6 weeks in California

19th of October 2016 – What I got:

  • a visa stamp
  • a campus card
  • a student ID
  • an affordable apartment in the Bay area
  • a social security number
  • American health care for my family
  • an American bank account
  • a talk at UC Berkeley
  • a talk at UC Davis
  • a talk at WSL
  • getting to know the best microbial genomicists at a local conference
  • living in a van for more than 3 weeks
  • living without a car in California
  • PIT tagging a juvenile rainbow trout
  • Driving alone on a 4-lane American highway
  • getting the phone number of 4 new people I like
  • getting a key to my office
  • learning to recognize the most common plants and animals in this state
  • swimming in the Pacific Ocean
  • getting everything ready for my first own scientific experiment
  • finding a lab to do molecular genetic analyses during my fieldwork session.

Die leere Wohnung

Wenn Studenten und Mitarbeiter an der Uni Berkeley mindestens zwei Kinder haben und wenig verdienen, dann dürfen sie in einem sogenannten Dorf in Albany eine subventionierte Wohnung beziehen. Genau von so einer Wohnung haben wir seit 2 Jahren geträumt. Wir haben sie bekommen. Bereits 2.5 Wochen nachdem wir nach Kalifornien gekommen sind und in einem kleinen Transporter gewohnt haben. Eigentlich habe ich eine Email bekommen mit der Nachricht, dass wir sicher bis im Februar keine subventionierte Wohnung kriegen werden weil viele andere in der Warteliste bedeutend ärmer sind als wir. Nachdem ich aber persönlich mit der ganzen Familie bei den Wohnungsvermittlern im Büro aufgetaucht bin haben sie uns per sofort eine Wohnung angeboten. Klammerbemerkung: Hier in Kalifornien läuft sehr viel so. Es gibt viel Bürokratie zu erledigen aber wenn man persönlich vorbei schaut sind die Leute sehr freundlich und vor allem hilfreich. Jetzt haben wir also so eine Wohnung.

Was braucht man in einer leeren 3-Zimmer Wohnung? Der 50-jährige Mann und die 30-jährige Frau mit 2 Kleinkindern und einem unerwarteten Mitbewohner Mitte 20 sitzen in einer sauberen, leeren Wohnung. Mein Stipendium beinhaltet Familienbeiträge und wir haben Erspartes mitgebracht. Nun können wir die Wohnung füllen. Diese Situation ist spannend und aufregend. Sie beinhaltet aber auch viele Entscheidungen. Fast zu viele Entscheidungen. Was braucht man überhaupt in einer Wohnung um glücklich zu sein. Kann man das generalisieren? Was brauche ich jeden Tag? Einen Wasserkocher, einen Dampfgarer, ein Bett mit einer bequemen Matratze, einen Staubsauger. Das waren meine ersten Gedanken. Dann habe ich an Linnea gedacht. Spielsachen, ein Kajütenbett, Schränke für Spielsachen. Einen Kühlschrank, eine Badewanne, WC Papier, Internet, ein Bett – das sagt Donny. Nichts, ich brauche nichts. Das sagt der Mitbewohner. Ein paar Kartonschachteln. Das sagt der post-doc der nicht mit uns wohnt. Der durchschnittliche Schweizer mit Nationalfonds Geld, der sein Stipendium an der Uni verbringt. Oder ist das mein Gewissen?

First Fieldwork in California

L.A. is huge. There is no Swiss comparison. Zürich or Geneva are little villages compared to it. San Francisco and the whole Bay area are also bigger than Switzerland and overpopulated. When you drive during the night it seems like the whole world is artificially illuminated. Thousands of cars, houses and signs are flashing. It is hard to believe that 150 years ago none of these people were here. This was a wild place with whales, sharks, condors, mountain lions and even golden bears. If you want to get a glimpse of the past you should go to the Angelo Coast Range Reserve. This is a reserve that is run by the University of California, Berkeley.


We drove up the coast the night before fieldwork and slept at Fort Bragg. We had dinner with the locals. A bar full of sailors, butchers and carpenters – us in the middle with the kids. And all these rough men turned soft and playful. Challenging Linnea in dominos and watching Donny feed Jacoby. Anyways, early in the morning we drove into the reserve and I helped Suzanne collect some data for her doctoral thesis. Donny stayed at the station during the day and I followed Suzanne into the woods. Climbing up the creeks against the flow and catching rainbow trout until it got dark. The mountain lions saw us but we never saw them. Suzanne caught her fish with electro shocks. While she administers current underwater we were trying to catch all the stunned critters with hand nets. We caught lots of salamanders (Dicamptodon spp.), frogs (Foothill yellow-legged frog / Rana boylei), crabs, and even a lamprey (Lampetra tridentate). And lots of rainbow trout, maybe some steelheads. Suzanne collected scales, tissue, wrote down sizes, weights, and stuck little PIT tags into the fish. She reminded me of myself working on my PhD. She is great and it seems she has it all under control. I am looking forward to collaborate with her next summer. We want to collect lots of juveniles and sample their gut microbes and at the same time we decided we should also have a look at the gut contents.

