Methylglyoxal-Stimulated Mesothelial Cells Prompted Fibroblast-to-Proto-Myofibroblast Transition.

During long-term peritoneal dialysis, peritoneal fibrosis (PF) often happens and results in ultrafiltration failure, which directly leads to the termination of dialysis. The accumulation of extracellular matrix produced from an increasing number of myofibroblasts was a hallmark characteristic of PF. To date, glucose degradation products (GDPs, i.

Genome-Wide Identification and Expression Profile of () Gene Family in L.

The biosynthesis of isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), which are essential for sesquiterpenes and triterpenes, respectively, is primarily governed by the mevalonate pathway, wherein () plays a pivotal role. This study identified eight members of the FPS gene family in , designated -, through bioinformatics analysis, revealing their distribution across several chromosomes and a notable tandem gene cluster. The genes exhibited strong hydrophilic properties and key functional motifs crucial for enzyme activity.

Glycosylation Pathways Targeted by Deregulated miRNAs in Autism Spectrum Disorder.

Autism Spectrum Disorder (ASD) is a complex condition with a multifactorial aetiology including both genetic and epigenetic factors. MicroRNAs (miRNAs) play a role in ASD and may influence metabolic pathways. Glycosylation (the glycoconjugate synthesis pathway) is a necessary process for the optimal development of the central nervous system (CNS).

Cytosine Methylation Changes the Preferred Cis-Regulatory Configuration of Arabidopsis WUSCHEL-Related Homeobox 14.

The Arabidopsis transcription factor WUSCHEL-related homeobox 14 (AtWOX14) plays versatile roles in plant growth and development. However, its biochemical specificity of DNA binding, its genome-wide regulatory targets, and how these are affected by DNA methylation remain uncharacterized. To clarify the biochemistry underlying the regulatory function of AtWOX14, using the recently developed 5mC-incorporation strategy, this study performed SELEX and DAP-seq for AtWOX14 both in the presence and absence of cytosine methylation, systematically curated 65 motif models and identified 51,039 genomic binding sites for AtWOX14, and examined how 5mC affects DNA binding of AtWOX14 through bioinformatic analyses.

Genome-Wide Identification of - () Gene Family and the Potential Function of Under Salt Stress in .

is an important medicinal herb known as a "natural antibiotic", which has been used in Southeast Asia for thousands of years. The () gene is an important regulatory factor for plant photoperiod flowering and stress response. However, there is currently no detailed research on the genes of .

Mechanism of Functional Compound Fruit Drinks in Regulating Serum Metabolism in Constipated Mice.

A compound fruit drink (CFD) is a functional beverage containing fruits, Chinese herbal medicine, and prebiotic fructose. Previous studies have shown the effect of a CFD on alleviating constipation and its impact on gut microbiota. However, a comprehensive analysis has not been reported in regard to the serum metabolism of CFDs.

Predaceous and Phytophagous Pentatomidae Insects Exhibit Contrasting Susceptibilities to Imidacloprid.

Imidacloprid, a widely used neonicotinoid insecticide, targets insect pests but also affects natural enemies. However, the effects of neonicotinoid insecticides on closely related insects remain unclear. We evaluated the harmful effects of imidacloprid on the phytophagous and predaceous .

Clinical and Genomic Features of Androgen Indifferent Prostate Cancer.

Androgen-indifferent prostate cancer (AIPC) is increasingly common and particularly lethal. Data describing these tumors are sparse, and AIPC remains a poorly understood malignancy. Utilizing the Oncology Research Information Exchange Network (ORIEN) database, we enriched for tumors with features of AIPC using previously described characteristics.

Establishing a General Atomistic Model for the Stratum Corneum Lipid Matrix Based on Experimental Data for Skin Permeation Studies.

Understanding the permeation of drugs through the intercellular lipid matrix of the stratum corneum layer of skin is crucial for effective transdermal delivery. Molecular dynamics simulations can provide molecular insights into the permeation process. In this study, we developed a new atomistic model representing the multilamellar arrangement of lipids in the stratum corneum intercellular space for permeation studies.

Utility of Protein Markers in COVID-19 Patients.

