Yoshio Kodera
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View article: Identification of Cancer-Associated Proteins in Colorectal Cancer Using Mass Spectrometry
Identification of Cancer-Associated Proteins in Colorectal Cancer Using Mass Spectrometry Open
Background: Colorectal cancer (CRC) is a leading cause of cancer-related mortality worldwide, with a multifactorial etiology involving genetic and environmental factors. Advanced proteomics offers valuable insights into the molecular mecha…
View article: Structure-activity relationship of an all-α-helical prenyltransferase reveals a mechanism for indole prenylation
Structure-activity relationship of an all-α-helical prenyltransferase reveals a mechanism for indole prenylation Open
Enzymes are involved in the biosynthesis of various secondary metabolites found in nature. The catalytic mechanism is regulated by the three-dimensional structure of the enzyme especially at the catalytic site, resulting in the natural pro…
View article: jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data
jPOST environment accelerates the reuse and reanalysis of public proteome mass spectrometry data Open
jPOST (https://jpostdb.org/) comprises jPOSTrepo (https://repository.jpostdb.org/) (over 2000 projects), a repository for proteome mass spectrometry data, the reanalysis of raw proteome data based on a standardised protocol using UniScore,…
View article: Molecular dynamics simulations reveal differences in the conformational stability of FtsZs derived from Staphylococcus aureus and Bacillus subtilis
Molecular dynamics simulations reveal differences in the conformational stability of FtsZs derived from Staphylococcus aureus and Bacillus subtilis Open
View article: Fibrocyte Phenotype of ENTPD1+CD55+ Cells and Its Association with Pain in Osteoarthritic Synovium
Fibrocyte Phenotype of ENTPD1+CD55+ Cells and Its Association with Pain in Osteoarthritic Synovium Open
Osteoarthritis (OA) is a prevalent degenerative joint disorder characterized by cartilage erosion, structural changes, and inflammation. Synovial fibroblasts play a crucial role in OA pathophysiology, with abnormal fibroblastic cells contr…
View article: Molecular dynamics simulations reveal differences in the conformational stability of FtsZs derived from Staphylococcus aureus and Bacillus subtilis
Molecular dynamics simulations reveal differences in the conformational stability of FtsZs derived from Staphylococcus aureus and Bacillus subtilis Open
FtsZ is highly conserved among bacteria and plays an essential role in bacterial cell division. The tense conformation of FtsZ bound to GTP assembles into a straight filament via head-to-tail associations, and then the upper subunit of Fts…
View article: CD39+CD55− Fb Subset Exhibits Myofibroblast-Like Phenotype and Is Associated with Pain in Osteoarthritis of the Knee
CD39+CD55− Fb Subset Exhibits Myofibroblast-Like Phenotype and Is Associated with Pain in Osteoarthritis of the Knee Open
Recent studies utilizing single-cell analysis have unveiled the presence of various fibroblast (Fb) subsets within the synovium under inflammatory conditions in osteoarthritis (OA), distinguishing them from those in rheumatoid arthritis (R…
View article: Interaction between membranous <scp>EBP50</scp> and myosin 9 as a favorable prognostic factor in ovarian clear cell carcinoma
Interaction between membranous <span>EBP50</span> and myosin 9 as a favorable prognostic factor in ovarian clear cell carcinoma Open
Ezrin‐radixin‐moesin‐binding phosphoprotein 50 (EBP50) is a scaffold protein that is required for epithelial polarity. Knockout (KO) of membranous EBP50 (Me‐EBP50) in ovarian clear cell carcinoma (OCCC) cells induced an epithelial–mesenchy…
View article: Assessment of inconsistencies in the solvent-accessible surfaces of proteins between crystal structures and solution structures observed by LC-MS
Assessment of inconsistencies in the solvent-accessible surfaces of proteins between crystal structures and solution structures observed by LC-MS Open
Structural proteomics techniques are useful for identifying the binding sites of proteins. The surface of a target protein with and without a bound binding partner is artificially labeled using a hydroxy radical, deuterium, or a low-molecu…
View article: A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation
A marine sponge-derived lectin reveals hidden pathway for thrombopoietin receptor activation Open
N-glycan-mediated activation of the thrombopoietin receptor (MPL) under pathological conditions has been implicated in myeloproliferative neoplasms induced by mutant calreticulin, which forms an endogenous receptor-agonist complex that tra…
View article: Importance of the Q/N-rich segment for protein stability of endogenous mouse TDP-43
Importance of the Q/N-rich segment for protein stability of endogenous mouse TDP-43 Open
View article: ANGT_HUMAN[448–462], an Anorexigenic Peptide Identified Using Plasma Peptidomics
ANGT_HUMAN[448–462], an Anorexigenic Peptide Identified Using Plasma Peptidomics Open
The discovery of bioactive peptides is an important research target that enables the elucidation of the pathophysiology of human diseases and provides seeds for drug discovery. Using a large number of native peptides previously identified …
View article: Hidden pathway for cytokine receptor activation: a marine sponge-derived lectin reveals sugar-mediated thrombopoietin receptor activation
Hidden pathway for cytokine receptor activation: a marine sponge-derived lectin reveals sugar-mediated thrombopoietin receptor activation Open
N-glycan-mediated activation of the thrombopoietin receptor (MPL) under pathological conditions has been implicated in myeloproliferative neoplasms induced by mutant calreticulin, which forms an endogenous receptor-agonist complex that tra…
View article: A novel peptide identified from visceral ganglia induces oocyte maturation, spermatozoa active motility, and spawning in the pen shell Atrina pectinata
