Farewell gala at Waikiki Aquarium

At this very moment I'm well on my way back home to Sweden, but still have a long way to go with a total flight time of 20 hours. I'm getting back to reality soon enough, well that's kind of how it feels after these five amazing weeks at C-MORE, Honolulu. Thankfully I will only have a few days back at work in Stockholm before I go on summer vacation for four weeks, making up for lost time with my family these past 6 months. It will be good.

So citing fellow course participant Michael Henson's Facebook post, "it feels surreal" that the course is over and a very awkward feeling saying goodbye to all these great people that I basically have spent every single day with for the past five weeks. Needless to say, it was a great bunch of people, students and faculty alike. I'm sure I will see most of them again sometime and there might even be opportunities for collaboration. To cite David Karl (the C-MORE director); "science is greater than any one individual", the new generation of scientists (including me) goes down a path of sharing knowledge to further our research to the benefit of all. That's exactly what Dave recognises and perhaps this is one of the contributing factors to why humanity has never seen a greater rate of progress in all fields and aspects. 30 years ago most methodologies and technologies (perhaps even including theories to some extent) never saw much change. Today, in 2015, and with the increasing development of the newly implemented metagenomic tools, we are looking at ever improving methods and new discoveries almost on a yearly basis. It is a staggering development which we all should be proud of and which I'm privileged to be part of.
Now I'm starting to sound like Dave, haha!

Anyway, the final day at C-MORE entailed a two hour long presentation which we students at the course had frantically put together the night before by fusing our individual stories from the data analyses to tell a coherent story of station ALOHA for all people interested (the presentation was open to the public). The lecture hall was almost filled up to the last seat which was really cool, and what was even cooler was that we even had the university dean and a US national science board member among the audience (in addition to all the renowned faculty of C-MORE, David Karl included).
I contributed with a small, but oh so important, story (which I of course told the audience) of nitrogen fixation at station ALOHA. Using metagenomics I wanted to address a few different questions on the subject; What organisms fix nitrogen at station ALOHA? At what depth do they do that? And finally, in what size fraction is most of the nitrogen fixation occurring? After successfully answering my questions I also used chemical and physical data profiles, plotted for comparison, to attempt to answer why I got these results.
In short (which was my conclusion slide during my part of the presentation) I found that the unicellular cyanobacteria and obligate symbiont, UCYN-A, was dominating nitrogen fixation at this time of year at station ALOHA. I also found that the relative abundance of genes for nitrogen fixation (nif-H, which I assumed to be a proxy for actual nitrogen fixation) was highest at the surface and decreased with depth.

The evening was spent at Waikiki Aquarium by the beach which was a farewell gala for us summer course students. All of C-MORE (and more) were invited and I had a great evening mingling with all the faculty a final time as well as hanging out with the rest of the students. Thanks Dave for the talk, the introductions to the rest of the renowned people attending and all the praise (weather it is actually true or not, you're a true inspiration).
I must say that it was a rather emotional evening which Mike set the bar for when he showed a self-made video compilation summing up the course (awesome job, Mike).
So at the end of our time at the Aquarium there were plenty of speeches of praise (specially by Dave), hugging and also a bit of crying. I wish the evening hadn't passed so quickly, but at least I had great concluding talks with everyone involved in the course.
Fittingly enough it just so happened that this very day was a regular day of fireworks at Waikiki. It really felt like it was just for us.
I'll see you soon again all the awesome people of C-MORE summer course 2015!

Now I'm going home with my head held high.

Short on time for final presentation

Just a quick update really. That's all I have time and energy for.
It has been an exhausting week of frantically analyzing and pursuing specific research questions on the samples, and ultimately data, that we pulled out from the cruise at station ALOHA.
I decided to investigate nitrogen fixation using metagenomics, since I'm an absolute beginner at metagenomics.
Tomorrow morning is the final (group)-presentation and there have been a few late nights. I'm probably looking at another one now.
That will be the end of the course, so when I'm done with that I can share my metagenomics work and findings in a bit more detail. Now I need to focus on getting everything right for tomorrow.
It will  be a big day tomorrow (presentation is open to the public). With that said, I leave you with a picture of an example of one step in the metagenomics workflow, for now.

Final week at C-MORE

I just started on my last week of work at the C-MORE summer course. What remains is an intense week of data analysis of the data we all generated from the lab work back at C-MORE hale. It includes many biochemical parameters as well as metagenomics. In the end we are supposed to take all these datasets and, as a group, try to make sense of them and tell a story to a general audience about what we found out at station ALOHA this past week. It will all be presented as a two-hour seminar on the last day.

