September 4, 2015

Whale Course Among UChicago-MBL Programs to be Held in Woods Hole

whale-and-calfThe first undergraduate course cultivated from the UChicago-partnership is set for the Fall of 2015.  Twelve UChicago undergraduates will spend the 10 weeks at the MBL for “The Whale: Biology, Culture and Evolution on Nantucket Sound,” a four course program that targets undergraduate, non-science majors interested in the maritime culture and entwined histories of whales and America.

Students will be exposed to New England maritime history and culture, and provided a comprehensive overview of biology that includes evolution, environmental science, biodiversity, physiology, and cell and developmental biology.

The lead instructors will be Karl Matlin, University of Chicago Professor of Surgery, teaching “Experimental Biology by the Sea,” Michael Rossi, University of Chicago Assistant Professor of the History of Medicine teaching, “Whales, Whaling, and American History,” and Robert Richards, University of Chicago Distinguished Professor in History of Science and Medicine teaching, “Darwin’s The Origin of Species and The Descent of Man.”

Guest lecturers include Mitch Sogin, MBL Distinguished Scientist and Professor in Molecular Biology, Cell and Biochemistry at Brown University, and Nathaniel Philbrick, noted author of In the Heart of the Sea and other works on whaling and the maritime history of New England.

The program will run from September 27 to December 6, 2015.

A “Quantitative Biology Boot Camp” targeted for all incoming graduate students from all programs in UChicago’s Biological Sciences Division is also scheduled for September 2015 at the MBL.

Co-directed by Stefano Allesina, an Assistant Professor, UChicago Department of Ecology & Evolution and Stephanie Palmer, an Assistant Professor, UChicago Department of Organismal Biology and Anatomy, the course will provide students with a working knowledge of computational and statistical approaches through their application to analysis of real world data sets.  Organizers also hope to foster future MBL-UChicago collaborations by exposing students to the full range of MBL’s research opportunities and resources .

The program will run from September 5 to 11, 2015.

In late August, 12 students from the University of Chicago Lab Schools will spend a week at the MBL engaged in intense biology experiences that both enhance and relate to the current High School curriculum. Experiences will include a trip on the MBL’s R/V Gemma to collect samples and gather data on the local marine intertidal ecosystem, visits to the salt marshes to study restoration ecology, learning about and utilizing cutting-edge microscopes made exclusively available to the MBL community as well as a community service project.

The program will run from August 23– August 30.

UChicago Metcalf Students to Conduct Summer Research at MBL

metcalf.2015.by.dan.cojanuDuring the summer of 2015, twelve undergraduates from the University of Chicago will gain substantive, project-based professional research experience at the Marine Biological Laboratory through the MBL/Jeff Metcalf Summer for Undergraduate Research Fellows program (SURF). The goal of the SURF Program is to introduce students to scientific research under the guidance and direction of MBL’s leading scientists.

“The Metcalf SURF Program represents the best of the MBL/UC partnership as it reflects the enthusiasm of both institutions for research and educational advancement,” says Beth Simmons, MBL-University of Chicago Assistant Director for Education Programs.

Reflective of the program’s past success, this year saw an increase in the number of applications from first to fourth-year students whom expressed interest in a variety of research areas including medicine, developmental biology, genetic diseases, neurology and immunology, oceanography, and ecology.

The twelve-week program encourages students to initiate a project proposal which couples the student with an MBL faculty scientist whose expertise mirrors the student’s research interests and career goals. Each advising scientist mentors and guides the student toward successful project completion. Student experiences vary with each discipline, providing both hands-on field and laboratory-based training in an effort to allow a comprehensive research experience.

The Program is enriched by weekly lunch-seminars with MBL faculty, networking opportunities with other undergraduates on campus, evening lectures, and a variety of cultural and social activities throughout the summer. Additional professional development series workshops are also offered to assist in navigating career and graduate school admissions processes.

SURF students culminate their experience with an undergraduate student symposium through which they have the opportunity to present their projects to their peers and the MBL community prior to submission of a final paper detailing the project, its goals and related successes.

