Biomedical subjects

S J Han

Publications and source records attributed to S J Han.

At least 19 recordsLinked to original sources

PubMed2006

Monte Carlo simulation of the photon beam characteristics from medical linear accelerators.

The MCNPX code has been employed on a personal computer to calculate the dosimetric characteristics of the photon beams from the 6 MV Siemens MX2 and the 10 MV Varian Clinac 2100C linear accelerators. A model of the treatment head includes the major geometric structure within the beam path. The model was used to calculate the energy spectra of the photon beam, percentage depth dose and the dose profiles. The accuracy of the calculated results is examined by comparing them with the measured dose distributions for the two machines. The computed and measured depth dose curves agree to within 2% for all the depths beyond the build-up region for both treatment machines. The calculations agree to within 2% of the measured profiles within the 100-50% dose level. It has been found that the MCNPX code is an effective tool for simulating the clinical photon beam.

Body Burden↗

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

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

Characterization of an oxygen-dependent inducible promoter, the nar promoter of Escherichia coli, to utilize in metabolic engineering.

The nar promoters, whose transcription is maximally induced under microaerobic conditions in the presence of nitrate ion, were characterized in fed-batch culture to determine whether they can be used for metabolic engineering, by which overall production of valuable chemicals can be increased. For this purpose, we tested whether the expression level of a reporter gene, the lacZ gene from the nar promoter, could be maintained constant throughout the induction period by manipulation of dissolved oxygen (DO) levels at a given nitrate ion concentration. First, E. coli was grown under aerobic conditions (DO 80%) to absorbance at 600 nm (OD(600)) of 35, then the nar promoter was induced by reduction of DO to different levels, combined with different frequencies and duration of alternating microaerobic and aerobic conditions throughout the entire induction period. For a wild-type nar promoter (pMW61) in a mutant host E. coli with a mutation in the narG gene on the chromosome of the host (RK5265), it was possible to maintain production of beta-galactosidase activity per cell (specific beta-galactosidase activity) at a constant rate at 5000, 10,000, 15,000, and 20,000 Miller units, using different combinations of nitrate ion concentrations (0.1%, 0.5%, and 1%) and DO levels. In addition, it was possible to maintain production of specific beta-galactosidase activity at a constant rate at about 10,000 Miller units in the absence of nitrate ion when a nitrate-independent nar promoter (pMW618) in the narL(-) mutant of the W3110 E. coli strain (W3110narL(-)) was used. Based on these results, we conclude that the nar promoter system provides a convenient expression system for metabolic engineering as well as for maximal production of recombinant proteins under conditions of fed-batch culture.

Chromosomes, Bacterial↗

PubMed2001

Molecular cloning and characterization of thermostable DNA ligase from Aquifex pyrophilus, a hyperthermophilic bacterium.

A DNA ligase gene from the hyperthermophilic bacterium Aquifex pyrophilus (Ap) was cloned and sequenced. An open reading frame of 2,157 bp that codes for a 82-kDa protein showed 40%-60% homology with a series of NAD+-dependent DNA ligases from different organisms. The recombinant enzyme Ap DNA ligase expressed in Escherichia coli was purified to homogeneity and characterized. The activity of Ap DNA ligase gradually increased in proportion to the concentration of monovalent salt up to 200 mM NaCl, 150 mM KCl, 200 mM NH4Cl, and 350 mM potassium glutamate. The optimum temperature and pH of Ap DNA ligase were greater than 65 degrees C and 8.0-8.6, respectively, for nick-closing activity. More than 75% of the ligation activity was retained after incubation at 95 degrees C for 60 min, whereas the half-lives of Thermus aquaticus and Escherichia coli DNA ligases at 95 degrees C were < or =15 min and 5 min, respectively. Thermostable Ap DNA ligase was applied to repeat expansion detection (RED) and could be a useful enzyme in DNA diagnostics.

Amino Acid Sequence↗

PubMed2001

Fistula-in-ano in infants: is nonoperative management effective?

