From The University of Delaware
And
The University of California-San Diego
6.27.24
Karen B. Roberts
Photos courtesy of the Lyman group and Jacob Winnikoff/UC San Diego
Animation by Sasiri Vargas-Urbano
This deep-sea ctenophore is about the size of a tennis ball and thrives two miles below the sea surface. Its scientific genus is Bathocyroe, which translates to “master of the deep.” University of Delaware researchers were part of a multi-institutional study that explored how these marine animals survive at extreme pressures.
UD researchers and collaborators explore how deep-sea animals perform under pressure.
A multi-institutional team that includes researchers from the University of Delaware, University of California San Diego and Monterey Bay Aquarium Research Institute (MBARI), among others, published a paper in Science on Thursday, June 27, that provides new insight on how deep-sea “comb jellies” called ctenophores adapt and survive at extreme pressures.
It turns out that part of the adaptation involves lipids, fatty chemical compounds found in the membrane of all living cells that perform essential functions, including storing energy, sending signals and controlling what passes through the cell membrane.
The work provides new knowledge about how marine organisms can adapt and survive in the ocean, now and potentially into the future. It also may inform what’s known about the human body — in particular, how a specific lipid called plasmalogen found in nerve cells might work in our brains.
UD biophysicist Edward Lyman and doctoral students Sasiri Vargas-Urbano and Miguel Pedraza Joya are among the co-authors on the paper. Other co-authors include first-author Jacob Winnikoff, a researcher at MBARI and University of California, Santa Cruz and San Diego, now at Harvard University, Steven Haddock, an MBARI marine biologist, and the project principal investigator Itay Budin, an assistant professor of chemistry and biochemistry at UC San Diego. Additional collaborators include researchers from UCSD Health Sciences, University of California Santa Cruz, the National Institutes of Health and Cornell Center for High Energy X-ray Sciences.
Adapting under extreme pressure
Ctenophores are predators found at various depths in the ocean, where they help regulate the marine ecosystem by eating fish and shellfish larvae, while serving as a food source for other marine animals. If you go back in time, UD’s Lyman said, the first thing that branches off from the rest of the animals is the ctenophores — a result just established last year by co-author Haddock.
“This means that you and I are more closely related to a jellyfish than a jellyfish is to a ctenophore,” Lyman said.
The deep ocean, meanwhile, is characterized by low temperature and high pressure. Lyman explained that ctenophores are great for teasing apart this problem of how marine organisms adapt to extreme pressure environments because there are multiple ctenophore species that live at the surface, up to two and half miles deep in the ocean, and only at the surface in the Arctic, where the temperature is generally the same as in the deep sea.
“Studying ctenophores, you can compare those organisms in a way that’s roughly controlled for temperature and now you can look at how the organism adapts only to changes in pressure,” said Lyman, a UD professor of physics and astronomy with expertise using molecular dynamics simulations to characterize lipids.
Haddock’s team at MBARI collected samples of 17 different species of ctenophores that live in different parts of the ocean and Budin’s lab analyzed their lipidomes — the chemical species found in the cell membrane — in an extensive survey.
In the work, the collaborative researchers compared the chemical composition of shallow- and deep-sea dwelling ctenophores and found an adaptation in the cellular membrane of those living in the deep that enables them to survive under extreme pressures. Budin’s preliminary research revealed that deep-sea ctenophores have a huge abundance of a particular type of lipid molecule called plasmalogen, which is present in our own membranes in small amounts.
“What makes plasmalogen lipids interesting is that they allow cell membranes to bend and deform, even in the deep ocean at high pressure, where membranes would otherwise be very stiff, and that’s a useful adaptation,” said Lyman.
Of molecules and membranes
A fundamental function of membranes is to let things in and out a cell or to enable cell division to replicate genetic material. To do this, the cell membrane must go from a generally flat state to one that is highly curved, so the researchers ran experiments and simulations to measure the shape of plasmalogen molecules under different conditions. This is because while all membranes are made from a mixture of different kinds of lipids, it’s the chemistry of a lipid molecule that determines whether it wants to reside in a membrane that’s flat or curved.
UD’s Vargas-Urbano leveraged molecular dynamics and the massive computational power of National Science Foundation supercomputers to model all the structures inside the ctenophore membranes and simulate how the molecules would move and interact with each other at high pressures. The process took a great deal of time.
