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Biomedical subjects

Jin Young Kim

Publications and source records attributed to Jin Young Kim.

At least 19 recordsLinked to original sources
PubMed2024

Proteomic Heterogeneity of the Extracellular Matrix Identifies Histologic Subtype-Specific Fibroblast in Gastric Cancer.

Gastric cancer (GC) is a highly heterogeneous disease regarding histologic features, genotypes, and molecular phenotypes. Here, we investigate extracellular matrix (ECM)-centric analysis, examining its association with histologic subtypes and patient prognosis in human GC. We performed quantitative proteomic analysis of decellularized GC tissues that characterizes tumorous ECM, highlighting proteomic heterogeneity in ECM components. We identified 20 tumor-enriched proteins including four glycoproteins, serpin family H member 1 (SERPINH1), annexin family (ANXA3/4/5/13), S100A family (S100A6/8/9), MMP14, and other matrisome-associated proteins. In addition, histopathological characteristics of GC reveals differential expression in ECM composition, with the poorly cohesive carcinoma-not otherwise specified (PCC-NOS) subtype being distinctly demarcated from other histologic subtypes. Integrating ECM proteomics with single-cell RNA sequencing, we identified crucial molecular markers in the PCC-NOS-specific stroma. PCC-NOS-enriched matrisome proteins and gene expression signatures of adipogenic cancer-associated fibroblasts (CAFadi) are closely linked, both associated with adverse outcomes in GC. Using tumor microarray analysis, we confirmed the CAFadi surface marker, ATP binding cassette subfamily A member 8 (ABCA8), predominantly present in PCC-NOS tumors. Our ECM-focused analysis paves the way for studies to determine their utility as biomarkers for patient stratification, offering valuable insights for linking molecular and histologic features in GC.

Humans↗
PubMed2006

Hormonal activity of AIMP1/p43 for glucose homeostasis.

AIMP1/p43 is known as a cytokine working in the control of angiogenesis, inflammation, and wound healing. Here we report its enrichment in pancreatic alpha cells and glucagon-like hormonal activity. AIMP1 is secreted from the pancreas upon glucose starvation. Exogenous infusion of AIMP1 increased plasma levels of glucose, glucagon, and fatty acid, and AIMP1-deficient mice showed reduced plasma glucose levels compared with the wild-type mice under fasting conditions. Thus, AIMP1 plays a glucagon-like role in glucose homeostasis.

3T3-L1 Cells↗
PubMed2006

G-rich, a Drosophila selenoprotein, is a Golgi-resident type III membrane protein.

G-rich is a Drosophila melanogaster selenoprotein, which is a homologue of human and mouse SelK. Subcellular localization analysis using GFP-tagged G-rich showed that G-rich was localized in the Golgi apparatus. The fusion protein was co-localized with the Golgi marker proteins but not with an endoplasmic reticulum (ER) marker protein in Drosophila SL2 cells. Bioinformatic analysis of G-rich suggests that this protein is either type II or type III transmembrane protein. To determine the type of transmembrane protein experimentally, GFP-G-rich in which GFP was tagged at the N-terminus of G-rich, or G-rich-GFP in which GFP was tagged at the C-terminus of G-rich, were expressed in SL2 cells. The tagged proteins were then digested with trypsin, and analyzed by Western blot analysis. The results showed that the C-terminus of the G-rich protein was exposed to the cytoplasm indicating it is a type III microsomal membrane protein. G-rich is the first selenoprotein identified in the Golgi apparatus.

Amino Acid Sequence↗
PubMed2006

Planar gold nanoparticle clusters as microscale mirrors.

Dispersible microscale mirror particles were synthesized by linkage of citrate-coated gold nanoparticles and 3-aminopropylsilyl-modified Ca2Nb3O10 perovskite nanoplates. The mirror particles reflect 14-19% of light in the 500-800 nm wavelength interval with retention of polarization. Due to their directional reflection properties, laser-irradiated micromirror dispersions in solvents exhibit Brownian motion-driven multicolor blinking behavior.

Journal Article↗
PubMed2006

Radiofrequency radiation does not induce stress response in human T-lymphocytes and rat primary astrocytes.

