Finding Caenorhabditis Nematodes in the Under-Explored Midwest

Blake David lindgren Author

04/07/2021 Added

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[00:00:02.142]Hello my name is Blake Lindgren
[00:00:03.640]and I'm presenting Finding
[00:00:04.840]Caenorhabditis Nematodes in the under
[00:00:06.455]Explored Midwest
[00:00:08.074]So the first thing you need to know
[00:00:10.318]What C Elegans is and what the project
[00:00:12.284]goals are C elegans is a free living
[00:00:14.705]Bactriovorus Nematode it lives in
[00:00:16.880]Decaying matter and is found across the world
[00:00:19.604]And is a powerful genetic model organism
[00:00:22.244]The project goals are obviously identify
[00:00:25.627]and find a source of C Elegans
[00:00:27.452]Contribute to C elegans biogeographic database
[00:00:30.989]and characterize isolation sites for
[00:00:33.353]C elegans
[00:00:34.627]So you know we're looking for C elegans
[00:00:37.679]and how do we get them is
[00:00:39.153]we isolate them which means we take
[00:00:41.483]Decaying matter which is rotting apples
[00:00:43.771]Rotten walnuts or compost or other things
[00:00:46.359]And we try to put them on plates and pick
[00:00:47.943]the worms off to keep them
[00:00:49.252]we have isolated previously
[00:00:51.343]Caenorhabditis sp. 8 and C briggsaes
[00:00:54.414]C elegans has not been isolated yet in
[00:00:57.216]the Midwest or in Nebraska
[00:00:59.636]This is the map of sites we are going to
[00:01:01.706]isolate or to get worms from where we
[00:01:04.051]going to sample from martins hillside
[00:01:05.450]orchard valas pumpkin patch and east side
[00:01:08.020]Campus from the university of Nebraska
[00:01:09.941]Which you can see here on the right side
[00:01:12.129]so the first place we went to was east side
[00:01:15.162]Campus and we were sampling the walnuts
[00:01:17.325]From there and we got three walnuts from
[00:01:19.140]the greenhouses over here and we got 22
[00:01:21.581]samples from the beehives over here on
[00:01:23.948]east campus we can see in these pictures
[00:01:27.692]the next place we went to was martins
[00:01:31.028]and Valas and I forgot to mention we did
[00:01:33.269]not get any nematodes form the greenhouses or the beehives
[00:01:37.622]The next place we went to was martins and
[00:01:39.814]when we went to martins we sampled 46 apples
[00:01:42.277]and we only 2 nematodes from a single apple
[00:01:45.782]from this side area over here'
[00:01:48.141]and the next place we went to was valas
[00:01:50.335]we sampled 31 apples and got zero nematodes
[00:01:53.451]from them as well
[00:01:54.463]and I should mention about the apples
[00:01:56.214]very quickly is this is not normal
[00:01:58.159]last year when they went to martins
[00:02:00.216]they gotten all there nematodes form one sampling
[00:02:04.880]and they didnt sample 90 apples they
[00:02:06.939]sampled the same amount of apples so this
[00:02:09.170]is very strange to say the least while we haven't
[00:02:11.971]sampled walnuts as I mentioned before this
[00:02:13.946]is far stranger because we have no reason
[00:02:17.197]to believe normal this has not happened before
[00:02:20.604]in the research years so its defiuntily
[00:02:23.248]a bit strange and something to keep note of
[00:02:25.179]so after that we only have 2 worms
[00:02:28.753]we need to move on and find something else
[00:02:30.738]so next thing we try to get is compost sampling
[00:02:32.998]and we got our compost SBS faculty and students
[00:02:37.539]And they got us 18 bags total
[00:02:40.529]out of the 18 bags 16 had worms and out
[00:02:44.754]of those 16 two different kinds of worms in them
[00:02:49.480]so when we sampled the bag we had two
[00:02:52.379]different district kind of worm's
[00:02:53.616]and this is the result tab of them and
[00:02:56.453]you can see we sampled alot but we didnt
[00:02:58.617]actually get that many compared to last year
[00:03:00.806]we definitely had to sample a lot more this year
[00:03:02.552]but 16 of the worm's came from compost
[00:03:05.598]2 of the worms came from apples
[00:03:07.290]and once again to mention this is not
[00:03:09.787]normal for apples apples should have
[00:03:11.607]given us a lot more compared to what we have
[00:03:13.974]gotten in years prior
[00:03:15.534]so we're kind of gonna go through the
[00:03:18.056]workflow really quick the first thing we
[00:03:19.654]have to do is we have to do is isolate
[00:03:20.976]our nematodes which we just did we have
[00:03:23.244]gotten our nematodes we got them on our
[00:03:25.274]plates and what's the next step and how do
[00:03:27.614]you tell worms apart so really your got to look
[00:03:29.676]for is the growth rate and the self fertility
[00:03:32.258]and we check those rates and ill explain them
[00:03:34.394]in a sec but after that you look at morphology
[00:03:37.001]and then you do a DNA sequencing of a gene
[00:03:40.161]now for the self futility and growth rate
[00:03:43.226]to briefly explain growth rates are
[00:03:45.983]comparative that's the best way to describe
[00:03:48.125]them but we do look at some other things
[00:03:49.933]we look at basically how fast they grow compared
[00:03:52.509]to other ones and how fast they grow
[00:03:54.477]compared to out C elegans that we have in
