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Weblog Cosmas Broek

Cosmas Broek is blogger for the MSc Plant Biotechnology. He started his master this year, after he finished his bachelor in Plant Sciences, also at Wageningen University.

I chose for Plant Biotechnology and the specialisation Functional Plant Genomics, because this allows me to really focus on plant physiology and morphology

Introduction

My name is Cosmas Broek and I’m the new blogger for the MSc Plant Biotechnology. I started my master this year, after I finished my bachelor in Plant Sciences, also at Wageningen University. I’ll tell in short how I ended up here:

It all started at the open day of the university in November 2009. Just one year before that I had decided to go and study chemical technology, but one day I suddenly lost interest in chemistry. So all of a sudden I had to find something else. The fact that I was lacking motivation for everything school-related at that time wasn’t helping either.

I accidentally stumbled upon plant sciences. Originally I did not even want to take a look at the study, because I thought a study solely about plants was boring and something for vegans and farmers. However, the study really appealed to me. I like biology, but not really the animal and human part of it, so this was the perfect alternative.

During my first year I was questioning if this was really the correct study for me, but by the time I had to choose a BSc thesis subject in my third year I knew this was my study. Again I couldn’t make a choice what to do for my thesis, but this time because I liked everything instead of nothing.

I decided to do my master in Wageningen as well, because I like the city and the education is very good. I chose for Plant Biotechnology and the specialisation Functional Plant Genomics, because this allows me to really focus on plant physiology and morphology (my favourite part of plant sciences) on the scale of single cells to whole plants.

Besides studying I am active in the study association as editor-in-chief (I like that word, it sounds classy…) of our magazine ‘Internodium’. I’m also the building representative of my student complex and I’m a tutor for secondary school children, although at the moment I’m not actually tutoring anyone....

In my spare time I like to write. Occasionally I draw or make my own board game (I bet that’s a hobby you’ve never heard of...) and whenever I have space in my room I grow some, mostly exotic, plants from seed. I also like to play computer games and hang with friends.

May 2015

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Did you ever get lost on a graveyard? Well... it’s quite a unique experience... I went to visit a friend.  Since I was in quite an isolated suburb, public transport would take me 45 minutes, which was only ten minutes faster compared to walking. So I decided to walk. The internet at my room was really bad and I couldn’t check the satellite images of the walk. I just memorized the streets and went off. It turned out that some of those streets were actually streets on a graveyard... and this graveyard was so big it even had a roundabout. Somewhere on this graveyard there was supposed to be a clear path that led through a tiny forest. That was the part where I got lost. In the end I did find this path: it was a small and muddy, mostly washed away by rain and it went down at a steep angle. At the bottom of the hill it stopped and I had to search my way through tall grass before I got back on a normal road again, with 2 cm of mud and grass under my shoes.

I also went there to check out the accommodation. He would be leaving shortly after that and then I would move in, because I did not feel at ease anymore at the place I first stayed. They seemed nice in the beginning, but as time got by, that changed and in the end they only acted nice. Long story short: it wasn’t a nice place to stay at and I couldn’t get along with them very well in the end (it turned out all the woman seemed to care about was money).

My new place is fantastic. I spent my free time relaxing in front of the fireplace together with the dog. I do get up rather early in the morning now to avoid rush hour in the train, but that also means that I have some nice morning views with the sunrise.

In the lab I did a first transient expression with Agrobacterium in Nicotiana benthamiana. The plasmids with fluorophores worked perfectly. This was just a control and in the beginning of next month I will actually test my plasmids with my gene of interest. So next time I might show some nice microscopy pictures again and I will also talk more about my other experiments then.


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April 2015

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I’m already in New Zealand for a month! I’m starting to get used to Auckland. For example: I know which way to look when I cross the road. I’m living in a nice suburb with lots of nature around me. The one downside is that it is difficult to go somewhere. Especially since Auckland is a car city, which means:

  1. public transport isn’t very good
  2. cycling is kind of suicide

Nevertheless, I did some hikes, visited a few nice beaches and went to see the city centre.

