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Biomedical subjects

B Kim

Publications and source records attributed to B Kim.

At least 127 records · Page 7Linked to original sources
PubMed1996

Retrotransposon reverse-transcriptase-mediated repair of chromosomal breaks.

The abundance of short and long interspersed nuclear sequences (SINEs and LINEs) and pseudogenes in eukaryotic genomes indicates that reverse transcriptase (RT)-mediated phenomena are important in genome evolution. However, the mechanisms involved in their spread are largely unknown. We have developed a selection system in the yeast Saccharomyces cerevisiae to test whether RT-mediated events could be linked to the repair of double-strand breaks (DSBs). Here we show that DSBs can be fixed by the insertion of complementary DNAs at the break site. In the presence of functional RT (from human L1, yeast Tyl or Crithidia CRE1), and in the absence of homologous recombination, an HO endonuclease-induced DSB at the mating type (MAT) locus is the primary site at which a marked cDNA is observed among surviving cells. The structure and junctional sequences of these insertions suggest that repair occurs primarily by non-homologous recombination. Our data support a role for endogenous retroelements in the repair of chromosomal breaks.

Animals↗
PubMed1996

Human immunodeficiency virus reverse transcriptase. Functional mutants obtained by random mutagenesis coupled with genetic selection in Escherichia coli.

We describe catalytically active mutants of HIV RT (human immunodeficiency virus reverse transcriptase) generated by random sequence mutagenesis and selected in Escherichia coli for ability to complement the temperature-sensitive phenotype of a DNA polymerase I (Pol Its) mutant. We targeted amino acids Asp-67 through Arg-78 in HIV RT, which form part of the beta3-beta4 flexible loop and harbor many of the currently known mutations that confer resistance to nucleoside analogs. DNA sequencing of 109 selected mutants that complement the Pol Its phenotype revealed substitutions at all 12 residues targeted, indicating that none of the wild-type amino acids is essential. However, single mutations were not observed at Trp-71, Arg-72, and Arg-78, consistent with evolutionary conservation of these residues among viral RTs and lack of variation at these positions among isolates from patients. The mutations we recovered included most of those associated with drug resistance as well as previously unidentified mutations. Purification and assay of 14 mutant proteins revealed correlation between their DNA-dependent DNA polymerize activity in vitro and ability to complement the Pol Its phenotype. Activity of several mutants was resistant to 3'-azidothymidine triphosphate. We conclude that random sequence mutagenesis coupled with positive genetic selection in E. coli yields large numbers of functional HIV RT mutants. Among these are less active variants which are unlikely to be isolated from HIV-infected individuals and which will be informative of the roles of individual amino acids in the catalytic functions of the enzyme.

Amino Acid Sequence↗
PubMed1996

Olmsted syndrome. Case report and identification of a keratin abnormality.

BACKGROUND: Olmsted syndrome is a rare disorder characterized by a mutilating palmoplantar keratoderma and periorificial keratotic plaques. It begins in early childhood and is complicated by the development of painful flexion contractures, constrictions, and autoamputations of the digits. Only 11 cases of Olmsted syndrome have been reported to date. However, no biochemical abnormalities in the skin were reported in any of these cases. OBSERVATIONS: We report the 12th case of Olmsted syndrome. In addition, we describe a keratin abnormality found in a skin specimen obtained from our patient. The specimen showed a suprabasilar staining pattern with AE1, an antibody that shows only basilar staining in normal skin. CONCLUSION: We report the 12th case of Olmsted syndrome, review the literature, and describe a keratin abnormality that was found in our patient's skin specimen.

Child↗
PubMed1996

Tolerance of different proteins for amino acid diversity.

Random mutagenesis of genes followed by positive genetic selection in bacteria requires that the variant molecules confer biological activity, and is thus the most demanding approach for generating new functionally active molecules. Furthermore, one can learn much about the protein in question by comparing the population of selected molecules to the library from which they were selected. Described here is a mathematical method designed to guide such comparisons. We use as examples the results of randomization-selection studies of four different proteins. There exists, in general, a positive correlation between the number of amino acid substitutions in a critical region of a protein and the likelihood of inactivation of that protein; a correlation long suspected, but developed here in detail. At this time, we are comparing regions in different proteins and our conclusions must be limited. However, the method presented can serve as a guideline for anticipating the yield of new active mutants in genetic complementation assays based on the extent of randomization.

Amino Acids↗
PubMed1996

Calcium regulation of thin filament movement in an in vitro motility assay.

