Genomic blueprint of Hahella chejuensis, a marine microbe producing an algicidal agent

Harmful algal blooms, caused by rapid growth and accumulation of certain microalgae in the ocean, pose considerable impacts on marine environments, aquatic industries and even public health. Here, we present the 7.2-megabase genome of the marine bacterium Hahella chejuensis including genes responsible for the biosynthesis of a pigment which has the lytic activity against a red-tide dinoflagellate. H.chejuensis is the first sequenced species in the Oceanospiralles clade, and sequence analysis revealed its distant relationship to the Pseudomonas group. The genome was well equipped with genes for basic metabolic capabilities and contained a large number of genes involved in regulation or transport as well as with characteristics as a marine heterotroph. Sequence analysis also revealed a multitude of genes of functional equivalence or of possible foreign origin. Functions encoded in the genomic islands include biosynthesis of exopolysacchrides, toxins, polyketides or non-ribosomal peptides, iron utilization, motility, type III protein secretion and pigmentation. Molecular structure of the algicidal pigment, which was determined through LC-ESI-MS/MS and NMR analyses, indicated that it is prodigiosin. In conclusion, our work provides new insights into mitigating algal blooms in addition to genetic make-up, physiology, biotic interactions and biological roles in the community of a marine bacterium.     

A computational approach for identifying pathogenicity islands in prokaryotic genomes

Background  

Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to now, computational approaches for identifying PAIs have been focused on the detection of genomic regions which only differ from the rest of the genome in their base composition and codon usage. These approaches often lead to the identification of genomic islands, rather than PAIs.     

Sodium ascorbate (vitamin C) induces apoptosis in melanoma cells via the down-regulation of transferrin receptor dependent iron uptake

Sodium ascorbate (vitamin C) has a reputation for inconsistent effects upon malignant tumor cells, which vary from growth stimulation to apoptosis induction. Melanoma cells were found to be more susceptible to vitamin C toxicity than any other tumor cells. The present study has shown that sodium ascorbate decreases cellular iron uptake by melanoma cells in a dose- and time-dependent fashion, indicating that intracellular iron levels may be a critical factor in sodium ascorbate-induced apoptosis. Indeed, sodium ascorbate-induced apoptosis is enhanced by the iron chelator, desferrioxamine (DFO) while it is inhibited by the iron donor, ferric ammonium citrate (FAC). Moreover, the inhibitory effects of sodium ascorbate on intracellular iron levels are blocked by addition of transferrin, suggesting that transferrin receptor (TfR) dependent pathway of iron uptake may be regulated by sodium ascorbate. Cells exposed to sodium ascorbate demonstrated down-regulation of TfR expression and this precedes sodium ascorbate-induced apoptosis. Taken together, sodium ascorbate-mediated apoptosis appears to be initiated by a reduction of TfR expression, resulting in a down-regulation of iron uptake followed by an induction of apoptosis. This study demonstrates the specific mechanism of sodium ascorbate-induced apoptosis and these findings support future clinical trial of sodium ascorbate in the prevention of human melanoma relapse.     

Junctional membrane inositol 1,4,5-trisphosphate receptor complex coordinates sensitization of the silent EGF-induced Ca2+ signaling

Ca(2+) is a highly versatile intracellular signal that regulates many different cellular processes, and cells have developed mechanisms to have exquisite control over Ca(2+) signaling. Epidermal growth factor (EGF), which fails to mobilize intracellular Ca(2+) when administrated alone, becomes capable of evoking [Ca(2+)](i) increase and exocytosis after bradykinin (BK) stimulation in chromaffin cells. Here, we provide evidence that this sensitization process is coordinated by a macromolecular signaling complex comprised of inositol 1,4,5-trisphosphate receptor type I (IP(3)R1), cAMP-dependent protein kinase (PKA), EGF receptor (EGFR), and an A-kinase anchoring protein, yotiao. The IP(3)R complex functions as a focal point to promote Ca(2+) release in two ways: (1) it facilitates PKA-dependent phosphorylation of IP(3)R1 in response to BK-induced elevation of cAMP, and (2) it couples the plasmalemmal EGFR with IP(3)R1 at the Ca(2+) store located juxtaposed to the plasma membrane. Our study illustrates how the junctional membrane IP(3)R complex connects different signaling pathways to define the fidelity and specificity of Ca(2+) signaling.     

