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Biomedical subjects

K Nam

Publications and source records attributed to K Nam.

At least 19 recordsLinked to original sources
PubMed2006

Determination of biodegradation potential by two culture-independent methods in PAH-contaminated soils.

Biodegradation potentials of polycyclic aromatic hydrocarbons (PAHs) were determined with soil samples collected from various depths of a PAH-contaminated site and of a site nearby where PAHs were not found. Putative dioxygenase genes were amplified by a primer set specific for initial dioxygenases and identified by web-based database homology search. They were further categorized into several groups of which four dioxygenases were selected as probes for DNA hybridization. The hybridization signals according to the presence of putative dioxygenases were positively related to the extent of PAH contamination. However, the signal intensities varied depending on the probes hybridized and moreover were not consistent with PAH biodegradation activities determined by CO2 evolution. Despite widely accepted advantages of molecular biodegradation assessment, our data clearly present the variations of assessment results depending on the genetic information used and suggest that the methodology may tend to underestimate the real biodegradation capacity of a site probably due to the limited dioxygenase database available at the moment. Therefore, the molecular assessment of biodegradation potential should involve a very careful primer and probe design and an extensive microbiological examination of a site of interest to accurately delineate the biodegradation potential of the site.

Amino Acid Sequence↗
PubMed2005

Determination of environmental factors influencing methane oxidation in a sandy landfill cover soil.

It is advantageous to use coarse soils as landfill cover because they allow better aeration of the biologically active zone. In this study, therefore, patterns of methane oxidation were investigated under various environmental conditions including soil moisture content, temperature, and the addition of NH4+ in a sandy landfill cover soil. The kinetics of CH4 oxidation was also studied at different moisture contents and temperatures. Soil moisture content of 10% (wt/wt) resulted in the maximum CH4 oxidation rate (19.2-22.4 nmol gsoil DW(-1) min(-1)). A Vmax value was not significantly different when the moisture content was more than 10%, but a Km value increased from 5.23 to 75.24 microM as the moisture content increased. The ratio of Vmax to Km was the highest at 10% moisture content. The CH4 oxidation rate increased as the incubation temperature increased, and Q10 values and optimum temperature were determined to be 2.57-2.69 and 30 degrees C, respectively. Both Vmax and Km values decreased at the temperatures below and above 30 degrees C. The addition of various levels of NH4+ resulted in increased or decreased CH4 oxidation rates, however, the initiation of appreciable CH4 oxidation was delayed with increasing amounts of NH4+ application in all samples tested. Among the environmental variables tested, moisture content control seems to be the most important and an efficient means of managing methane oxidation when sandy soils are used in landfill cover.

Bacteria, Anaerobic↗
PubMed2004

Auditory evoked field responses in the left hemisphere to morphosyntactic violations in Korean sentence.

To investigate multiple cortical regions associated with syntactic processes at the sentence level, auditory evoked field responses to morphosyntactic violations were measured over the left hemisphere of seven subjects. Subjects were asked to judge the acceptability of the final verb in verb-ending Korean sentence. Measured field data were transformed to the fields that would be detected on a standard sensing plane and averaged across subjects in different violation conditions. In the grand average data, we found distinct features at latencies of 400 ms and 600 ms, which seem to be specific to morphosyntactic processes. Equivalent current dipoles (ECDs) plotted on a standard brain indicate the inferior frontal region and the superior temporal gyrus for 400 ms component, and the middle temporal gyrus for 600 ms component. Our MEG study localized the distinct cortical regions involved in syntactic processes, which may be reflected in LAN and P600 of ERP.

Acoustic Stimulation↗
PubMed2004

Use of autotrophic sulfur-oxidizers to remove nitrate from bank filtrate in a permeable reactive barrier system.

