PANAMA

Well, on Friday, almost two weeks ago, we decided to fly to Panama. It just made sense to join our STRI collaborators during their field trip and to take Linnea out of school while her regular teacher was still sick. When we arrived at San Francisco airport very early in the morning of Saturday, the lady at the check-in told us that we could not fly to Panama because Linnea’s passport will expire on December 1st and to fly to Panama you would need your passport to be valid for 3 full months. This is where our Panama trip ended.

We went back home to Albany and slept for an hour. Then I had the brilliant idea of calling the Swiss embassy and asking them for an emergency passport. Unfortunately, they were closed on a Saturday. Donny spent some time on google and found out that today (!) there was the yearly passport day in San Francisco where people, especially families, can get passports. So, we drove to Berkeley, made passport photos, copied birth certificates, called grandma, and rushed to San Francisco. At the passport office, we got called up immediately and ordered Linnea’s passport. However, the friendly lady told us that it would take 4-6 weeks to mail the passport to us. If we wanted if faster it would cost extra and still take 2 weeks. Then, Donny started crying. He explained the lady that this trip to Panama could change our lives. He told them about me and my research and that he wanted to see the country before moving there with the kids. The lady left, talked to her supervisor and came back. She told us that Linnea’s passport will be ready in 2h.

Seven hours later we sat on the plane to Miami, 15 hours later we arrived in Panama City.

We arrived on a Sunday. The first evening we went for a 2h walk with the stroller and both kids to check out downtown Panama City. It was interesting, safe, but not very exciting. After a trip to ‘Price Smart’, the brother of ‘Sams’ we had gotten enough snacks for the rest of the days and enough of downtown City. On Monday, I went on a field trip with Jarrod and Harilaos. Jarod picked me up from my hotel and I helped him prepare tubes and stuff in the lab on the island of Naos for our dissections later that day. The lab is very impressive. They have every kind of equipment, from gel electrophoresis to fume hood and MiSeq sequencer. Better than most of the Swiss labs I have seen.

Then Harilaos invited me for coffee at his house. An old colonial house with lots of Coatimundis begging for toast.

Coatimundi

I liked the experienced greek and his strong, Italian coffee. He drove us across the country to the Carribean site, to Galeta, where we sampled urchins. We drove through a rainforest, the autopista and in the end a beautiful mangrove forest. There were several checkpoints where they asked us for identification and collection permits. At Galeta we met Haris’ technician Axel, his postdoc Carlos, and his intern Tanner. Here is a link to Carlos‘ personal blog!

We collected four different species of urchins (Diadema sp., Eucidaris sp., Echinometra lucintra, and Echinometra viridis).

Galeta:

Underwater:

Diadema in their natural habitat:

Three different species of Sea urchins in their natural habitat:

Then, we drove back to the laboratory and dissected them to identify the microbes living on and inside them. Harilaos, Jarrod and I dissected. We split the work up so that each of us would dissect at least 3 individuals of each species and we kept track of who did what. We collected their fecal pellets first. Then, we poked them with a syringe and sucked out their coelomic fluid. Then, we collected a few spines. After cutting the poor animal open, we also took a piece of their intestines and a piece of gonad.

Diadema dissections:

Eucideris dissections:

Late at night I made it back to the hotel and passed out pretty soon. The next day I went back to Naos and had more time to talk to Harilaos. He showed me all their facilities and how to keep urchins and crabs in tanks. Later that day he introduced me to Alexandra Hiller, a collaborator who works on Porcellanidae. We talked for several hours and she told me some fascinating stories. I got lots of ideas.

That night we went to see Dumas, a Panamanian friend who was in my PhD cohort at Lausanne University. He and his wife Emilie (jurasienne) have a nice little house in Paraiso. We stayed until late and talked. Linnea fell in love with Emilie. We played with their two dogs (Chocolate and Dubois – or something similar) and hung out in their hammock.

