Iceland – Day 5 – Glacier Walking

The landscape in Iceland is ever-changing. One minute you are surrounded by sheep and ponies in wide open grass fields and the next minute you are standing on top of a glacier looking at snow capped mountains all around you. You can get lost in a field of lava rocks covered in spongy green moss or spend the day gazing at blue waves crashing near the shoreline. Iceland is an island full of sensational scenery.

 

Today we went on a glacier walk. It was on Vatnajökull, the largest ice cap in Iceland. Guess what was filmed here. You guessed it! Game of Thrones. The second season was filmed where we took our walk. James Bond, Fast and the Furious and a new Jackie Chan movie have also been filmed at this glacier. But let’s be honest, as soon as our guide said “Game of Thrones”, the theme song started to play in my head and I was ready tah go!

20160416_122207

 

Our guides were hilarious. They took note of where 2 other glacier walk groups were heading and steered us away from them.   If you want more info on the company we used, just let me know!   We laced up our crampons (No, not tampons.  Gah, you’re sick!) and headed for the ice.

20160416_121745

 

The only rule for glacier walking is “Do Not Fall.” Christian and I found out how sharp glacier ice can be. No one fell, but we were both assaulted by the prickly frozen water. Our hands acquired some cuts just from being Curious Georges and touching the ice. Blood was spilled. (Game of Thrones theme music is still playing. Can you hear it?)

20160416_134354-2

We walked on the glacier for a little over an hour and DANG was it hot! My dad and I had definitely overdressed. But come on – who expects to be warm on a glacier? There is an advantage of being surrounded by tons of ice when you are sweaty. I’ll let you figure it out. We cooled down and enjoyed another fantabulous Icelandic landscape.

20160416_133456

20160416_132009

img_6596

Glow Worms – German Version

Hättet ihr gedacht, dass wir Menschen auf der genetischen Ebene Würmern relativ ähnlich sind? Viele Gene stellen in Würmern Proteine her, die identisch mit denen von Menschen sind. Wissenschaftler am Max-Planck-Institut für molekulare Zellbiologie und Genetik erforschen diese Proteine mit Hilfe des Fadenwurms Caenorhabditis elegans und hoffen, so auch besser verstehen zu können, welche Funktionen diese Gene bei uns Menschen erfüllen. Gut 80% der menschlichen Proteine haben eine Entsprechung in entwicklungsgeschichtlich sehr entfernten Organismen wie solchen Würmern.

 

Der Fadenwurm C. elegans lebt in nahrungsreicher Erde und frisst Bakterien, die auf organischem Material, das verrottet, zu Haufe vorkommen. Der Wurm hat zwar kein Atmungs- und Kreislaufsystem, verfügt aber trotzdem über einen Mund, eine Art Speiseröhre, einen Darm und ein Nervensystem. Ausgewachsen ist der Wurm ungefähr 1mm lang. Dieser minikleine Wurm kann sein ganzes Leben über mehr als 20.000 Proteine herstellen. Wenn wir verstehen, wie diese Proteine im Fadenwurm C. elegans funktionieren, können wir vielleicht Rückschlüsse darauf ziehen, welche Funktion sie bei uns Menschen haben.

worms

Fadenwürmer mit grün markierten Proteinen. Oben links: ein Ei, aus dem sich ein Wurm-Embryo entwickelt Oben rechts: Drei Würmer im Larvenstadium Unten links: Der Kopf eines ausgewachsenen Wurms Unten rechts: Der Schwanz eines ausgewachsenen Wurms

Abbildungen: Ich mit Transgeneomics-Facility am MPI-CBG

Die Proteine dieses Wurms sichtbar zu machen, ist relativ einfach, da der Wurm durchsichtig ist und sich somit perfekt zum Mikroskopieren eignet. Aber wie unterscheidet man unterschiedliche Proteine? Und wie macht man möglichst gute Bilder? Wir arbeiten mit Licht.