The 2015 Metcalf SURF students are:

Ruby An
“Optimizing the Performance of an Algae-to-Methane Coupled Bioreactor System Through Experimental and Modeling Approaches”
Mentors:  Zoe Cardon /Joe Vallino, Ecosystems Center

Caroline Owens  
“Atmospheric Delivery of Nitrogen to Ecosystem as a Stimulant of Harmful Algal Blooms (HABs)”
Mentor: Ivan Valiela, Ecosystems Center

Petra Byl    
“Microbial Influence on the Transformation of Ferrous and Ferric Iron in Siders Pond”
Mentors: Julie Huber, Bay Paul Center / Joe Vallino, Ecosystems Center

Clara Kao
“Zebrafish Cytoskeleton Architecture: Actin Filaments and Reconstruction”
Mentor: Jonathan Gitlin, Bell Center

Eva Kinnebrew    
Impact of Soil Nitrogen Levels on Species Diversity in Northeastern Grasslands and the Role of Grazing in Mediating the Nitrogen-Diversity Relationship”
Mentor: Chris Neill, Ecosystems Center

Corey Okinaka  
“Visual Function in Pupil Shape in Skates”
Mentor: Lydia Mathger, Bell Center

Leonard Shaw    
“Phosphorous Phase Associations as Indicators for Particle Cycling in the Water Column”
Mentor: Maureen Conte, Ecosystems Center

Hanna Weller    
“Shifting Perspectives: Quantifying Color Camouflage by Flounder in the Eyes of Different Predators”
Mentor: Roger Hanlon, Bell Center

Yangtian Yi
“Parkinson Disease Synoptic Nerves in Lamprey”
Mentor: Jennifer Morgan, Bell Center

Irene Zhang  
“Lifestyles and Hosts of Unknown Acidophilic Legionella  in the Rio Tinto”
Mentor: Linda Zettler, Bay Paul Center

MBL Announces New Recipients of MBL-UChicago-Argonne Collaboration Awards

mbl-uc-argonne.award.recipients.15The Marine Biological Laboratory (MBL) has announced new recipients of the MBL-UChicago-Argonne Collaboration Awards.

These awards support innovative scientific collaborations among faculty at the MBL and UChicago/Argonne, in service of laying the foundation for long-term interactions between the institutions. Teams of at least one UChicago/Argonne and one MBL resident scientist are eligible to receive the awards. The following projects were awarded:

“Structural investigations of a protein-primed reverse transcriptase”

Irina Arkhipova, Bay Paul Center, and collaborator Phoebe Rice, Department of Biochemistry & Molecular Biology, University of Chicago

“Color visual perception: advancing sensory ecology with innovative neural modeling and hyperspectral imaging”
Roger Hanlon, Bell Center, and collaborators Stephanie Palmer and Mark Westneat, Department of Organismal Biology and Anatomy, University of Chicago

“The molecular evolution of a neuron”
Jennifer Morgan, Bell Center, and collaborators Melina Hale, Department of Organismal Biology and Anatomy, University of Chicago, and Jeramiah Smith, Biology Department, University of Kentucky

“Can biodiversity and ecological function be restored to the residential landscape? A MBL-University of Chicago-Nature Conservancy workshop to develop science for testing the efficacy of backyard management”
Christopher Neill, Ecosystems Center, and collaborators Charles Catlett, Urban Center for Computation and Data, University of Chicago; Andrew Chien, Department of Computer Science, University of Chicago; and Tom Chase, The Nature Conservancy

UChicago and MBL Announce Recipients of Lillie Awards for Collaborative Research

research.awardees.feature.imgMBL, WOODS HOLE, MA—The University of Chicago and the Marine Biological Laboratory (MBL) have announced the 2015 recipients of the Frank R. Lillie Research Innovation Awards.

The grant program honors Frank R. Lillie, the early 20th-century embryologist who served as the MBL’s second director and as chair of UChicago’s Department of Zoology. Awards are open to collaborators from the MBL and the University of Chicago or Argonne National Laboratory.

A. Murat Eren and Eugene B. Chang will build an open-source software platform to investigate the intricate role of microbial communities in human digestive diseases.

