Living with type 1 diabetes!

I've been thinking about this blog post for a while now, but never really been sure as to if I should really write it and where (if I did) I should post it. Secondly there's also the decision whether to write it in English or in Swedish.

Stay active, stay strong, stay alive.

What I will tell you about ultimately concerns more than just me. More than just my son and family. More than just Sweden. Therefore I will write it in English and I will post it on my blog where I intended to write posts related to my science and experiences in the field. However, I would be lying if I said that none of this affects me both on a personal and professional level.

It is important that you know that my purpose with this post is purely to enlighten and give my views on the everyday life, the challenges, the outlook and the science of one of the the biggest, the quickest emerging and sadly also most underrated diseases in the western world. This is a tiny window into the life of my family and my son (and most likely other families battling type 1 diabetes), diagnosed with type 1 diabetes (Diabetes mellitus Type 1 - or just DM1). There are many details on diabetes that I will deliberately leave out, so please, for further reading internet is your best friend. Finally, I would very much appreciate if you, as a reader of this blog, would help me spread the word for the benefit of all the current and future children and adolescents in the world with the same diagnose.

What is type 1 diabetes?

First of all I would like to make a clear statement on the difference between type 1 diabetes and type 2 diabetes. Unfortunately media often refers to the disease as only diabetes, as if type 1 and type 2 were basically the same disease afflicting different age-groups. This couldn't possibly be further from the truth and it is a major driver of much prejudice against type 1 diabetes (most commonly afflicting children). The only thing the two have in common apart from the the name is that the body of the afflicted person can't produce enough of the hormone insulin, responsible for feeding our cells with sugar transported with our blood (thus keeping blood sugar on a healthy level), or lacks production altogether.
Type 1 diabetes is fundamentally different in the fact that it is (as of now) an irreversible autoimmune disease which current research propose is both genetically inherited (many genes involved which can be both dominant and recessive) and triggered by an environmental factor (possibly a common viral infection). In difference to type 2 diabetes there's therefore no way to prevent or mitigate the onset of type 1 diabetes by way of i.e healthier living. Developing type 1 diabetes basically means that you're the wrong genetical composition at the wrong place and time. Unlucky, right?
Autoimmune means that the own immune system somehow has been triggered to unrelentingly attack the insulin producing beta-cells in the pancreas, ultimately fully deactivating their ability to produce the essential insulin, which is the only hormone of its kind with the function of decreasing blood sugar (i.e both cortisol and adrenalin are hormones that increase blood sugar by stimulating the liver to release glucose).
Because of this lack of insulin, the afflicted person's only option is dependency on an outside source of insulin by injections, most commonly by use of needles or the rising technological tool, the insulin pump.

Portable "real-time" blood sugar monitoring with a six meter range.

In spite of advanced technological tools and rapid advances in scientific understanding, type 1 diabetes is a widespread and deadly disease which also (at least) doubles the risk of a "premature" death no matter how well it is treated. It is a constant battle of balance of blood sugar, something that the insulin pump has helped a lot to manage but still is nowhere near as effective as the own body. High blood sugar may lead to cell starvation (if insulin is lacking) and ketoacidosis (acidifying the blood and body) and further down the road a range of complications with function of bodily organs, especially kidneys and heart. On the other hand, low blood sugar may lead to insulin induced coma and death.

Current status and living with DM1

Type 1 Diabetes has an estimated 80.000 new cases worldwide each year, while the total number of people with the diagnose is unknown. It has also been observed to increase in magnitude by about 3 % per year in recent years. Looking at diabetes as a whole (both type 1 and 2) an estimated number of 387 million people worldwide has one of the two diseases (8 % of the world's population) and up to 4.9 million people die each year as a direct result of diabetes.
External insulin dependence (type 1) is a constant management of one's blood sugar which then of course, independent of treatment tools, requires plenty of medical consumables, to an estimated cost of $875 per month per diabetic (in the USA). You do the rest of the math.

Insulin pump consumables which are replaced every third day.

With that said, type 1 diabetes is a taxing disease to treat, with a never-ending learning curve which sometimes feel steep and at other times leave parents and medical personnel alike baffled. Either way, it is a constant home treatment which demand regular (mostly not medically trained) parents to take full responsibility for a deadly disease, where death as a result of unintentional mistreatment is a very real possibility. It is a very intimidating thought. At the same time the ultimate goal for all parents is to, with time, foster independent children. How much more difficult is that scenario for both parents and children when the fledgling leaves the nest for the first time carrying with him/her the responsibility of a deadly disease.
Parents have to first learn and then teach how to monitor blood sugar, using needles and a small computer. Continuous  monitoring with less need for needles is also possible if the treatment is by insulin pump but it still needs to be calibrated at least two times a day. Secondly, the correct insulin need at any given time (mostly for meals, if treatment is by pump) needs to be calculated and administered (by needles or pump). Thirdly, unexpectedly and/or unexplained high or low levels of blood sugar has to be dealt with. Every case of diabetes is as unique as the afflicted individual and is a highly personal story. Parents will often refer to it as an additional child to care for. That gives an estimate of the level of attention it requires. 24 hours a day, every day, for the rest of their lives.
The harsh reality is that, as of today, there's no cure for type 1 diabetes.

