It has been awhile but there are big things brewing here in the Punyasena Lab. More to come soon!
The lab’s pollen images from a recent PLoS ONE paper has found another public venue.This time, the technicolor 10-foot banner of Croton hirtus, Mabea occidentalis, and Agropyron repens pollen grains will be on display in Concourse A at Chicago’s Midway Airport. The banner, which was part of the University of Illinois Institute for Genomic Biology’s (IGB) Art of Science 2.0 exhibition, is now part of a rotating exhibit of images from IGB that will be on display at Midway starting in late July.
The display is now up in Concourse A. Read more about the exhibit here.
Derek – thanks in part to support from a Center for Latin American and Caribbean Studies (CLACS) Tinker grant – is back in Panama this month working at the Smithsonian Tropical Research Institute (STRI). He is visiting a long-time collaborator, J. Enrique Moreno, a STRI researcher at the Center for Tropical Paleoecology and Archaeology (CPTA). This is Derek’s second trip to STRI-CPTA. He is back working with the Alan Graham Tropical Pollen Reference Collection, curated by the lab group of STRI Staff Scientist Carlos Jaramillo. The Alan Graham Collection represents one of the largest modern reference collections of Neotropical pollen – with reference slides of over 25,000 species. Derek will be using the collection to help identify over 100 unknown pollen morphotypes from his counts of aerial pollen samples collected from Parque National San Lorenzo. Several hundred species of plants are potentially represented in the pollen rain of this high-diversity moist forest.
We are excited to announce that the lab recently received funding through the National Science Foundation’s Advances in Bioinformatics (NSF-ABI) program for a new three-year collaborative project. The proposal “ABI Innovation: Breaking through the taxonomic barrier of the fossil pollen record using bioimage informatics” links the high-throughput, super-resolution structured illumination microscopy being employed at the University of Illinois with the morphological algorithms being developed by Washington Mio’s lab at Florida State and the machine learning advances made by Charless Fowlkes at University of California, Irvine.
Funding includes support for a graduate student with interest in microscopy, machine learning, and mathematical morphology – as well as pollen-curious undergraduates. Please contact Surangi (punyasena AT life.illinois.edu) for more information.
Cassie Wesseln, a first-year PhD student and former undergraduate researcher in the Punyasena lab, received an Honorable Mention from the National Science Foundation (NSF) Graduate Research Fellowships Program (GRFP) earlier this year. The NSF GRFP is one of the most competitive national fellowships available to graduate students in their first two years of study. A belated congratulations to Cassie!
Cassie is also currently an NSF Integrated Graduate Research and Education Traineeship (IGERT) fellow. The IGERT fellowship in Vertically Integrated Training with Genomics – a Smithsonian Tropical Research Institute (STRI) and UIUC collaboration – included a semester in Panama (Spring 2013). As a result of the program, Cassie was able to participate in a Tropical Ecology course led by STRI staff scientists, and in seminars and field trips conducted by over thirty different STRI scientists and fellows. In four short months, she visited almost all of the STRI research stations in Panama. Cassie adds: “It was an incredible experience in which I learned a great deal about the tropical biology and the research opportunities at STRI.”
Luke and Shiv’s pollen images from our recent PLoS ONE paper are continuing to make a splash. First named University of Illinois Institute for Genomic Biology’s (IGB) Image of the Month in December 2011, then chosen as the featured image for the Art of Science 2.0 exhibition at the Indigo Gallery in April 2012, these Croton hirtus, Mabea occidentalis, and Agropyron repens pollen grains were recently selected to remain on permanent display in the science wing of at the Richland Community College in Decatur, Illinois. The images from the Art of Science exhibitions were brought to Richland’s gallery to engage community members in central Illinois in the diversity of research occurring at Urbana-Champaign.
The 2012 Art of Science theme of “cross-pollination” between the academic and local communities of Illinois lives on!
Derek’s paper – Variability within the 10-Year Pollen Rain of a Seasonal Neotropical Forest and Its Implications for Paleoenvironmental and Phenological Research – based on his MS research – is now out in virtual print in PLoS ONE (Jan 8, 2013). Co-authored with STRI collaborator, J. Enrique Moreno, this works captures the year-to-year variation in the pollen output of one site in Barro Colorado Island (BCI). This analysis uses 10 years of the two decades of aerial pollen samples Enrique has collect from two Panamanian forests: BCI and Parque National San Lorenzo.
The paper was featured in the STRI Newsletter.
Congratulations, Derek and Enrique!
Last year was a very productive one for the lab – with four papers in print and two in press by late December. We had seventeen accepted abstracts, posters, and talks at national and international meetings, which meant that we were traveling the world for most of the year – from Boulder to Woods Hole to Portland to Charlotte to Vienna to Tokyo to Dublin. These abstracts included talks by collaborators: David Tcheng, Washington Mio, and Carlos Jaramillo; as well as talks by the core lab: Luke, Derek (his first!), and Surangi. The lab organized two sessions: Advancing High-Resolution, High-Throughput Research in Paleoecology at IOPC/IPC in Tokyo and The Future of Quantitative Paleontology: Biometry, Computer Vision & Machine Learning at GSA in Charlotte. Many of the other talks were invited – so we are glad to see that there’s growing interest in what we do!
Surangi was invited to participate in the Palaeo50 workshop at Oxford University; she co-chaired the “Approaches” section. She also gave two invited departmental seminars, one close to home at Illinois State University and one at Utrecht University, Netherlands. She and David were also invited speakers at a Department of Homeland Security meeting on pollen forensics – a first for the lab!
Three new PhD students started in 2012. Two were not so new – Derek completed his MS in PEEC in December 2011 and Cassie had been an undergraduate researcher in the lab since August 2009. The newest graduate student, Aleja, completed her MS with Mark Bush at FIT and spent a year working with Carlos Jaramillo at the Center for Tropical Paleoecology and Archaeology at the Smithsonian Tropical Research Institute.
Two lab members moved on in 2012. Stefan completed his MS in Plant Biology in May and Luke started a tenure-track position as Lecturer at Plymouth University, UK in October.
Finally, 2012 also saw the start of our second NSF grant – this one from Macrosystems Biology, on the Automated Analysis of the Reproductive Response of Two Panamanian Forests to ENSO Climate Variation – A Machine Learning Pilot Study. With this project, we hope to expand our previous work on the automated identification of black and white spruce to a significantly larger and more complex data set.
Thanks to everyone for all their hard work and effort last year. Here’s to another great year!
Welcome to the new website for our lab group!
It’s been several years since we updated our original website. We have been busy with many new projects, and sadly, found our old website just a little too cumbersome to keep up to date. We have now migrated to the shiny new space provided by publish.illinois.edu and adopted WordPress. We hope that this will help us keep you (friends, collaborators, prospective students and the curious public) better informed on what is going on behind the doors of Morrill 139!
Not everything is quite yet finished, but our hope is that over the course of the next year, this website will become the go-to space to hear the latest on our research.