Biomedical subjects

S Kim

Publications and source records attributed to S Kim.

At least 613 records · Page 34Linked to original sources

PubMed1998

CD4 cell count as a surrogate endpoint in HIV clinical trials: a meta-analysis of studies of the AIDS Clinical Trials Group.

OBJECTIVE: To evaluate initial changes in CD4 cell count as a surrogate endpoint for clinical outcome in HIV-infected patients. DESIGN: Meta-analysis of all relevant Phase II and III randomized clinical trials undertaken by the Adult AIDS Clinical Trials Group. METHODS: Individual patient data were obtained from each clinical trial, and the difference between a pair of treatments in their effect on clinical outcome (AIDS or death, or death alone) during 2 years of follow-up was evaluated. The proportion of treatment effect explained (PTE) was the proportion of this difference explained by the change in CD4 cell count 6 months after starting treatment, evaluated using proportional hazards models. A weighted average PTE across treatment comparisons was obtained. The association between the difference between treatments in clinical outcome, expressed as hazard ratio, and the difference in mean change in CD4 cell count was evaluated using regression analysis. RESULTS: There were 15 clinical trials involving 24 treatment comparisons. The weighted average PTE for both progression to AIDS or death was 0.16 [95% confidence interval (Cl), 0.07-0.26] and for death was 0.10 (95% Cl, 0.00-0.20). There were significant associations between treatment differences in effect on AIDS or death, and on death alone, and the difference in mean change in CD4 cell count. A difference in mean change in CD4 cell count of 30 or 40 x 10(6)/l or more in favor of the test treatment indicated with high probability that there was a corresponding difference in progression to AIDS or death. CONCLUSIONS: The small PTE suggest that other mechanisms of drug action not captured by initial change in CD4 cells are important. CD4 cell count is a weak surrogate endpoint, but has some value as an aid for screening treatments for drug development or preliminary regulatory approval.

Anti-HIV Agents↗

PubMed1998

Vibrational spectrum associated with the reduction of tyrosyl radical D* in photosystem II: a comparative biochemical and kinetic study.

Photosystem II (PSII) contains a redox-active tyrosine, D. Difference FT-IR spectroscopy can be used to obtain structural information about this species, which is a neutral radical, D*, in the photooxidized form. Previously, we have used isotopic labeling, site-directed mutagenesis, and kinetics to assign a vibrational line at 1477 cm-1 to D*; these studies were performed on highly resolved PSII preparations at pH 7.5 ¿Kim et al. (1998) Biochim. Biophys. Acta 1364, 337-360; publisher's correction, Biochim. Biophys. Acta 1366, 330-354¿. Here, we use kinetics to assign vibrational features to tyrosyl radical, D*, in PSII membranes. EPR and fluorescence controls identify a time regime in which D* decay occurs independently of redox changes involving the PSII quinone acceptors. Difference FT-IR spectra, acquired over this time regime, exhibit decreases in the amplitude of a 1477 cm-1 line; quantitative comparison with EPR transients supports the assignment to D*. Conditions, requiring the use of phosphate/formate, have been described for observation of a dissimilar FT-IR spectrum, which has been assigned to tyrosyl radical D*; this spectrum lacks a 1477 cm-1 line ¿Hienerwadel et al. (1997) Biochemistry 36, 14712-14723¿. Under these conditions, we have observed (1) an acceleration in the rate of D* decay and a decrease in D* yield attributable to the presence of formate, (2) a proportional decrease in the amplitude of FT-IR spectra acquired over the time regime in which D* decays, (3) frequency shifts in the D* - D FT-IR spectrum, (4) large-scale structural changes, as assessed by the amide I line shape, and (5) contributions to the FT-IR spectrum from the phosphate/formate buffer in the absence of PSII. We conclude that changes in the FT-IR spectrum, observed in the presence of phosphate/formate, are caused by alterations in the environment of D* and by direct phosphate/formate contributions to the spectrum.

Amides↗

PubMed1998

Determination of amphetamine, methamphetamine and dimethamphetamine in human urine by solid-phase microextraction (SPME)-gas chromatography/mass spectrometry.