The next morning, we got picked up early and drove to the jungle of Gamboa. Our guide Carl (the owner of the Jungle Land Panama Ecolodge) drove us on a boat along the Panama Canal. He enjoys talking. We took several side rivers and met monkeys. Capuchin monkeys, Spider monkeys, Howler monkeys, and Cotton-top tamarin monkeys. Carl goes and feeds them every day, so they recognize him and jump on the boat when he shows up. Not sure what I should think about it. The French-Canadian tourists with flip flops and beers on our boat definitely enjoyed it.

The canal is pretty impressive. They are constantly dredging and making it wider and bigger. Some of their cranes are from Germany from post-war times.

On the canal:

2000 containers of toys, cars, crap from Asia to Europe…

Then we arrived at the lodge. It is a wild and fantastic place!!!

After a rich lunch, Linnea and I went kayaking while Donny and Jacoby took a little nap. Linnea is a great companion! She told me everything she knows about the jungle. We left the kayaks and took a little hike to a waterfall. I jumped down and Linnea was a bit jealous. I promised we could come back when she is a bit older and can jump too. She was sitting in the water and waiting for me until the little minnows started nibbling on her.

We stayed overnight at the lodge. I went swimming with Jacoby and we enjoyed all the night creatures. Linnea sat on the balcony at dark and looked at the bats. There were lots of them. During the day, we saw a lot of birds. However, I do not know them all by name. I am not a passionate birder. I recognized the Brown pelican, Snail Kites, Purple Marten, some swifts, hummingbirds,

On Thursday, we traveled back to the big city of Panama. On the way, we saw a sloth. People here like to take them down from the trees so that tourists can take pictures of them. That is pretty sad. It costs them a lot of energy to climb back up the trees. Their diet is not very nutrient rich and they need to save their energy!

I don’t even want to start writing about the sad Boa constrictor that is living with Carl. She does not live a very happy life.

On my last day I saw Alexandra one more time and we talked crabs.

Panama is beautiful. There is such a rich life here. Most people I met were very nice. However, it is also very complicated. Last night I went to a bar alone. I ordered a beer and a sandwich. The bartender told me that I was absolutely crazy to walk alone into a bar without speaking Spanish and being a white lady. It confuses me that I do not know the rules here in Panama. Three people pointed out that I am white during my trip. I do not fully understand what is going on. I am motivated to learn Spanish and I think it will help. However, as blond as I am, I think I will never be taken seriously in Panama. I find this pretty racist. I am feeding a family of four with a postdoc salary. My computer was stolen two weeks ago. I have almost no money left and still I got charged ten times more than locals. A weird feeling. Tomorrow we are flying to Florida for the weekend before returning back to California.

We saw alligators in the Everglades and I found a dead Porcellanid during snorkeling at Bill Baggs State Park in Key Biscayne while Donny took care of the last Baseball moves on my phone. This is called convenience.

Blog post functional visualization Kamchatka

We are reaching out to hear from others what tools they are using to assign and visualize gene functions in environmental samples of microbial communities.

 

Our dataset is simple. We did a metagenomic analysis of two pools (samples/sites). First, we co-assembled the whole metagenome for each pool. Then, we used anvi’o to bin individual bacterial and archaeal genomes within the pools. These genomes (bins) were then fed into RAST. This online software gives you a table of known genes for each bin. At the moment we have an array of tables with known microbial genes for each pool that we would like to visualize/summarize in an aesthetically pleasing way. We tried to use summary statistics in MG-RAST, but the upload failed eight times in a row (including several attempts of uploading individual bins as fasta files, co-assembled metagenomes as fasta files, and sequence reads before assembly as fastq files). The upload failures were identified as cashing problems or internal errors.

 

We went back to using anvi’o using NCBI COG assignments, following their infant gut pangenome tutorial (http://merenlab.org/tutorials/infant-gut/) which in the end gives you a similar output to RAST in tabular format.

 

What software are people using out there to compare, assign and visualize gene functions across samples and across bins? Can these tabular outputs be used as inputs for any software producing visually pleasing figures?

