A cuttlefish next to a checked wall pattern displays adaptive camouflage.
Photo courtesy of Kim Ulmer, MBL

The study, led by Kimberly Ulmer and Roger Hanlon in the MBL’s Program in Sensory Physiology and Behavior, is published in the April issue of the Biological Bulletin.

Many prior experiments have shown the influence of two-dimensional (2D) substrates, such as sand and gravel habitats, on camouflage, yet many marine habitats have three-dimensional (3D) structures, such as rocks and coral, among which cuttlefish camouflage from predators. In this study, Ulmer and Hanlon tested the relative influence of horizontal versus vertical visual cues on cuttlefish camouflage. They found that visual stimuli in the vertical dimension (2D or 3D) have a stronger influence on changeable camouflage than do 2D stimuli presented horizontally. This effect is noteworthy because in many of the experiments, the vertical stimuli represented only a small proportion of the total visual surrounds, indicating that cuttlefish are selectively responding to vertical cues.

Such choices highlight the selective decision-making that occurs in cuttlefish as they determine their camouflage body patterns.

Citation:

Ulmer KM, KC Buresch, MM Kossodo, LM Mathger, LA Siemann and RT Hanlon (2013) Vertical visual features have a strong influence on cuttlefish camouflage. Biological Bulletin 224: 110-118.

Arctic LTER greenhouses in peak autumn. Credit: Sadie Iverson

In 1989, MBL Senior Scientist Gaius Shaver and his colleagues set up a series of small experimental greenhouses on a hillside above the Toolik Field Station at the National Science Foundation Arctic Long Term Ecological Research site in northern Alaska. The clear plastic-covered greenhouses increase ambient soil temperatures by up to 2°C and are used by Shaver and other scientists to observe the effects of sustained warming on the Arctic environment. Today, the test plots are the longest-running climate warming study in the tundra.

New research from Seeta Sistla, a doctoral student at the University of California, Santa Barbara and a graduate of the Brown-MBL Partnership and Graduate Program in Biological and Environmental Sciences, her adviser, Josh Schimel, Shaver, and their colleagues reports the results the long-term warming experiment at the site.

The study reveals that decades of slow and steady warming have not changed the amounts of carbon in the soil, despite changes in vegetation and even the soil food web. Whether or not this phenomenon—no net loss of soil carbon despite long-term warming—is a transient phase that will eventually give way to increased decomposition activity and more carbon release, remains to be seen.

 “This work demonstrates why long-term ecological research, and especially long-term whole-ecosystem experiments, are a good thing,” says Shaver. “The experiment on which this paper is based was set up in 1989, when Seeta Sistla was about 6 years old.  There is no way she could have produced such a nice thesis if we had not set up these experiments so many years ago, not always knowing exactly how they would be used.”

The paper appeared in the May 15, 2013 Advance Online Publication of the journal Nature.

Other researchers participating in this study include John C. Moore and Rodney T. Simpson from Colorado State University, Fort Collins and Laura Gough from the University of Texas at Arlington.

Funding came from the National Science Foundation Long Term Ecological Research (LTER) Program, DOE Global Change Education Program Graduate Fellowship, a Leal Anne Kerry Mertes scholarship, and Explorer’s Club.

Gonzalez-Bellido and colleagues were honored for the “scientific excellence and originality” of their study of prey detection and interception in dragonflies.

The research was performed at Howard Hughes Medical Institute’s Janelia Farm Research Campus, where Gonzalez-Bellido was a postdoctoral scientist prior to joining the MBL’s Program in Sensory Physiology and Behavior in September 2011.

The study provides insight into basic visual-motor neural processing, and has implications for the development of “bioinspired” prosthetics for humans.

A green darner dragonfly, a member of the Aeshnidae family, in which Robert Olberg of Union College originally discovered the target-selective descending neurons (TSDNs). Credit: Brian Robert Marshall/Wikimedia

“I am honored to receive recognition for this work, for which we bridged the clinical and neuroethological fields, and developed new techniques,” says Gonzalez-Bellido. “This award has provided me with fuel to keep up the hard work and further my research plans.”

