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Biomedical subjects

J Kim

Publications and source records attributed to J Kim.

At least 415 records · Page 23Linked to original sources
PubMed2000

Apg9p/Cvt7p is an integral membrane protein required for transport vesicle formation in the Cvt and autophagy pathways.

In nutrient-rich, vegetative conditions, the yeast Saccharomyces cerevisiae transports a resident protease, aminopeptidase I (API), to the vacuole by the cytoplasm to vacuole targeting (Cvt) pathway, thus contributing to the degradative capacity of this organelle. When cells subsequently encounter starvation conditions, the machinery that recruited precursor API (prAPI) also sequesters bulk cytosol for delivery, breakdown, and recycling in the vacuole by the autophagy pathway. Each of these overlapping alternative transport pathways is specifically mobilized depending on environmental cues. The basic mechanism of cargo packaging and delivery involves the formation of a double-membrane transport vesicle around prAPI and/or bulk cytosol. Upon completion, these Cvt and autophagic vesicles are targeted to the vacuole to allow delivery of their lumenal contents. Key questions remain regarding the origin and formation of the transport vesicle. In this study, we have cloned the APG9/CVT7 gene and characterized the gene product. Apg9p/Cvt7p is the first characterized integral membrane protein required for Cvt and autophagy transport. Biochemical and morphological analyses indicate that Apg9p/Cvt7p is localized to large perivacuolar punctate structures, but does not colocalize with typical endomembrane marker proteins. Finally, we have isolated a temperature conditional allele of APG9/CVT7 and demonstrate the direct role of Apg9p/Cvt7p in the formation of the Cvt and autophagic vesicles. From these results, we propose that Apg9p/Cvt7p may serve as a marker for a specialized compartment essential for these vesicle-mediated alternative targeting pathways.

Animals↗
PubMed2000

An efficient approach for cloning the dNDP-glucose synthase gene from actinomycetes and its application in Streptomyces spectabilis, a spectinomycin producer.

Specifically designed PCR primers were applied to amplify a segment of dTDP-glucose synthase gene from six actinomycete strains. About 300-bp or 580-bp DNA fragments were obtained from all the organisms tested. By DNA sequence analysis, seven amplified fragments showed high homology with dTDP-glucose synthase genes that participate in the biosynthesis of secondary metabolites or in deoxy-sugar moieties in lipopolysaccharides. In addition, we have cloned a 45-kb region of DNA from Streptomyces spectabilis ATCC27741, a spectinomycin producer which contained the dTDP-glucose synthase and dTDP-glucose 4,6-dehydratase genes named spcD and spcE, respectively. The spcE gene was expressed in Escherichia coli and the activity was assayed in cell extracts. The enzyme showed substrate specificity only to dTDP-glucose.

Actinomycetales↗
PubMed2000

Stability of Si-interstitial defects: from point to extended defects

Trends in the growth of extended interstitial defects are extracted from extensive tight-binding and ab inito local density approximation simulations. With an increasing number of interstitials, the stable defect shape evolves from compact to chainlike to rodlike. The rodlike 311 defect, formed from (011) interstitial chains, is stabilized as it grows, elongating in the chain direction. Accurate parametrization of the defect-formation energy on the number of interstitials and interstitial chains, together with the anisotropy of the interstitial capture radius, enables macroscopic defect-growth simulations.

Journal Article↗
PubMed2000

Cynandione A from Cynanchum wilfordii protects cultured cortical neurons from toxicity induced by H2O2, L-glutamate, and kainate.