Linnean’s name for the rainbow trout is O. mykiss. In the South Fork Eel river watershed, where I went to visit Suzanne, O. mykiss individuals exhibit two different life-forms. Some individuals stay for their whole life in the river pools. These are the ‘actual rainbow trout’. Their counterparts swim down the river as juveniles and live for part of their lives in the Pacific Ocean. They come back as much bigger fish to spawn. These individuals are called ‘steelheads’. I want to find out if the gut microbes of juvenile rainbow trout and steelheads (before they leave) from the same river pools differ. My hypothesis is that their symbiont bacteria are different. I think that bacteria help the steelheads during the process of smolting – when they prepare to swim away.

Suzanne made me familiar with the typical fieldwork that is required to sample wild O. mykiss. We were crawling up and down the creeks with all the material. I really enjoyed the reserve and its wilderness. Most of the sampling techniques (sampling tissues and scales, measuring the fish) I already knew well. I was impressed how easy it seems to tag the fish with PIT tags and then how to scan them and recognize individuals. My task before next summer is to learn how to get stomach content samples from wild fish without hurting them. I am also thinking about getting ‘stool’ samples simultaneously.

Lucky, as I am, I joined the Eisen group right after the annual STAMPS course.


Holly and Guillaume took that course this summer and devoted the last three lab meetings on summarizing the most important bits from the course and sharing it with the rest of the group. I got all the course slides about the latest advancements and conclusions how to analyze microbial genomic data. It feels like I made the right choice of groups for my project. With Suzanne and the other people at ESPM I was deeply impressed about their expertise in ecology. In Jonathan’s group I met a bunch of people who are totally specialized on the analysis of microbial communities from different angles. Needless to say again that the Lake Arrowhead conference just blew me away. Hence, both aspects of my project, the host system and its symbionts are nicely covered.


into the wild


yellow legged frog


our van and home


giant salamander


giant rainbow trout…


giant lamprey

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Bacteria on naturally spawned trout eggs and regionally increasing temperatures

Freely available online!!!


Here we published a correlative study of bacterial assemblages on naturally-spawned brown trout (Salmo trutta) eggs. During my first year as a PhD student I collected brown trout eggs within a big river system in the canton of Berne. I joined Joachim Guthruf, a passionate brown trout specialist, who monitored natural spawning in the main river Aare and its tributaries. He studied the fish for days in order to see them spawning and mark the burial sites of the eggs. About three weeks later he would go back and dig out the eggs, count them and analyze the spawning success at the different spawning sites. I had the opportunity to join and help him during most his trips. While I helped him with his data acquisition, I also collected eggs at the late-eyed developmental stage for my own studies. I was interested in investigating the spatial pattern of host-associated bacterial communities in brown trout eggs across a rivers system. Recent experiments with salmonid embryos established important principles of microbial colonization, maternal transmission of bacteria, bacterial virulence factors, and host genetic responses to bacterial infections. This progress stands in sharp contrast to what is known about the diversity of host-associated bacteria of fish in their natural environment.


Salmo trutta


For this study we characterized bacteria at nine different locations. Eight locations were within the river Aare system and one location was in Sils/Maria, within a non-connected river system of a different river, the river Inn. Bacterial communities on brown trout eggs differed markedly from the composition of bacteria found in their water environment. However, they were strikingly similar across different habitats and rivers regardless of (i) geographic distance among spawning places (isolation-by-distance) and (ii) host genetic and morphological differentiation. These findings strongly suggest that brown trout have egg-specific microbiomes. In the paper we describe the trout egg-associated microbiomes in detail and report evidence that bacterial diversity increases with water temperature.