In order for a dragonfly to intercept its prey in midair (which dragonflies do with a 95% success rate), it needs to quickly track the prey and predict its future location. To understand how they undertake this complex task, Gonzalez-Bellido and her co-authors studied a small group of 16 motor neurons, called target-selective descending neurons (TSDNs), in the dragonfly Libellula luctuosa. These neurons, originally discovered by co-author Robert M. Olberg (Union College) in the green darner dragonfly, originate in the brain and extend to the thoracic ganglia, where the neural signal is interpreted and translated into wing muscle movements. Surprisingly, the scientists found that this small group of neurons can detect the direction of target prey with high accuracy and reliability across 360 degrees, and that this information is relayed from the brain to the wing motor centers in population vector form.

In 1988, co-author Apostolos Georgopoulos and his colleagues showed in monkeys that from the activity of neurons in the motor cortex, the population vector algorithm can predict the monkey’s upcoming arm movement. However, to achieve a more accurate prediction with this algorithm, upwards of 200 neurons were needed. Thus, the present discovery that a highly accurate neural code carrying information about target direction can be achieved with just 16 neurons is enlightening, and could have applications in the development of bioinspired robots. (Georgopolos is an MD-PhD at the University of Minnesota/Veterans Administration Medical Center who is interested in the development of prosthetics.)

Paloma Gonzalez-Bellido. Credit: HHMI/Janelia Farm

Randy Schekman, PhD, editor-in-chief of PNAS, describes the papers chosen for the Cozzarelli Prize as being “of exceptional interest… These papers are not merely technically superior but have had special impact and maybe novel techniques or novel applications of techniques, or very important discoveries.”

For this study, Gonzalez-Bellido and Trever Wardill (then at HHMI) developed a new protocol for labeling and confocal imaging of neurons in thick invertebrate tissue samples. In addition, her co-authors and former HHMI colleagues Hanchuan Peng and Jinzhu Yang developed a method for automatic 3D digital reconstruction (tracing) of neurons in microscopic images.

Gonzalez-Bellido sees the dragonfly as a promising model for understanding the evolution of neural systems. “It’s exciting that the same computation [the population vector algorithm] is used by monkeys and dragonflies for this task. Dragonflies belong to the most ancient groups of flying insects on earth, and they have changed little in 250 million years” she says.

The Cozzarelli Award was established in 2005 and named in 2007 to honor late PNAS editor-in-chief Nicholas R. Cozzarelli. Gonzalez-Bellido and the other awardees will be recognized at an awards ceremony during the National Academy of Sciences Annual Meeting on April 28, 2013, in Washington, D.C.

Out of more than 3,700 papers published in the journal last year, the editors selected Gonzalez-Bellido’s paper and five others for the Cozzarelli Prize.

Citation: 

Gonzalez-Bellido PT, Peng H, Yang J, Georgopoulos AP and Olberg RM (2012) Eight pairs of descending visual neurons in the dragonfly give wing motor centers accurate population vector of prey direction. PNAS 110: 696-701 /doi/10.1073/pnas.1210489109

A PNAS commentary on the paper is here.

The report highlights recent activities by 13 federal agencies to strengthen our scientific understanding of global changes including climate change, the threats and opportunities they present, and how they are likely to evolve over time.

In addition, Our Changing Planet showcases tangible results of work carried out by USGCRP agencies, including, for example, some of the most detailed, data rich maps of Alaskan permafrost ever generated; the most precise map ever produced of carbon stored in Earth’s tropical forests; critical information about the number and magnitude of extreme weather events in the United States; and updated maps that help gardeners and growers plan for harvesting seasons.

This report anticipates the USGCRP’s comprehensive Third National Climate Assessement, which will be released in early 2014. MBL Distinguished Scientist Jerry Mellilo chairs the advisory group that is preparing the National Climate Assessment, which presents the latest science about the current and projected effects of climate change across the United States.

The Deep Carbon Observatory (DCO), a $500 million, 10-year international program that aims to reveal the quantity, movements, forms and origins of carbon inside our planet, has released its first major product after three years of inquiry: the volume Carbon on Earth.

Mitchell Sogin, director of the MBL’s Bay Paul Center for Comparative Molecular Biology and Evolution, co-chairs the DCO’s Deep Life Directorate. This group is discovering and describing the microbes and viruses that live in the deep ocean and beneath the ocean floor, and how they interact with deep carbon cycles. Guiding questions include:

* What’s down there?

* Do different geological environments host different populations of microbes and viruses?

* How do they adapt to extreme environmental conditions in order to survive?

