Thank you!!!

Hi all,

Wow!!! The LilBUBome crowdfunding is over. We have to admit that these last 40 days of fundraising (and the previous days of preparation) have been quite exhausting – but also unbelievably exciting. This was our first experience with crowdfunding, and we always had the fear of not getting funded. Not because of the money, but because it would have meant that we did not manage to explain how amazingly interesting this project is. So we are really glad to have finally reached our goal (and a little bit more), and about all the positive feedback we have received!

A BIG THANK YOU goes undoubtedly to the 248 backers who decided to join the project. We appreciate not only your support but also your interaction with us. All of you contributed to achieve the first essential part of this project. And now it is our turn!!!!!

So, what´s next? Continue reading

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Our stretch goal: Maine Coons. The sky’s the limit for awesome cat genetics!

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A Maine Coon with polydactyly. [by Jorbasa, via flickr]

As we posted yesterday, we have reached the full amount needed to sequence BUBs genome. Thanks again to everyone who made this happen! But the fundraiser is still not over! You can still donate on the experiment.com site and we have 5 more days to prove that we can do even more awesome science – with your help! Here’s what we propose to do:

We’ve set our stretch goal to 30.000$ and the money that we raise will go towards Leslie Lyons’ 99 Lives Cat genome sequencing initiative. More specifically, we would like to sequence another cat breed, with traits that resemble those of LilBUB. This will help us understand BUB’s genome data better. At the same time we will get insight into the health and biology of this breed. And after a long discussion with Leslie this afternoon we have settled for Maine Coons.

Here’s why: Continue reading

Same, same, but different? Meet Rosie, another cat with osteopetrosis.

One of the great things about the LilBUBome is that it’s an open science project, so we get to interact a lot with people who are interested in our science. One of these people is Ann, whom we got to know through Mike (BUB’s dude). Ann had contacted Mike a few months ago, because she also has a cat, Rosie, who was recently diagnosed with osteopetrosis, and Ann wanted to know more about the disease.

Of course, we were really fascinated by Ann & Rosie’s story: osteopetrosis is a rare disease, and even more rare in cats. BUB seems unique, because she’s the only cat with a juvenile (early-onset) form of the disease. Rosie’s case seems different.

Rosie & Ziggy April 2015

A furball with piercing green eyes. Meet Rosie, another cat with osteopetrosis.

For example, she only developed osteopetrosis when she was older, so – unlike BUB –  she’s actually quite long and lean (BUB is probably so small because her osteopetrosis forced her bones to calcify and stop growing too quickly).

Also, Rosie has different symptoms than BUB, and also received a different treatment. However, similarly to BUB she seems to be doing fine, despite living with osteopetrosis.

So, similarly to human patients with osteopetrosis, the disease seems to be rather diverse in cats, too. To get a better picture, we asked Anne to tell us Rosie’s story. Continue reading

Ask an Expert – Prof. Uwe Kornak on BUB, Osteopetrosis, and Genetics.

Hi All,

as we mentioned before, we are connected with experts in cat genetics and bone disorders, who back us up on all the expertise we don’t have. With their help we think we have a very good chance of finding BUB’s mutation once we get her genome sequence.

It also has the big advantage that we can ask them basically anything. And so we did, when we asked Prof. Uwe Kornak from the Charité University Hospital about LilBUB, types of osteopetrosis and the diffences between mutations in animals and humans. Read on…… Continue reading

23 days later, this is where we’re at…

Hi All, 17 days of crowdfunding to go and last week was totally insane: we found a mutation in LilBUB’s genome, which we think causes her polydactyly (!). Also, traffic and support for the project just exploded – we’ve now raised an unbelievable 4,699$ (only 1,801$ to go)! We’ll be bringing you some more scientific content next week, but until then, there are a few things we wanted to say: Continue reading

Congratulations! It’s a Hemingway.

Hi All,

Last week Daniel was busy in the lab, doing a first experiment for the LilBUBome. And as we briefly posted yesterday: he found something really cool! We actually just wanted to test whether the DNA we extracted from BUB’s blood was of good quality. So we decided to do this by checking the DNA sequence of BUB’s ZRS.

Well, it turns out that with this experiment, we found out why BUB has polydactyly AND discovered at the same time that she’s (very, very, very distantly) related to Ernest Hemingway’s cats!

Here’s the full story. It’s a bit long, but worth the read… Continue reading

NerdTalk

OK people. We wanted to let you know how things sound and feel like in the lab. So this one is for those of you who are interested, have a little more background knowledge, or are scientists. These are some notes on what exactly we did to sequence LilBUB’s ZRS in a way that I’d write it in an email to Uschi or Dario or how I could reconstruct the experiment I did in my lab book. Continue reading

First bit of real research! How to make a LilBUBome – STEP 2. Sequence a target region

Hey All,

as we wrote you on Thursday, we’ve decided to do a lucky-guess experiment to look for mutations in a tiny part of LilBUB’s genome, a region called the ZRS. So, this week we’ve been working pretty hard to get a sample ready for sequencing, because May 1st is a bank holiday here in Germany. Well, it turns out I was too slow so now we’ll only get the result of what the exact DNA sequence of LilBUB’s 800bp ZRS is on Monday.

So, what did we do?

First, we extracted the DNA from some of the blood sample. We then used a technique called PCR to purify (and amplify) only the DNA contains the ZRS, so that we have a lot of material to analyze (here’s how it works).

After that, the first thing we checked is whether amplifying LilBUB’s DNA worked just like amplifying any other cat’s DNA (which I did as control in parallel – thanks to my neighbor Nadja for the sample). Turns out, BUB’s ZRS (remember, the part of the DNA that controls the number of digits) is the same size as that of the control. OK, nothing unusual so far.

The amplified ZRS of a control cat (left) and LilBUB (right)

But what about the actual DNA sequence? We sent only only the amplified bit of DNA in the picture above for sequencing (0.00023% of BUB’s genome) and until Monday we have to wait for the results. So let’s see, my guess is it’s like nothing unnormal in the sequence here as well.

Best

Daniel

The guessing game: searching the ZRS haystack for mutations

On Monday we had a state-of-the-crowdfunding meeting. We’re all really excited that we’ve already raised 28% of the money, and we’d love to share some of that excitement with you. So, after some discussion Daniel and Darío persuaded their boss to pay for a lucky-guess sequencing. This means we’re applying a magnifying glass at only a tiny part of the genome, because we’re hoping we might find something there. Basically, while searching for a needle in a whole bunch of haystacks, we’ve decided to focus on a single one (you can read more about different strategies for finding needles in genomic haystacks in our previous post: How to find a mutation? – Needles and haystacks).

The haystack we’ve decided to focus on is called the ZRS. The function and discovery of the ZRS warrants multiple blog posts in it’s own right, so let’s just say it’s a decent haystack to look at. First of all, it’s rather small: about 800 basepairs (building blocks of DNA), and only 0.000028% of the genome. Second, we know that there are a bunch of human patients, chicken, dogs and other cats with polydactyly, who all have mutations in the ZRS, so we figured: if we have to make a single guess this will be it.

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Polydactyly happens in many different species

Daniel started the experiments on Monday. We’ll keep you posted with progress!

– Uschi