ARABIDOPSIS RESPONSE TO THE CARCINOGEN BENZO[A]PYRENE A DISSERTATION SUBMITTED TO THE GRADUATE DIVISION OF THE UNIVERSITY OF HAW AIT IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY IN TROPICAL PLANT AND SOE. SCIENCES DECEMBER 2008 By Beth Irikura Dissertation Committee: Robert Pauli, Chairperson Henrik Albert Paul Moore Ming-Li Wang Paul Patek
194
Embed
ARABIDOPSIS RESPONSE TO THE CARCINOGEN BENZO ......Figure 5.5 Differential GO Annotation of Molecular Function in control vs. BaP exposed...
This document is posted to help you gain knowledge. Please leave a comment to let me know what you think about it! Share it to your friends and learn new things together.
Transcript
ARABIDOPSIS RESPONSE TO THE CARCINOGEN BENZO[A]PYRENE
A DISSERTATION SUBMITTED TO THE GRADUATE DIVISION OF THE UNIVERSITY OF HAW AIT IN PARTIAL FULFILLMENT OF THE
REQUIREMENTS FOR THE DEGREE OF
DOCTOR OF PHILOSOPHY
IN
TROPICAL PLANT AND SOE. SCIENCES
DECEMBER 2008
ByBeth Irikura
Dissertation Committee: Robert Pauli, Chairperson
Henrik Albert Paul Moore
Ming-Li Wang Paul Patek
We certify that we have read this dissertation and that, in our opinion, it is satisfactory in
scope and quality as a dissertation for the degree of Doctor of Philosophy in Tropical
I am fortunate to have been able to design a project that has held my interest throughout. Funding was provided in part by ARCS Foundation awards and a U.S. Dept, of Education GAANN Fellowship in Interdisciplinary Biotechnology. I’d like to acknowledge the people and situations that made this research possible. First, I thank my father for demonstrating a profound love of science, while encouraging his children to explore all other conceivable options.
My mother’s death by lung cancer at the age of 54 interrupted my college education, too late to stop me from getting a BA in English literature, but so early that it forced me to reevaluate priorities. My mother also pioneered in our family, showing that an artist could teach science. The last photo of my mother is from late 1983. She’s dressed up as a chicken, and she’s laughing. I like to think she was trying to signal the connection between avian sarcoma virus and cancer, which provided the first molecular understanding of cancer processes. At the time, that connection was just beginning to be deciphered, and public understanding was at the level of thinking maybe you shouldn’t eat too much chicken.
It’s hard to explain how I came to work with BaP, a chemical that very likely contributed to my mother’s death. My first project measured BaP interactions with monoclonal antibodies that had been produced by inducing cancers in mice. Yet without that initial work, it’s unlikely that I would have proposed this project. The ensuing years allowed me to develop as a scientist, and more importantly allowed the field to make major progress that I could later use. The situations and people that have impeded my progress (data not shown) have left some lasting scars, but the delay has meant that many exciting advances have been made in the meantime, which give my data a richer and more meaningful context. Without time served, this dissertation would be (even) more like an interpretive dance.
Heartfelt thanks to my current advisor and committee members for their participation, insight, and support. Research is only possible through the sacrifices of people wiser and more patient than us.
It is impossible and possibly impolitic to thank everyone who has helped, encouraged, or inspired me, but I am enormously grateful to all the people I’ve had the pleasure to work for and with. You know who you are; please accept my thanks. I thank my family for being beautiful, patient and there. To Kawai, Dasmin, Jonah, Joe, Kaimanu, Chase, Pele, Marley, Azzie and Ka‘eo: I’m sorry for working so much, I love you, go to college.
Finally, this is for Aike, who was always there.
IV
ABSTRACT
This project investigates the effects of the carcinogenic environmental pollutant
benzo[a]pyrene (BaP) on the model plant, Arabidopsis thaliana ecotype Columbia.
Previous research has demonstrated phytodegradation of BaP, in the presence and
absence of microorganisms. BaP and its metabolites have been detected in plant tissues,
but the parent compound is only found in parts-per-billion quantities in most plants.'
Increases in plant biomass and lifespan have been observed after growth in BaP, raising
questions about how plants are able to benefit from a compound that is detrimental to
most other eukaryotes. Since plants share many of the same molecules used by animals
in response to BaP (e.g. cytochrome P450, peroxidases, laccases, glutathione,
glycosylases and aminotransferases), it has been assumed that they employ similar
mechanisms to degrade BaP. Until now, investigations of these mechanisms were limited
by methodological constraints. In this study, we applied genetic and genomic tools to
determine specific gene expression responses to BaP in Arabidopsis. Particular attention
was paid to the mechanisms by which BaP tolerance was achieved in the plant. Much
research has shown functional equivalence between homologous genes in plants and
animals, hence the results of this study may have applications in biomedical research on
molecular mechanisms of BaP effects in mammals.
page
Acknowledgements.................................................................................................................. iv
Abstract...................................................................................................................................... v
Table of Contents..................................................................................................................... vi
List of Tables.......................................................................................................................... xii
List of Figures........................................................................................................................ xiii
List of Abbreviations..............................................................................................................xv
Appendix A. Mammalian genes up-regulated by BaP or BPDE............................... 128
Appendix B. Mammalian genes down-regulated by BaP or BPDE.......................... 133
Appendix C. Complete gene list for 4-wk exposure microarray results................... 138
Appendix D. Complete gene list for 24-hour exposure microarray results............... 146
Appendix E. Primers used for qRT- PCR....................................................................151
XI
LIST OF TABLES
Table 4.1 T-test for phenotypic differences between control plants and plants grown in 40 ppm BaP..........................................................................................................33
Table 5.1 Differences in the experimental conditions in the two 4-wk growthexperiments.......................................................................................................... 62
Table 5.2 Genes called Increased or Decreased in 4-wk GeneChip results.................. 63
Table 6.1 Twenty-eight genes represented by 25 probe sets that increased in the 24-hmicroarray results................................................................................................ 92
Table 6.2 Twenty-nine genes represented by 25 probe sets that decreased in the 24-hmicroarray results................................................................................................ 93
Table 6.3 Analysis of promoter motifs at 24 h and 4 wks............................................... 94
Table 6.4 BaP-upregulated genes containing DREs in 1 kb upstream are regulateddifferently by other abiotic stresses..................................................................95
X ll
LIST OF FIGURES
Figure 2.1 Phase I activation of BaP in animals (A) and diagram illustrating AhR-dependent effects of BaP (B)............................................................................24
Figure 4,1 Stratified seeds germinated faster on Difco Bacto agar with 50 ppm BaP in0.2% DMSO than on agar with DMSO alone..................................................35
Figure 4.2 Comparison of fluorescent bodies in root tissue.............................................36
Figure 4.3 Osmium tetraoxide stained roots suggest higher levels of phenolics and/orlipophilic metabolites in BaP-grown plants....................................................37
Figure 4.4 HPLC analysis of agar shows a decrease in BaP when plants are present.. .38
Figure 4.5 Darkening of media and roots in the presence of BaP.................................. 39
Figure 4.6 Types of nuclei observed in alkaline comet assay......................................... 40
Figure 4.7 DNA damage measured by comet assay........................................................ 41
Figure 4.8 Comet assay of sand-grown Arabidopsis shows individual differences inDNA damage within 24 h of exposure to BaP................................................42
Figure 5.1 Effects of methylobacteria on BaP-grown and control plants...................... 66
Figure 5.2 No clear phenotypic differences between soil-grown control plants andBaP-grown plants...............................................................................................67
Figure 5.3 Comparative distribution of cellular components based on Gene OntologyAnnotation...........................................................................................................68
Figure 5.4 Differential GO Annotation of Biological Processes in control V5. BaP-exposed plants.................................................................................................... 69
Figure 5.5 Differential GO Annotation of Molecular Function in control vs. BaP-exposed plants.................................................................................................... 70
Figure 5,6 Expression of 10 genes in soil-grown Arabidopsis, by qRT-PCR................71
Figure 5.7 Comparative expression of 10 genes measured in two independentexperiments, expressed as the ratio of BaP vs. control plants....................... 72
Figure 6.1 Specific gene expression in 24 h soil-grown plants by qRT-PCR................96
xiii
Figure 6.2 Comparison of GeneChip and qRT-PCR results for sand- and soil-grownplants, respectively............................................................................................97
Figure 6.3 Microarray results for 24-h BaP overlaid on map of abiotic stresses mediated by two DRE-binding transcription factors......................................................98
XIV
ABBREVIATIONS
a. a. Amino acids
ABA Abscisic acid
ABC ATP-Binding Cassette (ABC) superfamily; used here for At3g59140
ABRC Arabidopsis Biological Resource Center
AhR Aryl hydrocarbon receptor
Atl4a At3g28300, shares probe set with At3g28290, contains EOF repeats
1.8 255904_.at ATI G17860 trypsin and protease inhibitor / Kunitz family protein1.8 256883_ at AT3G26440 similar to ATI G130001.8 260391_.at AT1G74020 SS2 (STRICTOSIDINE SYNTHASE 2)1.8 262682 .at AT1G75900 family II extracellular lipase 3 (EXL3)1.8 262942_ at AT1G79450 LEM3 (ligand-effect modulator 3) / CDC50 family1.7 246125_.at AT5G19875 similar to AT2G31940.11.7 254234_.at AT4G23680 major latex protein-related / MLP-related1.7 254314,.at AT4G22470 protease inhibitor/seed storage/lipid transfer protein (LTP)1.7 258596,.at AT3G04510 similar to LSH1 Light-dependent Short Hypocotyls 11.7 265943. at AT2G19570 CDA1 (CYTIDINE DEAMINASE 1)1.7 267128..at AT2G23620 esterase, putative1.6 249955. at AT5G18840 sugar transporter, putative1.6 254040..at AT4G25900 aldose 1-epimerase family protein1.6 254500. at AT4G20110 vacuolar sorting receptor, putative1.6 255059. at AT4G09420 disease resistance protein (TIR-NBS class), putative1.6 258374..at AT3G14360 lipase class 3 family protein1.6 260408._at AT1G69880 ATH8 thioredoxin H-type 81.6 265111. at AT1G62510 protease inhibitor/seed storage/lipid transfer protein (LTP)1.6 266808’_at AT2G29995 similar to ATI G07175.11.5 246620._at AT5G36220 CYP81D1 (cytochrome P450 91 A l); oxygen binding1.5 262657._at AT1G14210 ribonuclease T2 family1.4 254818._at AT4G12470 protease inhibitor/seed storage/lipid transfer protein (LTP)1.4 264708._at AT1G09740 ethylene-responsive protein, putative
□ transport 19: 7%I unknown biological processes 87; 34%
GO Biological Process, BaP□ cell organization and biogenesis 4; 2%■ developmental processes 9; 4%□ DNA or RNA metabolism 0; 0%□ electron transport or energy pathways 6; 3%
[other biological processes 35; 17%I other cellular processes bU; 20%I other metabolic processes 76; 37%I protein metabolism 17: 8%____________
CTTTrp^^ponse to abiotic or biotic stimulus 39: 19^?T!> cT B response to stress 52; 25%
□ signal transduction 8; 4%■ transcription 7; 3%
C^ tra n s p o rt 27; 1 3~ ^T ^■ unknown biological processes 50; 24%
Figure 5.4 Differential GO annotation of biological processes in control vs. BaP-
exposed plants. Processes represented by more gene aimotations in control (down-
regulated in BaP/control) or in BaP (up-regulated) are circled.
69
GO Molecular Function, Control C O D N^or RNA bindingljr i ^■ hydrolase activity 31; 12%■ kinase activity 20; 8%□ nucleic acid binding 2; 1%
nucleotide binding■ other binding 33; 13%■ other enzyme activity 32; 13%■ other molecular functior^ 7: 3%
C j ^ o t e i n binding 24; l"o K ir2>□ receptor binding or actMty 3; 1%□ structural molecule activity 1; 0%■ transcription factor activity 21; 8%
rC S transferase activity 39;T b^^I>□ transporter activity 14: 6%
C jTunknow n molecular functions 80:~3?^>
GO Molecular Function, BaP□ DNA or RNA binding 7; 3%■ hydrolase activity 31; 15%■ kinase activity 6; 3%□ nucleic acid binding 0; 0%□ nucleotide binding 4; 2%
C jo t h e r binding 3 6 ; l 8 ^[other enzyme activity [5fher molecular functions 12;
concentrations produced stress symptoms in all plants. Each jar was spiked 27 d after
germination by adding 1 mL of new liquid MS containing either 60 pL DMSO, 60 pL
85
H2 O, or 750 pg BaP in 60 pL DMSO. The additions were performed in a sterile hood
with a sterile 5 mL syringe fitted with an 0.2 pm filter (RC431215, Coming, NY) and
mixed in by drawing liquid media in and out of a sterile 1 mL pipet tip lOx, taking care
not to contact the leaves. The final BaP concentration was 50 pg/mL (w/v) in 0.4%
DMSO (v/v). Light level was at 90 pE m’ s ’ for 8:16 h day/night, and temperature was
maintained between 22° and 24° C.
6.2.2 Affymetrix ATHl GeneChip analysis of plants grown in sand
Shoot tissue was harvested 24 h after BaP exposure, flash-frozen in liquid nitrogen,
and processed as before for microarray analysis (Ch. 5, Methods). Three biological
replicates of BaP and DMSO-only controls were analyzed, plus two no-solvent controls.
Each sample consisted of at least six pooled rosettes. Order of harvest was (1) DMSO
controls, (2) no-solvent controls, (3) BaP-exposed plants. After statistical analysis,
interesting genes were identified for further investigation.
6.2.3 Repeat of experiment in soil
For qRT-PCR analysis, seeds were surface-sterilized as before, stratified 3 d at 4°
C, and pipetted onto soil that had been sterilized by autoclaving at 120°C for 60 min (four
times over 4 days, to remove soil bacteria) in 400 mL glass beakers. Plants were grown
under short-day (8 h light) fluorescent lighting. Soil was not spiked with BaP until plants
were full-grown (about 4 wks after imbibition). Soil was spiked with 2 mg BaP in 160
pL DMSO, dispersed in 40 mL of water, for a final DMSO concentration of 0.4% (v/v)
and BaP at 50 mg/L (w/v). Controls were spiked with 160 pL DMSO in 40 mL water,
and no solvent controls were simply wetted with 40 mL water. Solutions were dispensed
with a glass pipet, so that liquid did not contact the leaves directly. Plants were harvested
8 6
as before at growth stage 3.9, to minimize differences between the two groups due to
developmental changes. Plants were also harvested at additional exposure times,
between one hour and 3 days after addition of BaP. Plants were again harvested in the
order of spiking (DMSO—no solvent—BaP), and to avoid time-of-day effects, samples
were processed quickly so that all treatments were harvested within 10 min of each other.
6.2.4 Quantitative RT-PCR of plants grown in soil
Primers were designed using Invitrogen OligoPerfect™ Designer, IDT Oligo
Analyzer (Integrated DNA Technologies), mFOLD,” ® and Universal Probe Library
(Roche). All primers were checked for cross-hybridization using BLASTn (NCBl).
RNA was isolated by Qiagen RNeasy Plant kit and DNase-digested with Roche DNase I.
After DNase reaction components were removed using a Qiagen RNeasy column, RNA
was quantified using a Thermo Scientific NanoDrop™ 1000 Spectrophotometer, and
reverse-transcribed with Bio-Rad iScript cDNA Synthesis kit. Quality and purity of
cDNA, and primer design, were evaluated with 3.5% agarose gel electrophoresis of PCR
products (Eppendorf) in 0.5x TBE. Quantitative RT-PCR was performed with 20 pL
rxns using Bio-Rad iQ SYBR Green Supermix on an IQ5 cycler (Bio-Rad). Reactions
included 125 to 500 nM primers and 20 ng cDNA or the equivalent negative control
(iScript reaction without reverse transcriptase) to test for genomic DNA (gDNA)
contamination or non-specific amplification. Data were considered acceptable if the
difference in threshold crossing values (delta-Ct, or dCt) between each cDNA and its
corresponding negative control was at least 10 cycles. Five potential reference genes
were selected based on the 4 wk and 24 h microarray data and reports of low genotoxic or
abiotic stress responses (checked with eFP Browser at the Bio-Array Resource for
87
Arabidopsis Functional Genomics)/^” Reference gene amplification results were
reviewed using GeNORM/^* and data were normalized to Tubulin 8 (At5g23860).
Background subtracted signals (raw data) were analyzed by PCR Miner (Stanford
University, Stanford, CA)^^” and compared in Microsoft Excel. Quantitative RT-PCR
products were checked for nonspecific amplification by melt curve analysis and by
electrophoresis on a 3.5% agarose gel in 0.5x TBE. The full list of primer sequences,
melting temperatures, and qRT-PCR parameters are given in Appendix E.
6.2.5 Data analysis and bioinformatics
As in Chapter 5, with additional analyses of genes from both time-points.
6.3 Results
6.3.1 General observations
Sand-grown plants were small in the enclosed, sterile, semi-hydroponic conditions.
The spiking had to be conducted in a sterile biological/chemical hood, so plants were
exposed briefly to temperatures of about 26° C as they were transported to another
building. By the next day, the BaP-exposed plants had visible anthocyanin pigmentation.
Plant phenotypes were more variable when plants were grown in soil. All plants
were healthier than enclosed plants grown in sterile agar, developing larger, thicker
leaves with more obvious trichomes. These observations were consistent with
expectations, since sterile growth conditions limit nutrient availability and gas exchange,
and most importantly, prevent beneficial interactions with endosymbiotic and soil
microorganisms.
6.3.2 Microarray analysis of 24 h gene expression in sand-grown plants
GeneChip analysis by MAS 5.0 and Data Mining Tool identified 28 probe sets as
‘Increased’ following BaP treatment, and 25 probe sets as ‘Decreased’, in at least 8 of 9
comparisons (Tables 6.1 and 6.2). The full list of differentially expressed genes is given
in Appendix D.
6.3.3 Gene expression changes after 24 h in soil-grown plants by qRT-PCR
The qRT-PCR results are presented in Figure 6.1. It was not possible to completely
remove gDNA from all RNA samples, so primers that spanned introns were used
wherever possible. Results were evaluated along with dCt values, and amplification of
nonspecific products was checked by agarose gel electrophoresis. In a very few
instances, as when a gene contained no introns, or expression levels were extremely low,
it was not possible to measure expression differences reliably.
6.3.4 Comparison of qRT-PCR and microarray results
Expression ratios of genes measured by qRT-PCR of soil-grown plants were plotted
against GeneChip results from the sterile agar experiment (Figure 6.2). The qRT-PCR
results showed striking agreement with the GeneChip results, even though the
experimental conditions were quite different.
6.3.5 Promoter analysis of genes identified by microarray
Databases of cis elements remain incomplete, and many families of transcription
factors have only a general conserved binding sequence, proposed on the basis of a single
family member’s interaction, or no suggested binding elements at all.’"** For this reason,
and to maximize data prospecting related to BaP response, transcription factor motifs
from other eukaryotes were considered. Predicted gene regulation was based upon a
89
search for short sequence motifs that were over- or underrepresented in microarray data,
compared with the occurrence in the genome as a whole and suggest response pathways
operating in the experiment. Motifs over-represented in promoters of genes up-regulated
by BaP include EE, DNA damage-inducible elements, E box, G box, C box, and 3
conserved WRKY elements. Over-represented down-regulated motifs included Myb,
bZIP/APl, AMLl, E box, GBLE, NAC and TATA boxes. Motif occurrence in 24 h and
4 wk up- or down-regulated gene sets are shown in Table 6.3.
6.3.6 Intersection of BaP and cold stress response
Many genes originally identified and armotated as cold responsive were up-
regulated in 24 h BaP-exposed plants. As some of these responses are mediated by ABA
and/or represent common stress pathways, this is not too surprising. Figure 6.3 outlines a
common stress signaling pathway mediated by two Drought-Responsive Element
Binding (DREB) transcription factors. Data from the eFP Browser was used to show the
different effects of abiotic stresses on DREB 1A and DREB2A expression levels after 24
hrs exposure to the stressor. DRE sequences in gene promoters are recognized by
DREB 1A and DREB2A in response to various abiotic stresses, and activate transcription
of the genes. Both of these transcription factors were increased in 24-h BaP microarrays
by 1.9x and 1.6x, respectively, and the prevalence of the promoter sequences increased
for genes up-regulated by BaP. Table 6.4 examines genes identified by microarray as up-
regulated in 24-h BaP response, which contain drought-responsive elements (DREs)
within 1 kb upstream of the start codon. Because of its chemical properties, BaP is likely
to elicit responses similar to oxidative, UV-B, and genotoxic (represented in eFP Browser
by experiments using Bleomycin and Mitomycin C) stresses. However, for these DRE-
90
containing and probable stress-regulated genes, there are significant differences. Note
that C0R15A is down-regulated in these three stresses, and none of the stresses elicit up-
regulation of RD29A, GRP7, or the small hydrophobic protein (all of which were
increased by BaP in both sand and soil experiments). Four other genes (ERD3, APRR3,
C0R15B, At5g23410) are also upregulated by cold and BaP, but not by oxidative, UV-B,
or genotoxic stress. In the up-regulation of ACA8, At5g50450, RPS27aA, COLIO, and
At2g22450, BaP response is only similar to cold stress, with other stresses not inducing
these genes significantly. Drought and heat stress bear almost no similarity to BaP stress
at 24 h post-exposure.
91
Table 6.1 Twenty-eight probe sets that increased in the 24 h microarray results. Genes
called ‘increased’ by the Affymetrix Data Mining Tool (DMT) in at least eight of nine
comparisons were included, with genes selected for qRT-PCR analysis in bold. Note:
probe sets may target more than one gene locus.