A novel peptide identified from visceral ganglia induces oocyte maturation, spermatozoa active motility, and spawning in the pen shell Atrina pectinata Open
The identification of novel peptides that regulate reproduction is essential for studying reproductive physiology in bivalves. Therefore, we aimed to identify peptides that affect the reproductive physiology of bivalves. We identified an o…
View article: Identification of novel biomarkers for ovarian clear cell carcinoma by shotgun proteomics using FFPE samples
Identification of novel biomarkers for ovarian clear cell carcinoma by shotgun proteomics using FFPE samples Open
Ovarian cancer is the leading cause of death in women with gynecologic malignancies, and especially, clear cell subtype (OCCCa) shows chemoresistance and clinical outcomes at advanced stages are generally unfavorable. To identify proteins …
View article: Importance of the Q/N-rich Segment for Protein Stability and Activity of Endogenous Mouse TDP-43
Importance of the Q/N-rich Segment for Protein Stability and Activity of Endogenous Mouse TDP-43 Open
TAR DNA-binding protein 43 kDa (TDP-43), a nuclear protein, plays an important role in the molecular pathogenesis of amyotrophic lateral sclerosis (ALS). TDP-43 aggregation and translocation out of the nucleus are crucial factors in ALS. T…
View article: LC–MS peak assignment based on unanimous selection by six machine learning algorithms
LC–MS peak assignment based on unanimous selection by six machine learning algorithms Open
View article: AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation
AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation Open
Background Phosphoinositide-3 kinase (PI3K)/AKT signaling participates in cellular proliferation, survival and tumorigenesis. The activation of AKT signaling promotes the cellular reprogramming including generation of induced pluripotent s…
View article: LC-MS Peak Assignment Based on Unanimous Selection by Six Machine Learning Algorithms
LC-MS Peak Assignment Based on Unanimous Selection by Six Machine Learning Algorithms Open
Recent Mass spectrometry (MS)-based techniques enable deep proteome coverage with relative quantitative analysis, resulting in increased identification of very weak signals accompanied by increased data size of liquid chromatography (LC)–M…
View article: GIP_HUMAN[22–51] is a new proatherogenic peptide identified by native plasma peptidomics
GIP_HUMAN[22–51] is a new proatherogenic peptide identified by native plasma peptidomics Open
View article: Highly accurate and precise quantification strategy using stable isotope dimethyl labeling coupled with GeLC-MS/MS
Highly accurate and precise quantification strategy using stable isotope dimethyl labeling coupled with GeLC-MS/MS Open
Shotgun proteomics is a powerful method for comprehensively identifying and quantifying tryptic peptides, but it is difficult to analyze proteolytic events. One-dimensional gel and liquid chromatography-tandem mass spectrometry (GeLC-MS/MS…
View article: Suprabasin-derived bioactive peptides identified by plasma peptidomics
Suprabasin-derived bioactive peptides identified by plasma peptidomics Open
Identification of low-abundance, low-molecular-weight native peptides using non-tryptic plasma has long remained an unmet challenge, leaving potential bioactive/biomarker peptides undiscovered. We have succeeded in efficiently removing hig…
View article: Additional file 1 of AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation
Additional file 1 of AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation Open
Additional file 1: Data 1 : Metabolome data for OSKA − 4OHT and OSKA + 4OHT at 10 dpi.
View article: Additional file 2 of AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation
Additional file 2 of AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation Open
Additional file 2: Auto ma ted shell scr ipt used for quantification of DNA methylation.
View article: Additional file 3 of AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation
Additional file 3 of AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation Open
Additional file 3: Automated shell script used for quantification of DNA methylation for Linux.
View article: Additional file 4 of AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation
Additional file 4 of AKT signaling is associated with epigenetic reprogramming via the upregulation of TET and its cofactor, alpha-ketoglutarate during iPSC generation Open
Additional file 4: Read me for automated shell script used for quantification of DNA m ethylation.
View article: Efficient extraction of proteins from formalin-fixed paraffin-embedded tissues requires higher concentration of tris(hydroxymethyl)aminomethane
Efficient extraction of proteins from formalin-fixed paraffin-embedded tissues requires higher concentration of tris(hydroxymethyl)aminomethane Open
BackgroundNumerous formaldehyde-fixed and paraffin-embedded clinical tissues have been created in the past decades and stored in pathological depositories at hospitals as well as in clinical laboratories worldwide. In addition to the archi…
View article: Epsin-mediated degradation of IP3R1 fuels atherosclerosis
Epsin-mediated degradation of IP3R1 fuels atherosclerosis Open
View article: Oxidised Met147 of human serum albumin is a biomarker of oxidative stress, reflecting glycaemic fluctuations and hypoglycaemia in diabetes
Oxidised Met147 of human serum albumin is a biomarker of oxidative stress, reflecting glycaemic fluctuations and hypoglycaemia in diabetes Open
View article: AKT Signaling Promotes Epigenetic Reprogramming via Upregulation of TET and its Cofactor, Alpha-Ketoglutarate, During iPSC Generation
AKT Signaling Promotes Epigenetic Reprogramming via Upregulation of TET and its Cofactor, Alpha-Ketoglutarate, During iPSC Generation Open