Expression, purification, and characterization of peptidyl-tRNA hydrolase from Staphylococcus aureus.

Bacterial peptidyl-tRNA hydrolase (Pth) activity ensures the rapid recycling of peptidyl-tRNAs that result from premature termination of translation. Pth has been shown to be essential for growth in Escherichia coli suggesting that its homologue in Staphylococcus aureus is a potential molecular therapeutic target for the development of antibacterial agents. In this report we describe the cloning of a DNA fragment (573 bp) containing the pth gene from a S. aureus (strain ISP3) genomic DNA library. Analysis of the predicted polypeptide sequence from the pth gene showed that the protein shared complete conservation of the three residues thought to be involved in the active site of E. coli Pth. The gene was cloned into a pQE-60 expression vector and expressed in E. coli, and the resulting His-tagged Pth protein was purified to greater than 95% purity from the soluble portion of the E. coli lysate in a single chromatographic step. His-tagged Pth was shown to be biologically active by its ability to hydrolyze diacetyl-[(3)H]Lys-tRNA(Lys) in a time- and concentration-dependent manner. Optimum hydrolyzing activity of Pth occurred at a pH value of 7.0 and a MgCl(2) concentration of 5 mM. The K(m) of the diacetyl-[(3)H]-Lys-tRNA(Lys) substrate for S. aureus Pth was determined to be 2.8 microM. A far UV circular dichroism spectrum revealed that His-tagged S. aureus Pth appears to have a structured core predominated by beta-sheet.     

Glucosamine-mediated detoxification of p-benzoquinone and its removal by chitosan

p-Benzoquinone non-enzymatically reacted with d-glucosamine at physiological pH and moderate temperature. The reaction of p-benzoquinone with glucosamine was signaled by changes in the UV and visible spectra. The reactivity proceeded fastest at pH values above 7, with a sharp drop from pH 6.5 to 7.0, and the reaction was negligible in acidic conditions. The order of reactivity of amino sugars was d-mannosamine > d-glucosamine > d-galactosamine. From the reaction mixture, four conversion products were isolated and none was toxic to Escherichia coli even at 500–700 g ml^–1, while p-benzoquinone was cytotoxic to E. coli at 20 g ml^–1. Chitosan could react with p-benzoquinone efficiently and remove this toxicant in aqueous solution.     

Development of a target component extraction method from GC-MS data with an in-house program for metabolite profiling

After gas chromatography-mass spectrometry (GC-MS) analysis, data processing, including retention time correction, spectral deconvolution, peak alignment, and normalization prior to statistical analysis, is an important step in metabolomics. Several commercial or free software packages have been introduced for data processing, but most of them are vendor dependent. To design a simple method for Agilent GC/MS data processing, we developed an in-house program, "CompExtractor", using Microsoft Visual Basic. We tailored the macro modules of an Agilent Chemstation and implanted them in the program. To verify the performance of CompExtractor processing, 30 samples from the three species of the genus Papaver were analyzed with Agilent 5973 MSD GC-MS. The results of CompExtractor processing were compared with those of AMDIS-SpectConnect processing by hierarchical cluster analysis (HCA) and principal component analysis (PCA). The two methods showed good classification according to their species in HCA. The PC1+PC2 scores were 54.32-63.62% for AMDIS-SpectConnect and 56.65-85.92% for CompExtractor in PCA. Although the CompExtractor processing method is an Agilent GC-MS-specific application and the target compounds must be selected first, it can extract the target compounds more precisely in the raw data file with batch mode and simultaneously assemble the matrix text file.     

