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Biomedical subjects

Y J Kim

Publications and source records attributed to Y J Kim.

At least 91 records · Page 5Linked to original sources
PubMed2001

The structural and functional organization of the yeast mediator complex.

The Mediator complex of Saccharomyces cerevisiae is required for diverse aspects of transcription by RNA polymerase II (pol II). Mediator is composed of two functionally distinct subcomplexes, Rgr1 and Srb4. To identify the structures and functions of each subcomplex, we expressed recombinant proteins for each subunit and assayed their interactions with each other and with basal transcription proteins. The Rgr1 subcomplex is composed of the Gal11 module, which binds activators, and the Med9/10 module. The Med9/10 module is required for both transcriptional activation and repression, and these activities appear to be carried out by two submodules. Proteins in the Med9 submodule interact physically and genetically with Srb10/11, suggesting that the Med9 submodule mediates the repression of pol II. Purified recombinant Srb4 subcomplex stimulated basal transcription of pol II but had little effect on activated transcription and phosphorylation of the C-terminal domain of the Rpb1 subunit of pol II. Both subcomplexes of Mediator interacted with a distinct set of basal transcription factors and pol II. The modular organization of Mediator and the associated functions suggest that the Mediator complex may recruit and/or stabilize the preinitiation complex through several points of contact with transcriptional regulators and basal transcription factors.

Fungal Proteins↗
PubMed2001

Blocking of c-FLIP(L)--independent cycloheximide-induced apoptosis or Fas-mediated apoptosis by the CC chemokine receptor 9/TECK interaction.

Chemokines play a pivotal role in regulating leukocyte migration as well as other biological functions. CC chemokine receptor 9 (CCR9) is a specific receptor for thymus-expressed CC chemokine (TECK). It is shown here that engagement of CCR9 with TECK leads to phosphorylation of Akt (protein kinase B), mitogen-activated protein kinases (MAPKs), glycogen synthase kinase--3 beta (GSK-3 beta), and a forkhead transcription factor, FKHR, in a human T-cell line, MOLT4, that naturally expresses CCR9. By means of chemical inhibitors, it is shown that phosphoinositide-3 kinase (PI-3 kinase), but not MAPK, is required for CCR9-mediated chemotaxis. Akt, GSK-3 beta, FKHR, and MAPK have been previously implicated in cell survival signals in response to an array of death stimuli. When MOLT4 cells, which expressed Fas as well as CXCR4, were stimulated with cycloheximide (CHX), an agonistic anti-Fas antibody, or a combination of these, the cells rapidly underwent apoptosis. However, costimulation of MOLT4 cells with TECK or stromal derived factor--1 significantly blocked CHX-mediated apoptosis, whereas stimulation only with TECK partially blocked Fas-mediated apoptosis. Concomitant with this blocking, cleavage of poly (adenosine 5'-diphosphate--ribose) polymerase and activation of caspase 3 were significantly attenuated, but the expression level of FLICE inhibitory protein c-FLIP(L), which had been shown to be regulated by CHX, was unchanged. This demonstrates that activation of CCR9 leads to phosphorylation of GSK-3 beta and FKHR and provides a cell survival signal to the receptor expressing cells against CHX. It also suggests the existence of a novel pathway leading to CHX-induced apoptosis independently of c-FLIP(L). (Blood. 2001;98:925-933)

Apoptosis↗
PubMed2001

Why is alkylation of an enolate accompanied by so much polyalkylation?

[reaction: see text] The lithium enolate 1-Li of 6-phenyl-alpha-tetralone forms a monomer-tetramer equilibrium in THF at 25 degrees C with K(1,4) = 4.7E+10 M(-3). The lithium enolate 2-Li, however, forms a monomer-dimer equilibrium with K(1,2) = 3800 M(-1). In both cases reaction with benzyl bromide is dominantly with the monomer. The results support an earlier conjecture of House that alkylation of an enolate is frequently accompanied by extensive polyalkylation because the less substituted enolates are more aggregated.

Journal Article↗
PubMed2001

Caffeine inhibits exercise-induced increase in tryptophan hydroxylase expression in dorsal and median raphe of Sprague-Dawley rats.

Effect of caffeine on the expression of tryptophan hydroxylase (TPH), rate limiting enzyme of serotonin synthesis, in dorsal and median raphe was investigated via immunohistochemistry. In exercise groups, Sprague-Dawley rats were put on treadmill running for 30 min per day for 6 consecutive days. On the seventh day, animals of control-with-caffeine group were injected subcutaneously with 4 mg/kg caffeine, while control-without-caffeine group were injected with 0.9% NaCl, sacrificed 2 h later. Exercise-with-caffeine group and exercise-without-caffeine group were injected with caffeine and NaCl, respectively; all-out time was determined 1 h after injection, and then sacrificed. Caffeine increased all-out time in exercised rats, and inhibited the exercise-induced elevation in TPH expression. The suppressive effect of caffeine on TPH expression in exercised rats can be suggested as one possible ergogenic mechanism of caffeine.

