Thesis DEFENSE
-
Upload
briena-healy -
Category
Documents
-
view
36 -
download
1
Transcript of Thesis DEFENSE
Density and flow effects on benthic black fly larvae
and
Identifying genomic regions responsible for altered reproductive traits of Arabidopsis
thaliana grown at an elevated carbon dioxide concentration
Briena E. HealyAdvisor: Dr. Jonathan T. Fingerut
Dr. Clint J. Springer
Thursday, July 12, 2012
Thesis Presentation
Briena Healy
Advisor: Dr. Jonathan Fingerut
Black Flies, Family Simuliidae
• Order Diptera, Family Simuliidae, sp. Simulium tribulatum.
•Common, usually a biting pest.
Hill, Catherine, and John MacDonald. Resources: Public Health and Medical Department at Purdue University, 2008. Web. Aug. 2011. <http://extension.entm.purdue.edu/publichealth/resources.html>.
Life cycle of the Black fly
Black Fly Larvae
• Found on solid substrates within streambeds.
• Heavily reliant upon flow at different scales
– Distribution
– Protection
– Food
FLOW
Research question
What effects distribution on the scale of a
single bed element?
Objectives of the study
• Density effects on distribution.
– What are the effects of neighboring larvae on distribution?
• Past experiences effecting behavior.– How do starting conditions effect final settlement location?
The one-stone model
Hemi-cylinder placed perpendicular to the flow
0.00%
20.00%
40.00%
60.00%
80.00%
100.00%
120.00%
-5 -4 -3 -2 -1 0
0.2
5
0.5
0.7
5 1
1.2
5
1.5
1.7
5 2 3 4 5
Rela
tive
fra
cti
on
of
Ma
x S
pe
ed
Distance from Top (cm)
Relative Flow Speed by Position at Different Settings
Slow Flow
Medium Flow
High Flow
Flow data
(12 cm/s)
(26 cm/s)
(56 cm/s)
The Database
Determining effects of Density
• Graphed the last known position for
– Individual Neonate (N) = low density
– Individual Late-Instar (LI)= low density
– Mass Addition Late-Instar (MA)= high density
-50
-45
-40
-35
-30
-25
-20
-15
-10
-5
0
-15 -10 -5 0 5 10 15 20 25 30
Individual Neonate positions under Medium (26 cm/s) Flow
Individual Neonate positionaldata under Medium Flow
5 10 15 20 25 30 35 40 45
0
1
2
3
4
5
6
7
8
9
10
Fre
qu
en
cy
Distance on the hemi-cylinder (mm)
Last position of Individual Neonates under Medium (26 cm/s ) flow
0.0%
10.0%
20.0%
30.0%
40.0%
50.0%
60.0%
70.0%
80.0%
90.0%
100.0%
0
2
4
6
8
10
12
14
16
18
Perc
en
t o
f M
ax F
low
Perc
en
t o
f th
e p
op
ula
tio
n
Distance on hemi-cylinder in cm
Mass Addition Late Instar
Individual Late Instar
Slow (12 cm/s) flow
Density on distribution
Density Effects Results
• Definite preference by larvae for fastest available flow
• Distributional spread differs with high density populations shifting towards suboptimal flows
• While distributions were not statistically different, descriptive statistics support the expected trend of distribution into faster flow
Determining effects of past experiences
• Calculated and compared the starting and ending flow conditions.
• Tortuosity of paths travelled in respect to starting velocity
Tortuosity: a winding or twisting path.
How twisty or circuitous is the path travelled
http://www.sciencedirect.com/science/article/pii/S0264817210001170
Straight Medium Curvy
1-2 3-5 6-10Ratio of Linear Distance:
Path shape
Flow effects on Late-Instar destination
• Larvae relocate themselves from an area of slower flow to an area of higher flow.
• Though larvae may start in the highest available flow, they don’t necessarily remain there due to turbulence.
