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Biomedical subjects

S T Kim

Publications and source records attributed to S T Kim.

At least 91 records · Page 5Linked to original sources
PubMed1996

Purification and characterization of Drosophila melanogaster photolyase.

Animal-type photolyases have very limited sequence homology to microbial-type photolyases. We wanted to find out whether the two types of enzymes have different or similar biochemical and photochemical properties. In particular, the chromophore/cofactor composition of animal photolyases is of special interest since the presence and nature of a second chromophore in these enzymes are not known in contrast to the microbial photolyases which contain FAD cofactor, and folate or deazaflavin as second chromophores. We overproduced the Drosophila melanogaster photolyase in Escherichia coli using the cloned gene. The enzyme contains FAD and folate and thus belongs in the folate class of enzymes but with an action spectrum peak at 420 nm.

Absorption↗
PubMed1996

Improved sample preparation for cross-sectional transmission electron microscopy of layered structures using rocking-angle ion-milling techniques.

The rocking-angle ion-milling technique has been employed to produce optimum Pt/Ti/SiO2/Si, W/TiN/SiO2/Si, and (Pb,La)TiO3/Pt/MgO samples for cross-sectional transmission electron microscopy (TEM). Because of the different ion-milling rates between film layers and substrate materials, no satisfactory cross-sectional TEM samples could be obtained when they were made by the conventional ion-milling method. The differential thinning problems could be effectively solved by optimizing both ion-milling rocking-angle and ion-beam incidence angle without the increase of overall milling time. It was found that the rocking-angle of around 40 degrees is good when the multilayer structure is composed of materials with great ion-milling rate differences, while the rocking angle of around 80 degrees is good when the ion-milling rate differences are relatively small.

Microscopy, Electron↗
PubMed1996

Endotoxin rejection by ultrafiltration through high-flux, hollow fiber filters.

The efficacy of endotoxin (ET) rejection of four hollow fiber membranes with comparable sieving properties was evaluated in an ultrafiltration experiment. The solution conditioned with type I lipopolysaccharide (LPS) from Escherichia coli, 80,000 endotoxin units (EU)/L, was filtered through polyesterpolymer alloy (PEPA), polymethyl methacrylate (PMMA), polyacrylonitrile (PAN), and polysulfone (PS) membranes. The ET activity of the filtrate was not detectable in PEPA and PMMA, 6.4 +/- .04 (mean +/- SD) EU/L in PAN, and 10.3 +/- 1.1 EU/L in PS. The ET activity of the filtrate of type II LPS from Acinetobacter solution, 80,000 EU/L, was not detectable in PEPA, 3.7 +/- 0.4 EU/L in PMMA, 16.5 +/- 1.5 EU/L in PAN, and 20.7 +/- 1.4 EU/L in the PS filter. The order of the rejection capability coincided with the adsorptive capacity as shown by the decrement in ET levels of solutions filled within the filter modules in the adsorption equilibrium experiment. In conclusion complete rejection of ET molecules can be achieved by ultrafiltration through hydrophobic membranes having a high adsorptive capacity in addition to an appropriate sieving property for ET molecules.

Acinetobacter↗
PubMed1996

Purification and partial characterization of (6-4) photoproduct DNA photolyase from Xenopus laevis.

The (6-4) photoproduct DNA photolyase was detected in two vertebrate animals Crotalus atrox (rattlesnake) and Xenopus laevis (South African clawed toad). The enzyme was extensively purified from X. laevis and characterized. The highly purified enzyme is fluorescent with an excitation maximum at 420-440 nm and emission maximum at 460-480 nm. The photorepair action spectrum matches the fluorescence excitation spectrum with a 430 nm maximum.

Animals↗
PubMed1996

Isolated hematuria in adults: IgA nephropathy is a predominant cause of hematuria compared with thin glomerular basement membrane nephropathy.

We examined kidney biopsy specimens obtained from 40 adult patients with isolated hematuria to determine the renal pathology and the incidence of thin glomerular basement membrane nephropathy (TGBMN). Light microscopy showed minor glomerular abnormalities in 26 patients (65%), focal and segmental lesions in 3 patients (8%), and mild diffuse proliferative glomerulonephritis in 11 patients (28%). Immunofluorescence microscopy showed IgA nephropathy (IgA-N) in 16 patients (40%), in whom no progressive lesions were identified. We measured the glomerular basement membrane (GBM) thickness using electron microscopy, and TGBMN was identified in 4 patients (10%). Our results suggest that IgA is a major pathological finding in adult patients with isolated hematuria. GBM thinning does not appear to be a major cause of glomerular hematuria.

Adolescent↗
PubMed1996

Successful treatment with fluconazole of protothecosis developing at the site of an intralesional corticosteroid injection.

