• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.83-85
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• 2000

A lot of microbial genome sequencing projects is being done in many genome centers around the world, since the first genome, Haemophilus influenzae, was sequenced in 1995. The deluge of microbial genome sequence data demands new and highly automatic data flow system in order for genome researchers to manage and analyze their own bulky sequence data from low-level to high-level. In such an aspect, we developed the automatic data management system for microbial genome projects, which consists mainly of local database, analysis programs, and user-friendly interface. We designed and implemented the local database for large-scale sequencing projects, which makes systematic and consistent data management and retrieval possible and is tightly coupled with analysis programs and web-based user interface, That is, parsing and storage of the results of analysis programs in local database is possible and user can retrieve the data in any level of data process by means of web-based graphical user interface. Contig assembly, homology search, and ORF prediction, which are essential in genome projects, make analysis programs in our system. All but Contig assembly program are open as public domain. These programs are connected with each other by means of a lot of utility programs. As a result, this system will maximize the efficiency in cost and time in genome research.

• Proceedings of the Korea Crystallographic Association Conference
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• 2003.05a
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• pp.17-17
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• 2003

tRNA (m¹ G37) methyltransferase (TrmD) catalyze s the trans for of a methyl group from S-adenosyl-L-methionine (AdoMet) to G/sup 37/ within a subset of bacterial tRNA species, which have a residue G at 36th position. The modified guanosine is adjacent to and 3' of the anticodon and is essential for the maintenance of the correct reading frame during translation. We have determined the first crystal structure of TrmD from Haemophilus influenzae, as a binary complex with either AdoMet or S-adenosyl-L-homocysteine (AdoHcy), as a ternary complex with AdoHcy/phosphate, and as an apo form. The structure indicates that TrmD functions as a dimer (Figure 1). It also suggests the binding mode of G/sup 36/G/sup 37/ in the active site of TrmD and catalytic mechanism. The N-terminal domain has a trefoil knot, in which AdoMet or AdoHcy is bound in a novel, bent conformation. The C-terminal domain shows a structural similarity to DNA binding domain of trp or tot repressor. We propose a plausible model for the TrmD₂-tRNA₂ complex, which provides insights into recognition of the general tRNA structure by TrmD (Figure 2).

• Molecules and Cells
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• v.20 no.3
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• pp.442-445
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• 2005

HP0894 (SwissProt/TrEMBL ID O25554) is an 88-residue conserved hypothetical protein from Helicobacter pylori strain 26695 with a calculated pI of 8.5 and a molecular weight of 10.38 kDa. Proteins with sequence similarity to HP0894 exist in Vibrio choierae, Enterococcus faecalis, Campylobacter jejuni, Streptococcus pneumoniae, Haemophilus influenzae, Escherichia coli O157, etc. Here we report the sequence-specific backbone resonance assignments of HP0894. About 97.5% (418/429) of the HN, N, CO, $C{\alpha}$, $C{\beta}$ resonances of the 88 residues of HP0894 were assigned. On the basis of these assignments, three helical regions and four strand regions were identified using the CSI program. This study is a prerequisite for calculating the solution structure of HP0894, and studying its interaction with its substrates, if any, and/or with other proteins.

• Biodesign
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• v.6 no.4
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• pp.96-99
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• 2018

The gram-positive bacterium Staphylococcus aureus is a common cause of abscesses, sinusitis and food poisoning. The emergence of antibiotic-resistant strains has caused significant clinical issues worldwide. The HslU-HslV complex was first identified as a prokaryotic homolog of eukaryotic proteasomes. HslU is an unfoldase that mediates the unfolding of the substrate proteins, and it works with the protease HslV in the complex. To date, the protein complex has been mostly studied in gram-negative bacteria. In this study, we report the purification and crystallization of the full-length HslU from S. aureus. The crystal diffracted X-rays to a $3.5{\AA}$ resolution, revealing that the crystals belong to space group $P2_1$, with unit cell parameters of a = 166.5, b = 189.6, $c=226.6{\AA}$, and ${\beta}=108.1^{\circ}$. We solved the phage problem by molecular replacement using the structure of HslU from Haemophilus influenzae as a search model. The cell content analysis with this molecular replacement solution revealed that 24 molecules are contained in the asymmetric unit. This structure provides insight into the structural and mechanistic difference of the HslUV complex of gram-positive bacteria.