My internship is really nice so far. I have a very nice office (see picture) which I share with a Malaysian PhD student. The group originally used to be on the top floor of the main building, but they are currently renovating that part. So now we are located inside a harvest processing building. In general this is really nice. We all got a nice office and the lab is just around the corner. Sometimes, however, there is a lot of noise, because some other people are processing their apple harvest: they turn on a big machine, put apples in on one side and collect them on the other side. The only difference I can spot is that the apples seem a little bit shinier when they exit the large machine...

In the lab I did my first PCR and ran my first gel in three years! Nowadays I often spent the biggest part of my day in the lab. Currently I’m busy with transformations for a transient expression in Nicotiana benthamiana. This basically means:

Design primers for the gene of interest. Put the primers with the DNA and all kinds of other stuff into a PCR machine and keep your fingers crossed. Squeeze amplified gene into a plasmid. Shove plasmid into E. coli, let them grow for a while, test to see if they have the plasmid and then kill them to extract the plasmids again. Shove these plasmids into A. tumefaciens, grow them for a while and test to see if they have the plasmid with correct insert.

Sometimes it’s just like cooking with a recipe. I really like it. Next month I’ll probably have some first results to talk about!


March 2015

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It was a long travel to the other side of the world, but: I’m in Auckland, New Zealand! It’s awesome here! Everything is so beautiful! The people from whom I rent the room are very nice and I already got a good tour around Auckland. It is so different from the Netherlands here: there is lots of nature and lots of nice parks with old trees, there are a lot of hills, the autumn is like Dutch summer, everybody is driving on the wrong side of the road, everybody seems to be happy, the streets are clean, people aren’t complete stressed-out monsters in traffic and there a very few bicycles (which is the only thing I don’t like).

On the first of April I’ll start my internship, which is already the last part of my MSc Plant Biotechnology. I will work on identifying new genes in the strigolactone hormone pathway in petunia. In the beginning of this month I already met my supervisor at the International Congress on Strigolactones. Although I couldn’t be at the congress all the time due to some experiments I was doing at that moment, it was really nice to already get some background knowledge on strigolactones.

This month I finished almost all my experiments, including the mitotic index. For the mitotic index I had to count roughly 40,000 cells, but I didn’t mind: it finally worked! In general my results, although some of them are a bit unexpected, are really nice and I can write a nice coherent thesis report with it. I already held my final presentation. I had to come early that morning to collect my last important results that I needed for the presentation. Now I only need the results of some experiments that needed more replicas, but my supervisor will collect those results for me.

I was a bit busy with getting everything arranged for my internship, so I did not managed to finish my thesis report on time. I still have to write the discussion. I hope I can finish that part quickly, because I don’t want to sit inside writing, when I can also go outdoors to see the beautiful nature and meet nice people.

February 2015

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And another month has passed. Time is going really fast. In one month I’ll be in New Zealand and before that I still have to finish my thesis. I’ve already started writing my thesis report in between my experiments, but it’s still a tight schedule… The seeds for the extra cultivars have arrived and I’m testing them right now. In the meantime I may have to redo some experiments, because some batches suddenly germinated slower than expected or they got infected (see picture). I sterilize the seeds, so I have little fungi, but now and then I get that nasty slimy looking infection. That one is really contagious and devastating and then I often have to redo the experiment. I won’t have enough time for some of those experiments, but luckily my supervisor will continue with them for me.

The mitotic index struggle still continued this month. The guy from the microscope first told me to put the embryos in the fixative for more than 12 hours, because the embryos were so large. After 18 hours of fixative they were indeed very well fixed: the stain couldn’t get it anymore…. On top of that the microscope guy suddenly told me that he rarely puts material in that fixative for more than one hour… not very helpful…

That wasn’t the only issue: the embryo cells are too dense for the microscope to penetrate deep into the tissue. But I have finally solved all those issues. I now isolate the root and shoot meristems from the embryos and focus on that. It is precision work to isolate them (like peeling cell layers of a very tiny onion), but it is doable.

Beside these troublesome experiments, I also got some very nice results and I had some nice activities with the chairgroup. There was a nice trip with the Seed Lab subgroup after which we cooked all together. With more than 20 people this was quite chaotic, but a lot of fun.

With most of the master students of the chairgroup we went to a pubquiz. We split into two groups. I was in the ‘Smart seeds’ group, representing the seed lab. Of course we won from the other group (‘MAX madness’)!   