0
2
4
6
8
10
12
0 2 4 6 8 10 12
End
ing
Ve
loci
ty (
cm/s
)
Starting Velocity (cm/s)
Late-Instar larvae In Low speed flow (12 cm/s)
-4
-2
0
2
4
6
8
10
0 2 4 6 8 10 12
Dif
fere
nce
bet
wee
n E
nd
ing-
Star
tin
g ve
loci
ty (
cm/s
)
Starting velocity (cm/s)
Difference in velocity for Late-Instar larvae under Low speed flow (12 cm/s)
Flow effects on Neonate destination
• No matter where they landed, they remained there.
• The majority have a difference in almost zero between their starting and ending velocities
0
2
4
6
8
10
12
0 2 4 6 8 10 12
End
ing
velo
city
(cm
/s)
Starting velocity (cm/s)
Neonate larvae in Low speed flow (12 cm/s)
-2
-1
0
1
2
3
0 2 4 6 8 10 12
Dif
fere
nce
bet
wee
n E
nd
ing-
Star
tin
g ve
loci
ty (
cm/s
)
Starting velocity (cm/s)
Difference in velocity for Neonate larvae under Low speed flow (12 cm/s)
Conclusions and possibilities for future endeavors
• High density flow has some effect on where within a current a larva ends
• Conditions of starting flow matter, but ontogeny can effect larval distribution
• Data remains unexamined in the database
Isolating genomic regions in Arabidopsis responsible for changes…
Briena Healy
Advisor: Dr. Clint Springer
Rising Atmospheric CO2
Photosynthesis +40%
Carbohydrates +45%
Total Mass +35%
Seed Yield +25%
Ainsworth et al. 2002
Plant LevelResponses
Ambient [CO2] = 350-370 ppm
Elevated [CO2] = 650-700 ppm
150 ppm
270 ppm350 ppm
700 ppm
Flowering Time and Elevated [CO2]
Springer & Ward, 2007
16
20
24
28
32Ireland
Norway
Sweden
Portugal
Austria
BC, Canada
Cape Verdi
Tadjikistan
Ukraine
Belgium
380 700
Tim
e o
f F
low
ering
(d
)
[CO2] (ppm)
Genetic Variation in Flowering Time
Springer & Ward. 2007 New Phytol.
What are the molecular and physiological mechanisms controlling reproductive responses to elevated atmospheric CO2 in Arabidopsis thaliana?
Research Question
© European Communities, 1995-2009
t
Goal= to identify regions of an organism’s genome that controls for a quantitative trait
Quantitative Trait Loci Analysis
Quantitative Trait = Characteristic of an organism that can be attributed to it’s genetic background
Mapping QTL Requires• An organism with a mapped genome.
• Genetic markers distributed throughout the genome
– Must be polymorphic markers
• Individuals homozygous at identified markers.
– Back-crossed populations
– Recombinant Inbred Lines
Objectives
• Identifying the significant QTLs controlling the flowering time in both CO2 concentrations.
• Identifying the significant QTLs controlling plant reproductive architecture in both CO2
concentrations.