• Clinical and Experimental Pediatrics
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• v.56 no.6
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• pp.231-234
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• 2013

This article contains the recommended immunization schedule by the Committee on Infectious Diseases of the Korean Pediatric Society, updated in March 2013, when Haemophilus influenzae type b vaccine is now included in the National Immunization Program in Korea. It also includes catch-up immunization schedule for children and adolescents who are behind the recommended schedule. These schedules are a minor revision of the corresponding parts of Immunization Guideline, 7th edition, of the Korean Pediatric Society, released in 2012. Pediatricians should be aware of these schedules to provide adequate immunization to Korean children and adolescents.

• Clinical and Experimental Pediatrics
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• v.59 no.12
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• pp.461-465
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• 2016

This report includes the recommended immunization schedule table for children and adolescents based on the 8th (2015) and revised 7th (2012) Immunization Guidelines released by the Committee on Infectious Diseases of the Korean Pediatric Society (KPS). Notable revised recommendations include: reorganization of the immunization table with a list of vaccines on the vertical axis and the corresponding age on the horizontal axis; reflecting the inclusion of Haemophilus influenzae type b vaccine, pneumococcal conjugate vaccine, and hepatitis A vaccine into the National Immunization Program since 2012; addition of general recommendations for 2 new Japanese encephalitis (JE) vaccines and their interchangeability with existing JE vaccines; addition of general recommendations for quadrivalent meningococcal conjugate vaccines and scope of the recommended targets for vaccination; and emphasizing catch-up immunization of Tdap vaccine. Detailed recommendations for each vaccine may be obtained from the full KPS 8th Immunization Guidelines.

• Clinical and Experimental Pediatrics
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• v.62 no.7
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• pp.252-256
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• 2019

The Committee on Infectious Diseases of the Korean Pediatric Society recommended immunization schedule for children and adolescents aged 18 years or younger in the 9th (2018) edition of Immunization guideline. This report provides the revised recommendations made by the committee and summarizes several changes from the 2015 guideline. National immunization program (NIP) launched a human papillomavirus (HPV) immunization for girls aged 12 years in 2016. NIP has also expanded age indication for inactivated influenza vaccine (IIV) to 12 years of age in the 2018-2019 season. Quadrivalent IIVs with a full dose (0.5 mL) are approved for all children of 6 months or older. Recommendations of live attenuated influenza vaccine were removed. For inactivated Japanese encephalitis vaccine, first 2 doses are considered as the primary series. Recommendations for use of newly introduced vaccines (diphtheria-tetanus-acellular pertussis/inactivated poliovirus/Haemophilus influenzae type b, 9-valent HPV, new varicella vaccine, new quadrivalent IIV, and attenuated oral typhoid vaccine) were added. Lastly, monitoring system for adverse events following immunization was updated. Other changes can be found in the 9th edition of Immunization guideline in detail.

• Tuberculosis and Respiratory Diseases
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• v.49 no.6
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• pp.740-751
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• 2000

Background : Moxifloxacin is a newly developed drug which is more potent and safe compared to previous fluoroquinolones. This drug effectively eradicates organisms such as beta-lactamase-producing or other resistant bacteria. Moxifloxacin is known to be effective in treating respiratory infections such as Streptococcus pneumoniae, Haemophilus influenzae, Moraxella catarrhalis, Chlamydia pneumoniaeme, Legionella spp. and Mycoplasma pneumoniae. Methods : In a multicenter, randomized, open, comparative study, the efficacy and safety of oral moxifloxacin taken 400 mg once a day and clarithromycin taken 500 mg twice daily for 7 days were compared for the treatment of Korean patients with acute exacerbations of chronic bronchitis. Results : A total of 170 patients were enrolled, and they were divided into two groups: 87 in the moxifloxacin group and 83 in the clarithromycin group. Of those enrolled, 76 (35 for bacteriologic efficacy) in the moxifloxacin group and 77 (31 for bacteriologic efficacy) in the clarithromycin group were included in the efficacy analysis. All were included in the safety analysis. Clinical success was noted in 70 (92.1%) of 76 moxifloxacin-treated patients and 71 (92.2%) of 77 clarithromycin-treated patients. Bacteriologic success rate seemed to be higher in moxifloxacin group (73.5%) than in clarithromycin group (54.8%), but statistically insignificant (p=0.098). Drug susceptibility among organisms initially isolated was higher in moxifloxacin group on Streptococcus pneumoniae, Pseudomonas aeruginosa, Klebsiella pneumoniae (p<0.001). Adverse events were reported by 12.8% of 86 patients receiving moxifloxacin and 21.7% of 83 patients receiving clarithromycin. Headache (4.7% vs 4.8%, moxifloxacin group vs clarithromycin group, respectively) and indigestion (2.3% vs 6.0%, moxifloxacin group vs clarithromycin group, respectively) were the most frequent side effects in the two groups. Conclusion : This study demonstrated that for the treatment of acute exacerbations of chronic bronchitis a 7-day course of moxifloxacin 400 mg od was clinically equivalent and microbiologically superior to clarithromycin 500 mg bid.

