Category Archives: Video

we be all night

Special thanks to Queen B for helping us give voice to our passion for science. More substantial posts to come once I figure out how to save my iPython scripts!

“Stuck in Lab” (feat. Sarah, Ruth, and Reyn)

I’ve been thinking, I’ve been thinking
I get filthy when that vector get into me
I’ve been thinking, I’ve been thinking
Why can’t I keep these slides in focus?
Laby I want you, na na
Why can’t I keep these slides in focus?
Laby I want you, na na

Primers on ice, primers on ice
Feeling like an animal with these cameras all in my grill
Flashing lights, flashing lights
These bands are faded, faded, faded
Laby, I want you, na na

Can’t keep my eyes off that UV
Laby I want you, na na
Stuck in lab, I want you

We woke up in the morning saying,
“How the hell did this shit happen?”
Oh laby, stuck in lab we be all night
Last thing I remember is your beautiful cultures spinning up in that flask
Stuck in lab

We be all night, in laaaab lab
We be all night, in laaaaab lab

We be all night,
And everything alright
No complaint, your FISH is so fluorescent under these lights
Laby, I’m thinking,
Park it in the rig 7 to 11
I’m sterilizing, st-sterilizing, if you scared, call that sales rep
I’m thinking, get my brain right
Filter water, oyster life
Kim wipes, we wipe it out like wash rags we wear it out
Laby, I’m thinking, I’m yelling, on the phone with the sales rep
Then I lay the transect halfway then write it on my clipboardt, clipboardt, clipboardt
Riding on that boat, riding, riding on that boat
I’m culling on that, culling, culling on that eel grass
Been spinning all this, spinning, spinning all in this good, good

We woke up in the morning saying,
“How the hell did this shit happen?”
Oh laby, stuck in lab we be all night
Last thing I remember is your beautiful cultures spinning up in that flask
Stuck in lab

We be all night, in laaaab lab
We be all night, in laaaaab lab

Hold up
That Lisa is the shit if I do say so myself
If I do say so myself, if I do say so myself
Hold up,
Intertidal got doused time to back up all of that mouth
That you had all in the car, talking ’bout you the baddest bitch thus far
Talking ’bout you be counting that turd, I wanna see all the laby that I heard
You know I can quantitate, hope you got a standard curve, Uh
PCR in the gel rig, fucked up my control
Put the product right to the side aint got the time to put gloves on, on site
Catch a charge I might, beat the rig up like Mike
In ’97 I bite, I’m Drew, Harvell Harvell
Laby no I don’t play, now bake the cake, DNA
Said, “bake the cake, DNA!”
I’m nice, for y’all to reach these heights you gonna need 3 genes
4, 5, 6 types, sleep tight
We count again in the morning, your hemocytes is my breakfast
We going in, we be all night

We be all night, in laaaab lab
We be all night, in laaaaab lab

Never tired, never tired
I been sipping, that’s the only thing that’s keeping me on fire, me on fire
Didn’t mean to spill that coffee all on my attire
I’ve been eating watermelon
I want your lesions right now, laby I want you, right now
Can’t keep my eyes off that UV
Laby I want you

We be all night, in laaaab lab
We be all night, in laaaaab lab

Processing all those oysters…Let the PCR begin

Many PCRs will ensue in the upcoming days. In regards to that, here is a video for your enjoyment.

M:          Yesterday Casey and I extracted DNA from the gill tissue and digestive glands of one oyster from each of the treatments of the oyster filtration of Laby experiment. We used the QIAGEN DNA Stool kit an all of the samples. We actually got the heat black to cooperate this time.Previously, I questioned the specificity of the ‘Laby 154′ primer set. To test specificity of this primer set (and the ‘Laby-WC’ primer set), we also extracted DNA from one of the trees outside of Lab 10. It is very unlikely that the marine protist, Labyrinthula, would be living on a terrestrial plant, but other epiphytes and the plant itself still have 18S DNA to possibly anneal to the “Laby 154′ primers and amplify. We added DNA from each sample to two PCR reaction mixtures; one with the ‘Laby-154′ primer set and another with the ‘Laby-WC’ primer set. Reaction were 10uL using BSA and GoTaq Green polymerase and 1uL of template DNA. We used the same thermocycler conditions as our previous PCR run with this primer set.