Locus ID AnnotationAT5G57110 autoinhibited calcium-transporting ATPase, ACA8AT5G52310 cold/desiccation-responsive protein RD29A/COR78AT5G48250 zinc finger (B-box type), similar to CONSTANS homologsAT5G42900 unknown expressed protein, similar to AT4G33980AT5G23240 DNAJ heat shock N-terminal domain-containing proteinAT3G59350 serine/threonine protein kinase, putativeAT4G34120 LEJ1 (LOSS OF THE TIMING OF ET AND JA BIOSYNTHESIS 1)AT4G33980 unknown expressed proteinAT1G07050 CONSTANS-like protein-related, similar to C0L15AT1G68050AT5G42730AT5G23410
FKF1/AD03, E3 ubiqultin llgase SCF complex F-box subunit, 2 loci similar to FKF1
AT1G67970 heat shock transcription factor HSFA8AT2G42530 cold-responslve protein COR15BAT4G17490 ethylene response factor ATERF-6AT4G16146 similar to AT1G69510AT4G37260 myb family transcription factor MYB73AT5G61380 TOCl (TIMING OF CAB EXPRESSION 1) transcription regulatorAT5G61600 ethylene-responsive element-binding family proteinAT5G60100 APRR3 (Pseudo-Response Regulator 3); transcription regulatorAT5G57220 CYP81F2 cytochrome P450AT5G50450 zinc finger (MYND type) family proteinAT3G55450 protein kinase, putative, similar to APK1BAT4G34950 nodulin family proteinAT4G33985 similar to AT2G15590AT4G24570 mitochondrial substrate carrier family proteinAT4G12280 AT4G12290 copper amine oxidase
Table 6.2 Twenty-nine genes represented by 25 probe sets that decreased in the 24 h
microarray results. Genes called ‘decreased’ by the Affymetrix Data Mining Tool
(DMT) in at least eight of nine comparisons were included, with genes selected for qRT-
PCR analysis in bold.
Locus ID AnnotationAT1G13650 similar to 18S pre-ribosomal assembly protein gar2-related AT2G03810ATIG 18620 similar to unknown protein AT1G74160AT1G55960 similar to unknown protein AT3G13062; Lipid-binding START domainAT1G64500 glutaredoxin family proteinAT1G69160 unknown proteinAT1G69530 ATEXPA1 (A. thaliana EXPANSIN A l)AT1G74670 gibberellin-responsive protein, putativeAT2G04039 similar to unnamed proteinAT2G30520 RPT2 (ROOT PHOTOTROPISM 2); protein bindingAT2G40205AT3G08520AT3G11120AT3G56020
603 ribosomal protein L41 (probe set targets 4 loci)
Table 6.4 BaP-upregulated genes containing DREs in 1 kb upstream are regulated differently by other abiotie stresses. The second column lists the fold changes from 24-h BaP microarrays; fold changes for other 24-h abiotic stresses archived in the eFP Browser are color-coded according to the key below.
Fold Change >50 >10 >2 0.5 >0.2
Genes in bold were also up-regulated in soil-grown plants, as measured by qRT-PCR.
Figure 6.3 Microarray results for 24-h BaP overlaid on map of abiotic stresses mediated by two DRE-binding transcription factors (following schematic of Sakuma, et al. 2006).*” Abiotic stresses that induce each DREB factor after 24 h are listed at the top, with corresponding fold changes underneath (data from eFP Browser). Numbers in red are fold changes in response to 24-h BaP, as measured by microarray. Fold changes in parentheses reflect genes with more than one type of DRE in promoter, and are listed in both columns. Bold red is used to show overrepresentation frequency of DRE motifs in 1 kb upstream of genes increased after 24-h BaP, compared with whole genome.
98
In mammals, the signaling response to BaP exposure begins with binding of BaP to
the aryl hydrocarbon receptor, AhR.’"” ’’*’ BaP-bound AhR then transloeates to the
nucleus where it dimerizes with the aryl hydrocarbon receptor nuclear translocator (Amt),
and the complex activates transcription of nuclear genes with xenobiotic response
elements (XRE) in their promoter regions. No specific homologs of AhR have been
identified in plants, but other members of the Per-Amt-Sim family, for which the PAS
domain was named, exist in plants. The genes in the PAS family have a wide range of
functions, including circadian clock regulation, xenobiotic response, development, and
cell lineage control. Besides the PAS domain, some members of this family have a basic-
helix-loop-helix domain (bHLH), potentially involved in transcriptional specificity and/or
dimerization.’"** The PAS domain is also the site of BaP binding to AhR. A recent report
identified genes that were down-regulated in pancreatie cancer as homologs of circadian
genes in Drosophila, confirming other evidence that dismption of circadian rhythms is
coincident with cancer.’"" The implication of this connection is that BaP may bind to the
PAS domain in cireadian genes. Experiments with AhR knockout mice showed that the
AhR ligand, dioxin, altered the light responsive circadian rhythms and the expression
levels of the two core clock genes Perl and BMALI?^^ The PAS-containing clock
signaling gene, FKFl, was up-regulated in Arabidopsis after 24 h of BaP exposure.
The xenobiotic response element (XRE) was found by motif analysis of upstream
promoter regions. In 4-wk treated plants, XRE motifs were present upstream of down-
regulated genes at a level almost twice the genomic level. This pattern held whether the
upstream region was 500 bases or 1000 bases from the start codon. This suggests a BaP-
6.4 Discussion
99
mediated mechanism, but without an AhR homolog. While generally considered an
enhancer element in BaP or dioxin response mediated by AhR, an XRE has been shown
to be required for dioxin-induced down-regulation of prostaglandin endoperoxide G/H
synthase-2 gene in rat thymocytes.’"’® It is also present in the promoter region of
CYP2C11, down-regulated in rats exposed to dioxin.’"”
An animal system that lacks a functional AhR would make a better comparison for
plant response. In a rat comeal epithelium culture lacking AhR protein, researchers
demonstrated that non-AhR-bound ARNT, HNFl, and HNF4 bound to the XRE region
and mediated constitutive induction of ALDH3?^^ Mutations in the XRE region
abolished binding and gene activation. The presence of an XRE in disproportionate
numbers of genes down-regulated by 4-wk BaP exposure (Table 6.3) could reflect
interference with XRE-mediated constitutive transcription. Specifically, BaP may bind to
a PAS or PAC-containing protein, favoring formation of a dimer with a protein that
normally would bind the XRE for constitutive activation. Thus the genes with XRE in
their promoters would appear down-regulated, because BaP dismpted their basal
transcription. Such crosstalk is very common, as AhR, ARNT, HNFl, HNF4, and many
others can bind the XRE in multiple homo- or heterodimer configurations. It is also
possible that the normal activation of these down-regulated genes is via endogenous plant
compounds such as those studied in animal systems for their ability to interfere with AhR
pathway activation. Epigallocatechin gallate (EGCG) has been shown’"’® to stabilize a
form of AhR complex which is then unable to bind the XRE motif or ARNT protein. In a
system such as Arabidopsis that may lack an AhR, EGCG may interact similarly with an
analogous protein. This interaction could easily interfere with constitutive regulation of a
1 0 0
large set of genes. This possibility is supported by the observation that genes producing
flavonoid compounds like EGCG are up-regulated in BaP-exposed plants (At5g63600
and At5gl3930, Appendix C). The determining factor in plant BaP response may start
upstream of the regulation of EGCG, and define one of the basic differences between
plant and animal BaP response.
Correlations between the 24 h response data and known circadian and cold response
pathways were found. Although the microarray data may have been skewed by the later
harvest of BaP-exposed plants to that of the DMSO control plants, the subsequent
experiment using plants grown in soil exercised good control over time of harvest, and
the qRT-PCR results verified that FKFl and TOCl were up-regulated in these plants as
well. These two genes are central to the circadian clock in Arabidopsis?^^ Genes
responding to 24 h cold treatment overlapped extensively with expression profiles of 3 h
osmotic and 0.5 h drought treatments.” '
Laboratory studies have shown that short day light regimes elicit enhanced immune
response in animals (c / Nelson et al. 1996),” ’ and that the immunity is mediated by
melatonin.” ’ This is presumably an adaptive advantage because short days coincide with
the onset of winter, with accompanying cold temperatures and often reductions in food
supplies. In plants, photoperiod responses, circadian rhythm, and cold signaling are
interrelated.” '' As light is fundamental for their survival, plants that develop efficient
mechanisms for sensing light fluctuations will maximize fitness. Since darkness is
accompanied by a decrease in temperature, it is reasonable to expect interplay between
light and cold signaling, and in plants, cold temperature has been shown to disrupt or
101
‘gate’ the circadian c l o c k . A l t h o u g h all plants were grown in the same short day
conditions, daylength could amplify an adaptive response induced by BaP.
HORMONES
Auxin-related response genes were altered in Arabidopsis after 24 h BaP exposure,
with a greater proportion up-regulated than down-regulated. The significance of this is
not entirely clear, although over half of auxin-responsive genes have been found to be
rhythmically expressed, suggesting that auxin response is controlled by the clock.^^^
Given that estimates of circadian regulated genes in Arabidopsis are between 10% and
16%,^^ this is an extremely large fraction. In the BaP response, more of the auxin-
responsive genes that were expressed at higher levels in the controls were circadian
regulated (23 out of 38), while those up-regulated by BaP were mostly not circadian (44
out of 46). These data suggested that auxin levels were higher in BaP-exposed plants,
which accords with previous findings that BaP concentrations that were not high enough
to inhibit growth produced higher auxin levels in f e r n s . C o v i n g t o n and Harmer
(2007) concluded that auxin signaling is regulated by the clock, but the clock is probably
not regulated by auxin. The AhR agonist dioxin disrupts the clock in animals,^^® and
genes involved in Phases I-III xenobiotic metabolism are regulated by circadian bZip
transcription factors. ®** In Arabidopsis, BaP appears both to disrupt the clock and to
increase levels of auxin. Therefore, the auxin-related genes that were decreased in 24 h
BaP exposure are likely to be down-regulated by the circadian clock, as an indirect effect
of BaP.
Regulation of the circadian clock is possible by a compound related to auxin
metabolism. Recent progress in the decades-old search for an endogenous AhR ligand
102
indicates that the tryptophan photoproduct 6-formylindolo[3,2-b]carbazole (FICZ) has
the highest AhR affinity of any compound tested.’®' Exposure to FICZ led to an increase
in CYP450 and other transcriptional targets of ligand-activated AhR, and also altered
expression of BMAL3 and Per clock genes.’®’ Furthermore, auxin, FICZ, and the
circadian regulator melatonin are all tryptophan derivatives. Perturbation of tryptophan
metabolism may itself affect circadian rhythms. Circadian cycling of melatonin and its
oxidative metabolite AFMK have been found in water hyacinth,’®’ and the authors
speculate that high levels of these compounds may contribute to this plant’s exceptional
phytoremediation abilities. Growth media supplementation with Trp resulted in higher
melatonin synthesis. Melatonin has been found to have auxin-like effects in plants,’®"*
and is synthesized at significantly higher levels in cold temperatures.’®® Lei et al. (2004)
found that melatonin prevented cold-induced apoptosis in carrot suspension eells,
possibly by inereasing levels of polyamines. Auxin also inereases polyamine synthesis,
so it is likely that auxin, melatonin, and polyamines act together in some way in cold and
circadian signaling.’®®
ABA biosynthesis genes were down-regulated by BaP in the microarray data
(Appendix D). This did not preclude extensive ABA signaling. The ABA response
element, ABRE, was over-represented in 1 kb and 3 kb upstream of genes inereased by
BaP response. The most flexible consensus ABRE sequence, [C/A]ACG[C/T]G[T/C/G],
may be targeted by HLH, bZIP, and Myc transcription factors in response to multiple
hormonal signals. It is difficult to untangle the exact factors involved, but the elear
down-regulation of ABA synthesis implied that another hormone signal was involved.
103
Ethylene appears to be an important signal in the short-term response to BaP. The
transcript for an enzyme that eatalyzes the first committed step of ethylene synthesis,
ACS6, was 2.9x greater in 24 h BaP-exposed plants. The ethylene response elements,
ERE, were greatly over-represented in the 3 kb upstream region of genes increased by
BaP exposure. Many ERE-binding proteins (EREBP), also known as ethylene response
factors (ERF), were up-regulated in BaP response. Ethylene acts as a second messenger
or co-hormone with cytokinin, brassinosteroid, auxin, JA, MJ, and SA, and extensive
cross-talk exists between ABA and ethylene.’*’ Nevertheless, it seemed that along with
many other biotic and abiotic stress responses, ethylene did aet in the BaP response.
Intuitively, since ethylene is involved in senescence, abscission, ripening, and selective
growth inhibition in the developing hypocotyl, it would be expected to be involved in
BaP response. In an unsuccessful response to a carcinogen, an organism would
experience uncontrolled growth or proliferation, suppression of apoptosis, and inhibition
of differentiation. Plants, more than animals, need plasticity to be able to isolate a
foreign body by walling it off, or even abscising an infected organ such as a leaf It is
also significant that BaP and ethylene are both combustion products, with cars estimated
to produce approximately 90% of airborne ethylene.’** Abeles et al. (1971) measured an
increase in beta-l,3-glucanase activity in bean plants exposed to unfiltered air containing
elevated levels of ethylene, and also in response to 10 pL/L ethylene for 24 h. Although
they described the enzyme as 3.2.1.6, (equivalent to GH16) they only measured activity
as glucose released from laminaria.’** A member of glycosyl hydrolase family 17
(GH17), At4g 16260, was up-regulated in 24 h BaP exposure. Members of GH17
(3.2.1.39) can also hydrolyze laminaria. Although our research was separated by almost
104
40 years, we seem to have measured a similar plant response to air pollutants. A beta-
glucan oligomer produced from laminaria by a beta-l,3-glucanase had antiproliferative
effects against human myeloid leukemia cells.
GENES
P450
At3g28740 is a member of the CYP450 genes known for their detoxification activity
in all phyla. XRE and AML motifs occur in the promoter region of this gene, with no EE
motifs. This gene was up-regulated in 24 h BOA treatment, but the authors only
identified W-box (WRKY transcription factor binding sites) and G box promoter
elements as putative regulatory sites.” ® Elicitation with cis-jasmonate resulted in high
expression of this P450, and changed the chemical profile of emitted volatile compounds
which repelled herbivorous insects and attracted insect parasitoids.” '
ABC/MRP14 and UGTl
Although the ABC transporter, At3g59140, is not induced in 24 h by bleomycin and
mitomycin C (eFP Browser), it is induced 1.38x by oxidative stress. The ABC
transporter family is well conserved and the closest human homolog to this protein is the
multidrug resistance-associated protein MRP2 (e=5 x lO'^-H). MRP2 is induced in
response to many different xenobiotics, and associated with resistance to chemotherapy
via enhanced drug clearance.” ’ Human MRP2 has been shown to be induced by
quercetin but not by dioxin.” ’ It is possible that this gene was not induced directly by
BaP, but by a plant flavonoid metabolite downstream of the initial chemical interaction.
In the same study, quercetin also induced UGT1A6, a member of the UGTl family
105
capable of glycosylation of quercetin and other compounds. UGT1A6 was induced by
dioxin, as UGTl was induced by BaP in our study. Quercetin has antitumor effects” "’
due to antioxidant potential and probably via its induction of MRP2, which helps to clear
carcinogens from the body.
The AtUGTl promoter contains two AML motifs, one XRE, and an EE. UGTl and
other enzymes involved in conjugation of both xenobiotic compounds like BaP and
native flavonoids were induced by BaP in 24 h. UGTl localizes to the callose synthase
complex during deposition of the phragmoplast.” ® UGTl was identified in a screen for
SA-responsive genes, believed to be regulated by bZIP transcription factors in an NPRl-
independent process.” ® It was up-regulated in 24 h exposure to the allelochemical
benzoxazolin-2(3H)-one (BOA), along with many other putative detoxification genes.” ®
It has also been shown to make glucose esters of para-aminobenzoate (pABA), which
appeared to be a vacuolar storage form of the folate precursor and sunscreen chemical.” ’
Similarly, UGTl can glucosylate ABA,” * presumably to limit the active pool of the
hormone.
GH17
At4gl6260 is a member of glycosyl hydrolase family 17 (GH17). A similar gene is
up-regulated very strongly in tomato leaves by ethylene, and less by MeJA.” ®
Oligosaccharides produced by this enzyme may induce defense response genes, based on
evidence from plant pathogen-derived saccharides.’*® GH17 also contains an RGD motif,
which could be involved in interaction with the EGF repeats of At 14a in an integrin-like
signaling pathway. GH17 was up-regulated at both exposure times.
106
A tU a
Atl4a contains an integrin-like domain that may interact with genes containing RGD
or KGE motifs. RGD is the motif bound by integrin in animals, which transduces signals
from EGFR and other cell surface receptors. This signaling is crucial to invasion and
metastasis,^*' with higher levels of integrins produced in tumor tissues. RGD analogues
are used to image tumor cells and neovasculature^*^ and are under investigation as
therapeutic tools.^*^ RGD, and KGE, which is a variant with similar amino acid
characteristics, have been shown to function in cell wall signaling in plants,^*"* and the
KGE motif was over-represented in genes up-regulated in 24 h BaP response (18% of
genes called increased, vs. 8% in the whole proteome).
At4s33980 and At5e42900
Both of these proteins contain KGE motifs, and have unknown functions. At4g33980
(called E4 in Figures 6.1 and 6.2) was highly up-regulated by BaP in 24 h, and contains
many potential regulatory motifs in its upstream sequence, including XRE, TATA, EE,
AML alternate, G BOX, GBLE, WRKY, and two motifs defined as DNA-damage
285inducible. It is similar in sequence to At5g42900, (E5 in Figures 6.1 and 6.2), which
was also highly up-regulated. It contains the same general battery of motifs, except an
AML consensus instead of the alternate motif, and no XRE. Neither belongs to the
common stress response gene cluster N 12, delineated by Ma et al. 2007.^*^ (None of the
down-regulated genes, and only 26 of 143 genes up-regulated in BaP response, were in
this cluster). Instead, they clustered with circadian genes in N52. The core clock gene
TOCl is coregulated with them. The other gene of interest in this group is FKFl.
107
FKFl rAtlg68050)
The probe set for FKFl also targets two other loei (AT5G23410 and the pseudogene
AT5G42730), but since FKFl up-regulation was confirmed by qRT-PCR, only
Atlg68050 will be discussed. FKFl is a flavin-binding keleh repeat F box protein that
contains two PAS and one PAC domain. E3 ubiquitin ligases help degrade proteins in a
clock-dependent marmer. FKFl enables degradation of CONSTANS proteins in the
control of flowering time, but its function in BaP response is uncertain. It is a likely
candidate for direct binding of BaP through its PAS domain, thereby initiating the
disruption of clock timing, which in animals has been shown to correlate with increased
287cancer risk. Quite recently, the Per2 gene has been defined as a tumor suppressor in
breast cancer,’** and shown to target estrogen receptor alpha for degradation. Per2 is
also up-regulated by estrogen, and is a major factor in estrogen receptor-positive breast
cancer and in normal reproductive health.’*" Where Per2 is a PAS-containing clock
protein that interacts with female hormones, FKFl is a PAS-containing protein that
affects floral induction and clock signaling.’"" Therefore, FKFl could be the site of BaP
interaction with Arabidopsis that perturbs the clock and initiates xenobiotic response
signaling. FKFl increases in cold treatment, and to a lesser extent in genotoxic stress
(eFP Browser). FKFl could also be a functional AhR homolog, since the AhR was
recently found to act as a ligand-activated E3 ubiquitin ligase.’"'
TOCl
TOCl is part of the central oscillator of the plant circadian clock.’"’ The observed
up-regulation of TOCl (Figure 6.2), or perhaps the oscillatory shift in its expression, in
response to BaP, accords with recent findings in animals that DNA damaging agents
108
perturb the clock.’”’ Gamma radiation advanced the phase of Perl and Perl expression
in rat cells, while MMS treatment disrupted the clock largely by indueing higher Per
gene expression. DNA damage is proposed as a universal clock regulator. The
mechanisms behind clock dysregulation are not elear, but BaP binding to PAS-eontaining
FKFl or another endogenous factor could be involved.
G/?F7(AT2G216601
Grp7 belongs to a family of genes, conserved in eukaryotes, that are induced by cold
and have important functions in immune response.’”"* Endometrial carcinoma is
associated with reduced or no expression of the human HomoloGene for Grp7, CIRPP^
CIRP is up-regulated by UV and the UV-mimetic compound A-acetoxy-2-
acetylaminofluorene.’”® CIRP is induced by eold or hypoxia, but does not require
activation by HIFl.’”’ In hypoxia, osmotic, or oxidative stress, CIRP migrates to the
cytoplasm and aggregates in stress granules.’”* Methylation of arginines in the RGG
domain of CIRP is required for translocation of the protein from the nucleus to the
cytoplasm, where it binds mRNA and represses translation.’”” The arginine
methyltransferase involved is a PRMTl,’”* and the Arabidopsis functional homolog,
PRMTl 1,’”” was also up-regulated following 24 h BaP exposure. CIRP homologs were
diumally regulated in bullfrog’”' and in mouse brain,’”’ and diurnal rhythms observed in
treefrog brain and eye appeared to be gated by eold and light.’”’
Like CIRP, Arabidopsis Grp7 links circadian rhythm with stress response pathways.
Grp7 transcription increases in cold and drought.’”"* It is autoregulated by its own
protein, whieh increases transcription of a short-lived, alternatively spliced mRNA.’”®
The high conservation of this RNA binding protein was demonstrated by studies that
109
showed that both Arabidopsis and human transportin-1 proteins facilitated nuclear import
of GRP7, and interacted with human hnRNP Al and yeast Nab2p.’®®
In plants, some glycine-rich proteins are localized to the cell wall matrix,’®’ and
GRPs have been identified in the xylem sap of different plant species.’®* These proteins
are incorporated into the cell wall during xylem formation and cell wall remodeling.’®®
GRP7 is highly expressed in trichomes and guard cells, regulating stomatal opening and
closing,” ® which places it at the interface with external environmental forces.
