Biochemical Profiling of Urine Metabolome in Premature Infants Based on LC-MS Considering Maternal Influence.

In this study, Liquid Chromatography-Mass Spectrometry (LC-MS)-based metabolomics profiling was conducted to elucidate the urinary profiles of premature infants during early and late postnatal stages. As a result, we discovered significant excretion of maternal drugs in early-stage infants and identified crucial metabolites like hormones and amino acids. These findings shed light on the maternal impact on neonatal metabolism and underscore the beneficial effects of breastfeeding on the metabolism of essential amino acids in infants.

Optimizing MS-Based Multi-Omics: Comparative Analysis of Protein, Metabolite, and Lipid Extraction Techniques.

Multi-omics integrates diverse types of biological information from genomic, proteomic, and metabolomics experiments to achieve a comprehensive understanding of complex cellular mechanisms. However, this approach is also challenging due to technical issues such as limited sample quantities, the complexity of data pre-processing, and reproducibility concerns. Furthermore, existing studies have primarily focused on technical performance assessment and the presentation of modified protocols through quantitative comparisons of the identified protein counts.

A review of suspension trapping digestion method in bottom-up proteomics.

The standard bottom-up proteomic workflow is comprised of sample preparation, data acquisition, and data analysis. While the latter two parts have made considerable advances in the last decade, sample preparation has remained an important challenge within the workflow due to the multi-step nature of complex biological samples, and still requires much development. Several sample preparation methods have been developed and used in the last two decades, including in-gel, in-solution, on-bead, filter-aided sample preparation, and suspension trapping, to improve reproducibility, efficiency, scalability, and reduce the handling time of this process.

Discovery of Post-Translational Modifications in .

is a cosmopolitan coccolithophore that plays an essential role in global carbon and sulfur cycling, and contributes to marine cloud formation and climate regulation. Previously, the proteomic profile of was investigated using a three-dimensional separation strategy combined with liquid chromatography-tandem mass spectrometry (LC-MS/MS). The current study reuses the MS/MS spectra obtained, for the global discovery of post-translational modifications (PTMs) in this species without specific enrichment methods.

Establishment of functional epithelial organoids from human lacrimal glands.

Background: Tear deficiency due to lacrimal gland (LG) dysfunction is one of the major causes of dry eye disease (DED). Therefore, LG stem cell-based therapies have been extensively reported to regenerate injured lacrimal tissue; however, the number of stem cells in the LG tissue is low, and 2D long-term cultivation reduces the differentiation capacity of stem cells. Nevertheless, 3D LG organoids could be an alternative for a DED therapy because it is capable of prolonged growth while maintaining the characteristics of the LG tissue.

UBA2 activates Wnt/β-catenin signaling pathway during protection of R28 retinal precursor cells from hypoxia by extracellular vesicles derived from placental mesenchymal stem cells.

Background: Stem cell transplantation has been proposed as an alternative treatment for intractable optic nerve disorders characterized by irrecoverable loss of cells. Mesenchymal stem cells, with varying tissue regeneration and recovery capabilities, are being considered for potential cell therapies. To overcome the limitations of cell therapy, we isolated exosomes from human placenta-derived mesenchymal stem cells (hPMSCs) and investigated their therapeutic effects in R28 cells (retinal precursor cells) exposed to CoCl.

Proteomic Profiling of Using a Three-Dimensional Separation Method Combined with Tandem Mass Spectrometry.

is one of the most abundant marine planktons, and it has a crucial feature in the carbon cycle. However, proteomic analyses of have not been done extensively. In this study, a three-dimensional liquid chromatography (3D-LC) system consisting of strong cation exchange, high- and low-pH reversed-phase liquid chromatography was established for in-depth proteomic profiling of .

Discovery of plasma biomarkers for predicting the severity of coronary artery atherosclerosis by quantitative proteomics.

Introduction: Cardiovascular disease (CVD) in patients with diabetes is the leading cause of death. Finding early biomarkers for detecting asymptomatic patients with CVD can improve survival. Recently, plasma proteomics-targeted selected reaction monitoring/multiple reaction monitoring analyses (MRM)-has emerged as highly specific and sensitive tools compared with classic ELISA methods.

Review of Three-Dimensional Liquid Chromatography Platforms for Bottom-Up Proteomics.

Proteomics is a large-scale study of proteins, aiming at the description and characterization of all expressed proteins in biological systems. The expressed proteins are typically highly complex and large in abundance range. To fulfill high accuracy and sensitivity of proteome analysis, the hybrid platforms of multidimensional (MD) separations and mass spectrometry have provided the most powerful solution.

De novo transcriptome profile of coccolithophorid alga Emiliania huxleyi CCMP371 at different calcium concentrations with proteome analysis.

The haptophyte alga Emiliania huxleyi is the most abundant coccolithophore in the modern ocean and produces elaborate calcite crystals, called coccolith, in a separate intracellular compartment known as the coccolith vesicle. Despite the importance of biomineralization in coccolithophores, the molecular mechanism underlying it remains unclear. Understanding this precise machinery at the molecular level will provide the knowledge needed to enable further manipulation of biomineralization.

Neural Ganglia Transcriptome and Peptidome Associated with Sexual Maturation in Female Pacific Abalone ().

Genetic information of reproduction and growth is essential for sustainable molluscan fisheries and aquaculture management. However, there is limited knowledge regarding the reproductive activity of the commercially important Pacific abalone . We performed de novo transcriptome sequencing of the ganglia in sexually immature and mature female Pacific abalone to better understand the sexual maturation process and the underlying molecular mechanisms.

Label-free quantitative proteomic analysis of human periodontal ligament stem cells by high-resolution mass spectrometry.