Oxidative stress has been implicated as a primary cause of neuronal death in certain neurodegenerative disorders and in aging brains. Natural products have been used in Asian societies for centuries for treating such neurodegenerative disorders as senile dementia. In an effort to identify active neuroprotective compounds from these products, we have employed cultures of rat cortical neurons as our screening system. A methanolic extract from dried roots of Cynanchum wilfordii Hemsley (Asclepiadaceae) significantly mitigated the neurotoxicity induced by H2O2 in this screening system. Activity-guided fractionation using several chromatographic techniques resulted in the isolation of the neuroprotective compound, cynandione A, a biacetophenone. At a concentration of 50 microM, cynandione A significantly reduced neurotoxicity induced by H2O2. Cynandione A significantly attenuated decreases in levels of glutathione, superoxide dismutase, and other enzymes that participate in the cellular defense against oxidative stress. Furthermore, cynandione A alleviated neurotoxicity induced by the excitotoxic neurotransmitter, L-glutamate, the neurotoxicity induced by kainate, but not that mediated by N-methyl-D-aspartate. Cynandione A was demonstrated to be a natural antioxidant as it facilitated the breakdown of hydrogen peroxide in vitro; however, no mechanism was uncovered to explain its neuroprotectant effects against glutamate and kainate. Therefore, cynandione A may be efficacious in protecting neurons from oxidative stress mediated via activation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate/kainate receptors since it exerted significant neuroprotective effects on cultured cortical neurons.

Animals↗
PubMed2000

Intrinsic effects of solvent polarity on enzymic activation energies.

The effect of organic solvents on subtilisin Carlsberg catalysis has been investigated with the aid of a thermodynamic analysis. Saturation solubility experiments were performed to provide a quantitative measure of substrate desolvation from the reaction medium. This enabled calculation of the intrinsic enzymic activation energy and resulted in a linear free energy relationship with respect to solvent polarity. The results indicate that the intrinsic activation energy of subtilisin catalysis is lowest in polar organic solvents, which may be due to transition state stabilization of the enzyme's polar transition state for transesterification.

Bacillus↗
PubMed2000

Molecular heterochrony in the early development of Drosophila.

Heterochrony, the relative change of developmental timing, is one of the major modes of macroevolutionary change; it identifies temporally disassociated units of developmental evolution. Here, we report the results of a fine-scale temporal study for the expression of the developmental gene hairy and morphological development in three species of Drosophila, D. melanogaster, D. simulans, and D. pseudoobscura. The results suggest that between and among closely related species, temporal displacement of ontogenetic trajectory is detected even at the earliest stage of development. Overall, D. simulans shows the earliest expression, followed by D. melanogaster, and then by D. pseudoobscura. Setting D. melanogaster as the standard, we find the approximate time to full expression is accelerated by 13 min, 48 s in D. simulans and retarded by 24 min in D. pseudoobscura. Morphologically, again with D. melanogaster setting the standard, initiation of cellularization is faster in D. simulans by 15 min, 42 s; and initiation of morphogenesis is faster in D. simulans by 18 min, 7 s. These results seem to be consistent with the finding that the approximate time to full expression of hairy is accelerated by 13 min, 48 s in D. simulans. On the other hand, the same morphological events are delayed by 5 min, 32 s, and by 11 min, 32 s, respectively, in D. pseudoobscura. These delays are small, compared with the 24-min delay in full expression. The timing changes, in total, seem consistent with continuous phyletic evolution of temporal trajectories. Finally, we speculate that epigenetic interactions of hairy expression timing and cell-cycle timing may have led to morphological differences in the terminal system of the larvae.

Animals↗
PubMed2000

The effect of long-term levodopa therapy on depression level in de novo patients with Parkinson's disease.

20) became non-depressed, while five patients (22%) among 23 initially non-depressed became depressed. With long-term levodopa therapy, the UPDRS-motor score significantly improved (35+/-15. 7-18+/-7.6), but the BDI score was unchanged (18+/-9.3-19+/-9.2). The initial BDI score was significantly and inversely correlated to the parkinsonian motor symptoms, but their percentage changes were not correlated to each other. These results provide strong support to previous observations that levodopa therapy does not alter parkinsonian depression as well as providing additional evidence to support the role of non-dopaminergic mechanisms in parkinsonian depression.

Depressive Disorder↗
PubMed2000

Dynamic distribution of an antigen involved in the differentiation of avian myoblasts: II. Possible association of beta1 integrin with myofibril organization.