A simple and rapid assay method for three stimulant drugs (amphetamine, methamphetamine, and dimethamphetamine) in human urine using solid-phase microextraction was developed. In solid-phase microextraction, the drugs were equilibrated between the adsorbent coated-fiber and aqueous sample matrix. After adsorption of the analytes, the fiber was directly transferred to the injector of a gas chromatograph, where the analytes were thermally desorbed and subsequently separated by the gas chromatograph and detected by mass spectrometer. The solid-phase microextraction method, which did not require solvents, was found to be a fast and simple analytical method. We optimized the solid-phase microextraction technique, for factors such as the NaCl salt effect (30%), pH effect (pH=12.4), equilibration time (30 min), desorption time (1 min) and coated-fiber type (100 microm poly(dimethylsiloxane)) and detected the stimulants in human urine, obtained from human subjects. The detection limits of each drug were below 1-10 ng/ml. The developed method can be applied to the abused drug test.

Amphetamine↗

PubMed1998

Benzylamine-based selective and orally bioavailable inhibitors of thrombin.

A series of p-aminomethylphenylalanine derivatives were investigated as novel thrombin inhibitors. This study led to potent inhibitors of thrombin (Ki up to 3.3 nM) that are trypsin-selective, highly orally bioavailable in rats, and highly permeable across Caco-2 cells. The P1 benzylamine binding mode in the thrombin active site was identified by X-ray crystallographic analysis.

Animals↗

PubMed1998

Constitutive and antibody-induced internalization of prostate-specific membrane antigen.

Prostate-specific membrane antigen (PSMA) is a cell surface glycoprotein expressed predominantly by prostate cancer cells. We have characterized four monoclonal antibodies that bind to the extracellular domain of PSMA (Liu et al., Cancer Res., 57: 3629-3634, 1997). Here we report that viable LNCaP cells internalize these antibodies. Laser scanning confocal microscopy reveals that the internalized antibodies accumulate in endosomes, and immunoelectron microscopy reveals that endocytosis of the PSMA-antibody complex occurs via clathrin-coated pits. In addition, a quantitative cell surface biotinylation assay demonstrates that PSMA is constitutively endocytosed in LNCaP cells and that anti-PSMA antibodies increase the rate of internalization of PSMA. These studies suggest that PSMA might function as a receptor mediating the internalization of a putative ligand. The availability of prostate-specific internalizing antibodies should aid the development of novel therapeutic methods to target the delivery of toxins, drugs, or short-range isotopes specifically to the interior of prostate cancer cells.

Antibodies, Monoclonal↗

PubMed1998

Zuotin, a ribosome-associated DnaJ molecular chaperone.

Correct folding of newly synthesized polypeptides is thought to be facilitated by Hsp70 molecular chaperones in conjunction with DnaJ cohort proteins. In Saccharomyces cerevisiae, SSB proteins are ribosome-associated Hsp70s which interact with the newly synthesized nascent polypeptide chain. Here we report that the phenotypes of an S.cerevisiae strain lacking the DnaJ-related protein Zuotin (Zuo1) are very similar to those of a strain lacking Ssb, including sensitivities to low temperatures, certain protein synthesis inhibitors and high osmolarity. Zuo1, which has been shown previously to be a nucleic acid-binding protein, is also a ribosome-associated protein localized predominantly in the cytosol. Analysis of zuo1 deletion and truncation mutants revealed a positive correlation between the ribosome association of Zuo1 and its ability to bind RNA. We propose that Zuo1 binds to ribosomes, in part, by interaction with ribosomal RNA and that Zuo1 functions with Ssb as a chaperone on the ribosome.

Cytosol↗

PubMed1998

Overexpression of the fanconi anemia group C gene (FAC) protects hematopoietic progenitors from death induced by Fas-mediated apoptosis.

Fanconi anemia is a rare, inherited disorder characterized by bone marrow failure, congenital malformations, and cancer susceptibility. The group C Fanconi anemia gene, FAC, identified by expression cloning methods, encodes a protein of unknown function that may be involved in the response to apoptotic stimuli. Hematopoietic progenitor cells from Fac knock-out mice are hypersensitive to IFN-gamma, a molecule that can induce apoptosis through up-regulation of the Fas death receptor. In this study, we used FAC-overexpressing transgenic mice to examine the relationship between FAC and Fas-triggered cell death. Hematopoietic progenitors from FAC-transgenic mice were up to 10-fold less sensitive to the cytolytic effect of Fas-ligation. Our experiments implicate FAC in the regulation of apoptosis mediated by the Fas death receptor.

