From The University of Arizona: “World Water Day brings work of UArizona researcher into focus” Raina Maier

From The University of Arizona

3.20.24
Media contact
Niranjana Rajalakshmi
Science Writer, University Communications
niranjanar@arizona.edu
917-415-3497

Researcher contact
Raina Maier
Department of Environmental Science
rmaier@arizona.edu
520-621-7231

Ahead of World Water Day on Friday, environmental science professor Raina Maier discusses the use of microbial surfactants or soaps for water remediation.

An acidic red lake that formed in the pit of an abandoned copper mine in Cyprus.

Raina Maier, a University of Arizona professor of environmental science, has a special connection to World Water Day. Her research in environmental microbiology and water remediation is positioned squarely at the confluence of science, sustainability and societal well-being.

World Water Day, officially designated in 1993 by the United Nations, is observed annually on March 22. The day was intended to inspire action regarding the global water crisis, with the ultimate focus being “water and sanitation for all by 2030.”

Raina Maier

This year’s “Water for Peace” campaign highlights how water scarcity, pollution and unequal access can exacerbate tensions between communities and nations.

Maier’s work focuses on the crucial role of microorganisms in water and soil environments and their application in metal extraction and environmental cleanup. In this Q&A, she talks about the microbially produced surfactants or soaps, their role in recovering critical metals from water streams and the biosurfactants’ overall effect on water treatment.

Q: Could you elaborate on the significance of using microbes for critical metal recovery?

A: A critical metal is a metal needed for electrification of society. They are important for making copper wires, batteries and electronics in general. As we transition from petroleum-based energy towards green energy and infrastructure, we need a growing amount of these metals. In collaboration with scientists from Clemson University and Georgia Tech University, we did a first analysis of the natural and waste waters in the U.S. and found that a significant portion of the U.S. demand for the critical rare earth elements could be met by harvesting the elements from these water sources.

That would reduce the need for hard rock mining, which requires large amounts of energy and water to take rock out of the ground, crush and extract metals from it. Harvesting metals directly from natural and waste waters has the potential to save a lot of energy. We are developing a harvesting technology that uses surfactants or soaps that are made by bacteria. In collaboration with University of Arizona chemists, we now can make these bacterial surfactants synthetically and apply them to selectively take the rare earth elements out of wastewater solutions. We are working with several mining companies who are interested in the technology to harvest metals from mining waste streams and want to help us move it along to commercialization.

Q: Can you explain in detail about how these biosurfactants capture metals?

A: I got interested in biosurfactants as a graduate student and continued studying them as a new faculty member at the University of Arizona. One of the discoveries my lab made in the early 1990s was that these surfactants could bind metals, thanks to the fact that the surfactants have complex structures that create a metal-binding pocket. The pocket is just the right size, so that it fits and binds large metals like rare earth elements better than common soil and water ions like calcium or magnesium. We have worked over the years to understand this metal binding and to develop technologies to recover metals from real world solutions.

Q: What type of microbes are they? How does this metal recovery work on a large scale?

A: Our initial work focused on a bacterial surfactant called rhamnolipid, which is produced by Pseudomonas aeruginosa and related species. Rhamnolipids have either one or two fatty acid or lipid tails that don’t like to mix with water, and one or two sugar heads that do like to mix with water. Bacterial rhamnolipids come as complex mixtures of 40 or more different rhamnolipids — the tails might be longer or shorter, or there could be one or two sugars, for instance. So, there is batch-to-batch variability when you produce these microbially. The thought behind making them synthetically is that not only can one make a single rhamnolipid, but one can choose the surfactant you want to make and make it with high purity and in large quantity. So, the ability to make these surfactants synthetically has opened a new door, because we now can choose the structure we want to make. We’re working with modelers at the University of Arizona to make rhamnolipid-like surfactants with different size pockets. This research is based on the hypothesis that we can tune the structure of the surfactant pocket to be selective for a particular metal or a rare earth element.

Q: Do these biosurfactants produce a qualitative change in the water streams?

A: Wastewater from mining activities, including acid mine drainage, contains a large variety of metals. It is estimated that acid mine drainage affects and degrades the quality of 10,000 miles of waterways in the United States. We are currently working with mining companies to create treatment platforms that would allow us to sequentially remove all metals from these mining waste streams to produce water that can be reused or returned to the environment. This involves using a variety of approaches and steps to first separate metals from each other and then recover them for reuse or disposal. The bioinspired surfactants are part of the last steps of this technology and are applied to selectively remove metals, like the rare earth elements, that are of value for reuse.

Q: Has critical metal recovery using biosurfactants been implemented already?

A: It has not been implemented in the field yet. But we have groundwater samples from the U.S. Department of Energy that contain uranium and we have several mining company wastewaters that are very complex with a multitude of metals at very different concentrations. We are working to develop strategies on these actual samples. So we moved from very fundamental research for understanding the surfactant-metal interactions, to working with model metal mixture solutions we’ve created in the lab, to now working with real world solutions. The next step is to build and test a pilot scale facility in the field, which is what we’re hoping to do soon.

Q: What other applications do these biosurfactants have pertaining to water?

A: These biosurfactants are truly amazing molecules. We have found that they have application for use in dust suppression. Right now, mining companies suppress dust on their roads and mine tailings piles by watering several times a day. But water is a precious commodity. So, we are testing adding these same surfactants to the water. These surfactants help for a crust formation on the mine tailings surface that reduces the need for such frequent water application.

Another area of interest is the treatment of groundwater that is contaminated with uranium. We have many such sites on the Navajo Nation in Arizona. Many of these communities don’t have access to advanced water treatment systems, so our team envisions building column systems packed with these surfactants that could locally treat groundwater to remove uranium and provide potable water.

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct.

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Please help promote STEM in your local schools.

Stem Education Coalition

The University of Arizona enrolls over 49,000 students in 19 separate colleges/schools, including The University of Arizona College of Medicine in Tucson and Phoenix and the James E. Rogers College of Law, and is affiliated with two academic medical centers (Banner – University Medical Center Tucson and Banner – University Medical Center Phoenix). The University of Arizona is one of three universities governed by the Arizona Board of Regents. The university is part of the Association of American Universities and is the only member from Arizona, and also part of the Universities Research Association.

Known as the Arizona Wildcats (often shortened to “Cats”), The University of Arizona’s intercollegiate athletic teams are members of the Pac-12 Conference of the NCAA. The University of Arizona athletes have won national titles in several sports, most notably men’s basketball, baseball, and softball. The official colors of the university and its athletic teams are cardinal red and navy blue.

After the passage of the Morrill Land-Grant Act of 1862, the push for a university in Arizona grew. The Arizona Territory’s “Thieving Thirteenth” Legislature approved The University of Arizona in 1885 and selected the city of Tucson to receive the appropriation to build the university. Tucson hoped to receive the appropriation for the territory’s mental hospital, which carried a $100,000 allocation instead of the $25,000 allotted to the territory’s only university Arizona State University was also chartered in 1885, but it was created as Arizona’s normal school, and not a university). Flooding on the Salt River delayed Tucson’s legislators, and by the time they reached Prescott, back-room deals allocating the most desirable territorial institutions had been made. Tucson was largely disappointed with receiving what was viewed as an inferior prize.