The ability of calcium to regulate thin filament sliding velocity was studied in an in vitro motility assay system using cardiac troponin and tropomyosin and rhodamine-phalloidin-labeled skeletal actin and skeletal heavy meromyosin to propel the filaments. Measurements showed that both the number of thin filaments sliding and their sliding speed (Sf) were dependent on the calcium concentration in the range of pCa 5 to 9. Thin filament motility was completely inhibited only if troponin and tropomyosin were added at a concentration of 100 nM to the motility assay solution and the pCa was more than 8. The filament sliding speed was dependent on the pCa in a noncooperative fashion (Hill coefficient = 1) and reached maximum at 5 microns/s at a pCa of 5. The number of filaments moving uniformly decreased from > 90% at pCa 5-6 to near zero in less than 1 pCa unit. This behavior may be explained by a hypothesis in which the regulatory proteins control the number of cross-bridge heads interacting with the thin filaments rather than the rate at which they individually hydrolyze ATP or translocate the thin filaments.

Animals↗
PubMed1996

Modulation of renal kallikrein production by dietary protein in streptozotocin-induced diabetic rats.

Renal kallikrein levels and excretion rates are increased in insulin-treated diabetic rats with hyperfiltration, and inhibition of kallikrein or blockade of kinin receptors reduces GFR and RPF. In contrast, insulin-deprived severely (SD) diabetic rats that display renal vasoconstriction show reduced levels and excretion rates of renal kallikrein. In these two models, dietary protein manipulation was utilized to study further the relationships between renal kallikrein and renal hemodynamic regulation. Insulin-deprived SD and insulin-treated moderately diabetic (MD) rats were fed a low (9%), normal (25%), and a high (50%) protein diet. In SD rats fed the 50% protein diet, GFR, RPF, and kallikrein excretion rate were increased compared with SD rats fed the 25% protein diet (GFR, 2.66 +/- 0.16 versus 1.74 +/- 0.30 mL/min; RPF, 7.78 +/- 0.58 versus 5.14 +/- 1.03 mL/min; total kallikrein, 248 +/- 24 versus 120 +/- 30 micrograms/24 h, SD 50% versus SD 25%, respectively; P < 0.005). In MD rats fed the 9% protein diet, GFR, RPF, and kallikrein excretion rate were significantly reduced compared with MD 25% protein-fed rats (GFR, 1.54 +/- 0.07 versus 1.95 +/- 0.09 mL/min; RPF, 5.58 +/- 0.35 versus 7.81 +/- 0.35 mL/min; total kallikrein, 119 +/- 8.3 versus 219 +/- 15 micrograms/24 h, MD 9% versus MD 25%, respectively; P < 0.005). Protein restriction in normal nondiabetic rats resulted in a twofold decrease in kallikrein mRNA levels. These findings suggest that the renal hemodynamic response to dietary protein manipulation in diabetic rats could be mediated via changes in renal kallikrein-kinin system activity.

Actins↗
PubMed1995

Homogeneous assays for riboflavin mediated by the interaction between enzyme-biotin and avidin-riboflavin conjugates.

Homogeneous-type enzyme-linked competitive binding assays utilizing the synthetic enzyme-biotin and avidin-riboflavin conjugates are developed for the detection of riboflavin as well as its binder protein. The activity of the enzyme-biotin conjugate is inhibited in the presence of the avidin-riboflavin conjugate, and the observed inhibition is reversed in an amount dependent on the concentration of riboflavin binding protein (RBP) added. Upon additions of free riboflavin to the mixture, activity is reinhibited in an amount proportional to the riboflavin concentration. Three different enzymes are examined as the labels: glucose-6-phosphate dehydrogenase, adenosine deaminase, and alkaline phosphatase. The catalytic activity of these enzymes, when conjugated with biotin, is shown to be inhibited to a significant degree (> 90%) by the binding of the avidin-riboflavin conjugate, and reversed upon additions of RBP.

Adenosine Deaminase↗
PubMed1995

Homology in structural organization between E. coli ClpAP protease and the eukaryotic 26 S proteasome.

Energy-dependent protein degradation is carried out by large multimeric protein complexes such as the proteasomes of eukaryotic and archaeal cells and the ATP-dependent proteases of eubacterial cells. Clp protease, a major multicomponent protease of Escherichia coli, consists of a proteolytic component, ClpP, in association with an ATP-hydrolyzing, chaperonin-like component, ClpA. To provide a structural basis for understanding the regulation and mechanism of action of Clp protease, we have used negative staining electron microscopy and image analysis to examine ClpA and ClpP separately, as well as active ClpAP complexes. Digitized images of ClpP and ClpA were analyzed using a novel algorithm designed to detect rotational symmetries. ClpP is composed of two rings of seven subunits superimposed in bipolar fashion along the axis of rotational symmetry. This structure is similar to that formed by the beta subunits of the eukaryotic and archaeal proteasomes. In the presence of MgATP, ClpA forms an oligomer with 6-fold symmetry when viewed en face. Side views of ClpA indicate that the subunits are bilobed with the respective domains forming two stacked rings. ClpAP complexes contain a tetradecamer of ClpP flanked at one or both ends with a hexamer of ClpA, resulting in a symmetry mismatch between the axially aligned molecules. Our findings demonstrate that, despite the lack of sequence similarity between ClpAP and proteasomes, these multimeric proteases nevertheless have a profound similarity in their underlying architecture that may reflect a common mechanism of action.

