Monday, June 21, 2010

The Acid Fairy

The Acid Fairy has killed my algae. Each day I left the lab and the algae seemed to be growing happily inside their cozy bottles. Each day I would return and the bottles would be turning more and more acidic. The only logical explanation was that someone was putting acid in my bottles. Sabotaging my experiment right under my nose!

Or.... it's science.... this same phenomenon of batch algae tests going acidic has been reported in other published studies, but not really explained.... so the next step in our experiment is to try to determine what's happening. We have a few possible scenarios: the bottles are contaminated (which some surely are) with bacteria, bacteria who produce fatty acids as a byproduct, the algae are using the glucose we added and producing carbon dioxide, or there is a fatty woman in a ballet costume adding fatty acids to our bottles at night.

Tomorrow we will get to the bottom of this. we are being trained on gas chromatography, which will allow us to test for the presence of fatty acids. we may also look at the other bacteria growing in some of the bottles to see if we can identify it..... but i think i already know what it is..... Acid Fairy!

we've also started a mini-batch test to get a better idea of what happened. we inoculated nine bottles with algae and different combinations of nutrients, glucose, and buffer. however, we are not sampling to keep them sterile to see if the same bacteria invades the experiment.....

we should hopefully have a better understanding of what's happening inside the bottle microcosm by the end of the week.... or at least have a better idea of where to set our traps....

Hup Holland Hup!

by De

So much has happened lately and I've been slacking on keeping everyone updated! The world cup has... BEGUN!! and thank goodness I'm in a country that likes soccer!! I've played since I was little and it's a lot of fun to see the Dutch get very patriotic for their team! The first game was on a Monday and this little city of Delft went completely ORANGE! The crazy outfits and ways that people were showing their team spirit made everyone be in such a great mood! (not to mention Holland is undefeated thus far..!)

Another bright note from the last week is that my mom came to visit me! Her and a friend from home came and stayed in Delft and instantly fell in love with the lifestyle over here! (I'm kind of surprised they made their flight home) I had a lot of fun seeing some friendly faces from back home and miss them already!

But on a more professional note.. things in the lab are definitely moving along.  Our SAT columns are getting closer and closer to being considered ripened as we speak.  There are small hiccups along the way, but for the most part everything has been very productive and a learning process on a daily basis!  We have characterized the columns twice now (once for pathogen removal and the second time for nutrient removal).  Through this process we now have a more exact idea about what is going on in the columns as the waste water runs through them.

More to come later for sure! Tot ziens!

Wednesday, June 16, 2010

New things through lists.

By Laurel
New things I am doing in the lab recently...
-Grinding plants with a pestel and mortar: haven't done this since 10th grade biology or something....
-Learning how to use the Atomic Adsorption Spectrometer
-Using my Biological Processes background to figure out where to get "primary effluent" with a concentration of ~30(+) mg/L NH4-N from at the local wastewater treatment plant

This week has been very busy for me, but with any sort of luck, help from lab staff, and hard work, I hope to have results by Friday!! I am really excited to see how they turn out. Even if I lost mass of my heavy metal, zinc. This excitement is why I am one of those crazy scientists....

New things I did this past weekend...
-Rode my bike from the Netherlands into Belgium, without even really noticing a border sign wherever I crossed the border
-Began to realize how to recognize a terrible map when I first see the map
-Strolled through a forest and viewed art sculptures in the forest: pretty amazing
-Ate Belgian frites with a ton of mayonnaise on top (and I hate U.S. mayonnaise....)
-Discovered salsa dancing in Delft

This summer is going by in a flash, as expected. I am trying to reconcile the fast-pace of events here in Europe with the knowledge that in Two month's time, I will be in a very different world, at a much slower pace, in the Peace Corps. Alone on long rides, just me and the bike (which is absolutely a great bike in my opinion), I can just focus on finding my way from point A to point B, at whichever speed I choose. Sometimes I feel like flying down the open bike road, and sometimes I get tired. I can say that biking is a sport I truly enjoy doing alone.

I also have to say that I love Delft. I love it more than any town I have been through by bike in the Netherlands. I would call it quaint, picturesque, laid back, small....