With no parties willing to provide land for the new institution, the citizens of Tucson prepared to return the money to the Territorial Legislature until two gamblers and a saloon keeper decided to donate the land to build the school. Construction of Old Main, the first building on campus, began on October 27, 1887, and classes met for the first time in 1891 with 32 students in Old Main, which is still in use today. Because there were no high schools in Arizona Territory, the university maintained separate preparatory classes for the first 23 years of operation.

Research

The University of Arizona is classified among “R1: Doctoral Universities – Very high research activity”. UArizona is the fourth most awarded public university by National Aeronautics and Space Administration for research. The University of Arizona was awarded over $300 million for its Lunar and Planetary Laboratory (LPL) to lead NASA’s 2007–08 mission to Mars to explore the Martian Arctic, and $800 million for its OSIRIS-REx mission, the first in U.S. history to sample an asteroid.

National Aeronautics Space Agency UArizona OSIRIS-REx Spacecraft.

The LPL’s work in the Cassini spacecraft orbit around Saturn is larger than any other university globally.

National Aeronautics and Space Administration/European Space Agency [La Agencia Espacial Europea][Agence spatiale européenne][Europäische Weltraumorganization](EU)/ASI Italian Space Agency [Agenzia Spaziale Italiana](IT) Cassini Spacecraft.

The University of Arizona laboratory designed and operated the atmospheric radiation investigations and imaging on the probe. The University of Arizona operates the HiRISE camera, a part of the Mars Reconnaissance Orbiter.

U Arizona NASA Mars Reconnaisance HiRISE Camera.

NASA Mars Reconnaissance Orbiter.

While using the HiRISE camera in 2011, University of Arizona alumnus Lujendra Ojha and his team discovered proof of liquid water on the surface of Mars—a discovery confirmed by NASA in 2015.

The University of Arizona receives more NASA grants annually than the next nine top NASA/JPL-Caltech-funded universities combined. The University of Arizona’s Lunar and Planetary Laboratory is actively involved in ten spacecraft missions: Cassini VIMS; Grail; the HiRISE camera orbiting Mars; the Juno mission orbiting Jupiter; Lunar Reconnaissance Orbiter (LRO); Maven, which will explore Mars’ upper atmosphere and interactions with the sun; Solar Probe Plus, a historic mission into the Sun’s atmosphere for the first time; Rosetta’s VIRTIS; WISE; and OSIRIS-REx, the first U.S. sample-return mission to a near-earth asteroid, which launched on September 8, 2016.

NASA – GRAIL [Gravity Recovery and Interior Laboratory] Flying in Formation. Artist’s Concept. Credit: NASA.

National Aeronautics Space Agency Juno at Jupiter.

NASA Lunar Reconnaissance Orbiter.

NASA Mars MAVEN.

NASA/Mars MAVEN

NASA Parker Solar Probe Plus named to honor Pioneering Physicist Eugene Parker. The Johns Hopkins University Applied Physics Lab.

NASA Parker Solar Probe Plus named to honor Pioneering Physicist Eugene Parker. The Johns Hopkins University Applied Physics Lab annotated.

National Aeronautics and Space Administration Wise/NEOWISE Telescope.

The University of Arizona students have been selected as Truman, Rhodes, Goldwater, and Fulbright Scholars. According to The Chronicle of Higher Education, UArizona is among the top producers of Fulbright awards.

The University of Arizona is a member of the Association of Universities for Research in Astronomy , a consortium of institutions pursuing research in astronomy. The association operates observatories and telescopes, notably Kitt Peak National Observatory just outside Tucson.

NSF NOIRLab NOAO Kitt Peak National Observatory on Kitt Peak in the Quinlan Mountains in the Arizona-Sonoran Desert on the Tohono O’odham Nation, 88 kilometers (55 mi) west-southwest of Tucson, Altitude 2,096 m (6,877 ft). annotated.

Led by Roger Angel, researchers in the Steward Observatory Mirror Lab at The University of Arizona are working in concert to build the world’s most advanced telescope. Known as the Giant Magellan Telescope (CL), it will produce images 10 times sharper than those from the Earth-orbiting Hubble Telescope.

Gregorian Optical Giant Magellan Telescope(CL) 21 meters, to be at the Carnegie Institution for Science’s Las Campanas Observatory(CL) some 115 km (71 mi) north-northeast of La Serena, Chile, over 2,500 m (8,200 ft) high. Credit: Giant Magellan Telescope–GMTO Corporation.

GMT will ultimately cost $1 billion. Researchers from at least nine institutions are working to secure the funding for the project. The telescope will include seven 18-ton mirrors capable of providing clear images of volcanoes and riverbeds on Mars and mountains on the moon at a rate 40 times faster than the world’s current large telescopes. The mirrors of the Giant Magellan Telescope will be built at The University of Arizona and transported to a permanent mountaintop site in the Chilean Andes where the telescope will be constructed.

Reaching Mars in March 2006, the Mars Reconnaissance Orbiter contained the HiRISE camera, with Principal Investigator Alfred McEwen as the lead on the project. This National Aeronautics and Space Agency mission to Mars carrying the UArizona-designed camera is capturing the highest-resolution images of the planet ever seen. The journey of the orbiter was 300 million miles. In August 2007, The University of Arizona, under the charge of Scientist Peter Smith, led the Phoenix Mars Mission, the first mission completely controlled by a university. Reaching the planet’s surface in May 2008, the mission’s purpose was to improve knowledge of the Martian Arctic. The Arizona Radio Observatory , a part of The University of Arizona Department of Astronomy Steward Observatory , operates the Submillimeter Telescope on Mount Graham.

U Arizona Submillimeter Telescope located on Mt. Graham near Safford, Arizona, Altitude 3,191 m (10,469 ft)

NRAO 12m Arizona Radio Telescope, at U Arizona Department of Astronomy and Steward Observatory at Kitt Peak National Observatory, In the Sonoran Desert on the Tohono O’odham Nation Arizona USA, Altitude 1,914 m (6,280 ft).

U Arizona Steward Observatory at NSF’s NOIRLab NOAO Kitt Peak National Observatory in the Arizona-Sonoran Desert 88 kilometers 55 mi west-southwest of Tucson, Arizona in the Quinlan Mountains of the Tohono O’odham Nation, altitude 2,096 m (6,877 ft).

The National Science Foundation funds the iPlant Collaborative in with a $50 million grant. In 2013, iPlant Collaborative received a $50 million renewal grant. Rebranded in late 2015 as “CyVerse”, the collaborative cloud-based data management platform is moving beyond life sciences to provide cloud-computing access across all scientific disciplines.

In June 2011, the university announced it would assume full ownership of the Biosphere 2 scientific research facility in Oracle, Arizona, north of Tucson, effective July 1. Biosphere 2 was constructed by private developers (funded mainly by Texas businessman and philanthropist Ed Bass) with its first closed system experiment commencing in 1991. The university had been the official management partner of the facility for research purposes since 2007.

University of Arizona mirror lab. Where else in the world can you find an astronomical observatory mirror lab under a football stadium?

University of Arizona’s Biosphere 2, located in the Sonoran desert. An entire ecosystem under a glass dome? Visit our campus, just once, and you’ll quickly understand why the UA is a university unlike any other.

University of Arizona Landscape Evolution Observatory at Biosphere 2

From The University of Tennessee-Knoxville Via phys.org For The American Society for Microbiology: “Subglacial microbial life on Earth and beyond”

From The University of Tennessee-Knoxville

Via

phys.org

For

The American Society for Microbiology

2.19.24

The search for life beyond Earth fascinates many and inspires big questions: Are we truly alone in the universe? Is our Earth unique? Is it possible that life beyond Earth may actually be far from little green aliens and much closer to the microbial life with which we share our planet?

