September 2, 2015

From Octopus Development to Arctic Change: UChicago Graduate Students Pursue Research Questions at the MBL

By Kelsey Calhoun

From octopus embryology to the proteins active in Arctic soil, University of Chicago graduate students are exploring a range of questions at the MBL this summer as recipients of a University of Chicago Graduate Student Research Award. Now in its second year, this program enables selected UChicago students to enroll in an MBL course or collaborate with an MBL research mentor. This year’s awardees are:

Caroline Albertin_smCarrie Albertin spent several weeks at the MBL investigating octopus development, as a follow-up to her recent work on octopus genomics. Albertin is first author of the cover story in Nature this week, which provides the first whole-genome analysis of an octopus (O. bimaculoides). This also represents the first complete sequencing of a cephalopod, a class of predatory molluscs that includes octopus, squid, cuttlefish, and nautilus. A sixth-year graduate student in Cliff Ragsdale’s lab in the Department of Organismal Biology and Anatomy at the University of Chicago, Albertin plans to defend her thesis soon after incorporating this summer’s work. Her MBL research was sponsored by Senior Scientist Roger Hanlon; she also worked closely with Research Associate Stephen Senft.

Albertin is interested in the unusual body plans of the cephalopods. The octopus, with its large brain and eight arms capable of grasping objects, is constructed very differently than most other animals, even other molluscs. “By sequencing the genome, you get access to the whole [genetic] toolkit the animal has” to develop its body plan, says Albertin. Genomic analysis also allowed her to “get a broad look of how to build a cephalopod,” she says, and uncovered quite a few surprises. Read more here “Octopus genome sequenced,” UChicago Medicine & Biological Sciences.

Albertin’s octopus developmental studies at the MBL this summer complement her genomic research. “These are two different snapshots of the same species,” she says. She took advantage of healthy specimens in the MBL’s Marine Resources Center and a powerful scanning electron microscope (SEM), which gives “a very different view [of structure] compared to a light microscope or even a confocal microscope,” she says. “You see all kinds of surface detail that you wouldn’t normally get.” Albertin used the SEM to look at various octopus body tissues and a technique called in situ hybridization to determine which genes are expressed as those tissues develop. The SEM data will add another dimension to the broader question that interests Albertin: “How do you get from a single cell to an eye, a brain, an arm?”

5-Katharine-Criswell-of-UChicago-at-MBL-Credit-Tom-Kleindinst_smKate Criswell attended the 2014 Embryology course as a recipient of a UChicago Graduate Research Award and came back to the MBL this summer, using part of her original award. Criswell returned to study the development of skates: flat, cartilaginous fish that resemble stingrays. Using a technique called fate mapping, Criswell is tracking how skate embryos grow and investigating what undeveloped tissues will become in the mature skate. She’s particularly interested in how the spine and the vertebrae form.

Not many scientists study skates, but for Criswell’s research questions, it’s one of the best experimental systems. As a fourth year-graduate student with Michael Coates, Professor of Organismal Biology and Anatomy at UChicago, Criswell sometimes has skates flown into the lab from a faraway ocean. However, she’s found it’s difficult to keep them healthy in the lab’s artificial seawater. In terms of experiments, “everything goes much more smoothly at the MBL,” Criswell says. She’s been able to collect a large amount of data with her MBL mentor, Whitman Center Investigator Andy Gillis of Dalhousie University, and she’ll analyze it over the winter.

This Chicago winter may be Criswell’s last, as she is about to graduate, but she hopes her work with skates—and her pilgrimages to the MBL—will continue. “The MBL has such a great, inspiring, positive, and creative atmosphere,” she says. Wherever Criswell goes after graduation, the MBL will likely be part of the plan.

Samuel Miller_smSamuel Miller, a fifth-year graduate student in Albert Colman’s lab in UChicago’s Department of the Geophysical Sciences, came to the MBL for its expertise in Arctic ecology. Miller studies frozen Arctic soils (permafrost) using proteomics, a method that investigates all the proteins present in a particular tissue, organism, or environmental sample. He’s interested in how permafrost soil microbes are responding to global warming. As the permafrost warms, proteins produced by microbes degrade frozen organic matter in the soil, which releases greenhouse gases, such as carbon dioxide. Understanding the types of soil proteins present will shed light on the response of the Arctic carbon cycle to a rapidly changing climate.

Miller is also identifying the microbial genes that encode Arctic soil proteins. This metagenomic approach is an essential complement to proteomics, since the DNA in a soil sample indicates the range of proteins that can potentially be expressed. His Graduate Research Award is supporting metagenomic analysis at UChicago, as well as a week at the MBL working with Senior Scientists Anne Giblin and Gus Shaver, both MBL Arctic researchers. Giblin and Shaver have long experience conducting research at Toolik Field Station in Alaska, where Miller collected soil cores last year.

3-Darcy-Ross-UChicago-Credit-DanielCojanu_smDarcy Ross also attended the Embryology course in 2014 and has returned to the MBL to continue her research. She is interested in the development of snail shells, specifically in the slipper snail (Crepidula fornicata). She wants to know how the shells form and what shell building involves, but the larger question behind her investigation concerns how shells have evolved.

The experiments Ross has designed can be conducted at UChicago, where Ross is a third-year graduate student with Neil Shubin, Bensley Professor of Organismal Biology and Anatomy. But the snails stay healthier in natural seawater at MBL, so Ross is working out of Shubin’s lab in the MBL’s Whitman Center this summer. Ross also has expert advice here. “One of the Embryology course faculty members, Jonathan Henry of the University of Illinois, is the snail guy,” Ross says. Henry, who is co-mentoring Ross’s MBL research, has developed techniques and protocols to explore these very small experimental subjects. Ross is using UV light and various drugs to determine which genes play a role in shell coiling, and she wants to know whether different species’ shells are built by disparate methods. “It’s time to start looking at the inside of the shell” and the story behind it, Ross says, “as well as the outside.”

