c-Myc Quadruplex-forming Sequence Pu-27 Induces Extensive Damage in Both Telomeric and Nontelomeric Regions of DNA

Quadruplex-forming DNA sequences are present throughout the eukaryotic genome, including in telomeric DNA. We have shown that the c-Myc promoter quadruplex-forming sequence Pu-27 selectively kills transformed cells (Sedoris, K. C., Thomas, S. D., Clarkson, C. R., Muench, D., Islam, A., Singh, R., and Miller, D. M. (2012) Genomic c-Myc quadruplex DNA selectively kills leukemia. Mol. Cancer Ther. 11, 66–76). In this study, we show that Pu-27 induces profound DNA damage, resulting in striking chromosomal abnormalities in the form of chromatid or chromosomal breaks, radial formation, and telomeric DNA loss, which induces γ-H2AX in U937 cells. Pu-27 down-regulates telomeric shelterin proteins, DNA damage response mediators (RAD17 and RAD50), double-stranded break repair molecule 53BP1, G₂ checkpoint regulators (CHK1 and CHK2), and anti-apoptosis gene survivin. Interestingly, there are no changes of DNA repair molecules H₂AX, BRCA1, and the telomere maintenance gene, hTERT. ΔB-U937, where U937 cells stably transfected with deleted basic domain of TRF2 is partially sensitive to Pu-27 but exhibits no changes in expression of shelterin proteins. However, there is an up-regulation of CHK1, CHK2, H₂AX, BRCA1, and survivin. Telomere dysfunction-induced foci assay revealed co-association of TRF1with γ-H2AX in ATM deficient cells, which are differentially sensitive to Pu-27 than ATM proficient cells. Alt (alternating lengthening of telomere) cells are relatively resistant to Pu-27, but there are no significant changes of telomerase activity in both Alt and non-Alt cells. Lastly, we show that this Pu-27-mediated sensitivity is p53-independent. The data therefore support two conclusions. First, Pu-27 induces DNA damage within both telomeric and nontelomeric regions of the genome. Second, Pu-27-mediated telomeric damage is due, at least in part, to compromise of the telomeric shelterin protein complex.     

Arthrobacter ginsengisoli sp. nov., isolated from soil of a ginseng field

A Gram-staining-positive, catalase-positive, oxidase-negative, non-motile, non-flagellate and rod-shaped bacterium, was designated as DCY81^T, and isolated from soil of a ginseng field in Pocheon province, Republic of Korea. The 16S rRNA gene sequence analysis revealed that strain DCY81^T belonged to the genus Arthrobacter. Major fatty acid was anteiso-C_15:0, while major polar lipids were diphosphatidyglycerol, phatidyglycerol, phosphatidylinositol, monogalactosyldiacylglycerol (GL1), and dimannosyldiacylglycerol (GL2). The dominant quinone was MK-9(H₂). The peptidoglycan type was A3α with an l-Lys–l-Ala–l-Thr–l-Ala interpeptide bridge. The DNA–DNA hybridization relatedness between strain DCY81^T and Arthrobacter siccitolerans LMG 27359^T (98.2 %), Arthrobacter sulfonivorans JCM 13520^T (97.81 %), Arthrobacter scleromae DSM 17756^T (97.59 %), Arthrobacter oxydans KCTC 3383^T (97.3 %) was 39.1 ± 0.2, 62.2 ± 1.6, 36.8 ± 1.1 and 48.3 ± 1.6 %, respectively which show that the genotypic separation of strain DCY81^T from the closest reference strain of the genus Arthrobacter. The DNA G+C content was 65.2 mol%. The genotypic analysis, physiological, and chemotaxonomic results indicate that strain DCY81^T represents a novel species of the genus Arthrobacter. Therefore, Arthrobacter ginsengisoli sp. nov., is proposed as the type strain (=KCTC 29225^T = JCM 19357^T).     

An alkaline and metallo-protein type endo xylanase from Streptomyces sp. CSWu-1

An alkaline xylanase (XynWu-1) from Streptomyces sp. CSWu-1 was isolated from the Korean soil sample, purified and biochemically characterized. The extracellular xylanase was purified 4.8 fold with a 16% yield using Sephadex G-50 followed by DEAE-Sepharose (fast flow) column chromatography. The molecular mass of the enzyme was approximately 37 kDa estimated by SDS-PAGE and xylan zymography. N-terminal amino acid sequence of XynWu-1 was AINVLVAALX. The enzyme was found to be stable in a broad range of pH (7.0 ～ 13.0) and to 50°C and have an optimal pH and temperature of 11.0 and 60°C, respectively. XynWu-1 activity was found to be affected by Mn²⁺ ion with highest activity at 6 mM and produced xylose, xylobiose, and xylotetraose as major hydrolyzed end products. It was found to degrade agro waste materials like corncob and wheat bran by XynWu-1 (2,000 U/g) as shown by electron microscopy. As being stable in extreme alkaline pH, diverse peculiar biochemical characteristics, and ability to produce oligosaccharide shows that XynWu-1 has potential application in various bioindustries like probiotics, ethanol, etc.     