Animals↗

PubMed1998

Regulation of prothrombin, thrombin receptor, and protease nexin-1 expression during development and after denervation in muscle.

Prothrombin, thrombin receptor (ThR), and protease nexin-1 (PN-1) mRNA levels in mouse muscle were quantified using competitive reverse transcriptase-polymerase chain reaction during development and after denervation to examine the possible role of thrombin in activity-dependent synapse elimination at the neuromuscular junction. The results showed that the levels of prothrombin and ThR were maximal at birth and decreased by two orders of magnitude by postnatal day 20 (P20). The level of PN-1 mRNA was fairly constant during development except for a 4-fold to 5-fold downregulation at P10 and P15, the periods of maximal synapse elimination at the rodent neuromuscular junction. The expression of prothrombin mRNA in muscle at birth was 41-fold and 22-fold lower than those of ThR and PN-1, respectively, and the level of difference between prothrombin and PN-1 reached almost three orders of magnitude at adulthood. Denervation of adult muscle resulted in a reversal of the relative expression levels of the three genes. There were rapid 8-fold and 10-fold increases in prothrombin and ThR mRNA, respectively, and a 2-fold decrease in PN-1 mRNA. The changes in mRNA levels of the three genes after denervation indicated that these genes were regulated in a innervation-dependent manner and that nerve activity may play an important regulatory role in the expression of prothrombin, ThR, and PN-1. The concurrent regulation of prothrombin and ThR suggests that thrombin-mediated cellular activities in muscle may be affected via the activation of ThR. An elevated level of local thrombin or thrombin-like activity might result from the decreased inhibitory activity of PN-1 during the period of peak synapse elimination in muscle development.

Amyloid beta-Protein Precursor↗

PubMed1998

Cloning and characterization of mitochondrial methionyl-tRNA synthetase from a pathogenic fungi Candida albicans.

A genomic sequence encoding mitochondrial methionyl-tRNA synthetase (MetRS) was determined from a pathogenic fungi Candida albicans. The gene is distinct from that encoding the cytoplasmic MetRS. The encoded protein consists of 577 amino acids (aa) and contains the class I defining sequences in the N-terminal domain and the conserved anticodon-binding amino acid, Trp, in the C-terminal domain. This protein showed the highest similarity with the mitochondrial MetRSs of Saccharomyces cerevisiae and Shizosaccharomyces pombe. The mitochondrial MetRSs of these fungi were distinguished from their cytoplasmic forms. The protein lacks the zinc binding motif in the N-terminal domain and the C-terminal dimerization appendix that are present in MetRSs of several other species. Escherichia coli tRNAMet was a substrate for the encoded protein as determined by genetic complementation and in vitro aminoacylation reaction. This cross-species aminoacylation activity suggests the conservation of interaction mode between tRNAMet and MetRS.

Amino Acid Sequence↗

PubMed1998

N-carbamoyl-L-glutamate plus L-arginine can protect ammonia intoxication in rats with reduced functional liver mass.

We previously reported the protective effect of N-carbamoyl-L-glutamate plus L-arginine in rats given a lethal dose (LD99.9) of ammonium acetate (Kim, S. et al., Proc. Natl. Acad. Sci. 69, 3530-3533, 1971; ref.1). The present study was undertaken to find out whether the same compounds could also be effective even after the functional mass of the liver was significantly reduced. Thus, the protective effect of these compounds in 70% partial hepatectomized rats following the injection of sublethal dose of ammonium acetate was assessed. The mixture could significantly decrease blood ammonia level compared with PBS-injected control group. In addition, abnormal behaviors observed in the control rats were significantly improved. The protective effect on the behavioral change seemed to be closely related with their effect on blood ammonia level, showing a strong correlation between the blood ammonia level and the behavioral score. The findings provide a rational basis for the clinical use of N-carbamoyl-L-glutamate plus L-arginine in the prevention and treatment of hyperammonemia encountered in liver diseases.