 

Fieldwork at Scott Creek with Katie Kobayashi

I had to show you these pictures from my field trip with Katie Kobayashi at Scott Creek in Santa Cruz. Katie is studying O. mykiss life-history strategies. She compares the diet of young fish that had been born this year. They are referred to as YOYs (young of the year). To find out what they are eating she makes them throw up. This is called ‚gastric lavage‘. She gently massages their abdomen while inserting a tube and flushing their stomachs out with water. Then she tags them with PIT tags (Passive Integrated Transponder). PIT tags will allow her to track the fish and find out whether they stayed in their natal rivers or whether they left to migrate into the ocean. Katie is studying whether their diet plays a role in deciding to leave or stay.

I tagged along with Katie and sampled stomach and gut microbes. The trip was a great success. Thanks to the heavy rainfalls last winter many fish managed to spawn and produce a lot of offspring. These YOYs are the ones that we are interested in. They seem to be doing very well this summer!

Scott Creek below the dam

Goin‘ fishin‘

My best friends – the Redwoods

Working with NOAA is always great!

Collecting precious data!

Und ein Film zum Abschluss:

Link to Youtube Video

ASF #147

I just came back from the American Fisheries Society conference in Tampa, Florida. This is one of the biggest conferences in fishery sciences- if not the biggest. At times we had 20 concurrent sessions on topics like fish migration, hatchery management practices, outreach, how to deal with lion fish invasions, imperiled aquatic species, and Darwinian selection. I presented my ongoing study on non-genetic paternal effects in salmonids at the Imperiled Aquatic Species and Genomics Symposium that was organized by Andrew Whiteley. The whole second day I spent at the Redefine Darwinian Fisheries Symposium (check out tweet here!).

@fishteph’s current group was represented by Stephanie Carlson, Sébastien Nusslé, Laura Härkönen, Suzanne Kelson, Jordan Wingenroth and I. We stayed at the Mariott Hotel right on the venue. We enjoyed ourselves a lot. Due to the close proximity we could engage in discussions and presentations with quick breaks at our rooms. Tampa was very hot and humid. Sometimes we just needed a quick dress change or two minutes of quiet time alone. Luckily, the hotel also had a spectacular pool.

I tried to get most out of the conference and went to social mixers, poster sessions, selected talks, networking events and the early morning spawning run. Gayle Zydlewski gave me, Louise Chavarie (@louisechavarie) and Lauren Laing (@LaurenVELaing) some good advice for our next career steps.

I want to highlight the great research of a few very nice researchers I met at this conference. Sarah Fitzpatrick is studying genetic rescue in guppies (her website). With a very intense field experiment and a lot of sequencing she could show that hybrids resulting from an experimental mix of two small and distinct populations in Trinidad (that differ mostly in predation rates) had a much higher fitness even after 10 generations of mixing. This mix of populations is called ‚genetic rescue‘ and could be applied to many small and endangered species. Mark Christie is applying *omics approaches to answer very interesting questions in salmon evolutionary history. He proved that one generation in a hatchery caused very strong selection on gene expression. Traits are selected that help the fish to cope better with the hatchery environment. He also studies steelheads that had been transferred from the Pacific to the Great Lakes in Michigan. They are still trying to migrate but now they move between the river and the lake. He compared steelhead genomes of the founder population, of samples at the time when individuals were brought to Lake Michigan, and of the current population in Lake Michigan. It appears that there is selection on genes for smoltification and ion transporters. These genes usually help the fish to adapt from freshwater to saltwater when they undergo their migrations. He could also show that Omy5 seems not to be under selection. Omy5 is the chromosome region that correlates with staying or leaving in O. mykiss (his website). Anna Kupalainen said if age at maturity is inherited by a single locus (original publication by Craig Primmer here) then populations are more likely to destabilize and go extinct – compared to a multilocus inheritance. Anna is a mathematician and modeler. She presented some phantastic approaches to infer fishery-induced selection (Anna’s google scholar profile). It is clear now that fishing is a very strong selective force acting on wild fish populations. Many fish species and populations are not only becoming smaller due to fishing out the bigger individuals, they also change in their behavior because behavioral traits are often correlated with being bigger and growing faster. This was nicely shown by Laura Härkönen. Sébastien Nusslé presented a new model how you can include environmental variables when estimating the strength of fishery-induced selection (Sébastien’s new position!). Lauren Laing is working on maternal and paternal epigenetic effects in sticklebacks and zebrafish. She uses full-factorial in vitro fertilization to raise offspring. Right after fertilization she induces non-genetic factors on them to see if this results in an epigenetic response. She showed during her talk that copper contamination can greatly affect embryonic gene expression and maybe also gene methylation (Lauren’s google scholar profile)

