G2PDeep-v2: a web-based deep-learning framework for phenotype prediction and biomarker discovery for all organisms using multi-omics data.

The G2PDeep-v2 server is a web-based platform powered by deep learning, for phenotype prediction and markers discovery from multi-omics data in any organisms including humans, plants, animals, and viruses. The server provides multiple services for researchers to create deep-learning models through an interactive interface and train these models using an automated hyperparameter tuning algorithm on high-performance computing resources. Users can visualize the results of phenotype and markers predictions and perform Gene Set Enrichment Analysis for the significant markers to provide insights into the molecular mechanisms underlying complex diseases, conditions and other biological phenotypes being studied.

Molecular dynamics of chemotactic signalling orchestrates dental pulp stem cell fibrosis during aging.

Aging often triggers dental pulp fibrosis, resulting in clinical repercussions such as increased susceptibility to dental infections, compromised tooth vitality, and reduced responsiveness to dental interventions. Despite its prevalence, the precise molecular mechanisms underlying this condition remains unclear. Leveraging single-cell transcriptome analysis from both our own and publicly available datasets, we identified Ccrl2 macrophages as particularly vulnerable during the early stages of aging.

From isolation to detection, advancing insights into endothelial matrix-bound vesicles.

Matrix-bound vesicles (MBVs), an integral part of the extracellular matrix (ECM), are emerging as pivotal factors in ECM-driven molecular signaling. This study is the first to report the isolation of MBVs from porcine arterial endothelial cell basement membranes (A-MBVs) and thyroid cartilage (C-MBVs), the latter serving as a negative control due to its minimal vascular characteristics. Using Transmission Electron Microscopy (TEM), Nano-Tracking Analysis (NTA), Electrochemical Impedance Spectroscopy (EIS), and Atomic Force Microscopy (AFM), we orthogonally characterized the isolated MBVs.

Global research hotspots and trends in oxidative stress-related diabetic nephropathy: a bibliometric study.

Background: Oxidative stress is widely acknowledged as a key pathogenic mechanism in diabetic nephropathy (DN). In recent years, the role of oxidative stress in DN has garnered increasing attention. However, no bibliometric analysis has yet been conducted on the relationship between oxidative stress and DN.

Computationally Assisted Noncanonical Amino Acid Incorporation.

Genetic encoding of noncanonical amino acids (ncAAs) with desired functionalities is an invaluable tool for the study of biological processes and the development of therapeutic drugs. However, existing ncAA incorporation strategies are rather time-consuming and have relatively low success rates. Here, we develop a virtual ncAA screener based on the analysis and modeling of the chemical properties of all reported ncAA substrates to virtually determine the recognition potential of candidate ncAAs.

When Photoelectrons Meet Gas Molecules: Determining the Role of Inelastic Scattering in Ambient Pressure X-ray Photoelectron Spectroscopy.

Inelastic photoelectron scattering (IPES) by gas molecules, a critical phenomenon observed in ambient pressure X-ray photoelectron spectroscopy (APXPS), complicates spectral interpretation due to kinetic energy loss in the primary spectrum and the appearance of additional features at higher binding energies. In this study, we systematically investigate IPES in various gas environments using APXPS, providing detailed insights into interactions between photoelectrons emitted from solid surfaces and surrounding gas molecules. Core-level XPS spectra of Au, Ag, Zn, and Cu metals were recorded over a wide kinetic energy range in the presence of CO, N, Ar, and H gases, demonstrating the universal nature of IPES across different systems.

Machine learning and metagenomics identifies uncharacterized taxa inferred to drive biogeochemical cycles in a subtropical hypereutrophic estuary.

Anthropogenic influences have drastically increased nutrient concentrations in many estuaries globally, and microbial communities have adapted to the resulting hypereutrophic ecosystems. However, our knowledge of the dominant microbial taxa and their potential functions in these ecosystems has remained sparse. Here, we study prokaryotic community dynamics in a temporal-spatial dataset, from a subtropical hypereutrophic estuary.

Anticarcinogenic cationic peptides derived from tryptic hydrolysis of β-lactoglobulin.

Introduction: This study investigated the tryptic hydrolysis of β-lactoglobulin (BLG) for 30, 60, 90, and 120 min at 1/200 E/S (enzyme/substrate ratio, w/w) to prepare potentially anticarcinogenic peptides.

Methods: The properties of hydrolysates were characterized, including degree of hydrolysis, free amino acids, SDS-PAGE, FTIR, and antioxidant activity employing DPPH-assay, β-carotene/linoleic acid, and FRAP assay.