A. Murat Eren and Eugene B. Chang will build an open-source software platform to investigate the intricate role of microbial communities in human digestive diseases.

The grants bring together interdisciplinary teams of scientists for a project that represents a new collaborative area of inquiry for the investigators. The goal is to stimulate “blue sky” thinking that has the potential to lead to significant external funding with a consortium of collaborators working together on a big problem.

One Lillie Award was given to MBL Assistant Research Scientist, A. Murat Eren and Eugene B. Chang, a Professor of Medicine at the University of Chicago, who will build a high-performance, open-source software platform to study metagenomics, a powerful tool that is used to analyze the genetic material of microbial communities extracted directly from the environment. Once built, the researchers plan to use the software to investigate the intricate role of microbial communities in human digestive diseases.

Another grant was awarded to MBL Associate Scientist Jianwu Tang and Yuki Hamada, an Associate Biophysical Remote Sensing Scientist at Argonne National Laboratory, who will develop a novel approach to measure plant photosynthesis and other ecosystem functions that can be used to quantify the impacts of environmental change on ecosystems and agricultural systems.

Jianwu Tang, Tomomi Tani, and Yuki Hamada (left to right) will develop a novel approach to measure plant photosynthesis and other ecosystem functions that can be used to quantify the impacts of environmental change on ecosystems and agricultural systems.

Jianwu Tang, Tomomi Tani, and Yuki Hamada (left to right) will develop a novel approach to measure plant photosynthesis and other ecosystem functions that can be used to quantify the impacts of environmental change on ecosystems and agricultural systems.

“The Lillie Awards are important to support and stimulate new collaborations between the MBL and the University of Chicago,” said MBL President and Director Huntington Willard. “The two projects that have been awarded have great potential for impacting both the science and its implications for the world we live in. This program is even more far-reaching, since it catalyzes interactions between our campuses at many different levels, which will have numerous payoffs down the line.”

Eren, a computer scientist by training, builds novel algorithms to make sense of complex datasets. As part of the MBL’s Josephine Bay Paul Center for Comparative Molecular Biology and Evolution, he recently developed oligotyping, a computational method that can help microbial ecologists investigate closely related bacterial groups with unprecedented sensitivity. At the University of Chicago, Chang leads a research program that aims to elucidate the role of microbial communities in the development and progression of human digestive diseases.

Eren and Chang’s project will contribute to the fields of microbiology and microbial ecology by tackling processing and visualization challenges that currently prevent researchers from having full control of their metagenomic data. Their software platform has the potential to transform how scientists interpret metagenomic data, which may have tremendous long-term implications on our understanding of the microbial world.

Understanding the response of natural ecosystems, agriculture, and urban ecosystems to the changing environment is critically important to guide sustainable development and protect the human environment. However, the ability to measure complex ecosystem functions (such as photosynthesis, respiration, water uptake, and nutrient cycling) and understand their processes on an ecosystem scale is limited.

Tang and Hamada’s project will address these challenges by building on Tang’s work in the MBL’s Ecosystems Center and developing a novel system to automatically measure plant fluorescence and its link to photosynthesis. This system will be integrated with Hamada’s work collecting ecosystem function data using Argonne’s EcoSpec tower-based hyperspectral remote sensing system, which explores the power of optical information to predict the dynamics of ecosystem functions. The team will further refine their approach by adding pixel-based fluorescence data and tapping the skills of MBL Associate Scientist Tomomi Tani who has been working on instrument development of fluorescent imaging for studying sub-cellular dynamics in living cells. Tang and Hamada expect their project to have a broad impact on the field in ecology, environmental science, agricultural science, remote sensing, and global change research.

The Lillie Awards will support up to two years of pilot research for a total of $125,000 per award. Recipients will be able to develop their projects over a period including two or three successive summers, working in residence as a team at the MBL, in addition to continued progress on the project during the traditional academic years in between MBL visits.

A complete list of 2015 Lillie Award recipients and their teams is listed below.