Acetates↗

PubMed1998

In vivo chiro-inositol metabolism in the rat: a defect in chiro-inositol synthesis from myo-inositol and an increased incorporation of chiro-[3H]inositol into phospholipid in the Goto-Kakizaki (G.K) rat.

We report our comparative studies of myo- and chiro-[3H]inositol distribution in control nondiabetic Wistar and spontaneous nonobese insulin-resistant Type II diabetic G.K. rat tissues following 78-h labeling period. From various tissue extracts, free inositols, inositol phosphates, and inositol phospholipids were isolated and analyzed. Our findings demonstrate (1) a significant difference in the metabolism of myo- and chiro-inositol in normal Wistar and G.K. rats, (2) a severe defect in conversion of myo-[3H]inositol to chiro-[3H]inositol at the inositol phospholipid level of insulin-sensitive tissues of the G.K. rat, (3) an increased incorporation of myo-[3H]inositol into purified inositol phospholipids of the G.K. rat consistent with a decreased conversion to chiro-[3H]inositol, (4) the presumed presence of a pathway which incorporates chiro-[3H]inositol into inositol phospholipids, and which is overactive in the G.K. rat compared to the Wistar rat, and (5) no or minimal conversion of chiro-[3H]inositol to myo-[3H]inositol.

Animals↗

PubMed1998

Differential accumulation of transcripts for ACC synthase and ACC oxidase homologs in etiolated mung bean hypocotyls in response to various stimuli.

Ethylene can be produced by a variety of developmental and environmental factors such as ripening, the plant hormone auxin, and mechanical wounding via a biosynthetic pathway including AdoMet synthase, ACC synthase, and ACC oxidase steps. ACC synthase and ACC oxidase are known to be encoded by multigene families, and are believed to be differentially expressed in response to various stimuli. In mung bean, ACC synthase is encoded by 7 genes, ACS1, ACS2 ACS3, ACS4, ACS5, ACS6, and ACS7, and ACC oxidase by 2 genes, ACO1 and ACO2. In this study, was have investigated differential accumulation of transcripts for ACC synthase and ACC oxidase homologs in etiolated mung bean hypocotyls under various conditions by the semiquantitative RT-PCR method. Primers which can specifically bind and amplify each cDNAs of ACS1, ACS2, ACS3, ACS4, ACS5, ACS6, ACS7, and ACO1, and ACO2 were designed and used to monitor the responses to various stimuli. Transcripts of ACO1 and ACO2 were accumulated constitutively in the hypocotyl segments even without andy treatment. After cold treatment on intact plant, transcripts of ACS5, ACS6, and ACS7 were accumulated in the hypocotyl segments. We also found the excision of hypocotyl segments and incubation in a buffer solution, a typical way of chemical treatments to hypocotyl segments, lowered the level of ACO2 transcripts with little change of the level of ACO1 transcripts. In response to incubation with IAA (0.1 mM) of excised hypocotyl segments, transcripts of ACS1, ACS6, and ACS7 were accumulated and the level of ACO2 transcripts was increased. Transcripts of ACS1, ACS2, ACS3, ACS5, ACS6 and ACS7 were induced by incubation with OGA (50 micrograms/ml), while the transcripts of ACS4 were accumulated and the level of ACO2 transcripts was increased by incubation with 1 mM LiCl. Our results strongly suggest that all seven ACC synthase genes and two ACC oxidase genes must be active and each gene is differentially regulated by a different subset of the inducing factors.

Adjuvants, Immunologic↗

PubMed1998

Expression of peroxisome proliferator-activated receptor gamma (PPARgamma) in rat aortic smooth muscle cells.

Peroxisome proliferator-activated receptor gamma (PPARgamma), a member of nuclear receptors, is expressed at a high level in adipose tissue and plays an important role in adipocyte differentiation. In the present study, we identified the expression of PPARgamma in rat aortic smooth muscle cells (RASMC) using reverse transcription-polymerase chain reaction and gel mobility shift assay. In addition, to investigate whether PPARgamma in RASMC is functional or not, we examined the effect of two specific ligands for PPARgamma, a thiazolidinedione anti-diabetic agent, troglitazone, and 15-deoxy-Delta12,14-prostaglandin J2, on the transcriptional activity of PPAR responsive element (PPRE). A significant increase in the activity of PPRE by addition of these ligands was found. These results suggest that in RASMC, target genes for PPARgamma may be activated by specific ligands for PPARgamma through PPRE in their promoters. In conclusion, PPARgamma is expressed and functional in vascular smooth muscle cells.