PURPOSE: Recently, a number of studies have reported positive results from the nonoperative management of fistula-in-ano in infancy, although it has not been of use in all patients. The purpose of this study was to discern the effective treatment methods of fistula-in-ano in infants. METHODS: A retrospective review was done of 310 children who required operative management for fistula-in-ano or perianal abscess between January 1991 and July 2000. Eighteen patients displayed an onset of symptoms at less than 1 year of age and a duration of symptoms longer than 12 months. The authors analyzed these patients' medical records. RESULTS: All patients were boys. The mean duration of the symptoms was 26.6 +/- 27.5 months. Fourteen patients had shown an onset of symptoms at less than 6 months of age. The longest duration was 10 years. The patients showed conservative periods of over 12 months because their parents did not want them to undergo surgery. The disease in these patients followed 2 patterns. One (6 patients) was an onset of symptoms followed by a silent fistula-in-ano state. The other (12 patients) was an onset of symptoms followed by an intermittent relapse of inflammation. All patients underwent fistulotomy, and none of them had recurrent fistula during the follow-up period. CONCLUSIONS: Although the advantages of a nonoperative management of fistula-in-ano in infants include the avoidance of general anesthesia and surgical intervention, the lesions cannot be cured by a period of conservation. Surgical management is more effective in respect to the time factor.

Child↗

PubMed2001

Biliary atresia associated with meconium peritonitis caused by perforation of small bowel atresia.

BACKGROUND/PURPOSE: This report describes our experiences with 5 cases of biliary atresia associated with meconium peritonitis caused by perforation of small bowel atresia. METHODS: A review of medical records was undertaken in an effort to recognize cases of biliary atresia associated with meconium peritonitis. RESULTS: Five patients of 171 with biliary atresia (2.9%) were detected to have meconium peritonitis caused by perforation of small bowel atresia. The biliary atresia was not suspected during the initial operation for meconium peritonitis. Total parenteral nutrition (TPN) made it difficult to make an early differential diagnosis of biliary atresia because of the presence of TPN-associated cholestatic jaundice, and the Roux-en-Y limb used for hepatic portoenterostomy could not be made long enough to prevent cholangitis caused by preexisting short bowel. The main complications were severe, intractable cholangitis, short bowel syndrome with malnutrition; TPN-associated liver injury; and wound problems. Two patients died of ascending cholangitis, 1 patient of liver failure that was exacerbated by TPN-associated liver injury, and 1 patient is awaiting a liver transplant. Only 1 patient is in good health, being anicteric and showing normal growth and development. CONCLUSIONS: Biliary atresia is evidently closely associated with meconium peritonitis caused by perforation of small bowel atresia. The management of these patients is more difficult than that of patients with the usual form of biliary atresia, because of the necessity for a long period of TPN and the combined short bowel syndrome. The ideal management of these conditions has yet to be determined.

Biliary Atresia↗

PubMed2001

The development of fetal surgery.

The history of fetal surgery features an absolute dependency upon the possibility of diagnosis before birth. Powerful new imaging methods, the techniques of sampling amniotic fluid and fetal tissue, and modern molecular genetics for the prenatal diagnosis of various congenital diseases have removed the veil of secrecy from the fetus. Even though most prenatally detected congenital malformations can be managed after maternal transport, a few simple anatomic defects require fetal surgery, albeit with predictably poor results. The understanding of intrauterine physiology and pathophysiology in several congenital malformations has been worked out in animal model study, and the natural history of congenital defects revealed by prenatal observations on human fetuses. Selection criteria for intrauterine intervention have been developed. Over the last two decades, surgical techniques for open and endoscopic fetal surgery have been defined and anesthesia and tocolysis for fetal surgery improved. As we enter the 21st century, this field of surgery will surely expand.

Animals↗

PubMed2001

[Anatomical study and clinical application of medial femoral condylar bone flap pedicled with the saphenous vessels].

OBJECTIVE: To investigate a new operative method for repairing nonunion and defect of tibia. METHODS: First, observe the relation between the joint branches of descending genicular artery and the saphenous branch of descending genicular artery in 10 cadevers. Then the medial femoral condylar bone flap pedicled with the saphenous vessels was prepared in 4 cadavers for simulated purpose. Clinically, two patients with tibial nonunion were treated by transplantation of this pedicled bone flap. RESULTS: In the 4 simulated operations, the ink which was injected into the femoral artery could be released from the joint branches. And in the clinical operation, the area of the pedicled bone flaps were 5.0 cm x 2.0 cm x 1.5 cm and 4.5 cm x 1.5 cm x 1.5 cm respectively. Followed up for 8 to 12 weeks, the fracture unioned well. CONCLUSION: This operation is simple and reliable, it is characterised by 1. unnecessary to anastomosis the vessels 2. reliable blood supply 3. high quality of bone flap 4. either bone flap or bone-skin flap can be chosen 5. long vessel pedicle.

