LA & NY

Leaving the "village" Santa Barbara behind me I'm visiting Los Angeles and New York during the winter break. Suddenly, sky scrapers, the metro and many more people are back in my life; it takes 1.5 hours to get with public transportation from the main airport in LA to the Walk of Fame. However, both locations are kind of "in the city center". Many friends told me that I would not like LA because it's not an actual city, but a bunch of clustered smaller towns or maybe not even towns, but living areas.

Walk of Fame in LA.

  The public transportation system itself worked well for us, but the people on the bus and in the metro were sometimes a bit "weird". Many were talking to themselves (I have to admit, sometimes it was hard to tell if they were speaking to their headset or not). Or shouting at other people, making noises and so on. I definitely don't want to be in the metro alone at night. Nevertheless, a one-day-ticket for the metro is 7$ which is really cheap compared to other large cities (Paris, ...). But apparently everybody who can effort a car does so and so the cities are unbelievable crowded (pedestrians are a rare species, don't even think of cyclists...).

I've just arrived in NY and my first impression is overwhelming - it's just unfortunate for LA that I go here directly afterwards...

Keep refrigerated

... and please think in Fahrenheit ;)

Winter in Santa Barbara

There are not many clouds in Santa Barbara most of the time, but now it's "winter" and "bad weather" appears. So we get clouds and temperatures below 10°C during the night. However, there's a huge advantage of clouds when it comes to sunsets (and of course some rain after a long drought is pleasant):

(I was asked if I use photoshop or anything else... but I didn't alter the image at all)

More images are at "Impressions".

Christmas tree at 20°C

The farmer's market in Goleta had an additional feature today: A huge, glittering Christmas tree! Some people were dressed up as Santa Claus with his angels and you could stop by for a photo with them. 

In addition to that, you can buy a lot of Christmas tree decorations for a reduced price at a decoration store next door:

The ugliest Christmas sweater alive

There's everything you can imagine decorated with the logo of my university here - pillow cases, pink Christmas tree balls (with a Hello-Kitty-symbol as well!), a lot of different clothing, drinking bottles of all kinds and sizes - and of course (we can't miss it, we're in the US!) Christmas sweaters:

I could just resist to buy one ;) The other day I went to buy clothes as well and there were even more sweaters in the same style. It's okay, since I had seen the video which is circulating on facebook which seems to be some kind of competition to wear the ugliest Christmas sweater you can find and dance to some Christmas music (sometimes accompanied by various family members with their favorite unfashionable sweater).

Group meeting

Today I presented my recent research results at our weekly group meeting. Usually we talk and discuss the work we did, but sometimes we chat about a paper if it's somebody's turn, but there are no new significant topics. I am also a member of another group which is so small that we don't present in turns every week, but we have visitors and meet with other groups.

Since the professor I work for, is right now not in California, we have a skype conference and two laptops (one for skype and one for the presentation).

The presentation today went well, I think, but I didn't find the remote control to switch on the projector, so I climbed on the table to turn it on manually ;) But later it turned out that there is no remote control and the control is built into the wall...

My love-hate-relationship to science

Honestly, I really started disliking the average image shape I had to process with the program Matlab for my current research project. I stared at my laptop screen 24/7 as it felt like. And the data was noisy and it looked like we were not getting anywhere.

But now! We tuned the algorithm and we believe that we can "see" the cortical actin concentration along the cell outline (that's kind of seeing where the "muscle" of the cell on the membrane is more active - we hope to show that). The reason why this is actually happening is not too simple and we're still thinking about it, but first of all, here's some  data:

Cortical actin concntration along a "master cell" under confinement (our average cell "to rule them all" ;)).

Ginger bread 2.0

A little bit more complicated than just attending the graduate housing ginger bread house building party is: making ginger bread with a ready mixture like this:

Well, it was not too easy, because we ended up with a very brittle dough so we added the tenfold amount of water ;) (just one order of magnitude, shouldn't matter too much ;)). So we couldn't make any cutting of shapes any more, but we had one huge ginger bread instead:

It was still stable enough that we could have build a house, but it was so nice, warm and ready, that we just started enjoying it. The next level will be actual self-made ginger bread, but I will have to translate the ingredients or that and it's not too common to bake huge amounts of ginger bread in the US.