Sunday, June 13, 2010

Introducing my mentor at UNESCO-IHE....Mrs. Valentine Uwamariya

Born in Rwanda, Mrs. Valentine Uwamariya graduated with her Bachelors (Chemistry) in 1999 with distinction from the National University of Rwanda. From June 2000, she has been working as assistant lecturer at the same university, in the Chemistry department. In 2003, she joined the University of Witwatersrand in South Africa where she obtained a Master of Science (Electrochemistry) in 2005 with distinction. In the same year she has been promoted to the grade of lecturer. Currently, she is a part time PhD student at UNESCO-IHE, Institute for water Education, in Water Supply and Sanitation Department. She works under the supervision of Prof. Gary Amy and Dr. Branislav Petrusevski. For her PhD her research is focused on "Adsorptive Removal of Heavy Metals from Groundwater by Iron (hydr)oxides-based Media."


Wednesday, June 9, 2010

Gl-AnMBR under Dutch conditions: an interdisciplinary approach between engineers and wizards


One of the most gratifying activities that you can do in Delft, and in the Netherlands in general, is biking. Right after work last Friday Ivy, Laurel and I took a bike ride to a beautiful park in Delft called "Delftse Hout". This park is right at the edge of the city limits and comprehends hectares of gorgeous land surrounding a lake. Biking in this park was a great pleasure. It was so pleasant that we forgot about the park limits and continued biking north up to the Hague's outer area. So many pretty spots in the way, sheeps, faissans, a wind mill, other lakes. No wonder why people around here don't really know about stress. How can you be stressed out with a landscape like this?. Of course, we are in summer time and it's a completely different story during winter.

 (Outer area of the Hague... preeeeetty!)

By now you might think all we do here is eating and traveling, but there is another activity that occupies the remaining 10% of the time (I'm just kidding Dr. Yeh). A major part of my research at IHE is to build a similar membrane set up as the one I have at USF and to run it under different operational conditions... Dutch conditions. So far, I've been successful on building the set up but the work is just starting. You see, Dutch conditions are a little rough in the edges. I was very spoiled back at the USF lab where I had all the supplies I could possibly think of to make my configuration more efficient. Under Dutch conditions however, I have to work with what is available since there is a major constrain of time in the research program. I have to say that lately I've been missing my lab more than ever, but at the same time I think I've become better at pulling rabbits out of hats and converting water into wine. I also want to acknowledge the very helpful IHE lab staff without which I couldn't have become the aprentice magician I am now. Being this said, I'm ready to test my set up, which is a great achievement since I only have 8 more weeks to go (WOW!).

Monday, June 7, 2010

Inoculation Day...

After working in the lab all day and coming home to work on my other project, I am a bit braindead... for some reason I can only think in haiku. So here are the day's events.... in 5-7-5...

Eukaryotic chaos
In swirling glass jars!

More to come later..... hopefully with stellar results....

Black or white... or red, yellow, blue, green, etc.

I wonder if Michael Jackson or Benetton ever got a real international encounter such as the one I recently experienced. A herd of very hungry people sits in a BBQ restaurant with the aim to take advantage of the special of the day, unlimited ribs for 10 euro. Thirteen people of 13 different countries sitting down in a wooden table with one, and only one thing in their minds... MEAT!. Colombia, Venezuela, Uruguay, Guatemala, Surinam, Germany, Belgium, Serbia, Portugal, Italia, China, Macedonia and Tailand-Norway (born in Tailand, raised in Norway) united by a delicious Dutch pork. No wonder why the Hague is the judicial capital of the United Nations. You must have a very nice rack of ribs to gain the attention of the world.
If you have noticed, a common factor among the bloggers on this column is the food. As I mentioned in previous blogs, going to the market is a very interesting experience. The adventure of finding what you like to eat with little knowledge of the Dutch language. I personally enjoy dark chocolate covered raisins very much and I've had several failed attempts in the search of them. But last week, I got it right!. After browsing the aisle of the grocery store for the the 100th time, there they were... waiting for me. It was a very satisfactory moment; in fact it was more than that. Compared to this covered raisins, Raisinets will cry out of disgrace. See with your own eyes how one of these raisins look like.

 (Dutch raisinet, the tip of my finger is used as a reference of the raisin size)

the guessing game


I bought something from Aldi today that comes in a box like grits and looks like it may actually be grits, but as I cannot read the box I will find out later if it truly is grits. Things like this simple surprise awaiting me has been one of the joyous experiences of living, shopping and eating in another country. 

This past week has brought a lot of accomplishments in the lab and has paved the way for many more.  I finally began the activity batch tests that I will be doing as part of Denys' evaluation of the inversed fluidized bed reactors that are being tested as a removal method for metals in wastewater using Sulfate reducing bacteria. 
 Using samples that Denys collected from her columns of both the liquid phase and the biofilm (shown in the above right image grown on polyethylene beads) and I will be testing their sulfide production and sulfate reduction while changing varies conditions. I have learned and practiced (about a million times now) a lot of new evaluation techniques to determine sulfide and sulfate concentration and am happy to be learning so many new lab techniques. I started a new experiment today and am excited to see how the week treats me. Hopefully all will go well and we will get some interesting and meaningful results. Either way they are cooking as we speak (or as I type?).