Single-celled organisms were the first life forms that evolved on Earth billions of years ago and have been around much longer than humans and other multicellular organisms. They are also metabolically diverse and can thrive in environments that we humans deem extreme—such as at the bottom of the ocean in piping-hot hydrothermal vents, in extremely salty lakes, and even within rocks.

Europa—an icy Jupiter moon

Europa via the Galileo Spacecraft, NASA/JPL/Caltech/SETI.

The first place to look for life outside Earth is within our solar system, where distances between us and potentially habitable worlds are still manageable for spacecraft flybys and even sampling missions. Venus, Mars, and many moons of Jupiter and Saturn are all of interest to astrobiologists, though Europa, one of Jupiter’s 95 moons, is a particularly promising candidate world. Europa is an icy ocean world where plumes of water spurt from an ocean below a thick ice crust.

Though the surface temperature perpetually lurks below a cool -220°F, Europa excites many astrobiologists as a possible site for life in our solar system because of its subglacial ocean. Water is important for the habitability of a planet by life as we know it; a polar solvent like water is essential for the biochemical reactions that drive all life on Earth and can also provide a thermally stable habitat for organisms to live and evolve.

Along with water, carbon is another important building block for life as we know it. All of life’s essential macromolecules are based on carbon—sugars, proteins, DNA, and lipids are all comprised of carbon atoms arranged in various shapes, including rings, sheets, and chains.

In Sept. 2023, two independent teams of scientists found that the solid carbon dioxide (CO2) on Europa’s surface most likely originates from its subglacial ocean, as its location on the surface coincides with geological features that indicate the transport of material from below the ice.

One team also hypothesized that the oceans are oxidized, a chemical condition that supports Earth’s current biosphere and thus favors habitability by life as we know it. Though scientists were not able to definitively determine the source of the CO2 on Europa, the confirmation that carbon exists on Europa has fueled the fire of astrobiologists who believe that it could host microbial life.

Signs of life like organic carbon and water are broadly known as biosignatures, chemical or physical markers that specifically require a biological origin. Though no single biosignature is enough to claim life in a faraway world, finding many complementary biosignatures on bodies like Europa can strengthen the argument that life, in some form, could exist beyond Earth.

From Europa to Antarctica—studying subglacial microbes

As a microbiological fieldwork site, Europa is about as unreachable as can be—it is over 390 million miles away, and unfathomably cold. How, then, can we determine whether life could survive under Europan conditions? One idea is to study Earth-based analog sites—extreme environments on Earth whose conditions mimic those of faraway worlds.

By characterizing the microbial life in these ecosystems, we can glean insight into how life can persist in places that are entirely inhospitable to most other life forms. Studying analog sites can also give us clues about what kinds of biosignatures may be important in different environments and help inform what researchers look for in data coming from future Europa-bound missions.

Jill Mikucki, Ph.D., an associate professor at the University of Tennessee, Knoxville, studies one such analog site: Blood Falls, a feature that colors the terminus of Taylor Glacier in the McMurdo Dry Valleys of Antarctica.

Blood Falls, Antarctica, where microbes live under the ice. Iron and other elements from the bedrock below the ice become oxidized when it interacts with air, producing the rusty red coloring. Credit: Jill Mikucki.

There, a briny, subglacial groundwater ecosystem leaks iron-containing brine to the surface. The iron oxidizes upon contact with air, tinting the outflowing saltwater a rusty red and giving Blood Falls its spooky appearance and name to match.

“It feels otherworldly to work and camp in the dry valleys,” Mikucki said. “It can be extremely quiet…penetratingly so. But if the wind picks up, it can roar.”

Part of Blood Falls’ attractiveness as an analog comes from its unique geo- and hydrological features. “I think Blood Falls makes a great analog for ocean world studies because it is one of the few places where liquid transits from the below the ice to the surface,” Mikucki explained. “Additionally, it is briny, so it’s like a mini ocean world that episodically spills out aliquots of subglacial fluids—and its microbial contents.”

These features are reminiscent of the Europan plumes spurting from underneath the ice. “At Blood Falls, we can study what life below the ice is like, what that transit to the surface involves, and what survival at the surface is like,” Mikucki said.

In 2009, Mikucki and colleagues published a paper [Science] detailing how microbes beneath Taylor Glacier may be cycling sulfur and using iron as a terminal electron acceptor, a role played by oxygen for many organisms on Earth’s surface.

This kind of metabolism occurs under anaerobic conditions (when oxygen is limited), which can happen in some environments when photosynthesizing organisms that produce O2 are absent. This ecosystem is buried deep under the ice and may have been isolated from the outside for over 1 million years.

Mikucki has been working on subglacial environments for over two decades but is still stunned by some of her and her team’s findings. For instance, the microbial cells grow very slowly under the ice, possibly taking a year or more to divide.

“Everything still boggles my mind,” she laughed. “I wonder how long this brine has been trapped below the Taylor Glacier—and how, where, under what circumstances it originated. How have these microbial communities persisted through this physical and chemical journey?” Could life persist in a similar fashion on Europa? The jury is still out, but efforts to gather more data are in the works.

Future missions to Europa

In the coming decades, we will get a better look at Europa through two missions: the European Space Agency’s JUICE (Jupiter Icy Moons Explorer), and NASA’s Europa Clipper.

The European Space Agency [La Agencia Espacial Europea] [Agence spatiale européenne][Europäische Weltraumorganization](EU) JUICE spacecraft.

European Space Agency [La Agencia Espacial Europea][Agence spatiale européenne][Europäische Weltraumorganization](EU) JUICE Schematic.

NASA Europa Clipper depiction.

NASA Europa Clipper Payload annotated.

While the JUICE mission, launched in April 2023, aims to characterize Europa and two other Jupiter moons, NASA’s Clipper mission (scheduled for launch in Oct. 2024) will focus on Europa.

The Clipper’s goal is to measure the thickness of the icy crust and exchange between surface and ocean, as well as study Europa’s composition and geology. The two spacecraft should reach their targets in the 2030s and can then begin gathering and sending back data.

The possibility that life exists beyond Earth—and that it may well be very different from what we have here—is both exciting and humbling. If we never find life beyond Earth, it will mean that what happened here was extraordinarily special. If we do, it might turn what we think we know about life on its head and show us that we are not alone in the vast cosmos.

See the full article here.

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply” near the bottom of the post.

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Please help promote STEM in your local schools.

Stem Education Coalition

The University of Tennessee-Knoxville is a public land-grant research university in Knoxville, Tennessee. Founded in 1794, two years before Tennessee became the 16th state, it is the flagship campus of the University of Tennessee system, with ten undergraduate colleges and eleven graduate colleges. It hosts more than 30,000 students from all 50 states and more than 100 foreign countries. It is classified among “R1: Doctoral Universities – Very high research activity”.

The University of Tennessee’s ties to the nearby DOE Oak Ridge National Laboratory, established under UT President Andrew Holt and continued under the UT–Battelle partnership, allow for considerable research opportunities for faculty and students. Also affiliated with the university are the Howard H. Baker Jr. Center for Public Policy, the University of Tennessee Anthropological Research Facility, and the University of Tennessee Arboretum, which occupies 250 acres (100 ha) of nearby Oak Ridge and features hundreds of species of plants indigenous to the region. The university is a direct partner of the University of Tennessee Medical Center, which is one of two Level I trauma centers in East Tennessee.