Finals done!

At the UCSB we live in a quarter system, i.e. there are no semester as most German universities structure their academic year, but quarters the year is divided into. This week was the last week of the fall quarter, so the final examinations were written. But unlike most German examinations, the graduate courses have a "take-home-final", so you get for example 24h for this homework. There's nearly no written 2-3h examination any more (that's the "undergraduate level of testing").

 

Comparison of the image of a cell nucleus once with a confocal microscope (left) and once including light form all heights (right). wikipedia

However, somehow I was lucky, and had "only" two presentations and one report to turn in. That was even the week before the finals' week :) So I've got more time to focus on research and next week I will get training on the confocal microscope which is a vital instrument in Biophysics: You can travel through your sample and focus on "slices". Often this microscope is combined with a fluorescent microscope so that only certain, dyed parts are illuminated and light from other slices (which are not in focus) is not included in the image.

Lebkuchen-House

Since we were lacking real "Lebkuchen" (or ginger bread) we took honey crackers to build a "Lebkuchen"-House. It was super fun, but the house didn't survive too long... But for our architecture we won a 5$ Starbucks gift card, yay! And if we want to build another one there are actually sets you can purchase at the supermarket (you might run into real Lebkuchen and not our pseudo-Lebkuchen substitute).

Tuition fees

Once upon a time, there were tuition fees in some counties in Germany and it was a huge debate and I can remember a lot of demonstrations until the fees were abandoned - yearly fees of about 1300 $. And in the US so many people pay the tenfold or even hundredfold amount per year! Most students start borrowing money on student loans so that after four years of undergraduate studies you've already collected a lot of debts to pay back. But imagine, you've started studying for some time and realize you are not going to make it or something happens and you don't graduate - there's still this huge amount of money left. As far as I got it, that will cause a different pressure on you to finally graduate. (Unlike in Germany where you "just" can skip or switch the subject - one year or even more does not matter too much.)

However, there's of course a movement against the fees, called the "Million Student March" - and again against this movements there are the really conservative voices, e.g.
Why I stand against the Million Student March
It's really fun to read ;)

Santa Monica

Today I've been to a Fulbright Lunch which was attended by a lot of international Fulbright scholars (not only students, but also professors and their families, postdocs,...). It took place in Santa Monica at a house on one of the hills from which you have got a beautiful view on the ocean and LA! Every scholar also brought a national dish from their country. It was super interesting and awesome!
Here are more pictures: http://masterusa-lotta.blogspot.de/p/impressions.html

Yosemite stories (1)

"Oh my goooosh, snooooow!!" - when we came close to Yosemite (after about 871429 hours of bus drive) we saw a not negligible amount of snow in the forest around us! It seemed to be another planet, not California. There were just some cabins around, no large buildings, no supermarket... and no signal! We had free wireless Internet access at our hostel, but I am not sure if Internet is the most important thing if you go hiking ;) I was more worried about not being able to call someone if any accident happened.

[The facts: The International Students Association of the UCSB organized a trip to the Yosemite National Park for four days leaving on Thanksgiving morning (Thursday), then there are two days of hiking in Yosemite and one day for driving back.]

After exploring and understanding the hostel (do not let children sleep on the upper bunk bed - I'll sleep at the bottom ;) ) we had a huge Thanksgiving Dinner on Thursday. It seems to be that you are not supposed to be able to stand up easily afterwards. Even for vegetarians there was a lot. The dessert would have been a meal for itself (pumpkin pie, apple pie, cream).

But you should have some space for "S'mores" afterwards at the campfire! Marshmallows are melted on a wooden stick just above the fire and then stuck between two crackers and chocolate. The name "S'mores" = "I want some more" is kind of understandable ;) (If you're not too tired by the bus ride and maybe didn't have Thanksgiving Dinner beforehand)

The next morning started with an awesome warm breakfast  (no muffin & coffee-style at all!) - that's probably the latest point where everybody stopped thinking about calories. But then again - 1.5 h bus tour to the hiking path in Yosemte NP.