Previous studies have shown that a monoclonal antibody, H-145, inhibits myotube formation of quail myoblasts transformed with a temperature-sensitive mutant of Rous sarcoma virus (QM-RSV cells) [Hyodo and Kim, 1994: Exp. Cell Res. 212:120-131]. The antigen recognized by H-145 (H-145 antigen), which is a glycoprotein with a molecular mass of about 116 kDa, is related to a step immediately before myoblast fusion. To determine the functional significance of H-145 antigen, we examined its dynamic state during myogenic differentiation of QM-RSV cells. H-145 antigen showed a unique and discrete distribution. In immature myotubes immediately after myoblast fusion, many ring-like structures of H-145 antigen appeared on the ventral surface of the cells, encircling the actin dots detected simultaneously by immunofluorescence and interference reflection microscopy. The core of the ring-like structures was filled with the termini of actin bundles, mainly formed by alpha-actin. Other cytoskeletal-associated proteins, such as vinculin and alpha-actinin, were also associated with these structures. The ring-like structures of H-145 antigen were observed only during a restricted period when myoblasts fused actively, suggesting their relationships to myotube formation and an early stage of myofibril formation. With maturation of the myotubes, most of the H-145 antigen became redistributed in linear arrays on the apical cell surface and was probably associated with the termini of actin bundles to organize myofibrils, suggesting that the antigen was also related to maturation of myotubes. Experiments using monoclonal antibodies against chick beta1 integrin showed that H-145 antigen is beta1 integrin or a very closely related derivation. Thus H-145 antigen (beta1 integrin) is possibly involved in both myoblast fusion and the myofibril organization in myotubes.

Actins↗
PubMed2000

Replication protein a 32 kDa subunit (RPA p32) binds the SH2 domain of STAT3 and regulates its transcriptional activity.

STATs (signal transducers and activators of transcription) are transcription factors that contain SH2 domains and are activated by tyrosine phosphorylation in response to cytokines and growth factors. Replication protein A (RPA) is a heterotrimeric complex that consists of three subunits, p70, p32 and p11, and has important functions in DNA replication and metabolism. Here, we present evidence that the RPA p32 subunit binds specifically to the SH2 domain of STAT3 in a phosphotyrosine-independent manner. We confirm their protein-protein interactions by yeast 2-hybrid analyses and in vitro binding assays using recombinant proteins generated from bacteria and in vitro translation. We also show that STAT3 binds to RPA p32 in vivo by conducting co-precipitation experiments. As the SH2 domain is highly involved in the tyrosine phosphorylation and the transcriptional activity of STAT3, over-expression of RPA p32 correspondingly augmented growth factor-stimulated tyrosine phosphorylation and transcription activities of STAT3.

Animals↗
PubMed2000

Slicing hyperdimensional oranges: the geometry of phylogenetic estimation.

A new view of phylogenetic estimation is presented where data sets, tree evolution models, and estimation methods are placed in a common geometric framework. Each of these objects is placed in a vector space where the character patterns are the basis vectors. This viewpoint allows intuitive understanding of various complex properties of the phylogeneticestimation problem structure. This is illustrated with examples discussing data set combinations, mixture models, consistency, and phylogenetic invariants.

Algorithms↗
PubMed2000

Modifier effects on supercritical CO2 extraction efficiency of cephalotaxine from Cephalotaxus wilsoniana leaves.

The effects of modifiers such as methanol, water, diethylamine in methanol (10 v/v %), and diethylamine in water (10 v/v %) were investigated at three different concentrations (1, 5, and 10 v/v %) of the modifiers in supercritical CO2 (SC-CO2) in order to enhance the supercritical fluid extraction (SFE) efficiency of cephalotaxine from Cephalotaxus wilsoniana leaves. Among the modifiers employed, methanol basified with diethylamine was found to greatly enhance the extraction efficiency relative to any other modifiers employed. The results suggest that cephalotaxine in plant matrices may be readily changed from SC-CO2-insoluble salt to SC-CO2-soluble free base by basified modifiers. In addition, SC-CO2 modified with basified methanol could enhance the extraction efficiency of cephalotaxine more than 30% when compared to the conventional organic solvent extraction.