The University of Tennessee is the only university in the nation to have three presidential papers editing projects. The university holds collections of the papers of all three U.S. presidents from Tennessee—Andrew Jackson, James K. Polk, and Andrew Johnson. Nine of its alumni have been selected as Rhodes Scholars and one alumnus, James M. Buchanan, received the 1986 Nobel Prize in Economics. UT is one of the oldest public universities in the United States and the oldest secular institution west of the Eastern Continental Divide.

The University of Tennessee was ranked very highly among public universities and national universities in the United States by U.S. News & World Report.

The University of Tennessee was ranked as the most LGBTQ-unfriendly university in the United States by The Princeton Review among all institutions it surveyed. The campus Pride Center has been defunded and vandalized several times.

Research

The total research endowment of the UT Knoxville campus is over $140,000,000. UT Knoxville boasts several faculty who are among the leading contributors to their fields, including Harry McSween, generally recognized as one of the world’s leading experts in the study of meteorites and a member of the science team for Mars Pathfinder and later a co-investigator for the Mars Odyssey and Mars Exploration Rovers projects. The university also hosts Barry T. Rouse, an international award-winning Distinguished Professor of Microbiology who has conducted multiple NIH-funded studies on the herpes simplex virus (HSV) and who is a leading researcher in his field. UT’s agricultural research programs are considered to be among the most accomplished in the nation, and the School of Agricultural Sciences and Natural Resources is home to the East Tennessee Clean Fuels Initiative, recognized by the United States Department of Energy as the “best local clean fuels program in America.”

The DOE’s Oak Ridge National Laboratory

The major hub of research at the University of Tennessee is The DOE’s Oak Ridge National Laboratory, one of the largest government laboratories in the United States. ORNL is a major center of civilian and governmental research and features two of the world’s most powerful supercomputers.

ORNL OLCF IBM Q AC922 SUMMIT supercomputer, was No.1 now No.7 on the TOP500.

ORNL Cray Frontier Shasta based Exascale supercomputer with Slingshot interconnect featuring high-performance AMD EPYC CPU and AMD Radeon Instinct GPU technology, at DOE’s Oak Ridge National Laboratory, No.1 on the TOP500.

From The College of Agriculture and Life Sciences And The College of Engineering At Cornell University: “Low-cost microbe can speed biological discovery”

From The College of Agriculture and Life Sciences

And

The College of Engineering

At

Cornell University

2.13.24
Blaine Friedlander
bpf2@cornell.edu

Media Contact
Becka Bowyer
rpb224@cornell.edu
6072204185

Cornell researchers have created a new version of a microbe to compete economically with E. coli – a bacteria commonly used as a research tool due to its ability to synthesize proteins – to conduct low-cost and scalable synthetic biological experiments.

As an inexpensive multiplier – much like having a photocopier in a test tube – the bacteria “Vibrio natriegens” could help labs test protein variants for creation of pharmaceuticals, synthetic fuels and sustainable compounds that battle weeds or pests. The microbe can work effectively without costly incubators, shakers or deep freezers and can be engineered within hours.

The laboratory of Buz Barstow has engineered the the bacteria Vibrio natriegens, shown here, to conduct low-cost science without expensive incubators, shakers or freezers. Credit: Bryce Brownfield/Provided.

The research published Feb. 13 in PNAS Nexus.

Vibrio natriegens genomically engineered for natural competence is transformable via direct addition of plasmid DNA to cells growing in a minimal competence media. Credit: Specht et al.

“It’s really easy to produce,” said lead author David Specht, Ph.D. ’21, a postdoctoral researcher in the laboratory of Buz Barstow, Ph.D. ’09, assistant professor of biological and environmental engineering in the College of Agriculture and Life Sciences.

To study proteins for creating medical cures or fashioning fuels, researchers use a plasmid (a small piece of DNA) that acts as the instruction manual to make the molecular machine – a protein – of interest. Currently, when researchers place a plasmid into E. coli, they can create many copies to test several variants.

E. coli cells help molecular biologists multiply and manipulate plasmids for protein engineering, but the process is expensive since they often purchase the bacteria from manufacturers, must keep it cold and maintain rooms of expensive equipment to sustain it. A modified E. coli, used for this purpose, is also very fragile.

“As scientists, we don’t often know precisely what those regulatory or molecular sequences should be to achieve our goals,” said Barstow, a faculty fellow at the Cornell Atkinson Center for Sustainability. “So we must test a lot of variants, and Vibrio natriegens allows researchers to scale up that process of testing.”

The microbe V. natriegens is not complicated, Specht said. “It’s so simple to make that someone with limited resources – like high school labs, home inventors or startup biological businesses – can do it,” he said.

Researcher Timothy Sheppard ’22, M.Eng. ’22, compared the simplicity of V. natriegens in conducting synthetic and molecular experiments to using a simple writing instrument hundreds of years old: “We’ve found nature’s pencil for cloning and conducting synthetic biology,” he said.

The process is inexpensive with V. natriegens, as it requires no capital equipment purchases and it can work at room temperature. The cells produced from V. natriegens grow quickly: According to the paper, a transformation started at 9 a.m. yields visible colonies by 5 p.m., each filled with masses of proteins.

“The microbe is a radically simple solution to a hard problem,” Barstow said.

In addition to Barstow, Specht and Sheppard, the co-authors of the research, “Efficient Natural Plasmid Transformation of Vibrio natriegens Enables Zero-capital Molecular Biology,” are Sijin Li, assistant professor in chemical and biomolecular engineering, Cornell Engineering; Greeshma Gadikota, associate professor in civil and environmental engineering (ENG); and Finn Kennedy ’25.

Funding for this research came from the Advanced Research Projects Agency-Energy (U.S. Department of Energy); a Cornell 2030 Project Fast Grant; and a gift from Mary Fernando Conrad ’83 and Tony Conrad.

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply” at the bottom of the post.

five-ways-keep-your-child-safe-school-shootings

Please help promote STEM in your local schools.

Stem Education Coalition

The Cornell University College of Engineering is a division of Cornell University that was founded in 1870 as the Sibley College of Mechanical Engineering and Mechanic Arts. It is one of four private undergraduate colleges at Cornell that are not statutory colleges.

It currently grants bachelors, masters, and doctoral degrees in a variety of engineering and applied science fields, and is the third largest undergraduate college at Cornell by student enrollment. The college offers over 450 engineering courses.

The College of Engineering was founded in 1870 as the Sibley College of Mechanical Engineering and Mechanic Arts. The program was housed in Sibley Hall on what has since become the Arts Quad, both of which are named for Hiram Sibley, the original benefactor whose contributions were used to establish the program. The college took its current name in 1919 when the Sibley College merged with the College of Civil Engineering. It was housed in Sibley, Lincoln, Franklin, Rand, and Morse Halls. In the 1950s the college moved to the southern end of Cornell’s campus.

The college is known for a number of firsts. In 1889, the college took over electrical engineering from the Department of Physics, establishing the first department in the United States in this field. The college awarded the nation’s first doctorates in both electrical engineering and industrial engineering. The Department of Computer Science, established in 1965 jointly under the College of Engineering and the College of Arts and Sciences, is also one of the oldest in the country.