Heat shock proteins (HSPs) are rapidly induced by a variety of stressors, including heat shock, ethanol, heavy metals, UV, and gamma-radiation. Mitogen-activated protein kinases (MAPKs) are also involved in the stress transduction pathways in all eukaryotes. In this study, we attempted to determine whether radiofrequency (RF) radiation is able to induce a non-thermal stress response. Human T-lymphocyte Jurkat cells and rat primary astrocytes were exposed to 1763 MHz of RF radiation at an average specific absorption rate (SAR) of either 2 W/kg or 20 W/kg, for 30 min or 1 h. Temperature was completely controlled at 37 +/- 0.2 degrees C throughout the exposure period. The sham exposures were performed under exactly identical experimental conditions without exposure to RF radiation. We assessed alterations in the expression of HSPs and the activation of MAPKs in the RF-exposed cells. No detectable difference was observed in the expression levels of HSP90, HSP70, and HSP27. The phosphorylation status of MAPKs, extracellular signal-regulated kinases (ERK1/2), c-Jun N-terminal protein kinases (JNK1/2), or p38, did not change significantly. In order to determine whether RF radiation can promote the effects of 12-O-tetradecanoylphorbol 13-acetate (TPA) on stress response, cells were exposed to RF radiation coupled with TPA treatment. When TPA alone was applied, the MAPKs were found to be phosphorylated in a dose-dependent manner. However, RF radiation did not result in any enhancement of TPA-induced MAPK phosphorylation. Neither TPA nor RF radiation exerted any detectable effect on the induction of HSPs. These results indicate that 1763 MHz RF radiation alone did not elicit any stress response, nor did it have any effect on TPA-induced MAPK phosphorylation, under our experimental conditions.

Animals↗
PubMed2006

Surgical anatomy of the middle turbinate.

Clinicians have encountered many variations of the middle turbinate. Previous descriptions of the middle turbinate were only focused on its size and shape and lacked surgical implications associated with endoscopic sinus surgery. Therefore, the aim of this study was to examine the surgical anatomy of the middle turbinate in hemisected cadaveric heads. The middle turbinates from 101 hemisections of adult Korean cadaveric heads were measured using digital calipers and a protractor. The middle turbinates were then classified according to their shape. The mean distance between the anterior attachment of the middle turbinate and the anterior attachment of the superior turbinate was 18.5 mm. The posterior end of the middle turbinate extended more posteriorly than that of the inferior turbinate in 40% of the cases, while in 26.3% of the cases, the posterior end of the inferior turbinate extended more posteriorly than that of the middle turbinate. The middle turbinate was classified into three types according to the shape of its anterior border. In type 1, the anterior border of the middle turbinate ran directly posteroinferiorly from its attachment to the conchal plate, and was observed in 45.3% of the cases. In type 2, the anterior border of the middle turbinate initially coursed inferiorly from the conchal plate and then turned in a posteroinferior direction. This type was observed in 44.2% of the cases. Type 3 involved 10.5% of the cases where the anterior border bulged anteriorly before it coursed posteroinferiorly. The information provided in this report should assist surgeons when performing partial middle turbinectomies.

Adult↗
PubMed2006

Mass spectrometric sequencing of endotoxin proteins of Bacillus thuringiensis ssp. konkukian extracted from polyacrylamide gels.

The amino acid sequences of the crystal proteins of Bacillus thuringiensis ssp. konkukian strain HL-47 are unknown. We used 1-D denaturing polyacrylamide electrophoresis, nano-ESI-Q-TOF-MS, and protein database searching to analyze these proteins. On SDS-PAGE gels, a preparation of purified crystal proteins exhibited 110, 102, 76, 55, 37, and 30 kDa protein bands. Immunoblotting of the gel with antiserum raised to this preparation revealed that four crystal proteins, of 110, 102, 55, and 37 kDa, reacted with the specific antiserum. The 102-kDa major protein reacted strongly. The other crystal proteins showed weak immunoreactivity. The 102 and 55 kDa proteins were analyzed by ESI-MS. The internal amino acid sequence of the 102-kDa major protein has similarity to the sequences of the surface layer protein of B. thuringiensis ssp. finitimus and B. anthracis. However, the internal amino acid sequences of the 55 kDa protein did not show any homology to proteins in the databases. Proteomic analysis of these proteins leads to the conclusion that the sequence data provided the protein databases of the crystal proteins of the konkukian ssp.

Amino Acid Sequence↗
PubMed2006

Human plasma proteome analysis by reversed sequence database search and molecular weight correlation based on a bacterial proteome analysis.

In shotgun proteomics, proteins can be fractionated by 1-D gel electrophoresis and digested into peptides, followed by liquid chromatography to separate the peptide mixture. Mass spectrometry generates hundreds of thousands of tandem mass spectra from these fractions, and proteins are identified by database searching. However, the search scores are usually not sufficient to distinguish the correct peptides. In this study, we propose a confident protein identification method for high-throughput analysis of human proteome. To build a filtering protocol in database search, we chose Pseudomonas putida KT2440 as a reference because this bacterial proteome contains fewer modifications and is simpler than the human proteome. First, the P. putida KT2440 proteome was filtered by reversed sequence database search and correlated by the molecular weight in 1-D-gel band positions. The characterization protocol was then applied to determine the criteria for clustering of the human plasma proteome into three different groups. This protein filtering method, based on bacterial proteome data analysis, represents a rapid way to generate higher confidence protein list of the human proteome, which includes some of heavily modified and cleaved proteins.