Adult↗

PubMed2000

Gram-negative bacteria-binding protein, a pattern recognition receptor for lipopolysaccharide and beta-1,3-glucan that mediates the signaling for the induction of innate immune genes in Drosophila melanogaster cells.

Pattern recognition receptors, non-clonal immune proteins recognizing common microbial components, are critical for non-self recognition and the subsequent induction of Rel/NF-kappaB-controlled innate immune genes. However, the molecular identities of such receptors are still obscure. Here, we present data showing that Drosophila possesses at least three cDNAs encoding members of the Gram-negative bacteria-binding protein (DGNBP) family, one of which, DGNBP-1, has been characterized. Western blot, flow cytometric, and confocal laser microscopic analyses demonstrate that DGNBP-1 exists in both a soluble and a glycosylphosphatidylinositol-anchored membrane form in culture medium supernatant and on Drosophila immunocompetent cells, respectively. DGNBP-1 has a high affinity to microbial immune elicitors such as lipopolysaccharide (LPS) and beta-1,3-glucan whereas no binding affinity is detected with peptidoglycan, beta-1,4-glucan, or chitin. Importantly, the overexpression of DGNBP-1 in Drosophila immunocompetent cells enhances LPS- and beta-1,3-glucan-induced innate immune gene (NF-kappaB-dependent antimicrobial peptide gene) expression, which can be specifically blocked by pretreatment with anti-DGNBP-1 antibody. These results suggest that DGNBP-1 functions as a pattern recognition receptor for LPS from Gram-negative bacteria and beta-1, 3-glucan from fungi and plays an important role in non-self recognition and the subsequent immune signal transmission for the induction of antimicrobial peptide genes in the Drosophila innate immune system.

Acute-Phase Proteins↗

PubMed2000

Behavior of lanthanides in countercurrent chromatography using dihexyl-N,N-diethylcarbamoyl methylene phosphonate as stationary phase.

Counter-current chromatography is a real liquid-liquid chromatography. The retention volume of the solute can be calculated from the batch distribution ratio in organic separations. In the separations of metal ion, there are several complex and dissociation reactions involved in the two phases, and the retention volume cannot be always predicted from the batch distribution ratio. A mass transfer model is proposed in this paper and an expression of V(R) is derived. The retention volume of metal ion is determined not only by the batch distribution ratio but also by the mechanism of the extraction reaction. When 25% dihexyl-N,N-diethylcarbamoyl methylenephosphonate in cyclohexane is used as stationary phase and 2.91 mol/l HNO3 as mobile phase, the dynamic distribution ratios obtained from the chromatogram are not equal to but proportional to the batch distribution coefficients. These results are in agreement with the theoretical expression.

Calibration↗

PubMed2000

Inhibition of mitogen-activated protein kinase by a Drosophila dual-specific phosphatase.

The Drosophila extracellular signal-regulated kinase (DERK) mitogen-activated protein kinase (MAPK) is involved in the regulation of multiple differentiation and developmental processes. Tight control of MAPK activity is critical for normal cell behaviour. We identified a novel Drosophila MAPK phosphatase (DMKP) cDNA from the expressed-sequence-tag database and characterized it. Analysis of the nucleotide sequence revealed an open reading frame encoding the 203-amino acid protein, with a calculated molecular mass of 23 kDa, which has a high amino acid sequence similarity with 'VH1-like' dual-specific phosphatases at the broad region near the catalytic sites. The expression of DMKP mRNA occurs from the late larval stages to adulthood in Drosophila development. The recombinant DMKP protein produced in yeast retained its phosphatase activity. When expressed in Schneider cells, DMKP dose-dependently inhibited DERK and Drosophila c-Jun N-terminal kinase activities with high selectivity towards DERK. However, DMKP did not have any affect on Drosophila p38 activity. When DMKP was expressed in yeast, it down-regulated the fus1-lacZ trans-reporter gene of the pheromone MAPK pathway without any significant effect on the high-osmolarity-glycerol-response pathway.

