Summer Interns 2014 : 10-July-2014 This page last changed on Jul 10, 2014 by thersh. This week, I ran multiple rounds of PCR on tissues from three different squid species and a nudibranch species. 2/4 rounds of PCR were successful (i.e. my primers amplified something). I ran the PCR products on a gel and cut out the most promising bands. I was able to get DNA from the bands, which was then sequenced. Good news: I have viable sequence for Pterygioteuthis! Basically, the photoprotein sequence that was found in a different species of squid appears to have similar genetic structure to the photoprotein sequence in Pterygioteuthis. Now I'll actually have something interesting to talk about during my presentation, even if nothing else happens during my project! Comments:
Another week gone, hard to imagine we're half way through. It's been a fairly productive week for me, despite my PC deciding to sulk on me at various points. My seafloor spreading data is all coming together. Having established lack of variation in extension due to faulting and fissure formation across the Alarcon Rise, I have shown notable variation in fault scarp orientation. I am now fine tuning the collected data, and gearing myself up for surveying one or possibly two more areas on the Alarcon Rise. Two would be wonderful, but I know time limits will come into play. I nearly missed Dilly's cookie break, but made it in time for the crumbs. In order to provide some variation from generating and recording data I have been working my way through all the Pink Floyd albums, so if anyone has walked by and heard me howling, "welcome to the machine," then I apologise for the noise disturbance, but ear plugs can be made available on request. Posted by kwillis at Jul 10, 2014 11:38
To get a better idea of how well the LISST-HOLO is able to characterize the plankton community structure, we will compare images to whole water samples collected at the same time. I am now going back to my roots and counting the plankton in those whole water samples at the scope. Posted by lziccarelli at Jul 10, 2014 14:15
This week has taught me to loath 3rd party freeware. Dependencies are the devil. But besides that I got an embedded system running ubuntu. I also successfully installed opencv (the freeware) on my linux box. I am currently developing code on it to mirror what I developed in matlab. However, this time I am programming with runtime in mind, trying various techniques to hopefully allow it to run in real time. I am having trouble with morphological operators in the less friendly c++ world. Next week I will continue my c++ code and maybe even successfully install opencv on the target. Posted by jsteck at Jul 10, 2014 16:55
My mentor was on vacation this week, but I still had so much fun learning from other MBARI staff members! Larry Bird taught me the basics of the lathe and mill. On Wednesday, we focused on welding, and I even got a little practice. I hope to find the time to get back there and refine my skills (welding is hard!!). Today, Mike was nice enough to walk me and Nate through some of the other machines. Always inspiring to talk to passionate people. I'm looking forward to going out next Monday on the Rachel Carson to get the benthic rover. I'll be working hard on decorating styrofoam cups over the weekend. Posted by cordelia at Jul 10, 2014 16:56
This week I have been working on several different parts for the AMP exhibit in the Aquarium. The earlier components that I designed are about to start being made, which will be really cool to see. I am currently working on a way to secure the motor and gearbox to the assembly by creating a mounting structure than can withstand the torsional forces that will be applied to it. Also Mike spent some time with Dilly and I in the machine shop and I think we both of us learned a lot! Posted by nreed at Jul 10, 2014 17:09
This week I was on the ship a lot, which is always fun, and on wednesday we cruised with the seminar speaker and she was wonderful to talk with. I just finished analyzing my last HD video tape for squid orientation and behavior; now I'm moving into the older tapes and I'll see how much info I can get out of them. I'll be over in Building G all by myself with just the smell of seagull poop to keep me company for the next bit of analysis. Posted by kthomas at Jul 10, 2014 17:10
Float is in the tank this week, and I'm off and running (profiling?). Ran into a small hiccup that gave a strong asymmetry in the actuator, but that was solved with a better suited check-valve. First steps at this point are to achieve a working velocity controller (descend @ 0.1m/s, achieve 0 velocity, ascend 0.05 m/s, etc.). From there go to depth control (go to 5m, 2m, 7m, etc.) Spent some time earlier in the week thinking about controller strategy/form, and have some ideas to model/play with. Also excited to get out on the Carson on Monday! Posted by lbarker at Jul 10, 2014 17:17
