Cytosolic retinoic acid-inducible gene I (RIG-I) is an important innate immune RNA sensor and can induce antiviral cytokines, e.g., interferon-β (IFN-β). Innate immune response to hepatitis B virus (HBV) plays a pivotal role in viral clearance and persistence. However, knowledge of the role that RIG-I plays in HBV infection is limited. The woodchuck is a valuable model for studying HBV infection. To characterize the molecular basis of woodchuck RIG-I (wRIG-I), we analyzed the complete coding sequences (CDSs) of wRIG-I, containing 2778 base pairs that encode 925 amino acids. The deduced wRIG-I protein was 106.847 kD with a theoretical isoelectric point (pI) of 6.07, and contained three important functional structures [caspase activation and recruitment domains (CARDs), DExD/H-box helicases, and a repressor domain (RD)]. In woodchuck fibroblastoma cell line (WH12/6), wRIG-I-targeted small interfering RNA (siRNA) down-regulated RIG-I and its downstrean effector-IFN-β transcripts under RIG-I' ligand, 5'-ppp double stranded RNA (dsRNA) stimulation. We also measured mRNA levels of wRIG-I in different tissues from healthy woodchucks and in the livers from woodchuck hepatitis virus (WHV)-infected woodchucks. The basal expression levels of wRIG-I were abundant in the kidney and liver. Importantly, wRIG-I was significantly up-regulated in acutely infected woodchuck livers, suggesting that RIG-I might be involved in WHV infection. These results may characterize RIG-I in the woodchuck model, providing a strong basis for further study on RIG-I-mediated innate immunity in HBV infection.
Animals ; Cell Line, Tumor ; Cloning, Molecular ; DEAD Box Protein 58 ; antagonists & inhibitors ; genetics ; immunology ; Fibroblasts ; immunology ; pathology ; Gene Expression ; Hepatitis B ; genetics ; immunology ; pathology ; veterinary ; Hepatitis B Virus, Woodchuck ; Immunity, Innate ; Interferon-beta ; genetics ; immunology ; Isoelectric Point ; Kidney ; immunology ; pathology ; virology ; Liver ; immunology ; pathology ; virology ; Marmota ; genetics ; immunology ; virology ; Open Reading Frames ; Protein Domains ; RNA, Double-Stranded ; RNA, Small Interfering ; genetics ; metabolism ; Rodent Diseases ; genetics ; immunology ; pathology ; virology

It is well known that proteins present in the primary urine are reabsorbed in the renal proximal tubules, and that this reabsorption is mediated via the megalincubilin complex and the neonatal Fcgamma receptor. However, the reabsorption is also thought to be influenced by an electrostatic interaction between protein molecules and the microvilli of the renal proximal tubules. By analyzing the charge diversity of urinary IgG, we showed that this reabsorption process occurs in a cationic charge-preferential manner. The charge-selective molecular sieving function of the glomerular capillary walls has long been a target of research since Brenner et al. demonstrated the existence of this function by a differential clearance study by using the anionic dextran sulfate polymer. However, conclusive evidence was not obtained when the study was performed using differential clearance of serum proteins. We noted that immunoglobulin (Ig) A and IgG have similar molecular sizes but distinct molecular isoelectric points. Therefore, we studied the differential clearance of these serum proteins (clearance IgA/ clearance IgG) in podocyte diseases and glomerulonephritis. In addition, we studied this differential clearance in patients with Dent disease rather than in normal subjects because the glomerular sieving function is considered to be normal in subjects with Dent disease. Our results clearly showed that the charge-selective barrier is operational in Dent disease, impaired in podocyte disease, and lacking in glomerulonephritis.
Blood Proteins ; Capillaries ; Child Health ; Dent Disease ; Dextran Sulfate ; Glomerulonephritis ; Humans ; Immunoglobulin A ; Immunoglobulin G ; Immunoglobulins ; Isoelectric Point ; Microvilli ; Nephritis ; Podocytes ; Polymers ; Proteinuria*

OBJECTIVETo explore the feasibility of membrane protein-based two-dimensional electrophoresis (2-DE) in the investigations of chondrocyte-related diseases and its complementarity with total protein-based 2-DE.