Next month I’ll be on the other side of the world and I’m looking forward to it!

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January 2015

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A new year has begun and everything is going very well. I’ve almost finished my desiccation tolerance experiments, the mitotic index problems are over, I have arranged my internship in New Zealand and I even had a better walk in the, again, first snow of this year. Although I have almost finished my desiccation tolerance experiments, this doesn’t mean I’ve got nothing to do anymore. I searched for some more drought sensitive and tolerant cultivars to test and those seeds will be here in two weeks (someone who’s visiting the IRRI in the Philippines now will bring them back personally). I won’t have much time to test them, but I’m really looking forward to it. With those cultivars I can test the hypothesis I have right now.

I don’t have to find a method to isolate all the cells from a rice embryo for the mitotic index. I will now use a very good fluorescence microscope from the chairgroup of Cell Biology which is able to scan through most of the embryo. I will make z-stacks from the embryos to later make a 3D reconstruction of them. I also have a better fixative, so the staining will probably work better too. Next week I will start with this and I’m expecting some nice results!

By the end of March I will go to Auckland, New Zealand to work on strigolactone hormones for four months. I’ve wanted this for a very long time and I’m really happy that it is finally arranged! I don’t even mind that it will be winter there (since winter there is more like a Dutch spring with a little bit more rain).

Last week I went to visit my girlfriend, who is doing an internship just across the border in Germany now. We visited a limestone mine in Valkenburg, which is in the southernmost part of the Netherlands. After that we went for a nice walk to some real, ankle-deep, snow. Of course we had to build a little snow man, which became a little bit bigger than expected.

I hope I can show you some nice pictures of the microscopy next month!


December 2014

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I just went for a walk with my girlfriend through the first snow of this year. Although most of the snow turned into greyish wet sludge after a while on the warm ground, the white roofs, bridges and grass fields were still really nice. It was a bit windy and cold and one of my shoes turned out not to be waterproof anymore, so now I’m heating up in the warm living room on the couch.

In the week before the holidays I got some nice results, there was a nice Christmas dinner with the chair group and I booked some progress with the mitotic index. A good way to start the holidays!

Also in my cultivar rice seeds the PEG treatment enhances the ability to re-establish desiccation tolerance in germinated rice seeds. One of the cultivars is better able to re-establish desiccation tolerance compared to the other two. A bit unexpected is that this is actually the more drought sensitive one. So it could be possible that desiccation tolerance and drought tolerance are two different systems in rice. I’m looking forward to research this some more.

The Christmas dinner was great. Everybody had to cook something, preferably from their home country. Since the chair group has a lot of nationalities, this resulted in all kinds of dishes. My main supervisor made a special alcoholic beverage of which I already forgot the name. He finished the last step right before the dinner: he built a pyramid of sugar cubes, soaked in 80% ethanol, on a grate and set them on fire. This resulted in caramelised sugar dripping into the beverage, which was very nice.

The stain I tried to colour the nuclei with did not work. Even with the help of my supervisor from my previous thesis, I could not get it working. This probably has something to do with the cell wall components that somehow block the stain from entering the cell. Then it turned out that there was a small fluorescence microscope at the lab that no one ever uses (while they are rather expensive...). So I switched to a fluorescence dye that works fine, but now I still need to dissolve the cell walls to be able to count everything and again the cell wall components are the problem, because I can’t get them dissolved (or the cellulase and pectinase I use are too old...).

November 2014

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I’ve got some very nice results. Most rice seeds have already lost the ability to re-establish desiccation tolerance after 15 hours of imbibitions. In that time there is not even radicle protrusion, only some swelling of the embryos. However, if I treat them with PEG, the seeds are able to re-establish desiccation tolerance up to 32 hours of imbibitions. By that time there is both radicle and coleoptile protrusion, so both root and shoot meristems are already out in the open.

Now I’m researching whether there is a physiological change at the germination stage in which the ability to re-establish desiccation tolerance lost. I’m looking at changes in sugar content and at the mitotic index (fraction of cells in mitosis). Someone helped me with my first sugar measurement trials, but unfortunately the computer that’s linked to the machine crashed and those data are lost... For the mitotic index I am going to count the cells with a simple stain and light microscopy. Unfortunately I haven’t got the stain working yet. It does stain my fingers though... and the 45% acetic acid I use to soften the cell walls to prepare my slides also works. Also tested that accidentally on my fingers (nothing serious though). But it’s not working on my rice embryos yet.