For many years, the college offered a five-year undergraduate degree program. However, in the 1960s, the course was shortened to four years for a B.S. degree with an optional fifth year leading to a masters of engineering degree. From the 1950s to the 1970s, Cornell offered a Master of Nuclear Engineering program, with graduates gaining employment in the nuclear industry. However, after the 1979 accident at Three Mile Island, employment opportunities in that field dimmed and the program was dropped. Cornell continued to operate its on-campus nuclear reactor as a research facility following the close of the program. For most of Cornell’s history, Geology was taught in the College of Arts and Sciences. However, in the 1970s, the department was shifted to the engineering college and Snee Hall was built to house the program. After World War II, the Graduate School of Aerospace Engineering was founded as a separate academic unit, but later merged into the engineering college.

Cornell Engineering is home to many teams that compete in student design competitions and other engineering competitions. Presently, there are teams that compete in the Baja SAE, Automotive X-Prize (see Cornell 100+ MPG Team), UNP Satellite Program, DARPA Grand Challenge, AUVSI Unmanned Aerial Systems and Underwater Vehicle Competition, Formula SAE, RoboCup, Solar Decathlon, Genetically Engineered Machines, and others.

The college is a leader in nanotechnology. In a survey done by a nanotechnology magazine Cornell University was ranked as being very high in nanotechnology commercialization and in terms of nanotechnology facilities, very high in nanotechnology research and nanotechnology industrial outreach.

Departments and schools

The college is the third-largest undergraduate college at Cornell by student enrollment. It is divided into twelve departments and schools:

School of Applied and Engineering Physics
Department of Biological and Environmental Engineering
Meinig School of Biomedical Engineering
Smith School of Chemical and Biomolecular Engineering
School of Civil & Environmental Engineering
Department of Computer Science
Department of Earth & Atmospheric Sciences
School of Electrical and Computer Engineering
Department of Materials Science and Engineering
Sibley School of Mechanical and Aerospace Engineering
School of Operations Research and Information Engineering
Department of Theoretical and Applied Mechanics
Department of Systems Engineering

Cornell CALS

As a premier institution of scientific learning, Cornell CALS connects the life, agricultural, environmental and social sciences to provide world-class education, spark unexpected discoveries and inspire pioneering solutions.

Cornell University’s College of Agriculture and Life Sciences tackles the challenges of our times through purpose-driven science that advances understanding and improves life.

Cornell CALS researches, teaches and explores the many aspects of discovery:
Agriculture
Biology
Climate Change
Environmental Science
Fauna
Flora
Food
Health & Nutrition

Once called “the first American university” by educational historian Frederick Rudolph, Cornell University represents a distinctive mix of eminent scholarship and democratic ideals. Adding practical subjects to the classics and admitting qualified students regardless of nationality, race, social circumstance, gender, or religion was quite a departure when Cornell was founded in 1865.

Today’s Cornell reflects this heritage of egalitarian excellence. It is home to the nation’s first colleges devoted to hotel administration, industrial and labor relations, and veterinary medicine. Both a private university and the land-grant institution of New York State, Cornell University is the most educationally diverse member of the Ivy League.

On the Ithaca campus alone students representing every state and many countries choose from among 4,000 courses in 11 undergraduate, graduate, and professional schools. Many undergraduates participate in a wide range of interdisciplinary programs, play meaningful roles in original research, and study in Cornell programs in Washington, New York City, and the world over.

Cornell University is a private, statutory, Ivy League and land-grant research university in Ithaca, New York. Founded in 1865 by Ezra Cornell and Andrew Dickson White, the university was intended to teach and make contributions in all fields of knowledge—from the classics to the sciences, and from the theoretical to the applied. These ideals, unconventional for the time, are captured in Cornell’s founding principle, a popular 1868 quotation from founder Ezra Cornell: “I would found an institution where any person can find instruction in any study.”

The university is broadly organized into seven undergraduate colleges and seven graduate divisions at its main Ithaca campus, with each college and division defining its specific admission standards and academic programs in near autonomy. The university also administers two satellite medical campuses, one in New York City and one in Education City, Qatar, and The Jacobs Technion-Cornell Institute in New York City, a graduate program that incorporates technology, business, and creative thinking. The program moved from Google’s Chelsea Building in New York City to its permanent campus on Roosevelt Island in September 2017.

Cornell is one of the few private land-grant universities in the United States. Of its seven undergraduate colleges, three are state-supported statutory or contract colleges through The State University of New York (SUNY) system, including its Agricultural and Human Ecology colleges as well as its Industrial Labor Relations school. Of Cornell’s graduate schools, only the veterinary college is state-supported. As a land grant college, Cornell operates a cooperative extension outreach program in every county of New York and receives annual funding from the State of New York for certain educational missions. The Cornell University Ithaca Campus comprises 745 acres, but is much larger when the Cornell Botanic Gardens (more than 4,300 acres) and the numerous university-owned lands in New York City are considered.

Alumni and affiliates of Cornell have reached many notable and influential positions in politics, media, and science. Nobel laureates, Turing Award winners and Fields Medalists have been affiliated with Cornell. Cornell counts more than 250,000 living alumni, and its former and present faculty and alumni include Marshall Scholars, Rhodes Scholars, Truman Scholars, Gates Scholars, Olympic Medalists, current Fortune 500 CEOs, and billionaire alumni. Since its founding, Cornell has been a co-educational, non-sectarian institution where admission has not been restricted by religion or race. The student body consists of undergraduate and graduate students from all 50 American states and many countries.

History

Cornell University was founded on April 27, 1865; the New York State (NYS) Senate authorized the university as the state’s land grant institution. Senator Ezra Cornell offered his farm in Ithaca, New York, as a site and $500,000 of his personal fortune as an initial endowment. Fellow senator and educator Andrew Dickson White agreed to be the first president. During the next three years, White oversaw the construction of the first two buildings and traveled to attract students and faculty. The university was inaugurated on October 7, 1868, and 412 men were enrolled the next day.

Cornell developed as a technologically innovative institution, applying its research to its own campus and to outreach efforts. For example, in 1883 it was one of the first university campuses to use electricity from a water-powered dynamo to light the grounds. Since 1894, Cornell has included colleges that are state funded and fulfill statutory requirements; it has also administered research and extension activities that have been jointly funded by state and federal matching programs.

Cornell has had active alumni since its earliest classes. It was one of the first universities to include alumni-elected representatives on its Board of Trustees. Cornell was also among the Ivies that had heightened student activism during the 1960s related to cultural issues; civil rights; and opposition to the Vietnam War, with protests and occupations resulting in the resignation of Cornell’s president and the restructuring of university governance. Today the university has more than 4,000 courses. Cornell is also known for the Residential Club Fire of 1967, a fire in the Residential Club building that killed eight students and one professor.

Since 2000, Cornell has been expanding its international programs. In 2004, the university opened the Weill Cornell Medical College in Qatar. It has partnerships with institutions in India, Singapore, and the People’s Republic of China. Former president Jeffrey S. Lehman described the university, with its high international profile, a “transnational university”. On March 9, 2004, Cornell and Stanford University laid the cornerstone for a new ‘Bridging the Rift Center’ to be built and jointly operated for education on the Israel–Jordan border.