• Pediatric Infection and Vaccine
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• v.22 no.2
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• pp.106-112
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• 2015

Purpose: The long-term administration of antibiotics interferes with bacterial culture in the middle ear fluids (MEFs) of young children with otitis media with effusion (OME). The purpose of this study is to determine whether molecular diagnostics can be used for rapid and direct detection of the bacterial pathogen in culture-negative MEFs. Methods: The specificity and sensitivity of both polymerase chain reaction (PCR) and loop-mediated isothermal amplification (LAMP) to the lytA gene of Streptococcus pneumoniae were comparatively tested and then applied for pneumococcal detection in the clinical MEFs. Results: The detection limit of the PCR assay was approximately $10^4$ colony forming units (CFU), whereas that of LAMP was less than 10 CFU for the detection of S. pneumoniae. Both PCR and LAMP did not amplify nucleic acid at over $10^6$ CFU of H. influenzae or M. catarrhalis, both of which were irrelevant bacterial species. Of 22 culture-negative MEFs from children with OME, LAMP positivity was found in twelve MEFs (54.5%, 12/22), only three of which were PCR-positive (25%, 3/12). Our results showed that the ability of LAMP to detect pneumococcal DNA is over four times higher than that of PCR (P<0.01). Conclusions: As a high-resolution tool able to detect nucleic acid levels equivalent to <10 CFU of S. pneumoniae in MEFs without any cross-reaction with other pathogens, lytA -specific LAMP may be applied for diagnosing pneumococcus infection in OME as well as evaluating the impact of a pneumococcal conjugate vaccine against OME.

• Clinical and Experimental Pediatrics
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• v.46 no.4
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• pp.345-350
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• 2003

Purpose : Bacterial meningitis is a serious infection of childhood associated with a significant morbidity and mortality. Repeated cerebrospinal fluid(CSF) examination is a useful prognostic indicator and a delayed sterilization is associated with a higher incidence of neurologic abnormalities. In this study we tried to determine the prognostic value of repeated CSF latex agglutination testing. Methods : We retrospectively evaluated 19 patients admitted to Ewha Womans University Mokdong Hospital for bacterial meningitis from January 1997 to June 2002. Bacterial meningitis was confirmed by a positive CSF culture and a positive CSF latex agglutination test. Repeated CSF examinations were done at three, seven, 14, 21 and 28 days after antibiotics therapy. Neuroradiologic studies were performed. Results : The mean age was $10.6{\pm}12.3months$(range; two to 33 months). The male to female ratio was 2.8 : 1. The causative organisms were Haemophilus influenzae type b 57.9%, Group B Streptococcus 21.1%, Streptococcus pneumoniae 15.7% and Escherichia coli 5.3%. Three days after the initiation of antibiotics therapy, repeated CSF latex agglutination tests persisted as positive in nine (47.4%) out of 19 cases, but all CSF cultures became negative. In those cases with negative latex agglutination tests three days after antibiotics therapy, neuroradiologic findings were completely normal. But, in cases with positive latex agglutination tests three days after antibiotics therapy, neuroradiologic abnormalities such as cerebral infarction, encephalomalasia occurred in 44.4%. Conclusion : Repeated CSF latex agglutination testing was valuable as a prognostic factor in bacterial meningitis. Neuroradiologic abnormalities may occur in cases with delayed clearance of CSF latex agglutination tests more often than in cases with negative latex agglutination tests three days after antibiotics therapy.