Today, I ran these PCR products on a 1% agarose gel made with 100mL 1xTBE buffer, stained with 5uL of EtBr at 80V for 1 hr.

R:

8.28.14

  • 1) Seawater and Oyster Treatment #1  Digestive Gland (SO1.1_DG)
  • 2) Seawater and Oyster Treatment #2 Digestive Gland (SO2.1_DG)
  • 3) Seawater and Oyster Treatment #3 Digestive Gland (SO3.1_DG)
  • 4) Seawater and Oyster and Laby Treatment #1 Digestive Gland (SOL1.1_DG)
  • 5) Seawater and Oyster and Laby Treatment #2 Digestive Gland (SOL2.1_DG)
  • 6) Seawater and Oyster and Laby Treatment #3 Digestive Gland (SOL3.1_DG)
  • 7) Seawater and Oyster Treatment #1 Gills (SO1.1_GL)
  • 8) Seawater and Oyster Treatment #2 Gills (SO2.1_GL)
  • 9) Seawater and Oyster Treatment #3 Gills (SO3.1_GL)
  • 10) Seawater and Oyster and Laby Treatment #1 Gills (SOL1.1_GL)
  • 11) Seawater and Oyster and Laby Treatment #2 Gills (SOL2.1_GL)
  • 12) Seawater and Oyster and Laby Treatment #3 Gills (SOL3.1_GL)
  • 13) Terrestrial Leaf DNA
  • 14) BLANK DNA EXTRACTION
  • (-) No Sample PCR control

D:       The Laby-154 primer set amplified everything including the terrestrial leaf sample (except the BLANK). I would conclude that this primer set is not specific to Labyrinthula sp. and therefore should not be used for its detection. However, amplification in all samples with this primer set means that good DNA was extracted and that this primer set may be used for a PCR control. The Laby-WC primer set did not amplify the terrestrial leaf. Instead we only got a band on #12 and a faint band on #7. These are both gill samples. It seems that Laby was not the digestive gland or not detectable in the digestive gland. This might make sense if the oysters are actually ingesting the protist then Laby DNA may already be degraded during the digestive process. The faint band in the treatment that did not have any inoculated Laby might suggest that there was already Laby in the seawater/attached to the oyster when entering the treatment. More of the oyster will need to be tested to see if this trend continues.

 

 

 

 

The coral microbiome: Thinking productively

Drew’s lecture on the coral microbiome sparked an interesting discussion today through which we considered what we know, what we’ve learned, and where we want to go. As was duly noted, the microbiome is a tricky beast to study in any organism! The complex community ecology of thousands of interacting organisms – which have no clear species distinctions p.s. – is a formidable challenge.

But what can we shoot for that’s realistic? Coral biologists have started by broadly characterizing differences at the community level between corals at different sites, of different disease statuses, and exposed to different temperatures and other stressors or treatments. There is also a pretty clear distinction between the bacterial microbiota of different species.

These broad characterizations are useful, but I think we’re all thirsting to make better use of the OTU-level data (OTU = operational taxonomic unit, often based on 97% sequence similarity or higher that is considered species-level). Part of the problem is the limited data on the ecological context for marine bacteria. I.e., we can’t start to interpret what’s happening with all the different OTUs without knowing what they do. Often we can’t even assign a sequence to a phylum. We literally only know that it is a bacterium. As a result, we have a daunting problem with 1000s (or more!) marine bacteria in a sample and no way to culture most of them.

Thinking comparatively across bobtail squid, humans, corals and other organisms may be one way to formulate clear hypotheses and new ways of doing things. We should also remember that we have a lot of information on the coral microbiome relative to the past, and new tools may help us make sense of the data.

Above all, this research presents a lot of really cool biological questions and allows us to test fascinating hypotheses. This NPR video that we watched in class today does a good job of communicating how fascinating this “universe” is!

In case anyone is interested in thinking about the microbiota in a very different context, here are a couple blog posts I wrote when I was working on public health at Environmental Defense Fund: 

A new power couple: The combined impact of the microbiome and chemical exposures on disease susceptibility (Part 1 of 2)

Part 2 of 2

Week 1 Video

Week 1 video posted!

Got to learn about pathogenic protists yesterday (bitter crab syndrome!) and transcriptions. In our free time we set up a sea star disease experiment to investigate the SSWD pathogen. Can’t believe we are almost done with week 2.