RD29A
The transcription factor RD29A (also known as COR78) is a major regulator of stress
response.’” It functions at the intersection of signaling pathways for cold or ABA, and
drought or salt responses. Cold or ABA can activate DREBIA. In response to stress
(drought, salt), ADRl is up-regulated, activating DREB2A. In Arabidopsis, ADRl was
1.4x up-regulated in the 24 h response, DREB2A was 1.6x up, and DREBIA was 1.9x up.
DREBIA and DREB2A are transcription factors that can bind A/GCCGACNN boxes,
activating transcription of known stress response genes, and both activate RD29A?^^
Figure 6.3 shows the central role of RD29A in abiotic stress signaling pathways mediated
by DREB transcription factors.
BoCAR6-4
Atlgl7665 is the Arabidopsis homolog of a gene that was identified in a screen for
Metallothionein 2 24 h Xenobiotic metabolism, stress response
TK6lymphoblastoidcells
1
Microsomal epoxide hydrolase
24 h Regulated by Nrf-2
M. musculus and nrf-2 k.o. mice
11
Myxovirusresistance
1 h BaP; 1 wkrecovery
Vascular smooth muscle cells
6
NAD(P)H:quinoneoxidoreductase
24 h Phase 2 detoxification
Regulated by Nrf-2
M. musculus and nrf-2 k.o. mice
11
N qol 1 h BaP; 1 wkrecovery
NAD(P)Hdehydrogenase
Vascular smooth muscle cells
6
Nrf-2 24 h TF Binds ARE to induce GST, NQO;suppressed by Keap-1
M. musculus and nrf-2 deficient mice
11
Nuclear protein 9 1 h BaP; 1 wkrecovery
Vascular smooth muscle cells 6
Oncoprotein induced transcript
1 h BaP; 1 wkrecovery
Vascular smooth muscle cells
6
130
Appendix A (Continued)Opioid receptor, sigma
1 h BaP; 1 wkrecovery
Vascular smooth muscle cells
6
0X 40 Ligand 24 h Growth factor, cytokine
TK6 lympho- blastoid cells
1
P21 24 h; 24 h
No increase in p21 protein (24); Increased protein (16)
Lung cancer cell lines(24); breast cancer lines(16)
5 ,8
P21-W AF Late (24 h)
Gl /S block P53 Normal mammary epithelial cells
13
P53 4, 8 & 24 h; 24 h
Breast cancer cells 5
P53R2 Late (24 h)
Normal mammary epithelial cells
13
P A K l 15-150min
P21-activated kinase
HeLa cells 15
PDGF-R-alpha 1 h BaP; 1 wkrecovery
Vascular smooth muscle cells
6
Pericentrin 2 1 h BaP; 1 wkrecovery
Vascular smooth muscle cells
6
Phenolsulfotransferase
24 h Xenobioticmetabolism
TK6 lympho- blastoid cells
1
R acl 1-6 h HeLa cells 15RNA Pol I 2h-14
daystranscription Rat liver 12
Secreted phosphoprotein 1
1 h BaP; 1 wkrecovery
BaP elicited ~ 11 fold increase; quinone and diol very little
Vascular smooth muscle cells
6
SE K l HeLa cells 15SSAT 24 h Amino acid
metabolismTK6 lympho- blastoid cells
1
STAT-3 24 h TF, intracellular transducer, effector, modulator
TK6lymphoblastoidcells
1
Sulfotransferase,hydroxysteroidpreferring
1 h BaP; 1 wkrecovery
Vascular smooth muscle cells
6
Thymidine kinase 24 h Nucleotidemetabolism
TK6 lymphoblastoid cells
1
Thymidylate kinase homolog
1 h BaP; 1 wkrecovery
Vascular smooth muscle cells
6
Tissue factor 24 h Cell surface antigen
TK6 lymphoblastoid cells
1
Tnf-aProtein
1-24 h apoptosis BaP-i-carbon black, but neither alone, induced TNF-a (protein)
RAW 264.7 macrophage cells
3
131
Appendix A (Continued)Transcription termination factor
1 h BaP; 1 wkrecovery
Vascular smooth muscle cells
6
UGT 0-20 h Phase II conjugation
Porcine bladder epithelial cells
14
WIPl 4 & lO h P53phosphorylationcontrol
P53-dep; feedback inhibition o f p38 MAPK p53 phosphorylation
Normal mammary epithelial cells
13
XPC Early(4h)
Recognition o f DNA damage; nucleotide excision repair
Normal mammary epithelial cells
13
Zfp-14 1 h BaP; 1 wkrecovery
Vascular smooth muscle cells
6
Zfp-35Protein
Zinc finger TF homology
Amnion epithelial cells
4
ZNF184Protein
Zinc finger TF Amnion epithelial cells
4
ZNF189Protein
Zinc finger TF homology
Amnion epithelial cells
4
132
Appendix B
Mammalian genes (or proteins) primarily down-regulated in response to BPDE or BaP
GeneTim e of Expression Function In terac ts with
BiologicalSystem Ref.
A4 1 h BaP; 1 wk recovery
Amyloid beta precursor
Vascular smooth muscle cells
6
AR 24, 48, 72 h Androgenreceptor
AhR/BPDE, Akt may ubiquitinate
Lung cells 7
A R P l 1 0 & 2 4 h TF Normalmammaryepithelialcells
13
BAXa 24 h Repressed by BaP, not BPDE
Breast cancer cells
5
Bcl-2 24 h Repressed by BaP, not BPDE
Breast cancer cells
5
BRCA-1 24 h Repressed by BaP & BPDE
Breast cancer cells
5
C184L-22 mr 1 h BaP; 1 wk recovery
Vascular smooth muscle cells
6
Claudin-7 1 h BaP; 1 wk recovery
Vascular smooth muscle cells
6
c-Jun 0.5 h Liver slices 10c-Myb 4 h Oncogene,
transcriptionalactivator
TK6 lympho- blastoid cells
1
c-Myc 4 & 2 4 h Oncogene,transcriptionalactivator
TK6 lympho- blastoid cells
1
Complement fac to r h precursor
1 h BaP; 1 wk recovery
Vascular smooth muscle cells
6
Connexin-32 4 h Cell-cell adhesion receptor
TK6 lympho- blastoid cells
1
Cyclin A 24 h Cell cycle TK6 lympho- blastoid cells
1
Decayacceleratingfactor
1 h BaP; 1 wk recovery
Vascular smooth muscle cells
6
Deoxycytidinekinase
4 h Nucleotide &xenobioticmetabolism
TK6 lympho- blastoid cells
1
D-interactingmyb-like
1 h BaP; 1 wk recovery
Vascular smooth muscle cells
6
DNATopoisomerase 11
4 h DNA synthesis,recombination,repair
TK6 lympho- blastoid cells
1
133
Appendix B (Continued)E2A 4 & lO h TF P21-W afl Normal
mammaryepithelialcells
13
Fern la 1 h BaP; 1 wk recovery
Vascular smooth muscle cells
6
Gl ucosylceram ide synthase
4 h Lipid metabolism TK6 lympho- blastoid cells
1
Growth Arrested Specific protein 1
4 h Cell cycle control TK6 lympho- blastoid cells
1
GTP binding protein- associated
1 h BaP; 1 wk recovery
Vascular smooth muscle cells
6
Heme oxygenase-1 24 h Xenobiotictransport
TK6 lympho- blastoid cells
1
Histidine decarboxylase 4 h Nucleotidemetabolism
TK6 lympho- blastoid cells
1
3-hydroxy-3-methylglutaryl-CoAligase
1 h BaP; 1 wk recovery
Vascular smooth muscle cells
6
HM G CoA Reductase 4 & 2 4 h Lipid metabolism TK6 lympho- blastoid cells
1
IkB-a 4 h TF TK6 lympho- blastoid cells
1
IAP-1 4 h Apoptosis TK6 lympho- blastoid cells
1
Immediate early response 1 h BaP; 1 wk recovery
Vascular smooth muscle cells
6
ILGF 1 h BaP; 1 wk recovery
Insulin-like growth factor
Vascular smooth muscle cells
6
ILG F binding protein 1 h BaP; 1 wk recovery
Vascular smooth muscle cells
6
Mannosidase 2aB 1 h BaP; 1 wk recovery
Vascular smooth muscle cells
6
Nuclear receptor binding factor
1 h BaP; 1 wk recovery
Vascular smooth muscle cells
6
Ornithine decarboxylase 24 h Amino acid metabolism
TK6 lympho- blastoid cells
1
PSScdc 24 h Cell cycle, intracellular transducer/effector /modulator
TK6 lympho- blastoid cells
1
PEP-ck PEP carboxy kinase; primary metabolism
Down regulated by ATF3? TK6 cell lines
1
Prolactin 24 h Hormone TK6 lympho- blastoid cells
1
134
Appendix B (Continued)Ref-1 24 h DNA damage
signaling & repairTK6 lympho- blastoid cells
RNA Pol II 2 h-14 days Transcription Compensated by Pol I Rat liver 12R N A P olIII 2 h-14 days Transcription Compensated by Pol I Rat liver 12SAMdC 24 h Amino acid
metabolismTK6 lympho- blastoid cells
Sarcoplasmic reticulum Ca2+ ATPase
4 h ATPasetransporter
TK6 lympho- blastoid cells
SHB/Src homology 2
4 h Adaptor and receptor- associated protein
TK6 lympho- blastoid eells
Small proline- rich protein
1 h BaP; 1 wk recovery
Vascular smooth muscle cells
SNF2L1Protein
SWI/SNF related, matrix associated, actin dependent regulator o f chromatin
Amnionepithelialcells
SOX4 24 h TF Normalmammaryepithelialcells
13
Transthyretin 4 h Extracellulartransporter/carrier
TK6 lympho- blastoid cells
Ubiquitin-conjugatingenzyme
1 h BaP; 1 wk recovery
Proteindegradation
Vascular smooth muscle cells
ZNF141Protein
Putative transeriptional repressor
Amnionepithelialcells
ZNF255Protein
Putative zinc finger TF
Amnionepithelialcells
References for Appendices A and B
1. Akerman, GS, Rosenzweig, BA, Domon, OE, McGarrity, LJ, Blankenship, LR, Tsai, CA, Culp, SJ, MacGregor, JT, Sistare, FD, Chen, JJ, and Morris, SM, 2004. Gene expression profiles and genetic damage in benzo(a)pyrene diol epoxide-exposed TK6 cells. Mutation Research/Fundamental and Molecular Mechanisms o f Mutagenesis 549:43-64.
2. Bral, CM and Ramos, KS, 1997. Identification of benzo[a]pyrene-inducible cis-acting elements within c-Ha-ras transcriptional regulatory sequences. Mol Pharmacol 52:974-982.
3. Chin, BY, Choi, ME, Burdick, MD, Stricter, RM, Risby, TH, and Choi, AMK, 1998. Induction of apoptosis by particulate matter; role of TNF-alpha and MAPK. Am J Physiol Lung Cell Mol Physiol 275:L942-949.
135
4. Gao, Z, Jin, J, Yang, J, and Yu, Y, 2004. Zinc finger proteins and other transcription regulators as response proteins in benzo[a]pyrene exposed cells. Mutation Research/Fundamental and Molecular Mechanisms o f Mutagenesis 550:11-24.
5. Jeffy, BD, Chimomas, RB, Chen, EJ, Gudas, JM, and Romagnolo, DF, 2002. Activation of the aromatic hydrocarbon receptor pathway is not suffieient for transcriptional repression of BRCA-1: requirements for metabolism of benzo[a]pyrene to 7r,8t-dihydroxy-9t, 10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. Cancer Res 62:113-121.
6. Jeffy, BD, Chimomas, RB, Chen, EJ, Gudas, JM, and Romagnolo, DF, 2002. Activation of the aromatic hydrocarbon receptor pathway is not sufficient for transcriptional repression of BRCA-1: requirements for metabolism of benzo[a]pyrene to 7r,8t-dihydroxy-9t, 10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. Cancer Res 62:113-121.
7. Lin, P, Chang, JT, Ko, JL, Liao, SH, and Lo, WS, 2004. Reduction of androgen receptor expression by benzo[alpha]pyrene and 7,8-dihydro-9,10-epoxy-7,8,9,10- tetrahydrobenzo[alpha]pyrene in human lung cells. Biochem Pharmacol 67:1523- 1530.
8. Nakanishi, Y, Pei, XH, Takayama, K, Bai, F, Izumi, M, Kimotsuki, K, Inoue, K, Minami, T, Wataya, H, and Hara, N, 2000. Polycyclic aromatic hydrocarbon carcinogens increase ubiquitination of p21 protein after the stabilization of p53 and the expression of p21. JRespir Cell Mol Biol 22:747-754.
9. Oguri, T, Singh, SV, Nemoto, K, and Lazo, JS, 2003. The carcinogen (7R,8S)- dihydroxy-(9S, 10R)-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene induees Cdc25B expression in human bronchial and lung cancer cells. Cancer Res 63:771-775.
10. Parrish, AR, Fisher, R, Bral, CM, Burghardt, RC, Gandolfi, AJ, Brendel, K, and Ramos, KS, 1998. Benzo(a)pyrene-induced alterations in growth-related gene expression and signaling in precision-cut adult rat liver and kidney sliees. Toxicol Appl Pharmacol 152:302-308.
11. Ramos-Gomez, M, Kwak, MK, Dolan, PM, Itoh, K, Yamamoto, M, Talalay, P, and Kensler, TW, 2001. Sensitivity to earcinogenesis is increased and chemoprotective efficacy of enzyme inducers is lost in nrf2 transcription factor-deficient mice. Proc Natl Acad Sci U S A 98:3410-3415.
12. Shah, G.M. and R.K. Bhattacharya, Modulation of transcription in rat liver by benzo[a]pyrene. Cancer Lett, 1987. 35(2): p. 191-8.
13. Wang, A, Gu, J, Judson-Kremer, K, Powell, KL, Mistry, H, Simhambhatla, P, Aldaz, CM, Gaddis, S, and MacLeod, MC, 2003. Response of human mammary epithelial eells to DNA damage indueed by BPDE: involvement of novel regulatory pathways. Carcinogenesis 24:225-234.
14. Wolf, A, Kutz, A, Plottner, S, Behm, C, Bolt, HM, Follmann, W, and Kuhlmann, J, 2005. The effect of benzo(a)pyrene on porcine urinary bladder epithelial cells analyzed for the expression of selected genes and cellular toxicological endpoints. Toxicology 207:255-269.
15. Yoshii, S, Tanaka, M, Otsuki, Y, Fujiyama, T, Kataoka, H, Arai, H, Hanai, H, and Sugimura, H, 2001. Involvement of Alpha-PAK-lnteracting Exchange Factor in the
136
PAKl-c-Jun NH2-Terminal Kinase 1 Activation and Apoptosis Induced by Benzo[a]pyrene. Mol Cell Biol 21:6796-6807.
137
Appendix C
Gene loci identified by microarray as up- or down-regulated by BaP in 4 weeks
Locus ID Annotation FCAT3G59930; [AT3G59930, defensin-like (DEFL)];
6.1AT5G33355 [AT5G33355, DEFL]AT5G38940; [AT5G38940, manganese/metal ion binding, nutrient reservoir];
Appendix C (Continued)AT3G14680 CYP72A14 cytochrome P450; oxygen binding 1.8AT3G21560 UGT84A2; UDP-glycosyltransferase/sinapate 1-glucosyltransferase 1.7AT3G26440 similar to unknown protein AT 1G13000; contains DUF707 1.AT2G02990 RNS1 (RIBONUCLEASE 1); endoribonuclease 1.AT2G05940 protein kinase, putative 1.AT4G22460 protease inhibitor/seed storage/lipid transfer protein (LTP) 1.AT3G18250 unknown protein 1.AT3G03520 phosphoesterase 1.AT5G19875 similar to oxidoreductase/transition metal ion binding AT2G31940 1.AT4G39270 leucine-rich repeat transmembrane protein kinase, putative 1.AT2G21180 similar to unknown protein AT5G19875 1.AT4G22470 protease inhibitor/seed storage/lipid transfer protein (LTP) 1.AT1G05710 ethylene-responsive protein, putative 1.AT3G54040 photoassimilate-responsive protein-related 1.AT2G19570 CDA1 (CYTIDINE DEAMINASE 1) 1.AT4G23680 major latex protein-related / MLP-related 1.AT4G00700 C2 domain-containing protein 1.AT3G04510 sim. to Light-dep. Short Hypocotyls 1 & to Rubisco, large chain; DUF640 1.AT4G30590 plastocyanin-like domain-containing protein 1.AT2G23620 esterase, putative 1.AT5G64110 peroxidase, putative 1.AT3G49120; [AT3G49120, PEROXIDASE 34];AT3G49110 [AT3G49110, PEROXIDASE 33] "AT5G13930 CHS (CHALCONE SYNTHASE); naringenin-chalcone synthase 1.AT5G48290 heavy-metal-associated domain-containing protein 1.AT4G23690 disease resistance-responsive family / dirigent family 1.AT5G38030 MATE efflux 1.AT4G32870 similar to unknown protein AT2G25770; contains domain Bet v1-like 1.AT3G48920 AtMYB45 (myb domain protein 45); DNA binding / transcription factor 1.6AT5G38780 S-adenosyl-L-methionine:carboxyl methyltransferase 1.6AT1G69880 ATH8 (thioredoxin H-type 8); thiol-disulfide exchange intermediate 1.6AT3G50570 hydroxyproline-rich glycoprotein 1.6AT1G09560 Germin-like protein 5; manganese ion/metal ion binding, nutrient reservoir 1.6AT 1G65500 similar to unknown protein AT 1G65490.1 1.6AT4G20110 vacuolar sorting receptor, putative 1.6AT5G18840 sugar transporter, putative 1.6AT5G44380 FAD-binding domain-containing protein 1.6AT2G17500 auxin efflux carrier 1.6AT3G22060 receptor protein kinase-related 1.6AT5G01050; [AT5G01050, laccase/diphenol oxidase];AT5G01040 [AT5G01040, LAC8(laccase8)]AT4G25810 XTR6 (Xyloglucan Endotransglycosylase 6); glycosylhydrolase 1.6AT2G29995 unknown protein 1.6AT3G62270 anion exchange 1.6AT4G16240 similar to glycine-rich protein AT5G46730 & AT2G05440 1.6AT1G63840 zinc finger (C3HC4-type RING finger) 1.6AT4G26150 zinc finger (GATA type) 1.6AT4G25900 aldose 1-epimerase 1.6AT4G18360 peroxisomal/glycolate oxidase/short chain a-hydroxy acid oxidase, put. 1.6
140
Appendix C (Continued)AT1G79530; [AT1G79530, GAPCP-1; GAP-dehydrogenase];AT1G16300 [AT1G16300, GAPCP-2]AT4G02280 SUS3; UGT/sucrose synthase 1.6AT2G32660 disease resistance / LRR 1.6AT2G16720 MYB7 (myb domain protein 7); DNA binding / transcription factor 1.6AT4G09500 glycosyltransferase 1.6AT4G09420 disease resistance protein (TIR-NBS class), putative 1.6AT5G46140 similarto unknown protein AT5G46130.1; contains DUF295 1.6AT4G01070 UDP-glucoronosyl/UDP-glucosyl transferase 1.6AT5G46050 ATPTR3/PTR3(PEPTIDE TRANSPORTER protein 3 1.6AT 1G63530 similar to hydroxyproline-rich glycoprotein AT 1G63540 1.6AT1G62510 protease inhibitor/seed storage/lipid transfer protein (LTP) 1.6AT4G32650 ATKC1 (A.t. K+ RECTIFYING CHANNEL 1); cyclic nucleotide binding 1.6AT3G46280 protein kinase-related 1.6AT 1G23800 ALDH2B7 3-chloroallyl aldehyde dehydrogenase (NAD) 1.6AT2G22170 lipid-associated 1.6AT2G02850 ARPN (PLANTACYANIN); copper ion binding 1.6AT3G14360 lipase class 3 1.6AT5G45380 sodium:solute symporter 1.6AT1G67360 rubber elongation factor (REF) 1.5AT1G14210 ribonuclease T2 1.5AT2G41380 embryo-abundant protein-related 1.5AT4G01610 cathepsin B-like cysteine protease, putative 1.5AT3G50480 HR4 (HOMOLOG OF RPW8 4) 1.5AT1G65510 similar to unknown protein ATI G65490.1 1.5AT5G36220 CYP81D1 (CYTOCHROME P450 91 A l); oxygen binding 1.5AT5G43060 cysteine proteinase, putative / thiol protease, putative 1.5AT4G37310 CYP81 HI cytochrome P450 1.5AT5G55170 SUM3 (SMALL UBIQUITIN-LIKE MODIFIER 3) 1.5AT4G37870 phosphoenolpyruvate carboxykinase (ATP) / PEPCK, putative 1.5AT4G23010 ATUTR2/UTR2 (UDP-GALACTOSE TRANSPORTER 2) 1.5AT3G02910 similar to unknown protein AT5G46720; contains UPF0131 1.5AT4G33420 peroxidase, putative 1.5AT4G21850 methionine sulfoxide reductase domain-containing protein 1.5AT3G29810 phytochelatin synthetase /COBRA cell expansion protein C0BL2 1.5AT5G45280 pectinacetylesterase, putative 1.5AT5G13180 ANAC083 (A.t. NAC domain containing protein 83); transcription factor 1.5AT1G10150 ATPP2-A10 (Phloem protein 2-A10) 0.7AT3G61060 ATPP2-A13 0.7AT5G61440 thioredoxin family 0.7AT4G39540 shikimate kinase family 0.7AT3G15070 zinc finger (C3HC4-type RING finger) family 0.7AT5G22270 similar to unknown protein AT3G11600.1 0.7AT5G52970 thylakoid lumen 15.0 kDa protein 0.7AT1G24575 unknown protein 0.7AT5G27950 kinesin motor protein-related 0.7AT1G33050 sim. to unknown protein AT4G 10470.1 & to Subtilisin-like serine protease 0.7AT1G74560 NRP1 (NAP1-RELATED protein 1); DNA/chromatin/histone binding 0.7
141