I've already been part of a lot of work, including both practical lab analyses and data handling. My midsummer was spent calculating low level nitrogen (LLN), bacterial production (radiolabeled Leu) and primary production (14C). Despite a 15 hour workday, my group is not quite done yet. It was a valiant effort that took most of the evening, but in the end we couldn't finalize our datasheets due to insufficient structure in some of the cruise work group's raw data. Annoying, but a wall of numbers without labels is hard to make any sense of.

Anyway, these last calculations will be finished today since most of it by now is just a matter of putting in the data (in the correct order) into the template spreadsheets that we prepared yesterday. This is why I sometimes love Excel. The initial calculations take some time but as soon as the first calculation spreadsheet is set up it is just a matter of entering the raw data into one column and Excel will take care of the rest to automatically give me the calculated numbers at the (far away) end of it. Beautiful.

The lab method I had the privilege to run was, as mentioned, LLN, which is a chemical and gas chromatography (GC) based method where we apply analytical chemistry to measure nitrogen concentrations in the upper surface waters that are too low (less than 1 µM) to be detected by conventional auto-detectors. It is therefore fully manual where we add a few chemicals to our sample together with a carrier gas which will transport the sample through the system and into the GC where the nitrogen concentration will be recorded as a peak on a histogram on a computer. This will ultimately give us concentrations down to the nano-scale. This fact of course makes the method extremely sensitive to contaminations.
Another upside is that due to all the bubbling chemicals, which changed colour when added, you felt a tiny bit like a mad scientist. Muahaha!

The final day of lecture is soon about to start. It will be a day full of omics, Galaxy and also some microbial culturing signed Scott Gifford, former student at this very course. I'm sure it's gonna be an interesting day!

Back at C-MORE hale

The last two days out at sea were stressful, confusing and filled with different kinds of tasks. All of the labs on board needed to be prepared for disembarking and ultimately sample processing while my group (amply named "Triple Threat" by the way, or "Muscles and the Bears" if you ask Grieg Steward) needed to run our productivity samples from last night in the scintillation instrument. This clever instrument registers radioactive decay in our samples (which we spike with 14C to measure primary production) by measuring fluorescence (light) emitted from an added chemical when it's hit by the radioactive particles of the decaying 14C.
But hey, lets start from the beginning, shall we.

It was a sunny morning, like every other morning at station ALOHA (just kidding, but it is actually a whole lot of sunshine out there).
My group did the last day of science on the primary productivity sampling which meant that we had an early morning preparing all our bottles and vials for the 03.00 CTD, spiking the water filled bottles and vials with either radiolabeled leucine (an amino acid) or radiocarbon, 14C, depending on if it was for measuring primary productivity (phytoplankton - photosynthesis) or bacterial production (heterotrophic plankton - eat stuff). This is a somewhat difficult distinguishment to make in some cases since some of the photosynthesising plankton are known to be mixotrophic (they both eat stuff and photosynthesise). An example of this is interestingly enough the most abundant microbe we have in our oceans, Proclorococcus.
Since the ocean is such a vast and diluted place, it kind of makes sense in terms of evolution and competitiveness to do both, whenever either of the strategies is the most efficient. I'm not sure if we have that many terrestrial examples, but I instantly think of plants that catch and digest flies.
It's an amusing thing to picture on land though; how a plant happily would live off the sun's rays until all of a sudden, an aggregate of whatever biochemical compound potentially favoring the plant, flies by and the plant would take a bite at it. It's like a scene out of Super Mario Bros. (for all you nerds out there). Anyway, that's reality for Proclorococcus, and that, ladies and gentlemen, is one of the many things that makes the ocean so intriguing.

After spiking our bottles and vials, they were fastened to arrays that ultimately went down at different depths along a line to be incubated, floating freely, for the most part of the day. In the evening we recovered them, or more specifically the deck group did, or as a matter of fact, they tried to.

Unfortunately the first mate steering the thrusters on the port side took the ship too close to the buoy marking the arrays and the floats attached to the buoy accidentally got caught in one of the back propellers. Needless to say, we were now sitting in a tight spot. Luckily someone had a GoPro with them and could lower it down to actually see how the line was entangled in the propeller, and it turned out it wasn't too bad. The crew got the zodiac in the water and pulled the whole array away from the ship, which solved all our problems, but of course, at this time we were almost two hours late and consequently me and my group had a late evening filtering our samples.

