Tuesday, December 3, 2013

Field experiment set-up

It was an awesome or terrible day, depending on how you look at it. We - Xue-Ping (research assistant), Shan-Hua (another PhD student), Wei-Jie (Dive guide) and I went to our field site to set-up the in-situ field experiment.

There are several goals on this trip :

1)  Cover half of each coral colonies (Acropora muricata) with transparent net. There are a total of three colonies. The hope of covering half of the coral colony is to dampen the water flow around it, but not affecting the light intensity too much. Of course, there is always a cut in light intensity when you cover the coral with a net. However, I did a preliminary test in the lab using a light meter, and the light was cut about 10% - 15% on an average, and there are still some peaks which are as high as the normal lighting conditions. Thus, I am willing to accept the small change in light intensity, knowing it shouldn't impact the coral too much with this minimal light intensity change.

Setting up the nets underwater is harder than it looks

2) Collect two samples of coral nubbins from each colonies, and will extract their mucus later in the lab. I am going to analyse the microbial communities in the mucus later on in Academia Sinica, Taipei

3) Collect surrounding reef water for analysing of microbial communities.

4) Get DivingPAM readings for the coral colonies. This reading tells the photosynthetic health of the coral, and I am using it as a indicator for coral stress. I hypotheses that the half of the coral within the net should experience higher stress than the other half which is not covered. This is due to the reduction in water flow (got to do with removal of waste, radical oxygen, transport of nutrients etc).

5) Shan-Hua is going to core a couple of coral colonies for her samples. She is examining the endolithic microbial communities in Isopora sp.

Well, it is a lot of work, but it does sound pretty simple. I mean some hammering, some manoeuvring of the nets around the corals, etc but it shouldn't be hard. I WAS WRONG! Well, Wei-Jie helped with all the hard work..hammering, drilling etc. I have to in charge of the nets, the reading of the DivingPAM etc. I was the only one who knew how to operate the DivingPAM, and thus it is my job. It wasn't a difficult job - point the optic fibre on the coral branch, wait for 5 secs, fired off a light source (from the DivingPAM), and read the value yield. I do not even need to record the values because it is automatically saved in the instrument, which I can retrieve later. However, there are a few "BUTS" -

1) I need to read the dark-adapted values, which means I can only use the DivingPAM during dusk hours. And since this is the first time, I also need to do another set of light-adapted values as a baseline. So I need to go once before the sunset to read the coral colonies. As a result, there was a lot of diving, 2 dives for DivingPAM readings, 2 dives for setting the nets up. And it was a chilling 23degC, and we were shivering!

2) For the reading on the DivingPAM, I need to ensure the values fall within a certain range before I fired off the light in the fibre optics. This means that for 9 readings on a single colony, I was staring at the small screen on the DivingPAM underwater for about 10 - 15mins. So it is like reading a book in a moving car - I got really SICK... and I throw up after every use of the DivingPAM!

Again, harder than it looks...especially when the current is going
Well, first day is over, and I got what I need for my samples...two more collection days to go!

All in a day's work
And now, for some surfing on the web...

Shan-Hua (left), Xue-Ping (right)


Sunday, November 24, 2013

Working in the new lab

I have been back from Kenting for a week now, and since been working in the lab at Academia Sinica. I have been working on extracting microbial DNA from the samples I collected in June. It is a LONG and TEDIOUS process. From previous posts, you probably knew that we moved to a new building. And I am the first one to work in the new lab - which means I have to figure out where are all the things (instrument, suppliers, kits etc) are... it was quite an adventure. The new place has a balcony which overlooks the hills, and my colleagues are out there occasionally to enjoy the views. On the other hand, I was too busy to enjoy any views. In fact, I was so busy that I am still working on weekends (both Sat and Sun). The way I see it, I am here to work, and not for vacation, so if I have the chance, I should be working. So, here I am again, on Sunday, and doing gel extractions.


Friday, November 15, 2013

Samples collection - Kenting

Last two days, I and Xue-Ping (research assistant at Academia Sinica) was out in Kenting, South Taiwan to collect my coral samples. I stayed in the new hostel at NMMBA (National Marine of Marine Biology and Aquarium). The place is very new and spacious! There are two levels, and each level has 8 double occupancy rooms. My room had two double beds, a nice flat-screen tv and a nice closet. Unfortunately, the internet here is VERY SLOW... well, you can't win all! :).. I guess the place is really for tourist because I rarely turn on the tv at all. Most of the time, I am either out in the lab preparing my tanks, or in the water collecting my samples.

Room

The new hostel

The purpose of this trip is to collect coral samples to acclimate for the next 2 weeks in the NMMBA tanks. Meanwhile, I would be back to Academia Sinica,Taipei to do some bench work. Besides collecting samples, I also scouted out 3 colonies outside the Nuclear Plant region for my field in-situ testing experiment. There will also be 3 other coral colonies, which I had already confirmed within the Nuclear Plant Inlet site. Therefore, I will be performing in-situ field testing on a total of 6 coral colonies at 2 different sites, which have different water flow characteristics and temperature differences. Wei-Jie, an experienced dive guide helped us with the coral samples collection and ID of the colonies. He is very experienced with helping scientific research, and he knows the area very well, making him a very important part of the experiment!

Acropora muricata colony 1

Acropora muricata colony 2
Acropora muricata colony 3
Wei-Jie busy collecting samples... I just need to stay out of his way

The plan was to be at NMMBA for 2 days for this trip. One day for samples collection and one day to prepare all the tanks ready for the experiment. I reckon there should be some fine tuning when we are back in December for the experiment. However, getting most of the tanks ready now means lesser work in December.

Tanks are ready

Coral nubbins are acclimating

Now... back to Taipei to do some more DNA extraction, and get ready to send the samples out for sequencing!...YAY! :)