METHODSKnee cartilage samples were obtained to isolate the chondrocytes with type II collagenase/hyaluronidase digestion. The membrane proteins and total proteins were extracted and loaded separately onto PH3.0-10.0 non-linear gel strip for 2-DE analysis. The qualities of membrane protein-based 2-DE gels were evaluated, and the difference between the distribution profiles of the membrane protein spots and that of the total protein were observed and their complementarities were evaluated.

RESULTSMembrane protein-based 2-DE generated high-quality gel images, and on each gel 412.3±13.5 protein spots were identified. These spots were distributed in the region of isoelectric point pH 5.0-9.0. In the gel images generated by the total proteins, 564.3±5.9 protein spots were identified in each image, and the spots were distributed in the region of isoelectric point pH 3.0-7.0.

CONCLUSIONMembrane protein-based 2-DE of the chondrocytes can generate high-quality gel images, and the isoelectric distribution of the protein spots is complementary to that of total protein, which provides valuable information for chondrocyte-related diseases.

Adult ; Chondrocytes ; chemistry ; Electrophoresis, Gel, Two-Dimensional ; methods ; Female ; Humans ; Isoelectric Point ; Male ; Membrane Proteins ; isolation & purification ; Middle Aged

In order to understand the protein functions that are related to disease, it is important to detect the correlation between amino acid mutations and isease. Many mutation studies about disease-related proteins have been carried out through molecular biology techniques, such as vector design, protein engineering, and protein crystallization. However, experimental protein mutation studies are time-consuming, be it in vivo or in vitro. We therefore performed a bioinformatic analysis of known disease-related mutations and their protein structure changes in order to analyze the correlation between mutation and disease. For this study, we selected 111 diseases that were related to 175 proteins from the PDB database and 710 mutations that were found in the protein structures. The mutations were acquired from the Human Gene Mutation Database (HGMD). We selected point mutations, excluding only insertions or deletions, for detecting structural changes. To detect a structural change by mutation, we analyzed not only the structural properties (distance of pocket and mutation, pocket size, surface size, and stability), but also the physico-chemical properties (weight, instability, isoelectric point (IEP), and GRAVY score) for the 710 mutations. We detected that the distance between the pocket and disease-related mutation lay within 20 A (98.5%, 700 proteins). We found that there was no significant correlation between structural stability and disease-causing mutations or between hydrophobicity changes and critical mutations. For large-scale mutational analysis of disease-causing mutations, our bioinformatics approach, using 710 structural mutations, called "Structural Mutatomics," can help researchers to detect disease-specific mutations and to understand the biological functions of disease-related proteins.
Computational Biology ; Crystallization ; Humans ; Hydrophobic and Hydrophilic Interactions ; Isoelectric Point ; Molecular Biology ; Point Mutation ; Protein Engineering ; Proteins

BACKGROUND: Prevalence of class A extended-spectrum beta-lactamases (ESBLs) has been investigated repeatedly in members of family Enterobacteriaceae in Korea, but only rarely in Acinetobacter baumannii and Pseudomonas aeruginosa. The aims of this study were to determine the prevalence of class A ESBL-producing A. baumannii and P. aeruginosa and to characterize the genotypes. METHODS: During the period of June to September 2004, clinical isolates of A. baumannii and P. aeruginosa were collected from patients in Kosin University Gospel Hospital, Busan, Korea. Antimicrobial susceptibility was determined by the disk diffusion and the agar dilution methods, and ESBLproduction by the double-disk synergy test. Transferability of ceftazidime-resistance of ESBL-producers were tested by conjugation. The isoelectric points of ESBLs were determined by isoelectric focusing. Searches for blaTEM, blaSHV, blaCTX-M, blaPER-1, blaVEB, and blaGES/IBC genes were performed by PCR amplification, and the genotypes of ESBLs were determined by a direct nucleotide sequence analysis of the amplified products. RESULTS: A total of 58 clinical isolates of A. baumannii and 77 P. aeruginosa were collected. Three (5.2%) isolates of A. baumannii and four (5.2%) P. aeruginosa isolates showed positive results in the double-disk synergy test using ceftazidime and imipenem disks, and one (1.7%) A. baumannii and two (2.6%) P. aeruginosa isolates showed positive results in that test using ceftazidime and cefoxitin disks. The most prevalent class A ESBL genotype in A. baumannii isolates was blaPER-1 (n=6), and blaSHV-12 gene was also found in one P. aeruginosa isolate. CONCLUSIONS: It is concluded that class A PER-1 ESBL-producing A. baumannii isolates are spreading, and SHV-12-producing P. aeruginosa has emerged in Korea. The spread of class A ESBLs could compromise the future usefulness of expanded-spectrum -lactam antibiotics for the treatment of A. baumannii and P. aeruginosa infections.
Acinetobacter baumannii* ; Acinetobacter* ; Agar ; Anti-Bacterial Agents ; Base Sequence ; beta-Lactamases* ; Busan ; Cefoxitin ; Ceftazidime ; Diffusion ; Enterobacteriaceae ; Genotype ; Humans ; Imipenem ; Isoelectric Focusing ; Isoelectric Point ; Korea ; Polymerase Chain Reaction ; Prevalence* ; Pseudomonas aeruginosa* ; Pseudomonas*