Animals↗
PubMed2001

Med9/Cse2 and Gal11 modules are required for transcriptional repression of distinct group of genes.

The yeast Mediator is composed of two subcomplexes, Rgr1 and Srb4, known to be required for diverse aspects of transcriptional regulation; however, their structural and functional organizations have not yet been deciphered in detail. Biochemical analyses designed to determine the subunit composition of the Rgr1 subcomplex revealed that the regulator-interacting subcomplex has a modular structure and is composed of the Gal11, Med9/Cse2, and Med10/Nut2 modules. Genome-wide gene expression and Northern analyses performed in the presence or absence of the various Mediator modules revealed a distinct requirement for the Gal11, Med9/Cse2, and Med10/Nut2 modules in transcriptional repression as well as activation. GST pull-down analysis revealed that the transcriptional repressor Tup1 binds to distinct but overlapping regions of the Gal11 module that were shown previously to be transcriptional activator binding sites. These data suggest that competition between transcriptional activators and repressors for a common binding site in the Mediator and distinct conformational changes in the Mediator induced by repressor binding may underlie the mechanism of transcriptional repression in eukaryotes.

Animals↗
PubMed2001

Auricular acupuncture decreases neuropeptide Y expression in the hypothalamus of food-deprived Sprague-Dawley rats.

The aim of the present study was to investigate whether stimulation of auricular acupuncture point has any effects on the expression of neuropeptide Y (NPY), appetite-inducing factor particularly abundant in the mammalian hypothalamus. In food-deprived condition, enhanced NPY expression was detected in both the arcuate nucleus (ARN) and the paraventricular nucleus (PVN) of the hypothalamus via immunohistochemistry in Sprague-Dawley rats. Needling the unfed rats on the auricular point resulted in decreased NPY levels in both the ARN and PVN, while it increased NPY levels in the ARN and PVN of fed rats. The present findings indicate that auricular acupuncture may affect NPY expression in the ARN and PVN of the hypothalamus.

Acupuncture, Ear↗
PubMed2001

Synthesis of the trisaccharide portion of the immunologic adjuvant QS-21A via sulfonium-mediated oxidative and dehydrative glycosylation.

[see structure]. The first synthesis of the trisaccharide fragment of the potent immunologic adjuvant QS-21A is reported. The key steps involve the application of sulfonium-mediated oxidative and dehydrative glycosidic couplings to construct the anomeric linkages in a short and convergent assembly of the branched trisaccharide.

Adjuvants, Immunologic↗
PubMed2001

Cyclophilin a binds to peroxiredoxins and activates its peroxidase activity.

Six distinct peroxiredoxin (Prx) proteins (Prx I-VI) from distinct genes have been identified in mammalian tissues. Prxs are members of a group of peroxidases that have conserved reactive cysteine residue(s) in the active site(s). An immediate physiological electron donor for the peroxidase catalysis for five Prx proteins (Prx I-V) has been identified as thioredoxin (Trx), but that for Prx VI (1-Cys Prx) is still unclear. To identify an immediate electron donor and a binding protein for Prx VI, we performed a Prx VI protein overlay assay. A 20-kDa binding protein was identified by the Prx VI protein overlay assay with flow-through fractions from a High-Q column with rat lung crude extracts. Using matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and MS-Fit, we identified the 20-kDa Prx VI-binding protein as a cyclophilin A (CyP-A). The binding of recombinant human CyP-A (hCyP-A) to Prx VI was confirmed by using the hCyP-A protein overlay assay and Western immunoblot analysis with hCyP-A-specific antibodies. hCyP-A enhanced the antioxidant activity of Prx VI, as well as the other known mammalian Prx isotypes. hCyP-A supported antioxidant activity of Prx II and Prx VI both against thiol (dithiothreitol)-containing metal-catalyzed oxidation (MCO) systems and ascorbate-containing MCO systems. Prx II was reduced by hCyP-A without help from any other reductant, and the reduction was cyclosporin A-independent. These results strongly suggest that CyP-A not only binds to Prx proteins but also supports its peroxidase activity as an immediate electron donor. In addition, Cys(115) and Cys(161) of hCyP-A were found to be involved in the activation and the reduction of Prx.