Research on DM1

In my molecular lab.

So what does science say? There is plenty of research being conducted around the world with different focus. Some research teams are focused on the demography of type 1 diabetes for a better understanding of the disease and possible prevention methods. There are hopes of developing a kind of vaccine for type 1 diabetes which would decrease or even mitigate the T-cells of the immune system's sensitivity to the insulin producing beta-cells in the pancreas. Secondly, as stated previously, this is also a billion dollar industry where companies make huge profits on providing new technology for rather hefty (in my opinion) prices. This is certainly a quickly developing industry where the aim is to make life easier for diabetics. The current "flagship-to-be" in this industry is the "virtual pancreas" which is very much like the current insulin pump but more compact, with a more advanced algorithm for automatically dispensing insulin as a reaction to increasing blood sugar (the current insulin pumps need to be configured and much of the insulin dispensing is by manual input) and being directly attached to the bodily systems by means of surgery.
However, as you can see, this is by no means a cure to the disease.
This is where the third field of type 1 diabetes research comes in, one which has been pioneered by Swedish researchers in Uppsala and Lund.
This research focuses on curing type 1 diabetes and the last few year's initial medical trials on human patients have shown great promise. Personally, I wouldn't go as far as calling it a major breakthrough, but the researchers are well on their way to countering one of the major issues of any treatment of the cause of the disease as well as restoring beta-cell activity and function. The T-cells of the immune system. They propose to use special cells from the own bone marrow to ward off the aggressive T-cells. There's also a possibility of shielding the beta-cells with reactive oxygen. The use of bone marrow proved successful in at least one medical trial where new type 1 diabetes patients showed full recovery of beta-cell function, thus external insulin independence, within a year after the study's conclusion. However, there are some drawbacks to consider.
This is only one case and it has not been replicated since.
Proper evaluation will take years and it is not known if the renewed beta-cell function is time limited. As an initial substitute for a cure I would argue that a major treatment session every 5 years (or whatever it might be in a worst case scenario) is better than the technological alternative.
It was only conducted on newly discovered diabetes, therefore we don't know if the same treatment will work after years with the disease. There is some hope in this reasoning though, since another team of researchers has shown that the T-cells don't, as previously thought, destroy the insulin producing beta-cells, but rather deactivate or suppress them. A course of events that can be reversed.

The disease, the onset and the society for a young diabetic

Tools for measuring blood sugar.

My personal opinions on type 1 diabetes in general and my life in specific living with the disease, are many and colorful even after just 7 months after the initial shock of my son being diagnosed with it. I think most people having to face the reality of type 1 diabetes go through a phase of denial before the ultimate acceptance. Same was true for me, but to be honest, as a parent and a scientist I think that I, at that point, at least owed it to my son to thoroughly investigate type 1 diabetes, its causes, method of diagnosis and possible explanations. The most unlucky coincidence was that he at the time had inhalation spray for child asthma which is known to increase blood sugar. We hoped for dear life that he would get better within a few weeks, but of course that never happened.
So this was where our journey, with my son, living as a healthy diabetic started, all the while looking to science for answers and hopes of a better life in the future. That, however, is no excuse to not live life to the fullest here and now, which I think is very important both for him and for us. Diabetes shouldn't govern our lives, then we aren't doing a good enough parental job, but rather that we plan and buffer for it. The difficulty in this rhetoric and way of living with type 1 diabetes is the constant ignorance and prejudice of the society (most of it anyway). Many times children with type 1 diabetes are excluded or denied participating in activities solely because of ignorance or fear derived of ignorance on involved adults part. All I ask is for children to be able to be children no matter their conditions, but to break that barrier in case of type 1 diabetes society in general, and people working with children in particular, need to be enlightened on what it is and how it is handled in daily life.
Personally I haven't had this argument yet, but I know that it will come soon enough, and I know it will be an essential one no matter the outcome. Equality is not for everyone when it requires a bit of extra time and effort, because nothing today is free. Though I am thankful that we, in Sweden at least, doesn't have to pay for the life-long treatment of type 1 diabetes.
On the other hand I'm concerned that the billion dollar industry that this constant treatment is, will hamper the progress of the true goal in this story, which is a cure. We have probably all heard the rumors about oil companies that buy and shut down projects for developing alternative fuels.
Further, the ignorance of type 1 diabetes is leading to insufficient funding in terms of charity foundations for research. As a scientist I know that every little penny counts but the neglect of type 1 diabetes is no petty sum. I don't want to discredit child cancer, which also is a terrible disease that still not every child recovers from, but purely for comparison, in Sweden, the foundation of child cancer receives about 208 million SEK yearly, while the child diabetes foundation only receives 8 million SEK yearly. I can't speak for the medical research field but for me as a marine biologist 10 million SEK will fund a rather extensive research project for a small team of scientists for several years. 200 million SEK is a lot of money in this context.