BACKGROUND: The purposes of this study were to investigate the prevalence of imipenem-resistant clinical Acinetobacter baumannii isolates and to determine the mechanism of the resistance. METHODS: During the period of June to September 2004, susceptibility to imipenem of A. baumannii isolates from a hospital in Busan, Korea were investigated. The isolates were screened for the production of carbapenemase and metallo-beta-lactamase by Modified-Hodge and EDTA-disk synergy tests, respectively; minimum inhibitory concentrations (MICs) were determined by agar dilution method. Genes coding for GES, IMP, VIM, SMP-1, GIM-1 and OXA type beta-lactamases were searched by PCR amplification, and the PCR products were subjected to direct sequencing. Isoelectric points of beta-lactamases were estimated by isoelectric focusing and the epidemiological relationships of isolates were investigated by enterobacterial repetitive intergenic consensus (ERIC) PCR. RESULTS: Fifty eight strains of A. baumannii were isolated from clinical specimens during the surveillance period, and 14 isolates (24.1%) were resistant to imipenem. Of the 14 isolates, 9 were tested positive in Modified-Hodge test and 2 were also positive in EDTA-disk synergy test. Genes encoding OXA-23 and IMP-1 were detected in 7 and 2 isolates, respectively. In IEF studies, OXA-23 and IMP-1 enzymes had corresponding pIs at 6.7 and 9.0, respectively. Seven OXA-23-producing and 2 IMP-1-producing isolates showed the same ERIC PCR patterns. CONCLUSION: It is concluded that 7 and 2 A. baumannii isolates from the patients in a hospital in Busan acquired resistance to imipenem by producing OXA-23 and IMP-1 beta-lactamases, respectively. The isolates producing these beta-lactamases might be originated from a common source.
Acinetobacter baumannii* ; Acinetobacter* ; Agar ; beta-Lactamases ; Busan ; Clinical Coding ; Consensus ; Humans ; Imipenem ; Isoelectric Focusing ; Isoelectric Point ; Korea ; Microbial Sensitivity Tests ; Molecular Epidemiology* ; Polymerase Chain Reaction ; Prevalence