We report a case of cutaneous protothecosis treated successfully with oral fluconazole. Fluconazole appears to be an effective alternative to conventional drugs for the treatment of cutaneous protothecosis. Cutaneous protothecosis is an uncommon infection due to achlorophyllic, saprophytic, algae-like unicellular organisms of the genus Prototheca that occurs mainly in immunocompromised patients. To date there is no standard treatment regimen. Surgical excision, oral ketoconazole, intravenous amphotericin B alone or in combination with oral tetracycline have been reported to be effective in the management of protothecosis. We report a 55-year-old immunocompetent woman with cutaneous protothecosis which developed at the site of intralesional triamcinolone acetonide injection, who was successfully treated with oral fluconazole.

Antifungal Agents↗
PubMed1995

Crystal structure of DNA photolyase from Escherichia coli.

Photolyase repairs ultraviolet (UV) damage to DNA by splitting the cyclobutane ring of the major UV photoproduct, the cis, syn-cyclobutane pyrimidine dimer (Pyr <> Pyr). The reaction is initiated by blue light and proceeds through long-range energy transfer, single electron transfer, and enzyme catalysis by a radical mechanism. The three-dimensional crystallographic structure of DNA photolyase from Escherichia coli is presented and the atomic model was refined to an R value of 0.172 at 2.3 A resolution. The polypeptide chain of 471 amino acids is folded into an amino-terminal alpha/beta domain resembling dinucleotide binding domains and a carboxyl-terminal helical domain; a loop of 72 residues connects the domains. The light-harvesting cofactor 5,10-methenyltetrahydrofolylpolyglutamate (MTHF) binds in a cleft between the two domains. Energy transfer from MTHF to the catalytic cofactor flavin adenine dinucleotide (FAD) occurs over a distance of 16.8 A. The FAD adopts a U-shaped conformation between two helix clusters in the center of the helical domain and is accessible through a hole in the surface of this domain. Dimensions and polarity of the hole match those of a Pyr <> Pyr dinucleotide, suggesting that the Pyr <> Pyr "flips out" of the helix to fit into this hole, and that electron transfer between the flavin and the Pyr <> Pyr occurs over van der Waals contact distance.

Amino Acid Sequence↗
PubMed1995

Putative blue-light photoreceptors from Arabidopsis thaliana and Sinapis alba with a high degree of sequence homology to DNA photolyase contain the two photolyase cofactors but lack DNA repair activity.

The putative blue-light photoreceptor genes of Arabidopsis thaliana and Sinapis alba (mustard) are highly homologous to the DNA repair genes encoding DNA photolyases. The photoreceptors from both organisms were overexpressed in Escherichia coli, purified, and characterized. The photoreceptors contain two chromophores which were identified as flavin adenine dinucleotide and methenyltetrahydrofolate. This chromophore composition suggests that the blue light photoreceptor may initiate signal transduction by a novel pathway which involves electron transfer. Despite the high degree of sequence identity to and identical chromophore composition with photolyases, neither photoreceptor has any photoreactivating activity.

Arabidopsis↗
PubMed1995

Structure and function of the UvrB protein.

UvrB plays a central role in (A)BC excinuclease. To identify the regions of UvrB which are involved in interacting with UvrA, UvrC, and DNA, deletion mutants, point mutants, and various fusion forms of UvrB were constructed and characterized. We found that the region encompassing amino acid residues 115-250 of UvrB binds to UvrA, while the region encompassing amino acid residues 547-673 binds to both UvrA and UvrC. In addition, the region between these two domains, which contains the helicase motifs II-VI, was found to be involved in binding to DNA. Within this DNA-binding region, two point mutants, E265A and E338A, were found to be unable to bind DNA while two residues, Phe-365 and Phe-496, were identified to interact with DNA. Furthermore, fluorescence quenching studies with mutants F365W and F496W and repair of thymine cyclobutane dimers by photoinduced electron transfer by these mutants suggest that residues Phe-365 and Phe-496 interact with DNA most likely through stacking interactions.

Adenosine Triphosphatases↗
PubMed1995

Low expression of adhesion molecules in a case of cutaneous T-cell lymphoma.