Blood Proteins↗
PubMed2006

Analysis of aromatic catabolic pathways in Pseudomonas putida KT 2440 using a combined proteomic approach: 2-DE/MS and cleavable isotope-coded affinity tag analysis.

Proteomic analysis of Pseudomonas putida KT2440 cultured in monocyclic aromatic compounds was performed using 2-DE/MS and cleavable isotope-coded affinity tag (ICAT) to determine whether proteins involved in aromatic compound degradation pathways were altered as predicted by genomic analysis (Jiménez et al., Environ Microbiol. 2002, 4, 824-841). Eighty unique proteins were identified by 2-DE/MS or MS/MS analysis from P. putida KT2440 cultured in the presence of six different organic compounds. Benzoate dioxygenase (BenA, BenD) and catechol 1,2-dioxygenase (CatA) were induced by benzoate. Protocatechuate 3,4-dixoygenase (PcaGH) was induced by p-hydroxybenzoate and vanilline. beta-Ketoadipyl CoA thiolase (PcaF) and 3-oxoadipate enol-lactone hydrolase (PcaD) were induced by benzoate, p-hydroxybenzoate and vanilline, suggesting that benzoate, p-hydroxybenzoate and vanilline were degraded by different dioxygenases and then converged in the same beta-ketoadipate degradation pathway. An additional 110 proteins, including 19 proteins from 2-DE analysis, were identified by cleavable ICAT analysis for benzoate-induced proteomes, which complemented the 2-DE results. Phenylethylamine exposure induced beta-ketoacyl CoA thiolase (PhaD) and ring-opening enzyme (PhaL), both enzymes of the phenylacetate (pha) biodegradation pathway. Phenylalanine induced 4-hydroxyphenyl-pyruvate dioxygenase (Hpd) and homogentisate 1,2-dioxygenase (HmgA), key enzymes in the homogentisate degradation pathway. Alkyl hydroperoxide reductase (AphC) was induced under all aromatic compounds conditions. These results suggest that proteome analysis complements and supports predictive information obtained by genomic sequence analysis.

Affinity Labels↗
PubMed2006

Profiling human brain proteome by multi-dimensional separations coupled with MS.

In our initial attempt to analyze the human brain proteome, we applied multi-dimensional protein separation and identification techniques using a combination of sample fractionation, 1-D SDS-PAGE, and MS analysis. The complexity of human brain proteome requires multiple fractionation strategies to extend the range and total number of proteins identified. According to the method of Klose (Methods Mol. Biol. 1999, 112, 67), proteins of the temporal lobe of human brain were fractionated into (i) cytoplasmic and nucleoplasmic, (ii) membrane and other structural, and (iii) DNA-binding proteins. Each fraction was then separated by SDS-PAGE, and the resulting gel line was cut into approximately 50 bands. After trypsin digestion, the resulting peptides from each band were analyzed by RP-LC/ESI-MS/MS using an LTQ spectrometer. The SEQUEST search program, which searched against the IPI database, was used for peptide sequence identification, and peptide sequences were validated by reversed sequence database search and filtered by the Protein Hit Score. Ultimately, 1533 proteins could be detected from the human brain. We classified the identified proteins according to their distribution on cellular components. Among these proteins, 24% were membrane proteins. Our results show that the multiple separation strategy is effective for high-throughput characterization of proteins from complex proteomic mixtures.

Brain↗
PubMed2005

Effect of FTY720 on chronic cyclosporine nephropathy in rats.

BACKGROUND: Long-term treatment with cyclosporine A (CsA) causes tubulointerstitial inflammation and fibrosis in the kidney. To define the role of lymphocytes in this process, the novel lymphocyte-specific inhibitor FTY720 was administered to rats with experimental model of chronic CsA nephropathy. METHODS: Sprague-Dawley rats were treated daily for 4 weeks with CsA (7.5 mg/kg), or both CsA and FTY720 (0.125 mg/kg). The effects of FTY720 on CsA-induced renal injury were evaluated using renal function tests and histopathology, and the expression of mediators of CsA-induced renal injury (osteopontin, transforming growth factor-beta1 [TGF-beta1], betaig-h3, and angiotensin II). RESULTS: FTY720 treatment significantly decreased T-lymphocyte accumulation in kidneys compared with CsA treatment alone. FTY720 treatment improved not only CsA-induced renal dysfunction but also renal histopathology, demonstrated by decreased macrophage infiltration and interstitial fibrosis. Increased osteopontin, TGF-beta1, betaig-h3, and angiotensin II expression in CsA-treated rat kidneys were decreased with FTY720 treatment. CONCLUSIONS: FTY720 treatment prevents CsA-induced renal injury.

Angiotensin II↗
PubMed2005

Planar polarized light emission from CdSe nanoparticle clusters.