BACKGROUND: Peroxiredoxins (Prxs) are a relatively newly recognized, novel family of peroxidases that reduce H2O2 and alkylhydroperoxide into water and alcohol, respectively. There are 6 known isoforms of Prxs present in human cells. Normally, Prxs exist in a head-to-tail homodimeric state in a reduced form. However, in the presence of excess H2O2, it can be oxidized on its catalytically active cysteine site into inactive oxidized forms. This study surveyed the types of the Prx isoforms present in the pulmonary epithelial, macrophage, endothelial, and other cell lines and observed their response to oxidative stress. METHODS: This study examined the effect of exogenous, excess H2O2 on the Prxs of established cell lines originating from the pulmonary epithelium, macrophages, and other cell lines, which are known to be exposed to high oxygen partial pressures or are believed to be subject to frequent oxidative stress, using non-reducing SDS polyacrylamide electrophoresis (PAGE) and 2 dimensional electrophoresis. RESULT: The addition of excess H2O2 to the culture media of the various cell-lines caused the immediate inactivation of Prxs, as evidenced by their inability to form dimers by a disulfide cross linkage. This was detected as a subsequent shift to its monomeric forms on the non-reducing SDS PAGE. These findings were further confirmed by 2 dimensional electrophoresis and immunoblot analysis by a shift toward a more acidic isoelectric point (pI). However, the subsequent reappearance of the dimeric Prxs with a comparable, corresponding decrease in the monomeric bands was noted on the non-reducing SDS PAGE as early as 30 minutes after the H2O2 treatment suggesting regeneration after oxidation. The regenerated dimers can again be converted to the inactivated form by a repeated H2O2 treatment, indicating that the protein is still catalytically active. The recovery of Prxs to the original dimeric state was not inhibited by a pre-treatment with cycloheximide, nor by a pretreatment with inhibitors of protein synthesis, which suggests that the reappearance of dimers occurs via a regeneration process rather than via the de novo synthesis of the active protein. CONCLUSION: The cells, in general, appeared to be equipped with an established system for regenerating inactivated Prxs, and this system may function as a molecular "on-off switch" in various oxidative signal transduction processes. The same mechanisms might applicable other proteins associated with signal transduction where the active catalytic site cysteines exist.
Catalytic Domain ; Cell Line* ; Culture Media ; Cycloheximide ; Cysteine ; Electrophoresis ; Electrophoresis, Polyacrylamide Gel ; Epithelium ; Humans ; Isoelectric Point ; Macrophages* ; Oxidative Stress ; Oxygen ; Partial Pressure ; Peroxidases ; Peroxiredoxins* ; Protein Isoforms* ; Regeneration* ; Signal Transduction

BACKGROUND AND OBJECTIVES: Calretinin is a neuron specific, high affinity cytosolic calcium-binding protein of the EF-hand family. In the mammalian inner ear, it is expressed in the organ of Corti and most of the spiral ganglion neurons. Authors observed the change of expression and amount of calretinin according to the maturation in the rat cochleae. MATERIALS AND METHOD: Sprague-Dawley rat cochleae collected from each stage (postnatal day (P) P5, P17, P35) were analyzed using 2D gel electrophoresis, proteomic analysis, Western blot analysis, and fluorescence immunocytochemistry. RESULTS: In P17 and P35, calretinin was identified at an isoelectric point (pI) of 4.9 and a molecular weight of 29 kDa in the analysis of the rat cochlea proteins using proteomic analysis. P17 and P35 revealed remarkable existence of calretinin in 2D gel electrophoresis and the Western blot, whereas P5 demonstrated no existence in 2D gel electrophoresis and weak expression in the Western blot. In fluorescence immunocytochemistry, P17 and P35 showed intense calretinin immunoreactivity in the inner hair cells and most ganglion neurons, but P5 displayed no immunoreactivity in inner hair cells and very weak expression in spiral ganglion cells. CONCLUSION: Compared with the early neonatal stage, an amount of calretinin remarkably increases during the critical period of the cochlear maturation and is maintained until the young adult stage. These results suggest that calretinin may have a specific role as a calcium-binding protein since the cochlear maturation in the rat inner ear.
Animals ; Blotting, Western ; Calbindin 2* ; Cochlea* ; Critical Period (Psychology) ; Cytosol ; Ear, Inner ; Electrophoresis, Gel, Two-Dimensional ; Fluorescence ; Ganglion Cysts ; Hair ; Humans ; Immunohistochemistry ; Isoelectric Point ; Molecular Weight ; Neurons ; Organ of Corti ; Rats* ; Rats, Sprague-Dawley ; Spiral Ganglion ; Young Adult