And it was absolutely worth it! We started with the small hike and saw some beautiful nice small stream, a huge amount of snow and the motive for the characteristic Mac desktop background! At the "top" of the path we took there was a smaller, short path which led to another water fall and these falls go a few hundred of meters downwards...

This was all so impressive that we finally concluded that the modern digital technologies are so advanced that everything still seemed real.

Yosemite (2)

... and there'll be a Yosemite (3) with all exciting stories, but for now, let's start with some more photos: http://masterusa-lotta.blogspot.de/p/impressions.html

Yosemite (1)

During Thanksgiving the International Students' Association organized a four-day-trip to the Yosmite National Park. And it was amazing! But also super snowy and the hiking path consisted sometimes of more ice than rock. I'll post more photos and infos soon, but here's a start:

My network

Two days ago I made my own network! (Non-social, sorry ;)) It's been a "small" microtubuli network or probably rather a bunch of microtubuli clustered together without adding any crosslinker. It took about 2.5 hours and it was mostly pipetting and waiting for the incubation time to pass.

 

Green: Microtubuli, red: actin, blue: nucleus (wikipedia).

Microtubuli are long, stable polymers (... "long" on a cell scale...) which make up a large part of the cytoskeleton and are vital for the cell shape and in general the cell's well-being. There's a common cancer medication, taxol, which stabilizes microtubuli in the cancer cells, so that they can't divide and the cells die.

Actually, we used taxol as well, to stabilize our microtubuli: We began with tubulin which is the protein microtubuli are made of and started adding taxol in small steps to the buffer-tubulin solution. After adding taxol you have to wait for some time so that the taxol can spread out. Tubulin polymerizes to microtubuli (i.e. connecting in a non-trivial way to form long, stiff rods). Some of the tubulin proteins were labeled with a fluorescent dye so we could see them under our TIRF microscope! :)

Asking for homework

Today I witnessed how a group of students (to be honest - somehow including myself) asked for homework - yes, indeed, to get another homework sheet for class. I said several times I would favor some voluntary problems just to get a better understanding of the topics we're talking about, so nobody would be stressed out because it's the ending of the quarter and some lectures require final exams, so you could do the homework any time you want (or not at all if you're not interested).
It's actually really helpful to have some problems to solve for yourself about the topics discussed in class, because otherwise everything seems "so clear" if somebody explains it, but it's a different cup of tea if you have to do it on your own.

However, we ended up with another (unplanned) homework set which is due in ten days - and even our professor didn't really want to give us one! In the class I'm talking about we don't have a grader, so our professor has to do all the grading and correcting of the homework...

Fortunately, the homework isn't too difficult! And now it's Thanksgiving and hopefully nobody is going to do anything. I'm going to the Yosemite National Park, so maybe there won't be too many entries for the next few days, but prospect-like photos afterwards.

Morning run

It's 6:30 am and I thought I should start enjoying November by a run on the beach. And it's beautiful! I wish I could do that every morning:

Turkey Trot

In order to get rid of additional pounds you might gain during Thanksgiving there's a short run (5 or 10 km) at the weekend before Thanksgiving at the lagoon of the UCSB. Of course, the original intention is not that directly connected to weight loss, but to support students to go to conferences associated with sports and leadership development.

Or, as the Daily Nexus describes it:
“The fund basically sends students to conferences and different activities that would promote Recreation Sports leadership,” Clarke said.
Chad Briner Student Staff Development Fund also helps expand leadership roles in the Rec Sports office through workshops aimed at strengthening the recreation sports programs and helping staff members continue to put on various activities, such as the Turkey Trot." (link)
http://www.gauchosplay.com/student-events/item/1128-turkey-trot

So, we had a great morning of fun and so many different people were running, that was fantastic! For example, I met one of my professors and his son; then there was a group of "old guys" as they called themselves who were running the 10 km under 50 min.! I felt old ;) The track was beautiful as we had a nice ocean view... but I could have stopped after 3.5 km - 5 km can become very long if you run under time pressure.

