DualNetM: an adaptive dual network framework for inferring functional-oriented markers.

Background: Understanding how genes regulate each other in cells is crucial for determining cell identity and development, and single-cell sequencing technologies facilitate such research through gene regulatory networks (GRNs). However, identifying important marker genes within these complex networks remains difficult.

Results: Consequently, we present DualNetM, a deep generative model with a dual-network framework for inferring functional-oriented markers.

Biological interpretation of DNA/RNA modification by ALKBH proteins and their role in human cancer.

AlkB homolog (ALKBH) belongs to 2-oxoglutarate (2OG) and ferrous iron-dependent oxygenases, which can catalyze the demethylation of DNA/RNA and play an important role in human diseases represented by cancer. Although ALKBH has been extensively studied, the biological explanation for its specific recognition of DNA/RNA and its mechanism of action in cancer remains unclear. This review explores the molecular mechanism of ALKBH protein binding to DNA/RNA through structural fitting and ChIP-Seq analysis and summarizes the structural biology factors that lead to its specific substrate recognition.

Machine Learning-Based identification of resistance genes associated with sunflower broomrape.

Background: Sunflowers (Helianthus annuus L.), a vital oil crop, are facing a severe challenge from broomrape (Orobanche cumana), a parasitic plant that seriously jeopardizes the growth and development of sunflowers, limits global production and leads to substantial economic losses, which urges the development of resistant sunflower varieties.

Results: This study aims to identify resistance genes from a comprehensive transcriptomic profile of 103 sunflower varieties based on gene expression data and then constructs predictive models with the key resistant genes.

Deciphering Sequence Determinants of Zygotic Genome Activation Genes: Insights From Machine Learning and the ZGAExplorer Platform.

The mammalian life cycle initiates with the transition of genetic control from the maternal to the embryonic genome during zygotic genome activation (ZGA), which becomes pivotal for development. Nevertheless, understanding the conservation of genes and transcription factors (TFs) that underlie mammalian ZGA remains limited. Here, we compiled a comprehensive set of ZGA genes from mice, humans, pigs, bovines and goats, including Nr5a2 and TPRX1/2.

Multi-omics approaches for biomarker discovery and precision diagnosis of prediabetes.

Recent advancements in multi-omics technologies have provided unprecedented opportunities to identify biomarkers associated with prediabetes, offering novel insights into its diagnosis and management. This review synthesizes the latest findings on prediabetes from multiple omics domains, including genomics, epigenomics, transcriptomics, proteomics, metabolomics, microbiomics, and radiomics. We explore how these technologies elucidate the molecular and cellular mechanisms underlying prediabetes and analyze potential biomarkers with predictive value in disease progression.

[Role of Mitophagy Affecting Macrophage Polarization in Immunomodulationin Sepsis and Traditional Chinese Medicine Intervention:A Review].

Sepsis,a syndrome characterized by organ dysfunction caused by infection,exhibits high incidence and mortality.The pathogenesis of sepsis is complex and involves a cascade of immune reactions,with no specific drugs currently available.Sepsis is mainly treated with Western medical supportive therapies such as antibiotics,hemodynamic management,and mechanical ventilation.

Review and new insights into the catalytic structural domains of the Fe(ll) and 2-Oxoglutarate families.

Histone lysine demethylase (KDM), AlkB homolog (ALKBH), and Ten-Eleven Translocation (TET) proteins are members of the 2-Oxoglutarate (2OG) and ferrous iron-dependent oxygenases, each of which harbors a catalytic domain centered on a double-stranded β-helix whose topology restricts the regions directly involved in substrate binding. However, they have different catalytic functions, and the deeply structural biological reasons are not yet clear. In this review, the catalytic domain features of the three protein families are summarized from both sequence and structural perspectives.

Noncoding RNAs in atherosclerosis: regulation and therapeutic potential.

Atherosclerosis, a chronic disease of arteries, results in high mortality worldwide as the leading cause of cardiovascular disease. The development of clinically relevant atherosclerosis involves the dysfunction of endothelial cells and vascular smooth muscle cells. A large amount of evidence indicates that noncoding RNAs, such as microRNAs (miRNAs), long noncoding RNAs (lncRNAs), and circular RNAs (circRNAs), are involved in various physiological and pathological processes.

Roles of mitochondrial fusion and fission in breast cancer progression: a systematic review.

Background: Mitochondria play critical roles in cellular physiological activity as cellular organelles. Under extracellular stimulation, mitochondria undergo constant fusion and fission to meet different cellular demands. Mitochondrial dynamics, which are involved in mitochondrial fusion and fission, are regulated by specialized proteins and lipids, and their dysregulation causes human diseases, such as cancer.