“Post-assembly metagenomics pipeline for comparative analysis of microbial populations”
Principal Investigators:
A. Murat Eren, Assistant Research Scientist, Marine Biological Laboratory
Eugene B. Chang, Professor, University of Chicago

“Using chlorophyll fluorescence and other hyperspectral reflectance signatures to investigate plant photosynthesis and other ecosystem functions”
Principal Investigators:
Jianwu Tang, Associate Scientist, Marine Biological Laboratory
Yuki Hamada, Associate Scientist, Argonne National Laboratory
Co-Investigator:
Tomomi Tani, Associate Scientist Marine Biological Laboratory

 

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The Marine Biological Laboratory (MBL) is dedicated to scientific discovery and improving the human condition through research and education in biology, biomedicine, and environmental science. Founded in Woods Hole, Massachusetts, in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.

 

MBL Announces First Recipients of MBL-UChicago/Argonne Collaboration Award

 The Marine Biological Laboratory (MBL) has announced the first recipients of the MBL-UChicago/Argonne Collaboration Awards.

These awards support innovative scientific collaborations among faculty at the MBL and UChicago/Argonne, in service of laying the foundation for long-term interactions between the institutions. Teams of at least one UChicago/Argonne and one MBL resident scientist are eligible to receive the awards. The following projects were awarded:

“High-Resolution Microbiome Informatics”— A. Murat Eren, Bay Paul Center, MBL, and collaborator Jack Gilbert, Department of Ecology & Evolution, University of Chicago, will work with co-investigators Jessica Mark Welch and Mitchell Sogin of the Bay Paul Center; Andrew Chien, Department of Computer Science, University of Chicago; and Eugene Chang, Department of Medicine, University of Chicago.

“Cytoskeletal Adaptation During Suspended Animation”Shalin Mehta, Cellular Dynamics Program, MBL and collaborator Patrick La Rivière, Department of Radiology, University of Chicago, will work with co-investigators Hari Shroff, National Institute of Biomedical Imaging and Bioengineering, and Jonathan Gitlin, Bell Center, MBL.

“Developing a Pan-Arctic Ecosystem Respiration Model”Edward Rastetter, Ecosystems Center, MBL, and collaborator Julie Jastrow, Biosciences Division, Argonne National Laboratory, will work with co-investigator Susan Natali, Woods Hole Research Center.

A second round of awards will be announced in December 2014.

New Internships Allow Eight UChicago Undergrads to Spend Summer at Marine Biological Laboratory

Dianna Douglas, University of Chicago

 

ight UChicago undergraduates will spend their summer at the MBL as research interns through the Metcalf program.

Eight UChicago undergraduates will spend their summer at the MBL as research interns through the Metcalf program.

Eight students in the College will spend their summer as research interns at the Marine Biological Laboratory in Massachusetts, marking a new phase in the affiliation between the lab and the University of Chicago that will allow students to pursue significant scientific projects.

“The student interns will make invaluable contributions this summer, while gaining important contacts and resources to navigate the complex process of finding a career path,” said John W. Boyer, dean of the College. “The Marine Biological Laboratory internships are an example of the faculty and laboratory collaborations that can help our students succeed in many careers.”

Funding for the internship comes through a partnership between the MBL and the College, and the interns will be part of UChicago’s Metcalf internship program in Career Advancement. Each student will live in or near the MBL campus in Woods Hole, Mass., a village on Cape Cod that attracts world-renowned scientists for intense, transformative research and advanced courses in a range of biological subjects. The MBL’s summer courses are famous for creating a distinctive environment of collaboration among instructors and students, often working with the latest technology to address research questions.

“It is a fantastic opportunity. We’re going to have a lot of exposure to the scientists, and will understand more things that are happening in the field,” said Medha Biswas, a second-year biology student, who will be part of the first group of interns. She visited the MBL during a Career Advancement trek over spring break.

This summer she will work on live imaging of synaptic proteins in the laboratory of William Green, professor of neuroscience at UChicago and a visiting fellow at the MBL.

While the MBL has hosted many scholars from UChicago during its summer programs, this is the first time that a formal internship program will bring a group of students to Woods Hole.

