1. Molecular dissection of internal organs with
involuntary muscle contraction in sheep
AGRICULTURE FLAGSHIP
Tamia Nguyen
5th February 2014
VACATION SCHOLARSHIP PROGRAM 2014
2. A 5-sentence story
• Sheep coverts plant materials into meat but also produces methane in the process.
• Methane production from sheep and cattle represents the largest single source of
methane emission in Australia and the largest source of emissions from agriculture
(71%) (Dept of Environment and Primary Industries, VIC, 2014)
• Methane is produced when bacteria fermentate the ingested plant materials in
rumen, the foregut of sheep.
• Yield of methane production is partly determined by the rate of passage through
rumen, which is controlled by rumen muscle wall.
• To further investigate the role of rumen muscle in methane production, first we need
reference gene(s) that can reliably report the abundance of rumen muscle.
2 | Molecular dissection of internal organs with involuntary muscle contraction in sheep| Tamia Nguyen
4. 4 |
Method
* Gene ontology (GO) term: controlled
vocabularies that describe gene products
in terms of their associated biological
processes, cellular components and
molecular functions.
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Molecular dissection of internal organs with involuntary muscle contraction in sheep| Tamia Nguyen
5. 5 |
Figure 1: Muscle coexpression network. This network consists of 5450 nodes and 176346 edges.
Molecular dissection of internal organs with involuntary muscle contraction in sheep| Tamia Nguyen
6. Analysis
• No significant enrichment of GO term
• Too much noise disrupts signal. Where does the noise come from?
• Too few replicates ( 3 individuals)
• Large biological variations between replicates (size, age, gender etc)
• Threshold not stringent enough (FDR < 0.01, RPKM > 1)
>10 000 genes identified as differentially expressed in total of 25 000 genes
6 |
Change of strategy
Use GO terms to compile a list of genes known to be involved in
muscle structure and activity
Then find a cluster that contains smooth muscle signature genes.
Molecular dissection of internal organs with involuntary muscle contraction in sheep| Tamia Nguyen
7. 7 |
Figure 2. Muscle gene network. This network consisted of 5450
nodes and 176346 edges. Cutoff of correlation coefficient was 0.7
• 265 genes had GO term related to
muscle structure or activity
• 125 had equivalent sheep genes
• 113 were differentially expressed
Cardiac and skeletal muscle
gene enriched
Smooth muscle
gene enriched
Molecular dissection of internal organs with involuntary muscle contraction in sheep| Tamia Nguyen
8. 8 | Molecular dissection of internal organs with involuntary muscle contraction in sheep| Tamia Nguyen
9. Reflection
9 | Molecular dissection of internal organs with involuntary muscle contraction in sheep| Tamia Nguyen
10. Acknowledgement
Supervisors:
Dr. Ruidong Xiang
Postdoctoral Fellow
CSIRO Agriculture Flagship
Dr Brian Paul Dalrymple
Senior Principal Research Scientist
CSIRO Agriculture Flagship
10 | Molecular dissection of internal organs with involuntary muscle contraction in sheep| Tamia Nguyen
11. CSIRO Animal, Food and Health Science
Tamia Nguyen
Summer student
t +61 732142619
e ngu11v@csiro.au
AGRICULTURE FLAGSHIP
Thank you
VACATION SCHOLARSHIP PROGRAM 2014
Apologies for it’s not the most coherent story
Methane is the second most prevalent greenhouse gas (just after that you-know-which gas)
http://www.depi.vic.gov.au/agriculture-and-food/dairy/emissions-in-dairy/methane-research
Long dorsal muscle = muscle on the back
On the choice of control – find sth muscle negative
We have tested all possibilities - find cerebrum to be the best – which we originally thought to be a good choice because blood vessels in the brain although there are a lot of them – they may be not as muscular as blood vessels everywhere else in the body as there is no need for them to contract or dilate significantly. Turns out we were a bit too optimistic, we later learn that cerebrum still contain an ineligible amount of vascular smooth muscle and it complicates our analysis. But it was the best choice that we have.
Explain the concept of “guilt by association’. If two genes show similar expression profiles, they may be involved in the same process or under the same regulatory regime.
Gene ontology (GO) term: controlled vocabularies that describe gene products in terms of their associated biological processes, cellular components and molecular functions.
.
Slide that shows the awful network: I enjoy exploring the network – why they are clustering together – at first – but then – too noisy –
Excuse my excitement
In my last slide I would like to acknowledge my supervisors Ruidong Xiang and Brian Dalrymple who have provided me with lots of guidance and support along the way and many more useful advices.
