Factors affecting nitrogenase activity associated with marsh grasses and their soils from eutrophic lakes

The acetylene reduction activity (ARA) of soil-plant cores and intact, soil-free plant-root systems was used to study the influence of soil moisture content, diurnal cycles of temperature and light, and inorganic N and P on the nitrogenase activity (AR) associated with Phalaris arundinacea L. and Phragmites australis (Cav.) Trin. from two eutrophic lakes (lochs), Balgavies and Forfar.A positive correlation (r = 0.81, n = 26) was established between AR and soil moisture content in individual soil-plant cores of Phalaris from Forfar Loch. Nitrogenase activity, soil moisture and NO₂⁻-N increased with decreasing distance from lake water in Balgavies Loch.Diurnal fluctuations in AR, probably attributable to a combined effect of soil temperature and illumination changes, were observed under field conditions for Phalaris and Phragmites. Under laboratory conditions, the shading and cutting of Phalaris shoots did not inhibit ARA, which suggested that new photosynthates did not necessarily supply substrate for activity in the short term.Partial and temporary inhibition of ARA was obtained in dissected soil-plant cores after a single application of NH₄⁺-N and NO₃⁻-N (350 μg N g⁻¹ fresh weight). At concentrations equivalent to 300 μg P g⁻¹ fresh weight of Phalaris cores, PO₄³⁻-P also caused partial and temporary inhibition of ARA of soil-free plant-root systems, but stimulated activity in intact simulated in situ systems.     

Land, Custom and Practice in the South Pacific

Land, Custom and Practice in the South Pacific, R. Gerard Ward and Elizabeth Kingdon. eds. Cambridge: Cambridge University Press, 1995. 290 pp.     

Evaluation of four membrane filter media in anaerobic-MF recovery of faecal coliforms from freshwater in Nigeria.

MacConkey (MC), membrane lauryl sulphate (MIS), membrane faecal coliform amended with rosolic acid (MFC + R) and without the acid (MFC - R) were evaluated in the anaerobic membrane filtration (anaerobic-MF) recovery of faecal coliform populations (FCs), genera and faecal coliform positive (FC-positive) strains isolated from various sources of freshwater, i.e., rivers, rural wells, unchlorinated distributive supplies and hand pumps. Mean counts (x 10(2)/100 ml) of presumptive (typical) FCs varied from 13.69 (MC) to 40.81 (MLS) in river samples, and from 2.0 (MC) to 4.19 (MFC + R) in wells. The proportion of FC-positive, typical FCs ranged from 48.66 (MIS) to 66-67% (MC) in rivers, and from 50 (MC) to 90.22% (MFC + R) in wells. More than 30% of the typical FCs from all sources on each medium was FC-negative. These usually formed small (ca 1.0 mm diam.) colonies on the test agar, and were prevalent in wells. Typical FCs and FC-positive strains were not recovered from piped supplies and hand pumps. In spite of anaerobic incubation, non-faecal coliforms (NFCs) were often higher than the FCs; the FC:NFC ratios for rivers ranged from 1.65 (MC) to 7.65 (MLS) and (MFC + R) but were < 1.0 for wells on each medium. Escherichia coli, Klebsiella and Enterobacter species were recovered on all media: approximately 35-64% of the strains confirmed as FCs were E. coli, 20-42% were Kl. pneumoniae. The FC counts on the media were variable, but the overall performance in recovering 'true' FCs was similar; < 70% of strains per medium were FC-positive. None could count E. coli exclusively.     

Characterization of extremely halophilic Archaea isolated from the Ayvalik Saltern,Turkey

Seven extremely halophilic strains were isolated from the Ayvalik Saltern in the north-eastern part of Turkey. Chemical analyses of the brine and salt samples were performed to measure their salt content, hardness and pH. Isolated strains were tested for their antibiotic sensitivities; cell and colony morphologies; hydrolysis of casein, starch, gelatin, Tween 20 and Tween 80; and oxidase and catalase activity. All strains were found to belong to the domain Archaea. Characterization of polar lipids by thin layer chromatography indicated that all isolates contained phytanyl diether derivatives of phosphatidylglycerol (PG), the methyl ester of phosphatidyl glycerophosphate (PGP-Me), and phosphatidylglycerosulphate (PGS). Four isolates had triglycosyl diether (TGD-2) as glycolipid, and the other three contained a sulphated diglycosyl diether instead. All isolates were examined for the presence of plasmids by agarose gel electrophoresis. Four strains were found to harbour plasmids ranging in size from 13.8 to 15.3 kbp. Correlation between the protein profiles in SDS–PAGE and the phenotypic properties of the strains was poor. The data presented here provide the first published account of the microbiota of the Ayvalik saltern, which provides a large part of the salt produced in Turkey.     