Appendix C (Continued)AT5G51830 pfkB-type carbohydrate kinase family 0.7AT3G25910 similar to unknown protein AT3G24740.2; similar to TRAF-like; DUF1644 0.7AT1G11260 STP1 (SUGAR TRANSPORTER 1); carbohydrate transporter 0.7AT5G16180 ATCRS1/CRS1 (A.f. ortholog of maize chloroplast splicing factor CRS1) 0.7AT1G48600 phosphoethanolamine N-methyltransferase 2, putative (NMT2) 0.7AT5G46710 zinc-binding family 0.7AT3G45300 IVD (ISOVALERYL-COA-DEHYDROGENASE) 0.7AT2G39310 jacalin lectin family 0.7AT4G33666 unknown protein 0.7AT5G23020 MAM-L, Methylthioalkylmalate synthase-like; 2-isopropylmalate synthase 0.7AT1G61800 GPT2 (glucose-6-phosphate/phosphate translocator 2); antiporter 0.7AT4G17490 ATERF6 (Ethylene Responsive Element Binding Factor 6); TF 0.7AT1G21100 O-methyltransferase, putative 0.7AT5G52310 COR78 (COLD REGULATED 78) 0.7AT1G15940 similar to binding AT1G80810; contains ARM repeat 0.7AT1G64490 sim. to unkn. protein AT5G42060 & to putative transcriptional coactivator 0.7AT4G19170 NCED4 (NINE-CIS-EPOXYCAROTENOID DIOXYGENASE 4) 0.7AT5G26740 similar to unknown protein AT3G05940.1; contains DUF300 0.6AT5G20150 SPX (SYG1/Pho81/XPR1) domain-containing protein 0.6AT2G41640 sim. to unknown protein AT3G57380.1 & to glycosyltransferase; DUF563 0.6AT1G03090 MCCA (3-methylcrotonyl-CoA carboxylase 1) 0.6AT5G57630 CIPK21 (CBL-INTERACTING protein KINASE 21); kinase 0.6AT4G28040 nodulin MtN21 family 0.6AT5G57340 similar to unknown protein AT5G67390.2 0.6AT5G24770; [AT5G24770, VSP2 (Vegetative Storage Protein 2); acid phosphatase];AT5G24780 [AT5G24780, VSP1; acid phosphatase] ° ®AT4G20820 FAD-binding domain-containing protein 0.6AT1G70290 ATTPS8 {A.t. trehalose phosphatase/synthase 8); glycosyl-transferring 0.6AT5G06560 similar to unknown protein AT3G11850.2; contains DUF593 0.6AT2G34620 mitochondrial transcription termination factor-related/mTERF-related 0.6AT4G26260 MI0X4 (MYO-INOSITOL OXYGENASE 4) 0.6AT3G22420 WNK2 (WITH NO K 2); kinase 0.6AT1G08630 THAI (THREONINE ALDOLASE 1); aldehyde-lyase 0.6AT4G17460 HAT1 (homeobox-leucine zipper protein 1); transcription factor 0.6AT 1G72070; [AT 1G72070, DNAJ heat shock N-terminal domain-containing protein];AT1G72060 [AT1G72060, serine-type endopeptidase inhibitor]AT4G19160 binding 0.6AT3G62950 glutaredoxin family 0.6AT4G00780 meprin and TRAF homology/MATH domain-containing protein 0.6AT5G55300 TOPI BETA (DNA TOPOISOMERASE 1 BETA); type I 0.6AT4G01560 MEE49 (maternal effect embryo arrest 49) 0.6AT1G10070 ATBCAT-2; branched-chain-amino-acid transaminase/catalytic 0.6AT1G02640 BXL2 (BETA-XYLOSIDASE 2); 0-glycosyl hydrolase 0.6AT1G35140 PHI-1 (PHOSPHATE-INDUCED 1) 0.6AT1G48160 signal recognition particle 19 kDa protein, putative/SRP19, putative 0.6AT3G44630 disease resistance protein RPP1-WsB-like (TIR-NBS-LRR class), putative 0.6AT4G10120 ATSPS4F; sucrose-phosphate synthase/transferase 0.6AT3G49780 ATPSK4 (PHYTOSULFOKINE 4 PRECURSOR); growth factor 0.6AT2G22990 SNG1 (SINAPOYLGLUCOSE 1); serine carboxypeptidase 0.6
142
Appendix C (Continued)AT1G17280; [AT1G17280, UBC34 ubiquitin-conjugating enzyme; ubiquitin-proteinAT5G50430 ligase]; [AT5G50430, UBC33; ubiquitin-protein ligase]AT 1G64660 ATMGL; catalytic/ methionine gamma-lyaseAT2G18300 basic helix-loop-helix (bHLH) family AT2G42530 cold-responsive/cold-regulated protein (cor15b)AT1G29395 COR414-TM1 (cold regulated 414 thylakoid membrane 1)AT4G33070 pyruvate decarboxylase, putativeAT1G21910 AP2 domain-containing transcription factor familyAT3G02550 lateral organ boundaries domain protein 41 (LBD41)AT2G02710 PAC motif-containing proteinAT3G21650 Ser/Thr protein phosphatase 2A (PP2A) regulatory subunit B', put. AT3G21260 GLTP3 (GLYCOLIPID TRANSFER protein 3)AT1G20650 protein kinaseAT2G22080 sim. to zinc finger protein-related AT5G63740.1; sim. to calcium-binding AT1G76590 zinc-binding family AT 1G04770 male sterility MSS familyAT3G52170 DNA bindingAT4G04630 similar to unknown protein AT4G21970.1; contains DUF584 AT5G48850 male sterility MSS familyAT1G53870; [AT1G53870, similar to unknown protein AT1G53890.1];AT1G53890 [AT1G53890, contains DUF567]AT2G41100 TCH3 (TOUCH 3)AT1G03610 similar to unknown protein AT4G03420.1; contains DUF789 AT 1G02660 lipase class 3AT2G17550 similar to unknown protein AT2G20240.1AT3G52072; [Potential natural antisense gene, locus overlaps with AT3G52070];AT3G52070 [AT3G52070, similar to hypothetical protein [M. truncatula]]AT2G22980 SCPL13; serine carboxypeptidaseAT4G09890 similar to unknown protein AT5G11970.1AT3G45780 PH0T1 (phototropin 1); kinaseAT1G73600 phosphoethanolamine N-methyltransferase 3, putative (NMT3)AT4G33050 EDA39 (embryo sac development arrest 39); calmodulin bindingAT2G18190 AAA-type ATPaseAT5G55620 similar to unknown protein AT3G09950.1AT5G35490 unknown proteinAT3G49160 pyruvate kinaseAT5G39890 similar to unknown protein AT5G15120; DUF1637 & Cupin, RmlC-type AT4G29950 microtubule-associated proteinAT1G76410 ATL8; protein binding/zinc ion bindingAT3G47340 ASN1 (DARK INDUCIBLE 6)AT4G36500 similar to unknown protein AT2G18210.1AT2G26530 AR781, similar to calmodulin-binding protein AT2G15760; DUF1645AT1G75020 LPAT4; acyltransferaseAT2G24600 ankyrin repeat familyAT3G55510 similar to unknown protein AT2G18220.1; contains UPF0120AT5G61020 ECT3 (evolutionary conserved C-terminal 3)AT3G44970 cytochrome P450AT2G03390 uvrB/uvrC motif-containing proteinAT5G23010 MAM1 (2-isopropylmalate synthase 3); 2-isopropylmalate synthase
AT3G03020 unknown proteinAT5G49360 BXL1 (BETA-XYLOSIDASE 1); 0-giycosyi hydroiase AT1G80920 J8; heat shock protein binding/unfoided protein bindingAT4G02800 similar to unknown protein AT5G01970.1AT4G12720 AtNUDT7 {A.t. NUDIX HYDROLASE HOMOLOG 7); hydrolase AT5G14470 GHMP kinase-relatedAT 1G80840 WRKY40 (WRKY DNA-binding protein 40); transcription factorAT4G37370 CYP81D8 cytochrome P450AT 1G36370 SHM7 (Serine/glycine hydroxymethyltransferase 7)AT3G05900 neurofilament protein-relatedAT5G11010 pre-mRNA cleavage complex-relatedAT5G18060 auxin-responsive protein, putativeAT3G10040 transcription factorAT4G24110 similar to Hypothetical protein [Oryza sativa]AT1G14280 PKS2 (PHYTOCHROME KINASE SUBSTRATE 2)AT5G22920 zinc finger (C3HC4-type RING finger)AT4G27450 sim. to unknown At3g15450; N-terminal nucleophile aminohydrolase dom.AT5G41080 glycerophosphoryl diester phosphodiesteraseAT5G44260 zinc finger (CCCH-type) familyAT2G26980 CIPK3 (CBL-INTERACTING protein KINASE 3)AT4G10270 wound-responsive familyAT1G35612 pseudogene of Ulpl protease family proteinAT2G15080 disease resistance familyAT3G29290 EMB2076 (EMBRYO DEFECTIVE 2076); bindingAT1G73540 ATNUDT21 {A.t. Nudix hydrolase homolog 21); hydrolaseAT2G04050 MATE efflux familyAT2G17850 similar to unknown protein AT5G66170.2; Rhodanese-like domainAT1G74670 gibberellin-responsive protein, putativeAT2G32880; [AT2G32880, MATH domain-containing protein];AT2G32870 [AT2G32870, MATH domain-containing protein]AT2G38470 WRKY33 (WRKY DNA-binding protein 33); transcription factorAT 1G05680 UDP-glucoronosyl/UDP-glucosyl transferase familyAT3G55980 zinc finger (CCCH-type) familyAT5G47240 ATNUDT8 (A.t. Nudix hydrolase homolog 8); hydrolaseAT1G64360 unknown proteinAT5G15960; [AT5G15960, KIN1];AT5G15970 [AT5G15970, KIN2 (COLD-RESPONSIVE 6.6)]AT3G02040 Senescence-Related Gene 3; glycerophosphodiester phosphodiesterase AT3G13080; [AT3G13080, ATMRP3 (A.t. multidrug resistance-associated protein 3)];AT1G71330 [AT1G71330, ATNAP5 (A.t. non-intrinsic ABC protein 5)]AT1G33055 unknown proteinAT2G45660 AGL20 (AGAMOUS-LIKE 20); transcription factorAT1G21110; [AT1G21110, 0-methyltransferase, putative];AT1G21120 [AT1G21120, 0-methyltransferase, putative]AT3G23030 IAA2 (indoleacetic acid-induced protein 2); transcription factor AT5G46240 KAT1, K+ ATPase; cyclic nucleotide binding/inward rectifier K+ channel AT5G56870 beta-galactosidase, putative/lactase, putative AT2G22880 VQ motif-containing proteinAT3G48710 GTP binding/RNA binding
Appendix C (Continued)0.60.60.60.60.60.60.60.60.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.50.5
0.5
0.50.50.50.50.5
0.5
0.4
0.4
0.40.4
0.4
0.40.40.40.40.3
144
Appendix C (Continued)AT5G66985 unknown protein 0.3AT5G12050 sim. to unknown prot. AT1G54200 & to putative ATP-dep. DNA helicase 0.3AT1G76650 calcium-binding EF hand 0.3
145
Gene loci identified by microarray as up- or down-regulated by BaP in 24 h
Appendix D
Locus ID FC AnnotationAt4g 17490 28.1 ATERF6 (Ethylene-Responsive binding Factor 6); TFAt5g42900 23.6 similar to unknown protein At4g33980At4g33980 19.1 similar to unknown protein At5g42900At2g14560 8.1 similarto unknown protein At1g33840; contains DUF567At1g17665 7.1 BoCAR; similar to CA-responsive protein [S. oleracea]At3g55980 7.1 zinc finger (CCCFI-type) familyAt5g45340 7.1 CYP707A3 (cytochrome P450)At1g07050 6.9 CONSTANS-like protein-relatedAt2g40080 6.5 ELF4 (EARLY FLOWERING 4)At4g24570 5.6 mitochondrial substrate carrier familyAt1g27730 4.7 STZ (SALT TOLERANCE ZINC FINGER); TFAt3g04640 4.7 glycine-rich proteinAt5g61600 4.7 ethylene-responsive element-binding familyAt4g29780 4.6 sim ilarto unknown protein At5g12010At5g52310 4.4 COR78 (COLD REGULATED 78)At5g23240 4.3 DNAJ heat shock N-terminal domain-containingAt1g80840 4.1 WRKY40 (WRKY DNA-binding protein 40); TFAt2g40140 4.1 CZF1/ZFAR1; transcription factorAt5g48250 4.1 zinc finger (B-box type) family proteinAt1g05575 3.9 unknown proteinAt2g40000 3.9 similar to unknown protein At3g55840At4g27280 3.8 calcium-binding EF hand familyAt5g51190 3.8 AP2 domain-containing transcription factor, putativeAt5g57220 3.8 CYP81F2 cytochrome P450At3g59350 3.7 serine/threonine protein kinase, putativeAt1g51090 3.6 heavy-metal-associated domain-containingAt5g50450 3.6 zinc finger (MYND type) familyAt3g50930 3.5 AAA-type ATPase family proteinAt4g11280 3.5 ACS6 (1-ACC SYNTHASE 6)At4g37260 3.5 AtMYB73/MYB73 (myb domain protein 73)At5g61380 3.5 T0C1 (TIMING OF CAB EXPRESSION 1)At1g61890 3.4 MATE efflux familyAt4g23810 3.4 WRKY53 transcription activator/TFAt5g57110 3.4 ACA8 (Autoinhibited Ca2+ -ATPASE, Isoform 8)At4g34131 3.3 UGT73B3; UDP/abscisic acid glucosyltransferaseAt4g34135 3.3 UGT73B2; UDP/flavonol 3-0-glucosyltransferaseAt5g 15960 3.3 KIN2 (COLD-RESPONSIVE 6.6)At5g15970 3.3 KIN1At2g21130 3.2 peptidyl-prolyl cis-trans isomerase / cyclophilin (CYP2)At4g 12280 3.2 copper amine oxidase familyAt4g12290 3.2 copper amine oxidase familyAt2g38470 3.1 WRKY33 (WRKY DNA-binding protein 33)At2g41640 3.1 similarto unknown protein At3g57380At3g05800 3.1 transcription factorAt5g04340 3.1 C2H2 zinc finger TF (ZAT6)At1g11210 3 similar to unknown protein A t lg l 1220; contains DUF761
At1g57980 3 purine permease-relatedAt1g57990 3 ATPUP18 (A.t. purine permease 18)At1g76600 3 similar to unknown protein At1g21010At4g16260 3 glycosyl hydrolase family 17At4g30650 3 hydrophobic/low temperature & salt responsive prot., putativeAt5g27420 3 zinc finger (C3HC4-type RING finger) familyAt5g44420 3 PDF1.2 (Low-molecular-weight cysteine-rich 77)At5g62360 3 invertase/pectin methylesterase inhibitor familyAt1g68050 2.9 FKFl, Flavin-binding Kelch domain F box; ubiquitin- ligaseAt1g77450 2.9 ANAC032 (Arabidopsis NAC domain containing TFAt4g31800 2.9 WRKY18 transcription factorAt5g23410 2.9 similar to FKFl; contains domain PTHR23244At5g42730 2.9 pseudogene similar to ACT domain-containing, F-boxAt5g60100 2.9 APRR3 (PSEUDO-RESPONSE REGULATOR 3)At1g 18570 2.8 MYB51 (MYB DOMAIN PROTEIN 51)At1g67970 2.8 AT-HSFA8 transcription factorAt4g17500 2.8 ATERF-1, Ethylene Responsive Element binding FactorAt1g 17420 2.7 L0X3 (Lipoxygenase 3)At5g11150 2.7 ATVAMP713 (vesicle-associated membrane protein)At5g17340 2.7 similar to unknown protein At3g03272At5g59550 2.7 zinc finger (C3HC4-type RING finger) familyAt1g17170 2.6 ATGSTU24 glutathione transferaseAt1g55450 2.6 embryo-abundant protein-relatedAt2g47890 2.6 zinc finger (B-box type) familyAt3g08720 2.6 ATPK19 (A.t. PROTEIN KINASE 19); kinaseAt3g20810 2.6 jumonji OmjC) domain-containing transcription factorAt5g10695 2.6 similar to unknown protein At5g57123At5g57630 2.6 CIPK21 (CBL-INTERACTING PROTEIN KINASE 21)At2g42530 2.5 C0R15BAt4g33050 2.5 EDA39 (embryo sac development arrest 39)At1g73540 2.4 ATNUDT21 (A.t. Nudix hydrolase homolog 21)At1g76790 2.4 0-methyltransferase family 2 proteinAt1g80590 2.4 WRKY66 (WRKY DNA-binding protein 66)At2g38790 2.4 unknown proteinAt4g01870 2.4 tolB protein-relatedAt4g27560 2.4 glycosyltransferase family proteinAt4g27570 2.4 glycosyltransferase family proteinAt4g36010 2.4 pathogenesis-related thaumatin familyAt5g06320 2.4 NHL3 (NDRI/HINI-like 3)At5g23660 2.4 MTN3 (HOMOLOG OF M. truncatula MTN3)At5g39020 2.4 protein kinase family proteinAt1g49230 2.3 zinc finger (C3HC4-type RING finger) familyAt1g72900 2.3 disease resistance protein (TIR-NBS class), putativeAt1g73500 2.3 ATMKK9 (A.t. MAP kinase kinase 9); kinaseAt2g16365 2.3 F-box family proteinAt2g26530 2.3 AR781At2g31880 2.3 LRR transmembrane protein kinase, putativeAt3g46620 2.3 zinc finger (C3HC4-type RING finger) familyAt3g56710 2.3 SIB1 (SIGMA FACTOR BINDING PROTEIN 1)
147
At4g34950 2.3 nodulin family proteinAt5g22250 2.3 CCR4-N0T transcription complex protein, putativeAt5g46710 2.3 zinc-binding family proteinAt1g05560 2.2 UGTl (UDP-glucosyl transferase 75B1)At1g28330 2.2 DRM1 (DORMANCY-ASSOCIATED PROTEIN 1)At1g69890 2.2 similar to unknown protein At1g27100At2g02390 2.2 ATGSTZ1 (GLUTATHIONE S-TRANSFERASE 18)At2g 19450 2.2 TAGl (Triacylglycerol Biosynthesis Defect 1)At2g26560 2.2 PLP2 (PHOSPHOLIPASE A 2A); nutrient reservoirAt2g36790 2.2 UGT73C6 (UDP-GLUCOSYL TRANSFERASE)At2g36970 2.2 UDP-glucoronosyl/UDP-glucosyl transferaseAt3g23605 2.2 UBX domain-containing proteinAt4g16146 2.2 similar to unknown protein At1g69510At5g 18470 2.2 curculin-like (mannose-binding) lectin familyAt5g60900 2.2 RLK1 (Receptor-Like Protein Kinase 1)At5g67480 2.2 BT4 (BTB and TAZ domain protein 4)At1g11130 2.1 SUB (STRUBBELIG); protein bindingA ll g 12200 2.1 flavin-containing monooxygenase familyAt1g21250 2.1 W AKl (CELL WALL-ASSOCIATED KINASE)At1g23410 2.1 ubiquitin extension protein, putative; RPS27aAt1g55850 2.1 ATCSLE1 (Cellulose synthase-like E l)At1g72940 2.1 disease resistance protein (TIR-NBS class), putativeAt1g73330 2.1 ATDR4 (A.t. drought-repressed 4)At1g76680 2.1 OPRl (12-oxophytodienoate reductase 1)At1g76690 2.1 0PR2 (12-oxophytodienoate reductase 2)At2g36800 2.1 DOGTl (DON-GLUCOSYLTRANSFERASE)At2g42540 2.1 C0R15A (COLD-REGULATED 15A)At3g28290 2.1 AT14AAt3g28300 2.1 AT14AAt3g59140 2.1 ATMRP14 (multidrug resistance-associated protein)At3g59820 2.1 calcium-binding mitochondrial protein-relatedAt4g36500 2.1 similar to unknown protein At2g18210At5g24470 2.1 APRR5 (PSEUDO-RESPONSE REGULATOR 5)At5g63790 2.1 ANAC102 transcription factorAt1g23830 2 similar to unknown protein At1g23840At1g27770 2 ACA1 (autoinhibited Ca2+ -ATPase 1)At2g21660 2 ATGRP7 (Cold, Circadian Rhythm, & RNA binding 2)At2g22450 2 riboflavin biosynthesis protein, putativeAt3g16530 2 legume lectin family proteinAt3g28740 2 cytochrome P450 family proteinAt4g19120 2 ERD3 (EARLY-RESPONSIVE TO DEHYDRATION 3)At4g19880 2 similar to unknown protein At5g45020At5g23050 2 acyl-activating enzyme 17 (AAE17)At5g39410 2 binding / catalyticAt5g54960 2 PDC2 (PYRUVATE DECARBOXYLASE-2)At2g07675 1.9 ribosomal protein SI 2 mitochondrial family
ATMG00980 1.9 ribosomal protein L2At1g02340 0.6 HFR1 (LONG HYPOCOTYL IN FAR-RED)A tig 10370 0.6 GSTU17/GST30/Early-Responsive to Dehydration 9
148
At1g34310 0.6 ARF12 (AUXIN RESPONSE FACTOR 12)At1g64670 0.6 BDG1 (B0DYGUARD1); hydrolaseAt2g21560 0.6 similar to unknown protein At4g39190At3g21670 0.6 nitrate transporter (NTP3)At3g28270 0.6 similar to A T U A At3g28290 & At3g28300; DUF677At4g30610 0.6 BRS1 (BRI1 SUPPRESSOR 1)At4g38850 0.6 SAUR_AC1 (SMALL AUXIN UP RNA 1)At5g02670 0.6 similar to poly(A)transferase/protein binding At3g06560At5g59780 0.6 MYB59 (myb domain protein 59)At1g07180 0.5 ATNDI1/NDA1 (Alternative NAD(P)H Dehydrogenase 1)At1g07350 0.5 transformer serine/arginine-rich ribonucleoprotein, putativeAt1g 13080 0.5 CYP71B2 CYTOCHROME P450A tig 14280 0.5 PKS2 (PHYTOCHROME KINASE SUBSTRATE 2)At1g29430 0.5 auxin-responsive family proteinAt1g32450 0.5 proton-dependent oligopeptide transport (POT) familyAt1g44000 0.5 similar to unknown protein At4g11911At1g62510 0.5 protease inhibitor/seed storage/lipid transfer protein (LTP)At1g62960 0.5 ACS10 (ACC SYNTHASE 10)At1g75180 0.5 similar to unknown protein At1g19400At1g79270 0.5 ECT8 (evolutionarily conserved C-terminal region 8)At2g 16370 0.5 THY-1 (THYMIDYLATE SYNTHASE 1)At2g 17830 0.5 F-box family proteinAt2g21185 0.5 unknown proteinAt2g21187 0.5 Potential natural antisense gene, overlaps with At2g21185At2g26690 0.5 nitrate transporter (NTP2)At2g30520 0.5 RPT2 (ROOT PHOTOTROPISM 2); protein bindingAt2g31380 0.5 STH (salt tolerance homologue); zinc ion binding TFAt2g32530 0.5 ATCSLB03 (Cellulose synthase-like B3)At2g32540 0.5 ATCSLB04 (Cellulose synthase-like B4)At2g37170 0.5 PIP2B (plasma membrane intrinsic protein 2;2)At2g37180 0.5 RD28 (plasma membrane intrinsic protein 2;3)At2g42190 0.5 sim. to unknown protein At3g57930; HMG-1 & HMG-Y domainAt2g43620 0.5 chitinase, putativeAt2g45660 0.5 AGL20 (AGAMOUS-LIKE 20); transcription factorAt3g01550 0.5 those phosphate/phosphate translocator, putativeAt3g11770 0.5 nucleic acid bindingAt3g12580 0.5 HSP70 (heat shock protein 70); ATP bindingAt3g14770 0.5 nodulin MtN3 family proteinAt3g15310 0.5 transposable element geneAt3g26310 0.5 CYP71B35 cytochrome P450At3g27170 0.5 CLC-B (chloride channel protein B)At3g48100 0.5 ARR5 (A.t. Response Regulator 5)At3g50560 0.5 short-chain dehydrogenase/reductase (SDR) familyAt3g54720 0.5 AMP1 (Altered Meristem Program 1); dipeptidaseAt3g55920 0.5 peptidyl-prolyl cis-trans isomerase/cyclophilin, putativeAt3g61890 0.5 ATHB-12 (A.t. HOMEOBOX PROTEIN 12)At3g63200 0.5 PLA IIIB/PLP9 (Patatin-like protein 9)At4g 12980 0.5 auxin-responsive protein, putativeAt4g22470 0.5 protease inhibitor/seed storage/lipid transfer protein (LTP)
149
