Lateolabrax maculatus).

Chinese sea bass (Lateolabrax maculatus) is a highly sought-after commercial seafood species in Asian regions due to its excellent nutritional value. With the rapid advancement of bioinformatics, higher standards for genome analysis compared to previously published reference genomes are now necessary. This study presents a gapless assembly of the Chinese sea bass genome, which has a length of 632.

Single-cell transcriptome landscape of zebrafish liver reveals hepatocytes and immune cell interactions in understanding nonalcoholic fatty liver disease.

Nonalcoholic fatty liver disease (NAFLD) is becoming the most common chronic liver disease in the world. Immunity is the major contributing factor in NAFLD; however, the interaction of immune cells and hepatocytes in disease progression has not been fully elucidated. As a popular species for studying NAFLD, zebrafish, whose liver is a complex immune system mediated by immune cells and non-immune cells in maintaining immune tolerance and homeostasis.

Molecular functional characterization of the setdb1 and its potential target gene sox5 illuminate the histone modification-mediated orchestration of gonadal development in Chinese tongue sole (Cynoglossus semilaevis).

SET (SuVar3-9, Enhancer of Zeste, Trithorax) domain bifurcated histone lysine methyltransferase 1, setdb1, is the predominant histone lysine methyltransferase catalyzing H3K9me3. Prior studies have illustrated that setdb1 and H3K9me3 critically regulate sex differentiation and gametogenesis. However, the molecular details by which setdb1 is involved in these processes in fish have been poorly reported.

Molecular phylogenetic relationships based on mitochondrial genomes of novel deep-sea corals (Octocorallia: Alcyonacea): Insights into slow evolution and adaptation to extreme deep-sea environments.

A total of 10 specimens of Alcyonacea corals were collected at depths ranging from 905 m to 1 633 m by the manned submersible Shenhai Yongshi during two cruises in the South China Sea (SCS). Based on mitochondrial genomic characteristics, morphological examination, and sclerite scanning electron microscopy, the samples were categorized into four suborders (Calcaxonia, Holaxonia, Scleraxonia, and Stolonifera), and identified as 9 possible new cold-water coral species. Assessments of GC-skew dissimilarity, phylogenetic distance, and average nucleotide identity (ANI) revealed a slow evolutionary rate for the octocoral mitochondrial sequences.

Transcriptome Analysis Revealed the Early Heat Stress Response in the Brain of Chinese Tongue Sole ().

As a common influencing factor in the environment, temperature greatly influences the fish that live in the water all their life. The essential economic fish Chinese tongue sole (), a benthic fish, will experience both physiological and behavioral changes due to increases in temperature. The brain, as the central hub of fish and a crucial regulatory organ, is particularly sensitive to temperature changes and will be affected.

Combined ATAC-seq, RNA-seq, and GWAS analysis reveals glycogen metabolism regulatory network in Jinjiang oyster ( ).

Glycogen serves as the principal energy reserve for metabolic processes in aquatic shellfish and substantially contributes to the flavor and quality of oysters. The Jinjiang oyster ( ) is an economically and ecologically important species in China. In the present study, RNA sequencing (RNA-seq) and assay for transposase-accessible chromatin using sequencing (ATAC-seq) were performed to investigate gene expression and chromatin accessibility variations in oysters with different glycogen contents.

The First High-Quality Chromosome-Level Genome of the Lutjanus erythropterus (Bloch, 1790) Using Single-Tube Long Fragment Reads and Hi-C Technologies.

Lutjanus erythropterus (Bloch, 1790), a Perciformes from the Lutjanidae family, is a commercially important species because of its taste and abundance. Despite the increase in genome resources in recent years, few genome assemblies are available within this fish family for comparative and functional studies. In this study, we determined the chromosomal genome of Crimson snapper using high-throughput Single-Tube Long Fragment Reads sequencing technology and Hi-C data.

Establishment and Characterization of a Spermatogonial Stem Cell Line from Tiger Puffer Fish ().

Tiger puffer fish () has become the main fish species cultured in China since the last century because of its high economic value. Male and female tiger puffer fish need 2 and 3 years each to reach sexual maturity, which limits the development of breeding research for this species. In recent years, in vitro culture of fish spermatogonial stem cells (SSCs) have shown potential in aquaculture.

Exosome delivery to the testes for dmrt1 suppression: A powerful tool for sex-determining gene studies.

Exosomes are endosome-derived extracellular vesicles about 100 nm in diameter. They are emerging as promising delivery platforms due to their advantages in biocompatibility and engineerability. However, research into and applications for engineered exosomes are still limited to a few areas of medicine in mammals.

The chromosome-level genome of Cherax quadricarinatus.

Red claw crayfish (Cherax quadricarinatus) is an aquatic crustacean with considerable potential for the commercial culture and an ideal model for studying the mechanism of sex determination. To provide better genomic resources, we assembled a chromosome-level genome with a size of 5.26 Gb and contig N50 of 144.

Evolution of the germline mutation rate across vertebrates.

The germline mutation rate determines the pace of genome evolution and is an evolving parameter itself. However, little is known about what determines its evolution, as most studies of mutation rates have focused on single species with different methodologies. Here we quantify germline mutation rates across vertebrates by sequencing and comparing the high-coverage genomes of 151 parent-offspring trios from 68 species of mammals, fishes, birds and reptiles.