NCI-60 Whole Exome Sequencing and Pharmacological CellMiner Analyses

Exome sequencing provides unprecedented insights into cancer biology and pharmacological response. Here we assess these two parameters for the NCI-60, which is among the richest genomic and pharmacological publicly available cancer cell line databases. Homozygous genetic variants that putatively affect protein function were identified in 1,199 genes (approximately 6% of all genes). Variants that are either enriched or depleted compared to non-cancerous genomes, and thus may be influential in cancer progression and differential drug response were identified for 2,546 genes. Potential gene knockouts are made available. Assessment of cell line response to 19,940 compounds, including 110 FDA-approved drugs, reveals ≈80-fold range in resistance versus sensitivity response across cell lines. 103,422 gene variants were significantly correlated with at least one compound (at p<0.0002). These include genes of known pharmacological importance such as IGF1R, BRAF, RAD52, MTOR, STAT2 and TSC2 as well as a large number of candidate genes such as NOM1, TLL2, and XDH. We introduce two new web-based CellMiner applications that enable exploration of variant-to-compound relationships for a broad range of researchers, especially those without bioinformatics support. The first tool, “Genetic variant versus drug visualization”, provides a visualization of significant correlations between drug activity-gene variant combinations. Examples are given for the known vemurafenib-BRAF, and novel ifosfamide-RAD52 pairings. The second, “Genetic variant summation” allows an assessment of cumulative genetic variations for up to 150 combined genes together; and is designed to identify the variant burden for molecular pathways or functional grouping of genes. An example of its use is provided for the EGFR-ERBB2 pathway gene variant data and the identification of correlated EGFR, ERBB2, MTOR, BRAF, MEK and ERK inhibitors. The new tools are implemented as an updated web-based CellMiner version, for which the present publication serves as a compendium.     

Extremely halophilic Archaea from Tuz Lake,Turkey, and the adjacent Kaldirim and Kayacik salterns

Tuz Lake is a hypersaline lake located in Central Anatolia, Turkey. The lake and its salterns, Kaldirim and Kayacik, are the major sources of solar salt for industrial applications in Turkey, especially in the food and leather industries. Use of the crude solar salt often results in microbial deterioration of the products. We therefore initiated a thorough characterization of the microbial communities in Tuz Lake and its adjacent salterns, and we present here the results of investigations on diversity of extremely halophilic Archaea. Twenty-seven colonies of aerobic red or pink Archaea (family Halobacteriaceae) were selected according to colony shape, size, consistency and pigmentation, and characterized according to their phenotypic characteristics, polar lipid contents, and antibiotic sensitivities. Furthermore, 16S rRNA genes of the isolates were screened by DGGE analysis and partially sequenced. Phylogenetic analysis showed that most isolates belonged to the genera Haloarcula, Halorubrum and Halobacterium. Haloarcula was found to be dominant both in Tuz Lake and in the saltern samples. Halorubrum species were isolated from Tuz Lake and from the Kaldirim saltern, and Halobacterium species were recovered from Tuz Lake and from the Kayacik saltern. All strains showed various activities of hydrolytic enzymes (proteases, amylases, cellulases, and others), activities which are responsible for the detrimental effects of the crude salt in food and leather products.     

Covalent immobilization of acetylcholinesterase on a novel polyacrylic acid‐based nanofiber membrane

In this study, polyacrylic acid‐based nanofiber (NF) membrane was prepared via electrospinning method. Acetylcholinesterase (AChE) from Electrophorus electricus was covalently immobilized onto polyacrylic acid‐based NF membrane by demonstrating efficient enzyme immobilization, and immobilization capacity of polymer membranes was found to be 0.4 mg/g. The novel NF membrane was synthesized via thermally activated surface reconstruction, and activation with carbonyldiimidazole upon electrospinning. The morphology of the polyacrylic acid‐based membrane was investigated by scanning electron microscopy, Fourier Transform Infrared Spectroscopy, and thermogravimetric analysis. The effect of temperature and pH on enzyme activity was investigated and maxima activities for free and immobilized enzyme were observed at 30 and 35°C, and pH 7.4 and 8.0, respectively. The effect of 1 mM Mn²⁺, Ni²⁺, Cu²⁺, Zn²⁺, Mg²⁺, Ca²⁺ ions on the stability of the immobilized AChE was also investigated. According to the Michaelis–Menten plot, AChE possessed a lower affinity to acetylthiocholine iodide after immobilization, and the Michaelis–Menten constant of immobilized and free AChE were found to be 0.5008 and 0.4733 mM, respectively. The immobilized AChE demonstrated satisfactory reusability, and even after 10 consecutive activity assay runs, AChE maintained ca. 87% of its initial activity. Free enzyme lost its activity completely within 60 days, while the immobilized enzyme retained approximately 70% of the initial activity under the same storage time. The favorable reusability of immobilized AChE enables the support to be employable to develop the AChE‐based biosensors.