This study was conducted to evaluate the potential applicability of an in situ biological reactive barrier system to treat nitrate-contaminated bank filtrate. The reactive barrier consisted of sulfur granules as an electron donor and autotrophic sulfur-oxidizing bacteria as a biological component. Limestone was also used to provide alkalinity. The results showed that the autotrophic sulfur oxidizers were successfully colonized on the surfaces of the sulfur particles and removed nitrate from synthetic bank filtrate. The sulfur-oxidizing activity continuously increased with time and then was maintained or slightly decreased after five days of column operation. Maximum nitrate removal efficiency and sulfur oxidation rate were observed at near neutral pH. Over 90% of the initial nitrate dissolved in synthetic bank filtrate was removed in all columns tested with some nitrite accumulation. However, nitrite accumulation was observed mainly during the initial operation period, and the concentration markedly diminished with time. The nitrite concentration in effluent was less than 2 mg-N/l after 12 days of column operation. When influent nitrate concentrations were 30, 40, and 60 mg-N/l and sulfur content in column was 75%, half-order autotrophic denitrification reaction rate constants were 31.73 x 10(-3), 33.3 x 10(-3), and 36.4 x 10(-3) mg(1/2)/l(1/2)min, respectively. Our data on the nitrate distribution profile along the column suggest that an appropriate wall thickness of a reactive barrier for autotrophic denitrification may be 30 cm when influent nitrate concentration is less than 60 mg-N/l.

Hydrogen-Ion Concentration↗
PubMed2004

Robust motor speed control under time varying loads in moving actuator type artificial heart (AnyHeart).

The Moving Actuator type artificial heart(AnyHeart) as well as many other artificial hearts uses a motor as its power source. For controllability of control parameters such as pump rate, pump output, blood pressure profile and flow form, the precise motor speed control is important. However, because the implantable device has limited carrying capacity of hardware components in size and number, applying diverse motor control methods are not possible. In addition, the existing PI (Proportional-Integral) motor controller does not show satisfactory performance. A new controller that is sufficiently robust for the changes of load and physical system parameters has been designed and tested. The robust speed controller is based on the sliding mode control method that is applicable to a system of which the ranges of uncertainty in physical parameters are known. In a mock circulation system test, the actual speed showed good tracking characteristics in respect to the reference speed. Fast follow-up characteristics were also observed under high afterload and speed conditions. The speed error, current and power consumption were reduced by about 40%. The proposed control technique overcomes the limitations of the PI controller, and makes important improvements in both performance and stability.

Algorithms↗
PubMed2003

Effect of soil aggregation on the biodegradation of phenanthrene aged in soil.

A study was conducted to determine the possible role of soil aggregates in the sequestration of phenanthrene and thus in the declined biodegradation of the hydrocarbon. Phenanthrene aged in Lima loam (2-mm aggregates) showed declined biodegradation with time of aging to the test bacterium P5-2 capable of using sorbed phenanthrene. In contrast, the compound aged in a soil reconstructed with 68% clay-silt and 32% sand that had been separated from the Lima loam was readily mineralized. The percentages of each fraction used were the same as those of the original soil. Biodegradation of aged phenanthrene was not affected significantly by varying the ratios of each fraction in reconstructed mixtures. In experiments with Lima loam, its clay-silt fraction, and its sand fraction, mineralization extent was much lower in soil aggregates compared with the other samples while all had similar organic carbon content of ca. 1.51%. This suggests that aggregation may be another important determinant in the reduced biodegradation of aged phenanthrene.

Biodegradation, Environmental↗
PubMed2003

AnyHeart: a single-piece heart-saving implantable artificial heart (BVAD)--monitoring and estimation.

AnyHeart is a single-piece, implantable biventricular assist device. This electromechanical BVAD has a moving-actuator mechanism. To monitor the status of AnyHeart from anywhere at any time, a portable personal digital assistant (PDA) monitor and web-based remote monitoring system were developed. The PDA local monitoring system has replaced bulky personal computer monitoring systems. The web-based remote monitoring system has several functions such as data collecting, storing, and posting through the internet. Basically, interventricular pressure (IVP) is a parameter indicating the filling level of the blood chambers of AnyHeart. The pump output can be estimated using IVP, which is acquired noninvasively from AnyHeart. With the proposed method, we can estimate the pump output with a small margin of error.

Computers, Handheld↗
PubMed2002

PAH utilization by Pseudomonas rhodesiae KK1 isolated from a former manufactured-gas plant site.