[00:03:55.944]lab because we do have some C elegans
[00:03:58.156]from other parts of the world
[00:03:59.557]but how fast do they just comparatively
[00:04:01.778]Because that's the best way to compare growth
[00:04:04.355]rates very easily at least in a short amount of time
[00:04:06.638]so fertility is also very important Because
[00:04:10.934]C elegans is a hermaphroditic worm
[00:04:14.055]Which means its self fertile it means it
[00:04:16.918]only needs itself to produce offspring
[00:04:18.673]and C elegans is a fast grower
[00:04:20.249]so you do that very simply by picking a
[00:04:22.689]female to a plate and waiting for it to
[00:04:25.398]reach maturity and then once it reaches maturity
[00:04:28.053]if it has offspring its self fertile
[00:04:30.564]because its by itself and it had to
[00:04:32.255]fertilize its own eggs
[00:04:33.538]So the next thing we look at is morphology
[00:04:37.374]and we really look at two big traits this
[00:04:39.681]can tell you alot about your worms the
[00:04:42.040]two big traits are buccal cavity and the
[00:04:44.398]pharynx you can see these two diagrams
[00:04:46.598]here and we check under a very powerful
[00:04:48.815]microspore to look at the buccal cavity
[00:04:51.241]and the pharynx ill show you better on a
[00:04:55.064]worm that I have so the left picture here is
[00:04:58.031]the buccal cavity and the pharynx is the
[00:05:03.659]right picture you can see the mouth structure
[00:05:09.101]its a very distinct feature and its a lot
[00:05:11.551]easier to tell apart then other features
[00:05:13.018]which is why we use this two predominantly
[00:05:14.892]so after you've gotten your worms and you've
[00:05:17.593]done fertility' tests and everything you
[00:05:19.677]have to ask what worms are you gonna
[00:05:22.326]sequence and which ones do you want to do first
[00:05:24.867]and which ones look the best
[00:05:26.309]so what your looking to do is
[00:05:27.907]tell your worms apart you cant do the
[00:05:30.056]whole DNA strain because that would be
[00:05:31.863]ridiculously long and a pain to deal with
[00:05:35.160]so instead a much easier way to do this
[00:05:38.304]is to take a conserved gene which is a
[00:05:42.047]specific kind of gene that basically
[00:05:44.874]allows you to easily compare your worms
[00:05:47.315]against each other because it is conserved
[00:05:49.958]this is a important part because it basically
[00:05:52.350]means there are very few changes and the
[00:05:54.815]changes that happen would be very specify
[00:05:56.758]to species so we do this by taking the
[00:05:59.150]18srRNA gene which once again a very specific
[00:06:03.674]gene all you really need to know is that
[00:06:05.655]it is conserved and it allows us to compare
[00:06:07.177]worms very easily and we do this by doing
[00:06:09.436]PCR and then gel extraction
[00:06:10.967]the results from that are here from one
[00:06:13.957]worm just for showing you
[00:06:16.349]on this example we have the results at the
[00:06:20.823]bottom here over at the qaury cover
[00:06:23.349]that is the percentage of likely hood
[00:06:27.823]it is that from the DNA we have its 99%
[00:06:30.624]for the top 2 and the top two are
[00:06:32.998]Rabdiltella axie which is a good likely hood
[00:06:37.974]that actually what it is and ill show
[00:06:40.489]you quickly were that is on the graph here
[00:06:42.452]now this red line here is the
[00:06:44.034]specific species and the bottom is C elegans
[00:06:52.618]and there distantly related but it is the
[00:06:55.232]result of them and that's how we compare them
[00:06:57.296]moving forward so really the future directions
[00:07:01.055]of this project is obviously characterize
[00:07:04.463]all the other C legans candidates we have
[00:07:07.280]and the ones don't have so we can double check
[00:07:09.254]they are not C elegans or related because
[00:07:11.605]morphology does not always tell you
[00:07:13.696]everything you need to know the other
[00:07:15.522]thing we need to do is investigate the lack
[00:07:17.157]of nematodes from apples that is very strange
[00:07:20.431]from this year I cant explain how strange
[00:07:24.847]that was when we sampled upwards of 90
[00:07:28.296]apples and only get 2 worms from that
[00:07:30.264]and last year they sampled 40 apples and
[00:07:33.805]got plenty of worms the next thing we need
[00:07:37.706]to do after that is to gather more samples
[00:07:40.656]not just from apples but from other things
[00:07:42.697]and see if C elegans is living in those
[00:07:47.369]so this is very important we do those things
[00:07:51.036]and the final thing id like to do is to
[00:07:52.469]acknowledge the people who helped me
[00:07:57.261]so id like to thank all of Herman lab
[00:07:59.504]but really id like to thank Dr Michael Herman
[00:08:03.711]Leah and most importantly Ashley
[00:08:07.204]they all really helped me but Ashley
[00:08:09.810]specifically but they all helped me
[00:08:12.875]and the program id like to thank is FYRE
[00:08:18.745]being a freshman it was most freshman
[00:08:21.830]don't get to do research and id just like
[00:08:23.563]to thank them

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Finding Caenorhabditis Nematodes in the Under-Explored Midwest

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