COVID-19 has been a challenge at the healthcare level not only in the early stages of the pandemic, but also in the subsequent appearance of long-term COVID-19. Several investigations have attempted to identify proteomic biomarkers in an attempt to improve clinical care, guide treatment and predict possible patient outcomes. Proteins such as C-reactive protein (CRP) or interleukin 6 (IL-6) are clear markers of severe disease, but many others have been proposed that could help in risk stratification and in the prediction of specific complications.

Don't Be Surprised When These Surprise You: Some Infrequently Studied Sphingoid Bases, Metabolites, and Factors That Should Be Kept in Mind During Sphingolipidomic Studies.

Sphingolipidomic mass spectrometry has provided valuable information-and surprises-about sphingolipid structures, metabolism, and functions in normal biological processes and disease. Nonetheless, many noteworthy compounds are not routinely determined, such as the following: most of the sphingoid bases that mammals biosynthesize de novo other than sphingosine (and sometimes sphinganine) or acquire from exogenous sources; infrequently considered metabolites of sphingoid bases, such as N-(methyl)-derivatives; "ceramides" other than the most common N-acylsphingosines; and complex sphingolipids other than sphingomyelins and simple glycosphingolipids, including glucosyl- and galactosylceramides, which are usually reported as "monohexosylceramides". These and other subspecies are discussed, as well as some of the circumstances when they are likely to be seen (or present and missed) due to experimental conditions that can influence sphingolipid metabolism, uptake from the diet or from the microbiome, or as artifacts produced during extraction and analysis.

Integrated Genetic Diversity and Multi-Omics Analysis of Colour Formation in Safflower.

Safflower ( L.) is a medicinal and edible cash crop that is widely cultivated worldwide. However, the genetic diversity of safflower germplasm resources and the reasons for the variations in safflower flower colour remain unclear.

Deciphering the Proteome and Phosphoproteome of Peanut ( L.) Pegs Penetrating into the Soil.

Peanut ( L.) is one of the most important crops for oil and protein production. The unique characteristic of peanut is geocarpy, which means that it blooms aerially and the peanut gynophores (pegs) penetrate into the soil, driving the fruit underground.

Identification of Immune Infiltration-Associated CC Motif Chemokine Ligands as Biomarkers and Targets for Colorectal Cancer Prevention and Immunotherapy.

Colorectal cancer (CRC) is the third most common cancer globally, with limited effective biomarkers and sensitive therapeutic targets. An increasing number of studies have highlighted the critical role of tumor microenvironment (TME) imbalances, particularly immune escape due to impaired chemokine-mediated trafficking, in tumorigenesis and progression. Notably, CC chemokines (CCLs) have been shown to either promote or inhibit angiogenesis, metastasis, and immune responses in tumors, thereby influencing cancer development and patient outcomes.

Enrichment of RedoxifibromiR miR-21-5p in Plasma Exosomes of Hypertensive Patients with Renal Injury.

Several microRNAs (miRNAs) emerged as powerful regulators of fibrotic processes, "fibromiRs", and can also influence the expression of genes responsible for the generation of reactive oxygen species, "redoximiRs". We aimed to investigate whether plasma exosomes from hypertensive and diabetes patients are enriched in fibromiRs and redoximiRs using deep sequencing technology and their association with relevant signalling pathways implicated in oxidative stress and fibrogenesis by GO terms and KEGG pathways. RNA-Seq analysis from P-EXO identified 31 differentially expressed (DE) miRNAs in patients compared to controls, of which 77% are biofluid specific.

Harnessing Molecular Insights for Translational Impact: Highlights from the Special Issue Titled "New Insights in Translational Bioinformatics".

The field of translational bioinformatics is rapidly evolving, driving the convergence of molecular sciences and computational methods with their applications in industrial and clinical practice [...

Ecometabolomics of Loggerhead Sea Turtles (): The Impact of Age on Metabolomic Profiles.

To investigate the impact of age on the metabolomic profile of loggerhead sea turtles (), this study analyzed 100 plasma samples of individuals across two age groups-50 post-hatchlings and 50 juveniles-from various locations along the Mediterranean coastline. Both targeted and untargeted metabolomic analyses were performed on the samples. Our results demonstrated a significant age-related effect on the metabolomic profiles in both analyses.