The next morning was early since I had already volunteered to help out recovering the sediment traps (which I was part of preparing and deploying on the first day). I was tasked with the grappling hook to catch and reel in the buoy and floats of the sediment traps. Suffice to say that it all went well.
The rest of the day was just a spectacle of preparing all our accumulated samples for disembarking and processing at C-MORE and then packing and cleaning the labs. The morning and noon was scheduled for different groups to have different tasks, but after that it was just a frenzy of people trying to find something to make use of themselves. After a couple of hours doing the same, I gave up (after at least cleaning and carrying around some stuff).

Since the sediment traps had drifted so far south-west during our week out at station ALOHA, the captain seized the opportunity to make a (by now) tiny detour west, along the eastern shores of one of the other Hawaiian islands, Kaua'i. Incredible scenery is all I can say. The cliffs seen in the picture are actually of mountain size, and by judging from some of the helicopters we saw flying along the cliff faces, I estimated the height to be approximately 1000-1500 m above the sea! To top that off we even had a group of dolphins putting up a show for us at the front of the ship. Amazing!

Next thing I knew, the last night at sea was gone, a great cruise was at its end and we were back in port, Honolulu, unloading the ship (where I fortified my new flattering nickname "Muscles") and heading back to C-MORE hale to plan for the upcoming intense lab days.

Deep cast and flow cytometry

Pipetting during DNA extraction.

Preparing a perfectly even gel for electrophoresis at sea.

The buoy marking the center of station ALOHA.

Subtropical open ocean sunrise at 06.00.

The final size of the cups after being lowered down to 4790 m.

Happy upcoming birthday, my son. This one is for you!

A selfie with the flow cytometer.

Be mindful of your surroundings when working in the rad-van.

I hope the pictures mostly speak for themselves. I was thinking that that should be it for this post but I just feel like I have to write a few lines about the deep cast and the flow cytometer. I was too excited about it, not to.
I can just mention that we did have a "biodiversity-day" (first two pictures) with Grieg Steward and Craig Nelson, who by the way were awesome to work with. This day comprised of DNA-extraction, PCR (polymerase chain reaction) and gel electrophoresis. This is what I do, so naturally it was my moment to shine!

Next up was the flow cytometer with Ken Dogget. This was an instrument/method I was most excited about on the entire cruise. It truly is an ingenious and complex instrument but the application still is fairly simple and unless you're a flow cytometer technician, most of the complicated work included is interpreting the data plots that the instrument gives.
So what the instrument actually does is counting and sorting cells in a water sample. Thats right individuals cells! Im far from an expert on this instrument after only working with it for a day but to simplify how it works, it uses laminar flow to dispense the sample into a so called interrogation zone (where the sample is read by the instrument). Here it shoots a laser beam at the sample which will scatter and fluoress when it hit cells. The angle and light is dependent on cell size and incorporated pigments (you can also dye your sample). This light signal is then picked up by detectors (they do have a fancy name which I can't remember now) which will eventually give a "pixel" in a scatter plot on a computer. Now it is a matter of interpretation and hopefully (and most often in these waters) you can see distinct clusters of cells (one pixel being one cell) and can then make out size ranges and/or pigment intensities of species or populations of microbes in the water, by visualizing them in different light (e.g. chlorophyll in red light).
So that was counting cells, but you can also sort cells, meaning that you can make the instrument put all cells (within a range) of your choosing in a tube, separating up to four species or populations at the same time, from the same sample water. This is achieved by use of electricity and polarization. So the tiny flow of your sample water going through the interrogation zone is made to vibrate, by adding a low voltage to the nozzle. This causes the water to make tiny waves which eventually break off into droplets. The trick here is to calculate and instruct the instrument as to how long it takes for a "laser-read" cell to end up in the first droplet formed down the flow. This droplet will then be charged and easily sorted. The calibration of this operation is mainly done using tiny cameras inside the instrument.
It might sound like this is a process which would take a while, and to be frank, yes it does, BUT the only reason for that is that we have such large quantities of microbes in our waters. The instrument is capable of counting and sorting at a staggering rate of 20 000 cells/sec!

Finally, I unfortunately lost one cup during the deep cast. I had made three, one for each of my kids back home. Apparently there's another deep cast going down later (2000 m) which should be enough to shrink the cups. So I made another cup. Here it is. Hopefully I won't lose it.

First days at sea

The first night on the ship was spent while still being moored in port. Me and my cabin mate's cabin was freezing because we couldn't find our thermostat. Stupid. Terrible night.
The following morning we set out from Honolulu on our half day transit to station ALOHA. Of course this time was filled with the regular safety instructions, drills, exploring the ship and signing our lives away (legal paperwork, thanks USA, sigh). We also had a science meeting just to go through the coming week.