“Scientific discovery moves forward when bright, young, curious minds are given the opportunity to explore without limits. These outstanding undergraduates are the perfect connection of real intellectual capital between our two great institutions and I have every anticipation of extraordinary accomplishments,” said Jonathan Gitlin, deputy director for research and programs at MBL.

Biswas said she is excited by the opportunity for these inaugural interns to show what UChicago students are capable of contributing at the MBL. The other interns—Rachel Folz, Shaunae Alex, Clara Kao, Lyda Harris, Para Mehta, Caroline Owens and Andrea Rummel—will work on projects as varied as suspended animation in zebrafish and the sedimentary layers of the salt marsh ecosystem.

Each of the student interns identified a faculty member at the MBL whose area of study intersected with their own work. They wrote proposals to the faculty members, explaining a research project that they hoped to pursue in collaboration with the laboratory scientists.

“We look forward to the energy and scholarship that the Chicago students will bring to our summer programs, and to seeing the results of the research and discoveries that will come out of their work,” said Joel Smith, a biologist at the MBL who has worked closely on bringing the UChicago interns to the lab this summer. The MBL’s renowned summer programs attract more than 1,700 scientists and advanced students from around the world.

The MBL interns will be part of the College’s largest group of Metcalf interns. More than 1,000 undergraduates will travel around the world through UChicago’s paid internship program to gain on-the-job skills and explore career opportunities this year.

UChicago and MBL Announce First Recipients of Lillie Awards for Collaborative Research

Contact: Gina Hebert
508-289-7725; ghebert@mbl.edu

Erik M. Jorgensen and Clare Waterman are the first two recipients of the Frank R. Lillie Research Innovation Awards. The awards will provide funding for scientists to develop novel, collaborative projects based at the MBL that will lead to transformative biological discoveries.

Erik M. Jorgensen and Clare Waterman are the first two recipients of the Frank R. Lillie Research Innovation Awards. The awards will provide funding for scientists to develop novel, collaborative projects based at the MBL that will lead to transformative biological discoveries.Waterman photo, credit: Tom Kleindinst/MBL

MBL, WOODS HOLE, MA—The University of Chicago and the Marine Biological Laboratory (MBL) today announced the first two recipients of the Frank R. Lillie Research Innovation Awards.

The newly established grant program honors Lillie, the early 20th-century embryologist who served as the MBL’s second director and as chair of UChicago’s Department of Zoology, and represents the first formal research opportunity between the University and the MBL since their affiliation in 2013. The awards will provide funding for scientists to develop novel, collaborative projects based at the MBL that will lead to transformative biological discoveries. Scientists throughout the MBL’s worldwide research community were eligible to receive the awards.

One grant was awarded to University of Utah neuroscientist Erik M. Jorgensen and his colleagues, who will address the fundamental question of how high-level brain processes such as memory are related to changes in the structure and function of neural connections.

Another grant was awarded to Clare Waterman of the National Institutes of Health. Waterman and a multidisciplinary team of cell biologists and experts in advanced microscopy will investigate basic molecular mechanisms of cellular movement, shape, and form, which are critical to understanding human disorders like cancer.

“This is innovative research by scientists who are leading their fields,” said Joan Ruderman, MBL President and Director. “They are asking bold questions that have the potential to change the way we understand fundamental biological processes. Frank Lillie was a visionary and these awards are visionary on the part of the University of Chicago and the MBL. The science has the potential to transform the understanding of basic biology and human health.”

“The collaborative advances that will emerge from these awards show the immense potential of the affiliation between the MBL and the University of Chicago,” said Neil Shubin, the Robert R. Bensley Professor in Organismal Biology and Anatomy at UChicago and senior advisor to the President and to the Vice President for Research and for National Laboratories. “These projects will bring together scientists who might not have interacted otherwise, with powerful benefits for our community of researchers and educators.”

Jorgensen and his colleagues from the University of Utah and Charité-Universitätsmedizin Berlin, one of the largest university hospitals in Europe, will use novel electron microscopy imaging techniques to investigate the cellular and molecular mechanisms underlying synaptic plasticity, a fundamental property of the nervous system. Synaptic plasticity describes the changes to structure and function that occur where nerve cells connect in the brain and is thought to underlie learning and memory. Abnormal synaptic plasticity is linked to neurodegenerative diseases such as Alzheimer’s disease.