“Simulations that are about 500 nanoseconds long could take about a month to create from the data,” said Vargas-Urbano. That’s the equivalent of a movie clip that lasts about 500 billionths of a second.
Meanwhile, Budin and Winnikoff used a special X-ray scattering beam line at Cornell to experimentally study how the structure of ctenophore membranes changed under various pressures. Looking at the structural properties of the lipid mixtures directly from the organisms at high-pressure was a crucial part of the project that helped the researchers discern that ctenophore lipidomes are specialized for high pressure.
The deep sea is under extreme pressures equal to that of hundreds of atmospheres, due to the weight of the water that lies above. Budin’s team at UC San Diego learned that if they exposed the cell membrane of E. coli, a human gut bacteria, to pressures found where the deepest ctenophore live (roughly 500 times the water pressure found on the ocean surface) then the microbes’ growth was severely restricted, Lyman said. However, when the researchers gave E. coli the ability to synthesize plasmalogen lipids and pressurized them the same way, then the cells could grow and divide normally.
Simulating the membrane in the computer and testing it under various temperatures and pressures across various timeframes allowed the UD team to validate that it is the plasmalogen lipids that keep the membranes fluid and deformable at high pressure.
“Using molecular-dynamic simulations to explore this system, we were able to test conditions that would be found even deeper in the sea than these ctenophore species actually live to see what happened,” said Vargas-Urbano.
This is because the deep-sea ctenophores contained more plasmalogen lipids in their cell membranes than other ctenophore species found at the sea surface and in the Arctic. In particular, the deep-dwelling ctenophores had higher concentrations of a plasmalogen known as PPE, which is characterized by a distinct cone shape. Simulations by the UD research team and artificial membrane experiments by Budin and Winnikoff showed the more PPE plasmalogen was present, the more the membranes curled up, even at low pressures.
One surprising result from the research, Lyman said, is that when they plotted the 17 ctenophore species studied, the researchers discovered a significant correlation between how much plasmalogen is found in the species’ cellular membrane and where it can live.
“If you take a deep-sea ctenophore and bring it to the surface, its membrane bends like crazy and that’s no good. If you take a surface-dwelling ctenophore and bring it to the deep, its membrane won’t bend anymore, also not good,” Lyman said.
But when the researchers compared the membrane of ctenophores living in surface waters and their deep-sea cousins in their natural environments, the species had similar properties in terms of how the molecules inside the cells adjust to keep the membrane stable.
The researchers called this effect “homeocurvature adaptation,” because the ctenophores—and their lipidomes—had adapted to the situation that they’re living in. This understanding may help explain a long-standing mystery of why deep-sea invertebrates, including ctenophores, disintegrate at the surface no matter how carefully they are handled. It seems in some cases the membranes actually are held together by the extreme pressure.
Human health implications of the work
Knowing how life adapts to high pressure and extreme environments such as the ocean can also inform what is known about the human body. Lyman explained that plasmalogen lipids present in ctenophores also are found in our bodies, most abundantly in neural tissue.
“Nerve cells in the brain transmit messages by sending chemicals from one cell to another. And there is an awful lot of plasmalogen at the site where all that synaptic transmission is happening in your neurons,” said Lyman.
The loss of plasmalogen is known to be associated with conditions such as Alzheimer’s disease, making new insights about the unique properties of plasmalogen lipids potentially useful in other areas of research.
Full list of authors: Daniel Milshteyn, Edward Dennis, Aaron Armando, Oswald Quehenberger and Itay Budin (all UC San Diego); Jacob Winnikoff (Harvard University); Sasiri J. Vargas-Urbano, Miguel Pedraza Joya and Edward Lyman (all University of Delaware); Alexander Sodt (National Institute of Child Health and Human Development); Richard E. Gillilan (Cornell University); and Steven H.D. Haddock (MBARI).
See the full article here .
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The University of California-San Diego is a public land-grant research university in San Diego, California. Established in 1960 near the pre-existing Scripps Institution of Oceanography, The University of California-San Diego is the southernmost of the ten campuses of the University of California, and offers over 200 undergraduate and graduate degree programs. The University of California-San Diego occupies 2,178 acres (881 ha) near the coast of the Pacific Ocean, with the main campus resting on approximately 1,152 acres (466 ha). The University of California-San Diego is ranked among the best universities in the world by major college and university rankings.