Neuroscientists Invited to Apply for a Travel Award to Attend the SPINES Neuroscience Symposium in Chicago

Monday, June 15, 2015, Chicago, IL

Contact: Chinonye Nnakwe, PhD
spinessymposium@gmail.com

Event: SPINES Neuroscience Symposium—Scientific Excellence and Lifelong Mentoring to Increase Diversity

Date and Location: October 16, 2015 – Hyatt Regency Chicago, 151 E. Wacker Dr., Chicago IL

Deadline to Apply for a Travel Award: June 30, 2015

The aim of the SPINES Neuroscience Symposium is to deepen our knowledge and understanding of current findings in neuroscience, recruit young and aspiring underrepresented scientists, as defined by the National Institutes of Health, to the field of neuroscience and to enhance retention and success of those already in scientific careers.

The planning committee seeks applicants to apply for a travel award. For further information and an application visit the website: http://www.mbl.edu/spines-symposium/travel-awards/

Applications from pre-doctoral and postdoctoral neuroscientists, and faculty/scientists from academia, industry and non-profit organizations are encouraged. There is a special interest in receiving applications from past and present SPINES students. The deadline to apply for a travel award is June 30, 2015.

About the Symposium
The SPINES Neuroscience Symposium will bring together a large contingent of underrepresented minority neuroscientists from multiple SPINES generations to provide encouragement, support, and networking, in the context of a scientific conference. Planned activities include scientific lectures, professional development workshops, lightning talks, mentoring sessions, and a showcase of the successes of SPINES student and faculty alumni.

About the SPINES Course
SPINES (Summer Program in Neuroscience, Ethics & Survival) is a novel professional development course offered each year at the Marine Biological Laboratory (MBL) to facilitate the careers of underrepresented doctoral and postdoctoral students and early career neuroscientists. It is considered a model for the successful training of early career scientists from underrepresented groups. The SPINES course has been offered for over 20 years and has hundreds of alumni — from those who are beginning their careers to those nearing retirement. The key ingredients for the success of SPINES are career-long mentoring, monitoring, networking, and understanding the current boundaries of neuroscience knowledge. No other experience, except graduate training, has such a profound effect upon a student’s research career, as does a summer course at the MBL. Many describe the effect as magical and transformative.

Additional Symposium Sponsors
Alzheimer’s Association
Grossman Institute for Neuroscience, Quantitative Biology and Human Behavior

MBL–UChicago Exploratory Research Seed Funds Announced

We are pleased to announce grants in support of collaborative research among UChicago and MBL faculty (both visiting and year round) at the MBL. The grants will seed novel research that initiates collaboration between individuals and institutions and can serve as the substrate for future grant proposals. The intent is to provide the basis for collaborative research between UChicago faculty and visiting and/or year-round faculty of the MBL.

These grants are intended to be exploratory funds: budgets are at a maximum of $25,000, proposals are short, target dates are quarterly, and review and funding will be rapid.

Applications are accepted in Fall, Winter, and Spring Quarters. The next round is due April 30, 2015.

Completed applications are due by midnight CST on April 30th.

 

Winter 2015 MBL – UChicago Exploratory Seed Fund Winners

Melina Hale, Jennifer Morgan
“Behavioral change and neural circuit reorganization during metamorphosis in Xenopus

Understanding of neural circuit development and evolution is limited by the difficulty of establishing neuron homology among organisms and species. How does the startle circuit reconfigure from driving unilateral axial bending to controlling bilateral limb movement during development and evolution? Here we focus on development and will examine the M-cell circuit through the transition from tadpole to frog in Xenopus laevis. This work will provide new insights into how neural circuits develop through major behavioral transitions and will inform examination of startle circuit evolution in tetrapods. Homology of the M-cells to hindbrain neurons of amniotes is unknown; ultimately we aim to trace the evolution of this neuron and its circuit across the water-to-land transition and through tetrapod diversity.

MBL Celebration of Discovery to Focus on Research and Education Partnerships and Opportunities

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

Marine Biological Laboratory Semester in Environmental Science Open to UChicago Students

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.

 

UChicago Innovation Fund Now Accepting Applications for Spring 2015

uc.innovator.fund

 

Fund Open to Resident MBL Faculty

The University of Chicago has built an array of programs to create an entrepreneurial ecosystem that can help researchers navigate the path toward commercialization and overcome the hurdles to attracting investment. These programs include the Chicago Innovation Exchange, The New Venture Challenge, accelerator and incubator programs, and the University of Chicago Innovation Fund.

About the Innovation Fund
The Innovation Fund is a philanthropic proof-of-concept fund created to support the evolution of your ideas into products and services. The Fund has now been expanded to $20 million dollars and is open to current UChicago and affiliated lab faculty, staff, and students with technologies in a wide variety of industries.

Applications are due via electronic submission by Thursday, March 12th.

Apply Now!

Eligibility
The Innovation Fund is intended to provide proof-of-concept funding for technologies / concepts which:

  • are submitted by a current University of Chicago Principal Investigator, student, affiliate (including national labs), or their representative,
  • possess the potential to have a substantial commercial impact but are too early to attract commercial investment,
  • and cannot be funded through existing granting mechanisms.

It is not intended to fund research / activities that are not directly driving towards an externally validated business outcome.

Contact
If you have any questions, contact Jason Pariso, The Director of Operations (jpariso@uchicago.edu), or Wolfgang Connell, Chicago Innovation Exchange Program Manager (wolfgangc16@uchicago.edu).

— The Innovation Fund Team