Nitrogen budgets for the Republic of Korea and the Yellow Sea region

Growing populations in northeast Asia have greatly altered the nitrogencycle, with increases in agricultural production to feed the population, andwith increases in N emissions and transboundary air pollution. For example,during the 1900's over 50% of the N deposition over Republic of Korea wasimported from abroad. In this paper, we present biogeochemical budgets ofN for the South Korean peninsula (the Republic of Korea) and for the YellowSea region. We quantify N inputs from atmospheric deposition, fertilizers,biological fixation, and imports of food, feed, and products. We quantifyoutputs in riverine export, crop uptake, denitrification, volatilization,runoff, sedimentation and sea water exchange. Calculations were conductedusing mean values from 1994–1997. All of the nitrogen budgets werepositive, with N inputs exceeding outputs. The excess N inputs gave rise toincreases in N storage in landfills and in groundwater. Annual accumulationof N in the Yellow sea, including inputs from South Korea and otherdrainage areas, was 1229 kt yr^–1 with a residence time for N ofapproximately 1.5 years, thus doubling N content in marine waters every 3years during 1994–1997. The human derived N inputs leads to excessiveeutrophication and pollution of the Yellow Sea.     

Mycelial protoplast isolation and regeneration of Lentinus lepideus

Generation of fungal protoplast is essential for fusion and transformation systems. Protoplast fusion offers great potential for the improvement of industrially important microorganisms. To establish conditions for the protoplast isolation and regeneration of the mycelia of Lentinus lepideus, various enzymes and osmotic stabilizers were examined. To investigate suitable medium for the culture of L. lepideus, the mycelia were grown in ten different media at 28 degrees C for 10 days. Among them potato dextrose agar (PDA) medium was found to be the best for colony growth. When Novozym 234, cellulase and beta-glucuronidase were added to the mycelia in combination or alone, Novozym 234 alone at the concentration of 10 mg/ml was the most effective for the protoplast yield. Purified spherical protoplasts of the mycelia were osmotically hypersensitive and further incubation of the mycelia with the lytic enzyme resulted in the older parts of the hyphae swollen. When we applied various osmotic stabilizers at the fixed concentration of 0.6 M on the protoplasts, the yields of protoplasts were increased until 4-hr incubation. However application of sucrose or MgSO4 led to further protection of protoplasts after that time and reached a plateau on 5- and 7-hr incubations, respectively. The suitable incubation time and optimal pH with the lytic enzyme for the maximum release of protoplasts were 6 hrs of incubation and pH 5, respectively. When we examined various osmotic stabilizers for the regeneration of the protoplast, the complete medium containing 0.6 M sucrose induced highest hyphal growth with regeneration frequency of 3.28%.     

Shh signaling is essential for rugae morphogenesis in mice

Palatal ridges, or rugae palatinae, are corrugated structures observed in the hard palate region. They are found in most mammalian species, but their number and arrangement are species-specific. Nine palatal rugae are found in the mouse secondary palate. Previous studies have shown that epithelial Shh signaling in the palatal ridge plays an important role during rugae development. Moreover, Wnt family members, including LEF1, play a functional role in orofacial morphogenesis. To explore the function of Shh during rugae development, we utilized the maternal transfer of 5E1 (anti-Shh antibody) to mouse embryos. 5E1 induced abnormal rugae patterning characterized by a spotted shape of palatal ridge rather than a stripe. The expression patterns of Shh and Shh-related genes, Sostdc1, Lef1 and Ptch1, were disrupted following 5E1 injection. Moreover, rugae-specific cell proliferation and inter-rugae-specific apoptosis were affected by inhibition of Shh signaling. We hypothesize that the altered gene expression patterns and the change in molecular events caused by the inhibition of Shh signaling may have induced abnormal rugae patterning. Furthermore, we propose a reaction–diffusion model generated by Wnt, Shh and Sostdc1 signaling. In this study, we show that Sostdc1, a secreted inhibitor of the Wnt pathway, is a downstream target of Shh and hypothesize that the interaction of Wnt, Shh and Sostdc1 is a pivotal mechanism controlling the spatial patterning of palatal rugae.     