Background And Objectives: Proteome analysis of periodontal ligament stem cells (PDLSCs) could be used to study the function of PDL tissue. We used a label-free quantitative proteomic technique to investigate differentially expressed proteins (DEPs) in human PDLSCs (hPDLSCs) compared to human bone marrow mesenchymal stem cells (hBMSCs) and identify proteins specific to hPDLSCs.

Material And Methods: hPDLSCs (n = 3) and hBMSCs (n = 3) were cultured and harvested for protein extraction and trypsin digestion.

Effects of FGF21-secreting adipose-derived stem cells in thioacetamide-induced hepatic fibrosis.

Mesenchymal stem cells (MSCs) have been investigated to treat liver diseases, but the efficiency of MSCs to treat chronic liver diseases is conflicting. FGF21 can reduce inflammation and fibrosis. We established FGF21-secreting adipose derived stem cells (FGF21_ADSCs) to enhance the effects of ADSCs and transplanted them into thioacetamide (TAA)-induced liver fibrosis mice via the tail vein.

Extensive Submacular Hemorrhage After Trabeculectomy With Mitomycin C.

Purpose: We report the occurrence of an extensive submacular hemorrhage after trabeculectomy with mitomycin C in a patient with an occult choroidal neovascular membrane (CNVM).

Patients And Methods: A 66-year-old man had a 3-year history of primary open-angle glaucoma in the left eye, which had been treated with topical antiglaucoma medication. The patient had age-related macular degeneration with an occult CNVM, for which he had received 5 intravitreal injections of ranibizumab and 5 intravitreal injections of bevacizumab in the left eye over a 3-year period.

Enhancement of the Antitumor Effect of Methotrexate on Colorectal Cancer Cells via Lactate Calcium Salt Targeting Methionine Metabolism.

Methionine (Met) is involved in one-carbon de novo nucleotide synthesis and is an essential amino acid for cell survival. The impact of lactate calcium salt (CaLa) on the Met metabolism was investigated to evaluate the enhanced antitumor effect of methotrexate (MTX) on colorectal cancer (CRC) cells. Met dependency relating to homocysteine (Hcy) and betaine was investigated in human CRC cells (HCT-116 and HT-29) using a viability assay and liquid chromatography-mass spectrometry.

Difference of Self-identity Levels between Strabismus Patients and Normal Controls.

Purpose: To evaluate differences in self-identity in patients diagnosed with strabismus, patients who underwent strabismus surgery, and healthy control individuals.

Methods: Self-identity testing was done during a military service physical examination. There were three subject groups: subjects with strabismus (group 1), subjects who had undergone corrective strabismus surgery (group 2), and subjects free of strabismus (group 3).

Integrated analysis of global proteome, phosphoproteome, and glycoproteome enables complementary interpretation of disease-related protein networks.

Multi-dimensional proteomic analyses provide different layers of protein information, including protein abundance and post-translational modifications. Here, we report an integrated analysis of protein expression, phosphorylation, and N-glycosylation by serial enrichments of phosphorylation and N-glycosylation (SEPG) from the same tissue samples. On average, the SEPG identified 142,106 unmodified peptides of 8,625 protein groups, 18,846 phosphopeptides (15,647 phosphosites), and 4,019 N-glycopeptides (2,634 N-glycosites) in tumor and adjacent normal tissues from three gastric cancer patients.

Electromagnetically induced transparency based on guided-mode resonances.

We present a novel, electromagnetically induced transparency system based on guided-mode resonances and numerically demonstrate its transmission characteristics through finite-difference time-domain simulations. The system is composed of two planar dielectric waveguides and a subwavelength grating. It is shown that by coupling the two resonant guide modes with a low- and high-quality factor, a narrow transparency window is generated inside a broad background transmission dip produced by the guided-mode resonance.

Aralia elata prevents neuronal death by downregulating tonicity response element binding protein in diabetic retinopathy.

Background/aims: The present study addresses the role of tonicity response element binding protein (TonEBP) in retinal ganglion cell (RGC) death in diabetic retinopathy and the impact of Aralia elata extract on the TonEBP/RGC interaction.

Methods: Diabetes was induced in C57BL/6 mice by intraperitoneal injection of streptozotocin (STZ). Control mice received phosphate-buffered saline.

Proteomic analysis of serum from patients with major depressive disorder to compare their depressive and remission statuses.

Objective: Currently, there are a few biological markers to aid in the diagnosis and treatment of depression. However, it is not sufficient for diagnosis. We attempted to identify differentially expressed proteins during depressive moods as putative diagnostic biomarkers by using quantitative proteomic analysis of serum.

Dihydrolipoyl dehydrogenase as a potential UVB target in skin epidermis; using an integrated approach of label-free quantitative proteomics and targeted metabolite analysis.

Unlabelled: Photodamage is extrinsically induced by overexposure to ultraviolet (UV) radiation, and it increases the risk of various skin disorders. Therefore, discovery of novel biomarkers of photodamage is important. In this study, using LC-MS/MS analysis of epidermis from UVB-irradiated hairless mice, we identified 57 proteins whose levels changed after UVB exposure, and selected 7 proteins related to the tricarboxylic acid (TCA) cycle through pathway analysis.

Fano resonance of self-collimated beams in two-dimensional photonic crystals.

We report that the Fano resonance of self-collimated beams can be achieved in a two-dimensional photonic crystal by introducing a Fano resonator that is composed of zigzag line defects. An asymmetric Fano line shape in a transmission spectrum is generated by the interference between radiated light beams from the resonator and self-collimated beams that directly pass through the resonator without resonance. It is shown that the Fano profile increases in sharpness as the number of zigzag line defects increases because the phase values of the radiated light beams change more rapidly when the number of defects increases.