Antineoplastic Agents, Phytogenic↗
PubMed2000

Isolation of luteolin 7-O-rutinoside and esculetin with potential antioxidant activity from the aerial parts of Artemisia montana.

The antioxidant activity of Artemisia montana was determined by measuring the radical scavenging effect on 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical and inhibitory activity against free radical generation of hepatocytes (AC2F). The methanol extract of A. montana showed strong radical scavenging activity at a concentration of 10.1 microg/ml, and thus fractionated by solvent extraction. Esculetin and luteolin 7-O-rutinoside (scolymoside) were isolated as the active principles from the EtOAc and Interphase fractions, respectively. The antioxidant activity of these compounds were comparable to that of L-ascorbic acid.

Antioxidants↗
PubMed2000

APO2L/TRAIL expression in human brain tumors.

APO2 ligand (APO2L)/TRAIL is a novel member of the tumor necrosis factor cytokine family and a potent inducer of apoptosis in tumor cell lines. We recently reported that APO2L is consistently expressed in low-grade astrocytomas, anaplastic astrocytomas, glioblastomas, and cell lines derived thereof, and that malignant glioma cell lines are susceptible to APO2L-induced apoptosis. In this study, we investigated whether APO2L is expressed in medulloblastoma or neuroblastoma cell lines and whether these cells are sensitive to APO2L-induced apoptosis. Immunoblot analyses revealed full-length APO2L protein expression in one (DAOY) of three medulloblastoma cell lines but not in two neuroblastoma cell lines (SKN-BE and SKN-LE). Viability assay performed after exposure to soluble APO2L for 16 h showed that DAOY medulloblastoma cells were the most sensitive and that apoptosis induced by APO2L was greatly enhanced when protein synthesis was inhibited by cycloheximide. Neuroblastoma cell lines were almost completely resistant to APO2L-induced apoptosis. We also carried out APO2L immunohistochemistry in a total of 115 tumors of the nervous system with different histogenesis and biological behavior. In all 9 pilocytic astrocytomas, the areas of dense fibrillary network showed diffuse and strong APO2L expression. In oligodendrogliomas, APO2L expression was observed in areas with a significant admixture of astrocytic cells, but was absent in neoplastic oligodendrocytes. In 13 of 14 ependymomas, APO2L was expressed in perivascular pseudorosettes. In all 12 medulloblastomas, strong APO2L expression was observed in intra-tumoral-reactive astrocytes, but neoplastic cells did not show APO2L immunoreactivity. Thus, the pattern of APO2L expression was largely similar to that of glial fibrillary acidic protein (GFAP), except for choroid plexus tumors and 3 of 8 anaplastic meningiomas, in which APO2L was focally expressed without concomitant GFAP expression. APO2L expression was absent in meningiomas, neurocytomas, and schwannomas. Thus, there is considerable heterogeneity of APO2L expression and susceptibility to APO2L-induced apoptosis among human brain tumors.

Apoptosis↗
PubMed2000

Genomic organization of the human leukocyte immunoglobulin-like receptors within the leukocyte receptor complex on chromosome 19q13.4.

The leukocyte immunoglobulin (Ig)-like receptors (LIRs) comprise a family of cell surface receptors that couple to either activating or inhibitory signals depending on the nature of their transmembrane and cytoplasmic domains. We describe the organization and fine localization of the genes for LIR-1 and LIR-5, which are inhibitory receptors, and LIR-6, which is an activating receptor. The genomic organization of all three genes is highly conserved from the signal peptide through the membrane-proximal Ig domain but diverges thereafter depending on the inhibitory or activating nature of the gene product. The 3' untranslated region of the gene for LIR-6 contains a 37-base pair repeat not present in the LIR-1 or LIR-5 genes. 5' rapid amplification of cDNA ends defined the putative transcription initiation site of the LIR-5 gene, which is TATA-less. A nucleotide substitution in the LIR-5 gene led to loss of an intron present in the 5' untranslated region of the LIR-1 and LIR-6 genes. Differences in the genomic structure of these three LIR genes suggests possible mechanisms for their differential expression in cells of hematopoietic lineage. The three genes are in a region of Chromosome 19q13.4 that is immediately centromeric of the killer cell Ig-like receptor genes and are separated from one another by approximately 20 to 30 kb, suggesting that they arose by gene duplication from a common ancestor.