At4g22570 0.5 APT3 (Adenine phosphoribosyltransferase 3)At4g23290 0.5 protein kinase family proteinAt4g34570 0.5 THY-2 (THYMIDYLATE SYNTHASE 2)At4g38860 0.5 auxin-responsive protein, putativeAt5g12050 0.5 similar to unnamed protein [\/. vinifera] (GB:CA045643.1)At5g12110 0.5 elongation factor IB alpha-subunit 1 (eEF1Balpha1)At5g27780 0.5 auxin-responsive family proteinAt5g35970 0.5 DNA-binding protein, putativeAt5g42460 0.5 F-box family proteinAt5g47370 0.5 HAT2; transcription factorAt5g48490 0.5 LTPAt5g64840 0.5 ATGCN5 (A.t. general control non-repressible 5)At5g64940 0.5 ATATH13 (ABC2 homolog 13)At5g66590 0.5 allergen V5/Tpx-1-related family proteinAt1g02820 0.4 late embryogenesis abundant 3 family / LEA3 familyAt1g 12650 0.4 contains DUF947 (lnterPro:IPR009292)At1g29460 0.4 auxin-responsive protein, putativeAt1g68190 0.4 zinc finger (B-box type) family proteinAt1g69160 0.4 unknown proteinAt1g69530 0.4 ATEXPA1 (A.t. EXPANSIN A l)At1g74670 0.4 gibberellin-responsive protein, putativeAt1g75100 0.4 JAC1; HSP bindingAt1g76110 0.4 high mobility group (HMG1/2), ARID/BRIGHT domainAt2g39705 0.4 DVL11/RTFL8 (ROTUNDIFOLIA LIKE 8)At2g40610 0.4 ATEXPA8 (A.t. EXPANSIN A8)At3g04810 0.4 ATNEK2; kinaseAt3g14200 0.4 DNAJ heat shock N-terminal domain-containing proteinAt3g17510 0.4 CIPK1 (CBL-INTEFtACTING PROTEIN KINASE 1)At3g47340 0.4 ASN1 (DARK INDUCIBLE 6)At3g54500 0.4 similar to dentin sialophosphoprotein-related At5g64170At3g57040 0.4 ARR9 (RESPONSE REACTOR 4); transcription regulatorAt5g35490 0.4 unknown proteinAt5g62280 0.4 similar to unknown protein At2g45360; contains DUF1442At1g 13650 0.3 similar to gar2-related At2g03810At1g55960 0.3 similar to unknown protein At3g13062; Lipid-binding STARTAt1g64500 0.3 glutaredoxin family proteinAt2g 15020 0.3 similar to unknown protein At5g64190At2g41250 0.3 haloacid dehalogenase-like hydrolase familyAt2g46830 0.3 CCA1 (CIRCADIAN CLOCK ASSOCIATED 1)At3g24500 0.3 MBF1C (Multiprotein Bridging Factor 1c)At4g25100 0.3 FSD1 (FE SUPEROXIDE DISMUTASE 1)At5g06980 0.3 similar to unknown protein At3g 12320At5g 15850 0.3 C0L1 (CONSTANS-LIKE 1); zinc ion binding TFAt5g52900 0.3 similar to unnamed protein [V. vinifera] (GB:CA049548.1)At1g73870 0.2 zinc finger (B-box type) familyAt2g46670 0.2 pseudo-response regulator/TOCI-like protein, putativeAt2g46790 0.2 APRR9 (PSEUDO-RESPONSE REGULATOR 9)At3g02380 0.2 COL2 (CONSTANS-LIKE 2); zinc ion binding TFAt3g12320 0.2 similar to unknown protein At5g06980
Note: All amplicons are between 60 and 140 nt. Tm at 59-60° C. The last column
represents final nanomolar primer concentrations used. If the two values differ, the first
value is for 24-h and the second is for 4-wk samples.
152
1 Fismes J, Perrin-Ganier C, Empereur-Bissoimet P, Morel JL (2002) Soil-to-Root Transfer and Translocation of Polycyclic Aromatic Hydrocarbons by Vegetables Grown on Industrial Contaminated Soils. J Environ Qual 31: 1649-1656
2 Forrest V, Cody T, Caruso J, Warshawsky D (1989) Influence of the carcinogenic pollutant benzo[a]pyrene on plant development: fern gametophytes. Chem Biol Interact 72: 295-307
3 Weberlotfi F, Pfohlleszkowicz A, Keith G, Pillay DTN, Dietrich A, Rether B, Guillemaut P (1992) Formation of Abnormal Hypermodified Nucleotides on Plant DNA Upon Xenobiotic Action. Plant Science 86: 13-19
4 Phillips DH (1983) Fifty years of benzo(a)pyrene. Nature 303: 468-4735 Meyer BK, Pray-Grant MG, Vanden Heuvel JP, Perdew GH (1998) Hepatitis B Virus
X-Associated Protein 2 Is a Subunit of the Unliganded Aryl Hydrocarbon Receptor Core Complex and Exhibits Transcriptional Enhancer Activity. Mol. Cell. Biol. 18: 978-988
6 Denison M, Fisher J, Whitlock J, Jr (1989) Protein-DNA interactions at recognition sites for the dioxin-Ah receptor complex. J. Biol. Chem. 264: 16478-16482
7 Wei SJ, Chang RL, Wong CQ, Bhachech N, Cui XX, Hennig E, Yagi H, Sayer JM,Jerina DM, Preston BD, et al. (1991) Dose-dependent differences in the profile ofmutations induced by an ultimate carcinogen from benzo[a]pyrene. Proc Natl Acad S ciU S A88: 11227-11230
8 Cherpillod P, Amstad PA (1995) Benzo[a]pyrene-induced mutagenesis of p53 hotspot codons 248 and 249 in human hepatocytes. Mol Carcinog 13: 15-20
9 Chen J, Zheng Y, West M, Tang M (1998) Carcinogens preferentially bind atmethylated CpG in the p53 mutational hot spots. Cancer Res 58: 2070-2075
10 Vahakangas KH, Bennett WP, Castren K, Welsh JA, Khan MA, Blomeke B, Alavanja MC, Harris CC (2001) p53 and K-ras mutations in lung cancers from former and never-smoking women. Cancer Res 61: 4350-4356
11 Kootstra A (1986) The dynamics of chromatin carcinogen interactions in the human cell. Nucl. Acids Res. 14: 9897-9909
12 Moorthy B, Miller KP, Jiang W, Williams ES, Kondraganti SR, Ramos KS (2003) Role of Cytochrome P4501B1 in Benzo[a]pyrene Bioactivation to DNA-Binding Metabolites in Mouse Vascular Smooth Muscle Cells: Evidence from 32P- Postlabeling for Formation of 3-Hydroxybenzo[a]pyrene and Benzo[a]pyrene-3,6- quinone as Major Proximate Genotoxic Intermediates. J Pharmacol Exp Ther 305: 394-401
13 Shen Y-M, Troxel AB, Vedantam S, Penning TM, Field J (2006) Comparison of p53 Mutations Induced by PAH o-Quinones with Those Caused by anti-Benzo[a]pyrene Diol Epoxide in Vitro: Role of Reactive Oxygen and Biological Selection. Chem. Res. Toxicol. 19: 1441-1450
14 Kirso U, Irha N (1998) Role of Algae in Fate of Carcinogenic Polycyclic Aromatic Hydrocarbons in the Aquatic Environment. Ecotoxicology and Environmental Safety 41: 83-89
7.3 References
153
15 Hussain SP, Hofseth LJ, Harris CC (2003) Radical causes of cancer. Nature Reviews Cancer 3: 276-285
16 Pappas P, Sotiropoulou M, Karamanakos P, Kostoula A, Levidiotou S, Marselos M (2003) Acute-phase response to benzo[a]pyrene and induction of rat ALDH3A1. Chemico-Biological Interactions 143-144: 55-62
17 Canuto RA, Ferro M, Muzio G, Bassi AM, Leonarduzzi G, Maggiora M, Adamo D, Poli G, Lindahl R (1994) Role of aldehyde metabolizing enzymes in mediating effects of aldehyde products of lipid peroxidation in liver cells. Carcinogenesis 15: 1359-1364
18 Strolin Benedetti M, Whomsley R, Baltes E (2006) Involvement of enzymes other than CYPs in the oxidative metabolism of xenobiotics. Expert Opinion on Drug Metabolism & Toxicology 2: 895-920
20 Smith TL, Merry ST, Harris DL, Joe Ford J, Ike J, Archibong AE, Ramesh A (2007) Species-specific testicular and hepatic microsomal metabolism of benzo(a)pyrene, an ubiquitous toxicant and endocrine disruptor. Toxicol In Vitro 21: 753-757
21 Lin P, Chang JT, Ko JL, Liao SH, Lo WS (2004) Reduction of androgen receptor expression by benzo[alpha]pyrene and 7,8-dihydro-9,10-epoxy-7,8,9,10- tetrahydrobenzo[alpha]pyrene in human lung cells. Biochem Pharmacol 67: 1523- 1530
22 Chakrabarti S, Hanes SD, Biswas DK (1982) Mechanism of action of benzo(a)pyrene and nicotine on hormone production by rat pituitary tumor cells. Biochem Biophys Res Commun 108: 596-603
23 Charles GD, Bartels MJ, Zacharewski TR, Gollapudi BB, Freshour NL, Camey EW (2000) Activity of benzo[a]pyrene and its hydroxylated metabolites in an estrogen receptor-alpha reporter gene assay. Toxicol Sci 55: 320-326
24 Chang LW, Chang Y-C, Ho C-C, Tsai M-H, Lin P (2007) Increase of carcinogenic risk via enhancement of cyclooxygenase-2 expression and hydroxyestradiol accumulation in human lung cells as a result of interaction between BaP and 17-beta estradiol. Carcinogenesis 28: 1606-1612
25 Jeffy BD, Chimomas RB, Chen EJ, Gudas JM, Romagnolo DF (2002) Activation of the aromatic hydrocarbon receptor pathway is not sufficient for transcriptional repression of BRCA-1: requirements for metabolism of benzo[a]pyrene to 7r,8t- dihydroxy-9t,10-epoxy-7,8,9,10-tetrahydrobenzo[a]pyrene. Cancer Res 62: 113-121
26 Hockings JK, Thome PA, Kemp MQ, Morgan SS, Selmin O, Romagnolo DF (2006) The Ligand Status of the Aromatic Hydrocarbon Receptor Modulates Transcriptional Activation of BRCA-1 Promoter by Estrogen. Cancer Res 66: 2224-2232
28 Forrest, et al. (1989)29 Reinert J (1952) Der Einfluk von 3,4-benzpyrene auf das flachenwachstum und den
auxinspiegel der prothallien von stenochlaena palustris. Zeitschrift fur Botanik 40: 187-192
154
30 Mockaitis K, Estelle M (2008) Auxin Receptors and Plant Development: A New Signaling Paradigm. Annual Review of Cell and Developmental Biology 24
31 Montagut C, Rovira A, Albanell J (2006) The proteasome: a novel target for anticancer therapy. Clin Transl Oncol 8: 313-317
32 Tsai KS, Yang RS, Liu SH (2004) Benzo[a]pyrene Regulates Osteoblast Proliferation through an Estrogen Receptor-Related Cyclooxygenase-2 Pathway. Chem. Res. Toxicol. 17: 679-684
33 Song S, Xu XC (2001) Effect of benzo[a]pyrene diol epoxide on expression of retinoic acid receptor-beta in immortalized esophageal epithelial cells and esophageal cancer cells. Biochem Biophys Res Commun 281: 872-877
34 Cote S, Siimett D, Momparler R (1998) Demethylation by 5-aza-29-deoxycytidine of specific 5-methylcytosine sites in the promoter region of the retinoic acid receptor beta gene in human colon carcinoma cells. Anticancer Drugs 9: 743-750
35 Song S, Lippman SM, Ye Y, Zou X, Xu X-C (2005) Induction of cyclooxygenase-2 by benzo[a]pyrene diol epoxide through inhibition of retinoic acid receptor-beta 2 expression. Oncogene 24: 8268-8276
36 Virmani AK, Rathi A, Zochbauer-Muller S, Sacchi N, Fukuyama Y, Bryant D, Maitra A, Heda S, Fong KM, Thunnissen F, Minna JD, Gazdar AF (2000) Promoter Methylation and Silencing of the Retinoic Acid Receptor-{beta} Gene in Lung Carcinomas. J Natl Cancer Inst 92: 1303-1307
37 Yu N, Wang M (2008) Anticancer drug discovery targeting DNA hypermethylation. CurrMed Chem 15: 1350-1375
38 Mishra MV, Bisht, K.S., Sun, L., Muldoon-Jacobs, K., Awwad, R., Kaushal, A., Nguyen, P., Huang, L., Pennington, J.D., Markovina, S., Bradbury, C.M., and Gius, D. (2008) DNMTl as a molecular target in a multimodality-resistant phenotype in tumor cells. Mol Cancer Res 6: 243-249
39 Olson PE, Flechter JS, Philp PR (2001) Natural attenuation/phytoremediation in the vadose zone of a former industrial sludge basin. Environ Sci Pollut Res Int 8: 243- 249
40 Contreras-Ramos SM, Alvarez-Bemal D, Dendooven L (2006) Eisenia fetida increased removal of polycyclic aromatic hydrocarbons from soil. Enviromnental Pollution 141: 396-401
41 Liu SL, Luo YM, Cao ZH, Wu LH, Ding KQ, Christie P (2004) Degradation of benzo[a]pyrene in soil with arbuscular mycorrhizal alfalfa. Environ Geochem Health 26: 285-294
42 Rentz JA, Alvarez PJ, Schnoor JL (2005) Benzo[a]pyrene co-metabolism in the presence of plant root extracts and exudates: Implications for phytoremediation. Environ Pollut 136: 477-484
43 Yi H, Crowley D (2007) Biostimulation of PAH degradation with plants containing high concentrations of linoleic acid. Environ Sci Technol 41: 4382-4388
44 Bardi L, Martini C, Opsi F, Bertolone E, Belviso S, Masoero G, Marzona M, Marsan FA (2007) Cyclodextrin-enhanced in situ bioremediation of polyaromatic hydrocarbons-contaminated soils and plant uptake. J Incl Phenom Macrocycl Chem 57
45 Durmishidze, et al. (1974)
155
46 Buadze O, Durmishidze SV, Kakhaya MD, Zaalishvili G (1979) The study of the effect of different concentrations of benzidine, benzanthacene and 3,4-benzpyrene on root ultra-structure of maize. In SV Durmishidze, ed. Metabolism of Chemical Pollution of Biosphere in Plants. Metsniereba, Tbilisi, pp 179-195
47 Harms H, Langebartels C (1986) Standardized plant cell suspension test systems for an ecotoxicologic evaluation of the metabolic fate of xenobiotics. Plant Sci. 45: 157- 164
48 Harms H (1983) Uptake and conversion of three different 5-ring polycyclic aromatic hydrocarbons (PAHs) in cell suspension cultures of various Chenopodiaceae species. Z. Naturforsch. 38C: 382-386
49 Cemiglia CE (1992) Biodegradation of polycyclic aromatic hydrocarbons. Biodegradation 3: 351-368
50 Harbome IB (1979) Variation in and functional significance of phenolic conjugation in plants. Rec. Adv. Phytochem. 12: 457-474
51 Dohn DR, Krieger RI 0981) Oxidative metabolism of foreign compounds by higher plants. DrugMetab. Rev. 12: 119-157
52 Kuhn A, Ballach HI, Wittig R (2004) Studies in the biodegradation of 5 PAHs (Phenanthrene, pyrene, fluoranthene, chrysene und benzo(a)pyrene) in the presence of rooted poplar cuttings. Environmental Science and Pollution Research 11: 22-32
53 Brady CA, Gill RA, Lynch PT (2003) Preliminary evidence for the metabolism of benzo(a) pyrene by Plantago lanceolata. Environ Geochem Health 25: 131-137
54 Forrest, et al. (1989)55 Alvarez-Bemal D, Contreras-Ramos S, Marsch R, Dendooven L (2007) Influence of
Catclaw Mimosa monancistra on the Dissipation of Soil PAHS. International Journal of Phytoremediation 9: 79 - 90
56 Campbell S, Paquin D, Awaya JD, Li QX (2002) Remediation of benzo[a]pyrene and chrysene-contaminated soil with industrial hemp (Cannabis sativa). Int J Phytoremediation 4: 157-168
57 Jones KC, Grimmer G, Jacob J, Johnston AE (1989) Changes in the polynuclear aromatic hydrocarbon content of wheat grain and pasture grassland over the last century from one site in the U.K. Sci Total Environ 78: 117-130
58 Howsam M, Jones KC, Ineson P (2001) PAHs associated with the leaves of three deciduous tree species. II: uptake during a growing season. Chemosphere 44: 155-164
59 Fismes, et al. (2002)60 Pilon-Smits E (2005) Phytoremediation. Annu Rev Plant Biol 56: 15-3961 Wolf AE, Dietz KJ, Schroder P (1996) Degradation of glutathione S-conjugates by a
carboxypeptidase in the plant vacuole. FEBS Lett 384: 31-3462 Wild E DJ, Thomas GO, Jones KC. (2005) Direct observation of organic contaminant
uptake, storage, and metabolism within plant roots. Environ Sci Technol. 39: 3695- 3702
64 Huang X-D, El-Alawi Y, Penrose DM, Glick BR, Greenberg BM (2004) A multiprocess phytoremediation system for removal of polycyclic aromatic hydrocarbons from contaminated soils. Environmental Pollution 130: 465-475
156
65 Brady, et al. (2003)66 Meudec A, Dussauze J, Deslandes E, Poupart N (2006) Evidence for bioaccumulation
of PAHs within internal shoot tissues by a halophytic plant artificially exposed to petroleum-polluted sediments. Chemosphere 65: 474-482
67 Ataria, et al. (2007)68 McGarry MA, Charles GD, Medrano T, Bubb MR, Grant MB, Campbell-Thompson
M, Shiverick KT (2002) Benzo(a)pyrene, but not 2,3,7,8-tetrachlorodibenzo-p-dioxin, alters cell adhesion proteins in human uterine RL95-2 cells. Biochem Biophys Res Commun294: 101-107
69 Ames BN, McCann J, Yamasaki E (1975) Methods for detecting carcinogens and mutagens with the Salmonella/mammalian-microsome mutagenicity test. Mutat Res 31: 347-364
70 Kontir DM, Glance CA, Colby HD, Miles PR (1986) Effects of organic solvent vehicles on benzo[a]pyrene metabolism in rabbit lung microsomes. Biochem Pharmacol 35: 2569-2575
71 Friend C, Scher W, Holland JG, Sato T (1971) Hemoglobin synthesis in murine virus- induced leukemic cells in vitro: stimulation of erythroid differentiation by dimethyl sulfoxide. Proc Natl Acad Sci U S A 68: 378-382
72 Carla M, Cuomo M, Arcangeli A, Olivotto M (1995) Adsorption properties of polar/apolar inducers at a charged interface and their relevance to leukemia cell differentiation. Biophys J 68: 2615-2621
73 Yao B, Fu J, Hu E, Qi Y, Zhou Z (2007) The Cdc25A is involved in S-phase checkpoint induced by benzo(a)pyrene. Toxicology 237: 210-217
74 Wang Y-F, Fan L-M, Zhang W-Z, Zhang W, Wu W-H (2004) Ca2-l--Permeable Channels in the Plasma Membrane of Arabidopsis Pollen Are Regulated by Actin Microfilaments. Plant Physiol. 136: 3892-3904
75 Hernandez-Allica J, Becerril JM, Garbisu C (2008) Assessment of the phytoextraction potential of high biomass crop plants. Environmental Pollution 152: 32-40
77 Yi & Crowley (2007)78 Rohloff J, Bones AM (2005) Volatile profiling of Arabidopsis thaliana - Putative
olfactory compounds in plant communication. Phytochemistry 66: 1941-195579 Baird WM, Zennie TM, Ferin M, Chae YH, Hatchell J, Cassady JM (1988)
Glucolimnanthin, a plant glucosinolate, increases the metabolism and DNA binding of benzo[a]pyrene in hamster embryo cell cultures. Carcinogenesis 9: 657-660
80 Perocco P, lori R, Barillari J, Broccoli M, Sapone A, Affatato A, Paolini M (2002) In vitro induction of benzo(a)pyrene cell-transforming activity by the glucosinolate gluconasturtiin found in cruciferous vegetables. Cancer Lett 184: 65-71
81 Telang NT, Katdare M, Bradlow HL, Osborne MP, Fishman J (1997) Inhibition of proliferation and modulation of estradiol metabolism: novel mechanisms for breast cancer prevention by the phytochemical indole-3-carbinol. Proc Soc Exp Biol Med 216: 246-252
82 Laky B, Knasmuller S, Gminski R, Mersch-Sundermaim V, Scharf G, Verkerk R, Freywald C, Uhl M, Kassie F (2002) Protective effects of Brussels sprouts towards B[a]P-induced DNA damage: a model study with the single-cell gel electrophoresis (SCGE)/Hep G2 assay. Food Chem Toxicol 40: 1077-1083
83 Fahey JW, Haristoy X, Dolan PM, Kensler TW, Scholtus 1, Stephenson KK, Talalay P, Lozniewski A (2002) Sulforaphane inhibits extracellular, intracellular, and antibiotic-resistant strains of Helicobacter pylori and prevents benzo[a]pyrene- induced stomach tumors. Proc Natl Acad Sci U S A 99: 7610-7615
84 Kazerouni N, Sinha R, Hsu C-H, Greenberg A, Rothman N (2001) Analysis of 200 food items for benzo[a]pyrene and estimation of its intake in an epidemiologic study. Food and Chemical Toxicology 39: 423-436
85 Final Report, EuroBionet, European Network for the Assessment of Air Quality by the Use of Bioindicator Plants, University of Hohenheim, 2004. Accessed on 7/24/2005 at http://www.uni-hohenheim.de/eurobionet/Finalreport-eng/6-Results.pdf
86 The Arabidopsis Genome Initiative, (2000). "Analysis of the genome sequence of the flowering yiXavA Arabidopsis thaliana." Nature 408(6814): 796-815.