Stellt euch vor, man könnte ein bestimmtes Protein in so einem Wurm überall aufleuchten lassen, und hätte schließlich einen leuchtenden Wurm, an dem man genau dieses Protein dann unter dem Mikroskop genau erforschen kann. Nun, genau das haben Wissenschaftler am MPI schon geschafft. Sie haben ein grün leuchtendes Gen (GFP – green fluorescent protein) als Markierung an ein Wurmprotein gehängt, das auch beim Menschen vorkommt. Das haben sie dann mit vielen anderen Proteinen genau so gemacht. Durch das angehängte GFP leuchtet das Protein unter UV-Licht grün und kann gut lokalisiert werden.

 

Die Mikroskopietechnik, die genutzt wird, um die grün leuchtenden Proteine zu erforschen, heißt SPIM – Selective Plane Illumination Microscopy. Hier nehmen Lichtscheiben die Probe ins Visier, die im 90°-Winkle zum Detektionsobjektiv liegt (das ist anders als bei anderen Mikroskopen). Bei dieser Mikroskopietechnik entfällt das Problem des optischen Bleichens – Licht kann die Fluoreszenz verschwinden lassen und damit die Probe unbrauchbar machen. Mit den Lichtscheiben kann man schnell ein 360°-Bild der Probe machen, und dann alles als 3D-Bild zusammensetzen.

 

Die Wissenschaftler am MPI-CBG nutzen SPIM, um Bilder von vielen verschiedenen, mit GFP markierten Proteinen im Fadenwurm aufzunehmen. Die Lichtscheibe erleuchtet einen hauchdünnen Schnitt durch die Probe. Der gesamte Rest des Wurms verbleibt im Dunkeln. Ist das leuchtende Protein in der erleuchteten Schnittfläche vorhanden, wird es sichtbar. Scheibe für Scheibe wird der Wurm so vom Kopf bis zum Schwanz durchleuchtet und wird währenddessen auch um 360° gedreht. Mit einer Software kann man daraus dann ein 3D-Bild rekonstruieren.

 

Ziel ist es, einen interaktiven Bildatlas der Wurmproteine zu erstellen. Damit hätte man die Möglichkeit, bestimmte Proteine zu bestimmten Zeitpunkten in der Entwicklung eines Wurmes zu lokalisieren. Schaut man sich die 3D-Bilder am Computer an, kann man den Wurm in alle Richtungen drehen und ein bestimmtes Protein sichtbar machen. Das kann viele Forschungsfragen beantworten: Wie viel vom Protein X ist in der Kopfregion, wie viel davon in der Schwanzregion vorhanden? Ist das Protein Y immer nur im Kopf des Wurms angesiedelt, oder ändert es seine Position um Laufe der Entwicklung auch? Interagieren Protein X und Y miteinander?

 

Dieses Wissen kann uns helfen, die Funktion bestimmter Proteine auch beim Menschen besser zu verstehen. Und das kann medizinische Bedeutung haben, weil es neue Ansätze für die Behandlung von Krankheiten wie Alzheimer, Parkinson oder Krebs liefern könnte.

Glow Worms – English Version

First published online for Germany’s Year of Light 2015, here is what I do these days.

Did you know that humans are genetically similar worms? Some worm genes make proteins that are similar to proteins in humans. Scientists at Max Planck Institute of Molecular Cell Biology and Genetics are using the worm, C. elegans, to study these proteins in hopes of gaining a better understanding of how the proteins function in humans.

C. elegans is a nematode worm. It can be found in nutrient rich soil often feeding on bacteria that thrive on decaying organic matter. Although lacking a circulatory and respiratory system, the worm has a mouth, pharynx, intestines and a nervous system. As an adult worm, it only grows to about 1mm in length. This tiny worm can generate over 20,000 proteins throughout its life. If we can understand how these proteins function in C. elegans we may be able to draw the same conclusions about their functions in human.

worms

Above: C. elegans worms with a GFP tagged protein, syp-1.  The green is the protein and the blue is the DNA inside the worm. Syp-1 plays a role in pairing chromosomes during meiosis. Top Left: egg, Top Right: Three worms at larvae stage 1, Bottom Left: Midsection of larvae stage 4, Bottom Right: Tail of adult. Taken by Me, while in the Transgeneomics Facility/Sarov Lab – MPI-CBG.

