Archive Page 2

Happy Birthday George!

George Matsumoto is the internship coordinator.  If you’ve been following our adventures over the past 5 weeks, you’ve been reading about many of the things he has organised for us.  Lunches and dinners out with seminar speakers, presenting how we got into marine science to high school kids, kayaking, being shown around the inner workings of the Monterey Bay Aquarium – these are just a few of the things that have made our internship here absolutely unforgettable, and they are all thanks to George!  So, seeing as today is his birthday, I thought we should make a bit of a fuss over him…

HAPPY BIRTHDAY George, have a good one and thanks again from your Fabulous Flying Interns!

The day we spent kayaking is a good example of George’s skill at turning a group of quiet, sleepy interns into bouncy and smiley (if not slightly wet) interns!

Smiles all round!!


A day in the life of… Sara

by Sara Thomas

Lab Environmental Sample Processor (ESP)

Mentor Post-doc Julie Robidart

A typical day in the ESP lab begins with loading a nifH template (nifH is a gene expression for nitrogen reductase) onto the Micro-Fluidic Block 2 (MFB2).  Although the MFB2 sits at my work station, its real home is on an ESP instrument.  The ESP will collect environmental water samples in-situ during deployment in micro-fluidic proportions which ultimately make its way to the MFB.  Once the sample reaches the MFB it undergoes a qPCR (quantitative polymerase chain reaction).  An in-situ qPCR experiment is exciting for micro-biologists and microbial oceanographers because it allows scientists to investigate marine biogeochemistry in near real time.  If it weren’t for the ESP, these samples could not be analyzed for their content for days after their collection.  My main task on the non-deployed MFB2 at my desk is to determine nifH standard curves for different groups of microbes.  I do this by loading known concentrations of templates and plotting the DNA amplification curves (fluorescence vs. cycle number) in Excel.  The process, run in triplicate, takes approximately 6 hours to complete.

Setting up a gel electrophoresis

After setting up the MFB2, I run over to the other lab and prepare what I call an “old- school” PCR where I test the primers I designed to target the idiA gene (expressed during iron deficiency) in the species Synechoccocus.  I prepare the appropriate master mixes and primer probes for my samples to prepare them for DNA amplification.  I can test for DNA amplification, and therefore if my primers worked, by running an agarose gel electrophoresis on the PCR product against DNA ladder standard material.  After sending an electrical current through my gel and buffer, I observe how chunks of DNA from the PCR product have moved (or raced) through the gel relative to the standards (I hope to see a tie at a certain ‘ladder step’ in each lane).

At this point in my day I secretly do a celebratory fist pump and heel click because my agarose gel has just told me that my PCR product is worthy of cloning which reinforces the success of my primer design.  I happily pull e-coli cells out of the -80°C freezer and introduce them to my PCR product via a cloning procedure.  Then I spread material onto an agar plate, throw them in an incubator at 37°C over night, and hope to see cultures waiting for me in the morning.

A bit about me!!

It wasn’t until recently that I discovered my interest in microbial oceanography.  I earned my B.S. in Global Environmental Science with a minor in Meteorology.  My major required an undergraduate thesis and so I performed a trace metal analysis where I investigated the spatial and vertical distribution of arsenic in soil cores collected from O’ahu- a project completely different from what I am doing now.  The C-MORE (Center for Microbial Oceanography; Research and Education) Scholar’s program provided support for this project and opened my eyes to the intriguing world of microbes through meetings and seminars.  My internship here is supported by C-MORE and I’m stoked to have a project that directly ties into research in microbial oceanography!

In Monterey with flatmates Izzy and Melissa

Life below the waves

Did you know?  MBARI has a YouTube channel!  Click here for videos of the deep sea world in action!

The half way point!

5 weeks have quickly passed us by and only another 5 lie ahead!  I was interested at this point to see what parts of the internship had really stood out for everyone so far.  These are the answers I got.

Izzy: The intern kayaking afternoon on the Elkhorn Slough and watching Becks walk straight into a screen door at Spencer’s house in Sonoma!