Research

Cornell, a research university, is ranked highly in producing the largest number of graduates who go on to pursue PhDs in engineering or the natural sciences at American institutions, and high in the world in producing graduates who pursue PhDs at American institutions in any field. Research is a central element of the university’s mission.

Cornell is a member of the Association of American Universities and is classified among “R1: Doctoral Universities – Very high research activity”.

Federal sources constitute the largest source of research funding. The agencies contributing the largest share of that investment are The Department of Health and Human Services and the National Science Foundation , accounting for 49.6% and 24.4% of all federal investment, respectively. Cornell is on the top-ten list of U.S. universities receiving the most patents and in forming start-up companies’

Since 1962, Cornell has been involved in unmanned missions to Mars. In the 21st century, Cornell had a hand in the Mars Exploration Rover Mission. Cornell’s Steve Squyres, Principal Investigator for the Athena Science Payload, led the selection of the landing zones and requested data collection features for the Spirit and Opportunity rovers. NASA-JPL/Caltech engineers took those requests and designed the rovers to meet them. The rovers, both of which have operated long past their original life expectancies, are responsible for the discoveries that were awarded 2004 Breakthrough of the Year honors by Science. Control of the Mars rovers has shifted between National Aeronautics and Space Administration’s Jet Propulsion Laboratory at Caltech and Cornell’s Space Sciences Building.

Further, Cornell researchers discovered the rings around the planet Uranus, and Cornell built and operated the telescope at Arecibo Observatory located in Arecibo, Puerto Rico until 2011, when they transferred the operations to SRI International, the Universities Space Research Association and the Metropolitan University of Puerto Rico [Universidad Metropolitana de Puerto Rico]. The telescope has now collapsed.

The Automotive Crash Injury Research Project was begun in 1952. It pioneered the use of crash testing, originally using corpses rather than dummies. The project discovered that improved door locks; energy-absorbing steering wheels; padded dashboards; and seat belts could prevent an extraordinary percentage of injuries.

In the early 1980s, Cornell deployed the first IBM 3090-400VF and coupled two IBM 3090-600E systems to investigate coarse-grained parallel computing. In 1984, the National Science Foundation began work on establishing five new supercomputer centers, including the Cornell Center for Advanced Computing, to provide high-speed computing resources for research within the United States. As a National Science Foundation center, Cornell deployed the first IBM Scalable Parallel supercomputer.

In the 1990s, Cornell developed scheduling software and deployed the first supercomputer built by Dell. Most recently, Cornell deployed Red Cloud, one of the first cloud computing services designed specifically for research. Today, the center is a partner on the National Science Foundation XSEDE-Extreme Science Engineering Discovery Environment supercomputing program, providing coordination for XSEDE architecture and design, systems reliability testing, and online training using the Cornell Virtual Workshop learning platform.

Cornell scientists have researched the fundamental particles of nature for more than 70 years. Cornell physicists, such as Hans Bethe, contributed not only to the foundations of nuclear physics but also participated in the Manhattan Project. In the 1930s, Cornell built the second cyclotron in the United States. In the 1950s, Cornell physicists became the first to study synchrotron radiation.

During the 1990s, the Cornell Electron Storage Ring, located beneath Alumni Field, was the world’s highest-luminosity electron-positron collider. After building the synchrotron at Cornell, Robert R. Wilson took a leave of absence to become the founding director of the DOE’s Fermi National Accelerator Laboratory, which involved designing and building the largest accelerator in the United States, the Tevatron.

Cornell’s accelerator and high-energy physics groups are involved in the design of the proposed ILC-International Linear Collider (JP) and plan to participate in its construction and operation.

ILC, being planned for the Kitakami highland, in the Iwate prefecture of northern Japan schematic,.

The International Linear Collider (JP) will complement the The European Organization for Nuclear Research [La Organización Europea para la Investigación Nuclear][Organization européenne pour la recherche nucléaire] [Europäische Organization für Kernforschung](CH)[CERN] Large Hadron Collider(CH) and shed light on questions such as the identity of dark matter and the existence of extra dimensions.

The Kavli Institute at Cornell (KIC) is devoted to the development and utilization of next-generation tools for exploring the nanoscale world.

As part of its research work, Cornell has established several research collaborations with universities around the globe. For example, a partnership with the University of Sussex(UK) (including the Institute of Development Studies at Sussex) allows research and teaching collaboration between the two institutions.

From “The Gazette” At Harvard University: “We are social beings. So are microbes”

From “The Gazette”

At

Harvard University

2.12.24
Anne J. Manning

When we pick up our neighbors’ bugs, we get the good as well as the bad and the ugly.

Evolutionary biology research team members: Amar Sarkar (from left), Rachel Carmody, and Cameron McInroy.
Credit: Jon Chase/Harvard Staff Photographer

The COVID-19 pandemic reminded us that social interactions transmit pathogens. But do humans spread “good” bugs, too?

Very much so, say a team of biologists who are probing the links between the microbiome and health. In a recent perspective piece in Cell, they explain why the “social microbiome” — the microbial metacommunity associated with a social network of humans or other animals — deserves attention.

Processes at different social-ecological scales influence the social microbiome, and health-relevant processes are affected by the social transmission of microbes. Credit: Cell.

The researchers pointed out that microbial sharing could play a role in individuals’ susceptibility to, and resilience against, both communicable and non-communicable diseases.

“When we think of factors that affect the microbiome, diet and antibiotics come to mind most readily,” said lead author Amar Sarkar, a Harvard Griffin Graduate School of Arts and Sciences student in the Department of Human Evolutionary Biology. “But the fact that our social interactions also affect the microbiome is less well appreciated.”

The researchers first introduced the concept of the social microbiome in a 2020 article in Nature Ecology and Evolution. There, Sarkar and co-authors suggested that the social microbiome could be viewed as a sort of archipelago, each of us being an “island” that hosts a distinct set of microbes. We share our microbes with one another, similar to how birds or insects might disperse across islands. Their latest analysis looks at why that framework matters.

Focusing on the gut microbiome and its implications for overall health, the researchers offer an analysis of social transmission of microbes at five levels, each increasing in ecological scale. They range from host-to-host interactions that spread through direct contact between individuals, like ­hugging and touching, all the way up to inter-species microbial mingling — think our close ties with our pets.

Social microbial transmission can take place from parent to infant early in life, and through direct and indirect contact with others throughout life. This is why household co-habitation leads to substantial microbial strain-sharing between family members. The researchers cite studies showing that individuals within a household shared a significant proportion of their gut microbial strains, and that villages could be distinguished on the basis of their social microbiomes.

The importance of microbial connections in human health outcomes is an area with enormous potential for discovery, according to the researchers. Many chronic conditions historically considered to be “noncommunicable” — including metabolic diseases, cardiovascular disease, autoimmune disorders, and certain cancers — are now being evaluated for their microbial causes and correlations. In many cases, the microbes that shape susceptibility to diseases, or responses to treatment, have been shown to be socially transmissible.

“If microbes contributing to disease can be transmitted between individuals, some noncommunicable conditions may in fact have a communicable component,” said Rachel Carmody, associate professor in Human Evolutionary Biology and co-senior author of the work. “While that may be a potentially unsettling thought, socially transmitted microbes may help protect against these conditions, too.” For example, studies have shown that mice living in the same cage can transmit microbes that increase resilience against colitis or improve their responsiveness to cancer therapy.