The University of California-San Diego consists of twelve undergraduate, graduate and professional schools as well as seven undergraduate residential colleges. It regularly receives over 140,000 applications for undergraduate admissions. The University of California-San Diego San Diego Health, the region’s only academic health system, provides patient care, conducts medical research and educates future health care professionals at The University of California-San Diego Medical Center, Hillcrest, Jacobs Medical Center, Moores Cancer Center, Sulpizio Cardiovascular Center, Shiley Eye Institute, Institute for Genomic Medicine, Koman Family Outpatient Pavilion and various express care and urgent care clinics throughout San Diego.
The University of California-San Diego operates 19 organized research units as well as eight School of Medicine research units, six research centers at Scripps Institution of Oceanography and two multi-campus initiatives. The University of California-San Diego is also closely affiliated with several regional research centers, such as The Salk Institute, the Sanford Burnham Prebys Medical Discovery Institute, the Sanford Consortium for Regenerative Medicine, and The Scripps Research Institute. It is classified among “R1: Doctoral Universities – Very high research activity”.
The University of California-San Diego is considered one of the country’s “Public Ivies”. The University of California-San Diego faculty, researchers, and alumni have won Nobel Prizes as well as Fields Medals, National Medals of Science, MacArthur Fellowships, and Pulitzer Prizes. Additionally, of the current faculty, a number have been elected to The National Academy of Engineering, The National Academy of Sciences, The National Academy of Medicine and to The American Academy of Arts and Sciences.
History
When the Regents of the University of California originally authorized The University of California-San Diego campus in 1956, it was planned to be a graduate and research institution, providing instruction in the sciences, mathematics, and engineering. Local citizens supported the idea, voting the same year to transfer to the university 59 acres (24 ha) of mesa land on the coast near the preexisting Scripps Institution of Oceanography. The Regents requested an additional gift of 550 acres (220 ha) of undeveloped mesa land northeast of Scripps, as well as 500 acres (200 ha) on the former site of Camp Matthews from the federal government, but Roger Revelle, then director of Scripps Institution and main advocate for establishing the new campus, jeopardized the site selection by exposing the La Jolla community’s exclusive real estate business practices, which were antagonistic to minority racial and religious groups. This outraged local conservatives, as well as Regent Edwin W. Pauley.
University of California President Clark Kerr satisfied San Diego city donors by changing the proposed name from University of California, La Jolla, to University of California-San Diego. The city voted in agreement to its part in 1958, and the University of California approved construction of the new campus in 1960. Because of the clash with Pauley, Revelle was not made chancellor. Herbert York, first director of The DOE’s Lawrence Livermore National Laboratory, was designated instead. York planned the main campus according to the “Oxbridge” model, relying on many of Revelle’s ideas.
According to Kerr, “San Diego always asked for the best,” though this created much friction throughout the University of California system, including with Kerr himself, because The University of California-San Diego often seemed to be “asking for too much and too fast.” Kerr attributed The University of California-San Diego’s “special personality” to Scripps, which for over five decades had been the most isolated University of California unit in every sense: geographically, financially, and institutionally. It was a great shock to the Scripps community to learn that Scripps was now expected to become the nucleus of a new University of California campus and would now be the object of far more attention from both the university administration in Berkeley and the state government in Sacramento.
The University of California-San Diego was the first general campus of the University of California to be designed “from the top down” in terms of research emphasis. Local leaders disagreed on whether the new school should be a technical research institute or a more broadly based school that included undergraduates as well. John Jay Hopkins of General Dynamics Corporation pledged one million dollars for the former while the City Council offered free land for the latter. The original authorization for The University of California-San Diego campus given by the University of California Regents in 1956 approved a “graduate program in science and technology” that included undergraduate programs, a compromise that won both the support of General Dynamics and the city voters’ approval.
Nobel laureate Harold Urey, a physicist from the University of Chicago, and Hans Suess, who had published the first paper on the greenhouse effect with Revelle in the previous year, were early recruits to the faculty in 1958. Maria Goeppert-Mayer, later the second female Nobel laureate in physics, was appointed professor of physics in 1960. The graduate division of the school opened in 1960 with 20 faculty in residence, with instruction offered in the fields of physics, biology, chemistry, and earth science. Before the main campus completed construction, classes were held in the Scripps Institution of Oceanography.
