LC-MS-Based Direct Quantification of MicroRNAs in Rat Blood.

MicroRNA (miRNA) has recently garnered significant research attention, owing to its potential as a diagnostic biomarker and therapeutic target. Liquid chromatography-mass spectrometry (LC-MS) offers accurate quantification, multiplexing capacity, and high compatibility with various matrices. These advantages establish it as a preferred technique for detecting miRNA in biological samples.

SUMO-specific protease 2 regulates lipid droplet size through ERRα-mediated CIDEA expression in adipocytes.

Lipid droplets are not only lipid storage sites but also are closely related to lipid metabolism. Lipid droplet growth increases lipid storage capacity and suppresses lipolysis via lipase associated with the lipid droplet surface. The cell death-inducing DFF45-like effector (CIDE) family of proteins mediates lipid droplet fusion, which mainly contributes to lipid droplet growth.

The dehiscence process in seeds and the stigmasterol biosynthesis pathway in terms of metabolomics.

Background: Ginseng, officially known as Meyer, has been traditionally used as a medicinal herb, particularly in Asia. Ginseng is propagated from seeds; however, seed germination is challenging, especially in its natural environment on farms. The seeds typically exhibit morphophysiological dormancy and require release from both morphological and physiological dormancy before germination.

Isolation and Metabolic Assessment of Cancer Cell Mitochondria.

Mitochondrial metabolism plays an essential role in various biological processes of cancer cells. Herein, we established an experimental procedure for the metabolic assessment of mitochondria in cancer cells. We examined procedures for mitochondrial isolation coupled with various mitochondrial extraction buffers in three major cancer cell lines (PANC1, A549, and MDA-MB-231) and identified a potentially optimal and generalized approach.

Biotherapeutic Products, Cellular Factories, and Multiomics Integration in Metabolic Engineering.

Since the introduction of the first monoclonal antibody, biopharmaceuticals and biotherapeutic products manufactured in cellular factories are on the rise in modern medicine and therapeutics. Dynamic and real-time innovation strategies for operational implementation of biotherapeutic production are rapidly emerging. The advances in related fields such as genome editing technology, systems biology, and machine learning/artificial intelligence are expected to introduce innovative solutions in every aspect of the mammalian cell culture-based biotherapeutic production.

Comprehensive phenotyping and multi-omic profiling in the toxicity assessment of nanopolystyrene with different surface properties.

There is a growing concern regarding the toxic effects of terrestrial nanoplastic contaminants. However, an all-encompassing phenotyping- and omics-based strategy for the toxicity assessment of nanoplastics with different surface properties on soil living organisms remains to be established. Herein, we devised a comprehensive phenotyping and multi-omic profiling method to examine the molecular disturbance of nanopolystyrene (PS)-exposed Caenorhabditis elegans.

Research Quality-Based Multivariate Modeling for Comparison of the Pharmacological Effects of Black and Red Ginseng.

Black ginseng has various pharmacological activities, but only few studies have compared its pharmacological effects with those of red ginseng. We conducted an integrative systematic literature evaluation and developed a non-inferiority test based on the multivariate modeling approach to compare the pharmacological effects of red ginseng and black ginseng. We searched reported studies on the pharmaceutical effects and composition of ginsenosides and assigned numeric scores using nonlinear principal component analysis, based on discretization measures for the included publications.

Ginger on Human Health: A Comprehensive Systematic Review of 109 Randomized Controlled Trials.

Clinical applications of ginger with an expectation of clinical benefits are receiving significant attention. This systematic review aims to provide a comprehensive discussion in terms of the clinical effects of ginger in all reported areas. Following the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guideline, randomized controlled trials on the effects of ginger were investigated.

Comprehensive Multi-Omics Analysis Reveals Aberrant Metabolism of Epstein-Barr-Virus-Associated Gastric Carcinoma.

The metabolic landscape of Epstein-Barr-virus-associated gastric cancer (EBVaGC) remains to be elucidated. In this study, we used transcriptomics, metabolomics, and lipidomics to comprehensively investigate aberrant metabolism in EBVaGC. Specifically, we conducted gene expression analyses using microarray-based data from gastric adenocarcinoma epithelial cell lines and tissue samples from patients with clinically advanced gastric carcinoma.

Steroidomics for the Prevention, Assessment, and Management of Cancers: A Systematic Review and Functional Analysis.

Steroidomics, an analytical technique for steroid biomarker mining, has received much attention in recent years. This systematic review and functional analysis, following the PRISMA statement, aims to provide a comprehensive review and an appraisal of the developments and fundamental issues in steroid high-throughput analysis, with a focus on cancer research. We also discuss potential pitfalls and proposed recommendations for steroidomics-based clinical research.