But back to the good news: my cultivar rice seeds have arrived! I read in the literature that some cultivars can take up to 7 days to germinate, so I started some germination tests right away. Luckily they germinate within 1 day. I now have all germination stages of my three cultivars, including some very nice pictures. The seeds were delivered while still husked. So I’m spending quite some time now dehusking the seeds one by one (to make sure that the embryos stay intact). But I don’t really mind it: I’m expecting a lot from these seeds. I asked another MSc student to take some pictures for my blog while I was dehusking the seeds (picture 1) and not long after that he had taken a lot of pictures; including all kinds of close ups, someone else who tried to work in the lab and a funny (partly) selfie with me (picture 2).

So far everything is going very well and maybe I have some new nice results by the end of this month. But for now: merry Christmas and a happy New Year!

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October 2014

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Last week I had to write down step by step all the things I had to do for my experiment. Both when and where, because the two laboratories I use are on two different floors. Especially when I have to do something in the early morning, I have to make sure that I prepare as much as possible the day before. I can’t have more than an hour delay for some steps and if there is a meeting in the morning as well, I have even less time.

So on Thursday evening I had to make a stock for several polyethylene glycol (PEG) solutions (I’ll tell more about this PEG later), create an ethanol and bleach stock for seed sterilization and move it to the other laboratory, put 300 seeds in an empty tube and label 27 petri dishes. The next morning, I immediately started to sterilize the 300 seeds in the tube, which takes half an hour. In the meantime I washed and prepared three trays to put them in later. Then I took some trays with seeds from the day before and went to the other lab, while still regularly shaken the tube with the seeds and the bleach. There I transferred three times three replicas of twenty seeds to the different PEG solutions. Then I went back to the other lab to sow the seeds I had just sterilized. I was supposed to do that all within an hour, because at 9 o‘clock there was a meeting, but even with that much preparation and planning it still took me more than an hour. This was only the planning for one evening and one morning... I’ve done a lot more running up and down the stairs, from lab to lab.

I’m working with PEG now; this is a polymer that can enhance the ability of germinated seeds to re-establish desiccation tolerance. I will tell more about that next time, because I (likely) have some nice results from it then as well (that experiment is still running right now and I’ll have the results next week).

We also had a nice bowling activity with the chairgroup of Plant Physiology. It was so nice that I forgot to make a picture of it for this blog. I also talked to the head of the chairgroup there and he is going to help me to find an internship in New Zealand!  

September 2014

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A new year has started and so my major thesis has begun. Now I’m sitting here while more and more people around me are leaving and it is slowly becoming dark outside. From 16:30 to 21:30 I have to go to the lab every hour and weight the seeds that I put in an incubator to dry at 32% relative humidity. I am now working with rice seeds. I am looking at the capability of rice seeds to re-establish drought tolerance after they have germinated. This is very interesting, because seeds are desiccation tolerance, but they quickly loose this feature when they germinate.

The day I started my thesis, my supervisor left to China until the 22nd of September. So I was all alone... but because I started already, I was still in time for the annual barbeque of the chair group! This was very nice and good to get to know some people. Of course my supervisor gave me some instructions and a list of people I could ask help from, but now and then it was quite a hassle to find things and start experiments.

I had some more starting hassles. In the beginning my seed embryos got all white and fluffy, which looked cute but unfortunately was fungus. Then they grow too slow, so they were still too young to look at on Friday evening. After that, with other growing conditions, they grew too fast and when I came back the following morning they were too old. Right now they are doing perfect and I expect some nice results at the end of this week.

A lot of students are doing their thesis here right now, which is nice, but there are too little computers available for all the students that are doing a thesis here. The students’ desks are also flex desks, so you have to empty it and log off when you are away for 45 minutes, i.e. every single time you go to the lab to do something... (Although I have all the computers for myself right now). 

Another hour has passed, I have to go look at my seeds again. Next time I hope I can talk about some of the nice results I get from this and following experiments!

