Download Omics tools for assessing effects of environmental stressors on the

Omics tools for assessing effects of environmental
stressors on the northern Atlantic key species Calanus finmarchicus
Bjørn Henrik Hansen, Trond R. Størseth, Kolbjørn Zahlsen and Dag Altin
Calanus finmarchicus
Main objectives of the project:
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Marine ecological key species
2-3 mm pelagic copepod (zooplankton, microcrustacean)
300 mill tons annual production in the North Atlantic and
Barents Seas
Short generation time (~80 days in culture)
Up to 50% of dry weight is lipids  Very important food
resource for commercial fish
Important transfer route of environmental contaminants in
the marine food web
Launch a large-scale EST sequencing program
Develop a custom-made oligonucleotide microarray
 transcriptomics
Develop methods for metabolic profiling and fingerprinting
 metabonomics
Use bioinformatics tools in order to analyze and correlate
omics output for controlled exposure experiments
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TRANSCRIPTOMICS
454 FLX sequencing
Assembly and annotation
Probe design and array
construction
Experimental design
Exposure experiment
Library construction and sequencing
We already have established three SSH libraries
from copepods exposed to a mixture of stressors.
Here a normalized library will be constructed by
EcoArray Inc..
454 FLX sequencing
The normalized library will be sequenced by 454
FLX sequencing by EcoArray Inc./University of
Florida.
GC-MS and LC-MS
Chromatographic methods will also be used to further study lipophilic endogenous
metabolites in particular.
Sequence annotation and array construction
Sequences will be assembled and annotated
(Blast2GO) before probes are designed and
oligoarray produced (Agilent).
TRANSCRIPTOMICS
Image processing
Data management
Quality control
Normalization
Expression profiles
1.5e+07
FACH3/ile
1.0e+07
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thr
pro
asn
val
FAallylic
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pro
FAb
ile FAb
5.0e+06
cys
lys
ile
cys
bglc
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FAa
ile
met
met
0.0e+00
thr
4
3
2
1
ppm
FITNESS-RELATED
ENDPOINTS
Narcosis and survival
Altered reproduction
Developmental effects
Biometry/morphology
DNA damage
SINTEF Materials and Chemistry
Contact person: Bjørn Henrik Hansen ([email protected])
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0.0
loading value
Integration,
visualization
and analysis
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ile
ile
met
Gene functional groups,
pathways, networks (gene
ontology, KEGG maps)
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FAn-3CH3
thr
Data interpretation
Literature mining
Subjective biological interpretation
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2.0e+07
FACH2
phosphocholines
bglc
Statistics
Using PLS/PCA we visualize differences in metabolic profiles between different
experimental groups.
Determine list of
expressed genes
METABOLOMICS
Calanus culture
High Resolution Magic Angle Spinning NMR
Whole copepods were analyzed (n=5) with HR MAS NMR, and of the resulting
spectrum 60 metabolites were resolved and characterized.
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Normalized library
Pooled sample
Copepods exposed to heavy metals (mercury and
copper), oil, heat, CO2, H2O2 and sampled at
different developmental stages.
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Pooled sample (different dev.
stages and exposures)
METABOLOMICS
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1000
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Determine list of
expressed metabolites
variable
Phenotypic
anchoring
of gene
expression
“Marker” gene identification
Identify novel functions of known
genes and possible functions of
uncharacterized genes
Effects of stressors
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