Integrated metabolomics signature for assessing the longevity of Panax ginseng seeds.

Background: Panax ginseng seeds have strong dormancy and a prolonged germination period in comparison to other seeds; thus, it is a great challenge to propagate ginseng. Seed longevity is closely associated with germination rate and viability, so we assumed that if a seed loses its viability, specific metabolic alterations regarding plant growth factors might occur. In this study, we divided ginseng seeds into normal and accelerated-aging groups.

An Integrative Data Mining and Omics-Based Translational Model for the Identification and Validation of Oncogenic Biomarkers of Pancreatic Cancer.

Substantial alterations at the multi-omics level of pancreatic cancer (PC) impede the possibility to diagnose and treat patients in early stages. Herein, we conducted an integrative omics-based translational analysis, utilizing next-generation sequencing, transcriptome meta-analysis, and immunohistochemistry, combined with statistical learning, to validate multiplex biomarker candidates for the diagnosis, prognosis, and management of PC. Experiment-based validation was conducted and supportive evidence for the essentiality of the candidates in PC were found at gene expression or protein level by practical biochemical methods.

Efficacy of Integrating a Novel 16-Gene Biomarker Panel and Intelligence Classifiers for Differential Diagnosis of Rheumatoid Arthritis and Osteoarthritis.

Introducing novel biomarkers for accurately detecting and differentiating rheumatoid arthritis (RA) and osteoarthritis (OA) using clinical samples is essential. In the current study, we searched for a novel data-driven gene signature of synovial tissues to differentiate RA from OA patients. Fifty-three RA, 41 OA, and 25 normal microarray-based transcriptome samples were utilized.

Systematic assessment of cervical cancer initiation and progression uncovers genetic panels for deep learning-based early diagnosis and proposes novel diagnostic and prognostic biomarkers.

Although many outstanding achievements in the management of cervical cancer (CxCa) have obtained, it still imposes a major burden which has prompted scientists to discover and validate new CxCa biomarkers to improve the diagnostic and prognostic assessment of CxCa. In this study, eight different gene expression data sets containing 202 cancer, 115 cervical intraepithelial neoplasia (CIN), and 105 normal samples were utilized for an integrative systems biology assessment in a multi-stage carcinogenesis manner. Deep learning-based diagnostic models were established based on the genetic panels of intrinsic genes of cervical carcinogenesis as well as on the unbiased variable selection approach.

Multi-platform metabolomics and a genetic approach support the authentication of agarwood produced by Aquilaria crassna and Aquilaria malaccensis.

Agarwood, the resinous heartwood produced by some Aquilaria species such as Aquilaria crassna, Aquilaria malaccensis and Aquilaria sinensis, has been traditionally and widely used in medicine, incenses and especially perfumes. However, up to now, the authentication of agarwood has been largely based on morphological characteristics, a method which is prone to errors and lacks reproducibility. Hence, in this study, we applied metabolomics and a genetic approach to the authentication of two common agarwood chips, those produced by Aquilaria crassna and Aquilaria malaccensis.

A 1H NMR-based metabolomics approach to evaluate the geographical authenticity of herbal medicine and its application in building a model effectively assessing the mixing proportion of intentional admixtures: A case study of Panax ginseng: Metabolomics for the authenticity of herbal medicine.

Ginseng, the root of Panax ginseng has long been the subject of adulteration, especially regarding its origins. Here, 60 ginseng samples from Korea and China initially displayed similar genetic makeup when investigated by DNA-based technique with 23 chloroplast intergenic space regions. Hence, (1)H NMR-based metabolomics with orthogonal projections on the latent structure-discrimination analysis (OPLS-DA) were applied and successfully distinguished between samples from two countries using seven primary metabolites as discrimination markers.

Ca2+ signaling induced by sphingosine 1-phosphate and lysophosphatidic acid in mouse B cells.

Lysophospholipids (LPLs) such as lysophosphatidic acid (LPA) and sphingosine 1-phosphate (S1P) are chemotactic for lymphocytes, and increases of in cytosolic [Ca(2+)] signal the regulation of lymphocyte activation and migration. Here, the authors investigated the effects of LPA and S1P on [Ca(2+)](c) in mouse B cell lines (WEHI-231 and Bal-17) and primary B cells isolated from mouse spleen and bone marrow, and focused on the modulation of store-operated Ca(2+) entry (SOCE) by LPLs. In Bal-17 (a mature B cell line) both LPA and S1P induced a transient [Ca(2+)](c) increase via a phospholipase C pathway.