* How does biological carbon link to the slower deep cycle, and is biologically processed carbon represented in deep-Earth reservoirs?

* Did deep biochemistry play a central role in life’s origins?

The variety of bacterial life at extreme high-pressure depths worldwide constitutes a subterranean “Galapagos,” DCO scientists say, adding that such subsurface life comprises a large portion of Earth’s total biomass — estimated in the late 1990s to be a third to a half of all life, though that figure is now considered high.

DNA has unearthed a marvel of diversity among deep single-celled micro-organisms, notably Archaea. And deep fungi-organisms with complex cell structures (eukaryotes) in the marine subsurface, have been a scientific surprise.

“Given the extraordinarily low rates of respiration, subsurface microbes must reproduce very slowly, if at all,” says Deep Life Directorate member Steven D’Hondt of the University of Rhode Island. “They take at least hundreds to thousands of years to reproduce and it’s conceivable that they live without dividing for millions to tens of millions of years,” he says. Still to be determined, Dr. D’Hondt notes, is the extent to which these organisms are “microbial zombies, incapable of being revived to a normal state.”

Sogin and MBL scientist Julie Huber, a microbial oceanographer who is also involved with the Deep Life Directorate, are this week attending the Deep Carbon Observatory’s International Science Meeting at the National Academy of Sciences in Washington, DC.

While we know approximately the thickness of Earth’s layers, the quantities of carbon below the surface in each layer remain a mystery. In fact, even the estimates of the carbon in the crust are quite uncertain. Fluxes between the layers complicate the mystery and the quest of the Deep Carbon Observatory. Credit: Deep Carbon Observatory

The symposium “Innovations in Imaging: Seeing is Believing” was organized by Amy Gladfelter of Dartmouth College, an MBL Whitman Investigator.

Fluorescence image of a living cell (MDCK) expressing septin molecules linked to green fluorescent protein (GFP). The image was recorded with the Fluorescence LC-PolScope and shows fluorescent septin fibers in color, indicating that the fluorescence is polarized and the septin molecules are aligned in the fibers. Credit: Rudolf Oldenbourg/MBL

“We are beginning to understand the basis for cell organization at unprecedented spatial and temporal resolution through the creative application of fundamental physics to microscopy,” Gladfelter stated. “This symposium will help motivate the next phase of interdisciplinary approaches to advance the visualization of life, from the scale of a single molecule to the whole organism.”

The data collected in biological images, Gladfelter noted, not only illuminates basic cellular processes, but is useful for medical purposes: to diagnose a metastasizing cancer or microbial infection, for example, or to screen chemical libraries for new pharmaceuticals.

“These images bring us to a beautiful world beyond the grasp of our normal senses,” Gladfelter stated. “In this way microscopes give us beauty and [biological or medical] application, often in the same image.”

The capacity of microscopes to reach beyond the senses is well appreciated by Oldenbourg, who spoke on New Frontiers in Polarized Light Microscopy for Live Cell Imaging.
(Oldenbourg’s MBL co-authors are Michael Shribak, Tomomi Tani, and Shinya Inoué.)

“Polarization is a basic property of light that is often overlooked, because the human eye is not sensitive to polarization. Therefore, we don’t have an intuitive understanding of it and optical phenomena that are based on polarization either elude us or we find them difficult to comprehend,” Oldenbourg stated.

“Like most scientific instruments, the polarized light microscope translates polarization effects so they can be perceived by our senses, in this case by our eyes, and makes them amenable to quantitative and analytical analysis. At the MBL, we are developing polarized light imaging techniques, including fluorescence polarization … for generating time-lapse images that clearly reveal the otherwise invisible dynamics of single molecules and molecular assemblies in organelles, cells, and tissues.”

The events of cell division during meiosis I in a living insect spermatocyte, beginning at diakinesis through telophase to the near completion of cytokinesis. Testes from the Crane fly Nephrotoma suturalis were observed with time-lapse liquid crystal polarized light microscopy (LC-PolScope, MBL, Woods Hole MA, and PerkinElmer, Hopkinton MA). Movie images display the naturally occurring birefringence of cell organelles and structures that are made up of aligned molecules, such as the meiotic spindle and mitochondria. Horizontal image width is 56 µm. Credits: James LaFountain and Rudolf Oldenbourg/MBL

Other talks in the symposium included:

Navigating the Dynamic Cell
Jennifer Lippincott-Swartz (National Institutes of Heath/MBL Physiology Course)

Imaging Three-Dimensional Dynamics in Cells and Embryos
Eric Betzig (Howard Hughes Medical Institute/MBL Physiology Course and MBL Neurobiology Course)

Structured Illumination and the Analysis of Single Molecules in Cells
Rainer Heintzmann (King’s College, London)

Imaging Single Cells in the Breast Tumor Microenvironment
John Condeelis (Albert Einstein College of Medicine)

Single Molecule Imaging in Live Cells
Amy S. Gladfelter (Dartmouth College/MBL Whitman Investigator)

The head of the marine invertebrate amphioxus (Branchiostoma floridae), magnified 15 times. Amphioxus are the most ancient of the chordates (animals whose features include a nerve cord), according to molecular analysis. They are important to the study of the origin of vertebrates. Photo by Maria del Pilar Gomez. Click for larger version.

Nasi and his wife, MBL adjunct scientist Maria del Pilar Gomez, are interested in photo-transduction, the conversion of light by light-sensitive cells into electrical signals that are sent to the brain. The lancelet, also called amphioxus, doesn’t have eyes or a true brain. But what it does have in surprising abundance is melanopsin, a photopigment that is also produced by the third class of light-sensitive cells in the mammalian retina, besides the rods and cones. This third class of cells, called “intrinsically photosensitive retinal ganglion cells” (ipRGCs), were discovered in 2002 by Brown University’s David Berson and colleagues. Now sometimes called “circadian receptors,” they are involved in non-visual, light-dependent functions, such as adjustment of the animal’s circadian rhythms.

“It seemed like colossal overkill that amphioxus have melanopsin-producing cells,” Nasi says. “These animals do nothing. If you switch on a light, they dance and float to the top of the tank, and then they drop back down to the bottom. That’s it for the day.” But that mystery aside, Gomez and Nasi realized that studying amphioxus could help reveal the evolutionary history of the circadian receptors.

Amphioxus can grow as long as 2.5 inches and are typically found half-burrowed in sand. Photo by Hans Hillewaert.

As so it has. In 2009, Gomez and Nasi isolated the animal’s melanopsin-producing cells and described how they transduce light. In their recent paper, they tackled the puzzling question of why the light response of these amphioxus cells is several orders of magnitude higher than that of their more sophisticated, presumed descendents, the ipRGCs. (In mammals, the ipRGCs relay information on light and dark to the biological clock in the hypothalamus, where it is crucial for the regulation of circadian rhythms and associated control of hormonal secretion.)

By detailing how the large light response occurs in the amphioxus cells, Gomez and Nasi could relate their observations to the functional changes that may have occurred as the circadian receptors evolved and “eventually tailored their performance to the requirements of a reporter of day and night, rather than to a light sensor meant to mediate spatial vision.” The light-sensing cells of amphioxus, they discovered, may be the ”missing link“ between the visual cells of invertebrates and the circadian receptors in our own eyes.

Citations

Ferrer C., Melagón G., del Pilar Gomez M., and Nasi E. (2012) Dissecting the Determinants of Light Sensitivity in Amphioxus Microvillar Photoreceptors: Possible Evolutionary Implications for Melanopsin Signaling. J. Neurosci. 32: 17977-17987.

del Pilar Gomez M., Angueyra J.M, and Nasi E. (2009) Light-transduction in melanopsin-expressing photoreceptors of Amphioxus. PNAS 16: 9081-9086.

Enrico Nasi and Maria Gomez (second and third from left) with some of their students from the Universidad Nacional, de Colombia, where they hold faculty appointments. Nasi and Gomez regularly bring students to the MBL, where they are affiliated with the Program in Sensory Physiology and Behavior in addition to Cellular Dynamics.

A federal advisory committee chaired by MBL Distinguished Scientist Jerry M. Melillo has released a draft of the  Third National Climate Assessment Report  for public comment. The report presents the latest science about the current and projected effects of climate change across the United States. It is a scientific document—not a policy document—and does not make recommendations regarding responses to climate change. It does, however, describe some of the actions that society is already taking, and can take, to adapt to and mitigate climate change.

“Climate change is already affecting the American people,” the report begins. “Certain types of weather events have become more frequent and/or intense, including heat waves, heavy downpours, and, in some regions, floods and droughts. Sea level is rising, oceans are becoming more acidic, and glaciers and sea ice are melting. These changes are part of the pattern of global climate change, which is primarily driven by human activity.”