Bartolome: Seeing the Tuna Conservation and Research Center during our behind the scenes tour of the Monterey bay Aquarium, and WimbleBARI!!!

Katie L: The kayaking day and seeing a sunfish during our family trip to the Channel Islands.

Sara: The massive sunfish at the Tuna Conservation and Research Center, and getting my DNA to amplify!

Katie M: Ari Shapiro’s seminar on communicating science.

Dan: Getting to see how the massive jellyfish exhibit at Monterey Bay Aquarium really works on our behind the scenes tour.

Chris: The day on the R/V Zephyr.  It was an AUV dive (autonomous underwater vehicle) and I was able to watch the launch and talk to both the scientists and the engineers involved.

Becks: The day at sea on the R/V Point Lobos, watching the video the ROV was sending up from the depths then getting to drive it!  And the afternoon we came across a sea otter on the way back from a lunch time trip to the fruit market.  It was floating in the water right next to us cleaning itself and watching the world go by.  If it hadn’t eventually swam off I think I’d still be there.


Waking up on Sunday morning you could tell something was different, something was in the air.  An unusual hush had fallen over the fields surrounding Marina.  Doors and windows were closed.  The children didn’t play on the streets that day.  There was an uncomfortable tension and everyone knew it was just on the verge of breaking.  They waited….  and then, through the fog, figures were discerned.  Figures in spandex, headbands and trainers that were blindingly white.  The interns had arrived on the tennis court.  It was WimbleBARI!!!

That’s right, after a week of sleepless nights, secret practice sessions, hours pouring over the details of famous matches and a lot of effort from our coordinator Isobel ‘The Pink’ Yeo, it was finally time for the interns tennis tournament.

As all veterans of WimbleBARI know, there is nothing more important than the costumes, and this was a particulary good year.  We were treated to the aesthetic delights of Team Pink, Team Purple (Spandex a go-go) and Team Monochrome, not to mention ‘The Trash Man’!

Team Pink

Team Purple (including the crippled Sara's wheelchair pusher)

Heartwarming sportmanship between Team Monochrome, The Trashman and Tony

Even the sun decided to join in!  We had two heated group stages and already the crowds had been shocked more than they could handle.  A number of ‘first timers’ turned out to be nothing but sharks, running away with the points and smashing the balls down the outside line.  Calls for Hawkeye fell on deaf ears, the umpires word was final (and, as the umpire depended on who was left with the scoring clip board, the final decisions were unnervingly fickle…)

Many games were played, many tears were bitterly shed; we were down to the semi finals…  Then, in an unprecedented twist to the story, a new team walked into the court.  It was as we feared, none other than Katie ‘The Smasher’ Lodes and her formidable husband Andy.  The legends were true!  No one dared speak as they placed themselves straight into the semi-finals.  The remaining two pairs, Chris and Sandeep, and Becks and Bart, quaked in their tennis shoes.  The other players hid on the sidelines and thanked their luck for missing that final shot, little had they realised at the time that it had bought them safety!

A nervous crowd

The first semi began, a terrifying battle to the end!  Chris astounded everyone with his sheer nerve in the face of the Lodes partnership.  Sandeep perfected his ball-dodging technique beautifully.  But the battle did not last, Chris and Sandeep were thrown out of the tournament and the Lodes’ roared in triumph – only one more partnership stood between them and the Championship!

Semi-final 1

Becks (who had really much preferred being a ball girl) and The Hustler (also known as Bart) were next to face The Smasher.  Understandably, a terrible fear had been borne in their hearts after watching the last game.  Becks and Bart fell to the Lodes partnership quickly, and all too soon (especially for the umpire, who had to be alerted to the fact that it was Championship Point) it was over….

Celebrations!  It was time to pop the cheap cava like they do on tv!!!  Then down to the field to have a BBQ and relax in the waning sunlight.

Well done Katie and Andy, and a special thanks to our two excellent ball girls, Sophie and Margie!

