The Partner University Fund is a Franco-American initiative whose goal is to support high-level and cutting-edge partnerships between French and American universities and research institutes. Established in 2007, the Partner University Fund provides the most talented scholars in both countries with the opportunity to cross national boundaries and pursue a long tradition of fruitful academic cooperation. The Partner University Fund is a program of the French Embassy in the United States and the FACE Foundation and is supported by American donors and the French government. Learn more...
The Ocean Observatory of Villefranche-sur-Mer (OOV) is one of three oceanography research institutes of Université Pierre et Marie Curie. It hosts several research teams and an ecosystem monitoring observatory, which has been taking daily samples of water and biological organisms in Villefranche's bay since 1966. In three historical buildings, on a total of 8500 m2, it hosts about 90 teaching and research staff (faculty, researchers, engineers), nearly as many non-permanent staff (students, contract employees), and about 50 support staff (administrative personnel, IT, machine shop, sailors, etc.). — Learn more...
The Rosenstiel School of Marine and Atmospheric Science (RSMAS), of the University of Miami, is a the leading academic oceanographic research institutions in the world. The School's basic and applied research interests encompass virtually all marine-related sciences. The Rosenstiel School's main campus is located on Virginia Key, Florida. It forms part of a specially designated 65-acre marine research and education park that includes two NOAA laboratories and a dedicated marine and science technology high school. RSMAS itself hosts about 220 faculty and research staff, almost as many Ph.D. students, and 80 support staff. — Learn more...
Through this PUF-sponsored project we have been able to study the orientation of fish larvae during the day and relate it to physical forcings such the position of the sun in the sky. It is already pretty crazy to think that those cm-sized organisms are able to detect the position of the sun from underwater and orient with respect to it. However, fish larvae are known to settle on the coast at night, not during the day. So while the sun would be a useful cue for large scale navigation in the ocean, they have to use some other cue to settle at night.
But studying behaviour at night is, of course, more challenging than during the day. Only a handful studies have tackled the question and always used traps or lab experimental settings, never in situ observations. We set out to change this and observe larvae in the DISC at night. To do so, we needed a way to see without being seen. Because light wavelengths in the red color range are quickly absorbed in water, most sea creatures do not "see" the reds. We went even beyond red and used infra-red LEDs to light up the DISC observation area, just to be sure we would not disturb the organisms. But infra-red is basically heat and the LEDs heat up very much during prolonged use, which makes them difficult to attach to a transparent plastic instrument. Furthermore, while CCD sensors on digital cameras record infra-red just fine, these wavelengths are problematic for picture quality in normal-life applications and all lenses include an infra-red filter to block them out. So it took over a year of development with Bellamare to get to a working system, comprised of very bright infra-red LEDs (to shine through red-absorbing water) potted in custom aluminium and epoxy housings, a large Lithium battery pack to power them for a few hours, a modified GoPro camera with a customised lens, etc. The result is below: a nice, focused image, captured in complete darkness!
Thanks to the new extension of the project (as explained in the previous post), we could plan the first in situ observations of fish larvae at night, offshore Miami. The "DISCo night" team was lead by Professor Claire Paris and comprised Captain Evan D'Alessandro, Craig Raffenberg and Alessandro Cresci (Pr Paris' students), and Pr Jean-Olivier Irisson, from UPMC. Between July 29th and August 5th, we caught many larvae of the bicolor Damselfish (Stegastes partitus) and deployed the DISC for four nights to observe their behaviour. Instead of the usual time-lapse pictures, we captured video to get a better understanding of their behaviour. In turn, this required some non-negligible changes to discr, the software written to analyse DISC data. A few bad weather days in the middle of the week allowed to prototype those changes.
The bad weather days and the abundance of larvae were also an incentive to test the new lab-based experimental setup of Pr Paris, at RSMAS. Her wet lab is equipped with a cylindrical aquarium large enough to fit the DISC (and a PhD student, if needed), light-insulating curtains, and an array of lighting systems allowing to simulate full daylight, select some wavelengths, or use wavelengths invisible to humans such as UV or infra-red. Damselfish larvae were observed in the DISC, while it was rotating in this setup, during the day (using simulated daylight) and at night (using infra-red). The goal of these first experiments is to determine if larvae still orient indoors, which would suggest that this behaviour is somewhat ingrained and not conditioned by external stimuli. Now we need to analyse the data!