The draft then details climate change impacts on specific U.S. regions and sectors, including agriculture and human health, based on input from more than 240 scientist-authors.

The draft report is available for download at http://ncadac.globalchange.gov. Public comments will be accepted until April 12, 2013 and must submitted online. In addition to the public review, the report will also undergo a review by the National Academies of Sciences. The authors will use the public comments to revise the report before submitting it to the federal government for consideration in the Third National Climate Assessment (NCA) Report (to be published in early 2014).

Dr. Melillo’s research focuses on the impacts of human activities on terrestrial ecosystems. He has studied carbon and nitrogen cycling in ecosystems across the globe and has played a prominent role in international climate change policy throughout his career. In 2009, Dr. Melillo co-authored the landmark report to Congress, “Global Climate Change Impacts in the United States,” issued by the U.S. Global Change Research Program. He was also a lead author on both the 1990 and 1995 Assessment Reports of the Intergovernmental Panel on Climate Change (IPCC), and he served in President Clinton’s Office of Science and Technology Policy from 1996 to 1997.

The Global Change Research Act of 1990 requires a National Climate Assessment at least every four years.

Snow falls on an experimental plot at Harvard Forest in Petersham, Mass., where Jerry Melillo and colleagues have studied how warming temperatures affect carbon and nitrogen cycling in soil and vegetation. Photo courtesy of Jerry Melillo. Click here for full-size image

In the case of the MBL Physiology course, one outcome has been—paradoxically—an extraordinary level of new knowledge and publications generated by student-and-faculty teams.

In the Dec. 21 issue of Science magazine, several scientists who have directed the Physiology course detail their winning formula for instilling in students the passion for and ability to conduct “real research,” as lead author Ron Vale of University of California, San Francisco, describes it.

The article presents the overwhelmingly positive feedback from a poll of Physiology course alumni from 2004 to 2010; and the remarkable list of 23 research papers and 59 meeting abstracts that developed out of Physiology course projects from 2005 to 2012.

Physiology course students, faculty, and family members with a sand sculpture they made of the mitotic spindle. Photo courtesy of Ron Vale.

Vale and Tim Mitchison of Harvard Medical School co-directed the Physiology course from 2004 to 2009 and revamped it in significant ways: (1) an equal number of students from cell biology and from physical sciences are admitted (2) students go through a “boot camp” to learn research techniques outside their fields and to begin thinking and stretching beyond their comfort zones (3) faculty give students the kernel of a “real” research problem – not an exercise – and the students develop an experimental plan, reporting back on what they found at the end of 11 intense days (often working 14 hours a day!)

And if they find nothing? Not a problem! “That’s most of what is going on!” Vale says. “Learning from failure is a crucial part of being a scientist.” The atmosphere the course intentionally creates is “intense, yet low-risk,” minimizing “the fear of failure or of appearing ignorant, factors that impede students, as well as senior scientists, from venturing into new fields or learning new approaches,” the article states.

Very often, students and faculty become so inspired by a research problem that they continue to work on it after the course ends, at their home institutions. That is how the seven-week Physiology course has generated so many publications.

The positive impact on students is evident from the alumni poll, which includes comments like, “I am now much more likely to try new experiments even though they seem nearly impossible. This attitude has had a very positive influence on the fun I have being a scientist, which is also reflected in the results.”

“People have a tremendous amount of fun in the Physiology course, whether their project gets a good result or not,” Vale says. “They appreciate the experience of going after a real research problem, of being surrounded by faculty and fellow students who are excited by the thrill of the chase … We are trying to learn something new, and we don’t necessarily know how to get there. That is science!”

The current co-directors of the Physiology course, Dyche Mullins of University of California, San Francisco, and Clare Waterman of the National Heart Lung and Blood Institute, have preserved the basic structure and spirit that Vale and Mitchison brought to the course.

Physiology is one of 22 courses the MBL offers for advanced, laboratory-based research training in fields such as cellular physiology, embryology, neurobiology, and microbiology.

Citation:

Vale RD, DeRisi J, Phillips R, Mullins RD, Waterman C, and Mitchison TJ (2012) Interdisciplinary Graduate Training in Teaching Labs. Science 338: 1542-1543.