Systematic probing of an atomic charge set of sialic acid disaccharides for the rational molecular modeling of avian influenza virus based on molecular dynamics simulations

A systematic searching approach for an atomic charge set through molecular dynamics simulations is introduced to calculate a reasonable sialic acid carbohydrate conformation with respect to the experimentally observed structures. The present molecular dynamics simulation study demonstrated that B3LYP/6-31G is the most suitable basis set for the sialic acid disaccharides, attaining good agreement with experimental data.     

Degradation of endocrine disrupting chemicals by genetic transformants in Irpex lacteus with an inducible laccase gene of Phlebia tremellosa

Irpex lacteus was genetically transformed using an laccase expression vector to get increased laccase producing strains. Stable integration of the vector was confirmed by PCR using the vector-specific primers, and the transformants showed increased laccase activities. When the transformants were grown with several endocrine disrupting chemicals, laccase activity of each transformant was induced up to six times higher than that of the wild type. They showed increased degrading activities against EDCs as well as increased removal rates of estrogenic activities generated by the EDCs than the wild type, and the laccase expression was increased during the degradations of the EDCs.     

The study of antagonistic interactions among pelagic bacteria: a promising way to coin environmental friendly antifouling compounds

Ten strains of marine bacteria (SCH0401–SCH0410) were isolated from Ayajin, the east coast of South Korea. In spectrophotometer based chemotaxis assay the ethyl acetate extract (300 μg) of SCH0402 decreased the optical density (OD) of the motile target strains SCH0401, SCH0402, SCH0407 and SCH0408 by two to six times when compared to control. Tributyltin oxide (TBTO) decreased the OD of all target strains by only two times. The most active strain SCH0402 was identified as Shewanella oneidensis by using 16S rDNA gene sequence analysis. Similarly, the target motile strains SCH0401, SCH0402, SCH0407 and SCH0408 were identified as Alteromonas marina, Shewanella oneidensis, Roseobacter gallaeciensis and Bacillus atrophaeus, respectively. The growth inhibition zone produced by the test bacterial extracts against the target strains were three to eight times smaller when compared to that of TBTO. Even though, SCH0402 showed six times weaker antibacterial activity, the repellent activity was three times stronger than TBTO. Therefore, the higher negative chemotactic activity would be better to select eco-friendly antifouling compounds than the other antibacterial activities.     

Dasania marina gen. nov., sp. nov., of the order Pseudomonadales, isolated from Arctic marine sediment

An obligately aerobic bacterium, strain KOPRI 20902T, was isolated from a marine sediment in Ny-Arlesund, Spitsbergen Islands, Norway. Cells were irregular rods and motile with polar monotrichous flagellum. The optimum growth temperature was 17-22 degrees . Cells grew best in pH 7.0-10.0 and 3-4% sea salts (corresponding to 2.3-3.1% NaCl). The novel strain required Ca2+ or Mg2+ in addition to NaCl for growth. Sequence analysis of 16S rRNA gene revealed that the Arctic isolate is distantly related with established species (<92.4% sequence similarity) and formed a monophyletic group with Cellvibrio, which formed a distinct phylogenetic lineage in the order Pseudomonadales. Predominant cellular fatty acids [C16:1 omega7c/15:0 iso 2OH (45.3%), C16:0 (18.4%), ECL 11.799 (11.2%), C10:0 3OH (10.4%)]; DNA G+C content (37.0 mol%); nitrate reduction to nitrogen; absence of aesculin hydrolysis, N-acetyl-beta-glucosaminidase and esterase; no assimilation of arabinose, galactose, glucose, lactose, maltose, and trehalose differentiated the strain from the genus Cellvibrio. Based on the phylogenetic and phenotypic characteristics, Dasania marina gen. nov., sp. nov. is proposed in the order Pseudomonadales. Strain KOPRI 20902T (=KCTC 12566T=JCM 13441T) is the type strain of Dasania marina.     

Mutant selection of <Emphasis Type="Italic">Hahella chejuensis</Emphasis> KCTC 2396 and statistical optimization of medium components for prodigiosin yield-up

Prodigiosin is a natural red pigment with algicidal activity against Cochlodinium polykrikoides, a major harmful red-tide microalga. To increase the yield of prodigiosin, a mutant of Hahella chejuenesis KCTC 2396, assigned M3349, was developed by an antibiotic mutagenesis using chloramphenicol. When cultured in Sucrose-based Marine Broth medium (SMB), M3349 could produce prodigiosin at 1.628+/-0.06 g/L, while wild type producing at 0.658+/-0.12 g/L under the same conditions. To increase the yield of prodigiosin production by M3349, significant medium components were determined using a two-level Plackett-Burman statistical design technique. Among fourteen components included in SMB medium, NaCl, Na2SiO3, MgCl2, H3BO3, Na2HPO4, Na2SO4, and CaCl2 were determined to be important for prodigiosin production. The medium formulation was finally optimized using a Box-Behnken design as follows: sucrose 10.0, peptone 8.0, yeast extract 2.0, NaCl 10.0, Na2SO4 12.0, CaCl2 1.8, MgCl2 0.7 g/L; and H3BO3 22.0, Na2HPO4 20.0, Na2SiO3 8.0 mg/L. The predicted maximum yield of prodigiosin in the optimized medium was 2.43 g/L by the Box-Behnken design, while the practical production was 2.60+/-0.176 g/L, which was 3.9 times higher than wild type with SMB Medium (0.658 g/L).     