Simplified feeding strategies for the fed-batch cultivation of Kluyveromyces lactis GG799 for enhanced recombinant xylanase production

A xylanase gene (xyn2) from Trichoderma reesei ATCC 58350 was previously cloned and expressed in Kluyveromyces lactis GG799. The production of the recombinant xylanase was conducted in a developed medium with an optimised batch and with fed-batches that were processed with glucose. The glucose served as a carbon source for cell growth and as an inducer for xylanase production. In a 1-L batch system, a glucose concentration of 20 g L^?1 and 80 % dissolved oxygen were found to provide the best conditions for the tested ranges. A xylanase activity of 75.53 U mL^?1 was obtained. However, in the batch mode, glucose depletions reduced the synthesis of recombinant xylanase by K. lactis GG799. To maximise the production of xylanase, further optimisation was performed using exponential feeding. We investigated the effects of various nitrogen sources combined with the carbon to nitrogen (C/N) molar ratio on the production of xylanase. Of the various nitrogen sources, yeast extract was found to be the most useful for recombinant xylanase production. The highest xylanase production (110.13 U mL^?1) was measured at a C/N ratio of 50.08. These conditions led to a 45.8 % increase in xylanase activity compared with the batch cultures. Interestingly, the further addition of 500 g L^?1 glucose led to a 6.2-fold increase (465.07 U mL^?1) in recombinant xylanase activity. These findings, together with those of the exponential feeding strategy, indicate that the composition of the C/N molar ratio has a substantial impact on recombinant protein production in K. lactis.     

Involvement of NHERF1 in apical membrane localization of MRP4 in polarized kidney cells

Multidrug resistance protein 4 (MRP4/ABCC4), a member of the ATP-binding cassette protein superfamily, confers resistance to nucleoside and nucleotide analogs as well as camptothecin derivatives. MRP4 also mediates the efflux of certain cyclic nucleotides, eicosanoids, conjugated steroids, and uric acid. Depending on the cell type, MRP4 may localize to either apical or basolateral membranes in polarized cells. The adaptor protein NHERF1 has previously been implicated in MRP4 internalization in non-polarized cells. We have now found that NHERF1 levels are very low in polarized MDCKI cells which express MRP4 on basolateral membranes relative to polarized LLC-PK1 cells which express MRP4 on apical membranes. Furthermore, ectopic expression of FLAG-tagged NHERF1 in MDCKI cells and in MDCKI cells stably expressing eGFP-tagged MRP4 causes endogenous MRP4 and eGFP-MRP4, respectively, to traffic to the apical membranes. These data establish NHERF1 as a major determinant of MRP4 trafficking to apical membranes of mammalian kidney cells.     

Novozym 435 for production of biodiesel from unrefined palm oil: Comparison of methanolysis methods

Biodiesel (BD) is commonly produced from refined vegetable oils by alkali-catalyzed methanolysis. Unrefined vegetable oils are economically attractive but not suitable for alkali catalysis because of their high content of free fatty acids (FFAs). Novozym 435 (immobilized Candida antarctica lipase B), which accepts both FFA and oil as substrates, was, therefore, employed to convert unrefined palm oil to BD. Three different methanolysis methods, namely, t-butanol mediated system (method-1), LiCl solution based controlled release system for methanol (method-2) and solvent-free system with three successive additions of methanol (method-3), were compared. The optimal methanol to oil molar ratios in the method-1, -2 and -3 are 6:1, 3:1 and 3:1, respectively. BD yield at an optimal methanol concentration reaches 91–92% after 10, 20 and 24 h in the method-1, -2 and -3, respectively. BD yield remains the same over five repeated cycles in the method-1, while it drops to 68 and 71% by the fifth cycle in the method-2 and -3, respectively. The results show that the method-1 is the most effective for production of BD from a low cost feedstock like unrefined palm oil.     

Diet and prey selection in larval and juvenile Japanese anchovy Engraulisjaponicus in Ariake Bay, Japan

We studied the diet of larval and juvenile Japanese anchovy Engraulis japonicus in the upper Ariake Bay, Japan. Diet was analyzed by examining the digestive tracts; feeding intensity, proportion of empty guts, and prey selectivity were calculated. Anchovy density was negatively influenced by temperature and positively by salinity and prey density. Diet was dominated by Acartia omorii, which was positively selected with two other copepods, Calanus sinicus and Pseudodiaptomus marinus. In contrast, Oithona davisae was highly dominant in the environment but was absent in anchovy guts; thus, this copepod was negatively selected, with two others, Tortanus derjugini and Sinocalanus sinensis. Overall, larger prey were positively selected and smaller ones were negatively selected; value of electivity index correlated negatively with prey size. Larvae [<18 mm of standard length (SL)] showed significantly lower feeding intensities and higher rates of empty guts than juveniles (≥18 mm SL). In juveniles, feeding intensity increased steadily as the fish grew in size, with a corresponding reduction in empty guts. Feeding intensity correlated positively and empty gut correlated negatively with fish size. We suggest that larger prey are important diets for postlarval Japanese anchovy in Ariake Bay.     

High levels of genetic variability and differentiation in hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) populations revealed by PCR-RFLP analysis of the mitochondrial DNA D-loop region

The hilsa shad, Tenualosa ilisha (Clupeidae, Clupeiformes) is an important anadromous clupeid species from the Western division of the Indo-Pacific region. It constitutes the largest single fishable species in Bangladesh. Information on genetic variability and population structure is very important for both management and conservation purposes. Past reports on the population structure of T. ilisha involving morphometric, allozyme and RAPD analyses are contradictory. We examined genetic variability and divergence in two riverine (the Jamuna and the Meghna), two estuarine (Kuakata and Sundarbans) and one marine (Cox's Bazar) populations of T. ilisha by applying PCR-RFLP analysis of the mtDNA D-loop region. The amplified PCR products were restricted with four restriction enzymes namely, XbaI, EcoRI, EcoRV, and HaeIII. High levels of haplotype and gene diversity within and significant differentiations among, populations of T. ilisha were observed in this study. Significant F(ST) values indicated differentiation among the river, estuary and marine populations. The UPGMA dendrogram based on genetic distance resulted in two major clusters, although, these were subsequently divided into three, corresponding to the riverine, estuarine and marine populations. The study underlines the usefulness of RFLP of mtDNA D-loop region as molecular markers, and detected at least two differentiated populations of T. ilisha in Bangladesh waters.