The conference ended with an evening at the Tampa Aquarium and then a long night saying goodbye to Séb in the lobby. I tried my red snapper, my key lime pie and I saw alligators, ‚gator gars and non-native pythons. Now we are flying back to Oakland. Tired. One eye crying for Séb and one laughing to see our families again.

A few fotos:

Big fish

Us staring at the sun

Fieldwork for my fellowship project

After all the preparations and concerns for state and federal permits to work with an endangered species, I finally got out into the field and collected data for my second Swiss National Science project. Everything worked out. I got a satisfyingly big sample size and I feel very relieved. I had the greatest people helping me and spent an unforgettable time in nature. Elder Creek and Fox Creek in the South Fork Eel River system, Big Creek in Big Sur and Scott Creek close to Santa Cruz. All the microbes are resting in RNA/DNA shield buffer from ZymoBiomics and I am breathing in and out on my couch.

My sister helped me at Fox Creek. It has been 25 years since I last spent time alone with her. This was a unique experience. We drove into the wild, talked, enjoyed the Angelo Coast Range Reserve, the Pacific Coast, Piaci Pizza and a lot of E-fishing.

Shortly thereafter I brought Sabina back to Berkeley to turn around myself and collect in Elder Creek. Thanks to Suzanne the impossible was rendered possible, Suzanne always finds a way. After a lot of rock hopping we could also cross Elder off of my list. Chapeau and all my respect to Suzanne’s hard working interns who helped us fish, measure and tag, and most of all, carry buckets. The Angelo is the most special place where I have experienced nature. It is remote and wild. Kristen Shekelle, an undergrad scientist in the Carlson group, underlined this by showing me a few pictures of racoons, black bears and a mountain lion! (as well as Phil Georgakakos who photobombed the motion cameras a couple of times).

Back in Berkeley we had some permit issues. My heart fell into my pants and I had to shiver for a few days before Stephanie could resolve it and I continued my sampling streak. I spent a wonderful time at the Big Creek reserve last week with Dave Rundio, Heidi Fish and Russell Neches – my devoted field workers. My SAAB was packed with field material, tent, sleeping bag and camera. My colleagues at NOAA offered to help me with my project and I got spoiled with a huge 4WD truck, chairs to sit on in the field and two personal assistants. My friend Russell (a rockstar physicist) got his feet wet and kept us entertained during the long ride from Santa Cruz to the Big Creek Reserve. Highway 1 is still closed and we had to drive through the Salinas Valley and Fort Hunter Liggett. I think I slept most of the drive. Getting my samples after weeks of preparations was a huge relief and I felt the tension to disappear. At the same time I just let myself doze off in the shaking NOAA vehicle.

The last two days I spent in the Santa Cruz area working with Katie Kobayashi and her crew. She is studying food webs and makes O. mykiss regurgitate their food; that is, gastric lavage. I tagged along and sampled symbiotic microbes. Now we have all the measurements we need, fish are photographed and tagged and I am getting ready for my last sampling sites. It finally happened.

In a week the Carlson group is taking off for Tampa, FL. I will blog next time from Florida.

 

Sierra Nevada World Music Festival 2017

in Boonville.