QUOD ERAT FACIENDUM: sequence analysis of the H2-D and H2-Q regions of 129/SvJ mice

The H2-D and -Q regions of the mouse major histocompatibility complex ( Mhc or H2) have been sequenced from strain 129/SvJ (haplotype bc), revealing a D/Q region different from all other investigated haplotypes, including the closely related b haplotype. The 300-kb class I-rich region consists of the classical class I, H2-D, and 11 non-classical class I genes. The Q region was formed by two series of tandem duplications. Comparison of the segment between the D and Q1 genes with the H2-K region provides evidence that class I genes were translocated from the K region to the D region, and gives a new explanation for the weak locus specificity of the H-Kand H2-Dalleles.     

Ornithine-urea cycle and urea synthesis in African lungfishes, Protopterus aethiopicus and Protopterus annectens, exposed to terrestrial conditions for six days

The objectives of this study were (1) to determine the type of carbamoyl phosphate synthetase (CPS) present, and the compartmentalization of arginase, in the livers of the African lungfishes, Protopterus aethiopicus and Protopterus annectens, and (2) to elucidate if these two lungfishes were capable of increasing the rates of urea synthesis and capacities of the ornithine-urea cycle (OUC) during 6 days of aerial exposure without undergoing aestivation. Like another African lungfish, Protopterus dolloi, reported elsewhere, the CPS activities from the livers of P. aethiopicus and P. annectens had properties similar to that of the marine ray (Taeniura lymma), but dissimilar to that of the mouse (Mus musculus). Hence, they possessed CPS III, and not CPS I as reported previously. CPS III was present exclusively in the liver mitochondria of both lungfishes, but the majority of the arginase activities were present in the cytosolic fractions of their livers. Glutamine synthetase (GS) activity was also detected in the hepatic mitochondria of both specimens. Therefore, our results suggest that the evolution of CPS III to CPS I might not have occurred before the evolution of extant lungfishes as suggested previously, prompting an examination of the current view on the evolution of CPS and OUC in vertebrates. Aerial exposure led to significant decreases in rates of ammonia excretion in P. aethiopicus and P. annectens, but there were no accumulations of ammonia in their tissues. However, urea contents in their tissues increased significantly after 6 days of aerial exposure. The estimated rates of urea synthesis in P. aethiopicus and P. annectens increased 1.2- and 1.47-fold, respectively, which were smaller than that in P. dolloi (8.6-fold) reported elsewhere. In addition, unlike P. dolloi, 6 days of aerial exposure had no significant effects on the hepatic CPS III activities of P. aethiopicus and P. annectens. In contrast, aerial exposure induced relatively greater degrees of reductions in ammonia production in P. aethiopicus (34%) and P. annectens (37%) than P. dolloi (28%) as previously reported. Thus, our results suggest that various species of African lungfishes respond to aerial exposure differently with respect to nitrogen metabolism and excretion, and it can be concluded that P. aethiopicus and P. annectens depended more on reductions in ammonia production than on increases in urea synthesis to ameliorate ammonia toxicity when exposed to terrestrial conditions.     

Involvement of human MOF in ATM function

We have determined that hMOF, the human ortholog of the Drosophila MOF gene (males absent on the first), encoding a protein with histone acetyltransferase activity, interacts with the ATM (ataxia-telangiectasia-mutated) protein. Cellular exposure to ionizing radiation (IR) enhances hMOF-dependent acetylation of its target substrate, lysine 16 (K16) of histone H4 independently of ATM function. Blocking the IR-induced increase in acetylation of histone H4 at K16, either by the expression of a dominant negative mutant DeltahMOF or by RNA interference-mediated hMOF knockdown, resulted in decreased ATM autophosphorylation, ATM kinase activity, and the phosphorylation of downstream effectors of ATM and DNA repair while increasing cell killing. In addition, decreased hMOF activity was associated with loss of the cell cycle checkpoint response to DNA double-strand breaks. The overexpression of wild-type hMOF yielded the opposite results, i.e., a modest increase in cell survival and enhanced DNA repair after IR exposure. These results suggest that hMOF influences the function of ATM.