The poo results: duck all?

Ouch, what a title.

 I had some wonderful news yesterday. Remember that I forgot to put my tubes extracted DNA in the freezer on Friday. After a very tense night, I sent an email to Supervisor first thing on Saturday explaining what had happened, and it turns out that he knew someone who would be in the lab. She, the hero, found my tubes and froze them.

So, we got all of the tubes out yesterday morning to measure them. The thing is, we don't actually know that there's DNA in there at the end of the process: it's just a drop of clear liquid. We use a clever little machine called a Qubit to see if any DNA is actually present, and estimate its concentration. We ran all of the samples through. Here are the results (samples of the same letter are from ducks of the same species from the same location):

Sample	Preparator	Left out overnight	DNA (ng/µl)
A1	Me	N	-
A2	Me	Y	-
A3	Me	Y	-
A4	Me	Y	-
A5	Me	Y	-
B1	Me	Y	-
C1	S	N	22.00
C2	S	N	4.77
C3	S	N	5.52
C4	S	N	16.20
C5	S	N	3.49
C6	S	N	4.98
C7	Me	N	6.90
C8	Me	N	5.58
C9	Me	N	-
C10	Me	N	10.40
D1	Me	Y	-
D2	Me	Y	-
D3	Me	Y	-

 

Only 3/13 of my samples had any DNA in them. Most of mine were left out, which could have degraded any DNA into uselessness, and all of those left out failed. Unfortunately, of the five I did the day before, under supervision and that definitely did go in the freezer, two failed. And they were from different types of duck. So it looks like I need more practice at this!

I ran two more samples yesterday. We shall see how they come out this morning...

The training montage: DNA from duck poo

My project will involve searching for the DNA of parasitic worms. Unfortunately, getting DNA out of the materials I'll be working with, soil and spirit-preserved worms, is not straightforward. So this week I've been learning how to extract DNA from something easier: duck poo.

My supervisor has several samples of duck poo in his freezer for a project looking at parasitic worms in birds. They'll eventually collect samples from across Europe and see whether the phylogenies of the worms are connected to the migration patterns of the birds. These initial samples were just to test that they could get parasite DNA from these particular duck species. So they could withstand the fairly cack-handed treatment that I was likely to give them! At least, I hope so. We haven't actually measured the results yet.

I ended up running thirteen samples through the complicated recipe of chemicals and machinery. The first few were supervised and, though we haven't yet measured any of the DNA, seemed to come out fine. We're going to measure the DNA from all of the samples in one go, so we put it in the freezer for later.

The second lot I did by myself on Friday, my first solo labwork since playing with Drosophila a couple of years ago. Everything was going well. I finished up and went out to call my supervisor, thinking we might have time to measure the DNA before the end of the day. But it was a bit late after all, so we cleared up and talked over the plans for Monday. Then I left.

It was about  22:00 when I realised I hadn't ever put that DNA in the freezer. Today (Monday), I discover whether it survived!

Hyde Park

My supervisor has been teaching nearly all week, leaving me with lots of time and a dwindling pile of work. So, this afternoon I decided to take advantage of the beautiful weather and go for a walk. I walked through Hyde Park on my way to catch a train last term, but didn't have my camera on me. Not today! It's time for a list-of-pictures post!

In another excellent stroke of luck, there were lots of roadworks at the start of the massive road that cuts straight through the park:

Which meant that the road inside the park was like this:

Rather than, like, the A45. It was actually quiet. Wonderful.

So I got onto the grass, took off my shoes and socks and set about finding interesting organisms. First up was an exotic but undeniably attractive Egyptian goose:

I also got a photo of it walking. I've always underestimated how much goose-stepping actually resembles geese stepping:

Note also the offended swans.

Next to that lake edge was a stand of trees. And in the trees there was, rather unexpectedly, a heron:

And nearly enough pigeons that the branches may have broken if they'd all jumped at once:

There were pigeons on the ground being amusing too.

Courtship going round in circles

Not a flamingo

But sadly, that was when my camera batteries died for good. Because after that I saw:

• Great crested grebes
• Lesser black-backed gulls
• A coot nest
• Tufted ducks
• A cormorant
• A tree that had covered the ground around it in the softest white seed-down
• A magpie rummaging through a bin (I threw its rejects back in afterwards)
• Horseguards in training, basically playing polo with spears
• A bee swarm that I nearly walked into

 If Free Time is going to become more of a thing, I will be back again soon!

