Post on 20-Jan-2016
description
Effect of thyroid hormone concentration on the transcriptional response
underlying induced metamorphosis in the Mexican axolotl (Ambystoma)
Robert B. Page1, S. Randal Voss1, Amy K. Samuels1, Jeramiah J. Smith1, Srikrishna
Putta1, and Christopher K. Beachy2*
1Department of Biology and Spinal Cord and Brain Injury Research Center, University of Kentucky; and
2Department of Biology and Amphibian Growth Project, Minot State University
Ambystoma mexicanum
+ 5 nM TH
Ambystoma mavortium (tigrinum)
Comparisons of standard metamorphic gene expression and morphology profile with endocrine-disrupted profile in
salamander
metamorphosis
metamorphosis
Paedomorphosis(= metamorphic
failure)
skinliverbraintail
Collect mRNA cDNA microarray
Grow salamanders in experimental design
Basically…..
cDNA
cDNA
T
T
T
T
T
T
epithelial membrane protein 1
28 days after immersion in 5 nM TH
no TH 5 nM TH
0 days
2 days
12 days
28 days
CONTROL T4 IMMERSION50 nM TH
T4 IMMERSION
DESIGN
control
5 nM TH
50 nM TH
15 DAYS POST-EXPOSURE
ANALYSIS PART I:UNIVARIATE ANALYSIS
A series (4844) of one-factor ANOVAs comparing expression level among treatment groups (I.e., 0, 5, and 50 nM TH)
Used to identify genes for multivariate analysis
Linear and quadratic regression analyses
Volcano Plot representing univariate analyses
P = 0.05
4844to802 loci forconsideration(= DEGs)
2X up or down expressionrelative to controls
ANALYSIS PART II:MULTIVARIATE ANALYSIS
Principal Components Analysis
Bioinformatic comparison to other microarray databases: metamorphosis in Xenopus
day 2
day 28
day 12
day 0
day 2
day 28
day 12
day 0
day 2
day 28
day 12
day 0
day 2
day 28
day 12
A phylogeny of model craniates that have a genome project
mou
se
hum
an
chick
Xenop
us
axolo
tl
zebr
afish
Mammalia
Amniota
Lissamphibia
Tetrapoda
Osteichthyes
WHY SALAMANDER?--phylogenetic place
--natural history
--experimental possibilities and husbandry
Bioinformatic Comparison with Xenopus
TH-skin TH-intestine(this study, 2008,BMC Genomics 9:78)
(Buccholz et al., 2007,Dev. Biol. 303:576-590)
1997 DEGs802 DEGs
020406080
100
same different
n = 111
EXPRESSION PATTERN
% o
f ge
nes
CommonDEGs
Finishing up-TH dose influence timing of onset-Sets of transcription responses
-Diversity in expression
To view microarray database, visit-www.ambystoma.org