Animals↗
PubMed2001

Structure and expression of the Arabidopsis thaliana homeobox gene Athb-12.

We have isolated the Arabidopsis thaliana homeobox gene Athb-12, determined its structure and activation domain, demonstrated that its promoter is inducible in response to abscisic acid (ABA) treatment, and characterized the cellular distribution of its transcripts. The single intron of the gene interrupted the leucine-zipper domain region. The 5' regulatory region of Athb-12 can drive beta-glucuronidase (GUS) expression in tobacco transgenic plants. Athb-12 gene expression was further examined using in situ hybridization to determine the cellular distribution of Athb-12 transcripts during ABA induction. A complex pattern of Athb-12 expression was observed, often associated with regions of developing vascular tissues. Analysis of chimeras constructed from Athb-12 and the DNA-binding domain of the Saccharomyces cerevisiae transcription factor GAL4 revealed that the activation domain of Athb-12 lies in the C-terminal region (amino acids 180 to 235). Taken together, our data suggest that Athb-12 is a transcriptional activator important in regulating certain developmental processes as well as in the plant's response to water stress involving ABA-mediated gene expression.

5' Untranslated Regions↗
PubMed2001

Mutation in PMR1, a Ca(2+)-ATPase in Golgi, confers salt tolerance in Saccharomyces cerevisiae by inducing expression of PMR2, an Na(+)-ATPase in plasma membrane.

Sodium tolerance in yeast is enhanced by continuous activation of calcineurin, a Ca(2+)/calmodulin-dependent protein phosphatase that is required for modulation of the Na(+) efflux mechanism. We isolated several salt-tolerant mutations with the treatment of ethylmethane sulfonate under high salt stress. One of the mutations was mapped in the PMR1 gene. Pmr1p, the P-type Ca(2+)-ATPase in the Golgi apparatus, regulates a cytosolic Ca(2+) level in various responses. Cytosolic Ca(2+) concentration in the pmr1 mutant is highly maintained, and thus calcineurin is activated continuously. The treatment of FK506, a specific inhibitor of calcineurin, abolishes the salt-tolerant phenotype of the pmr1 mutant. Activated calcineurin induces the expression of PMR2, encoding the P-type Na(+)-ATPase, through the specific transcription factor, Tcn1p/Crz1p. Also, expression of the PMR2::lacZ reporter gene in the pmr1 mutant was higher than that in wild type. We propose that the pmr1 mutation confers salt tolerance through continuous activation of calcineurin and that Pmr1p might act as a major Ca(2+)-ATPase under high salt stress.

Adenosine Triphosphatases↗
PubMed2001

The product of an oculopharyngeal muscular dystrophy gene, poly(A)-binding protein 2, interacts with SKIP and stimulates muscle-specific gene expression.

Oculopharyngeal muscular dystrophy (OPMD) is caused by short expansions of the GCG trinucleotide repeat encoding the polyalanine tract of the poly(A)-binding protein 2 (PABP2). PABP2 binds to the growing poly(A) tail, stimulating its extension during the polyadenylation process, and limits the length of the newly synthesized poly(A) tail. Whereas PABP2 is expressed ubiquitously, the clinical and pathological features of OPMD patients are restricted to the skeletal muscle. To elucidate the possible role of PABP2 in skeletal muscle, we established the stable C2 cell lines expressing human PABP2. These stable cell lines showed morphologically enhanced myotube formation accompanied by an increased expression of myogenic factors, MyoD and myogenin. In nuclear run-on assay, the transcription rate of the MyoD gene was significantly increased by PABP2 transfection. We found the N-terminal region of PABP2 was responsible for the up-regulation of these myogenic factors. Furthermore, Ski-interacting protein (SKIP) was isolated as a binding protein for PABP2 using the yeast two-hybrid system. The interaction of PABP2 and SKIP was confirmed by glutathione S-transferase-pulldown assay and immunoprecipitation. Confocal laser scanning showed PABP2 was co-localized with SKIP in nuclear speckles. The reporter assays showed that PABP2 co-operated with SKIP to synergistically activate E-box-mediated transcription through MYOD: Moreover, both PABP2 and SKIP were directly associated with MyoD to form a single complex. These findings suggest that PABP2 and SKIP directly control the expression of muscle-specific genes at the transcription level.

Animals↗
PubMed2001

Expression and characterization of a recombinant Fab fragment derived from an anti-human alpha-fetoprotein monoclonal antibody.