By 1963, new facilities on the mesa had been finished for the School of Science and Engineering, and new buildings were under construction for Social Sciences and Humanities. Ten additional faculty in those disciplines were hired, and the whole site was designated the First College, later renamed after Roger Revelle, of the new campus. York resigned as chancellor that year and was replaced by John Semple Galbraith. The undergraduate program accepted its first class of 181 freshman at Revelle College in 1964. Second College was founded in 1964, on the land deeded by the federal government, and named after environmentalist John Muir two years later. The University of California-San Diego School of Medicine also accepted its first students in 1966.
Political theorist Herbert Marcuse joined the faculty in 1965. A champion of the New Left, he reportedly was the first protester to occupy the administration building in a demonstration organized by his student, political activist Angela Davis. The American Legion offered to buy out the remainder of Marcuse’s contract for $20,000; the Regents censured Chancellor William J. McGill for defending Marcuse on the basis of academic freedom, but further action was averted after local leaders expressed support for Marcuse. Further student unrest was felt at the university, as the United States increased its involvement in the Vietnam War during the mid-1960s, when a student raised a Viet Minh flag over the campus. Protests escalated as the war continued and were only exacerbated after the National Guard fired on student protesters at Kent State University in 1970. Over 200 students occupied Urey Hall, with one student setting himself on fire in protest of the war.
Early research activity and faculty quality, notably in the sciences, was integral to shaping the focus and culture of the university. Even before The University of California-San Diego had its own campus, faculty recruits had already made significant research breakthroughs, such as the Keeling Curve, a graph that plots rapidly increasing carbon dioxide levels in the atmosphere and was the first significant evidence for global climate change; the Kohn–Sham equations, used to investigate particular atoms and molecules in quantum chemistry; and the Miller–Urey experiment, which gave birth to the field of prebiotic chemistry.
Engineering, particularly computer science, became an important part of the university’s academics as it matured. University researchers helped develop The University of California-San Diego Pascal, an early machine-independent programming language that later heavily influenced Java; the National Science Foundation Network, a precursor to the Internet; and the Network News Transfer Protocol during the late 1970s to 1980s. In economics, the methods for analyzing economic time series with time-varying volatility (ARCH), and with common trends (co-integration) were developed. The University of California-San Diego maintained its research intense character after its founding, racking up many Nobel Laureates affiliated within 50 years of history.
Under Richard C. Atkinson’s leadership as chancellor from 1980 to 1995, The University of California-San Diego strengthened its ties with the city of San Diego by encouraging technology transfer with developing companies, transforming San Diego into a world leader in technology-based industries. He oversaw a rapid expansion of the School of Engineering, later renamed after Qualcomm founder Irwin M. Jacobs, with the construction of the San Diego Supercomputer Center and establishment of the computer science, electrical engineering, and bioengineering departments. Private donations increased from $15 million to nearly $50 million annually, faculty expanded by nearly 50%, and enrollment grew during his administration. By the end of his chancellorship, the quality of The University of California-San Diego graduate programs was ranked highly in the nation by The National Research Council.
The University of California-San Diego continued to undergo further expansion during the first decade of the new millennium with the establishment and construction of two new professional schools — the Skaggs School of Pharmacy and Rady School of Management—and the California Institute for Telecommunications and Information Technology, a research institute run jointly with University of California-Irvine. The University of California-San Diego also reached two financial milestones during this time, becoming the first university in the western region to raise over $1 billion in its eight-year fundraising campaign in 2007 and also obtaining an additional $1 billion through research contracts and grants in a single fiscal year for the first time. Despite this, due to the California budget crisis, the university loaned $40 million against its own assets in 2009 to offset a significant reduction in state educational appropriations. The salary of Pradeep Khosla, who became chancellor in 2012, has been the subject of controversy amidst continued budget cuts and tuition increases.
On November 27, 2017, The University of California-San Diego announced it would leave its longtime athletic home of the California Collegiate Athletic Association, an NCAA Division II league, to begin a transition to Division I in 2020. At that time, it would join the Big West Conference, already home to four other UC campuses (Davis, Irvine, Riverside, and Santa Barbara). The transition period would run through the 2023–24 school year. The university prepared to transition to NCAA Division I competition on July 1, 2020.