The rest of the day was just full of preparations for the coming day and lots of good food in between. I was on the team responsible for setting up and deploying the sediment traps. These traps are nothing more than long plastic tubes which are designed to catch sinking particles in the water column at various depths. To keep the caught particles in the traps we filled them up with high salinity water and a preservative chemical.
It was a very mixed work-load which involved chemical preparation, pipetting, filtration and finally deploying the sediment traps by help of a crane, 1 km of rope, a dozen floats and a buoy. Since the last part of the work was conducted at back deck, it involved a lot more practical, hands on work where life vest and hard hat was required.

The second day started relatively late, at 09.00 where we sampled the third CTD (the water collector which is lowered down to a pre-set depth to collect water on its way up while also continuously measuring parameters like e.g. oxygen and fluorescence) of the day.
Since we will always be assisted by senior scientists on the course during our sampling and methodology, there is already a set routine and everything ran very smooth. We filtered water and stored away samples in the -20 freezer for e.g. ATP (adenosine tri-phosphate, which is the "energy currency" of all living cells), phosphorus, nitrate, and POC (particulate organic carbon).
So it was quick work and we were done by dinner, which was good for next up was the CTD or deck work which started at 2.30 the following night.

So the third day was an early one and I treated myself to a very early breakfast which honestly did wonders to everything but my mood this morning. I just couldn't fall asleep as early as I should have. We prepared the CTD, including loading the niskin bottles (so they can later be fired in the water column to enclose water from a certain depth), setting up the software for monitoring and recording the operation and putting out ropes for safely guiding the CTD in and out of the water when it is being deployed using a crane. Finally we also instructed the crane operator via radio as where to stop the CTD to fire niskin bottles and then helped recover the CTD when back at the surface.

All in all, very practical work which usually took an hour to one and a half. That meant that we had some time between CTD deployments (every third hour) and also when it was in the water (unless you were monitoring the operation and firing niskin bottles).
This down-time became a bit tedious at the end of the day but at least we stayed productive by decorating styrofoam cups. These cups will be submerged together with the CTD on the last day (purely for fun) when there will be a 4000 meter cast.
With that said you can all try and figure out what will happen with the cups during that operation. I will post the result at the end of the cruise.

Research cruise postponed

By this time I should have been way out to sea, soon nearing station ALOHA (abbreviation for A Long-term Oligotrophic Habitat Assessment), which basically is a position some 10 hours by ship north of Oahu and Honolulu. To clarify; it's just a pre-decided patch of ocean marked with a single buoy.
Anyway, that didn't happen. The reason being some kind of engine failure of the research vessel, the R/V Kilo Moana. Thankfully it was quickly repaired and so we are finally scheduled to depart Honolulu tomorrow morning (local time), 2 days late.

During the wait for the ship to be repaired we had the days filled with Illumina sequencing and genomics theory as well as mathematical exercises where we calculated estimates of microbes and genetic material in the surface waters of station ALOHA. Not easy, but very interesting. There's a lot of stuff out there, both bound in cells and dissolved in the sea water.
Before going to the ship, we had a tour in the labs that we will use after the cruise. I've never seen such spacious and well organized labs, and on top of that they were filled with fancy instruments. Half of them I couldn't even tell what they were for. They even had an automatic pipetting instrument which did all pipetting work on 96-well plates by itself. Lastly, we were introduced to Illumina's prototype Next Seq.

Tonight is my first night on board, and it also marks the first day of my second research cruise. It will be a relatively short cruise (7 days is the current preliminary number due to the delay) where we will head out to station ALOHA (which actually is the same sampling location as for the Hawaii Ocean Time-series (HOT) which is an oceanographic monitoring program running since 1988), and sample as much as we can possibly manage. We have been divided into 5 groups (3-4 students in each group) which will rotate on a schedule of 5 different methodologies or sampling subjects. So my order of sampling is already decided and will be as follows: biomass, CTD, diversity, flow cytometry and finally productivity.
There will be loads of new methods to learn and get hands on experience of, which is great! I'm really looking forward to broadening my skills as a researcher. We will do many of the analysis preparations on board so once we get back to the lab we will start running the genome sequencing and metagenomics analysis which I'm looking forward to the most. It's a tough schedule but if the faculty are convinced we will manage then I am too I guess.

So far I've just had a short time to explore the ship, but what I've seen makes it fairly different from the last cruise ship I was on, the R/V L'Atalante.