Pseudomonas rhodesiae KK1 was isolated from a former manufactured-gas plant site, due to its ability to grow rapidly in a mixture of polycyclic aromatic hydrocarbons (PAHs). Radiorespirometric analysis revealed that strain KK1 was found to be able to mineralize anthracene, naphthalene and phenanthrene. Notably, phenanthrene-grown cells were able to mineralize anthracene much more rapidly than naphthalene-grown cells. Comparative analysis of amino acid sequences from 17 randomly selected dioxygenases capable of hydroxylating unactivated aromatic nuclei indicated that the enzymes for catabolism of PAHs, such as naphthalene and phenanthrene, might exist redundantly in strain KK1. Northern hybridization for cells grown on naphthalene or phenanthrene, using the putative naphthalene or phenanthrene dioxygenase gene fragment as a probe, suggested that the enzyme for naphthalene catabolism might share some homology in deduced amino acid sequences with phenanthrene dioxygenases. Also, it was found that three lipids (17:0 cyclo, 18:1 omega7c, 19:0 cyclo) increased in response to both naphthalene and phenanthrene, while the shift of other lipids varied from substrate to substrate.

Anthracenes↗
PubMed2002

Role of loosely bound humic substances and humin in the bioavailability of phenanthrene aged in soil.

A study was conducted to determine a possible role of loosely bound humic substances (i.e., humic and fulvic acids) in bioavailability of aged phenanthrene with time. In this study, long-term residence of phenanthrene in soil is defined as aging or sequestration, and the effect was determined by the declined bioavailability to bacteria of the polycyclic aromatic hydrocarbon with increased residence time. After 1, 7, and 100 days of aging of phenanthrene in Lima loam, about 90-93% of initial phenanthrene was recovered from the humin-mineral fraction of Lima loam whereas less than 12% was found in humic and fulvic acids of the same soil. Mineralization rates of phenanthrene aged in the humin-mineral fraction significantly decreased with time by the test bacterium P5-2. In terms of extents of mineralization, the difference with time was not appreciable, but still significant at P<0.05. Additional decreases in the rates and extents of mineralization were observed with the whole soil (i.e. Lima loam) to which phenanthrene had been aged. Data suggest that major sequestration sites for phenanthrene may reside in the humin-mineral fraction, and probably humic and fulvic acids may act as a physico-chemical barrier to bacterial degradation so that the compound's bioavailability may be limited.

Benzopyrans↗
PubMed2001

Evidence for expression of estrogen receptor cofactor messenger ribonucleic acid in the ovary and uterus of domesticated animals (sheep, cow and pig).

Expression levels of estrogen receptor cofactors (coactivators or corepressors) in specific tissue compartments and cells are thought to influence the expression of estrogen responsive genes and thereby influence overall hormonal responsiveness of target tissues. To date, the presence of cofactors has been reported in tissues from humans, rats and mice. We analyzed the presence and distribution of messenger ribonucleic acids (mRNAs) encoding several transcriptional cofactors in the ovary and uterus of three domestic animal species, the sheep, cow and pig. Northern analysis for cofactors SRC-1, GRIP1, RAC3, p300, RIP140, and SPA showed expression in ovaries from all three species. In addition, lower expression of SRC-1, GRIP1, RAC3, p300, and RIP140 mRNAs was observed during the luteal phase (day 10-12 of the estrous cycle) than at estrus (day 0); however, SPA transcript levels remained unchanged. We then examined expression of mRNAs for changing (SRC-1, RIP140) and constitutively expressed (SPA) cofactors in ovine ovaries. SRC-1 and RIP140 transcripts in corpus luteum were lower compared to the surrounding ovarian tissue. SPA mRNA expression, however, was similar in corpus luteum and surrounding tissues. To determine which ovarian cell types express SRC-1, RIP140, and SPA, in situ hybridization was performed on sheep ovaries. Silver grains corresponding to these cofactors were seen in ovarian granulosa, theca and stromal cells, but appeared to be most abundant in the granulosa cells. Expression of SRC-1 and RIP140 in corpus luteum, however, was reduced compared to expression in follicular cells. Finally, we examined cofactor expression in ovine, bovine, and porcine uterus. Northern blot analysis for SRC-1, GRIP1, RAC3, p300, and RIP140 mRNAs showed higher expression in extracts of the endometrium compared to whole uterus. We provide the first evidence for the presence of estrogen receptor cofactor mRNAs in the ovary and uterus of three domestic animal species. We suggest that coactivators are conserved among species and associated with hormonal responsiveness of reproductive tract tissues in sheep, cow and pig.

Animals↗
PubMed2001

Enhanced degradation of polycyclic aromatic hydrocarbons by biodegradation combined with a modified Fenton reaction.