Surface ultrastructure of Metagonimus miyatai metacercariae and adults

A scanning electron microscopic study was performed to observe surface ultrastructures of excysted metacercariae and adults of Metagonimus miyatai. Metacercariae were collected from the scale of the pale chub (Zacco platypus), and adult flukes were harvested 1-4 weeks after infection to rats. In excysted metacercariae, the oral sucker was devoid of tegumental spines and had type I and type II sensory papillae. Anteriorly to the ventral sucker, spines were dense and digitated into 5-7 points, whereas near the posterior end of the body spines were sparse and digitated into 2-3 points. In one-week adults, 7 type II sensory papillae were arranged around the lip of the oral sucker, and at inner side of the lip one pair of small and two pairs of large type 1 sensory papillae were seen on each side. The distribution of tegumental spines was similar to that of metacercariae, but they were more differentiated with 9-11 pointed tips. In two- to four-week old adults, the surface ultrastructure was nearly the same as in one-week old adults, however, sperms were frequently seen entering into the Laurer''s canal. Conclusively, the surface ultrastructure of M. miyatai was generally similar to that of M. yokogawai, however, differentiation of tegumental spines and distribution of sensory papillae around the oral sucker were different between the two species, which may be of taxonomic significance.     

Comparison of Ionized Calcium-binding Adapter Molecule 1-Immunoreactive Microglia in the Spinal Cord Between Young Adult and Aged Dogs

Microglia are main form of active immune defense, and they are constantly moving and analyzing the CNS for damaged neurons and infectious agents. In this study, we compared microglia in the spinal cord of the young adult (1–2 years old) and aged (10–12 years old) German Shepherd dogs via immunohistochemistry and western blot analysis for ionized calcium-binding adapter molecule 1 (Iba-1), a microglial marker. In addition, we also observed the interferon-γ (IFN-γ), a pro-inflammatory cytokine, and interleukin-1β (IL-1β), produced by activated microglia/macrophage, protein levels in these groups. At first, we found that neuronal nuclei (NeuN, a neuronal marker)-immunoreactive neurons were distributed throughout the grey mate of the spinal cord, and there were no significant differences between the adult and aged groups. Most of Iba-1-immunoreactive microglia were morphologically ramified microglia (resting form) in the adult group, while some Iba-1-immunoreactive microglia were morphologically activated microglia in the aged group. In western blot analysis, Iba-1, IFN-γ and IL-1β expression were increased in the aged group. This result may be associated with age-dependent changes in the spinal cord.     

Urokinase-Type Plasminogen Activator Induces BV-2 Microglial Cell Migration Through Activation of Matrix Metalloproteinase-9

In response to brain injury, microglia migrate and accumulate in the affected sites, which is an important step in the regulation of inflammation and neuronal degeneration/regeneration. In this study, we investigated the effect of urokinase-type plasminogen activator (uPA) on the BV-2 microglial cell migration. At resting state, BV-2 microglial cells secreted uPA and the release of uPA was increased by ATP, a chemoattractant released from injured neuron. The migration of BV-2 cell was significantly induced by uPA and inhibited by uPA inhibitors. In this condition, uPA increased the activity of matrix metalloproteinase (MMP-9) and the inhibition of MMP activity with pharmacological inhibitors against either uPA (amiloride) or MMP (phenanthrolene and SB-3CT) effectively prevented BV2 cell migration. Interestingly, the level of MMP-9 protein and mRNA in the cell were not changed by uPA. These results suggest that the increase of MMP-9 activity by uPA is regulated at the post-translational level, possibly via increased activation of the enzyme. Unlike the uPA inhibitor, plasmin inhibitor PAI-1 only partially inhibited uPA-induced cell migration and MMP-9 activation. The incubation of recombinant MMP-9 with uPA resulted in the activation of MMP-9. These results suggest that uPA plays a critical role in BV-2 microglial cell migration by activating pro-MMP-9, in part by its direct action on MMP-9 and also in part by the activation of plasminogen/plasmin cascade.