Imaging this creature’s proteins is a fairly simplified task as the worm is transparent, making it perfect for microscopy work. But how do we distinguish between different proteins in the worm? And how do we get the best image possible? We use light.

Imagine if we could light up one specific protein in the entire worm, essentially creating a glowing worm that we could use to study one protein at a time under a microscope. Well that is what the scientists at MPI have done. Using molecular biology techniques, they have attached a green fluorescent tag (or green fluorescent protein – GFP) to a worm protein that exists also in humans. And they have done this for many different proteins. The GFP tag makes the protein glow green under fluorescent light and allows the scientists to track the protein inside the worm.

The particular microscopy method employed to study these fluorescent worm proteins is known as SPIM. SPIM stands for Selective Plane Illumination Microscopy and uses sheets of light perpendicular to the detection lens to bring a specimen in to focus. This is different from other microscopes in many ways. It allows the scientist to avoid a lot of photo bleaching – a phenomenon where light fades the fluorescence in a sample, rendering it unusable. The light sheet SPIM also allows for quick 360o imaging and 3D reconstruction of specimens.

The scientists at MPI used SPIM to take pictures of many different GFP tagged proteins in C. elegans. A thin sheet of fluorescent light illuminates a tiny section along the worm body. Every other part of the worm is in the dark. If a fluorescent protein is present in this tiny lit up section, it will become visible. The light is repositioned on a different tiny section along the worm body and pictures are taken in this fashion along the entire length of the worm, from head to tail. The worm is also rotated a full 360o while pictures are being acquired via the light sheet illumination. After all of the 2D pictures are taken, a computer program uses the fluorescent light data in each image to construct the pictures into a final 3D image.

One goal of these images is to complete an interactive Pictionary of worm proteins, providing a visual tool to track where specific proteins are located during the different stages of the worm life cycle. Viewing the 3D image on a computer, one can rotate the worm in the x, y and z-axis allowing the visualization of one specific protein throughout the entire worm. This provides a multitude of answers to questions about worm proteins. How much of Protein A is present in the head of the worm as opposed to the body or the tail? Is Protein B always in the head of the worm or does its position change throughout the worm’s life cycle? Is it possible that Protein A and Protein B interact with each other?

If we can make conclusions about these human-like worm proteins, we will gain an understanding of how these proteins function in humans. This alone could lead to medical advancements in treating human diseases such as Alzheimer’s disease, spinal muscular atrophy, Parkinson’s disease and cancer.

Expat in Germany

January 10, 2014

I have lived 2 hours south of Berlin for 7 months and up until December had only been there once, to fly out of the airport.  Finally, I made a trip to this international city for a weekend with a good friend (A friend who has now left me for Belgium.  Thanks a lot, friend. ::wink::).

First impression:  This city is HUGE.  It’s so spread out compared to Dresden.  Then again, Dresden is pretty small.  Maybe that’s why I like it so much.  One point, Dresden.

Second impression:  It’s dirty.  Dresden is clean.  Berlin has tons of graffiti and trash lining its streets.  Two points, Dresden.

Third impression:  The people I met can pinpoint an East German by attitude, clothing and whether or not he/she had a baby by the age of 22.  I found this hilarious but also true.  The history of East/West Germany is still affecting the way people live here.  One point, Berlin.

Game over.  Dresden wins!!  Ok, I’m a bit biased.  Berlin is probably a lovely city, but I didn’t have a lot of time to see the sights.  We were there for a house party and it was also too cold for me to muster up any enthusiasm for sight-seeing.  But hey Berlin, you’re only 2 hours away… that’s what I’ll probably tell myself for the next 7 months to come.

mm

A Legal Alien

May 7, 2013:
It’s official!  I am a legal alien living in Germany.  I received my work permit at the immigration office this afternoon.  So I’m celebrating with a new dress and a bottle of vino!

Prost!  I guess I’ll continue this over a glass of my tempranillo…

Other accomplishments of the day:

1.  5K run along The Elbe to Schillerplatz.