A study has been conducted to enhance degradation of a mixture of polycyclic aromatic hydrocarbons (PAHs) by combining biodegradation with hydrogen peroxide oxidation in a former manufactured gas plant (MGP) soil. An active bacterial consortium enriched from the MGP surface soil (0-2 m) biodegraded more than 90% of PAHs including 2-, 3-, and 4-ring hydrocarbons in a model soil. The consortium was also able to transform about 50% of 4- and 5-ring hydrocarbons in the MGP soil. As a chemical oxidant, Fenton's reagent (H2O2 + Fe2+) was very efficient in the destruction of a mixture of PAHs (i.e., naphthalene (NAP), fluorene (FLU), phenanthrene (PHE), anthracene (ANT), pyrene (PYR), chrysene (CHR), and benzo(a)pyrene (BaP)) in the model soil; noticeably, 84.5% and 96.7% of initial PYR and BaP were degraded, respectively. In the MGP soil, the same treatment destroyed more than 80% of 2- and 3-ring hydrocarbons and 20-40% of 4- and 5-ring compounds. However, the low pH requirement (pH 2-3) for optimum Fenton reaction made the process incompatible with biological treatment and posed potential hazards to the soil ecosystem where the reagent was used. In order to overcome such limitation, a modified Fenton-type reaction was performed at near neutral pH by using ferric ions and chelating agents such as catechol and gallic acid. By the combined treatment of the modified Fenton reaction and biodegradation, more than 98% of 2- or 3-ring hydrocarbons and between 70% and 85% of 4- or 5-ring compounds were degraded in the MGP soil, while maintaining its pH about 6-6.5.

Biodegradation, Environmental↗
PubMed2000

Human RNA lariat debranching enzyme cDNA complements the phenotypes of Saccharomyces cerevisiae dbr1 and Schizosaccharomyces pombe dbr1 mutants.

The cDNA encoding the human RNA lariat debranching enzyme (hDBR1) was identified and cloned by searching the Expressed Sequence Tag (EST) database and screening a HeLa cDNA library, based on predicted amino acid sequence homologies with the Saccharomyces cerevisiae, Schizosaccharomyces pombe and Caenorhabditis elegans debranching enzymes. The hDBR1 cDNA expressed in Escherichia coli showed debranching activity in vitro and was also shown to be functional in an interspecies specific complementation experiment. hDBR1 cDNA in a S. cerevisiae expression vector complemented the intron accumulation phenotype of a S. cerevisiae dbr1 null mutant. Integration of the cDNA for hDBR1 into the ura4 locus of S. pombe also complemented both the intron accumulation and slow growth phenotypes of a S. pombe dbr1 null mutant strain. Comparison of the amino acid sequence of hDBR1 with the other DBR protein sequences showed several conserved regions, with 40, 44 and 43% identity to the S. cerevisiae, S. pombe and C. elegans debranching enzymes, respectively.

Amino Acid Sequence↗
PubMed2000

Lagrangian chaos and the effect of drag on the enstrophy cascade in two-dimensional turbulence

We investigate the effect of drag force on the enstrophy cascade of two-dimensional Navier-Stokes turbulence. We find a power law decrease of the energy wave number (k) spectrum that is faster than the classical (no-drag) prediction of k(-3). It is shown that the enstrophy cascade with drag can be analyzed by making use of a previous theory for finite lifetime passive scalars advected by a Lagrangian chaotic fluid flow. Using this we relate the power law exponent of the energy wave number spectrum to the distribution of finite time Lyapunov exponents and the drag coefficient.

Journal Article↗
PubMed2000

Combined ozonation and biodegradation for remediation of mixtures of polycyclic aromatic hydrocarbons in soil.

A study was conducted to investigate the feasibility of a combined treatment (i.e., ozonation and biodegradation) to overcome the inherent bacterial bioavailability limitation, and hence bioremediation limitation, of polycyclic aromatic hydrocarbons in soil. Ozonation was very efficient in the removal of naphthalene, fluorene, phenanthrene, and anthracene, but not for pyrene, chrysene, and benzo(a)pyrene from soil freshly spiked with the hydrocarbons. A similar result was obtained from coal tar-contaminated soil. Elimination of polycyclic aromatic hydrocarbons increased appreciably in sand containing 0.03% organic carbon, indicating the adverse effect of organic carbon on the efficiency of ozone treatment. In spiked and coal tar-contaminated soils, ozonation followed by biodegradation significantly increased the degradation of various polycyclic aromatic hydrocarbons including chrysene and benzo(a)pyrene which were not degraded by the test bacterial consortium alone. In particular, the effect of the combined treatment was more pronounced in coal tar-contaminated soil than in sterile soil spiked with hydrocarbons, probably due to the augmented biological activity of the introduced consortium. The results suggest that a combined treatment including ozonation and biodegradation may be a promising bioremediation technology in soil contaminated with mixtures of polycyclic aromatic hydrocarbons such as former manufactured gas plant sites.