The past weekend was fairly exciting. On Saturday De and I ventured to Amsterdam to walk around and see the Anne Frank Huis. 
 I thought Amsterdam was beautiful, and as a guy in the gift shop told me delft is somewhat it's miniature, which I decided to be very true. The canals are much wider and the building are taller (and lean a little more). From above and maps the city appears to be laid out like a spiderweb consisting of canals and roads and who wouldn't want to get stuck in it? It was a beautiful day and people were riding in their boats and enjoying the weekend and life. The Anne Frank Huis was also a very moving experience and its difficult to imagine the life that she saw and the positive view of people she maintained and relayed through her diary. 

After arriving back in Delft from Amsterdam, we ventured to the market to participate in the MooiWeerSpelen festival. Delft always has something new going on and it has been great to observe and play in the new culture.  The festival contained many theatrical acts that were scattered throughout squares in the city. The festival lasted well into the night on Saturday with the last act finishing around 12:30(or 00:30), but we were home in bed before the night drew to a close for the many performers.

 We did venture out again on Sunday to the festival despite the rain and saw some really neat acts. 

Even in the rain delft is a very gentle and beautiful city. It has been quite easy to feel comfortable here and although we have only been here a month now, it seems like much longer.

Sunday, June 6, 2010

Experiments, a labyrinth, and dunes

By Laurel
This week in the lab, I conducted the first run of an experiment for my project. I learned many things along the course of the week. To describe it without photos....

My experiments contain an adsorption step and a desorption step. The heavy metal I am working with is Zinc. I first made a Hoagland solution, which is a solution for growing aqueous plants, containing nutrients and trace elements. Using a scheme of controls, I added Zinc to some of the samples and incubated all of the samples in small plastic trays overnight. During this step, in the samples containing Zinc, the some of the Zinc will adsorb to the surface area of the duckweed plants. Also during this step, some of the adsorbed Zinc will be uptaken into the plant cells. The goal of my experiments is to find out how much Zinc is uptaken and how much is just adsorbed to the plant, and show this using a mass balance on Zinc.

The second step in my experiments is the desorption step. For this step, I added EDTA diNa to some of the samples, which is a metal chelator, meaning it binds to metals. Adding EDTA will desorb the metals that have been adsorbed to the surface of the plants, but will not change the fate of the metals that have already been uptaken into the plant cells. In this way, we hope to be able to distinguish how much of the metal is adsorbed the the plants, but not uptaken.

Following the adsorption and desorption of the Zinc, I collected and acidified water samples from all of the respective samples in the experimental scheme. What is left to do is analysis. I will digest the plant samples from this experiment with nitric acid and the digested plant samples and water samples will be analyzed on the Atomic Adsorption Spectrometer.

I am enjoying my time thus far working with plants. You have to get them to grow for you in the lab so that you can do experiments without collecting plants from the wild again. Part of my lab time always includes checking in on the plants, feeding them primary effluent, harvesting them so they don't get overcrowded, making sure the light intensity is right for them....

My story this week is about a 30 mile bike ride I went on (by the map, not including me getting somewhat off the paths and also riding around exploring) yesterday. Due to an excellent bike and much stretching, I am happy to say my knee felt perfectly fine at the end of the ride!

Luckily for me, I picked up a good bike map which includes Den Haag and the Dunes on the coast from the Den Haag tourist office before leaving on my bike ride.... It was another gorgeous sunny day in the province of South Holland, and I decided that I would ride to the coast near Den Haag and then bike along the dunes north for a while and then turn around and bike back.

I took a more scenic route north (not the one that runs straight to Den Haag), but one that ends up on the coast further south of Den Haag. On the way to the coast, I was biking down a forested trail when all of a sudden, I came upon a hedge on the side of the path. The hedge was surrounded by farm fields- maybe hay. I turned my head and did a double take because it was no ordinary hedge. I had just stumbled upon a labyrinth! The labyrinth is an ancient meditation and spiritual tool- not a maze, but a path winding inward to a central circle. You may think of the greek myth of the Minotaur in the labyrinth. Anyway, this labyrinth did have dead ends, so it was not the traditional labyrinth in the sense of having only one path to the center. I walked through it, reaching the center which was a spiraled raised circular platform of stone. The labyrinth is obviously maintained, but I wonder how old it is. It could be very old indeed.