Well, I did not expect I would have such a good time with Donny and the kids at the world music festival. It was too hot and too loud. It was at times 41° C in the shade! But we had a great time. Donny talked to many artists, collected jingles, interviewed, and we enjoyed the songs. Linnea made friends in the family zone. We arrived late so we could say a proper good bye to the Nusslés and we left early so we would not cook in the heat. After watching the kids during all my field trips and meetings, Donny deserved this special treat. It feels good to be married to a DJ.

hanging

family picture

teaching him some dance moves

my friend the redwood

DJW with Christopher Ellis (youngest male progeny of the Godfather of Jamaican Rocksteady)

DJW with Gappy Ranks from Oakland (Jacoby Lee Williams)

Linnea with Marla Brown – daughter of legendary Dennis Brown

Linnea going wild

Lee Scratch Perry during his interview

DJW with Macka B

DJW and Gentleman (my first live Reggae act 16 years ago)

Big Sur Feldarbeit

Ich habe Feldarbeit in Big Sur gemacht. Zusammen mit Tommy Williams von NOAA (National Oceanic and Atmospheric Administration) und seiner Gruppe. Landscape Ecology Group. Ich kann es selber immer noch kaum glauben. Das war nun schon seit mehreren Jahren mein Traum und jetzt hat es einfach stattgefunden.

Big Sur ist der schönste Ort den ich kenne. Diese Küstenregion ist magisch. Ich kann es gar nicht richtig beschreiben. Wenn ich dort bin, dann passiert etwas mit mir. Die Küste ist wild und das Meer ist rau. Momentan ist die einzige Strasse, Highway 1, gesperrt. Big Sur ist eine lange Bergkette die steil ins Meer abfällt. Es hat viel Nebel, der langsam über die Hügel schleicht. Wenn es lange trocken ist und dann viel regnet, dann gibt es viele Erdrutsche. Dieser Frühling war besonders schlimm. Jetzt ist der HWY1 zu, für mindestens ein Jahr! So mussten wir mit unseren grossen Autos durch das Salinas Tal fahren, dann durch ein Militärgebiet (Fort Hunter Liggett) und auf einer kleinen, kurvigen Strasse über die Berge durch den Los Padres National Forest. Salinas ist eines der produktivsten Ebenen in ganz Amerika, wenn nicht das Produktivste. Die Bauern da verdienen Milliarden. Die Erde ist fruchtbar, es hat viel Sonne und das Wasser nehmen sie vom Grundwasser. Den Fischen bleibt kaum eine Chance. Ich solle unbedingt die Bücher von John Steinbeck lesen. Ich möchte auch das Buch „Cadillac Desert“ von Marc Reisner empfehlen. Das muss man unbedingt lesen. Es geht darin um den Konsum von Wasser im Amerikanischen Westen.

Im Militärgebiet findet man eine aussergewöhnlich hohe Biodiversität. Übrigens auch einen der ältesten Eichenwälder im ganzen Land. Dann fährt man über die trockenen Hügel mit Kakteen und runter in die feuchte und magische Küste. Wir mussten für 2km auf dem HWY1 fahren. Diese Strecke wird jeweils am Morgen und am Abend einmal geöffnet, damit die wenigen Leute, die da wohnen rein und raus und die Kinder zur Schule gehen können. Als wir da gewartet haben, haben wir Maple Mike kennengelernt. Er bewacht die Absperrung. 7 Tage die Woche. 14 Stunden am Tag. Er spricht mit Eichhörnchen und mag Müesli Stengel mit Ahornsirup. Seine Tochter möchte Biologin werden. So hat Tommy sie eingeladen, einmal mit uns ins Big Creek Reserve zu kommen. Dort haben wir Feldarbeit gemacht. Es ist ein Park des UC (University of California) Systems. Genau wie der Angelo Park wo ich das letzte Mal war.

Big Creek Reserve

Tommy untersucht wie Fischpopulationen Änderungen in ihrer Umwelt wahrnehmen und darauf reagieren. Im Big Creek in Big Sur macht er eine Langzeitstudie. Jedes Jahr seit 12 Jahren fängt er Fische während drei verschiedenen Zeitpunkten im Jahr, dies alle 25m in einem Flusssystem von 7 Kilometern. Die Fische werden markiert (mit PIT tag), gemessen und wieder frei gelassen. Mit Sendern im Feld misst er kontinuierlich, wie sich die Fische bewegen. Mit seiner Rückfangmethode misst er, wie sich die Populationsgrösse und Dichte verändert. Die Fische seiner Studie sind Regenbogenforellen und Steelheads. Drum bin ich ja auch auf ihn gestossen. Ein zentrales Thema seiner Studien sind die verschiedenen Überlebensstrategien dieser Fische – ob sie ihr Leben lang im Fluss bleiben oder ins Meer wandern, gross und fett werden, und dann zurück kommen zum Laichen. Big Creek fliesst direkt ins Meer. Atemberaubend.