The two-body-problem

There's a very nice "publication" online dealing with some really special problem in physics, the "two-body-problem" - it's actually a proposal. For original size, here's the link: http://imgur.com/SKNl3VR .

Faraday - we made it!

A: "Why don't we kill all the IgE in a cancer patient? I mean, then there's no mediator for the allergic reaction and the patient will be fine, right?!"

B: "Mh, I think there's some function to IgE despite just reacting in a harming, allergic way..."

A: "Oh, wait, ... I just looked it up, IgE is super important, never mind, guys..."

That's a brief abstract of our Faraday discussion on Monday and Tuesday night and it was super fun! For the Faraday discussion some people prepared a presentation (5 min.) and others read all the papers which were going to be outlined. The readers have to come up with questions, so that you have an actual question / discussion session (20 min.).

And it's not an answer-response game! There've been many different ideas to questions and cross-links between the papers, so you could compare the research results and find even contradictory outcomes!

Our discussion was about lipids and their function as drug carriers (often used for cancer medication). But after about ten papers we were really glad to have a slightly different topic ;) I learned a lot about the different antibodies our immunsystem has (e.g. IgE, IgG, ...) and additionally, I did not read my paper to present it, but to answer questions, so I had to find the "difficult" points in it. That's a lot more interesting! I can only recommend this style of paper discussion!

Physics Circus

A frozen banana is super fascinating: Last Friday, an elementary school visited the UCSB and some volunteers from the "Physics Circus" performed a show with fancy physics experiments. We started with a demonstration of what's called the angular momentum. Somebody was sitting on a turning chair, got weights into his hands and was spun around. It's quite difficult to keep the balance, but you're faster with the weights pulled in (the energy is not invested in carrying the weights "the longer way" far away from the body, so it goes into the turning speed - that's at least the fast, non-formula explanation).

Physics Circus T-Shirt.

The phase transition part was probably most exciting, because a huge container of liquid nitrogen froze everything, including a banana which became so hard that you could nail with it. Flowers became stiff and broke - and (the highlight!) marshmallows "sounded" like rocks on a board because they were iced. But everybody still got a frozen marshmallow and they're edible!

Pummelo

Every Friday the Physics graduate students have a "happy hour", I mean, an "h-bar hour" how we call it. Today's special attraction was a drink in a pummelo. The pummelo was caved and the flesh was replaced by some liquid. It apparently still tasted of pummelo! I've just never seen a pummelo before, so that was really exciting (I heard of it, but that was really special today - always these weird Europeans who only now potatoes ;) ).

PPP

Published paper pressure - slight shakiness of any human being entering nearly any stage of academia and looking at other people's CVs. 

Since I had my first internship in a lab, people talked about papers and how many they should publish, they actually had published and the wish they had published (and all three numbers are different...). I heard of a frequency of about one paper per year you should stick to as a graduate student. But then somebody else told be that he'd been working on an algorithm to simulate proteins for three years and hadn't written any paper, but now he just has to alter a tiny detail and publishes again - every three months.
You could also start reading CVs of researchers which are online sometimes, but that's not recommendable because you might start feeling bad for every free minute you had in the last few days (including eating).

Thus, I tell myself not to freak out when I'm asked for my number of publications and conference talks. Of course, it's nice to have a large number of papers, but there's way more than that which makes a good researcher, e.g. the actual content and quality of the paper, the gained skills and experiences, funding, open-mindedness, etc. So I try to be a person, not a paper ;)

Race

On Saturday morning we had our first "race" as a rowing team. It was at Newport Beach which is near LA and to be on the water at 8 am on Saturday, we left Santa Barbara in the evening and stayed with the parents of a team mate. That was super nice and interesting because I saw an actual American home and the family was really nice, providing us with pizza, drinks and breakfast and coffee in the morning. Although you're not hungry at 4:30 am when you get up, eating something before a competition is a really good idea ;)

At Newport Beach.