BACKGROUND: Acinetobacter baumannii is a glucose-nonfermenting gram-negative rod and is a well-recognized nosocomial pathogen. In recent years, A. baumannii strains showing resistance to carbapenems by producing metallo-beta-lactamases or OXA-type beta-lactamases have increased, and it is considered to be a serious clinical problem. But genotypes of carbapenemases produced by A. baumannii isolates in Korea have been rarely reported. The purpose of this study was to investigate the prevalence of imipenem-resistant A. baumannii and to determine the mechanism of resistance. METHODS: During the period of January through September, 2003, susceptibilities to imipenem of A. baumannii isolates from patients admitted in Kosin University Gospel Hospital in Busan, Korea were investigated. The modified Hodge and EDTA-disk synergy tests were performed for screening of carbapenemase and metallo-beta-lactamase-production. Minimal inhibitory concentrations (MICs) were determined by the agar dilution method. For detection of IMP, VIM and OXA-type beta-lactamases genes, polymerase chain reactions (PCR) were performed, and the DNA sequences of OXA-type beta-lactamases genes were determined by using the dideoxy-chain termination method. The isoelectric points of beta-lactamases were determined by isoelectric focusing. Pulsed-field gel electrophresis (PFGE) of the SmaI-digested genomic DNA was performed. RESULTS: A total of 193 strains of A. baumannii were collected from patients during the surveillance period. Twenty-seven percents (52/193) of A. baumannii isolates were resistant to imipenem. Among the 52 imipenem-resistant isolates, 41 isolates (78.8%) showed positive results in the modified Hodge test, but none of the isolates showed positive results in the EDTA-disk synergy test. Thirty-eight modified Hodge test-positive isolates harbored blaOXA-23 gene, but none of the isolates harbored IMP- or VIM-type metallo-beta-lactamases genes. Analytical isoelectric focusing revealed that all the 38 isolates had a nitrocefin-positive band at pI of 6.65. Thirty-five OXA-23-producing isolatesshowed a similar PFGE pattern when digested by SmaI endonuclease. CONCLUSION: Thirty-eight clinical isolates of A. baumannii acquired resistance to imipenem by producing OXA-23 beta-lactamase. Among them were 35 isolates thought to be originated from the same source, because they contained a similar chromosomal type. To the best of our knowledge, this is the first time that OXA-23 beta-lactamase has been detected in Korea.
Acinetobacter baumannii* ; Acinetobacter* ; Agar ; Base Sequence ; beta-Lactamases ; Busan* ; Carbapenems ; DNA ; Genotype ; Humans ; Imipenem ; Isoelectric Focusing ; Isoelectric Point ; Korea* ; Mass Screening ; Polymerase Chain Reaction ; Prevalence*

BACKGROUND: In recent years, Acinetobacter baumannii isolates acquired resistance to cefepime have increased significantly. The aim of this study was to survey the prevalence of PER-1 extendedspectrum beta -lactamase (ESBL)-producing A. baumannii isolates in a University Hospital, Busan, Korea. METHODS: Antimicrobial susceptibilities were tested by the disk diffusion method, and double disk synergy test was performed for screening of ESBL-production. MICs were determined by agar dilution method. The isoelectric points of beta -lactamases were determined by isoelectric focusing. Transferability of cefepime-resistance were tested by conjugation. blaPER-1 and blaPER-2 alleles were detected by PCR, and the DNA sequences of amplified products were determined by using the dideoxy-chain termination method. RESULTS: Among 51 clinical isolates of A. baumannii intermediate or resistant to cefepime, 10 isolates (19.6%) showed positive results in double disk synergy test. PCR-based experiments detected blaPER-1 gene in all the 10 isolates. All the isolates contained three beta -lactamase bands: pI 5.3, 7.9, and 9.4. MICs of ampicillin, piperacillin, cephalothin, cefoxitin, cefoperazone, ceftazidime, cefotaxime, cefepime, and aztreonam were >256 mg/L, respectively, and them of imipenem were 8-16 mg/L. CONCLUSION: The prevalence of PER-1-producing A. baumannii strains in Busan was less than that of in Seoul. But an outbreak of infection caused by this strain in an intensive care unit shows that spread of PER-1-producing A. baumannii strains can be anticipated in a near future. Prevention of hospital infection by these resistant microorganisms are needed.
Acinetobacter baumannii* ; Acinetobacter* ; Agar ; Alleles ; Ampicillin ; Aztreonam ; Base Sequence ; Busan* ; Cefoperazone ; Cefotaxime ; Cefoxitin ; Ceftazidime ; Cephalothin ; Cross Infection ; Diffusion ; Imipenem ; Intensive Care Units ; Isoelectric Focusing ; Isoelectric Point ; Korea* ; Mass Screening ; Piperacillin ; Polymerase Chain Reaction ; Prevalence* ; Seoul