87 Bergkvist A, Forootan A, Zoric N, Strombom L, Sjoback R, Kubista M (2008) Tutorial: Choosing a Normalization Strategy for RT-PCR GenEx System Aids in the Selection of Reference Genes for Standardizing mRNA Measurements. Genetic Engineering & Biotechnology News 28
88 Balen B, Krsnik-Rasol M, Zamfir A, Milosevic J, Vakhrushev S, Peter-Katalinic J (2006 ) Glycoproteomic survey of Mammillaria gracillis tissues grown in vitro. JOURNAL OF PROTEOME RESEARCH 5: 1658-1666
89 Hakomori S (2001) Tumor-associated carbohydrate antigens defining tumor malignancy: basis for development of anti-cancer vaccines. Adv Exp Med Biol 491: 369-402
90 http ://www.arabidopsis. org/portals/genAnnotation/genome_snapshot.j sp91 Ma S, Gong Q, Bohnert HJ (2007) An Arabidopsis gene network based on the
graphical Gaussian model. Genome Res. 17: 1614-162592 Obayashi T KK, Nakai K, Shibaoka M, Hayashi S, Saeki M, Shibata D, Saito K, Ohta
H. (2007) ATTED-11: a database of co-expressed genes and cis elements for identifying co-regulated gene groups in Arabidopsis. Nucleic Acids Res.: D863-871
93 Thierry-Mieg DT-MaJ (2006) AceView: a comprehensive cDNA-supported gene and transcripts annotation. Genome Biology 7: S12
94 Bodour AA WJ, Brusseau ML, Maier RM (2003) Temporal change in culturable phenanthrene degraders in response to long-term exposure to phenanthrene in a soil column system. Environ Microbiol 5: 888-895
95 Allen-Jennings AE, Hartman MG, Kociba GJ, Hai T (2002) The Roles of ATF3 in Liver Dysfunction and the Regulation of Phosphoenolpyruvate Carboxykinase Gene Expression. J. Biol. Chem. 277: 20020-20025
96 Akerman GS, Rosenzweig BA, Domon OE, McGarrity LJ, Blankenship LR, Tsai CA, Culp SJ, MacGregor JT, Sistare FD, Chen JJ, Morris SM (2004) Gene expression profiles and genetic damage in benzo(a)pyrene diol epoxide-exposed TK6 cells. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 549: 43- 64
97 Alkio M, Tabuchi TM, Wang X, Colon-Carmona A (2005) Stress responses to polycyclic aromatic hydrocarbons in Arabidopsis include growth inhibition and hypersensitive response-like symptoms. J. Exp. Bot. 56: 2983-2994
98 Smith A, Nourizadeh S, Peer W, Xu J, Bandyopadhyay A, Murphy A, Goldsbourgh P (2003) Arabidopsis AtGSTF2 is regulated by ethylene and auxin, and encodes a glutathione S-transferase that interacts with flavonoids. The Plant Journal 36: 433- 442
99 Tanaka S, Brentner LB, Merchie KM, Schnoor JL, Yoon JM, Van Aken B (2007) Analysis of Gene Expression in Poplar Trees (Populus Deltoides x Nigra, DN34) Exposed to the Toxic Explosive Hexahydro-l,3,5-Trinitro-l,3,5-Triazine (RDX). International Journal of Phytoremediation 9: 15-30
100 Ohkama-Ohtsu N, Zhao P, Xiang C, Oliver DJ (2007) Glutathione conjugates in the vacuole are degraded by [gamma]-glutamyl transpeptidase GGT3 in Arabidopsis. The Plant Journal 49: 878-888
101 Lieberman MW, Wiseman AL, Shi ZZ, Carter BZ, Barrios R, Ou CN, Chevez- Barrios P, Wang Y, Habib GM, Goodman JC, Huang SL, Lebovitz RM, Matzuk MM (1996) Growth retardation and cysteine deficiency in gamma-glutamyl transpeptidase-deficient mice. Proc Natl Acad Sci U S A 93: 7923-7926
102 Schroder P, Scheer C, Diekmaim F, Stampfl A (2007) How plants cope with foreign compounds. Translocation of xenobiotic glutathione conjugates in roots of barley (Hordeum vulgare). Environ Sci Pollut Res Int 14: 114-122
103 Ekman DR, Lorenz WW, Przybyla AE, Wolfe NL, Dean JFD (2003) SAGE Analysis of Transcriptome Responses in Arabidopsis Roots Exposed to 2,4,6- Trinitrotoluene. Plant Physiol. 133: 1397-1406
104 Baerson SR, Sanchez-Moreiras A, Pedrol-Bonjoch N, Schulz M, Kagan LA, Agarwal AK, Reigosa MJ, Duke SO (2005) Detoxification and Transcriptome Response in Arabidopsis Seedlings Exposed to the Allelochemical Benzoxazolin- 2(3H)-one. J. Biol. Chem. 280: 21867-21881
105 Gaspar T (1995) The concept of cancer in in vitro plant cultures and the implication of habituation to hormones and hyperhydricity. Plant Tissue Cult Biotechnol. 1:126-136
106 Huebner R, Todaro G (1969) Oncogenes of RNA tumor viruses as determinants of cancer. Proc Natl Acad Sci U S A 64: 1087-1094
107 Sjolund R, Shih C (1970) Viruslike particles in nuclei of cultured plant cells which have lost the ability to differentiate. Proc Natl Acad Sci U S A 66: 25-31
108 Forrest, et al. (1989)109 Ishio S, Nakagawa H, Tomiyama T (1972) Algal cancer and its causes, II.
Separation of carcinogenic compounds from sea bottom mud polluted by wastes of the coal chemical industry. Bull Jpn Soc Sci Fish 38: 571-576
110 Ullrich Cl, Aloni R (2000) Vascularization is a general requirement for growth of plant and animal tumours. J. Exp. Bot. 51: 1951-1960
111 Ditt RF, Kerr KF, de Figueiredo P, Delrow J, Comai L, Nester EW (2006) The Arabidopsis thaliana transcriptome in response to Agrobacterium tumefaciens. Mol Plant Microbe Interact 19: 665-681
159
112 Deeken R, Engelmaim JC, Efetova M, Cziijak T, Muller T, Kaiser WM, Tietz O, Krischke M, Mueller MJ, Palme K, Dandekar T, Hedrich R (2006) An Integrated View of Gene Expression and Solute Profiles of Arabidopsis Tumors: A Genome- Wide Approach. Plant Cell 18: 3617-3634
113 Weiler E, Schroder J (1987) Hormone genes and crown gall disease. Trends in Biochemical Sciences 12: 271-275
114 Aloni R (1980) Role of auxin and sucrose in the differentiation of sieve and tracheary elements in plant tissue cultures. Planta 150: 255-263
115 Franchini G, Wong-Staal F, Baluda MA, Lengel C, Tronick SR (1983) Structural organization and expression of human DNA sequences related to the transforming gene of avian myeloblastosis virus. Proceedings of the National Academy of Sciences of the United States of America 80: 7385-7389
116 Janicke RU, Porter AG, Kush A (1998) A novel Arabidopsis thaliana protein protects tumor cells from tumor necrosis factor-induced apoptosis. Biochim Biophys Acta 1402: 70-78
117 Gorecka K, Konopka-Postupolska D, Hennig J, Buchet R, Pikula S (2005) Peroxidase activity of annexin 1 from Arabidopsis thaliana. Biochemical and Biophysical Research Communications 336: 868-875
118 Jami SK, Clark GB, Turlapati SA, Handley C, Roux SJ, Kirti PB Ectopic expression of an annexin from Brassica juncea confers tolerance to abiotic and biotic stress treatments in transgenic tobacco. Plant Physiology and Biochemistry In Press, Corrected Proof
119 Phillips (1983)120 Lee C-M, Chen S-Y, Lee Y-CG, Huang C-YF, Chen Y-MA (2006) Benzo[a]pyrene
and glycine N-methyltransferse Interactions: Gene expression profiles of the liver detoxification pathway. Toxicology and Applied Pharmacology 214: 126-135
121 Hockley SL, Arlt VM, Jahnke G, Hartwig A, Giddings I, Phillips DH (2008) Identification through microarray gene expression analysis of cellular responses to benzo(a)pyrene and its diol-epoxide that are dependent or independent of p52
122 Liu SL, Luo YM, Cao ZH, Wu LH, Ding KQ, Christie P (2004) Degradation of benzo[a]pyrene in soil with arbuscular mycorrhizal alfalfa. Environ Geochem Health 26: 285-293
123 Xing W, Luo Y, Wu L, Song J, Christie P (2006) Accumulation and phytoavailability of benzo[a]pyrene in an acid sandy soil. Environ Geochem Health 28: 153-158
124 Durmishidze SV, Devdariani TV, Kavtaradze LK, Kvartskhava L (1974) [Assimilation and transformation of 3,4-benzpyrene by plants in sterile conditions]. Dokl AkadNauk SSSR218: 1468-1471
125 Sage E, Haseltine W (1984) High ratio of alkali-sensitive lesions to total DNA modification induced by benzo(a)pyrene diol epoxide. J. Biol. Chem. 259: 11098- 11102
126 Cherpillod,etal. (1995)127 Chen,etal. (1998)
160
128 Graf W, Nowak W (1966) Promotion of growth in lower and higher plants by carcinogenic polycyclic aromatic compounds [in German], Arch Hyg Bakteriol 150: 513-528
129 Menke M, Chen I, Angelis KJ, Schubert I (2001) DNA damage and repair in Arabidopsis thaliana as measured by the comet assay after treatment with different classes of genotoxins. Mutat Res 493: 87-93
130 Garcia O, Mandina T, Lamadrid Al, Diaz A, Remigio A, Gonzalez Y, Piloto J, Gonzalez JE, Alvarez A (2004) Sensitivity and variability of visual scoring in the comet assay: Results of an inter-laboratory scoring exercise with the use of silver staining. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 556: 25-34
131 Walker TS, Bais HP, Halligan KM, Stermitz FR, Vivanco JM (2003) Metabolic profiling of root exudates of Arabidopsis thaliana. J Agric Food Chem 51: 2548- 2554
132 Qiu X (2000) Effects of plant flavonoids on the fate of polynuclear aromatic hydrocarbons in rhizosphere soil. Doctoral. West Virginia University, Morgantown, West Virginia
133 Jones K C,etal. (1989)134 Alvarez-Bemal, et al. (2007)135 Brady, et al. (2003)136 Gomes M, Santella R (1990) Immunologic methods for the detection of
benzo[a]pyrene metabolites in urine. Chem Res Toxicol 3: 307-310137 Plant A, Benson D, Smith L (1985) Cellular uptake and intracellular localization of
benzo(a)pyrene by digital fluorescence imaging microscopy. J. Cell Biol. 100: 1295-1308
138 Verdin A, Lounes-Hadj Sahraoui A, Newsam R, Robinson G, Durand R (2005) Polycyclic aromatic hydrocarbons storage by Fusarium solani in intracellular lipid vesicles. Environmental Pollution 133: 283-291
139 Maher VM LSJ, Straat PA, Ts'o PO. (1971) Mutagenic action, loss of transforming activity, and inhibition of deoxyribonucleic acid template activity in vitro caused by chemical linkage of carcinogenic polycyclic hydrocarbons to deoxyribonucleic acid. JBacteriol. 108: 202-212
140 Parodi S TM, Pala M, Santi L. (1981) Alkaline DNA fragmentation in vivo: borderline or negative results obtained respectively with 7,12- dimethylbenz[a]anthracene and benzo[a]pyrene. Tumori 67: 87-93
141 Barnes I, Hjorth J, Mihalopoulos N (2006) Dimethyl Sulfide and Dimethyl Sulfoxide and Their Oxidation in the Atmosphere. Chem. Rev. 106: 940-975
142 Rundell M, Wagner E, Plewa M (2003) The comet assay: genotoxic damage or nuclear fragmentation? Environ Mol Mutagen 42: 61-67
143 Chandna S (2004) Single-cell gel electrophoresis assay monitors precise kinetics of DNA fragmentation induced during programmed cell death. Cytometry Part A 61 A:127-133
144 Hartmann A AE, Beevers C, Brendler-Schwaab S, Burlinson B, Clay P, Collins A, Smith A, Speit G, Thybaud V, Tice RR (2003) Recommendations for conducting
161
the in vivo alkaline comet assay. 4th International Comet Assay Workshop. Mutagenesis 18; 45-51
145 Menke, et al. (2001)146 Olive P, Durand R (2005) Heterogeneity in DNA damage using the comet assay.
Cytometry Part A 66A: 1 -8147 Buchmann CA, Nersesyan A, Kopp B, Schauberger D, Darroudi F, Grummt T,
Krupitza G, Kundi M, Schulte-Hermann R, Knasmueller S (2007) Dihydroxy-7- methoxy-1,4-benzoxazin-3 -one (DIMBOA) and 2,4-dihydroxy-1,4-benzoxazin-3 - one (DIBOA), two naturally occurring benzoxazinones contained in sprouts of Gramineae are potent aneugens in human-derived liver eells (HepG2). Cancer Letters 246; 290-299
148 Comet Assay Forum posts, 2003-2005. http://www.comet.itreindia.org/index.asp.149 Speit G, Witton-Davies T, Heepchantree W, Trenz K, Hoffmaim H (2003)
Investigations on the effect of cigarette smoking in the comet assay. Mutation Research/Genetic Toxicology and Environmental Mutagenesis 542: 33-42
150 Koppen G, Toncelli LM, Triest L, Verschaeve L (1999) The comet assay: a tool to study alteration of DNA integrity in developing plant leaves. Mech Ageing Dev 110;13-24
151 Gichner T, Plewa MJ (1998) Induction of somatic DNA damage as measured by single cell gel electrophoresis and point mutation in leaves of tobacco plants. Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis 401: 143-152
152 Gichner T, Lovecka P, Kochankova L, Mackova M, Demnerova K (2007) Monitoring toxicity, DNA damage, and somatic mutations in tobacco plants growing in soil heavily polluted with polychlorinated biphenyls. Mutation Research/Genetic Toxicology and Environmental Mutagenesis 629: 1-6
153 Corpe W, Basile D (1982) Methanol-utilizing bacteria associated with green plants. Dev Ind Microbiol 23: 483^93
154 Koenig RL, Morris RO, Polacco JC (2002) tRNA is the source of low-level trans- zeatin production in Methylobacterium spp. J Bacteriol 184; 1832-1842
155 Bodour, et al. (2003)156 Andreoni V, Cavalca L, Rao MA, Nocerino G, Bemasconi S, DellAmico E,
Colombo M, Gianfreda L (2004) Bacterial communities and enzyme activities of PAHs polluted soils. Chemosphere 57: 401-412
157 Huang X-D, El-Alawi Y, Penrose DM, Glick BR, Greenberg BM (2004) A multiprocess phytoremediation system for removal of polycyclic aromatic hydrocarbons from contaminated soils. Environmental Pollution 130: 465-477
158 Huang, et al. (2004)159 Boyes DC, Zayed AM, Ascenzi R, McCaskill AJ, Hoffman NE, Davis KR, Gorlach
J (2001) Growth Stage-Based Phenotypic Analysis of Arabidopsis: A Model for High Throughput Functional Genomics in Plants. Plant Cell 13: 1499-1510
160 Moreno RL, Goosen T, Kent UM, Chung F-L, Hollenberg PF (2001) Differential Effects of Naturally Occurring Isothiocyanates on the Activities of Cytochrome P450 2E1 and the Mutant P450 2E1 T303A. Archives of Biochemistry and Biophysics 391: 99-110
162 Rulli SJ, Jr, Arikawa E, Yang J (2008) Cross-platform comparisons of algorithms for calculating real-time PCR amplification efficiencies. FASEB J. 22: 621.625
163 Rhee SY, Beavis W, Berardini TZ, Chen G, Dixon D, Doyle A, Garcia-Hemandez M, Huala E, Lander G, Montoya M, Miller N, Mueller LA, Mundodi S, Reiser L, Tacklind J, Weems DC, Wu Y, Xu I, Yoo D, Yoon J, Zhang P (2003) The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community. Nucleic Acids Res 31: 224-228