 
I think we were on the water at around 07:30 am and it was already getting really warm! We had to race for 10 min with a certain split (number of strokes per minute) and who got furthest, won the race. But during the first twenty seconds, two boats crashed! We had to re-start etc. After some time we were finally rowing together which was fantastic! The boat becomes faster and it feels lighter.

After cleaning the boats we went to a shopping mall to get lunch and there was already a Christmas tree built up! But we were wearing shorts and rowing T-shirts - we still have to work on the Christmas atmosphere a bit ;)

Actin network

About a week ago I started creating my own in silico actin network (I'm kind of proud that I learned next to the expressions in vitro (experiment outside a biosystem, e.g. on a petri dish) and in vivo (in a biosystem), in silico which is any "experiment" carried out by computational simulations).

 

 Color-coded actin filaments in a cell (merged stack of images from a confocal microscope, not all filaments are in one plane!).

The network starts with the creation of actin filaments, which are polymers (long chains of the same chemical unit, which is repeated). Actin networks are super important, since they determine the structure and form of cells, but are also involved in muscle activity. After creating the actin filaments, I added nodes wherever the filaments had a common point. But if I do that I have to make sure that my entire network is actually connected and I don't get several, separate clusters of actin networks! In my code, this becomes a long "while" loop which started taking a lot of time when I run it. I understand more and more why people want more computational power for simulations... It's so exhausting to sit in front of a screen and wait for 4 min. or the like and you can't start doing something else! I could start collecting statistical data of the muscovy ducks (Flugenten) in front of my window and the likelihood that they survive Christmas ;)

6k

For simplicity (and probably for coolness), some people introduced the expression "k€" which corresponds to "kilo-€" - I'm in favor of "10³€", but that's probably too scientific. However, our "k" was the 6 km-test in rowing we did on Tuesday (caution: no ft-measure!). We basically rowed 6 km without a stop on ergs (the machines you row on) as fast as we could. That takes about 25-35 minutes and afterwards you're done for the day; oh, well, nearly, we got the rowing shirts saying "UCSB ROWING" on them, which is quite nice.

 This morning at the lagoon, 6:10 am.

And good to wear at the soccer match on the same day at the evening! We won, but my contribution was only of decorative function, I think. It was great fun though and we're admitted to the play-offs.

But don't worry, I do something else than sports here as well: My simulated actin network "worked out" ;) and I did some signal-to-noise ratios on the intensity profiles I extracted from the sea urchin fluorescent images so far.

Faraday discussions

I am used to the probably most common time of seminars where everybody presents a paper for maybe 20 min., everybody else listens and then there should be questions - often, that part's finished after 5 min. and the next talk starts. After a couple of presentations I usually really have to concentrate to listen up and to raise a question.

 Taxus baccata / yew tree - its bark provides a chemical for producing taxol, one of the most common anti-cancer drugs.

To keep everybody a bit more awake and to rise the audience's activity, we will have "Faraday discussions" in one of my lectures (Biomaterials). In Faraday discussions the presentation-question-ratio is nearly inversed, i.e. we will have five minutes of presentation and 20 minutes for questions (if not even more!). The terms and conditions are, that the non-presenting people have to read all papers which are going to be presented and have to send two questions per paper to the instructor beforehand. It seems that the presenters get the easier part this time, but you still have to answer questions for 20 minutes ;) Indeed, there might not be only questions, but also comparisons to other papers because they all concern the same topic (hydrophobic drug carriers - that's exciting and new!). I'll talk about hypersensitivity reactions (HSR) which are caused by common cancer drugs.

However, (which might be even more difficult) you have to sum up a paper in 5-7 minutes! I got a review which is twelve pages long ;) - this is going to be fun and a really good challenge, I think.

During the next session we are going to switch roles, so I'll be part of the audience (together with all the people who are presenters this time) an the audience will give the talks. But the group numbers are not exactly equal and I got lucky, so I won't have to read eleven papers, but only nine in two weeks ;).