“We observe instances where social microbial transmission protects against disease, and instances where it promotes disease, but further work to probe these effects in humans is necessary,” said co-author Cameron McInroy ’22, a teaching fellow in the same department. “Key challenges lie in pinpointing the microbes and transmission contexts controlling these risk-decreasing and risk-increasing effects, understanding how they work, and ultimately harnessing them for our benefit.”

The researchers considered the impact of the social microbiome for antibiotic use. Antibiotic exposures can be thought of as disturbances to the microbiome ecosystem, similar to how fires disturb forest ecosystems. Altering the gut microbiome, sometimes for extended periods, can increase the risk of acute infections such as Clostridioides difficile. Social interactions after antibiotic exposure could help the microbiome recover from these antibiotic-induced disturbances.

The researchers also looked at the global problem of antibiotic-resistant microbes arising and spreading due to exploitation of antibiotic drugs. The transmission of such microbes may have more social components than are currently appreciated, the researchers say. For example, individuals who share a household might acquire antibiotic-resistant microbes from each other if some members are under prolonged antibiotic treatment. What’s more, cultures, societies, and countries differ in their usage of antibiotics, they say, creating “culture-dependent transmission landscapes” for antibiotic-resistant microbes.

Evolutionary biologists have long proposed that important benefits of group living — such as protection from predation, improved territorial defense, and social learning — come at the price of higher pathogen transmission. In their article, the researchers raise the prospect that some social behaviors may also have evolved to transmit beneficial bacteria among individuals.

“Social interactions can provide conduits for pathogen transmission, but beneficial microbes are also known to be transmitted through these interactions,” said co-senior author Andrew Moeller of Princeton University. “It may be that, in some contexts, the benefits provided by socially transmitted mutualists outweigh the costs incurred by socially transmitted pathogens.”

The authors of Microbial transmission in the social microbiome and host health and disease were supported in part by the National Science Foundation, National Institutes of Health, National Cancer Institute, and National Institute of General Medical Sciences.

See the full article here .

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Harvard University is the oldest institution of higher education in the United States, established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. It was named after the College’s first benefactor, the young minister John Harvard of Charlestown, who upon his death in 1638 left his library and half his estate to the institution. A statue of John Harvard stands today in front of University Hall in Harvard Yard, and is perhaps the University’s best-known landmark.

Harvard University has 12 degree-granting Schools in addition to the Radcliffe Institute for Advanced Study. The University has grown from nine students with a single master to an enrollment of more than 20,000 degree candidates including undergraduate, graduate, and professional students. There are more than 360,000 living alumni in the U.S. and over 190 other countries.

The Massachusetts colonial legislature, the General Court, authorized Harvard University’s founding. In its early years, Harvard College primarily trained Congregational and Unitarian clergy, although it has never been formally affiliated with any denomination. Its curriculum and student body were gradually secularized during the 18th century, and by the 19th century, Harvard University (US) had emerged as the central cultural establishment among the Boston elite. Following the American Civil War, President Charles William Eliot’s long tenure (1869–1909) transformed the college and affiliated professional schools into a modern research university; Harvard became a founding member of the Association of American Universities in 1900. James B. Conant led the university through the Great Depression and World War II; he liberalized admissions after the war.

The university is composed of ten academic faculties plus the Radcliffe Institute for Advanced Study. Arts and Sciences offers study in a wide range of academic disciplines for undergraduates and for graduates, while the other faculties offer only graduate degrees, mostly professional. Harvard has three main campuses: the 209-acre (85 ha) Cambridge campus centered on Harvard Yard; an adjoining campus immediately across the Charles River in the Allston neighborhood of Boston; and the medical campus in Boston’s Longwood Medical Area. Harvard University’s endowment is valued at $41.9 billion, making it the largest of any academic institution. Endowment income helps enable the undergraduate college to admit students regardless of financial need and provide generous financial aid with no loans The Harvard Library is the world’s largest academic library system, comprising 79 individual libraries holding about 20.4 million items.

Harvard University has more alumni, faculty, and researchers who have won Nobel Prizes and Fields Medals than any other university in the world and more alumni who have been members of the U.S. Congress, MacArthur Fellows, Rhodes Scholars, and Marshall Scholars than any other university in the United States. Its alumni also include U.S. presidents and many living billionaires, the most of any university. Turing Award laureates have been Harvard affiliates. Students and alumni have also won Academy Awards, Pulitzer Prizes, and Olympic medals (many gold), and they have founded many notable companies.

Colonial

Harvard University was established in 1636 by vote of the Great and General Court of the Massachusetts Bay Colony. In 1638, it acquired British North America’s first known printing press. In 1639, it was named Harvard College after deceased clergyman John Harvard, an alumnus of the University of Cambridge (UK) who had left the school £779 and his library of some 400 volumes. The charter creating the Harvard Corporation was granted in 1650.

A 1643 publication gave the school’s purpose as “to advance learning and perpetuate it to posterity, dreading to leave an illiterate ministry to the churches when our present ministers shall lie in the dust.” It trained many Puritan ministers in its early years and offered a classic curriculum based on the English university model—many leaders in the colony had attended the University of Cambridge—but conformed to the tenets of Puritanism. Harvard University has never affiliated with any particular denomination, though many of its earliest graduates went on to become clergymen in Congregational and Unitarian churches.

Increase Mather served as president from 1681 to 1701. In 1708, John Leverett became the first president who was not also a clergyman, marking a turning of the college away from Puritanism and toward intellectual independence.

19th century

In the 19th century, Enlightenment ideas of reason and free will were widespread among Congregational ministers, putting those ministers and their congregations in tension with more traditionalist, Calvinist parties. When Hollis Professor of Divinity David Tappan died in 1803 and President Joseph Willard died a year later, a struggle broke out over their replacements. Henry Ware was elected to the Hollis chair in 1805, and the liberal Samuel Webber was appointed to the presidency two years later, signaling the shift from the dominance of traditional ideas at Harvard to the dominance of liberal, Arminian ideas.

Charles William Eliot, president 1869–1909, eliminated the favored position of Christianity from the curriculum while opening it to student self-direction. Though Eliot was the crucial figure in the secularization of American higher education, he was motivated not by a desire to secularize education but by Transcendentalist Unitarian convictions influenced by William Ellery Channing and Ralph Waldo Emerson.

20th century

In the 20th century, Harvard University’s reputation grew as a burgeoning endowment and prominent professors expanded the university’s scope. Rapid enrollment growth continued as new graduate schools were begun and the undergraduate college expanded. Radcliffe College, established in 1879 as the female counterpart of Harvard College, became one of the most prominent schools for women in the United States. Harvard University became a founding member of the Association of American Universities in 1900.

The student body in the early decades of the century was predominantly “old-stock, high-status Protestants, especially Episcopalians, Congregationalists, and Presbyterians.” A 1923 proposal by President A. Lawrence Lowell that Jews be limited to 15% of undergraduates was rejected, but Lowell did ban blacks from freshman dormitories.

President James B. Conant reinvigorated creative scholarship to guarantee Harvard University’s preeminence among research institutions. He saw higher education as a vehicle of opportunity for the talented rather than an entitlement for the wealthy, so Conant devised programs to identify, recruit, and support talented youth. In 1943, he asked the faculty to make a definitive statement about what general education ought to be, at the secondary as well as at the college level. The resulting Report, published in 1945, was one of the most influential manifestos in 20th century American education.