A case of cutaneous T-cell lymphoma (CTCL) with low expression of the adhesion molecules lymphocyte function-associated antigen-1 (LFA-1), intercellular adhesion molecule-1 (ICAM-1), and very late antigen-4 (VLA-4) is described. The patient was a 90-year-old man with red round homogeneous tumors on his scalp, trunk, and extremities. He had no history of definite erythema or plaque stage. A biopsy sample taken from a tumor revealed massive infiltration of atypical lymphocytes in the reticular dermis and subcutis with a definite clear zone. The atypical lymphocytes were medium-sized with slightly convoluted nuclei. Immunohistochemically, the infiltrates showed the phenotype of so-called memory T cells. On the basis of these features, the case was diagnosed as CTCL. Expression of LFA-1, ICAM-1 and VLA-4 on the infiltrates was 9%, 13% and 11%, respectively, which is much lower than that in classic mycosis fungoides. This finding suggests that loss of these adhesion molecules may contribute to loss of epidermotropism in the advanced stage of CTCL.

Aged↗
PubMed1995

Peripheral T-cell lymphoma involving subcutaneous tissue.

The peripheral T-cell lymphomas, presumably derived from various immunocompetent peripheral T-cell system components, form a heterogeneous group of non-Hodgkin's lymphomas. We describe two patients with peripheral T-cell lymphoma primarily involving subcutaneous tissue. They presented with multiple subcutaneous nodules. Skin biopsy specimens in both patients demonstrated a lobular subcutaneous infiltrate. The infiltrate consisted of small and medium-sized atypical lymphoid cells. Both patients had a protracted clinical course before they were diagnosed as having malignant lymphoma. We detected latent Epstein-Barr virus infection in the skin lesions of case 2. Latent Epstein-Barr virus infection might be related to the development of this variant of peripheral T-cell lymphoma.

Adult↗
PubMed1995

Photorepair of nonadjacent pyrimidine dimers by DNA photolyase.

Photolyases reverse the harmful effects of UV light on cells by converting pyrimidine dimers (Pyr[]Pyr) into two pyrimidine monomers by utilizing near-UV and visible light. Previous work has shown that photolyase repairs T[c,s]T and T[t,s]T in DNA as well as U[]U in RNA, all of which are formed by joining the two adjacent pyrimidines in a light-dependent reaction. In this report, we show that Pyr[]Pyr formed in nonadjacent pyrimidines are also substrates for DNA photolyase.

DNA Repair↗
PubMed1994

Characterisation of D-arabinono-1,4-lactone oxidase from Candida albicans ATCC 10231.

D-Erythroascorbic acid was detected from the cell extracts of a dimorphic fungus, Candida albicans. Its concentration in yeast cells grown at 25 degrees C was estimated to be about 0.45 mumol/ml cell water. D-Arabinono-1,4-lactone oxidase, which catalyses the final step in the biosynthesis of D-erythroascorbic acid, was purified 639-fold from the mitochondrial fraction of C. albicans to apparent homogeneity, with an overall yield of 21.2%, by a purification procedure consisting of Triton X-100 solubilisation, ammonium sulphate precipitation, anion-exchange, hydrophobic-interaction, gel-filtration and dye-ligand chromatographies. Gel-filtration chromatography and polyacrylamide-gradient gel electrophoresis in the presence of deoxycholate gave apparent molecular masses of 110 kDa and 84.4 kDa, respectively. SDS/PAGE showed only one protein band corresponding to a molecular mass of 66.7 kDa. Considering the binding of detergents, the enzyme is suggested to be a single polypeptide. The enzyme showed a typical fluorescence excitation spectrum of a flavin-containing enzyme. The flavin was not released by treatment with SDS, CCl3CO2H or boiling, indicating that it may be covalently bound to the enzyme protein. The enzyme was optimally active at 40 degrees C and at pH 6.1. The enzyme was stable in the range pH 7.5-10. An apparent Km value for D-arabinono-1,4-lactone was 44.1 mM. L-Galactono-1,4-lactone, L-gulono-1,4-lactone and L-xylono-1,4-lactone could also serve as substrates. Competitive inhibition was demonstrated with D-glucono-1,5-lactone, L-arabinono-1,4-lactone, D-galactono-1,4-lactone and D-gulono-1,4-lactone. p-Chloromercuribenzoate, N-ethylmaleimide, iodoacetic acid, iodoacetamide and divalent metal ions such as Cd2+, Hg2+, Mn2+ and Zn2+ exhibited inhibitory effects on the enzyme.

Ascorbic Acid↗
PubMed1994

Characterization of a medium wavelength type DNA photolyase: purification and properties of photolyase from Bacillus firmus.

The gene for the apoenzyme of Bacillus firmus photolyase was cloned and sequenced. The enzyme was overproduced in Escherichia coli, purified, and characterized. It has the unique property of having the maximum activity over a wavelength range where all other known photolyases exhibit modest activity. The enzyme contains reduced FAD and methenyltetrahydrofolate and has an absorption and action spectrum peak at 410 nm, and it repairs DNA with a quantum yield of phi approximately 0.75.

Amino Acid Sequence↗