This paper describes synthesis and optical properties of planar clusters of CdSe nanocrystals. The clusters emit linearly polarized light in the plane of the cluster. The emission wavelength of the clusters can be adjusted between 568 and 639 nm with the size of the CdSe nanocrystals. Planar CdSe microclusters were synthesized by reaction of trioctylphosphine oxide-coated CdSe/CdS nanocrystals with 3-aminopropylsilyl-modified Ca(2)Nb(3)O(10) nanosheets in THF. The clusters are 3.92 +/- 1.18 mum length/width and 91 +/- 37 nm thickness, and they consist of alternating layers of Ca(2)Nb(3)O(10) to which CdSe nanocrystals are attached with densities of 5300 +/-310 particles per side of a single Ca(2)Nb(3)O(10) sheet. The chemical inertness of the clusters in coordinating solvents suggests covalent interactions between the aminopropyl groups and CdSe nanocrystals. Upon excitation at lambda(exc) = 400 nm, the clusters emit green (568 nm), orange (589 nm), or red (639 nm) light, depending on the size of the CdSe crystals. The light is emitted preferentially in the cluster plane and it is linearly polarized along the cluster edges. Combined fluorescence microscopy and atomic force microscopy reveal that the directional emission efficiency depends linearly on the thickness of the clusters, which varies between 70 and 180 nm. The ability to manipulate the direction and polarization of the photoemission of CdSe nanoparticles via assembly into 2D structures is of interest for applications of these and similar structures in advanced optical materials and devices.

Journal Article↗
PubMed2005

ZnO-CdSe nanoparticle clusters as directional photoemitters with tunable wavelength.

Reaction of 3-aminopropylsilyl-modified ZnO microrods with trioctylphosphineoxide-coated CdSe/CdS core/shell nanocrystals in THF produces rod-shaped nanoparticle clusters that show directional photoemission that can be tuned with the size of the CdSe nanocrystals. The observed waveguiding effect of these microstructures is due to total internal reflection of light at the cluster-air interface.

Journal Article↗
PubMed2005

Synthesis and real-time magnetic manipulation of a biaxial superparamagnetic colloid.

Superparamagnetic colloidal plates were synthesized from tetrabutylammonium stabilized Ca(2)Nb(3)O(10) nanosheets and oleic acid-stabilized Fe(3)O(4) nanoparticles. Modification with 3-aminopropyltrimethoxysilane produces amine-terminated Ca(2)Nb(3)O(10) with an amine concentration of 0.43 +/- 0.06 groups per Ca(2)Nb(3)O(10) unit as follows from spectroscopic quantification with trinitrobenzenesulfonic acid as a dye. Treatment of the modified sheets in THF/ethanol with 5.3 nm oleic acid-stabilized magnetite nanoparticles yields pseudo-2D assemblies that consist of 2 nm thick nanosheets decorated on both sides with a dense collection (9.3 +/- 0.5 x 10(3) particles per square micrometer per side) of magnetite particles. In noncoordinating or weakly coordinating solvents, these composite particles further aggregate into stacked aggregates with a mean edge length of 1.6 +/- 0.7 microm and a thickness of 79 +/- 30 nm. The colloidal plates were characterized by elemental analysis, X-ray powder diffraction, and infrared and UV/vis spectroscopy. SQUID measurements show that films of the aligned particles are superparamagnetic at room temperature. The magnetic hysteresis that is observed at 5 K reveals that the plates have a magnetic anisotropy with the easy axis in the plane of the plates and the hard axis perpendicular to it. Calculations show that the magnetic anisotropy is a direct consequence of the two-dimensional distribution of the magnetic nanoparticles on the sheets. Optical microscopy reveals that when suspended in ethanol or THF, the colloidal plates can be rotated in real time with a variable external magnetic field (200 Oe). Magnetic alignment of the particles in suspensions also produces asymmetric light scattering patterns and magnetic birefringence. These effects and the observed magneto-orientational properties make the biaxial colloids interesting as components in displays and as magnetic actuators.

Journal Article↗
PubMed2005

Spontaneous and simultaneous rupture of both quadriceps tendons in a patient with chronic renal failure. A case studied by MRI both preoperatively and postoperatively.

Spontaneous bilateral rupture of the quadriceps tendons without a significant history of trauma is an uncommon disease. It is generally associated with chronic metabolic disorders such as chronic renal failure and secondary hyperparathyroidism. Here, we report a case of spontaneous bilateral tendon rupture in a patient on chronic hemodialysis for the past 5 years. We performed a preoperative MRI to confirm the diagnosis; then we repaired the ruptured quadriceps tendons and reviewed the patient both clinically and by performing MRI postoperatively 4 yrs later. The patient attained the full function of the quadriceps tendon.

Adult↗