Animals↗

PubMed1998

Conservation of structure and function between human and murine IL-16.

IL-16 is a proinflammatory cytokine that signals via CD4, inducing chemotactic and immunomodulatory responses of CD4+ lymphocytes, monocytes, and eosinophils. Comparative analysis of murine and human IL-16 homologs could reveal conserved structures that would help to identify key functional regions of these cytokines. To that end, we cloned the murine IL-16 cDNA and found a high degree of amino acid similarity comparing the predicted murine and human IL-16 precursor proteins (pro-IL-16). The highest similarity (82.1%) was found in the C-terminal region, which is cleaved from pro-IL-16 to yield biologically active IL-16. Chemotaxis experiments with IL-16 of murine and human origin, using murine splenocytes or human T lymphocytes as targets, showed cross-species stimulation of motility. Synthetic oligopeptides and anti-peptide Ab were produced, based on the sequences of three predicted hydrophilic domains of IL-16 potentially presented in exposed positions. None of these peptides had intrinsic IL-16 bioactivity, but one (corresponding to a hydrophilic C-terminal domain of IL-16) partially displaced binding of OKT4 mAb to human lymphocytes. This peptide, and its cognate Ab, also inhibited IL-16 chemoattractant activity for human and murine cells. These studies demonstrate a high degree of structural and functional similarity between human and murine IL-16 and suggest that amino acids in the C terminus are critical for its chemoattractant function. The data suggest cross-species conservation of IL-16 receptor structures as well. Inhibitory peptides may be useful in disease states where the proinflammatory functions of IL-16 are detrimental to the host.

Amino Acid Sequence↗

PubMed1998

Human general transcription factor TFIIB: conformational variability and interaction with VP16 activation domain.

Human TFIIB, an essential factor in transcription of protein-coding genes by RNA polymerase II, consists of an amino-terminal zinc binding domain (TFIIBn) connected by a linker of about 60 residues to a carboxy-terminal core domain (TFIIBc). The TFIIB core domain has two internally repeated motifs, each comprising five alpha-helices arranged as in the cyclin box. Compared to the crystal structure of TFIIBc in complex with TBP and a TATA-containing oligonucleotide, the NMR-derived solution structure of free TFIIBc is more compact, with a different repeat-repeat orientation and a significantly shorter first helix in the second repeat. Analysis of backbone 15N relaxation parameters indicates the presence of relatively large amplitude, nanosecond time-scale motions in the TFIIBc interrepeat linker and structural fluctuations throughout the backbone. Interaction of TFIIBc with the acidic activation domain of VP16 or with TFIIBn induces 1H-15N chemical shift and line width changes concentrated in the first repeat, interrepeat linker and the first helix of the second repeat. These results suggest that TFIIB is somewhat pliable and that the conformation of the C-terminal core domain can be modulated by interaction with the N-terminal zinc binding domain. Furthermore, binding of the VP16 activation domain may promote TFIIBc conformations primed for binding to a TBP-DNA complex.

Binding Sites↗

PubMed1998

Infrared spectroscopic identification of the C-O stretching vibration associated with the tyrosyl Z. and D. radicals In photosystem II

