Initial results: new egg-laying mutants?

tl;dr: Using the data collected so far, we’ve already identified some mutants that look like they have different egg laying rates than the reference strain.  These could point to previously unknown roles for the mutated genes in nervous system function.  See the plot below for a summary of some of the results.

Following the dedicated work of so many worm watchers, we got classifications for all of the data that we initially uploaded to the site (thanks again!).  Since then, we’ve had a chance to look at some of the results.

Remember that the goal of this project is to find genes that play roles in behaviour.  The way we do that is by looking at mutant worms with known genetic changes to see if they behave differently.  If they do, then that’s a hint that the altered gene affects behaviour.  Many of the genes we are focussing on are likely to function in nerve cells so these results can provide new starting points for learning how brains work at the molecular level.

With a project like Worm Watch Lab, each video gets classified by multiple people.  We can compare different people’s annotations to help filter out mistakes and refine the timing of egg laying events.  Bertie Gyenes, a graduate student in my lab, has followed up on the work Vicky talked about in her blog post.

subspecial_illAt this point, we’ve just done some preliminary analysis of the average egg laying rate (how many eggs worms lay per video).  The plot summarises this data.  Each bar shows the range of egg laying rates observed for a given strain (the red crosses are individual outlying worms) and the dashed orange line shows the rate typically observed for the laboratory reference strain N2.  The plot only shows data for the mutants with the lowest and highest egg laying rates.  As you can see, many of the worms with low rates are called egl.  That’s because these genes were initially discovered by screening for mutants with abnormal egg laying.  These are expected hits.  What you can also see are worms with unusually high egg laying rates.  Many of these, including the current record holder in our dataset dnc-1 were not previously known to have abnormal egg laying rates, which means we already have hints of new discoveries in the data that’s been categorised so far!

If you’re interested in learning more about any of these genes, just go to http://wormbase.org/ and put the gene name into the search bar.  Sometimes you can learn interesting things about the genes.  For example, mutations in the human version of dnc-1 can lead to Charcot-Marie-Tooth disease.

We’re getting ready to upload some new videos to Worm Watch Lab soon.  Please consider contributing some more annotations for the next batch of data.  It will be exciting to see what else we’ll find.

Tip 2: Pause and Scroll

In her latest post, Vicky shows how to make your annotations more accurate by pausing and scrolling while WormWatching.

-André

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Hey guys!

I’ve noticed from the data and on the discussion board that many of you miss the egg and press ‘z’ a little too late. Not to worry! This next tip will show you how to go back to the egg-laying event and press ‘z’ at the right time. It’s really simple.

Tip Of The Day: Press ‘z’ while the video is paused

It’s so easy to miss an egg, especially when the worm is moving so quickly! Have a look at this example:

Did you see the egg-laying first time? Believe me, I didn’t!

If you miss an egg-laying, pause the video by clicking on it. Scroll back to exactly when the worm lays the egg and press ‘z’. The time is recorded on the right hand side of the video.

Wormwatching just got a whole lot easier!

Until next time ~~~

Tip 1: Only mark fresh eggs

This is the first in a series of posts Vicky will be publishing in which she shares some tips for accurate worm watching based on the annotations she’s analysing.

-André

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Hello once again, Wormwatchers!

To continue on from the Top Ten graph in my last post, here is another graph giving the number of users recording times in a 30 second video containing only one egg-laying event. Here is the link to this video:

The red dotted line marks the time of the egg-laying event. As you can see, most users press ‘z’ close to the actual event, but a few users seem to go astray.

badspread_ oneegg

Help is at hand! From now, I will be posting tips to help you on the way to becoming a professional Wormwatcher!

Tip of the day: Do not mark eggs that are already there!

It’s very tempting to press ‘z’ when you already see an egg, but ONLY press ‘z’ when the egg appears from the middle of the worm while you’re watching. Have a look at 0:27 of this video where an egg appears next to the red spot:

There are already two eggs at the start of this video, and these must NOT be marked.

 Screen Shot 2014-07-30 at 11.14.03

A few of you go into a clicking frenzy as soon as you see one egg. Only click ONCE when you see ONE egg-laying event. Rest assured that the time appears on the right hand side of the video and it is recorded. If you see another egg, press ‘z’ once again to record the next egg. If you make a mistake and accidentally press ‘z’, you can remove the time by clicking the cross next to it like so:

Screen Shot 2014-07-30 at 11.30.50So, one press per egg, please!