Elbe

2.  Found my new apartment in Blasewitz.  After running to the bridge at Schillerplatz, I walked my stink and sweat around town until I found the exact address of the place I will call home on Friday.  I walked through a midday market and found myself here:

Schillerplatz

Does it look familiar?  It should.  Check out the previous post.  IT’S REAL!  IT’S REAL!  Not like Santa Claus or the Tooth Fairy.  My apartment really is here.  Are you kidding me?!  Someone pinch me, I’m dreaming.  I live a few steps away from a tea shop.  Given my obsession with Earl Grey, I find it highly appropriate and mildly disturbing, like someone is saying, “I will give you an all access pass for now, but you better be ready to pay up in the future.”  Good thing I’m in academia and don’t have any thing to give back.  Sucker butt.

3.  A delicious home cooked dinner consisting of fresh made chicken filled ravioli in a tomato basil sauce.  It goes well with the wine.

So it may not seem like I accomplished a lot today, but I am exhausted from being an excited expat for the past couple of days.  I arrived last Thursday, after almost a complete day (yes, 24 hours) of traveling.  I managed to drag my jet lag to a seminar on prions the following Friday and I met my boss for the first time.  Appropriate that our fist meeting was over a couple of beers, right?!  GO GERMANY!  That same evening, I took my first trip to the grocery store (which I will now call Netto or Lidl or something else that will totally confuse me when I read this again in America).  Guess what I was excited to find.  Earl Grey!  Gimme that.

Earl Grey

Since Friday, I have been to the Zimmer and the Frauenkirche, both took my breath away.

The Zimmer (a palace):

zimmer

The Frauenkirche (a church):

Frauenkirche

I also found this restaurant that I was so excited to try before I moved here:

Alte

It was worth hunting down.  The view of the platz was incredible.  The food was delicious.  I will be making a second visit for the creme brulee.

The view:

platz

There is still so much more to do and see and I’m ready for all of it.  Tomorrow is my first day at work.  The following day is a holiday!  I just found that out.  Ich liebe Deutschland!  I guess I’ll have to make another trip to the grocery store, I mean I mean… Netto, before tomorrow night if there’s going to be any at-home wine drinking on Thursday.

The 7 Day Countdown to Moving Day

April 24, 2013

My new home

In one week, I will say “Auf Wiedersehen” to USA and “Hallo” to Dresden, Germany. I have never been so anxious, nervous, excited and stressed out. If I ever decide to do this again, pray I read this and remember how stressed I am at this very moment.

Friends and family all want to say goodbye during these last days in the States and I just don’t have the time right now. I thought I did a good job of planning and trying to see everyone before this final 7 Day Countdown and I am so grateful to have such good friends, but I am about to scream and then go run into a hole and hide until May 1st arrives with my airplane.

Let’s move on to nervousness. Ich bin nervös. How do I say “mascara” in German? Where do I buy pillows? Which direction is the US Embassy (thanks Liz!)? Will people be willing to help me if I forget all the German I know?

And now the exciting part. I’M MOVING TO GERMANY!   Thank you Kirsten, for reminding me why I’m doing this and how excited I should be.  Finally! I am doing something I’ve wanted to do since college. Ok, so it was always Italy where I envisioned living amongst the natives. But Italy is going down the crapper right now, along with Greece and Spain. I visited Germany twice last year and fell in love (plus I’m half German, is that racist?).  So, Germany it is! I’ve always wanted to live somewhere where I didn’t speak the language, and I’m doing it! Boom.

In 7 Days, this picture will be my new home.

Iceland – Day 4 – Forgetful yogurt

Day 4 was a day for conquering challenges.

We were served a huge breakfast at Guesthouse Nonni, which I mentioned before in Day 3. My belly gladly invited the challenge as I am always up for trying new foods – it is my favorite way to engage in different cultures. I experience the world through my taste buds and my memories are often linked to something I have eaten. I will always remember Nonni for the Icelandic pancakes, pate and homemade bread.