Research
Applied Physics and Mathematics
The Nature Index lists The University of California-San Diego highly in the United States for research output by article count. The university operates several organized research units, including the Center for Astrophysics and Space Sciences (CASS), the Center for Drug Discovery Innovation, and the Institute for Neural Computation. The University of California-San Diego also maintains close ties to the nearby Scripps Research Institute and Salk Institute for Biological Studies. In 1977, The University of California-San Diego developed and released the University of California-San Diego Pascal programming language. The university was designated as one of the original national Alzheimer’s disease research centers in 1984 by the National Institute on Aging. In 2018, The University of California-San Diego received $10.5 million from The DOE’s National Nuclear Security Administration to establish the Center for Matters under Extreme Pressure (CMEC).
The University of California-San Diego founded The San Diego Supercomputer Center in 1985, which provides high performance computing for research in various scientific disciplines. In 2000, The University of California-San Diego partnered with The University of California-Irvine to create the Qualcomm Institute, which integrates research in photonics, nanotechnology, and wireless telecommunication to develop solutions to problems in energy, health, and the environment.
The University of California-San Diego also operates the Scripps Institution of Oceanography, one of the largest centers of research in earth science in the world, which predates the university itself. Together, SDSC and SIO, along with funding partner universities California Institute of Technology, San Diego State University, and The University of California-Santa Barbara, manage the High Performance Wireless Research and Education Network.
The University of Delaware is a public land-grant research university located in Newark, Delaware. University of Delaware (US) is the largest university in Delaware. It offers three associate’s programs, 148 bachelor’s programs, 121 master’s programs (with 13 joint degrees), and 55 doctoral programs across its eight colleges. The main campus is in Newark, with satellite campuses in Dover, the Wilmington area, Lewes, and Georgetown. It is considered a large institution with approximately 18,200 undergraduate and 4,200 graduate students. It is a privately governed university which receives public funding for being a land-grant, sea-grant, and space-grant state-supported research institution.
The University of Delaware is classified among “R1: Doctoral Universities – Very high research activity”. It is recognized with the Community Engagement Classification by the Carnegie Foundation for the Advancement of Teaching.
The University of Delaware is one of only four schools in North America with a major in art conservation. In 1923, it was the first American university to offer a study-abroad program.
The University of Delaware traces its origins to a “Free School,” founded in New London, Pennsylvania in 1743. The school moved to Newark, Delaware by 1765, becoming the Newark Academy. The academy trustees secured a charter for Newark College in 1833 and the academy became part of the college, which changed its name to Delaware College in 1843. While it is not considered one of the colonial colleges because it was not a chartered institution of higher education during the colonial era, its original class of ten students included George Read, Thomas McKean, and James Smith, all three of whom went on to sign the Declaration of Independence. Read also later signed the United States Constitution.
Science, Technology and Advanced Research (STAR) Campus
On October 23, 2009, The University of Delaware signed an agreement with Chrysler to purchase a shuttered vehicle assembly plant adjacent to the university for $24.25 million as part of Chrysler’s bankruptcy restructuring plan. The university has developed the 272-acre (1.10 km^2) site into the Science, Technology and Advanced Research (STAR) Campus. The site is the new home of University of Delaware’s College of Health Sciences, which includes teaching and research laboratories and several public health clinics. The STAR Campus also includes research facilities for University of Delaware’s vehicle-to-grid technology, as well as Delaware Technology Park, SevOne, CareNow, Independent Prosthetics and Orthotics, and the East Coast headquarters of Bloom Energy. The University of Delaware opened the Ammon Pinozzotto Biopharmaceutical Innovation Center, which will become the new home of the UD-led National Institute for Innovation in Manufacturing Biopharmaceuticals. Also, Chemours recently opened its global research and development facility, known as the Discovery Hub, on the STAR Campus in 2020. The new Newark Regional Transportation Center on the STAR Campus will serve passengers of Amtrak and regional rail.
Academics
The university is organized into nine colleges:
Alfred Lerner College of Business and Economics
College of Agriculture and Natural Resources
College of Arts and Sciences
College of Earth, Ocean and Environment
College of Education and Human Development
College of Engineering
College of Health Sciences
Graduate College
Honors College
There are also five schools:
Joseph R. Biden, Jr. School of Public Policy and Administration (part of the College of Arts & Sciences)
School of Education (part of the College of Education & Human Development)
School of Marine Science and Policy (part of the College of Earth, Ocean and Environment)
School of Nursing (part of the College of Health Sciences)
School of Music (part of the College of Arts & Sciences)
sciencesprings 