PS: I don't have any clue why it's called "Faraday" discussion - there's nothing on the Internet about it. I can only speculate, that Faraday liked to discuss, what a guess...

And that's been Halloween.

Apparently Halloween was yesterday, that's at least what the date says. And nothing happened. Nothing means that there were more police officers than partying people around. When you go to the students' district, Isla Vista, there's usually a huge party going on and you hear music from everywhere - unlike Halloween, no music, overall quietness, and people running around in costumes. So we had a nice walk through Isla Vista as if it was a normal autumn afternoon walk and everybody had dressed up.

Isla Vista: after Halloween = before Halloween.

So the most important part of Halloween was the preparation (which costume???) and the security. And: Food! There was free food from in our resident halls for a small Halloween-warm-up party which was nice - you can make a lot of things with pumpkin!

So let's prepare for Christmas now, it's nearly tomorrow...

All laws strictly enforced

It's only one day left to Halloween - that's like no day left, therefore as the average, Halloween loving person you go to a supermarket and get everything containing the word "Halloween", "autumn" and especially today "50% off!". Nearly all costumes were gone today (and K-Mart, which is a store for everything but not fresh food here, dedicated about five lines for Halloween costumes!).

When I biked away from the grocery shopping area (of course equipped for Halloween) this inviting sign greeted me about a mile away from campus:

Thus, watch out. Isla Vista (the student town close to campus) is just about a mile away! My post yesterday about the fence surrounding the graduate student houses has to be corrected: There are two fences guarding us! The one, on the photo from yesterday, and another one in the middle of the street, which separates Isla Vista and the graduate student housing.

We're fenced in

As I got up in the morning to go to the rowing session at 6:15 am, I was confronted with a new obstacle: THE fence around San Clemente, the apartment complex in which the graduate students live. It's about 2.00 m high and very long (it's basically surrounding all houses, so maybe up to 2 km).

The reason is, that we've got less than 100 h left to count down for Halloween! We are told to "keep it safe, keep it local". (We are told not to freak out, but somehow this fence and many, many police officers from all over the US make me a tiny little bit nervous...)

There's a video how to keep it safe and local:
https://www.youtube.com/watch?v=bzj0rLqltQ8&feature=youtu.be

In Germany, there was a wall, but now, here's a fence.

Progress

After rowing and playing soccer yesterday (12 h is for sure enough time for rest for your body ;)), I was very productive today and improved the plot I posted yesterday a lot! Now the parts I plot are equally long (if they are on the same half of the cell I analyze), the background noise is the same for all and even a factor of pi found the right way into my integral :-)

But don't worry, this took a lot of time. But it's great and fun and the codes will be useful for other cells as well!

It's worth coding six weeks

Since some time I work on the image processing of fluorescent images of embryonic sea urchin cells during their first division cycles. Sounds dry? It's amazing! You see actual cells and some fascinating details with fluorescent microscopy (e. g. the two new nuclei forming!).

 Intensities of a symmetric cell shape after dividing into four quarters. (I can't display all the data, sorry, it's not public.)

We focus on the actin concentration during the division since actin is one of the most important structural proteins in the cell membrane. Knowing, where actin is, might shed light on a higher activity and forces which are responsible for the shape the cell has.

In other words: Hold a elastic ball or maybe even better a piece of putt and form a sphere. Now try to push it in the middle and get two approximately spherical pieces out of it. And that's what's happening in the cell, but there are no mini-fingers pushing anything, the cell does it itself... over and over again!

Today I processed an image which resulted in the intensity plots in the image up there. It might look very unspectacular, but it took some time and effort to track the right points. After processing more images we might be able to make a general statement - and publish a paper! Only the image processing (getting the cell membrane coordinates) might be worth one :-)

Rowing training

It's Friday morning, 06:15 am, and we start the rowing training: Running stairs in the university's stadium up and down with a partner! It's still dark when we're starting, but it's getting lighter and usually we are rewarded with a wonderful sun rise! Here's a short video of the training session last Friday:
https://www.youtube.com/watch?v=g1fbwwbZXTw