Things are looking up this week. I feel like I have a clear goal ahead of me now. Gonna be doing tons of VARS searching and spreadsheets. This entails looking for repeatable patterns in monthly abundances of rare species found in Monterey Bay's mid-water, classifying them, and argue their importantance lolz Posted by wtruong at Jul 10, 2014 17:21
This week my project took an interesting turn. My mentor and I have decided that a cool way to tease out LRAUV malfunctions could be the difference between observed LRAUV behavior and simulated behavior based on LRAUV theoretical equations of motion. And so this week I ended up bashing my head against the books and writing code for such a model. The 6 DOF model is pretty much written and next I'll be feeding it with historical data and comparing outputs with what the LRAUV actually ended up doing in past deployments. Can't wait to see what comes out the other end! Oh, I also added beaker as my profile picture to Jons request! Posted by byraanan at Jul 10, 2014 17:27
It was great this week to get out to sea and spend some time getting to know Kelly, our guest speaker. She was full of great advice and was certainly a fun person to talk to. Aside from that, the data collection and entry continues! I am very excited to start crunching the numbers soon to see what we will come up with! Posted by bburford at Jul 11, 2014 09:43
This week I spent most of my time doing transfers for my cultures. I still have the 14 flasks of RCC299 that I'm using for my preliminary nutrient depletion experiment, and yesterday I diluted them for the last time down to 150,000 cells/mL (very low!!). I diluted them to a very low concentration because this way there will be more generations, and a better more defined growth curve (more checkpoints before they level off into stationary phase). Posted by amaitland at Jul 11, 2014 11:45
Ah the half way point. I have just finished the data collection and done preliminary data workup towards answering my first question: at what rate(s) are traces in the seabed created and degraded at Station M? (and are there differences in these rates between traces?) To answer this, I have looked through >12000 photos spanning 18 months from the time lapse camera, and measured the size and area that each trace covers, noting the creation start and end times, and the last visible time. I am comparing this to environmental data. The preliminary work up suggests that the creation rates of seastar feeding impression spike about 5 months after the deposition of detritus - this means that sea stars like their food to be 'old', not fresh. Patterns in the creation rates of echinoid traces are not as easily teased out. Next week I will decide whether to look at another year's worth of time lapse images, or whether to move on to looking at differences in density and diversity of traces using images from the rover. Oh, and I'll try not to get seasick on the Carson on Monday! Posted by jdurden at Jul 13, 2014 13:01
This week was mostly spent up in Santa Cruz getting to prepare and run my full suite of samples for grain size analysis. I should now have data needed at least be able to write something for the project! Not much else to report other than getting through the logging - 2 transects done, 1 to go. I should be able to get the last one complete this week along with having a look at the grain size data. Posted by wsymons at Jul 13, 2014 15:38
I am afraid I have made less progress than I wished this week due to limited throughput of the sequencer. However, I have started to write my report for the internship and could analyze at least some more genes. At the moment a greater challenge consists in going through all the data other people produced, extracting the relevant information and understanding how they came to their results. Posted by cbreusing at Jul 13, 2014 16:19
Can't believe we are already half way through! This week went very well. I have started my main experiment so hopefully by wednesday of next week I will be able to tell which phosphorus concentration is considered a deplete condition for the phytoplankton. This week I have also finished my application for the SACNAS conference! Posted by zjensvold at Jul 13, 2014 21:17
Apologies for being so late on this one. Last week was hectic but productive! I went out on the water by Hopkins TWICE: once with Chris, Jeff, and Jules to deploy the pH sensors, and once with Kerry Nickols to learn CTD and bottle sampling techniques. We saw some cute seals. It was great. Looking forward to collecting more samples throughout my project. I'll be filling 36 bottles tomorrow (nutes, chl, DIC, and salts). Posted by jlafian at Jul 14, 2014 17:26

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