For starters, this ship is smaller. It is 56 m long (30 m shorter) and 26 m wide (actually 11 m wider), and the reason for the odd proportions is that it is basically a catamaran.
In addition to the pure physical, arrangements on board are a lot different. No housekeeping, no waiter and no alcohol, which isn't necessarily a bad thing. I will probably write more on this topic during the cruise. Buffé is awesome and there is always snacks of every single kind (fruit, chocolate, candy, grain bars, muffins, cookies, ice cream, bread, cereals, soft drinks etc,) available. How great is that!? I can definitely do without beer when there's ice cream readily available 24/7!

A session of stupid questions

First of all, happy national day to me and all other Swedes back home and around the globe. The only feel of the national day that I got today (so far at least) was actually provided by Google, so cheers.

Today finalized the week of omics and metagenomics and was concluded with a laid back session of "stupid questions", or "daft questions only" as Mick Follows put it last week. The point was to address questions, by students and faculty alike, that might be either embarrassingly simple or just "out-of-the-blue complex" to be put out there back in our home labs. To further the laid back atmosphere beer was served. Awesome!

So to be honest, I think most of the questions were really good (just as last week) so either I'm daft or the session just helped people to ask questions they have been pondering a while after not having the time to ask them after each lecture (for some reason we are constantly behind schedule every day).

We also learned a meta-omics software today, called Galaxy. It is used to analyse and visualize different omic datasets using various tools. The protocol is called a "pipeline" which has different purposes and tools depending on the data. It was interesting but unfortunately not very rewarding since the sessions was very short (no time to actually go through what the different tool settings actually meant) and since it is web-based with a local server it was impossible to do any analyses when 20 people accessed it at the same time. We will have more time to do proper analyses with real data after the upcoming cruise but until then I guess I'll have to be satisfied with knowing how to navigating the software.

So lunch time introductions continue every day and I start to see some kind of pattern in people's stories. 1. No one really knew what they wanted to do growing up, some was even sure that science was not for them. 2. Microbial oceanography is a relatively small and intriguing field where many of the scientists started out in neurobiology thinking that to be a cool field, and ending in microbial oceanography since that truly IS a cool field. 3. There's a fundamental difference between how we use University studies in Sweden and the U.S. In Sweden you often study to find out what you want to do (it's free) and in the U.S. you work to find out what you want to do (studies are expensive). 4. With that said, a lot of scientists on the course have had some pretty dodgy jobs over the years while many of my friends in Sweden have never had a job outside of academia.

Oh, and finally; apparently I'm the first Swede to attend the course (in its 10 years history) and the first participant to represent Stockholm University.

By the way (on the stupid questions session) I found this on the roof of our lecture hall. Anyone have a guess on what it actually is? :-)

Lunch-time introductions

I've been extremely busy these last few days. I haven't even had the time or the energy to write anything. The days so far have been very long and very intense. Total information overload, which is good I guess. That is why I'm here, to learn as much as possible from the very best. At the same time though, it definitely takes its toll. I'm not used to sitting down and listen for hours on end so the coffee breaks with awesome snacks and pastries are lifesavers together with the occasional interactive lecture by the faculty.

To make a long story short (because now I'm tired), this is without a doubt one of the best and most satisfying courses I've ever had the fortune to participate in. I've met so many new people in my community of microbial oceanography, world leading experts and emerging experts. Everyone have been very friendly and we've been encouraged to build on these networks for future collaboration to more easily further our research. It's an ingenious concept but like everything else of use or value it requires some effort.

A few days ago I held an introductory talk on myself, which was actually something I've never done before. It was an odd feeling to stand in front of everyone, student and faculty alike and tell them about my life, early career and choices/interests that brought me to where I am now. However, most people seemed genuinely interested which was very satisfying, especially since I think that I do have a good story to tell, having been outside of academia for most of my early career (in difference to most other researchers).

This week we started with the lectures on and preparations for the genomics and transcriptomics sampling (as well as Illumina sequencing) that will be done and processed before the end of the course. This is in my opinion a complex methodology which I have very limited experience and knowledge of. A good reason for staying on my toes. At the same time it's a really cool scientific approach which I'm hoping to apply on my own research back in Stockholm so I'm really trying to make the most of it. I also learned how the flow cytometer works today, which was awesome. I've always wondered about that, especially since a lot of people seem to use that instrument. Basically it is single cell counting and sorting at an extremely high rate. The design of the instrument is relatively simple which just makes the instrument better, and who doesn't like shooting intense rays of laser at stuff, eh?