Tumor necrosis factor-induced nonapoptotic cell death requires receptor-interacting protein-mediated cellular reactive oxygen species accumulation

The mechanism of tumor necrosis factor (TNF)-induced nonapoptotic cell death is largely unknown, although the mechanism of TNF-induced apoptosis has been studied extensively. In wild-type mouse embryonic fibroblast cells under a caspase-inhibited condition, TNF effectively induced cell death that morphologically resembled necrosis. In this study, we utilized gene knockout mouse embryonic fibroblasts cells and found that tumor necrosis factor receptor (TNFR) I mediates TNF-induced necrotic cell death, and that RIP, FADD, and TRAF2 are critical components of the signaling cascade of this TNF-induced necrotic cell death. Inhibitors of NF-kappaB facilitated TNF-induced necrotic cell death, suggesting that NF-kappaB suppresses the necrotic cell death pathway. JNK, p38, and ERK activation seem not to be required for this type of cell death because mitogen-activated protein kinase inhibitors did not significantly affect TNF-induced necrotic cell death. In agreement with the previous reports that the reactive oxygen species (ROS) may play an important role in this type of cell death, the ROS scavenger butylated hydroxyanisole efficiently blocked TNF-induced necrotic cell death. Interestingly, during TNF-induced necrotic cell death, the cellular ROS level was significantly elevated in wild type, but not in RIP(-/-), TRAF2(-/-), and FADD(-/-) cells. These results suggest that RIP, TRAF2, and FADD are crucial in mediating ROS accumulation in TNF-induced necrotic cell death.     

(-)-3,5-Dicaffeoyl-muco-quinic acid isolated from Aster scaber contributes to the differentiation of PC12 cells: through tyrosine kinase cascade signaling

Aster scaber T. (Asteraceae) has been used in traditional Korean and Chinese medicine to treat bruises, snakebites, headaches, and dizziness. (-)-3,5-Dicaffeoyl-muco-quinic acid (DQ) isolated from A. scaber induced neurite outgrowth in PC12 cells. It has been reported that the activation of the extracellular signal regulated kinase 1/2 (Erk 1/2) and phosphoinositide 3 (PI3) kinase plays a crucial role in the NGF-induced differentiation of PC12 cells. This study showed that the effect of DQ on neurite outgrowth is mediated via the Erk 1/2 and PI3 kinase-dependent pathways like NGF. Furthermore, DQ stimulated the phosphorylation of Trk A. Overall, DQ elicited the differentiation of PC12 cells through Trk A phosphorylation followed by Erk 1/2 and PI3 kinase activation.     

The identification and characterization of xenoantigenic nonhuman carbohydrate sequences in membrane proteins from porcine kidney

The immunogenic nonhuman carbohydrate sequences in membrane proteins from porcine kidney were identified and characterized using MALDI-TOF MS and ESI-QTOF-MS. The MALDI profile, investigated by incubation with exoglycosidases, showed a series of about 40 carbohydrates that were identified as high mannose glycans (Man(3-9)GlcNAc2) and complex bi-, tri-, and tetra-antennary glycans with and without core fucose. The antennae of many of the complex glycans were terminated with alpha-galactose residues, with the numbers of these residues ranging from one up to the number of antennae. Negative ion ESI-MS/MS spectra confirmed the location of the alpha-galactose residues on the ends of the antennae. This total glycan profile of the membrane proteins from porcine kidney will thus provide important information for the study of molecular interactions between antigenic carbohydrates and proteins in xenotransplantation.     