After the labyrinth, I continued on to the coast. I learned over time how to properly read the bike junctions on the map and how to look for the bike signposts that cover this country, but tend to disappear in a city or metropolitan area. I ate lunch by the North Sea. I had reached the dunes, or duins in Dutch.

The dunes were very pretty. I wished I had brought a bike lock to lock the bike and be able to walk on some walking paths through the dunes. Anyway, I carried my bike up to a lookout over the dunes and listened to whoever was opening for the outdoor Bon Jovi concert yesterday that was outdoors and thus amplified so I could hear it in the nearby dunes.

Up the coast, and the dunes were beautiful, but tiring because they were actually hills for a change from the flat landscape. Very suddenly, though, the dunes disappeared behind me and everything was flat again. By that time, I was tired, and instead of turning around as I would have had to do in most places, I decided to take a train home. You have to love the Netherlands for that combination: great bike trails and great public transit.

Inland to Leiden. When I reached Leiden, it was 4 p.m., and a little early to be going home. Instead I biked around looking for a castle marked on my map. I never found the castle, but I got to see a bit of the city of Leiden, which is located on the River Rhine, and has many nice places to eat or sit next to the river. It was a very pretty area, and I want to go back there some evening by train to explore it and hopefully find the castle, which is open to the public.

Back in Delft, the Mooi Weer Spelen festival was taking place. People were crowded into the central square for performances. The highlight was a night performance which included 8 dancers, a singer and a band, a crane, and a large steel ball. I will leave that to someone else to describe.

Friday, June 4, 2010

Almost There....

This week I spent preparing for my coming experiments... Because I don't have as much lab experience as some others in our lab, making solutions and other simpler tasks can take me a bit longer... but I take it all in as a learning experience...

Unlike other students, I'm not working directly with another student at IHE. The original plan was to continue another student's work, but due to time constraints we have a Plan B. This is the plan I've spent this week developing and finalizing (with much help!).

I will be conducting batch tests with different species of algae. I am investigating the optimal growth conditions for high nutrient loading under varying light regimes for each species. Other studies have tested species under high nutrient loading, but optimizing multiple parameter environments has not been well-covered. After running a series of batch tests, we are hoping to be able to pinpoint optimal growth conditions under these conditions, with a hope to expand to other parameters in the future.

After this week: preparing growth medium, determining trial matrices, finding out where things are in the lab, getting trained on various equipment, making mistakes and fixing them, finalizing the protocol... it's time for inoculation! Monday will be the day the algae garden is started... and hopefully they are happy there!

Wednesday, June 2, 2010


by De

This weekend was full of many surprises..  beach soccer in the city center aaaaand a HAIL STORM!! Oh my, there I was, sitting at the train station awaiting my friends arrival when ice came pouring from the sky!! Shortly after it poured... then all of a sudden the sun came out! (And I thought Florida's weather was crazy!)

This week Ana, myself and Chol went on a field trip to the wastewater treatment plant in Hoek Van Holland.  Sidenote: On the way, I learned that in dutch, IHE is pronounced E-Hi-A! Back to the real story.. we went to the WWTP to collect water to use for our SAT columns.  Due to the rain (and hail) during the previous days leading up to the trip, we were slightly skeptical as to whether or not the water we were to collect would be too diluted for our purposes.  It was very interesting to be able to kind of roam around the plant without supervision! (Pictures on the next trip for sure!)  After returning to E-Hi-A (hehe) and testing the water we brought back with us, the water did seem a little too diluted so we will be visiting the WWTP again next week.

These last couples weeks have been very productive in learning how to use the different machines to run different tests.  Now I can safely say that I can perform tests to monitor DOC, UV, Ammonium concentrations and am learning about COD and plate counts!

Plate counts.. sooooo cool!! I had to run downstairs to get my camera so that I could have pictures to share! Peter, the lab staff in charge of the microbiology aspects of the lab explained to Chol and myself the process and idea behind plate counts.  Yesterday we spread our water sample on a plate and today it looked like this...
Each little dot is a colony that represents a bacteria.  The pink ones are coliforms, the blue ones are e-coli and the green are salmonella.

This plate (different from the previous plate) consisted of 106,000 coliforms and 14,000 e-coli per 100 mL.  Only one of the plates showed a salmonella colony (the most dangerous of the bacteria).

On a not so happy note, we've had some strange complications measuring COD.  We prepared solutions to form a calibration curve... 

but when using the spectrophotometer, the absorbance value continued to increase slowly (rather than give one reading).  More to come on this later...
There was an error in this gadget