Adenosine Triphosphatases↗
PubMed1995

Human immunodeficiency virus reverse transcriptase substitutes for DNA polymerase I in Escherichia coli.

We present evidence that human immunodeficiency virus (HIV) reverse transcriptase (RT) can substitute for DNA polymerase I in bacteria. Expression of HIV RT enables an Escherichia coli mutant, polA12 recA718, containing a temperature-sensitive mutation in DNA polymerase I, to grow at a nonpermissive temperature. The plasmid pBR322 contains a DNA polymerase I-dependent origin of replication. Expression of HIV RT enables the same E. coli mutant to maintain this plasmid at a nonpermissive temperature. Furthermore, expression of HIV RT in this mutant renders it sensitive to 3'-azido-3'-deoxythymidine, a commonly used anti-AIDS drug that targets HIV RT. These combined findings on the genetic complementation of DNA polymerase I by HIV RT provide a bacterial assay to screen for drugs directed against HIV RT. Genetic complementation provides a method for positive selection of large numbers of functional HIV RT mutants for studies on structure-function relationships.

DNA Polymerase I↗
PubMed1995

Force-endurance relationship: does it matter if gloves are donned?

The human hand is a very useful multipurpose tool in all environments. However, performance capabilities are compromised considerably when gloves are donned. This is especially true for extra-vehicular activity (EVA) gloves used in a space environment. The primary aim of this study was to establish exertion and endurance limits for specific tasks. The objective of this study was to develop grip force endurance relations. Six subjects participated in a factorial experiment involving three hand conditions, three pressure differentials, and four levels of force exertion. The results indicate that while the force that could be exerted depended on the glove, pressure differential, and the level of exertion, the endurance time at any exertion level depended just on the level of exertion expressed as a percentage of maximum exertion possible at that condition. The impact of these findings for practitioners as well as theoreticians is discussed.

Journal Article↗
PubMed1995

Validation of a noninvasive method to measure brain temperature in vivo using 1H NMR spectroscopy.

The goal of this study was to evaluate the potential of using the difference between the 1H NMR frequencies of water and N-acetylaspartic acid (NAA) to measure brain temperature noninvasively. All water-suppressed and non-water-suppressed 1H NMR spectra were obtained at a field strength of 4.7 T using a surface coil. Experiments performed on model solutions revealed a decrease in the difference between NMR frequencies for NAA and water as a linear function of increasing temperature from 14 to 45 degrees C. Changing pH in the range 5.5-7.6 produced no discernible trends for concurrent changes in the slope and intercept of the linear relationship. There were minor changes in slope and intercept for solutions containing 80 or 100 mg of protein/ml versus no protein, but these changes were not considered to be of sufficient magnitude to deter the use of this approach to measure brain temperature. The protein content of swine cerebral cortex was found to remain constant from newborn to 1 month old (78 +/- 12 mg/g; n = 41). Therefore, data collected for the model solution containing 80 mg of protein/ml were used as a calibration curve to calculate brain temperature in eight swine during control, hypothermia, ischemia, postischemia, or death, over a temperature range of 23-40 degrees C. A plot of 61 temperatures determined from 1H NMR versus temperatures measured from an optical fiber probe sensor implanted 1 cm into the cerebral cortex showed excellent linear agreement (slope = 1.00 +/- 0.03, r2 = 0.96). We conclude that 1H NMR spectroscopy presents a practical means of making noninvasive measurements of brain temperature with an accuracy of better than +/- 1 degree C.

Animals↗
PubMed1995

A screen in Escherichia coli for nucleoside analogs that target human immunodeficiency virus (HIV) reverse transcriptase: coexpression of HIV reverse transcriptase and herpes simplex virus thymidine kinase.

Human immunodeficiency virus (HIV) reverse transcriptase substitutes for temperature-sensitive DNA polymerase I (Pol Its) in Escherichia coli, providing a screen for anti-HIV reverse transcriptase nucleoside analogs in bacteria. Since phosphorylation of nucleosides in E. coli is limited to thymidine and its derivatives, we coexpressed herpes simplex virus thymidine kinase, an enzyme that phosphorylates a wide variety of nucleoside analogs, together with HIV reverse transcriptase. Coexpression of herpes simplex virus thymidine kinase and HIV reverse transcriptase rendered Pol Its cells sensitive to dideoxycytidine. Studies with different nucleoside analogs indicate that this bacterial screening system is able to select and identify nucleoside analogs that specifically target HIV reverse transcriptase.

Antiviral Agents↗