164 Obayashi, et al. (2007)165 Yanaka N (2007) Mammalian Glycerophosphodiester Phosphodiesterases.
Bioscience, Biotechnology, and Biochemistry 71: 1811-1818166 Kadkhoda K, Pourpak Z, Akbar Pourfathallah A, Kazemnejad A (2004) The ex
vivo study of synergistic effects of polycyclic aromatic hydrocarbon, benzo(a)pyrene with ovalbumin on systemic immune responses by oral route. Toxicology 199: 261-265
167 Burchiel SW, Lauer FT, McDonald JD, Reed MD (2004) Systemic immunotoxicity in AJ mice following 6-month whole body inhalation exposure to diesel exhaust. Toxicology and Applied Pharmacology 196: 337-345
168 Wiese FW, Thompson PA, Kadlubar FF (2001) Carcinogen substrate specificity of human COX-1 and COX-2. Carcinogenesis 22: 5-10
169 Diaz AR, A.M.; Jimenez, S.A. (1992) Alternative splicing of human prostaglandin G/H synthase mRNA and evidence of differential regulation of the resulting transcripts by transforming growth factor beta-1, interleukin 1-beta, and tumor necrosis factor alpha. J. Biol. Chem. 267: 10816-10822
170 Tsujii M, Kawano S, Tsuji S, Sawaoka H, Hori M, DuBois RN (1998) Cyclooxygenase regulates angiogenesis induced by colon cancer cells. Cell 93: 705- 716
171 Hamberg M, Sanz A, Castresana C (1999) alpha-oxidation of fatty acids in higher plants. Identification of a pathogen-inducible oxygenase (piox) as an alpha- dioxygenase and biosynthesis of 2-hydroperoxylinolenic acid. J Biol Chem 274: 24503-24512
172 Camarero S, Canas Al, Nousiainen P, Record E, Lomascolo A, Martinez MJ, Martinez AT (2008) p-Hydroxycinnamic Acids as Natural Mediators for Laccase Oxidation of Recaleitrant Compounds. Environ. Sci. Technol. 42: 6703-6709
173 van der Trenck T, Sandermann HJ (1981) Incorporation of benzo[alpha]pyrene quinones into lignin. FEBS Lett. 125: 72-77
174 Passardi F, Cosio C, Penel C, Dunand C (2005) Peroxidases have more functions than a Swiss army knife. Plant Cell Reports 24: 255-264
175 Schopfer P, Liszkay A, Bechtold M, Frahry G, Wagner A (2002) Evidence that hydroxyl radicals mediate auxin-induced extension growth. Planta 214: 821-828
176 Abercrombie JM, Halfhill MD, Ranjan P, Rao MR, Saxton AM, Yuan JS, Stewart CN, Jr. (2008) Transcriptional responses of Arabidopsis thaliana plants to As (V) stress. BMC Plant Biol 8: 87
163
177 Welinder K, Justesen A, Kjaersgard I, Jensen R, Rasmussen S, Jespersen H, Duroux L (2002) Structural diversity and transcription of class III peroxidases from Arabidopsis thaliana. European Journal of Biochemistry 269: 6063-6081
178 Baerson, et al. (2005)179 Weston D, Gunter L, Rogers A, Wullschleger S (2008) Connecting genes,
coexpression modules, and molecular signatures to environmental stress phenotypes in plants. BMC Systems Biology 2: 16
180 Cole S, Bhardwaj G, Gerlach J, Mackie J, Grant C, Almquist K, Stewart A, Kurz E, Duncan A, Deeley R (1992) Overexpression of a transporter gene in a multidrug- resistant human lung cancer cell line. Science 256: 1650-1654
181 Calcagno AM, Fostel JM, To KK, Salcido CD, Martin SE, Chewning KJ, Wu CP, Varticovski L, Bates SE, Caplen NJ, Ambudkar SV (2008) Single-step doxorubicin- selected cancer cells overexpress the ABCG2 drug transporter through epigenetic changes. Br J Cancer 98: 1515-1524
182 Tommasini R, Vogt E, Schmid J, Fromentau M, Amrhein N, Martinoia E (1997) Differential expression of genes coding for ABC transporters after treatment of Arabidopsis thaliana with xenobiotics. FEBS Letters 411: 206-208
183 Yang XP, Freeman LA, Knapper CL, Amar MJ, Remaley A, Brewer HB, Jr., Santamarina-Fojo S (2002) The E-box motif in the proximal ABCAl promoter mediates transcriptional repression of the ABCAl gene. J Lipid Res 43: 297-306
184 Wagner BL, Valledor AF, Shao G, Daige CL, Bischoff ED, Petrowski M, Jepsen K, Baek SH, Heyman RA, Rosenfeld MG, Schulman IG, Glass CK (2003) Promoter- specific roles for liver X receptor/corepressor complexes in the regulation of ABCAl and SREBPl gene expression. Mol Cell Biol 23: 5780-5789
185 Hagen SG, Monroe DG, Dean DM, Sanders MM (2000) Repression of chick multidrug resistance-associated protein 1 (chMRPl) gene expression by estrogen. Gene 257: 243-249
186 http://www.cazy.org/fam/GH17.html. Accessed 10/13/08.187 http://bbc.botany.utoronto.ca/efip188 Hincha DK, Meins Jr F, Schmitt JM (1997) [beta]-l,3-Glucanase Is Cryoprotective
in Vitro and Is Accumulated in Leaves during Cold Acclimation. Plant Physiol 114: 1077-1083
189 Shibuya N, Minami E (2001) Oligosaccharide signalling for defence responses in plant. Physiological and Molecular Plant Pathology 59: 223-233
190 Hakomori S-i (2008) Structure and function of glycosphingolipids and sphingolipids: Recollections and future trends. Biochimica et Biophysica Acta (BBA) - General Subjects. Glycobiology and Sphingobiology 1780: 325-346
191 http://prevention.cancer.gov/programs-resources/groups/cb/programs/glycome,192 Suzuki A, Shijubo N, Yamada G, Ichimiya S, Satoh M, Abe S, Sato N (2005)
Napsin A is useful to distinguish primary lung adenocarcinoma from adenocarcinomas of other organs. Pathol Res Pract 201: 579-586
193 Simoes I, Mueller EC, Otto A, Bur D, Cheung AY, Faro C, Pires E (2005) Molecular analysis of the interaction between cardosin A and phospholipase D(alpha). Identification of RGD/KGE sequences as binding motifs for C2 domains. Febs J 272: 5786-5792
194 Knoepp SM, Chahal MS, Xie Y, Zhang Z, Brauner DJ, Hallman MA, Robinson SA, Han S, Imai M, Tomlinson S, Meier KE (2008) Effects of Active and Inactive Phospholipase D2 on Signal Transduction, Adhesion, Migration, Invasion, and Metastasis in EL4 Lymphoma Cells. Mol Pharmacol 74: 574-584
195 Slaaby R, Jensen T, Hansen HS, Frohman MA, Seedorf K (1998) PLD2 Complexes with the EGF Receptor and Undergoes Tyrosine Phosphorylation at a Single Site upon Agonist Stimulation. J. Biol. Chem. 273: 33722-33727
196 Bill HM, Knudsen B, Moores SL, Muthuswamy SK, Rao VR, Brugge JS, Miranti CK (2004) Epidermal Growth Factor Receptor-Dependent Regulation of Integrin- Mediated Signaling and Cell Cycle Entry in Epithelial Cells. Mol. Cell. Biol. 24: 8586-8599
197 Ohri S, Vashishta A, Proctor M, Fusek M, Vetvicka V (2008) The propeptide of cathepsin D increases proliferation, invasion and metastasis of breast cancer cells. International Journal of Oncology 32: 491-498
198 Perchick GB, Jabbour HN (2003) Cyclooxygenase-2 Overexpression Inhibits Cathepsin D-Mediated Cleavage of Plasminogen to the Potent Antiangiogenic Factor Angiostatin. Endocrinology 144: 5322-5328
199 Payie KG, Tanaka T, Gal S, Yada RY (2003) Constmction, expression and characterization of a chimaeric mammalian-plant aspartic proteinase. Biochem. J. 372: 671-678
200 Poulos AR, E.; Shankaran, P.; Callahan, J. W. (1984) Studies on the activation of the enzymatic hydrolysis of sphingomyelin liposomes. Biochim. Biophys. Acta 793: 141-148
201 Yuan WQ, X.; Tsang, P.; Kang, S.-J.; Illaniorov, P. A.; Besra, G. S.; Gumperz, J.; Cresswell, P. (2007) Saposin B is the dominant saposin that facilitates lipid binding to human CD Id molecules. Proc. Nat. Acad. Sci. 104: 5551-5556
202 Egas C, Lavoura N, Resende R, Brito RMM, Pires E, de Lima MCP, Faro C (2000) The Saposin-like Domain of the Plant Aspartic Proteinase Precursor Is a Potent Inducer of Vesicle Leakage. J. Biol. Chem. 275: 38190-38196
203 Ruysschaert JM, Goormaghtigh E, Homble F, Andersson M, Liepinsh E, Otting G (1998) Lipid membrane binding of NK-lysin. FEBS Lett 425: 341-343
204 Ramalho-Santos M VP, Cortes L, Samyn B, Van Beeumen J, Pires E, Faro C (1998) Identification and proteolytic processing of procardosin A. Eur J Biochem. 255: 133-138
205 Akiyama M, Maki H, Sekiguchi M, Horiuchi T (1989) A specific role of MutT protein: to prevent dG.dA mispairing in DNA replication. Proceedings of the National Academy of Sciences of the United States of America 86: 3949-3952
206 Mo JY, Maki H, Sekiguchi M (1992) Hydrolytic elimination of a mutagenic nucleotide, 8-oxodGTP, by human 18-kilodalton protein: sanitization of nucleotide pool. Proceedings of the National Academy of Sciences of the United States of America 89: 11021-11025
207 Murphy P, Knee R (1994) Identification and characterization of an antisense RNA transcript (gfg) from the human basic fibroblast growth factor gene. Mol Endocrinol 8: 852-857
165
208 Baguma-Nibasheka M, Li AW, Murphy PR (2007) The fibroblast growth factor-2 antisense gene inhibits nuclear accumulation of FGF-2 and delays cell cycle progression in C6 glioma cells. Mol Cell Endocrinol 267: 127-136
209 Asa SL, Ramyar L, Murphy PR, Li AW, Ezzat S (2001) The Endogenous Fibroblast Growth Factor-2 Antisense Gene Product Regulates Pituitary Cell Growth and Hormone Production. Mol Endocrinol 15: 589-599
210 Ogawa T, Ueda Y, Yoshimura K, Shigeoka S (2005) Comprehensive analysis of cytosolic Nudix hydrolases'm Arabidopsis thaliana. J Biol Chem 280: 25277-25282
211 Ge X, Li G-J, Wang S-B, Zhu H, Zhu T, Wang X, Xia Y (2007) AtNUDT7, a Negative Regulator of Basal Immimity in Arabidopsis, Modulates Two Distinct Defense Response Pathways and Is Involved in Maintaining Redox Homeostasis. Plant Physiol. 145:204-215
212 Bartsch M, Gobbato E, Bednarek P, Debey S, Schultze JL, Bautor J, Parker JE(2006) Salicylic acid-independent ENHANCED DISEASE SUSCEPTIBILITY 1 signaling in Arabidopsis immunity and cell death is regulated by the monooxygenase FMOl and the Nudix hydrolase NUDT7. Plant Cell 18: 1038-1051
213 Baguma-Nibasheka, et al. (2007)214 Jambunathan N, Mahalingam R (2006) Analysis of Arabidopsis Growth Factor
Gene 1 (GFGl) encoding a nudix hydrolase during oxidative signaling. Planta 224: 1-11
215 Singhal, et al. (2008)216 Murphy, et al. (1994)217 Asa, etal. (2001)218 Yokota J, Tsunetsugu-Yokota Y, Battifora H, Le Fevre C, Cline MJ (1986)
Alterations of myc, myb, and rasHa proto-oncogenes in cancers are frequent and show clinical correlation. Science 231: 261-265
219 Yanhui C, Xiaoyuan Y, Kun H, Meihua L, Jigang L, Zhaofeng G, Zhiqiang L, Yunfei Z, Xiaoxiao W, Xiaoming Q, Yunping S, Li Z, Xiaohui D, Jingchu L, Xing- Wang D, Zhangliang C, Hongya G, Li-Jia Q (2006) The MYB Transcription Factor Superfamily of Arabidopsis: Expression Analysis and Phylogenetic Comparison with the Rice MYB Family. Plant Molecular Biology 60: 107-124
220 Stracke R, Werber M, Weisshaar B (2001) The R2R3-MYB gene family in Arabidopsis thaliana. Current Opinion in Plant Biology 4: 447-456
221 Taki N, Sasaki-Sekimoto Y, Obayashi T, Kikuta A, Kobayashi K, Ainai T, Yagi K, Sakurai N, Suzuki H, Masuda T, Takamiya K, Shibata D, Kobayashi Y, Ohta H (2005) 12-oxo-phytodienoic acid triggers expression of a distinct set of genes and plays a role in wound-induced gene expression in Arabidopsis. Plant Physiol 139: 1268-1283
222 Jin H, Cominelli E, Bailey P, Parr A, Mehrtens F, Jones J, Tonelli C, Weisshaar B, Martin C (2000) Transcriptional repression by AtMYB4 controls production of UV- protecting sunscreens in Arabidopsis. EMBO J 19: 6150-6161
223 Ruegger M, Meyer K, Cusumano JC, Chappie C (1999) Regulation of Ferulate-5- Hydroxylase Expression in Arabidopsis in the Context of Sinapate Ester Biosynthesis. Plant Physiol. 119: 101-110
166
224 Fabbri M, Delp G, Schmidt O, Theopold U (2000) Animal and Plant Members of a Gene Family with Similarity to Alkaloid-Synthesizing Enzymes. Biochemical and Biophysical Research Communications 271: 191-196
225 Theopold U, Samakovlis C, Erdjument-Bromage H, Dillon N, Axelsson B, Schmidt O, Tempst P, Hultmark D (1996) Helix pomatia lectin, an inducer of Drosophila immune response, binds to hemomucin, a novel surface mucin. J Biol Chem 271: 12708-12715
226 Albrektsen T, Richter HE, Clausen JT, Fleckner J (2001 ) Identification of a novel integral plasma membrane protein induced during adipocyte differentiation. Biochem. J. 359: 393-402
227 Facchini PJ, Bird DA, St-Pierre B (2004) Can Arabidopsis make complex alkaloids? Trends in Plant Science 9: 116-122
228 Luijendijk TJC, Vandermeijden, E., and Verpoorte, R. (1996) Involvement of strictosidine as a defensive chemical in Catharanthus
229 Parrish AR, Fisher R, Bral CM, Burghardt RC, Gandolfi AJ, Brendel K, Ramos KS (1998) Benzo(a)pyrene-induced alterations in growth-related gene expression and signaling in precision-cut adult rat liver and kidney slices. Toxicol Appl Pharmacol 152: 302-308
230 Gwinn MR, Weston A (2008) Application of oligonucleotide microarray technology to toxic occupational exposures. J Toxicol Environ Health A 71: 315- 324
231 Bols NC, Schirmer K, Joyce EM, Dixon DG, Greenberg BM, Whyte JJ (1999) Ability of Polycyclic Aromatic Hydrocarbons to Induce 7-Ethoxyresorufm-o- deethylase Activity in a Trout Liver Cell Line. Ecotoxicology and Environmental Safety 44: 118-128
232 Houser WH, Raha A, Vickers M (1992) Induction of CYPlAl gene expression in H4-II-E rat hepatoma cells by benzo[e]pyrene. Mol Carcinog 5: 232-237
233 Piskorska-Pliszczynska J, Keys B, Safe S, Newman MS (1986) The cytosolic receptor binding affinities and AHH induction potencies of 29 polynuclear aromatic hydrocarbons. Toxicol Lett 34: 67-74
234 Ahn S, Wemer D, Luthy R (2005) Physicochemical characterization of coke-plant soil for the assessment of polycyclic aromatic hydrocarbon availability and the feasibility of phytoremediation. Environ Toxicol Chem. 24: 2185-2195
235 Ataria JM, O'Halloran K, Gooneratne R (2007) Hepatic and immune biological effect assays in C57BL/6 mice to measure polycyclic aromatic hydrocarbon bioavailability under laboratory exposures with increasing environmental relevance. Environ Sci Pollut Res Int 14: 256-265
236 Zuker M (2003) Mfold web server for nucleic acid folding and hybridization prediction. Nucl. Acids Res. 31: 3406-3415
237 Winter D, Vinegar B, Nahal H, Ammar R, Wilson G, Provart N (2007) An "electronic fluorescent pictograph" browser for exploring and analyzing large-scale biological data sets. PLoS ONE 2: e717
238 Vandesompele J, De Preter K, Pattyn F, Poppe B, Van Roy N, De Paepe A, Speleman F (2002) Accurate normalization of real-time quantitative RT-PCR data
167
by geometric averaging of multiple internal control genes. Genome Biology 3: research0034.0031 - research0034.0011
239 Zhao & Femald RD (2005)240 The Database of Arabidopsis Transcription Factors, http://datf.cbi.pku.edu.cn/241 Dolwick K, Swanson H, Bradfield C (1993) In vitro analysis of Ah receptor
domains involved in ligand-activated DNA recognition. Proc. Natl. Acad. Sci. 90: 8566-8570
242 Pandini A, Denison MS, Song Y, Soshilov AA, Bonati L (2007) Structural and Functional Characterization of the Aryl Hydrocarbon Receptor Ligand Binding Domain by Homology Modeling and Mutational Analysis. Biochemistry 46: 696- 708
243 Crews ST (1998) Control of cell lineage-specific development and transcription by bHLH-PAS proteins. Genes Dev. 12: 607-620
244 Pogue-Geile KL, Lyons-Weiler J, Whitcomb DC (2006) Molecular overlap of fly circadian rhythms and human pancreatic cancer. Cancer Letters 243: 55-57
245 Mukai M, Lin T-M, Peterson RE, Cooke PS, Tischkau SA (2008) Behavioral Rhythmicity of Mice Lacking AhR and Attenuation of Light-Induced Phase Shift by 2,3,7,8-Tetrachlorodibenzo-p-Dioxin. J Biol Rhythms 23: 200-210
246 Olnes MJ, Verma M, Kurl RN (1996) 2,3,7,8-tetrachlorodibenzo-p-dioxin modulates expression of the prostaglandin G/H synthase-2 gene in rat thymocytes. Journal of Pharmacology and Experimental Therapeutics 279: 1566-1573
247 Sawaya R, Riddick D (2008) Cytochrome P4502C11 5 '-flanking region and promoter: Regulation by aromatic hydrocarbons in vitro. Toxicology 248: 104-112
248 Boesch JS, Miskimins R, Miskimins WK, Lindahl R (1999) The Same Xenobiotic Response Element Is Required for Constitutive and Inducible Expression of the Mammalian Aldehyde Dehydrogenase-3 Gene. Archives of Biochemistry and Biophysics 361: 223-230
249 Palermo CM, Westlake CA, Gasiewicz TA (2005) Epigallocatechin Gallate Inhibits Aryl Hydrocarbon Receptor Gene Transcription through an Indirect Mechanism Involving Binding to a 90 kDa Heat Shock Protein†. Biochemistry 44: 5041-5052
250 Sawa M, Nusinow DA, Kay SA, Imaizumi T (2007) FKFl and GIGANTEA Complex Formation Is Required for Day-Length Measurement in Arabidopsis. Science 318: 261-265
251 Weston, et al. (2008)252 Nelson R, Demas G (1996) Seasonal changes in immune function. Q Rev Biol 71:
511-548253 Nelson R, Drazen D (2000) Melatonin mediates seasonal changes in immune
function. Ann N Y Acad Sci 917: 404-415254 Bieniawska Z, Espinoza C, Schlereth A, Sulpice R, Hincha DK, Hannah MA (2008)
Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcrip tome. Plant Physiol 147: 263-279
255 Covington MF, Harmer SL (2007) The circadian clock regulates auxin signaling and responses in Arabidopsis. PLoS Biol 5: e222
256 Michael T, McClung C (2003) Enhancer trapping reveals widespread circadian clock transcriptional control in Arabidopsis. Plant Physiol 132: 629-639
257 Forrest, et al. (1989)258 Reinert(1952)259 Mukai, et al. (2008)260 Gachon F (2007) Physiological function of PARbZip circadian clock-controlled
transcription factors. Annals of Medicine 39: 562 - 571261 Bergander L, Wahlstrom N, Alsberg T, Bergman J, Rannug A, Rannug U (2003)
Characterization of in vitro metabolites of the aryl hydrocarbon receptor ligand 6- formylindolo[3,2-b]carbazole by liquid chromatography-mass spectrometry and NMR. Drug Metab Dispos 31: 233-241
262 Mukai M, Tischkau SA (2007) Effeets of Tryptophan Photoproduets in the Circadian Timing System: Searching for a Physiological Role for Aryl Hydrocarbon Receptor. Toxicol. Sci. 95: 172-181
263 Tan D-X, Manchester EC, Di Mascio P, Martinez GR, Prado FM, Reiter RJ (2007) Novel rhythms of N1-acetyl-N2-formyl-5-methoxykynuramine and its precursor melatonin in water hyaeinth: importance for phytoremediation. FASEB J. 21: 1724- 1729
264 Amao M, and Hemandez-Ruiz, J. (2007) Melatonin promotes adventitious and lateral root regeneration in etiolated hypocotyls of Lupinus albus L. J. Pineal Res. 42: 147-152
265 Tan DX, Manchester EC, Reiter RJ, Qi WB, Karbownik M, Calvo JR (2000) Significance of melatonin in antioxidative defense system: reactions and products. Biol. Signals. Recept. 9: 137-159
266 Hemandez-Ruiz J, Cano A, Amao MB (2005) Melatonin acts as a growth- stimulating compound in some monocot species. J Pineal Res 39: 137-142
267 Schaller GE, Kieber JJ (2002) Ethylene. The Arabidopsis Book268 Abeles FB, Forrence LE, Leather GR (1971) Ethylene Air Pollution: Effects of
Ambient Levels of Ethylene on the Glucanase Content of Bean Leaves. Plant Physiol. 48: 504-505
269 Pang Z, Otaka K, Maoka T, Hidaka K, Ishijima S, Oda M, Ohnishi M (2005)Stmcture of beta-Glucan Oligomer from Laminarin and Its Effect on HumanMonocytes to Inhibit the Proliferation of U937 Cells. Bioscience, Biotechnology, and Biochemistry 69: 553-558
270 Baerson, et al. (2005)271 Bmce TJA, Matthes MC, Chamberlain K, Woodcock CM, Mohib A, Webster B,
Smart LE, Birkett MA, Pickett JA, Napier JA (2008) cis -Jasmone inducesArabidopsis genes that affect the chemieal ecology of multitrophic interactions with aphids and their parasitoids. Proceedings of the National Academy of Sciences 105: 4553-4558
272 Gerk PM, Vore M (2002) Regulation of Expression of the Multidmg Resistance- Associated Protein 2 (MRP2) and Its Role in Dmg Disposition. J Pharmacol Exp Ther302:407-415
273 Bock K, Eckle T, Ouzzine M, Foumel-Gigleux S (2000) Coordinate induction by antioxidants of UDP-glucuronosyltransferase UGT1A6 and the apical conjugate
169
export pump MRP2 (multidrug resistance protein 2) in Caco-2 cells. Biochem Pharmacol 59: 467-470
274 Paliwal S (2005) Induction of cancer-specific cytotoxicity towards human prostate and skin cells using quercetin and ultrasound. British Journal of Cancer 92: 499- 502
275 Hong Z, Zhang Z, Olson JM, Verma DPS (2001) A Novel UDP-Glucose Transferase Is Part of the Callose Synthase Complex and Interacts with Phragmoplastin at the Forming Cell Plate. Plant Cell 13: 769-780
276 Blanco F, Garreton V, Frey N, Dominguez C, Perez-Acle T, Van der Straeten D, Jordana X, Holuigue L (2005) Identification of NPRl-Dependent and Independent Genes Early Induced by Salicylic Acid Treatment in Arabidopsis. Plant Molecular Biology 59: 927-944
277 Eudes A, Bozzo GG, Waller JC, Naponelli V, Lim E-K, Bowles DJ, Gregory JF, III, Hanson AD (2008) Metabolism of the Folate Precursor p-Aminobenzoate in Plants: GLUCOSE ESTER FORMATION AND VACUOLAR STORAGE J. Biol. Chem. 283: 15451-15459
278 Lim E-K, Doucet C, Hou B, Jackson R, Abrams S, Bowles D (2005) Resolution of (-i-)-abscisic acid using an Arabidopsis glycosyltransferase. TETRAHEDRON ASYMMETRY 16: 143
279 Wu C-T, Bradford KJ (2003) Class I Chitinase and {beta}-l,3-Glucanase Are Differentially Regulated by Wounding, Methyl Jasmonate, Ethylene, and Gibberellin in Tomato Seeds and Leaves. Plant Physiol. 133: 263-273
280 Shibuya & Minami (2001)281 Saiki I (1997) Cell adhesion molecules and cancer metastasis. Jpn J Pharmacol 75:
215-242282 Pasqualini R, Koivunen E, Ruoslahti E. v Integrins as receptors for tumor targeting
hy circulating ligands. Nat Biotechnol. 1997;15:542-546.283 Nagarajan SR, Devadas B, Malecha JW, Lu HF, Ruminski PG, Rico JG, Rogers
TE, Marrufo LD, Collins JT, Kleine HP, Lantz MK, Zhu J, Green NF, Russell MA, Landis BH, Miller LM, Meyer DM, Duffin TD, Engleman VW, Finn MB, Freeman SK, Griggs DW, Williams ML, Nickols MA, Pegg JA, Shannon KE, Steininger C, Westlin MM, Nickols GA, Keene JL (2007) R-isomers of Arg-Gly-Asp (RGD) mimics as potent alphavbeta3 inhibitors. Bioorg Med Chem 15: 3783-3800
284 Simoes, et al. (2005)285 Cliften P, Sudarsanam P, Desikan A, Fulton L, Fulton B, Majors J, Waterston R,
Cohen BA, Johnston M (2003) Finding Functional Features in Saccharomyces Genomes by Phylogenetic Footprinting. Science 301: 71-76
286 Ma S, Bohnert HJ (2007) Integration of Arabidopsis thaliana stress-related transcript profiles, promoter structures, and cell-specific expression. Genome Biol 8: R49