This project should have been over for a while now but, as the title of this post (and Lenny Kravitz) says, things are never really over. Thanks to careful spending (and a few cancellations…) we actually had funds remaining on the US side. And thanks to the open minds and great support of the PUF project managers, we are allowed to use them, as per a second no-cost extension of the project!
We would like to take this opportunity to deeply thank the managing officers of the PUF program. The financial support of the PUF has been extremely useful and, almost as importantly, enjoyable to use.
The project started late because it took forever to sign the contracts thanks to the heaviness and slowness of the administrative systems of both universities. This was almost painless for the project itself because we were easily granted a no-cost extension every year, to account for the delay in the activities of the project.
On the research side, when the shipping company vastly underestimated the cost of shipping ISIIS to France and we had to reallocate funds in the first year to cover part of these expenses, they understood it was out of our hands and supported us. When we lost a DISC instrument at sea during the second year and had to quickly turn around and order another one with funds that were supposed to be dedicated to a sound recording system (and therefore postpone that part of the project), they accepted that this decision was making the best out of a bad situation. Finally, when we shifted focus from the influence of sound on the orientation of fish larvae to the observation of their orientation at night, because given the evolution of the field in the ~3 years since we wrote the initial proposal, this seemed like a more topical question, they trusted our decision.
On the educational side also, things changed quite a bit along the course of the project. The number of French students ready to leave for a second year of Masters was less than we expected, so we opened this opportunity to first year students. The number of US students who wanted to travel to France to take a multivariate statistics class was more than we could handle, so we had the professors travel to the US instead. In all cases, we accounted for these changes in the yearly reports, explained them and they were understood.
In an era when most funding agencies almost require you to get three quotes and a PO to buy a pencil, working with project managers who understand the inherent uncertainty associated with doing something new, be it in research or education, who are supportive and understanding, is extremely refreshing. And in the end, science wins, because we, as researchers and professors, can focus on advancing the field, on building new things, on creating new ways to train students instead of becoming accountants and form-fillers. So, once again, we thank the PUF very, very much for their support and we hope we made the best out of it.
In what will probably be the last mobility event of this 3-years PUF program, Claire Paris, the coordinator of the US part of this project, came to France to teach a class on the Lagrangian modelling of marine larvae, in the numerical modelling class of Villefranche-sur-mer. She taught this class last year for the first time (at exactly the same date, on Dec 11th!) and the class was again well received. Knowing the level of experience of the students allowed to better focus the computer lab exercices of the afternoon. During the class, the students were able to learn about the intricacies of the Connectivity Modelling System first hand, from the mouth of its creator! During the lab that we co-taught, students built a simple advection-diffusion model in a idealised current field before analysing the results of real CMS simulations that were run for them before the class. Altogether, this made for a rich and diverse experience. Here is a picture of the group of students in Villefranche together with myself, Jean-Olivier Irisson, or Simon Ramondenc, a PhD student from Villefranche who co-tutored the lab part, (far left) and Claire Paris (far right).
After Jessica in Miami, last week, it was now Robin Faillettaz' turn to defend his PhD thesis, in Villefranche-sur-Mer. His thesis work was an integral part of this PUF project: the VISUFRONT cruise (using ISIIS and UVP) in 2013, the behavioural experiments and the joint efforts for image analysis in 2014, and now his defense, in 2015. His work dealt with the distribution and behaviour of fish larvae, in response to their physical and chemical environment.