Amino Acid Sequence↗

PubMed2000

Development and characterization of an oxygen-dependent inducible promoter system, the modified nar promoter in a mutant Escherichia coli.

A nar promoter system (a modified nar promoter in a mutant host Escherichia coli (pMW618/W3110narL(-))), which is maximally induced under microaerobic conditions, was developed and characterized through batch and fed-batch culture to see whether the modified nar promoter can be used as an oxygen-dependent inducible promoter in the absence of nitrate ion. The modified nar promoter (pMW618) derived by mutations at -10 and -35 regions of the wild-type nar promoter does not require nitrate ion for the full induction, while a mutant host E. coli, W3110narL(-), does not express nitrate-dependent regulatory protein, NARL, from the host chromosome. In this study, it was found from fed-batch culture that the specific beta-galactosidase activity expressed from the lacZ gene fused to the modified nar promoter in the absence of nitrate ion was maximal when E. coli was grown under aerobic conditions (dissolved oxygen (DO) at 80%) to absorbance at 600 nm (OD(600)) of 35, and then the modified nar promoter was induced by lowering DO to 1-2% with alternating microaerobic and aerobic conditions. The maximal specific beta-galactosidase activity became 58,000 Miller at OD(600) of 160 with an induction ratio of 20. On the basis of these results, we conclude that the modified nar promoter system (pMW618/W3110narL(-)), requiring only reduction of DO for the full induction, provides a convenient and effective high-level expression system under conditions of fed-batch culture.

Bacteriological Techniques↗

PubMed2000

Lipopolysaccharide-activated kinase, an essential component for the induction of the antimicrobial peptide genes in Drosophila melanogaster cells.

Eukaryotic organisms use a similar Rel/NF-kappaB signaling cascade for the induction of innate immune genes. In Drosophila, lipopolysaccharide (LPS) signal-induced activation of the Rel/NF-kappaB family transcription factors is an essential step in the transcriptional activation of inducible antimicrobial peptide genes. However, the mechanism by which the LPS-induced signaling pathway proceeds remains largely unknown. Here we have cloned a novel Drosophila LPS-activated kinase (DLAK) that is structurally related to mammalian IkappaB kinases. DLAK is expressed and transiently activated in LPS-responsive Drosophila cells following LPS stimulation. Furthermore, DLAK can interact with Cactus, a Drosophila IkappaB and phosphorylate recombinant Cactus, in vitro. Overexpression of dominant-negative mutant DLAK (DLAK(K50A)) blocks LPS-induced Cactus degradation. DLAK-bound Cactus can be degraded in a LPS signal-dependent fashion, whereas the DLAK(K50A) mutant-bound Cactus is completely resistant to degradation in the presence of LPS. The DLAK(K50A) mutant also inhibits nuclear kappaB binding activity and kappaB-dependent diptericin reporter gene activity in a dose-dependent manner, but the kappaB-dependent diptericin reporter gene activity can be rescued by overexpression of wild type DLAK. Moreover, mRNA analysis of various kappaB-dependent antimicrobial peptide genes shows that LPS inducibility of these genes is greatly impaired in cells overexpressing DLAK(K50A). These results establish that DLAK is a novel LPS-activated kinase, which is an essential signaling component for the induction of antimicrobial peptide genes following LPS treatment in Drosophila cells.

Amino Acid Sequence↗

PubMed2000

Selective involvement of reactive oxygen intermediates in platelet-activating factor-mediated activation of NF-kappaB.

