Ahn, Joo-Myung

Gu, Man Bock

Hwang, Ee Taek

Kim, Byoung Chan

Kolkar Mohammed, Javed Hussain Niazi

English

Sabanci University Research Database

S94 Abstracts / Journal of Bioscience and Bioengineering 108 (2009) S75–S95in dry chamber for 2 days 0.7 mL of the cell suspensionwas inoculatedinto a vessel of model soil and kept at 30 °C. N-hexadecane wasquantified with FID-GC after extraction with chloroform.As the results, it was found that the degradation rate reachedplateau over the hexadecane concentration of 1.1 mg (g-soil)−1. Thissuggests that the rate-limiting step in the degradation of hexadecanein soil is not the transportation of the hydrophobic substance throughaqueous phase but the reactions that degrade the substance. Thus, wetried to clarify the rate-limiting reaction in the metabolic degradationpathway of hexadecane and on the other hand to prolong thedegradation reaction of Y. lipolytica.doi:10.1016/j.jbiosc.2009.08.274EN-P42Characterization of thermostable polyester-degrading enzymefrom Thermobifida alba AHK119Uschara Thumarat,1 Xiaopin Hu,2 Ryota Nakamura,3 Hideyuki Suzuki,3Hitomi Ohara,1 and Fusako Kawai1R&D Center for Bio-based Materials, Kyoto Institute of Technology,Kyoto, Japan,1 Department of Plant Pathology, Northwest A&FUniversity, Shaanxi, China2 and Graduate School of Science andTechnology, Kyoto Institute of Technology, Kyoto, Japan3Polyesters are categorized into three, that is, aliphatic, aromaticand aliphatic-aromatic ones. Aliphatic polyesters have high biode-gradability, but low physical properties. Aromatic polyesters haveexcellent physical properties, but low biodegradability. Aliphatic–aromatic polyesters are designed for biodegradable plastics withphysical properties enough for practical uses. Thermobifida albaAHK119 was isolated from compost, which are able to degrade oneof commercially available aliphatic-aromatic polyesters with highmelting temperature over 200 °C. The gene (est) encoding for amature polyester depolymerase of 301 amino acids was cloned fromThermobifida alba AHK119 and showed the high identity with thegenes encoding for lipolytic enzymes from several origins. Thepolyester depolymerase contains a catalytic triad formed by Ser, Aspand His, where Ser is conserved in an active site motif of lipase/esterase (GXSXGG). The presence of signal peptide (34 amino acidsof N-terminus), and 3D modeling suggested that the gene codes forthe extracellular esterase. The polyester depolymerase gene wasexpressed in different systems of pQE-80L and pET23a in E. coliBL21 (DE3) and Rosetta-gami (DE3). Most part of activity wasexpressed as pellets in BL21 (DE3), but as soluble form in Roseta-gami (DE3). The 6xhistidine-tagged recombinant enzyme waspurified from cell-free extracts of Rosetta-gami (DE3) harboringpET23a-est, using a Ni-NTA agarose column. The molecular mass ofpolyester depolymerase was determined to be approximately30 kDa by SDS-PAGE, and gel filtration, suggesting monomerenzyme. The highest activity was observed when p-nitrophenylhexanoate (C6) was used as a synthetic substrate. The purifiedenzyme was characterized with regard to thermostability, substratespecificity and substrate binding ability. In addition, the inductivityof the enzyme by polyesters was compared with known polyester-degrading enzymes.doi:10.1016/j.jbiosc.2009.08.275EN-P43A novel endophytic bacterium, Achromobacter xylosoxidans, helpsplants against pollutant stress and improves phytoremediationYing-NingHo, Chun-Hao Shih, Shu-ChuanHsiao, and Chieh-ChenHuangDepartment of Life Sciences, National Chung Hsing University,Taichung, TaiwanPhytoremediation has been considered as an in situ bioprocess toclean up environmental contaminated soil and water. Plants can act assolar-powered-pump treatment systems relying on their roots to takeup contaminants and transport them through various plant tissueswhere the contaminants could be metabolized. However, using plantsalone for remediation confronts many limitations. Recently, theapplication of endophytic bacteria (endophytes) has been extendedto remediate contaminated soils in association with plants. In thisstudy, 188 strains of the endophytes were isolated from reed(Phragmites australis), Ipomoea aquatica, and vetiver (Vetiveria ziza-nioides (L.) Nash). Some of the isolates demonstrated tolerance toheavy metals and aromatic compounds. Twenty-nine strains ofendophytes grew well in the presence of naphthalene, catechol andphenol. While those strains performed not only tolerance but also canutilize aromatic compounds as sole carbon sources. One of theendophytic isolate Achromobacter xylosoxidans F3B was furtherstudied to show its assistance for phytoremediation. Inoculation ofA. xylosoxidans F3B to Arabidopsis thaliana resulted in a significantincrease in root length, fresh weight in catechol and phenol-addedagar. The presence of A. xylosoxidans F3B provides the protectionagainst the phytotoxic effects of catechol and phenol. The results showthe potential of endophytic bacteria helping plants to toleratepollutant stress and improving