Results: BLG tryptic hydrolysate produced after 60 min hydrolysis recorded the highest antioxidant activity, and LCMS analysis revealed 162 peptides of molecular masses ranging from 800 to 5671Da, most of them are of hydrophobic nature.

Low Molecular Weight Biobased Aromatics from Pyrolysis Liquids Using Zeolites: Yield Improvements by Using Pyrolysis Oil Fractions.

Pyrolysis liquids from lignocellulosic biomass have the potential to be used as a feed for aromatics such as benzene, toluene, and xylenes (BTX) using catalytic upgrading with zeolites. We here report an experimental study on the conversion of various pyrolysis oil fractions to determine the most suitable one for BTX synthesis. For this purpose, the pyrolysis liquid was fractionated using several extraction/distillation steps to give four fractions with different chemical compositions.

Novel D-Ribofuranosyl Tetrazoles: Synthesis, Characterization, In Vitro Antimicrobial Activity, and Computational Studies.

The goal of this study was to synthesize and evaluate new antimicrobial compounds. We specifically focused on the development of 2,5-disubstituted tetrazole derivatives containing the O-methyl-2,3-O-isopropylidene-(D)-ribofuranoside groups through N-alkylation reactions. The synthesized compounds were characterized using H and C nuclear magnetic resonance (NMR) spectroscopy.

Identifying Natural Products as Feline Coronavirus M Inhibitors by Structural-Based Virtual Screening and Enzyme-Based Assays.

The main protease (M) is a pivotal target in the life cycle of feline coronavirus (FCoV), which causes a high mortality feline disease, feline infectious peritonitis (FIP). Virtual screening was performed against the feline coronavirus M to find active compounds with low toxicity from a library of natural products. Eighty-six compounds were selected by using the rank of docking score and binding pose analysis.

Chiral Recognition of Butylone by Methylated β-Cyclodextrin Inclusion Complexes: Molecular Calculations and Two-Level Factorial Designs.

The integration of molecular docking and AM1 calculations has elucidated the complexation behavior of butylone enantiomers with methylated β-cyclodextrin derivatives. Our study reveals that butylone can adopt two distinct conformations within the β-cyclodextrin cavity, with one conformation being preferentially stabilized due to its favorable binding energy. This conformation preference is influenced by the methylation at the O2, O3, and O6 positions of β-cyclodextrin, which significantly affects complex stability and solvation properties.

Protective effects of resveratrol on the expression of , and genes in the ovary and their activity in the serum of rats exposed to lead acetate: An experimental study.

Background: Lead (Pb) could be toxic to the female reproductive system, and resveratrol (Res) may overcome this toxicity.

Objective: To investigate the Res impact on the catalase (), glutathione peroxidase (), and superoxide dismutase () gene expression in the ovary and on the Cat and Gpx enzyme activity in the serum of rats exposed to lead acetate.

Materials And Methods: In this experimental study, 33 female Wistar rats (8-10 wk, 180-200 gr) were divided into 6 groups: a control group (normal saline), a Res group (40 mg/kg), and a Pb group (lead acetate 30 mg/kg).

Evolutionary patterns of the SSU rRNA (V4 region) secondary structure in genus (Ciliophora, Spirotrichea): insights into cryptic species and primitive traits.

The genus , a group of ciliated protists, has attracted attention as a model organism due to its widespread distribution and ease of cultivation. This study examines the evolutionary patterns of the SSU rRNA secondary structure within this genus, aiming to elucidate its role in supporting evolutionary relationships and uncovering cryptic species. By predicting the secondary structure of SSU rRNA and applying the CBC (Compensatory Base Change) concept analysis, we examined 69 species of the genus , with 57 SSU rRNA gene sequences retrieved from GenBank and 12 newly sequenced specimens from South Korea.

SSR marker-based genetic diversity and structure analyses of var. from different populations.

Background: var. is a variety in the section of the genus of the family Theaceae which is native to Fangchenggang, Guangxi, China. To date, the genetic diversity and structure of this variety remains to be understood.

Molecular characterization and genome sequencing of selected highly resistant clinical isolates of and its association with the clustered regularly interspaced palindromic repeat/Cas system.