His jury was composed of two reviewers: Howard Browman, from the IMR in Norway, and Paolo Guidetti, from the University of Nice; one president: Eric Thiebaut, from UPMC, Marine Station of Roscoff; one examiner: Claire Paris, from RSMAS, University of Miami –the co-supervisor of this project– (Ana Sabatés, from the CSIC in Barcelona, was also supposed to be here but could not attend because of a personal matter); and his two advisors: Philippe Koubbi and myself. After 45 mins (precisely!) of presentation and over two hours of questions and discussion, the jury declared his thesis worthy of the grade of doctor and his overall presentation "exceptional".
Congratulations to Robin, who I was very happy to supervise for the last three years. This project is a success in a great part because of his hard work. Below are a few pictures, before, during and after the defense!
Jessica Luo was a RSMAS PhD student under the supervision of Bob Cowen, the original coordinator of this PUF program at RSMAS (before he moved to Oregon State University). She is not a student anymore now but a doctor, after brilliantly defending her dissertation on Oct 30th, at RSMAS!
She studied gelatinous zooplankton (i.e. jellies) using the data and images collected by the In Situ Ichthyoplankton Imaging System (ISIIS). During her PhD, she also came to Villefranche for a class and learn image analysis tools, she participated in the VISUFRONT cruise funded by this PUF project, collaborated with Robin Faillettaz (a PhD student at OOV who will also defend soon) and myself. I was very happy to be part of her PhD thesis committee, to be present at her defense, and to be co-author on one of her dissertation papers. From what I saw in her manuscript, there are many more to come.
Jessica also invested a lot of time in the planktonportal project, a collaborative science website where enthusiasts can help identify plankton on ISIIS images. As a nice gift to Jessica, yshish (the very active volunteer moderator of that project) organised a contest to reach 1,000,000 plankton identifications on the project. That incredible milestone was met (and even exceeded) by the time Jessica defended. Big shoutout to the planktonportal community!
For the next year, Jessica will continue to work with Bob Cowen and Su Sponaugle in Oregon, which will give her the opportunity to publish all the good science she presented us and to do further research with plankton images and data, in tandem with us in Villefranche.
This week was my last trip to Miami as part of this PUF program. It was full of new ideas and events (as the other posts on this blog indicate) and also familiar: I got to meet again with old friends and collaborators at RSMAS and I spent the week with Pr Claire Paris, the coordinator of the PUF program for RSMAS.
We discussed our respective works on fish larvae orientation and the Drifting In Situ Chamber, the instrument she pioneered and which we now both use. I had the opportunity to present the research done with that instrument in Villefranche through a seminar titled "Mediterranean fish larvae: orienteering champions". We discussed both old data (which will soon turn into new papers!) and the developments of the instrument, in particular for the work of her numerous PhD students: Matt Foretich who works on olfaction (and whose thesis committee I sit on), Alessandro Cresci who works on magnetic orientation (and who recently came to Villefranche for a class), and Romain Chaput (pictured below) who will work on group orientation, who did his Master's degree internship with Pr Paris through this PUF program and now starts a PhD with her. Romain and Claire asked me to also be part of his committee and I gladly accepted. Not only do I enjoy working with Claire but I have also been particularly interested in the question of the dynamics of groups of fish since some work we did together on that topic a few years ago (which got submitted for publication this very week!)
So overall, another very enjoyable week, full of work and promises. The last as part of this PUF program but hopefully (surely!) not the last in this fruitful partnership.
Teams at OOV and RSMAS (and now OSU) have been working with instruments that allow us to take images of planktonic animals in situ: the Underwater Video Profiler (UVP) at OOV and the In Situ Ichthyoplankton Imaging System (ISIIS) at RSMAS/OSU. Half of the research done through this PUF project was built on those instruments, coupling them for the VISUFRONT cruise during the first year of the project. We worked on analysing the images and data recorded by these instruments since then.