Although it has been suggested that some biological activities of platelet-activating factor (PAF) are mediated by, at least in part, reactive oxygen intermediates (ROI), the precise mechanisms underlying the interaction between the two remains to be elucidated. Antioxidants, such as alpha-tocopherol acid succinate, N-acetyl-L-Cysteine, pyrrolidinedithiocarbamate failed to inhibit PAF-induced immediate systemic reactions such as lethality, symptoms of disseminated intravascular coagulation, and histological changes such as pulmonary edema and hemorrhage in renal medullae 10 min following PAF injection. In contrast. antioxidants significantly inhibited both the in vivo and in vitro PAF-induced NF-kappaB activation and NF-kappaB-dependent TNF-alpha expression. The effects of the antioxidants were due to their inhibition of PAF-induced degradation of IkappaBalpha, a protein responsible for keeping NF-kappaB in an inactive form. A protein tyrosine kinase and N-tosyl-L-phenylalanine chloromethyl ketone sensitive serine protease were involved in both PAF- and H2O2-induced NF-kappaB activation. Collectively, these data indicate that the PAF-induced NF-kappaB activation is selectively mediated through the generation of ROI.

Acetylcysteine↗

PubMed2000

REP1, a basic helix-loop-helix protein, is required for a branch pathway of phytochrome A signaling in arabidopsis.

Phytochromes are primary photoreceptors mediating diverse responses ranging from induction of germination to floral induction in higher plants. We have isolated novel recessive rep1 (reduced phytochrome signaling 1) mutants, which exhibit a long-hypocotyl phenotype only under far-red light but not under red light. Physiological characterization showed that rep1 mutations greatly reduced a subset of phytochrome A-regulated responses, including the inhibition of hypocotyl elongation, cotyledon expansion, modulation of gravitropic growth of hypocotyl, and induction of the CAB (encoding chlorophyll a/b binding protein) gene, without affecting the accumulation of anthocyanin, far-red-preconditioned blocking of greening, induction of germination, and induction of CHS (encoding chalcone synthase) and FNR (encoding ferredoxin-NADP(+) oxidoreductase) genes. These results suggest that REP1 is a positive signaling component, functioning in a branch of the phytochrome A signaling pathway. Molecular cloning and characterization of the REP1 gene revealed that it encodes a light-inducible, putative transcription factor containing the basic helix-loop-helix motif.

Arabidopsis↗

PubMed2000

In vivo requirement of activator-specific binding targets of mediator.

There has been no unequivocal demonstration that the activator binding targets identified in vitro play a key role in transcriptional activation in vivo. To examine whether activator-Mediator interactions are required for gene transcription under physiological conditions, we performed functional analyses with Mediator components that interact specifically with natural yeast activators. Different activators interact with Mediator via distinct binding targets. Deletion of a distinct activator binding region of Mediator completely compromised gene activation in vivo by some, but not all, transcriptional activators. These demonstrate that the activator-specific targets in Mediator are essential for transcriptional activation in living cells, but their requirement was affected by the nature of the activator-DNA interaction and the existence of a postrecruitment activation process.

Binding Sites↗

PubMed2000

Biliary atresia in neonates and infants: triangular area of high signal intensity in the porta hepatis at T2-weighted MR cholangiography with US and histopathologic correlation.

PURPOSE: To correlate a triangular area of high signal intensity in the porta hepatis on T2-weighted magnetic resonance (MR) cholangiograms of biliary atresia with ultrasonographic (US) and histopathologic findings in a portal mass observed during a Kasai procedure. MATERIALS AND METHODS: Twenty-one consecutive neonates and infants (age range, 13-88 days; mean age, 59 days) with cholestasis underwent US and single-shot MR cholangiography. In 12 patients with biliary atresia diagnosed at histopathologic examination, MR cholangiographic findings in the porta hepatis were correlated with US and histopathologic findings in the portal mass. RESULTS: At US, eight of the 12 patients had round, linear, or tubular hypoechoic portions within a triangular cord; MR cholangiography revealed a triangular area of high signal intensity confined to the porta hepatis. Histopathologic examination of the portal mass revealed a cystic or cleftlike lesion surrounded by loose myxoid mesenchyme and platelike fetal bile ducts. Neither the large cystic lesion without ductal epithelium nor the small cleftlike lesion with scanty epithelium demonstrated bile staining. Similar areas of high signal intensity were not seen on T2-weighted images in the remaining patients (four with biliary atresia and nine with neonatal hepatitis). CONCLUSION: In biliary atresia, T2-weighted single-shot MR cholangiography can show a triangular area of high signal intensity in the porta hepatis that may represent cystic dilatation of the fetal bile duct.

Bile↗