Aeschenfeld2 Forellen_Graben IMG_3518 IMG_3584I worked a very long time on this manuscript and I learned some very important conceptual points about working with environmental sampling of bacterial communities. First, I think it is extremely important to collect water samples or any kind of environmental samples when characterizing host-associated bacteria in their natural environment. This allows the discrimination of bacteria that are specifically associated with a host and bacteria that seem to be omnipresent in their environment. Second, I find it important to sample blank samples and sequence them. It is an illusion to think that we can work under sterile conditions in the field. So why not capturing all kinds of contaminations that we collect in the course of the study and subtract this from the real samples? We already followed this approach in our Aquatic Sciences paper earlier this year (blog post about it). Recently, Noah Fierer also tweeted about the importance of this approach and I must admit that I was very proud I already have published some articles where we took care of this issue. Third, we were dealing with some pretty low sample sizes for some locations. As we had to find a way to optimize the rather expensive sequencing technique (454 Pyrosequencing, Roche), we ended up pooling all the different sites where brown trout bury their eggs for each spawning location so the comparisons between locations could not be based anymore on variance estimates. Consequently, our data only allowed for (i) correlations of water temperature with bacterial community diversity, (ii) correlations of geographic and host genetic distance among spawning places with phylogenetic distance of bacterial communities, (iii) characterizations of core bacterial communities on all brown trout eggs, and (iv) comparisons of egg samples and water samples with regard to bacterial composition and its putative function. With regard to the comparison between the bacterial communities of the main river Aare with its tributaries we added a bootstrapping approach that is similar to a power analysis. Here we increased the number of samples for the main river Aare and its tributaries sequentially, using simulations, and investigated how many samples would be needed to find a significant difference in bacterial composition given the observed distribution of bacteria in our dataset. With regard to relationships between phylogenetic distance of bacterial communities among spawning places with geographic distance and host genetic distance respectively, we also analyzed the effect of reducing the number of pairwise comparisons on slope estimates and discussed this in the light of low sample sizes.


At this point I would like to thank Joachim for his time in the field with me, his patience and his generosity, sharing all this insider information about the local brown trout populations. I am also grateful to Claus and Luca for letting me follow my own curiosity and helping me a great deal with the writing for this manuscript. Aude, my first Master student at the University of Lausanne helped me a lot with the wet lab work for this manuscript, which was very time consuming and also under time pressure as I was expecting my daughter Linnea at that time. Finally, Frédéric supported me with the statistical analysis after the first revision by two very competent Scientific Reports reviewers. He backed up my statistical approaches and pointed out some weaknesses. I am very happy that this article is out now!

Tanking up energy

Hello? Can you hear me?

Please don’t go. Surround me with your love. Understand me. I need you now. Surround me with your words. Understand me. I need your love. I need your love. I need your love. After a week without sleep. The submission of three major fellowship proposals. The data analysis for another manuscript. And hours and hours of teaching lab practices to a beginner. My body full of stress hormones. I need to hide in your arms. My energy is limited. Look at our beautiful daughter. Surround me. I need you now. I do not want anything more than sleeping in the living room while you are talking and she is playing. Paradise.

Üseri Zwetschge

Üseri Zwetschge

Au üseri Zwetschge...

Au üseri Zwetschge…

Paper out!

Here is the Link!

I guess I should keep this going and write a little story for everybody about each of my manuscripts that some nice editors decide to accept.

This one here is about gene expression in whitefish embryos. Regarding the blog I wrote about the Aquatic Science paper, this could be interpreted as a continuation, a different perspective of our study system. Here we collected sperm and unfertilized eggs from whitefish that can be found in lake Geneva (Coregonus palaea). We fertilized the eggs in vitro and in a full-factorial breeding design. That means that we took the eggs of 4 females and the sperm of 4 males and then crossed them in all possible combinations. This gave us 16 little Tupperware buckets with freshly fertilized eggs. These we brought to the University where we have climate chambers at a constant temperature of 6.5° Celsius. All eggs were filled into individual wells with 2ml of standardized water. In their little microcosmos they grew and developed into embryos. At the late-eyed developmental stage when the blood circulation system is fully functional, we infected 13 replicates of each family with a nasty bacterial pathogen that can be found across many Swiss lakes and rivers Pseudomonas fluorescens. We also added some nutrients that these bacteria like. As a control we added only the nutrients without the pathogen to another 13 replicates of the same families. We already knew from previous studies that at this stage of development it matters who the father of the embryos was with regard to mortality and performance of the embryos under stress. Since the father only provided sperm and no paternal care, father effects can be interpreted as genetic effects. That means, he contributes genes to the embryos only. Once the embryo is old enough it starts expressing these genes and they have an impact on how it will perform under stress. However, what we did not know yet was which genes might be involved. So my goal for this study was to give these significant genetic effects a name.

Whitefish, an economically important fish species for the gastronomy in Switzerland

Whitefish, an economically important fish species for the gastronomy in Switzerland

my husband waiting for me outside the cold climate chamber

my husband waiting for me outside the cold climate chamber

Wells where embryos are raised.

Wells where embryos are raised.