My coming to RSMAS this week was an occasion to discuss plankton imaging again, two years later, with Bob Cowen. It was a long, interesting and fruitful discussion. It seems we are at a tipping point for plankton imaging. On the RSMAS/OSU side, ISIIS has now been used in several projects and multiple scientific papers have been and are being written. An automated image processing and segmenting routine is operational and fast. The planktonportal.org collaborative website for plankton identification generates a steady stream of human-validated identifications for images taken by ISIIS. The kaggle Data Science Bowl competition spurred several promising algorithms for automated image classification. On the OOV side, the UVP is being miniaturised to be included in autonomous underwater instruments and collect more data in more places. A web application for semi-automated, collaborative image classification by scientists has been developed and is ready for UVP and ISIIS images. Dr Ben Graham, one of the authors of a winning algorithms of the kaggle competition will be coming to OOV to discuss including his work as the classification backend of this application. And, on both sides of the Atlantic, the instruments and associated tools are becoming standard enough to be considered by environment monitoring programs.
So overall, the times are exciting and full of opportunities for all the teams involved in this PUF program!
I am Katell Guizien, a CNRS researcher, and I work in one of the three marine stations of UPMC, in Banyuls-sur-Mer. Connectivity is a central part of my research line on the conditions for persistence of benthic invertebrates populations. Having a project to transpose in the Caribbean sea the methodology I developed for populations in the Gulf of Lions, a region of the Mediterranean sea, I grabbed this unique opportunity offered by the PUF project to visit Claire Paris in RSMAS. I went to Miami in July for a very short but intense week!
Claire and I spent many hours every day confronting our approaches and thoughts about marine connectivity, applied to Caribbean fish and Mediterranean benthic invertebrates, respectively! We exchanged about hydrodynamical models resolution, experimental methodology to study larval motility behaviour and discovered how convergent our experiences were. We need to share our views about connectivity. The week was also very positive to establish new connections with atmospherical modellers and planting seeds for a sabbatical stay at RSMAS to develop the Caribbean project! I ended my week there by giving a seminar about Biodiversity conservation and larval dispersal, illustrated on the Gulf of Lions test case.
My name is Alessandro Cresci and currently I am a graduate student at the RSMAS, University of Miami, advised by Dr. Claire Paris. Thank to the exchange program with the UMPC I was able to attend the summer class in multivariate statistics in Villefranche, with Dr. J-O Irisson, Dr. S-D Ayata and Dr. S.Gasparini.
I am personally very grateful for this enriching and extremely helpful experience.
My research is focused on the study of the orienting abilities of marine fish larvae, and in particular on the magnetic sense. Before joining the class, I could conduct experiments in Norway at the marine station of Austevoll in order to collect data about the orientation of the post-larval glass eels in their natural environment utilizing the DISC (Drifting In Situ Chamber) technology. The class in multivariate statistics allowed me to improve my knowledge on the analytical techniques, which provided me of new tools for exploring my data, and relate the behavior of my eels to many environmental parameters. Moreover, the class has a full module dedicated to the statistical analysis by the software R. This gave me the possibility to successfully utilize R in the analysis on my DISC data and to highlight new, unknown aspects of the behavior of the glass eels.
This summer class has been of great utility for my research and I was able to submit a manuscript to Nature Communications.
I would recommend to everybody to make this great experience of study in the unique colors of the Mediterranean Sea.
I was looking for an internship in oceanography and I was lucky to be involved in this project during one full-on month. Initially, it was planned that I would observe larvae in the DISC at night, to push the fish larvae behaviour research started last year further. Unfortunately, the infrared light system was not ready yet, so I ended up DISCing during the day (too bad, I had to sleep at night!). This allowed to verify whether the results found last year were robust. Fifty Chromis chromis larvae were tested in the DISC; 30 were observed the same day (a new record for the largest number of observations in one day!) with perfect experimental conditions (and sighting of an ocean sunfish!).
I also measured the swimming speed of Diplodus annularis in a swimming chamber. I can say that during two days, I was the only person being cold whereas the outside temperature was 30°C or more. The 33 Diplodus annularis swam between 5 cm/s and 25 cm/s. The next step was extracting lipids from the fish muscle in order to know if the individual speed was related to the body condition of the individual. The final results from this will come next year.
My internship was a great opportunity to learn about fish larvae and why they should be studied. I am very grateful to Jean-Olivier Irisson and Robin Faillettaz for their trust, their patience and their knowledge. I have shared great moments with them.