Our impressive ball girls

Project updates and cookie breaks!!

Every Monday at 2:15 pm, one of the researchers at MBARI gives a presentation about their project.  These project updates are a great way for everyone here to stay up to date about what other work is going on.  It can also give you ideas about your own work, or you may be able to suggest a solution to another group’s problems.  Basically it keeps up good communication within the institute, and for the interns it’s a great way for us to see all the different things that can be done under one scientific roof!

Last Monday we heard from Izzy’s mentor David Clague, who talked to us about submarine volcanism (= volcanoes deep under the water!).  As well as telling us about some of his research group’s current work, David showed us some amazing videos of underwater eruptions.

You should have a look at the research group’s webpage!

After the presentation comes the cookie break.  Although this may sound like a way for us to take 30 minutes off work and eat lots of sugary snacks I can assure you it’s a very important part of the week!  It gives everyone a chance to chat in a relaxed atmosphere and the interns can talk to people they wouldn’t normally get the chance to see in their average work day.  The cookie break was geology-themed this week as Melissa Meiner Johnson baked up “sediment core” and “MB-System GUI” cakes, and “methane hydrate” lemonade!

Methane hydrate lemonade

Sediment core cake

An important part of the MBARI working week!

Where there's cake, there are interns...

Behind the scenes at Monterey Bay Aquarium

After already visiting the aquarium twice we’ve all had the chance for a good look round the exhibits.  The sea otters are my favourite, I could watch them all day!  Others would maybe choose the huge outer bay tank or the seahorses.  Although it’s generally agreed that nothing is more fun that flashing our MBARI cards at the front desk and waltzing on in for free!  (A perk of the job!)

Last week we were treated to a behind the scenes tour of the aquarium.  We spent around two hours exploring what goes on behind the intriguing ‘Staff Only’ signs, and it was definitely one of the high points of the internship so far.

Another of my favourite exhibits is the kelp forest.  These huge plants are at home in the waters off California and play a number of extremely important roles.  For instance, they are a main food source for sea urchins and without these urchins, otters have nothing to eat!  The size of these forests also act to protect coastal areas from storms.  So next time you see a piece of seaweed on the beach just remember how these plants are critical for both sea otters and humans!

The kelp forest viewed from the aquarium

The kelp forest exhibit from above

As you can see in the picture above, there is a lot of equipment around the top of the kelp forest exhibit.  A constant spray of salt water comes from around the sides to make sure that any kelp leaves above the water are kept moist.  There is also a wave generator at the end – this is used to give an authentic movement to the exhibit but is also important for the kelp’s health as it provides fresh water to the leaves and helps with gas exchange.  Some of the equipment is also used to manage the pH of water as very acidic or alkaline conditions would be harmful for these giant plants.

Next stop was the huge open water tank.  The window for this exhibit is one of the largest in the world and through it you can watch blue and yellowfin tuna, pelagic rays, a hammerhead shark, a Galapagos shark, barracudas, dolphinfish and a massive school of Pacific sardines.  We were lucky enough to arrive at feeding time so we witnessed a frenzy of activity in the water!

Some of the fish are fed individually and have learnt to come to the side of the tank to receive food.  This is why, when we walked up to see the tank from above, the hammerhead was swimming around at our feet!

The outer bay tank

... and from above!

We also had the chance to see some of the animals that are not currently on display, like these green turtles…

Next to the aquarium is the Hopkins Marine Station Tuna Research and Conservation Center.  There were a lot of tunas here, and we saw one that was in a respirometer.  This machine measures the amount of oxygen being used by the animal, and from this the metabolic rate can be calculated (basically how much energy the animal uses).  They also had a sunfish in one of the tanks.  These are strange looking fish as their body seems to finish after the dorsal and anal fins so they can look like they’ve been chopped in half!

A pretty chilled out sunfish

Like the hammerhead, this guy also thought we had some food for him so we got a good look up close!

Overall, another great day and another brilliant experience to take home with us!