Photosystem II (PSII) is a multisubunit complex, which catalyzes the photo-induced oxidation of water and reduction of plastoquinone. Difference Fourier-transform infrared (FT-IR) spectroscopy can be used to obtain information about the structural changes accompanying oxidation of the redox-active tyrosines, D and Z, in PSII. The focus of our work is the assignment of the 1478 cm-1 vibration, which is observable in difference infrared spectra associated with these tyrosyl radicals. The first set of FT-IR experiments is performed with continuous illumination. Use of cyanobacterial strains, in which isotopomers of tyrosine have been incorporated, supports the assignment of a positive 1478/1477 cm-1 mode to the C-O stretching vibration of the tyrosyl radicals. In negative controls, the intensity of this spectral feature decreases. The negative controls involve the use of inhibitors or site-directed mutants, in which the oxidation of Z or D is eliminated, respectively. The assignment of the 1478/1477 cm-1 mode is also based on control EPR and fluorescence measurements, which demonstrate that no detectable Fe+2QA- signal is generated under FT-IR experimental conditions. Additionally, the difference infrared spectrum, associated with formation of the S2QA- state, argues against the assignment of the positive 1478 cm-1 line to the C-O vibration of QA-. In the second set of FT-IR experiments, single turnover flashes are employed, and infrared difference spectra are recorded as a function of time after photoexcitation. Comparison to kinetic transients generated in control EPR experiments shows that the decay of the 1477 cm-1 line precisely parallels the decay of the D. EPR signal. Taken together, these two experimental approaches strongly support the assignment of a component of the 1478/1477 cm-1 vibrational lines to the C-O stretching modes of tyrosyl radicals in PSII. Possible reasons for the apparently contradictory results of Hienerwadel et al. (1996) Biochemistry 35, 15,447-15,460 and Hienerwadel et al. (1997) Biochemistry 36, 14,705-14,711 are discussed. Copyright 1998 Elsevier Science B.V. All rights reserved.

Journal Article↗

PubMed1998

Selective targeting of Kupffer cells with liposomal butyrate augments portal venous transfusion-induced immunosuppression.

BACKGROUND: Enhanced Kupffer cell production of the immunosuppressive arachidonic acid metabolite prostaglandin E2 (PGE2) has been shown to be a mechanism of the immunosuppressive effect of portal venous transfusions (PVT). Butyrate, a four-carbon short-chain fatty acid, has received increased attention because of its ability to enhance gene transcription. This study tested the hypothesis that the intrahepatic delivery of butyrate enhances Kupffer cell PGE2 production and thus augments the immunosuppressive effect of PVT. METHODS: Butyrate was incorporated into liposomes and administered intravenously to Lewis rats. Control rats were administered liposomes without butyrate. Twenty-four hours after liposome injection, rats were administered a PVT of 1 ml of Wistar-Furth blood. Kupffer cells were isolated, and PGE2 and tumor necrosis factor-alpha levels were measured in the culture medium after 24 hr. Additionally, Kupffer cells from butyrate-treated and control animals were added to one-way mixed lymphocyte reaction cultures. RESULTS: Intrahepatic delivery of butyrate via liposomes increased Kupffer cell PGE2 (3800+/-1220 vs. 1010+/-119 pg/ml, P<0.05) and decreased tumor necrosis factor-alpha (1670+/-81 vs. 3360+/-415 pg/ml, P<0.01) production as compared with controls. Butyrate also augmented the Kupffer cell-mediated immunosuppression as demonstrated by significant depression of the mixed lymphocyte reaction (690+/-119 vs. 3850+/-148 cpm, P<0.01). CONCLUSION: The results support the hypothesis that intrahepatic delivery of butyrate enhances Kupffer cell PGE2 production, and specific targeting of Kupffer cells with liposomes containing immunomodulating agents such as butyrate may be a useful means of augmenting immunosuppression protocols in organ transplantation.

Animals↗

PubMed1998

Biochemical and phylogenetic analyses of methionyl-tRNA synthetase isolated from a pathogenic microorganism, Mycobacterium tuberculosis.

Mycobacterium tuberculosis methionyl-tRNA synthetase (MetRS) has been cloned and characterized. The protein contains class I signature sequences but lacks the Zn2+ binding motif and the C-terminal dimerization appendix that are found in MetRSs from several organisms including E. coli MetRS. Consistent with these features, the enzyme behaved as a monomer in a gel filtration chromatography and did not contain the bound Zn2+. Nonetheless, it was active to the tRNAMet of E. coli as determined by in vivo genetic complementation and in vitro reaction. Phylogenetic analysis separated the M. tuberculosis and E. coli MetRSs into prokaryote and eukaryote-archaea group, respectively. This result is consistent with the taxonomic locations of the organism but is an interesting contrast to the case of its paralogous protein, isoleucyl-tRNA synthetase, and suggests that the two enzymes evolved in separate idiosyncratic pathways.

Amino Acid Sequence↗