“One of the great remaining mysteries in neuroscience surrounds the issues in the brain that make us uniquely human—how we think, sleep, learn, and remember things,” said Jonathan Gitlin, MBL’s Deputy Director for Research and Programs. “Memory is one of the most vibrant and important functions in the human brain, yet we don’t know how it works at a fundamental level. How can we approach diseases of memory? This is the frontier, and the new project brings forward cell biology and imaging, which are areas of incredible focus for our partnership with UChicago.”

Waterman’s research team includes scientists from the NIH, Harvard Medical School, the National Center for Biological Sciences in India, and investigators from the MBL’s Cellular Dynamics Program. They will use new technologies in polarization microscopy developed by MBL scientists to study molecules important to cell structure, movement, and form. Cell migration is critical for wound healing, immune response, and development.

“In human disorders like cancer, you want to inhibit cell movement, while in infection, you want to move it along,” says Gitlin. “The fundamental aspects of knowing how cells take shape and move are critical to understanding the cell biological basis of human health and disease.”

Several of Jorgensen’s and Waterman’s team members have long histories with the MBL, having served as faculty members in MBL courses and as visiting investigators. In addition, both projects were seeded at the MBL in previous summers. Jorgensen and fellow team member, Shigeki Watanabe spent three summers at the MBL developing the imaging techniques featured in their project. Waterman initiated her project with colleague Satyajit Mayor as part of an MBL Physiology course in 2012 while she was serving as course director and he as an instructor. Two other team members obtained preliminary data for the project while participating as students in the course.

The Lillie Awards will support two years of research for a total of $125,000 per award. Jorgensen and Waterman and their teams will initiate their projects this summer. A complete list of research teams and their affiliations is listed below.

“Ultrafast endocytosis of AMPA receptors during long-term synaptic depression”
Principal Investigator:
Erik M. Jorgensen, Professor, University of Utah; HHMI Investigator; MBL Neurobiology course faculty (2004-2008); MBL Visiting Investigator, (2008-2010)

Co-Investigators:
Christian Rosenmund, Professor, Charité – Universitätsmedizin Berlin; MBL Neurobiology course faculty (2008)
Shigeki Watanabe, Post-doctoral fellow, University of Utah; MBL Visiting Investigator (2008-2010)
Benjamin R. Rost, Post-doctoral fellow, Charité – Universitätsmedizin Berlin

 

“Integrin activation and organization by actin dynamics during cell migration”
Principal Investigator:
Clare Waterman, NIH Distinguished Investigator, National Heart, Lung, and Blood Institute, National Institutes of Health; MBL Physiology course student (1993); Physiology course instructor (2003-2007); Physiology course director (2008-2013)

Co-Investigators:
Timothy Springer, Latham Family Professor, Harvard Medical School
Satyajit Mayor, Dean and professor, National Center for Biological Sciences, Bangalore, India; MBL Physiology course instructor (2012-2013)
Tomomi Tani, Associate Scientist, Cellular Dynamics Program, MBL
Rudolf Oldenbourg, Director, Cellular Dynamics Program, Senior Scientist, MBL
Vinay Swaminathan, Post-doctoral fellow, National Heart, Lung, and Blood Institute, National Institutes of Health; MBL Physiology course student (2012); MBL Physiology course teaching assistant (2013)
Pontus Nordenfelt, Post-doctoral fellow, Harvard Medical School; MBL Physiology course student (2012); MBL Physiology course teaching assistant (2013)
Joseph K. Mathew, Graduate student, National Center for Biological Sciences, Bangalore, India; MBL Physiology course teaching assistant (2013)
Shalin Mehta, Post-doctoral fellow, Cellular Dynamics Program, MBL

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The Marine Biological Laboratory (MBL) is dedicated to scientific discovery and improving the human condition through research and education in biology, biomedicine, and environmental science. Founded in Woods Hole, Massachusetts, in 1888, the MBL is a private, nonprofit institution and an affiliate of the University of Chicago.