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June 2014

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We’ve got an entire practical room for ourselves. Now and then a PhD’er comes in to use one or two of the twenty fume hoods, but most of the time we are on our own, surrounded by all sorts of fancy coloured fabrics. Some of these fabrics are cut into pieces, with all kinds of decoloured spots on them. Together with two others from my ACT group, we are testing an alternative method to get a rain pattern on textile for our commissioner: bleaching. Although this may sound a bit destructive, we managed to get some nice patterns with multiple of our bleaching agents. We also had two other alternative methods, but unfortunately there was not enough time (and money) to experimentally test them as well.

In the meantime I have followed two MOS modules (some sort of mini-courses): project planning and scientific writing skills. The project planning module taught me the basics of project planning and what kind of problems can commonly occur during a project. I wish I had followed this MOS module before I started my thesis! The other module had its lectures on Friday afternoon and some people did not really like this. I didn’t really mind, because the lecturer was a fun guy and he gave some very useful information. For this module we had to improve an old report, so I could spend even more time on my thesis report…

I’m now entering the last week of this year. We have already written our main report for ACT and are now finishing up our experiments and reports on the experiments, for which we requested some extra time. Now we only have to prepare a presentation and each of us has to write a final reflection paper and discuss that with our coach, because ACT also involves a lot of self reflection and ‘personal development’; a little bit too much if you ask me…. After this last week my long awaited summer vacation will finally start! Two months of relaxing before I start my second and very likely already last year of my master.

Enjoy your holidays!

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May 2014

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It's almost half past nine. I was a bit late today and got stranded in rush hour. After a bicycle traffic jam at the traffic lights (I had to wait for two rounds before I could cross the street), I ended up in another jam at the doors of the university building. When I finally got to the lecture room it was already largely filled. I managed to find a spot somewhere and watched as more and more people entered the room until there were no seats left and people had to sit on the ground. It is the largest group ever for the both famous and notorious Academic Consultancy Training (ACT).

At the end of the introduction the coaches were shown on the screen with information on were to exit the lecture room and meet him/her to prevent total chaos. It took a while, but then suddenly my coach appeared on the screen. I walked toward the meeting spot, eager to meet my group and hoping that it would be a good group with nice people in it....

Luckily I have a very nice group of six! One is from Germany, but she has already done a bachelor in the Netherlands and speaks Dutch, like the rest of us. This is easy for the random chitchat and although we are not that multicultural, we are multidisciplinary with three students of molecular life sciences, one of plant sciences, one of plant biotechnology and one of communication sciences.

Our project is about reactive inks. Our commissioner is an artist who 'imprints' rain on textile by putting ink on it which reacts on the rain falling on it. After 5 minutes in the rain she brings it back in and sends it away to let the ink be fixated.

We work on this project in our personal room. This room is in one of the older buildings of the university in another part of Wageningen (on the 'mountain' of Wageningen). It is a bit more quite there (so no rush hour...), but we are accompanied by quacking frogs in the pond below (you can see the pond and the building in the picture; our room is on the top floor, a little left of the ginkgo). 

Next time I'll tell more about our project and also about the two MOS modules (some sort of miniature courses) I am following right now.

April 2014

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When you literally dream about the genetic pathways you learned the day before, it’s usually a sign you’ve been learning enough. Miraculously, I also dreamed about genes in pathways that I hadn’t learned yet. So maybe if I sleep enough, I’ll learn everything automatically…

It is currently self study week. I made an elaborate planning to get everything learned on time. This usually means going through four lectures a day, which does not seem very intensive in the beginning, but after a while I am happy that I can do some other stuff like writing this blog to let my mind process all the newly learned information. In the meantime I have finished my draft thesis report. I strongly suggest that if you ever still have to write your thesis report while you already started following courses again, you pick fixed days and times to work on it. If you don’t, you get the feeling that you never have time for yourself, because you’re always thinking ‘I could also/should use this time to work on my thesis’.

In the ‘Plant cell and tissue culture’ course my lab partner and I managed to have zero contaminations in our plates. Well, we did have one, but that was because some other people damaged our parafilm in the growth chamber. Even when my lab partner pressed a little too hard on one of the lids, crushing and pushing it into the medium, we did not have a contamination. I really liked the course and enjoyed to see new plants form from all kinds of plant material.