Pharmacodynamic Mechanisms of Cicadae Periostracum in Parkinson's Disease: A Metabolomics-Based Study.

Cicadae Periostracum (CP) is a traditional Chinese animal-derived medicine with the potential to treat Parkinson's disease (PD). This study aims to explore the pharmacodynamic mechanisms of CP against PD-based on metabolomics technology and provide a theoretical basis for developing new anti-PD medicine. First, MPP-induced SH-SY5Y cells were used to evaluate the anti-PD activity of CP.

Proteomic Profiling of Extracellular Vesicles in Inflammatory Bowel Diseases.

The proteomic analysis of serum extracellular vesicles (EVs) could be a useful tool for studying the pathophysiology of Crohn's disease (CD) and ulcerative colitis (UC), as well as for biomarker discovery. To characterize the proteomic composition of serum EVs in patients with CD and UC to identify biomarkers and molecular pathways associated with pathogenesis and activity. Methods: Serum EVs were enriched and analyzed in patients with quiescent CD, active CD (aCD), quiescent UC, active UC (aUC), and healthy controls (HCs) (n = 30 per group).

Integration of ATAC-Seq and RNA-Seq Reveals the Role of in Red Light-Induced Fruit Ripening in Strawberry.

Light is an important environmental factor affecting the ripening and quality of strawberry fruit. Previous studies have shown that red light treatment can promote strawberry ripening. Gene expression is closely associated with chromatin openness, and changes in chromatin accessibility are crucial for the binding of transcription factors to downstream regulatory sequences.

Lessons from Deep Learning Structural Prediction of Multistate Multidomain Proteins-The Case Study of Coiled-Coil NOD-like Receptors.

We test here the prediction capabilities of the new generation of deep learning predictors in the more challenging situation of multistate multidomain proteins by using as a case study a coiled-coil family of Nucleotide-binding Oligomerization Domain-like (NOD-like) receptors from and a few extra examples for reference. Results reveal a truly remarkable ability of these platforms to correctly predict the 3D structure of modules that fold in well-established topologies. A lower performance is noticed in modeling morphing regions of these proteins, such as the coiled coils.

Cyclophilin A Regulates Tripartite Motif 5 Alpha Restriction of HIV-1.

The peptidyl-prolyl isomerase A (PPIA), also known as cyclophilin A (CYPA), is involved in multiple steps of the HIV-1 replication cycle. CYPA regulates the restriction of many host factors by interacting with the CYPA-binding loop on the HIV-1 capsid (CA) surface. TRIM5 (tripartite motif protein 5) in primates is a key species-specific restriction factor defining the HIV-1 pandemic.

A Comparative Transcriptome and Proteome Analysis of the Molecular Mechanism Underlying Anterior to Dorsal Eye Rotation in the Celestial-Eye Goldfish ().

Goldfish (), subjected to millennia of artificial selection and breeding, have diversified into numerous ornamental varieties, such as the celestial-eye (CE) goldfish, noted for its unique dorsal eye rotation. Previous studies have primarily focused on anatomical modifications in CE goldfish eyes, yet the molecular underpinnings of their distinctive eye orientation remain poorly understood. This study employed high-throughput transcriptome and proteome sequencing on 110-day-old full-sibling CE goldfish, which displayed either anterior or upward eye rotations.

Responsivity of Two Pea Genotypes to the Symbiosis with Rhizobia and Arbuscular Mycorrhiza Fungi-A Proteomics Aspect of the "Efficiency of Interactions with Beneficial Soil Microorganisms" Trait.

It is well known that individual pea ( L.) cultivars differ in their symbiotic responsivity. This trait is typically manifested with an increase in seed weights, due to inoculation with rhizobial bacteria and arbuscular mycorrhizal fungi.

Dysregulation of FURIN and Other Proprotein Convertase Genes in the Progression from HPV Infection to Cancer.

Productive infections of oncogenic human papillomaviruses (HPVs) are closely linked to the differentiation of host epithelial cells, a process that the virus manipulates to create conditions favorable to produce virion progeny. This viral interference involves altering the expression of numerous host genes. Among these, proprotein convertases (PCs) have emerged as potential oncogenes due to their central role in cellular functions.