Happy Wormwatching!

~~~

Top worm watchers so far

This is the first post from Vicky who is working in my lab for the summer.  She’s doing a first pass through all the data you’ve collected so far and will be writing a few posts like this so that you can see how the project’s progressing.

-Andre

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1476126_10202635002742051_1739207330_nHello Wormwatchers! My name is Vicky and I am an undergraduate student from Cambridge University working in Andre’s Behavioural Genomics lab at the MRC over the summer. My job will be to collect all the data from the past year’s worm watch project and to optimise the data for later analysis. Soon we will be able to see which mutant worms have a change in egg-laying behaviour and also whether this can be linked to other behaviours.

Since June last year, more than 200,000 videos have been watched by more than 20,000 people, so a big thank you to those of you taking part in this fantastic project. Your diligent worm watching abilities are most important for this project to succeed.

First things first, I can already see there are some particularly dedicated users so I have found the Top Ten, who have watched the most videos without an  unreasonably high average egg-finding rate.  This is a first-pass way of filtering out the users you’ve been discussing on the talk page that are recording way too many eggs.

Congratulations to shawym3 for topping the chart!

figure2I know a few of you in the top ten are not far off and for the rest of you it looks very close, so keep up the good work! We really appreciate your input! Remember, it’s important for us not only for people to go through the large set of videos, but also to get accurate annotations for the egg-laying events.

For those of you who have not made the top ten and who have quite a tight life schedule, wormwatching for 15 minutes per day for a week will get you through AT LEAST 30 videos. I have gone through about 60 videos in 15 minutes, so in a week that could be at least 420 videos! Easy!

If you are new to worm watching, it is important you understand the tutorial first and make sure you are familiar with what you have to do before getting into the real thing.  If you are unsure of anything in the videos you can comment on the discussion board.

Finally, all I have to say is..

..get Wormwatching! ~ ~ ~

A protective instinct and live birth

Although worms aren’t known to care for their offspring directly in any way, mothers are concerned for the environment their wormy children will grow up in.  You can see this self-sacrifice if there is no bacterial food around.  Without food, worms stop laying eggs because hatching into starvation wouldn’t be good for the little ones.  In extreme cases, you see a “bag of worms” phenotype: offspring hatch inside their mothers and eventually eat their way out!  Fortunately for the worm in this video, it found a patch of food soon enough that it could start laying eggs again.  And not a moment too soon.  Have a look:

The worm in the top left corner of the frame lays five already-hatched larvae and an egg all at the same time.  The mother almost looks relieved afterwards.

Long-lived mutants and healthy aging

Cynthia Kenyon is a scientist at UCSF who uses C. elegans to study how animals age and how changing genes can make them live longer, more active lives.  One reason this field generates so much excitement is the hope that conserved genes, that is genes that are shared by worms and humans, operate in a similar way and that we might one day understand them well enough to intervene in human ageing and significantly extend our healthy lifespan.  In worms at least, this extension can be dramatic.  Watch the TED talk for more:

Daring escape from a death star

One of the more unusual talks at last year’s International Worm Meeting was given by Jonathan Hodgkin from the University of Oxford about a deadly bacterial infection in worms.  Now their paper‘s out so I can share some of the gory details with you!

One aspect of bacterial infections that I find interesting in worms is that bacteria are both their main source of food and a potentially deadly source of infection.  Sometimes they kill in spectacular fashion.  The paper reporting the results of Jonathan’s experiments was just published in Current Biology and it’s open access, so you can go read the original paper in full if you’d like to learn more.  Perhaps their most striking finding  is that a newly described strain of bacteria wages asymmetric warfare against worms: although the bacteria are much smaller, they are able to very effectively capture swimming worms by sticking them together at their tails:

wormstar

Worms trapped by bacteria strike a death star pose. One lucky worm escapes.

The trapped worms die relatively quickly and are consumed by the bacteria.  A gruesome but efficient way for the bacteria to thrive.  But it’s not hopeless for our courageous friends the worms.  Larval worms trapped in a death star are able to take extreme measures to escape by performing autotomy.  That’s right, they cut themselves in half.

worm-autotomy

An adult worm that escaped from a worm death star at an earlier larval stage. Although missing a significant part of its tail, it’s able to self-fertilise and survive.

Even the truncated worms are often able to self-fertilise.  Sometimes extreme measures work for worms, as they do for humans.