Life Cycle Assessment of a Personal Computer and its Effective Recycling Rate (7 pp)

Background, Aims and Scope Telecommunication and information technology, dramatically emerged during the last decade, has generated environmental problems by accelerating mass production, mass consumption, and mass disposal of personal computers (PCs) in Korea. In addition, it has led the Korean new economy. The Korean government has encouraged researchers and industry to study the environmental impact, adequate disposal treatment, and the reasonable recycling rate of an end-of-life personal computer. The main purpose of this research is to investigate the life cycle environmental impact of PCs and to determine the desirable or feasible recycle rate of an end-of-life PC. An LCA on a PC was performed based on different recycling scenario. Target audiences are new product developers, designers, product recovery managers and environmental policy makers who are interested in the environmental impact of PCs and recycling of end-of-life products. Methods A target product is a Pentium IV personal computer made in Korea in 2001, excluding the monitor and peripheral equipment. The procedure of the LCA followed the ISO14040 series. System boundary includes the entire life cycle of the product, including pre-manufacturing (the electrical parts and components manufacturing), manufacturing, transportation, use, and disposal. The LCI and impact assessment database for a PC was constructed using SIMAPRO version 4.0 software and LCI information was compiled by site-specific data and the Korean national database. The LCA was performed on different recycling scenarios: one being that of the current recycling rate of 46%, and the other being the ideal condition of a 100% recycling rate. Results and Discussion Abiotic depletion, global warming, ecotoxicity, human toxicity, acidification, ozone layer depletion, photo-oxidant formation, and eutrophication are adopted as the impact categories. The pre-manufacturing stage was a significant stage for all of the environmental parameters, besides human toxicity potential. PC manufacturing consists of rather simple processes such as assembly and packaging. For improving the environmental performance of PCs, environmental management approaches of design for the environment and green procurement are recommended. The use stage had a significant potential due to the electricity consumption produced by burning fossil fuel. The disposal stage's contribution to environmental impact was largest in human toxicity, and second largest in ozone layer depletion potential. The PC recycling was shown to inhibit all environmental impacts with the exception of the ozone depletion and ecotoxicity potential. The increase of light oil, nitric acid, sulfuric acid, and deoxidating agent consumption during the recycling process contributes to the environmental impact of ozone and ecotoxicity parameters. Current recovery and recycling technologies should be taken into account for enhancing the benefits of recycling. Anyway, the effectiveness of recycling was highlighted by this study. PC recycling reduces the total environmental impact of the product. The PC recycling is recommended to be raised up to at least 63% in order to reduce the environmental burdens of a PC in other life cycle stages. Conclusion and Recommendation This study implies that design for the environment (DfE) in the product design stage and green procurement are recommended for improving the entire environmental performance of electronic equipment such as PCs. The recycling of waste PCs clearly reduces the environmental burden. There are, however, trade-offs among environmental parameters according to the PC recycling rate. Current recycling methods are not effective in reducing ozone depletion and ecotoxicity environmental impact. The product recovery is another key for efficient recycling. Efficient reverse logistics to collect and transport end-of-life PCs should be taken into account to enhance recycling effects. There were several electrical parts not included in this assessment, due to the unavailability of adequate data. Further studies with more detail and reliable inventories for electrical parts and sub-components are recommended. Furthermore, costs of recycling should also be treated in further research.     

Regioselectivity of 7-O-methyltransferase of poplar to flavones

POMT-7, an O-methyltransferase from poplar (Populus deltoids) was used to modify a variety of flavonoid compounds. POMT-7 was able to transfer a methyl group to several flavonoids containing a C-7 hydroxyl group. However, POMT-7 showed a higher affinity toward flavonol and flavone such as apigenin, kaempferol, luteolin, and quercetin than flavanone and isoflavone. Based on comparison of HPLC retention times with authentic compounds and corresponding nuclear magnetic resonance spectroscopy data, the methylation position of the reaction products was determined to be at the hydroxyl group of C-7. Biotransformation kinetics indicated that the enzyme converted more than 80% of the apigenin, kaempferol, luteolin and quercetin substrates, which were added at concentration of 70 microM, into corresponding 7-methoxy compounds within 24 h.