Methods• Grew 98 RILs of the cross Columbia (Col) ×
Landsberg erecta (Ler)
• Used two [CO2]
– e[CO2]: 1000 ppm
– a[CO2]: 400 ppm
• Recorded time to flowering
• Counted resulting architecture
• Calculated means for individual lines at both [CO2] Ungerer et al. 2003
Averages days until Flowering
0
10
20
30
40
50
60
70
5 10 15 20 25 30 35 40 45
Fre
qu
en
cy
Average days
a[CO2] e[CO2]
Average Total Silique number
0
1
2
3
4
5
6
7
8
9
50
10
0
15
0
20
0
25
0
30
0
35
0
40
0
45
0
50
0
55
0
60
0
65
0
70
0
75
0
80
0
85
0
90
0
95
0
10
00
10
50
11
00
11
50
12
00
12
50
Fre
qu
en
cy
Average number of siliques
a[CO2] e[CO2]
0
5
10
15
20
25
50 100 150 200 250 300 350 400
Fre
qu
en
cy
Average number of Primary Siliques
Primary Siliques a[CO2]e[CO2]
0
2
4
6
8
10
12
14
16
5 10 15 20 25 30 35 40 45 50 55 60 65
Fre
qu
en
cy
Proportion of Primary Silique number: Primary Axes number
Primary Siliques/Primary Axes a[CO2]
e[CO2]
0
5
10
15
20
25
30
2 4 6 8 10
Fre
qu
en
cy
Average number of Primary Axes
Primary Axesa[CO2]e[CO2]
0
2
4
6
8
10
12
14
16
5 10 15 20 25 30 35 40 45 50 55 60 65 70 75 80
Fre
qu
en
cy
Average number of Secondary Axes number
Secondary Axes a[CO2]e[CO2]
0
1
2
3
4
5
6
7
8
9
10
50
10
0
15
0
20
0
25
0
30
0
35
0
40
0
45
0
50
0
55
0
60
0
65
0
70
0
75
0
80
0
85
0
90
0
95
0
10
00
Fre
qu
en
cy
Average number of Secondary Silique number
Secondary Siliques a[CO2]
e[CO2]
0
5
10
15
20
25
30
5 10 15 20 25 30 35 40 45
Fre
qu
en
cy
Proportion of Secondary Silique number: Secondary Axes number
Secondary Siliques/Secondary Axes a[CO2]e[CO2]
The existence of a significant QTL varying by CO2 concentration
Summary QTL table slideTrait CO2 concentration Number of sig. QTL Chromosome
Flowering Time Elevated 1 2
Ambient 4 1, 4, 5, 6
Total Siliques Elevated 2 5
Ambient 2 1
Primary Axes Elevated 1 5
Ambient - -
Primary Siliques Elevated 1 1, 5, 5
Ambient 3 5
Primary Siliques/ Primary Axes
Elevated3
4, 5, 5
Ambient - -
Secondary Axes Elevated 7 1, 1, 2, 3, 3, 5, 5
Ambient 8 1, 1, 1, 2, 3, 3, 4, 5
Secondary Siliques Elevated 3 2, 5, 5
Ambient 1 4
Secondary Siliques/ Secondary Axes
Elevated - -
Ambient 1 4
Number of QTL by Trait
0
1
2
3
4
5
6
7
8
9
Nu
mb
er
of
QTL
Reproductive Trait
Ambient
Elevated
0
2
4
6
8
10
12
1 2 3 4 5
Nu
mb
er
of
QTL
Chromosome
a[CO2]
e[CO2]
Interaction ANOVA table
Characteristic Chromosome Marker Significance
Primary Axes 1 CO2 * jcc3 0.04Primary Axes 1 CO2 * R64 0.04Primary Siliques/Primary Axes 3 CO2 * ATA1 0.02
Primary Siliques/Primary Axes 3 CO2 * atts3983 0.058Secondary Siliques/Secondary Axes 2 CO2 * BIO2b 0.002
Two-way ANOVA results indicating significant CO2 x genomic marker interaction for measured A. thaliana architectural traits (p <0.05)
• Looked at the nature of the effect of the marker on CO2 response
• These markers showed significant marker x CO2 interactions
Conclusions
• Plant reproduction increases as [CO2] increases
– Driven by meristematic activity
• Growth at e[CO2] alters the number and location of regions of control within the genome
• Effect of [CO2] on traits will depend on the genetic background present at loci.
Implications
• QTL identified represent portions of the genome that are most likely to undergo selection in future conditions
• The identified genomic regions can also
be used as targets for crop breeding programs.
Acknowledgements• Dr. Jonathan Fingerut• Dr. Clint Springer• Dr. Scott McRobert• SJU Department of Biology• Dana Semos, Sabrina Fecher, Holly Clark• Dr. Nick Nicolaides
• My Family & Friends• Fellow graduate students• Kristina Orbe
BIOLOGY