Our next challenge was to explore 2 waterfalls. Ok, not so much of a challenge except for the courage it took me to walk out on the metal grate platform at the top of the 2nd waterfall. I am not a fan of heights. The backs of my legs get weak just thinking about looking over an edge. While Christian had already explored the highest point of the waterfall, climbing and squatting close to the edge, I had yet to make it out on the platform. After a few cautious test steps and watching others walk on the platform worry-free, I tip toed out there. OHHHH! Looking down at the water falling below was a trip. I didn’t stay on the platform for long, but enough time to get a couple of pictures:

img_6544

photo-apr-15-2-28-55-pm-2

 

Here he goes again… scaring me by being so close to the edge:

photo-apr-15-2-39-16-pm-2

img_6549

 

With a bit of adrenaline pumping, we next made our way to THE EVENT of the day. Snowmobiling. On a glacier. Covering a volcano. This was the most expensive thing we planned for the trip (178 euros a person!) but it was by far the most fun, exciting and memorable experience. After gearing up, we looked like astronauts.

DCIM100GOPRO

DCIM100GOPRO

 

We climbed a ladder into a huge transport vehicle and settled in for a bumpy 20 minute ride over volcanic terrain. After hopping up and down in our seats, we arrived on the glacier where our snowmobiles were parked and waiting for us. We picked our vehicle and I hopped on the back. Christian drove the entire time and I was in charge of the GoPro – which means I held on to the snowmobile with one hand for most of the trip! (I will upload the video and link it here) I had that snowmobile in a death grip after we took off. Thirty kilometers per hour doesn’t seem very fast, but on a snowmobile it is fast enough! We rode to the top of the glacier in a single file line and I was screaming and laughing the whole way there.

I was relieved to have a break from riding. It was fun, but also scary at times. My butt came out of the seat a couple of times and at one point, we were riding on only the left skate of the snowmobile. The chance to hop off and enjoy the view of the volcano, glacier and surrounding mountains was welcomed!

We had a chance to stop 3 times on our tour, because apparently we were riding lightning fast. Holy shit, we could have slowed down?? If you ever do a snowmobiling tour, I would suggest taking your time if you don’t have a need for speed. The 15 or so other riders we were with happened to be all men in their 30s, from the Netherlands and I’m pretty sure they all had on shirts that said either “I wanna go fast, daddy!” or “If you’re not first, you’re last.” I know my dad and Annie would have loved to ride slower.

20160415_181826

The views were breathtaking. THIS is what made my experience. Seeing the world from up here, on a beautiful day with blue skies and the ones I love will be something I cherish for the rest of my life.

20160415_174809

We celebrated our victory with a beer in the cutest little town of (appropriately named) Vik.

20160415_204019

Wondering what the yogurt title is all about? The name of the glacier we toured is called:

Eyjafjallajökull

Exactly. Repeat, very quickly after me, “I forgot my yogurt.” That’s how you pronounce Eyjafjallajökull.

 

Iceland – Day 3 – Waterfalls

Our road trip started today. We departed Reykjavik and headed northeast towards Þingvellir National Park. Hiking was on the to do list, so we parked at an information center just outside the park and hiked our way in. We trekked for about an hour until we reached The Rock – the meeting place for Icelandic Parliament back in the day.

 

I imagine Thor was there, giving speeches about how he maintains his golden locks hair under a helmet bearing the weight of two huge feathered wings.   Thor’s helmet is also the nickname of NGC 2359, a nebula some 15,000 light years away in the constellation of Canis Major.

screen-shot-2016-05-17-at-8-08-39-am

 

(from http://www.pa.msu.edu/people/horvatin/images/constellations/canis_major.jpg)

 

What was I talking about? Day 3. After the park hike, we drove through Laugarvatn and made our way to Gullfoss waterfall. The family that owns the land at Gullfoss has never allowed companies harvest the energy of the waterfall for electricity. They are afraid it will take away from the beauty Gullfoss. Right on!

 

We took a few pics out in the wind… it was SO windy around the waterfall. Luckily, Christian’s colleagues suggested he take a scarf to cover his face. He was warm enough to go trekking beyond the visitor ropes, giving me a mild heart attack while fearing he would fall into Gullfoss.

img_6455-2

 

(Christian took the above pic while standing beyond the roped in boundary)

With the wind at our backs, we continued to Hella (pronounced “Hetla”). I had booked 2 rooms at Guesthouse Nonni in this little town. The house was perfect for us. We were the only ones staying there, except for the owners who sleep downstairs and open their kitchen in the morning for breakfast. Annie and my dad played their instruments all night – free concert! Yay yay. Then the owner of the house made us such a big and delicious breakfast in the morning with all the fixins! They had waffles and homemade bread (cooked using geothermal heat) and orange juice and pate and I could go on and on and on…

But I won’t. Until Day 4.