287 Hansen J. Increased breast cancer risk among women who work predominantly at night. Epidemiology. 2001;12:74-77.
288 Xiang S, Coffelt S, Mao L, Yuan L, Cheng Q, Hill S (2008) Period-2: a tumor suppressor gene in breast cancer. Journal of Circadian Rhythms 6: 4
170
289 Gery S, Virk RK, Chumakov K, Yu A, Koeffler HP (2007) The clock gene Per2 links the circadian system to the estrogen receptor. Oncogene 26: 7916-7919
290 Sawa, et al. (2007)291 Ohtake F, Baba A, Takada I, Okada M, Iwasaki K, Miki H, Takahashi S,
Kouzmenko A, Nohara K, Chiba T, Fujii-Kuriyama Y, Kato S (2007) Dioxin receptor is a ligand-dependent E3 ubiquitin ligase. Nature 446: 562-566
292 Alabadi D, Oyama T, Yanovsky MJ, Harmon FG, Mas P, Kay SA (2001) Reciprocal Regulation Between TOCl and LHY/CCAl Within the Arabidopsis Circadian Clock. Science 293: 880-883
293 Oklejewicz M, Destici E, Tamanini F, Hut RA, Janssens R, van der Horst GTJ (2008) Phase Resetting of the Mammalian Circadian Clock by DNA Damage. Current Biology 18: 286-291
294 Fu Z, Guo M, Jeong B, Tian F, Elthon T, Cemy R, Staiger D, Alfano J (2007) A type III effector ADP-ribosylates RNA-binding proteins and quells plant immunity. Nature 447: 284-288
295 Hamid AA, Mandai M, Fujita J, Nanbu K, Kariya M, Kusakari T, Fukuhara K, Fujii S (2003) Expression of cold-inducible RNA-binding protein in the normal endometrium, endometrial hyperplasia, and endometrial carcinoma. Int J Gynecol Pathol 22: 240-247
296 Sheikh MS, Carrier F, Papathanasiou MA, Hollander MC, Zhan Q, Yu K, Fomace Jr. AJ (1997) Identification of Several Human Homologs of Hamster DNA Damage-inducible Transcripts. Cloning and characterization of a novel UV- inducible cDNA that codes for a putative RNA-binding protein. J Biol Chem 272: 26720-26726
297 Wellmann S, Buhrer C, Moderegger E, Zelmer A, Kirschner R, Koehne P, Fujita J, Seeger K (2004) Oxygen-regulated expression of the RNA-binding proteins RBM3 and CIRP by a HIF-1-independent mechanism. J Cell Sci 117: 1785-1794
298 De Leeuw F, Zhang T, Wauquier C, Huez G, Kruys V, Gueydan C (2007) The cold-inducible RNA-binding protein migrates from the nucleus to cytoplasmic stress granules by a methylation-dependent mechanism and acts as a translational repressor. Experimental Cell Research 313: 4130-4144
299 Aoki K, Ishii Y, Matsumoto K, Tsujimoto M (2002) Methylation of Xenopus CIRP2 regulates its arginine- and glycine-rich region-mediated nucleocytoplasmic distribution. Nucleic Acids Res 30: 5182-5192
300 Scebba F, Morena De Bastiani GB, Andrea Andreucci, Alvaro Galli, Letizia Pitto,(2007) PRM Tll: a new Arabidopsis MBD7 protein partner with arginine methyltransferase activity. The Plant Journal 52: 210-222
301 Saito T, Sugimoto K, Adachi Y, Wu Q, Mori K (2000) Cloning and characterization of amphibian cold inducible RNA-binding protein. Comp Biochem Physiol B Biochem Mol Biol 125: 237-245
302 Nishiyama H, Xue J-H, Sato T, Fukuyama H, Mizuno N, Houtani T, Sugimoto T, Fujita J (1998) Diurnal Change of the Cold-inducible RNA-Binding Protein (Cirp) Expression in Mouse Brain. Biochemical and Biophysical Research Communications 245: 534-538
171
303 Sugimoto K, Jiang H (2008) Cold stress and light signals induce the expression of cold-inducible RNA binding protein (cirp) in the brain and eye of the Japanese treefrog (Hyla japonica). Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology 151: 628-636
304 Carpenter CD, Kreps JA, Simon AE (1994) Genes encoding glycine-rich Arabidopsis thaliana proteins with RNA-binding motifs are influenced by cold treatment and an endogenous circadian rhythm. Plant Physiol 104: 1015-1025
305 Schdning JC, Streitner C, Page DR, Hennig S, Uchida K, Wolf E, Furuya M, Staiger D (2007) Auto-regulation of the circadian slave oscillator component AtGRP7 and regulation of its targets is impaired by a single RNA recognition motif point mutation. The Plant Journal 52: 1119-1130
306 Ziemienowicz A, Haasen D, Staiger D, Merkle T (2003) Arabidopsis transportinl is the nuclear import receptor for the circadian clock-regulated RNA-binding protein AtGRP7. Plant Molecular Biology 53: 201-212
307 Ringli C, Keller B, Ryser U (2001) Glycine-rich proteins as structural components of plant cell walls. Cell Mol Life Sci 58: 1430-1437
308 Kehr J, Buhtz A, Giavalisco P (2005) Analysis of xylem sap proteins from Brassica napus. BMC Plant Biol. 5
309 Ringli, etal. (2001)310 Kim JS, Jung HJ, Lee HJ, Kim KA, Goh C-H, Woo Y, Oh SH, Han YS, Kang H
(2008) Glycine-rich RNA-binding protein7 affects abiotic stress responses by regulating stomata opening and closing in Arabidopsis thaliana. The Plant Journal 0: online
311 Kreps JA, Wu Y, Chang HS, Zhu T, Wang X, Harper JF (2002) Transcriptome changes for Arabidopsis in response to salt, osmotic, and cold stress. Plant Physiol 130: 2129-2141
312 Sakuma Y, Maruyama K, Osakabe Y, Qin F, Seki M, Shinozaki K, Yamaguchi- Shinozaki K (2006) Functional Analysis of an Arabidopsis Transcription Factor, DREB2A, Involved in Drought-Responsive Gene Expression. Plant Cell 18: 1292- 1309
313 Eason JR, Patel D, Ryan D, Page B, Hedderley D, Watson L, West P (2007) Controlled atmosphere treatment of broccoli after harvest delays senescence and induces the expression of novel BoCAR genes. Plant Physiology and Biochemistry 45: 445-456
314 Li Z-D, Liu L-Z, Shi X, Fang J, Jiang B-H (2007) Benzo[a]pyrene-3,6-dione inhibited VEGF expression through inducing HIF-1 [alpha] degradation. Biochemical and Biophysical Research Communications 357: 517-523
315 Gong Z, Koiwa H, Cushman MA, Ray A, Bufford D, Kore-eda S, Matsumoto TK, Zhu J, Cushman JC, Bressan RA, Hasegawa PM (2001) Genes That Are Uniquely Stress Regulated in Salt Overly Sensitive (sos) Mutants. Plant Physiol. 126: 363- 375
316 Kilian J, Whitehead D, Horak J, Wanke D, Weinl S, Batistic O, D'Angelo C, Bomberg-Bauer E, Kudla J, K. H (2007) The AtGenExpress global stress expression data set: protocols, evaluation and model data analysis of UV-B light, drought and cold stress responses. Plant J. 50: 347-363
172
317 Collins BM, McCoy AJ, Kent HM, Evans PR, Owen DJ (2002) Molecular architecture and functional model of the endocytic AP2 complex. Cell 109: 523-535
318 Steffen A, Le Dez G, Poincloux R, Recchi C, Nassoy P, Rottner K, Galli T, Chavrier P (2008) MTl-MMP-Dependent Invasion Is Regulated by TI- VAMP/VAMP7. Current Biology 18: 926-931
319 Leshem Y, Melamed-Book N, Cagnac O, Ronen G, Nishri Y, Solomon M, Cohen G, Levine A Suppression of Arabidopsis vesicle-SNARE expression inhibited fusion of H202-containing vesicles with tonoplast and increased salt tolerance. Proc Natl Acad Sci U S A 103: 18008-18013
320 Obayashi, et al. (2007)321 Kohom BD, Kobayashi M, Johansen S, Friedman HP, Fischer A, Byers N (2006)
Wall-associated kinase 1 (WAKl) is crosslinked in endomembranes, and transport to the cell surface requires correct cell-wall synthesis. J Cell Sci 119: 2282-2286
322 Dinchuk JE, Focht RJ, Kelley JA, Henderson NL, Zolotarjova NI, Wynn R, Neff NT, Link J, Huber RM, Bum TC, Rupar MJ, Cunningham MR, Selling BH, Ma J, Stem AA, Hollis GF, Stein RB, Friedman PA (2002) Absence of Post-translational Aspartyl beta -Hydroxylation of Epidermal Growth Factor Domains in Mice Leads to Developmental Defects and an Increased Incidence of Intestinal Neoplasia. J. Biol. Chem. 277: 12970-12977
323 He ZH, He D, Kohom BD (1998) Requirement for the induced expression of a cell wall associated receptor kinase for survival during the pathogen response. Plant J 14: 55-63
324 Wagner TA, Kohom BD (2001) Wall-associated kinases are expressed throughout plant development and are required for cell expansion. Plant Cell 13: 303-318
325 Cosgrove D (1998) Molecular regulation of plant cell wall extensibility. Gravit Space Biol Bull 11: 61-70
326 Park AR, Cho SK, Yun UJ, Jin MY, Lee SH, Sachetto-Martins G, Park OK (2001) Interaction of the Arabidopsis receptor protein kinase Wakl with a glycine-rich protein, AtGRP-3. J Biol Chem 276: 26688-26693
327 Suzuki T, Minehata K-i, Akagi K, Jenkins NA, Copeland NG (2006) Tumor suppressor gene identification using retroviral insertional mutagenesis in Blm- deficient mice. EMBO J. 25: 3422-3431
328 Zhang Y, Lu Y, Yuan B-Z, Castranova V, Shi X, Stauffer JL, Demers LM, Chen F (2005) The Human mineral dust-induced gene, mdig, is a cell growth regulating gene associated with lung cancer. 24: 4873-4882
329 Pfau R, Tzatsos A, Kampranis SC, Serebrennikova OB, Bear SE, Tsichlis PN(2008) Members of a family of JmjC domain-containing oncoproteins immortalize embryonic fibroblasts via a JmjC domain-dependent process. Proc Natl Acad Sci U S A 105: 1907-1912
330 Gayther SA, Batley SJ, Linger L, Bannister A, Thorpe K, Chin S-F, Daigo Y, Russell P, Wilson A, Sowter HM, Delhanty JDA, Ponder BAJ, Kouzarides T, Caldas C (2000) Mutations tmncating the EP300 acetylase in human cancers. Nature Genet. 24: 300-303
173
331 Kobayashi A, Numayama-Tsuruta K, Sogawa K, Fujii-Kuriyama Y (1997) CBP/p300 functions as a possible transcriptional coactivator of Ah receptor nuclear translocator (Amt). J Biochem 122; 703-710
332 Figueroa P, Gusmaroli G, Serino G, Habashi J, Ma L, Shen Y, Feng S, Bostick M, Callis J, Hellmann H, Deng XW (2005) Arabidopsis has two redundant Cullin3 proteins that are essential for embryo development and that interact with RBXl and BTB proteins to form multisubunit E3 ubiquitin ligase complexes in vivo. Plant Cell 17: 1180-1195
333 Du L, Poovaiah BW (2004) A novel family of Ca2+/calmodulin-binding proteins involved in transcriptional regulation: interaction with fsh/Ring3 class transcription activators. Plant Mol Biol 54: 549-569
334 Rohde M, Daugaard M, Jensen MH, Helin K, Nylandsted J, Jaattela M (2005) Members of the heat-shock protein 70 family promote cancer cell growth by distinct mechanisms. Genes Dev. 19; 570-582
335 Gong Z, Yang J, Yang M, Wang F, Wei Q, Tanguay RM, Wu T (2006) Benzo(a)pyrene inhibits expression of inducible heat shock protein 70 in vascular endothelial cells. Toxicology Letters 166: 229-236
336 Gachon F (2007)337 Toyoda M, Kojima M, Takeuchi T (2000) Jumonji is a nuelear protein that
participates in the negative regulation of cell growth. Biochem Biophys Res Commun 274: 332-336
338 van der Trenck & Sandermann (1981)339 Ivanovic V, Weinstein IB (1982) Benzo[a]pyrene and other inducers of eytochrome
P I-450 inhibit binding of epidermal growth factor to cell surface receptors. Carcinogenesis 3; 505-510
340 Li Z-D, Liu L-Z, Shi X, Fang J, Jiang B-H (2007) Benzo[a]pyrene-3,6-dione inhibited VEGF expression through inducing HIF-1 [alpha] degradation. Biochemical and Biophysical Research Communications 357: 517-524
341 Moradei O, Vaisburg A, Martell RE (2008) Histone deacetylase inhibitors in cancer therapy: new compounds and clinical update of benzamide-type agents. Curr Top Med Chem 8: 841-858
342 Tonon G (2008) From oncogene to network addiction; the new frontier of cancer genomics and therapeutics. Future Oncol 4: 569-577
343 Hauser AT, Jung M (2008) Targeting Epigenetie Mechanisms: Potential of Natural Products in Cancer Chemoprevention. Planta Med. Plant Cell Physiol. 43: 136-140
344 Willingham AT, Gingeras TR (2006) TUF Love for "Junk" DNA. Cell 125: 1215- 1220
345 Venter JC, Adams MD, Myers EW, et al. (2001) The Sequence of the Human Genome. Science 291: 1304-1351
346 Gilbert W (1986) Origin of life: The RNA world. Nature 319: 618347 Ehrenfreund P, Rasmussen S, Cleaves J, Chen L (2006) Experimentally Tracing the
Key Steps in the Origin of Life: The Aromatic World. Astrobiology 6; 490-520348 Jones S, Zhang X, Parsons DW, Lin JC-H, Leary RJ, Angenendt P, Mankoo P,
Carter H, Kamiyama H, Jimeno A, Hong S-M, Fu B, Lin M-T, Calhoun ES, Kamiyama M, Walter K, Nikolskaya T, Nikolsky Y, Hartigan J, Smith DR, Hidalgo
174
M, Leach SD, Klein AP, Jaffee EM, Goggins M, Maitra A, laeobuzio-Donahue C, Eshleman JR, Kem SE, Hruban RH, Karchin R, Papadopoulos N, Parmigiani G, Vogelstein B, Velculescu VE, Kinzler KW (2008) Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses. Science 321: 1801-1806
349 Alam S, Conway MJ, Chen H-S, Meyers C (2008) The Cigarette Smoke Carcinogen Benzo[a]pyrene Enhances Human Papillomavirus Synthesis. J. Virol. 82: 1053-1058
350 McGarry, et al. (2002)351 Kadkhoda K, Pourfathollah AA, Pourpak Z, Kazemnejad A (2005) The cumulative
activity of benzo(a)pyrene on systemic immune responses with mite allergen extract after intranasal instillation and ex vivo response to ovalbumin in mice. Toxicology Letters 157: 31-39
352 Katdare M, Osborne MP, Telang NT (1998) Inhibition of aberrant proliferation and induction of apoptosis in pre-neoplastic human mammary epithelial cells by natural phytochemicals. Oncol Rep 5:311-315
353 Kang ZC, Tsai SJ, Lee H (1999) Quercetin inhibits benzo[a]pyrene-induced DNA adducts in human Hep G2 cells by altering cytochrome P-450 lA l gene expression. Nutr Cancer 35: 175-179
354 Werck-Reichhart D, Bak S, Paquette S (2002) Cytochromes P450. The Arabidopsis Book: 1-28
355 Kaiser J (2008) CANCER GENETICS: A Detailed Genetic Portrait of the Deadliest Human Cancers. Science 321: 1280a-1281
356 Heinonen H, Nieminen A, Saarela M, Kallioniemi A, Klefstrom J, Hautaniemi S, Monni O (2008) Deciphering downstream gene targets of PI3K/mTOR/p70S6K pathway in breast cancer. BMC Genomics 9: 348
357 Frew AJ, Lindemann RK, Martin BP, Clarke CJ, Sharkey J, Anthony DA, Banks KM, Haynes NM, Gangatirkar P, Stanley K, Bolden JE, Takeda K, Yagita H, Secrist JP, Smyth MJ, Johnstone RW (2008) Combination therapy of established cancer using a histone deacetylase inhibitor and a TRAIL receptor agonist. Proc Natl Acad Sc iUS A 105: 11317-11322
358 Goymer P (2008) Cancer: The menace of evolution. Nature 754: 1046-1048359 McKenna DJ, Rajab NF, McKeown SR, McKerr G, McKelvey-Martin VJ (2003)
Use of the comet-FISH assay to demonstrate repair of the TP53 gene region in two human bladder carcinoma cell lines. Radiat Res 159: 49-57
360 Nedelcu AM (2006) Evidence for p53-like-mediated stress responses in green algae. FEBS Letters 580: 3013-3017
361 Xiang, et al. (2008)362 Gayther, et al. (2000)363 Harris RE, Beebe-Donk J, Alshafie GA (2008) Similar reductions in the risk of
human colon cancer by selective and nonselective cyclooxygenase-2 (COX-2) inhibitors. BMC Cancer 8: 237
364 Schonthal AH, Chen TC, Hofman FM, Louie SG, Petasis NA (2008) Celecoxib analogs that lack COX-2 inhibitory function: preclinical development of novel anticancer drugs. Expert Opin Investig Dmgs 17: 197-208
175
365 Chuang HC, Kardosh A, Gaffney KJ, Petasis NA, Schonthal AH (2008) COX-2 inhibition is neither necessary nor sufficient for celecoxib to suppress tumor cell proliferation and focus formation in vitro. Mol Cancer 7: 38
366 Simoes, et al. (2005)367 http://www.netl.doe.gov/publications/others/pdf/Oil Peaking NETL.pdf and
http://www.eia.doe.gOv/emeu/aer/txt/stb0501.xls, accessed 10/18/08.368 eFP Browser, at http://bbc.botany.utoronto.ca/efp/cgi-bin/efpWeb.cgi. Accessed
10/18/08.369 Tokunaga H, Takebayashi Y, Utsunomiya H, Akahira JI, Higashimoto M, Mashiko
M, Ito K, Niikura H, Takenoshita SI, Yaegashi N (2008) Clinicopathological significance of circadian rhythm-related gene expression levels in patients with epithelial ovarian cancer. Acta Obstet Gynecol Scand: 1-11