The presence of the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system in the superbug presents a unique opportunity to precisely target and edit bacterial genomes to modify their drug resistance. The objective was to detect the prevalence of CRISPR in extensively and pan-drug-resistant and to determine the utility of whole-genome sequencing (WGS) for the analysis of the entire genome for such strains. The antimicrobial susceptibilities of one hundred isolates were assessed using the antibiotic susceptibility test (AST) card of the VITEK system.

Elucidating genetic intersections: Co-differentially expressed genes in myasthenia gravis and idiopathic inflammatory myopathies and their role in comorbid pathogenesis.

Background: Myasthenia gravis (MG) and idiopathic inflammatory myopathies (IIM) are autoimmune disorders that can co-occur, complicating diagnosis and treatment. The molecular mechanisms underlying this comorbidity are not well understood.

Objective: This study aims to identify common differentially expressed genes (co-DEGs) between MG and IIM to elucidate shared pathogenic pathways and potential therapeutic targets.

Comprehensive analysis reveals cholesterol metabolism-related signature for predicting prognosis and guiding individualized treatment of glioma.

Objective: Gliomas are the most common intracranial tumors with the highest degree of malignancy. Disturbed cholesterol metabolism is one of the key features of many malignant tumors, including gliomas. This study aimed to investigate the significance of cholesterol metabolism-related genes in prognostic prediction and in guiding individualized treatment of patients with gliomas.

PPARG/SPP1/CD44 signaling pathway in alveolar macrophages: Mechanisms of lipid dysregulation and therapeutic targets in idiopathic pulmonary fibrosis.

Idiopathic pulmonary fibrosis (IPF) is a chronic and progressive interstitial lung disease. It is characterized by inflammation and fibrosis in the lung parenchyma and interstitium. Given its poor prognosis and limited treatment options, understanding the underlying molecular mechanisms is crucial.

Gastroprotective properties of flavonoid-rich extract of against ethanol-induced gastric ulcer in mice.

has been traditionally used in northeastern Algeria for treating gastrointestinal disorders, particularly ulcers. This study aimed to assess the gastroprotective, anti-inflammatory, and antioxidant properties of a crude hydroalcoholic extract derived from the leaves of , as well as its subsequent fractions. The gastroprotective effect was studied in an ethanol-induced ulcer model in mice.

ALKBH5 alleviates lower extremity arteriosclerosis by regulating ITGB1 demethylation and influencing macrophage polarization.

Objective: M6A methylation-regulated macrophages play an important role in the occurrence and development of arteriosclerosis. However, their role in lower extremity arteriosclerosis remains unclear. Therefore, this study aims to explore the key factors that regulate arteriosclerosis methylation in the lower extremities and the mechanism by which they affect arteriosclerosis by influencing macrophage polarization.

Computational network analysis of two popular skin cancers provides insights into the molecular mechanisms and reveals common therapeutic targets.

Basal Cell Carcinoma (BCC) and Actinic Keratosis (AK) are prevalent skin conditions with significant health complications. The molecular mechanisms underlying these conditions and their potential shared pathways remain ambiguous despite their prevalence. Therefore, this study aims to elucidate the common molecular pathways and potential therapeutic targets for BCC and AK through comprehensive computational network analysis.

Molecular docking and molecular dynamics simulation studies of inhibitor candidates against 3-hydroxykynurenine transaminase and implications on vector control.

Isoxazole and oxadiazole derivatives inhibiting 3-hydroxykynurenine transaminase (3HKT) are potential larvicidal candidates. This study aims to identify more suited potential inhibitors of 3HKT (3HKT) through molecular docking and molecular dynamics simulation. A total of 958 compounds were docked against 3HKT (PDB ID: 2CH2) using Autodock vina and Autodock4.

Molecular and cellular regulators of embryo implantation and their application in improving the implantation potential of IVF-derived blastocysts.

Background: In vitro fertilization (IVF) and embryo transfer (ET) are widely used in reproductive biology. Despite the transfer of high-quality blastocysts, the implantation rate of IVF-derived blastocysts remains low after ET.

Methods: This article provides a comprehensive review of current research on embryo implantation regulators and their application to improve the implantation potential of IVF-derived blastocysts.

Transcriptomic and metabolomic analysis reveals the molecular mechanism of exogenous melatonin improves salt tolerance in eggplants.

Introduction: Melatonin significantly enhances the tolerance of plants to biotic and abiotic stress, and plays an important role in plant resistance to salt stress. However, its role and molecular mechanisms in eggplant salt stress resistance have been rarely reported. In previous studies, we experimentally demonstrated that melatonin can enhance the salt stress resistance of eggplants.