Accordingly two days after treatment, we collected 3 embryos from each family and treatment and extracted all the gene expression products in their whole body, the so-called RNA. These are the gene products in all animals and plants that will be translated into proteins, which make up what we are. With the use of next-generation sequencing, we digitalized all this information. That means, that only messenger RNAs are filtered out, tagged according to which individual they belong to, pooled and then translated into letters. For this process we collaborated with a Swiss company in Geneva Fasteris. Months later, I received a huuuuuge text file that I could then use to satisfy my hunger for learning bioinformatics tools. With the help of a very friendly guy at Fasteris I found most overlapping sequences of text and aligned everything to a collection of longer text segments (contigs). These were then compared to an online reference of gene expression reads. The amount of data we produced was extremely big. Since I was only interested in genes that are differentially expressed between embryos in our treatment and control group, I decided to quantify the reads first and only compare the ones to a reference, that are also different between the two groups. Many of the reads did not result in a match, however, 1096 did and those could be characterized further. They told us which functional pathways are already active at this early stage of fish development and they gave us some insight into what defense mechanisms these embryos already have.

Whitefish embryos at the late-eyed developmental stage

Whitefish embryos at the late-eyed developmental stage

There is some background information to this paper. First, I must admit that I convinced my PhD supervisor to conduct this experiment because I wanted to get the chance to learn more about bioinformatics. I was the one responsible for the experimental treatment, the laboratory analysis of extracting RNA, and the one who did all the bioinformatics and data analyses. It was also the first manuscript that I wrote mostly on my own. It is not a very ground-breaking story. I would call it a lesson.

This project was always a side project during my PhD. We started with the fieldwork in 2010 when I just began my doctoral studies in Lausanne. The lab work was done in the end of 2011. I had serious troubles getting RNA of good quality from these embryos. We did not extract RNA directly but froze the embryos first for a couple of months at -80° Celsius. I would not recommend that to anybody. I was very busy working on different projects, some of them I considered my main projects at that time, and therefore this side project had to wait several times.

From the 16 families I managed to get a rather high amount of good quality RNA from 4 families. I made sure that I would have gene products from the same mother, crossed with 4 different fathers. I would say that this is the heart of this study. We could reduce variation in gene expression due to maternal effects. Different genotypes from the fathers were investigated against a constant background of the same mother. The whitefish external breeding system allowed us to control for host genotypes and contrast environment-induced changes in gene expression. I am discussing this strength of the study in the paper and encourage other scientists to use the same host system of fish with an external breeding system to investigate gene expression due to different treatments. It does not only present a way to reduce variation in expression due to maternal and environmental effects, it also provides the possibility to study gene expression in natural populations and their ecologically-relevant context.

FSI_blog2I also would like to add that it was very pleasant to work with Laurent Farinelli at Fasteris. He is one of the founders of the Illumina sequencing methodology and he had the balls to start his own company. Now he is collaborating on many very exciting projects and he delivers high quality data and an exceptional service. I enjoyed my few meetings in Geneva at his company.

To end the story of this paper I have to mention that I finally sent the extracted RNA for sequencing in summer 2012. I received the data during my maternity leave and already started playing with it. In 2013 I managed to assemble all reads. I had to digest quite a bit of theory about partly assembled gene expression reads (transcriptomes) and I learned how to use a high-performance computing system (clusters at the SIB). In 2014 I did the differential gene expression analysis and compared reads of interest to different online reference databanks. Here I could rely on the theory about differential gene expression in lung cancer datasets that I was exposed to during my internship at Novartis. This project would not have been possible without the help of several co-workers at UNIL, such as Oksana Riba, Kate Ridout, Paris Veltsos and my co-author Emily Clark. At this point I would like to thank them again for their help and advice.

At the moment I am supervising a Master student who is applying the same experimental set-up in grayling (Thymallus thymallus). He is looking at sex-specific gene expression of grayling embryos under estrogen stress. In this project we also did all the steps from fieldwork until bioinformatics ourselves. However, he can rely on several collaborators who are specialized in the different aspects of the project and as a Master student he concentrates on only one project at a time. I am very excited to see him advancing so fast.


This post goes out for Martin Kapun.


150g flour

2 eggs

0.5 dl milk

salt and nutmeg

40g butter

Peterli (cut in small pieces)

Basilicum (cut in small pieces)

Krauseminze (cut in small pieces)

100g bacon (cut in small pieces)

2 Landjäger (cut in small pieces)

1 Salsiz (cut in small pieces)

75 g Sbrinz, grated

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Mix flour, eggs and milk to a nice dough and let it stand at room temperature for 30min. Add spices, herbs and meat. Mix well. Take a tea spoon full and throw it on a leaf of Capuns. Pack it up nicely.

Cook up a big pan of water and add the packages for 7min. Take them carefully out and let them dry a bit. Put them in an oven form and add melted butter and graded cheese. Ready to eat.

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