I am very happy to live in California and work in the UC system. As Jonathan said, I believe in equality and fairness.
These are emails I got from the UC system. They are comforting. The people are still out there and there is a lot to do.
Die letzte Woche war bestimmt von Jetlag und Vorbereitungen für mein erstes SNF Projekt. Zum Glück hat mir Mami geholfen. So konnte ich alles reibungslos erledigen während sie meine Wäsche wusch und auf Jacoby schaute.
Gestern ging es dann auf Laichfischfang. Es war streng und sehr schön. Der Glenner floss wild zwischen den Valser Steinen und das Herbstwetter sorgte für eine wundervolle Stimmung. Die Forellen liessen nicht auf sich warten. Auch im Ferrera Bach fanden wir später viele.
Ich möchte mich hiermit bei all den Fischern und den Wildhütern Arnold Caminada, Moritz Schmid, Gieri Derungs, Gion Bundi, Pirmina Caminada, Patric Ragettli, Thomas Durschei und Martin Cavegn für ihre grosse Hilfe bedanken. Und natürlich Roland, der wichtigste von allen! Wir werden noch viele gemeinsame Stunden verbringen…
Bei meinen Recherchen habe ich noch diese Webseite über Pirmina gefunden:
Es war mir eine grosse Freude, Pirmina gestern kennenzulernen!
19th of October 2016 – What I got:
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?
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.
Click on this link to share my first experience with google documents!
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.
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.
I 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!
Wunderschöner, gemütlicher Tag im Regen. Der alte Rhein reisst und tobt. Wir haben in der Stube gezeltet und Spiele gespielt. Jetzt schlafen Donny und Linnea. Jacoby und ich schreiben an einem Manuskript. Jacoby zappelt und streckt sich. So soll es sein.
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.