Alpha-fetoprotein (AFP) is a well-known molecular marker indicating the development of cancer as well as fetal abnormalities such as open neural tube defects. Accordingly the measurement of serum AFP is important for the diagnosis of hepatocellular carcinoma (HCC) and other abnormalities. Monoclonal antibodies (McAb) to AFP were produced to develop an immunoassay kit, and to study the possibility of an antibody (Ab) therapy. The immunoglobulin genes were cloned from hybridoma cells, and expressed in E. coli as an Fab soluble into a culture medium. The Fab of anti-AFP McAb exhibited binding to AFP and similar affinity compared to the original IgG. This recombinant antibody can be studied further for in vivo imaging and immunotherapeutics.

Amino Acid Sequence↗
PubMed2001

Structures and related properties of AgX bearing 3,3'-thiobispyridine (X- = NO3-, BF4-, CLO4-, and PF6-.

Infinite molecular helices [Ag(3,3'-Py2S)]X (3,3'-Py2S = 3,3'-thiobispyridine; X- = BF4-, ClO4-, and PF6-) have been rationally constructed or induced. Crystallographic characterization (X- = BF-, monoclinic P2(1)/n, a = 8.946(3) A, b = 14.130(2) A, c = 10.124(2) A, beta = 107.83(2) degrees, V = 1218.3(5) A3, Z = 4, R = 0.0351; X- = ClO4-, monoclinic P2(1)/n, a = 8.884(1) A, b = 14.305(3) A, c = 10.110(1) A, beta = 106.78(1) degrees, V = 1230.1(3) A3, Z = 4, R = 0.0417; X- = PF6-, monoclinic P2(1)/c, a = 10.959(2) A, b = 9.808(2) A, c = 14.065(3) A, beta = 112.03(2) degrees, V = 1401.4(5) A3, Z = 4, R = 0.0442) reveals that the skeletal structure is an oblong cylindrical cationic helix consisting of alternating Ag(I) and 3,3'-Py2S species and that its counteranions are pinched in two columns inside each helix. The formation of the helical coordination polymer appears to be primarily associated with a suitable combination of the skewed conformer of 3,3'-Py2S and the potential linear geometry of the N-Ag(I)-N bond. However, the framework of the nitrate analogue [Ag(3,3'-Py2S)NO3] (monoclinic P2(1)/c, a = 8.177(2) A, b = 10.291(1) A, c = 14.771(2) A, beta = 102.19(1) degrees, V = 1214.9(4) A3, Z = 4, R = 0.0300) is a two-dimensional network consisting of an 18-membered ring unit, where each 3,3'-Py2S acts as a N,N',S- tridentate ligand connecting three tetrahedral silver(I) ions with the monodentate nitrate weakly bonded to the silver (Ag.O = 2.65(1) A) rather than acting as a counteranion. The anion exchange of [Ag(3,3'-Py2S)NO3] with BF4-, ClO4-, or PF6- has been accomplished in aqueous media. The two-dimensional networks are easily converted into the helices via the anion exchange, but the reverse anion exchange proceeds slightly. Thermal analyses indicate a relationship between the thermal stabilities and the structural properties.

Anions↗
PubMed2001

Angiogenic activity of pyruvic acid in in vivo and in vitro angiogenesis models.

The excessive growth of a tumor requires high rates of glucose uptake and glycolysis and continuous recruitment of new blood vessels. Here, we provide several lines of evidence showing that pyruvic acid, the end product of glycolysis, exhibits strong angiogenic activity. Pyruvic acid promoted angiogenesis in chorioallantoic membrane assay and in vivo mouse Matrigel plug assay. Pyruvic acid also positively affects angiogenic cascade, DNA synthesis, migration, and tube formation in bovine aortic endothelial cells. Furthermore, mRNA expression of fibroblast growth factor receptor-2 and vascular endothelial growth factor was enhanced by pyruvic acid. These results strongly suggest that pyruvic acid plays an important role in angiogenesis for tumor growth and metastasis.

Allantois↗
PubMed2001

Critical spin dynamics of the 2D quantum Heisenberg antiferromagnets Sr2CuO2Cl2 and Sr2Cu3O4Cl2.

We report a neutron scattering study of the long-wavelength dynamic spin correlations in the model two-dimensional S = 1/2 square lattice Heisenberg antiferromagnets Sr2CuO2Cl2 and Sr2Cu3O4Cl2. The characteristic energy scale, omega(0)(T/J), is determined by measuring the quasielastic peak width in the paramagnetic phase over a wide range of temperature ( 0.2 less similarT/J less similar0.7). The obtained values for omega(0)(T/J) agree quantitatively between the two compounds and also with values deduced from quantum Monte Carlo simulations. The combined data show scaling behavior, omega approximately xi(-z), over the entire temperature range with z = 1.0(1), in agreement with dynamic scaling theory.

Journal Article↗