Tours

Today I had my lab induction, which was mostly a tour of some very clean rooms with some extremely expensive machines that I might actually need to use in the near future. Sure hope my tendency to spill liquid and drop things won't be a problem.

I also had a quick tour around the parasite collections from their lone, rather harried curator. She showed me the banks of old wooden cabinets containing thousands upon thousands of microscope slides, each with a few specimens of tiny worms fixed in yellowish discs of preservative. The cabinets start right by my office; one is topped with shelves that include those wonderful Australian anurans.

Big worms are kept in the spirit collection. I didn't realise this, but five or six floors of that wing of the building are spirit storage. Each time I think I've appreciated how big the museum is, I move to a new collection area and get my mind blown again! The big worms are stored in jars ranging from the size in which you might buy spices to great urns of several litres. A selection of the most impressive are actually stored back out in an office. It's not worth keeping them in stores because they so often get displayed. The curator proudly pointed out the museum's biggest worm (I think it was 13 m): a Diphyllobothrium tapeworm from an orca. Its name was Eric. "Don't ask me where the name came from", she said.

Finally, in an almighty breakthrough, I found a settings menu on the Mac and can now perform right-clicks.

Come into my office...

...which I share with up to five other people and can get a bit crowded. But it's a nice little room with a wonderful view of the wildlife garden. 'My' desk is free of the personal junk that accumulates when it belongs to someone properly, but the far left side is the tea station. This is roughly 50cm² containing:

• One mug
• One jar of teabags
• Three boxes of tea
• Three bags of sugar
• Three empty coffee jars
• One large bottle of rum

I left the office midmorning for my first departmental coffee. I enjoyed the change of chair while my supervisor and his friends complained, venomously but justifiably, about a new piece of kit that didn't work as well as the seller said it would.

I got to stretch my legs again a couple of hours later, thanks to a fire alarm. Fortunately it was nothing serious, and forcing all of the Darwin Centre personnel to collect in one small meeting point meant I bumped into a few friendly faces. Many of my classmates had also started their projects this week. We're mostly all at the same stage: reading. I read a lot. I feel slightly more educated about DNA today. Tomorrow is my lab induction, after which people will expect me to know what I'm doing!

(The mutual misunderstandings between me and the Mac continue)

Day one of The Project

My year in London has been split more or less in half. Up until April's wonderful wonderful 90%-not-working break, I'd been in the taught half. I went to lectures and wrote essays and did practicals. Today was the first day of the research half.

I arrived at the library by 07:30 as usual (peak trains are just sooo much more expensive) and checked my emails. Turns out my supervisor starts his day at 08:30, so my morning internet trawl will be cut a little short. This is probably for the best. I went down the road to the museum and got rather lost because the routes around the whale installation building site had changed since I was last here, but arrived with a couple of minutes to spare outside his office.

I waited by looking over a big shelving unit, mostly groaning under the weight of parasitological books and journals, but with one space dedicated to taxidermied anurans enjoying Australian beer. I didn't ask.

Trying to get a spare computer in the office to work for me was a comedy of errors. Apart from anything else, today was an exercise in IT. I've barely used Macs before. I still haven't quite accepted that " is @ and the scroll goes upside down. The mouse makes a loud scraping noise over the desk as I wave my arm around, arcing the cursor from one end of the excessively gigantic screen to the other. It took me ages to realise that Photoshop did actually use layers because the layer box was nearly half a metre away from my image. Anyway.

This project is about finding remains of human intestinal parasites in soil. An archaeologist has sent the museum some samples from Russian graves, a few centuries old. The samples were taken from the pelvic regions, so if the people had any worms living in their intestines, we might be able to find some eggs. We're also going to try and extract some DNA, but there's a fair chance that the only thing that will prove is that soil contains bacteria. As a second angle, we'd also like to try and sequence some DNA from museum specimens of these worms too. Those animals will be intact, but preservatives can degrade DNA too. It's tricky stuff.

Today was mostly reading papers. I read a good textbook on palaeoparasitology over the break, but the DNA side is quite recent and not much has transferred to secondary sources yet. Also, textbooks are generally written clearly and explain their jargon. Papers can be impenetrable. I shall be ploughing through for some time yet.