Diese Jahr hat es ganz viele YOY’s. Das sind Young Of the Year – Fische, die in diesem Frühling geboren sind. Das ist super für mein Projekt! Ich untersuche deren Symbiose mit Bakterien. Letzten Winter hat es nach Jahrzehnten von Dürre in Kalifornien richtig viel geregnet. Die Fische haben darauf reagiert.

Wir haben jedoch auch viele kranke Fische gefunden. Black spot disease. Das ist ein Parasit, ein Saugwurm. Er lebt in Unterwasser Schnecken. Diese werden von den Fischen gefressen. Diese werden wiederum von Vögeln gefressen. Die Vögel kacken in den Fluss und das wird dann von Schnecken gefressen. So schliesst sich der Kreis. Fische mit dieser Krankheit kriegen auffällige schwarze Flecken und können sich schlechter verstecken. Neascus

Neben den Forellen haben wir ab und zu auch eine Groppe (Cottus bairdii) gefangen. Die sind so herzig.

Ab und zu haben auch ein paar Orchideen geblüht. Diese hier sind speziell an Flüsse angepasst. Sie kommen nur hier an der Westküste Mexiko’s, Amerika’s und Kanada’s vor. Genau wie meine Regenbogenforellen.

Und natürlich die scheuen Pumas!

Irgendwie hat es mich traurig gestimmt, dass der HWY1 jetzt einfach zu ist. Man sieht da so viele schöne Sachen. Diesmal hatte es viele wilde Blumen in voller Blüte und auf der anderen Seite im Meer haben wir Seehunde, Delfine und Buckelwale im Vorbeifahren beobachtet. Das wollte ich alles meinem Mami zeigen. Da hinunter zu fahren ist meine schönste Erinnerung in Kalifornien. Mit einem Stop im Nepenthe Café. Beni war einmal dabei. Zum Glück.

Hier ein Blick aus der Dusche im Big Creek Reserve:

Ich versuche herauszufinden, warum mir dieser Ort so gefällt. Zum einen sind es wohl die wilden Mammutbäume. Die leben da. Viele von ihnen sind mehr als 2000 Jahre alt. Sie brauchen Feuer um zu keimen. Und sie brauchen Feuer, um andere Baumarten abzuwehren, denn nur sie überleben einen Waldbrand. Wenn ein Sturm oder ein Erdrutsch kommt, dann kippen sie in den Bach und sterben. Aber halt. Die Wurzeln bleiben meist erhalten und schon bald keim ein neuer Spross. Und lebt weiter. Dann wachsen sie schnell und riesig in den Himmel. Wie ganz stille Riesen. Ich liebe diese Bäume.

Ich kann es kaum glauben. Ich arbeite mit NOAA. Die Arbeit war sehr streng und man musste richtig fit sein. Ich habe mich wohl gefühlt. Für das nächste Mal, meint Tommy, soll ich meine kleine Familie mitbringen…

Alltag

Ja, es gibt gar nicht soviel zu erzählen, da ich in den letzten Wochen vor allem mit Bioinformatik und Bewerbungen schreiben beschäftigt war. Es läuft viel hier in unserem Alltag. Donny und ich versuchen gesund zu kochen und haben einen kleinen Garten. Bei der Arbeit läuft alles rund. Ich habe mich etwas mit anvi’o aus dem Meren lab auseinander gesetzt. Das hat viel Spass gemacht.

Link dazu

Donny’s Eltern waren hier zu Besuch und wir hatten es sehr schön.

Wir haben uns an das Leben hier gewöhnt. Ich bin gerne auf dem „Bulb“. Die Kinder spielen da und ich habe für die Kalifornische Autoprüfung gelernt.