My lab partner and I also got a ‘certificate’ for having the most functional meristems recovered from one single Brussels sprout of our group (see the picture, some of them even started flowering already).

Next month I will start ACT, a multidisciplinary group project usually for a company. I’ll tell more about it next time. For now I just have my fingers crossed. I’ve heard stories about very nice groups that had a great time and scaring stories about not so nice and stressful groups…

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March 2014

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I did not manage to finish my thesis before the deadline. When I told my supervisor I wouldn’t be able to finish my report on time, he wasn’t surprised at all and told me almost no one makes it on time. This was both very soothing and troubling at the same time... Now I’m following two courses and work on my thesis in the few spare hours I have. I actually planned to work on it during my weekends, but somehow they all end up fully booked with other activities.

I’m following the courses ‘Regulation of plant development’ and ‘Plant cell and tissue culture’. The first course is mostly lectures. This year the class is very small with only 15 people. Actually even smaller during the lectures, because I often skip them…. Not because I’m lazy, but I’m just not good in listening to a lecturer for a prolonged time. I usually end up doodling. Therefore I just read the material and look at the presentations at home. The course is very interesting. It is really fascinating how an embryo develops into a healthy plant and how a plant reacts on environmental cues. But sometimes all those different genetic pathways that are discussed can become a bit boring.

The other course involves a lot of practicals in the flow cabinet. Under sterile conditions we have to grow and regenerate all kinds of plant cells and tissues, like apical meristems of Brussels sprouts and tobacco and tomato leaf disks transformed with Agrobacterium. I can’t wait to see some fancy fungi and bacteria some groups accidentally got in at the end of the course.

I did need to get used to working in a flow cabinet for a course instead of for my thesis. Now I’m following a protocol and do all kinds of small, separate practicals and most plant material is non-GM and can go into a normal bin, which feels very strange to do. (Although when we did have some GMO’s I accidentally threw it in the normal bin as well…)

I hope to have my thesis report, or at least a draft, finished by the end of the next month. Next time I’ll tell more about these two courses and my time management to get everything done.

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February 2014

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February went by incredibly fast and on top of that it also has just 28 days! I got the feeling I missed some days this month. Suddenly the end of my thesis is getting terrifying close…. Like I wrote in my last blog, this month was indeed a very good month: I now have a girlfriend! She is doing a thesis as well and we both reached the writing-part, the most notorious part of a thesis. I hope that we can stimulate each other instead of distracting each other from writing….

I’m now collecting my last results. Only one afternoon with the microscope left and then the last part of the analysis and the writing starts. I have collected some very nice time lapses, especially after I started to use the correct hormone concentration to induce the plants. It took quite some hours to collect all that data and I’ve seen so much microtubules that I can almost dream about them.

With all the data I was able to identify four distinct phases from induction to actual protoxylem formation. There is no time left to do some modeling to analyze the image, so I have to make an easy, but thorough guide to distinguish between the four phases.

I added an image that nicely illustrates how microtubule orientation is regulated to give rise to the ring-patterned protoxylem. To the untrained eye it might look like some random white lines, but trust me: it is much more than that. On the left you can see that the microtubules are nicely packed together. Some try to escape, but soon face a catastrophe and depolymerize back into the bundle. It is a pity that I can’t put the movie up here, which would’ve illustrated it even better. Than you can really see all those microtubules shooting out and breaking down again. On the right you can see the secondary cell wall that is being formed at the position of the microtubule bands. I would identify this as the 3rd phase. In the 4th phase the bands would be even more compact and the secondary cell wall thicker.

I have some nice results to write about now and I am confident that I will finish my thesis on time, but still: wish me luck! I’ll tell you next month if I finished it on time and how all the writing went.

January 2014

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How easy would it be if you could just use an instant–growth on your plants and skip all the waiting. Now I have to wait for my mutant lines to set seed, then sow those seeds, wait again until they flower, so I can make crosses and then wait for the seeds of those crosses.

My thorough analysis of the protoxylem showed some minor differences among the lines, but this could also be normal variation mixed with some wishful thinking. All I can hope for now is that the microtubules show some remarkable aberrations, but by the time I finally have the right crosses, I am probably finished with my thesis...