Benzo(a)pyrene↗
PubMed2000

Peripheral blood extrathymic CD4(+)CD8(+) T cells with high cytotoxic activity are from the same lineage as CD4(+)CD8(-) T cells in cynomolgus monkeys.

We have previously reported that CD4/CD8 double-positive (DP) T cells with the resting memory phenotype are present in the periphery of healthy cynomolgus monkeys. In the present study, we performed functional studies on the T cells. The expression of CD4 and CD8 on DP, CD4 single-positive (SP) or CD8 SP T cells was stable in cultures with either mitogen or anti-CD3 antibody stimulation. In spite of lacking CD28 expression, DP T cells showed similar proliferative ability and apoptosis sensitivity to CD4 SP and CD8 SP T cells. DP T cells showed both helper and cytotoxic activities. Although the helper activity of DP T cells was lower than that of CD4 SP T cells, cytotoxic activity was comparable to that of CD8 SP T cells. Fresh DP T cells killed target cells mainly by the perforin-granzyme pathway. In addition, fresh DP T cells expressed a high level of mRNA for IFN-gamma and produced a high level of IFN-gamma when they were activated by anti-CD3 antibody ligation. On the other hand, several expanded DP T cell clones shared TCR V(beta) with expanded CD4 SP T cell clones, strongly suggesting that those two corresponding clones with DP and CD4 SP phenotypes might be derived from the same ancestor T cell. These results showed that the DP T cells are a novel T cell subset with functions overlapping with those of CD4 SP and CD8 SP T cells, and that they might play protective and regulatory roles in secondary immune response in cynomolgus monkeys.

Animals↗
PubMed2000

Target waves in the complex ginzburg-landau equation

We introduce a spatially localized inhomogeneity into the two-dimensional complex Ginzburg-Landau equation. We observe that this can produce two types of target wave patterns: stationary and breathing. In both cases, far from the target center, the field variables correspond to an outward propagating periodic traveling wave. In the breathing case, however, the region in the vicinity of the target center experiences a periodic temporal modulation at a frequency, in addition to that of the wave frequency of the faraway outward waves. Thus at a fixed point near the target, the breathing case yields a quasiperiodic time variation of the field. We investigate the transition between stationary and breathing targets, and note the existence of hysteresis. We also discuss the competition between the two types of target waves and spiral waves.

Journal Article↗
PubMed1999

Arginine in the beginning of the 1A rod domain of the keratin 10 gene is the hot spot for the mutation in epidermolytic hyperkeratosis.

Keratin intermediate filaments are expressed in specific type I/type II pairs in the stage of differentiation of keratinocytes. The mutations in the keratin genes expressed in the epidermis are etiologically responsible for several epidermal genetic skin diseases, such as epidermolysis bullosa simplex, epidermolytic hyperkeratosis (EHK), ichthyosis bullosa of Siemens, palmoplantar keratoderma, pachyonchia congenita and white sponge nevus. The mutations of keratins 1/10 which are expressed in spinous and granular layers are confirmed to cause EHK. There are several trials to correlate between the clinical phenotypes and sites of mutations of the keratin genes. One of these is that EHK is divided into two groups: the palms and soles involvement (PS) group and the non-palms and soles (NPS) group. So far the PS group had the mutations in the keratin 1 and the NPS group in keratin 10. Most of the mutations of the NPS group were reported in the beginning of the 1A rod domain and over 2/3 of the mutations in the 1A rod domain were the base pair substitution of arginine. Here we find two different mutations in two unrelated Korean kindreds classified as NPS group-R156C and R156H-in the 1A rod domain of keratin 10. Our results are compatible with the above classification and suggest that the arginine in the beginning of the 1A rod domain is the hot spot for the mutation of the keratin 10 gene.

Arginine↗