Antigens, CD↗
PubMed2000

Characterization of an extracellular poly(3-hydroxy-5-phenylvalerate) depolymerase from Xanthomonas sp. JS02.

A bacterium, JS02, capable of degrading an aromatic medium-chain-length polyhydroxyalkanoate (PHA(MCL)), poly(3-hydroxy-5-phenylvalerate) (PHPV), was isolated from wastewater-treatment sludge (Ju et al. 1998), and was identified as a Xanthomonas species. An extracellular PHPV depolymerase was purified from the concentrated culture broth of Xanthomonas sp. JS02 by using a chromatography series on Sephadex G-75, QAE-Sephadex A-50 and hydroxyapatite. The molecular mass of the purified enzyme was estimated to be 41.7 kDa. The purified enzyme could hydrolyse PHPV and p-nitrophenyl (PNP)-esters of fatty acids, but did not hydrolyse short-chain-length PHAs, though the culture supernatant could hydrolyse them. The optimum pH range was 8.0-9.0 and the optimum temperature was 60 degrees C for PNP-octanoate hydrolysis. The Km values for PNP-hexanoate and PNP-octanoate were 10.9 and 0.88 microM, respectively.

Biodegradation, Environmental↗
PubMed2000

Inhibition of apamin-sensitive K+ current by hypoxia in adult rat adrenal chromaffin cells.

The effect of hypoxia on small-conductance Ca(2+)-activated K+ current was investigated in a study of adult rat adrenomedullary chromaffin cells (AMCs), which were maintained in short-term culture. The nystatin-perforated, whole-cell patchclamp technique was used to study the effect of hypoxia with minimum perturbation of the intracellular milieu. Under voltage-clamp conditions, acute hypoxia (P(O2) approximately equal to 25 mmHg) suppressed the whole-cell outward currents of more than half the AMCs (24/46). This suppression was eliminated after application of apamin (400 nM), a selective inhibitor of small-conductance Ca(2+)-activated K+ current (I(SK)(Ca)) (n=5), suggesting that an apamin-sensitive component of whole-cell currents is suppressed during hypoxia. In contrast to I(SK)(Ca), Ca2+ current (I(Ca)) (n=10) was not affected by hypoxia. Finally, under current-clamp conditions, hypoxia reversibly depolarized the resting membrane potential of adult AMCs (34/40). Apamin, however, eliminated the hypoxia-induced depolarization (400 nM) (7/8), suggesting that hypoxic depolarization is related to the suppression of I(SK(Ca). From the above results, we conclude that adult AMCs are sensitive to hypoxia, and that I(SK)(Ca) contributes to the hypoxia-induced suppression of whole-cell outward current and depolarization of the resting membrane potential in adult AMCs.

Adrenal Medulla↗
PubMed2000

Constraint structure analysis of gene expression.

A microarray experiment gives a snapshot of the state of an organism in terms of the relative abundances of its mRNA transcripts, locating the organism at a point in a high dimensional state space where each axis represents the relative expression level of a single gene. Multiple experiments generate a cloud of points in this gene expression space. We present a geometric approach to analyzing the covariational properties of such a cloud and use a dataset from Saccharomyces cerevisiae as an illustration. In particular, we use singular value decomposition to identify significant linear sub-structures in the data and analyze the contributions of both individual genes and functional classes of genes to these major directions of variation. Analyzing the publicly available yeast expression data, we show that under all experimental conditions the variation in expression is limited to a small number of linear dimensions. Projections of individual gene axes onto the significant dimensions can order the contribution of individual genes to variation in expression within an experiment. We show that no particular groups of genes characterize particular experimental conditions. Instead, the particular structure of the coordinated expression of the entire genome characterizes a particular experiment.

Gene Expression↗