 

The sky that night in Hella was incredible.  We even saw the Northern Lights again.

img_6461

Boobies – 560 Breast Cancer Cases

A lab in the UK sequences the genomes of 560 different breast cancer tumors and has published a list of genes that, if mutated, could cause tumor growth. I’m sure there are other papers out there like this, but who has time to read? This one caught my eye on BBC this morning.

The list consists of 93 genes. They give the information in a simple figure:

naturebreastcancer1

Ok, maybe it isn’t SO simple. I do have the slight advantage of reading scientific papers, albeit I should read more of them for work. Let’s ignore Part A. There is a better figure for that, below. Part B lists the 93 genes that can play a part in breast cancer development. They’ve told us which genes are estrogen receptor positive (ER +) and which ones are negative… important if your doctor wants to treat your breast cancer with hormone therapy. If the genes mutated in your breast cancer are ER+, that means they are fed by estrogen in your body. Hormone therapy to reduce/remove estrogen could reduce or even eliminate your breast cancer. If the genes mutated in your breast cancer are ER-, hormone therapy won’t help eliminate the cancer.

The figure below shows the frequency of different types of mutations in the tumors as well as the chromosomes involved. I love it! I love that I can finally just look at a chromosome map and see where breast cancer mutations most likely occur.

bc

The Ven diagram (ooooh, look at the pretty colors!) breaks down the ER+ and ER- into numerical data. It also shows how many HER2 mutations they came across and classified them into ER+ and ER-. An early breast cancer drug discovery showed that if HER2 is mutated, it could be treated with Herceptin. This diagram shows that of the 73 HER2 mutations they found, 27 of them will not respond to Herceptin treatment (because they are ER -). Neat, huh?

They saw substitutions, rearrangments and inserts and deletions (indels) in the DNA sequences that are not normal and put them in an easy-to-read pie chart. Mmmm, pie charts. Sixth grade math. Yummy!

Now can someone tell me why HER2 is not on the list of 93 genes??

It’s because HER2 is also known as ERBB2. Why? I don’t know. But the figures in this paper are still sexy.

Nik-Zainal, S., Davies, H., Staaf, J., Ramakrishna, M., Glodzik, D., Zou, X., et al. (2016). Landscape of somatic mutations in 560 breast cancer whole-genome sequences, advance online publication SP – EP . doi:10.1038/nature17676

I love the smell of bacteria in the morning!

June 8, 2016:

This morning I spilled bacteria on my hair. Bacteria! On my hair! Gross.

Oh, the joys of being a research scientist.

I immediately looked for the ethanol spray bottle and doused my locks with it. Now my hair will be completely dried out. Great. But I didn’t stop there. I found the bactericidal spray and swished that on my hair too. Then I ran to the bathroom and washed my hair with hand soap.

Then I remembered feeling some bacteria drop on my foot. Yep – I wasn’t wearing the best shoes for bench-work. My toe was on fire! I swear it was. Even though this bacteria is harmless, I swear the little buggers were eating my flesh. So I triple wiped my foot with ethanol, bactericide and hand soap.

I think I’m ok, but I will smell my hair for the rest of the day.

PhotoContest_small-71

(photo credit: S. Hasse)

If you’re wondering, “Why bacteria?” here is why…

In molecular biology, we use a bacteria strain, E. coli, to make DNA for us. We have usually manipulated the DNA in vitro, on a small scale. A common manipulation in my lab is to simply add a fluorescent tag to a gene so that we can see it under the microscope. Hey gene, whatcha doin??!  (We actually look at the protein associated with the gene under the microscope, but let’s just keep it simple for now). If we want to actually use the fluorescent DNA for anything other than small scale in vitro tests, we need TONS more DNA. So we put our manipulated DNA into E. coli and the bacteria “grows” the DNA for us. We basically utilize E. coli’s DNA replication machinery to make more DNA, then discard the E. coli – which is what ended up in my hair. Yuck.