Role models and the future

On clear and calm waters.

There are many examples of public figures in Sweden that have learned to master their type 1 diabetes and still be successful (and a role model), but many chose not to tell their story and many yet are never confirmed cases. Why this is I will probably never know, but I guess that type 1 diabetes, being a disease, is frowned upon. It is a brand that people will get and it is a brand that of course never will further a career. It would be a purely altruistic act, an important one that I wished that more public figures would do to inspire our young and enlighten our ignorant.
I will keep supporting my son in his decisions, in life, and spur him on where needed. Because if there is something that I will teach him, then it is definitely that living as a healthy diabetic should never be a limitation of ones dreams and goals, but if anything, merely a speed bump in the road.
So speaking about myself, I'm now pondering where this road will take us. I'm sure it will be a good place in the end, but what will that end look like.
I'm a scientist and I'm passionate about my field, but it has crossed my mind on more than one occasion if my future instead lies in diabetes research rather than marine biology. It is not as easy as that though, since I've learned how our oceanic systems work, not our bodily systems. There's a fundamental difference although it is biology, and there will probably be plenty of pitfalls for a marine biologist. But how would you start to explain to your growing son why daddy didn't use his research to at least attempt to find a cure?

References:

Out of convenience I pulled most of the above numbers and facts from https://en.wikipedia.org/wiki/Diabetes_mellitus and linked pages.
Also, check out the first successful medical trial on curing type 1 diabetes in this paper:
PO. Carlsson, E. Schwarcz, O. Korsgren, and K. Le Blanc. Preserved b-Cell Function in
Type 1 Diabetes by Mesenchymal Stromal Cells Diabetes Volume 64, February 2015.
If you can't access it, contact me and I'm happy to share it with you.

Comment, share and donate to bring hope of a better future, hopefully without type 1 diabetes!

Future endeavours

Before my flight on the very last day I had a few hours to spare. I chose to spend those hours at Pearl Harbour, which was a very interesting and humbling experience and I'm happy I went. So many details about the horrible WWII happenings at Pearl Harbour that I didn't know about.

After a terrible few flights (including a 17 hours involuntary stop in Salt Lake City due to an engine malfunction) I finally arrived back home with my family. Almost a full day late.
My plan was to be back at the lab in Stockholm before my supervisor leaves on summer vacation, which for obvious reasons didn't happen.
In this case it's great that my work is so flexible and I could show up later to get acquainted with the new lab and my new (empty) office. The new building which the department is moving into (kind of a physical merge) should have been mostly done by now, but no. This place is still a barren and somewhat messy construction site, and I have to step over construction workers on my way to the lab on the fourth floor. At least the lab is neatly set up already thanks to the rest of my group.

Officially I now have my first ever paid vacation. I never realised that I had all these perks doing my PhD in Sweden, but now I'm very grateful for it. Still I have tasks with deadlines approaching, but at least I can now spend some well earned time with my family after being gone for three months already this year. There is always more work to do, but for now it can wait.

So Sweden treated me with the best week of the summer so far when I got home, and now it's raining again. It was a nice feeling to be back, enjoying a beer in the sun, going for a swim, having a family barbecue and taking the kids outside. Hopefully July will be good (my vacation).

In August it is back to the lab again with lots of practical lab work (DNA-extraction and qPCR) to accumulate much needed data, analyse that data and put together an "award-winning" poster for the SAME conference in Uppsala, 23rd of August. So if you're going to that conference I'll see you there, specially during the poster presentations.
In addition to the conference I have plenty of future endeavours during the coming autumn. I will finally attend the introductory course on research studies in biology, which also is the first course in pedagogics which will make me eligible to teach on undergraduate courses. That is also exactly what I will do right after. One or two weeks (depending on the number of applicants) of assisting on a basic course at the Stockholm University field station Tovetorp.
Finally I also have another deadline on a writing assignment, but for now I'm fully committed to my vacation.
Thanks, have a nice summer and stay tuned in late summer!

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.