In the meantime I’m looking at the change in orientation and dynamics of microtubules when a cell is first initialized to form protoxylem until protoxylem formation. Since this can take up to 48 hours and, with the quality I want, I can only image one cell for approximately 10 minutes this is quite some work. Luckily I don’t have to make a time lapse for every 10 minutes. I skip the first 12 hours, because not much is happening than and after that I take steps of 3 hours. For those of you who are quick with numbers and think that it’s a piece of cake to make only 12 time lapses: it is a little bit more complicated. First of all I had to make a planning to induce all the plants on the correct time, keeping into account that the building is closed at night. This is not the most difficult part, because time is a reliable constant. Plants however, are not. Only half of the plants still produces the fluorescent labelled proteins to visualize the microtubules. Also the construct to induce protoxylem formation by adding a hormone is not working in all the plants and even if it is working the cells are sporadically and more or less randomly induced. So I’ll be screening over hundred plants for my 12 time lapses. 

The first month of 2014 is already over. It was a busy and a lovely month for me. However, I am almost sure February will be better…but I’ll tell you about that next time.

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December 2013

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Harvesting Arabidopsis seeds three afternoons in a row can be rather boring. Especially because you have to keep focused to prevent those tiny seeds from going everywhere and contaminating the different batches. One day I forgot about the time and when I left the growth chamber the corridor was pitch black and the door to the main corridor was closed. Luckily it wasn’t locked and it wasn’t that late… It just gets dark early…

I have finished screening the protoxylem of my T-DNA knock-out lines. On first sight there does not seem to be that much variation, but I still have to process the images for a proper analysis. My supervisor has a script for this to do it automatically. If I manage to get it working, I do hope to see some aberrations.

If this is not the case, it wouldn’t be a disaster. There are still some other lines that do have some differences. It would actually be a pity if I didn’t use them, since I spent three afternoons harvesting seeds from them!

I already wanted to make some crosses, but the plants with the fluorescent labels were not watered very well and before I noticed that, most of them were already dead. One of them was still okay, but exactly that one had silenced the gene with the fluorescence label….

My exam of the course ‘Cell Biology and Advanced Imaging Technologies’ went well. I was even disappointed that the questions were only about a part of the material we had to learn, which is usually a good sign. Because we had to write quite a lot at the exam, I took an old fashioned fountain pen with me. Those pens just slides over the paper, so no painful fingers and wrist for me this time!

For the next two and a half months I will be working solely on my thesis. I hope I can make some rapid progress than.

Until next month and have a happy New Year!

November 2013

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Four weeks ago I set a new personal record for ‘longest time non-stop in the same university building’: eleven and a half hours. It would’ve been better if it was twelve hours, but I had nothing to do anymore for that last half hour and wanted to go home. In the morning I worked on my minor thesis, for lunch I went to ‘het hok’ (the room of the study association), in the afternoon I had lectures and a computer practical for the course ‘Cell Biology and Advanced Imaging Technologies’ and in the evening I made a new edition of the Internodium together with my committee.

I’m doing my minor thesis at the Laboratory of Cell Biology chair group. I look for aberrations in the protoxylem and in microtubule orientation and dynamics in Arabidopsis mutants with xylem and/or miocrotubule associated gene knock-outs. I recently got the seeds of the mutants and now I’m growing the plants to create a seed stock and to make crosses with a line that contains fluorescence labeled proteins to visualize the microtubules.

Right now I’m screening the protoxylem of these lines by staining the roots of seedlings. The microscope I use for this is quite impressive and a lot larger than the basic light microscopes most of us have used. A few meters of table is filled with this microscope and other necessary equipment. I have to switch approximately ten switches just to get everything on. I really like to work with the microscope, it gives me the feeling that I’m looking into a completely different world. Next month I am going to analyze this protoxylem data. Hopefully I find some clear aberrations…

In the afternoon I follow the course ‘Cell Biology and Advanced Imaging Technologies’ which is about microscopes and microscopic techniques and approaches. It is impressive what kinds of things are possible with the many types of microscopes that exist nowadays. I like the fact that I am already working with a microscope in the morning, because it somehow makes it easier for me to understand all those different microscopic techniques and I also learn things that I can directly apply in my thesis.

Next month I’ll tell you if I found some aberrations and how my exam went…