Green Eggs and Worms

Bring a conversation starter to your next holiday party: a plate of worm-shaped cookies!

Worm cookie!

Oh, honey, look, it laid an egg!

The recipe is for a fairly standard butter cookie and is adapted from Cook’s Country (note, this recipe will make a lot of worms):

Ingredients Preparation
2 3/4 cups all-purpose white flour
1 1/4 cups granulated sugar
1 teaspoon baking powder
1/4 teaspoon table salt
2 large egg yolks
3/8 cup sour cream
1 tablespoon vanilla
1 1/2 sticks (12 tablespoons/175 g) unsalted butter
1. Melt the butter and set aside to cool slightly.2. In a large bowl, combine dry ingredients and whisk together.

3. In a smaller bowl, whisk egg yolks, sour cream, and vanilla until combined. Slowly add melted butter, whisking constantly, until mixture is smooth and homogeneous.

4. Pour wet ingredient mixture into dry ingredients; mix until flour is completely incorporated and the dough roughly makes a ball.

5. Turn dough out onto sheet of parchment paper (lightly floured if necessary), and separate into two halves.

Once the dough is prepared, it will probably have to be chilled for about an hour in the refrigerator before it’s ready to be rolled out. At that point, pre-heat the oven to 325F (160C) and lay out a piece of parchment paper on the counter. Knead and then roll the dough out to about 1/8-inch thick (that’s just over 3 mm). You can lightly flour the paper to prevent sticking, but the more flour you use, the tougher your cookies will end up being. If the dough warms to the point where it’s too floppy to work with, just put it back in the refrigerator for a few minutes.

Cookies being rolled out

To prevent sticking, occasionally (and carefully) flip the dough sheet over.

Once the dough is rolled out, begin cutting out worm shapes. Use a sharp knife and don’t worry about gaps in the dough: you can recycle scraps into another dough ball and re-roll it out (possibly after re-chilling it).

Bake the cookies for 10-12 minutes — ish. The cooking time varies somewhat depending on whether you’re using a conventional oven or a convection/fan oven. If it’s the latter, it might take much less time. I’d recommend setting a timer for about 7 minutes, rotating the cookie sheet, and then just keeping an eye on it until it’s golden brown around the edges.

Once they’re finished, you can decorate the cookies with a simple icing (1/2 cup icing sugar for every tablespoon of liquid such as milk or lemon juice) and sprinkles/colored sugar/chocolate chips, or frost them, or just dab a bit of icing on a few that you’ve decided look like the egg-layin’ type:

Worms! Lots of worms!

“I think some of those got a little more than golden brown.”
“…that’s just because I like my worms extra crispy.”

No matter what, worm cookies are a sure way to get people talking at your next get-together!

Worm sex

In the last post, I wrote about how C. elegans usually comes in the form of a self-fertilising hermaphrodite and that this is useful for studying behavioural genetics.  But, another important part of genetics is making crosses so that different genes can be exchanged between strains to study how they affect an organism.  Fortunately, there are also male C. elegans that are happy to exchange their genetic material with the hermaphrodites and although the hermaphrodites don’t strictly need the attention, the they don’t seem to mind.

Maureen Barr and Rene Garcia provide a technical, but not all together dry, description of the essentials in their WormBook chapter:

“In a stereotyped mating event, the male initially responds to hermaphrodite contact by placing his tail flush on her body; he begins moving backwards along her body until he reaches her head or tail, where he then turns via a sharp ventral coil. He continues backing until his tail contacts the vulva; at that region of the hermaphrodite, he stops moving, inserts his spicules, and ejaculates into the hermaphrodite uterus.”

This video from Steve Cook and Scott Emmons pretty much says (and shows!) it all:

Self-fertilising Hermaphrodites!

Many nematode species, including our favourite C. elegans, are self-fertilising hermaphrodites. This essentially means that they are females that are able to produce their own sperm. Selfing (as it is sometimes called) might seem a strange way of reproducing, but it can have advantages: for example, even a single worm may be able to successfully invade a new environment and produce many offspring.

For scientists like me that are interested in behavioural genetics, it makes it possible to study some mutations that it would not be possible to propagate in animals that couldn’t self. Take unc-7 mutants. As you can see in this video, worms with mutations in their unc-7 gene are not able to move normally.

That’s why they’re called “unc,” which stands for uncoordinated. The unc-7 gene makes a protein that connects neurons together and when it’s broken or absent, the neurons don’t communicate properly and that leads to abnormal motion.

If we had to rely on males to find and fertilise females, these mutants would be difficult to raise, but because they can reproduce by selfing, even severely uncoordinated worms can often survive perfectly well in the lab. That means we can study their behaviour (including egg laying!) and learn about how genes that lead to uncoordination work.

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