the efficiency of phytoremediation.Keywords: Phytoremediation, Endophytic bacteria, Achromobacterxylosoxidans, Biodegrading.doi:10.1016/j.jbiosc.2009.08.276EN-P44Prediction and classification of the modes of genotoxic actionsusing bacterial biosensors and cell array chipJoo-Myung Ahn,1 Ee Taek Hwang,1 Byoung Chan Kim,2Javed H. Niazi,1,3 and Man Bock Gu1Korea University, Seoul, Republic of Korea,1 Istitut Pasteur Korea,Gyeonggi-do, Republic of Korea2 and Sabanci University, Istanbul,Turkey3We report on a novel approach to predict the mode of genotoxicaction of chemicals using a series of DNA damage specific biolumi-nescent bacteria. One such test popularly known is Ames test based onbacterial bioassay, which has limitation for determining the potentialmode of DNA damage. In this study, we aim to classify genotoxic modeof toxic action and apply this for cell array chip using sevenrecombinant bioluminescence bacteria. For this, a group of sevendifferent DNA-damage sensing recombinant bioluminescent strainswere employed. Each of these strains were tested against model DNAdamaging agents, such as mitomycin C (MMC), 1-methyl-1-nitroso-N-S95Abstracts / Journal of Bioscience and Bioengineering 108 (2009) S75–S95methylguanidine (MNNG), nalidixic acid (Nal) and 4-nitroquinoline N-oxide (4-NQO). In a classification, we employed one of the sensingparameter, minimum detectable concentration (MDC), which can beused as an indicator of the assay's capability. The differential responsepatterns and its strength of these strains to various model genotox-icants allowed classifying the chemical's potential genotoxic mode. Asa result, these biosensors were grouped based on their responses to aspecific mode of genotoxic action, such as (a) DNA damage cascaderesponse (biosensor with nrdA-, dinI- and sbmC-lux), (b) SOSresponse or DNA repair (strains carrying recA-, recN- and sulA-lux),and (c) DNA damage potentially by alkylation (biosensor with alkA-lux). The application of classified three groups was conducted andidentified via 17 different chemical tests and construction ofgenotoxicity cell array chip. Finally, genotoxicity classification wasconfigured different DNA damage mechanism and cell array chipapproach showed the possible novel genotoxic assay for the pre-screening steps of new drugs or to characterize unknown or newlysynthesized chemicals, food and environment samples.doi:10.1016/j.jbiosc.2009.08.277EN-P45Analysis of protein expression profiles of As(III), As(V), Cd andbinary heavy metal mixture in Daphnia magnaEun-Suk Lim,1 Thai-Hoang Le,1 Yang-Hoon Kim,2 and Jiho Min1Chonbuk National University, Jeonju, Republic of Korea1 and ChungbukNational Univeristy, Cheongju, Republic of Korea2Proteomics related toxicology has provided innovative approachesto novel biomarkers screening, toxic materials screening, and riskassessments. The application of proteomic analysis in the field ofaquatic toxicology has recently started to increase, but until now, littleattention has been given to the integrated analysis of molecularresponses and higher-level effects within the same study. In this study,protein expression profiles provided significant insights into thetoxicity mechanisms for the Daphnia magna, post exposure of heavymetals. We performed proteomic analysis of D. magna in response toAs(III), As(V), Cd, As(III)+As(V), As(III)+Cd and As(V)+Cd as a heavymetal, by using two-dimensional gel electrophoresis (2-DE) and foundthat protein profiles from D. magna were shown different expressionpatterns for the each heavy metals. D. magna protein expressionpatterns of binary mixtures are not the simple sum of their individualcompounds' fingerprint. For example, the changed spots are 42 and 46in daphnia exposed to As(III) and Cd, respectively. In addition, thechanged spots are 31 in daphnia exposed to binarymixture, As(III) andCd. In comparison with results of single and binary mixture, thenumber of spots only found in As(III), Cd and binary mixture of As(III)and Cd are 23, 24 and 12, respectively. It means that the proteinexpression patterns of binary mixtures would be the results ofadditive molecular combinations of both individual compounds.Therefore, D. magna protein expression patterns of binary mixturesare not the simple sum of their individual compounds' fingerprint. The23, 24 changed spots by As(III) and Cd can be used as novel biomarkercandidates to detect As(III) and Cd.Acknowledgment: This study was supported by the 21C FrontierMicrobial Genomics and Applications Center Program, grant No. 11-2008-10-002-00, Ministry of Education, Science and Technology,Republic of Korea. The authors are grateful for their supports.doi:10.1016/j.jbiosc.2009.08.278

Prediction and classification of the modes of genotoxic actions using bacterial biosensors and cell array chip

http://research.sabanciuniv.edu/13970/1/abstracts.pdf

Prediction and classification of the modes of genotoxic actions using bacterial biosensors and cell array chip

Abstract

Similar works

Full text

Available Versions

Sabanci University Research Database