Between 1945 and 1960, admissions were opened up to bring in a more diverse group of students. No longer drawing mostly from select New England prep schools, the undergraduate college became accessible to striving middle class students from public schools; many more Jews and Catholics were admitted, but few blacks, Hispanics, or Asians. Throughout the rest of the 20th century, Harvard became more diverse.

Harvard University’s graduate schools began admitting women in small numbers in the late 19th century. During World War II, students at Radcliffe College (which since 1879 had been paying Harvard University professors to repeat their lectures for women) began attending Harvard University classes alongside men. Women were first admitted to the medical school in 1945. Since 1971, Harvard University has controlled essentially all aspects of undergraduate admission, instruction, and housing for Radcliffe women. In 1999, Radcliffe was formally merged into Harvard University.

21st century

Drew Gilpin Faust, previously the dean of the Radcliffe Institute for Advanced Study, became Harvard University’s first woman president on July 1, 2007. She was succeeded by Lawrence Bacow on July 1, 2018.

From The DOE’s Lawrence Berkeley National Laboratory: “Improving Climate Predictions by Unlocking the Secrets of Soil Microbes”

From The DOE’s Lawrence Berkeley National Laboratory

2.5.24
Julie Bobyock

Microbe models leverage extensive genomic data to power soil-carbon simulations. Illustration by Victor O. Leshyk.

Scientists are using the DNA from soil microbes to model how they function and use carbon, ultimately helping to advance the accuracy of climate models.

Climate models are essential to predicting and addressing climate change, but can fail to adequately represent soil microbes, a critical player in ecosystem soil carbon sequestration that affects the global carbon cycle. A team of scientists led by the Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) has developed a new model that incorporates genetic information from microbes. This new model enables the scientists to better understand how certain soil microbes efficiently store carbon supplied by plant roots, and could inform agricultural strategies to preserve carbon in the soil in support of plant growth and climate change mitigation.

“Our research demonstrates the advantage of assembling the genetic information of microorganisms directly from soil. Previously, we only had information about a small number of microbes studied in the lab,” said Berkeley Lab Postdoctoral Researcher Gianna Marschmann, the paper’s lead author. “Having genome information allows us to create better models capable of predicting how various plant types, crops, or even specific cultivars can collaborate with soil microbes to better capture carbon. Simultaneously, this collaboration can enhance soil health.”

This research is described in a new paper that was recently published in the journal Nature Microbiology. The corresponding authors are Eoin Brodie of Berkeley Lab, and Jennifer Pett-Ridge of Lawrence Livermore National Lab, who leads the “Microbes Persist” Soil Microbiome Scientific Focus Area project that is funded by the DOE Office of Science in support of this work.

Fig. 1: Overview of DEBmicroTrait.

a, Schematic of the DEBmicroTrait model showing dynamic energy budget (DEB) allocation for a single-reserve (E), single-structure (V) heterotrophic microorganism [67*] feeding on different substrates (S). Diffusion-limited substrate uptake occurs through specific substrate binding sites (coloured according to substrate chemical class). Substrate uptake kinetics are described by the ECA40. Reserve and structural biomass are conceptualized as generalized chemical compounds characterized by macromolecular composition (CaHbOcNd) and chemical potential (μ(E, V)). Top: the coupling of catabolism and anabolism, that is, the catabolic and anabolic reactions through which energy is obtained and utilized for a metabolism in which the C source is also used as the electron donor50. The coupling between catabolism and anabolism exists both in reserve assimilation and structural (and extracellular enzyme) synthesis. Bottom: the sequential assimilation (pA), partitioning and dissipation of substrate and reserve compounds, with maintenance (pM) taking priority over growth (pG) and extracellular enzyme production (pX). The turnover of reserve and structure (γ(E, V)) is density-dependent75. Essential fluxes are labelled and defined (see also Supplementary Table 1). b, Workflow combining biophysical theory and genome inference to constrain DEBmicroTrait model parameters: (1) Cell size covaries with genome size76. (2) Codon-usage bias sets an upper bound on protein translation power (kE72). (3) The number of ribosomal RNA operons predicts translation efficiency (yVE77). (4) The cellular composition influences C supply and demand, which in turn determines the substrate binding site density required to enable substrate uptake at a rate commensurate with the maximum specific growth rate (ρporter84). Binding sites can be allocated according to relative gene frequencies of transporter genes in the genome (zρ). (5) Basal maintenance rate is proportional to cell volume (kM73). Glycoside hydrolase gene frequencies scale the constitutive extracellular enzyme production rate (zX71).
*Science paper references.
See the science paper for further instructive material with images.

Seeing the Unseen: Microbial Impact on Soil Health and Carbon

Soil microbes help plants access soil nutrients and resist drought, disease, and pests. Their impacts on the carbon cycle are particularly important to represent in climate models because they affect the amount of carbon stored in soil or released into the atmosphere as carbon dioxide during the process of decomposition. By building their own bodies from that carbon, microbes can stabilize (or store) it in the soil, and influence how much, and for how long carbon remains stored belowground. The relevance of these functions to agriculture and climate are being observed like never before.

However, with just one gram of soil containing up to 10 billion microorganisms and thousands of different species, the vast majority of microbes have never been studied in the lab. Until recently, the data scientists had to inform these models came from only a tiny minority of lab-studied microbes, with many unrelated to those needing representation in climate models.

“This is like building an ecosystem model for a desert based on information from plants that only grow in a tropical forest,” explained Brodie.

The World Beneath our Feet

To address this challenge, the team of scientists used genome information directly to build a model capable of being tailored to any ecosystem in need of study, from California’s grasslands to thawing permafrost in the Arctic. With the model using genomes to provide insights into how soil microbes function, the team applied this approach to study plant-microbiome interactions in a California rangeland. Rangelands are economically and ecologically important in California, making up more than 40% of the land area.

Research focused on the microbes living around plant roots (called the rhizosphere). This is an important environment to study because, despite being only 1-2% of Earth’s soil volume, this root zone is estimated to hold up to 30-40% of Earth’s carbon stored in soils, with much of that carbon being released by roots as they grow.

To build the model, scientists simulated microbes growing in the root environment, using data from the University of California Hopland Research and Extension Center. Nevertheless, the approach is not limited to a particular ecosystem. Since certain genetic information corresponds to specific traits, just as in humans, the relationship between the genomes (what the model is based on) and the microbial traits is transferable to microbes and ecosystems all over the world.

The team developed a new way to predict important traits of microbes affecting how quickly they use carbon and nutrients supplied by plant roots. Using the model, the researchers demonstrated that as plants grow and release carbon, distinct microbial growth strategies emerge because of the interaction between root chemistry and microbial traits. In particular, they found that microbes with a slower growth rate were favored by types of carbon released during later stages of plant development and were surprisingly efficient in using carbon – allowing them to store more of this key element in the soil.

The Root of the Matter

This new observation provides a basis for improving how root-microbe interactions are represented in models, and enhances the ability to predict how microbes impact changes to the global carbon cycle in climate models.

“This newfound knowledge has important implications for agriculture and soil health. With the models we are building, it is increasingly possible to leverage new understanding of how carbon cycles through soil. This in turn opens up possibilities to recommend strategies for preserving valuable carbon in the soil to support biodiversity and plant growth at scales feasible to measure the impact,” Marschmann said.

The research highlights the power of using modeling approaches based on genetic information to predict microbial traits that can help shed light on the soil microbiome and its impact on the environment.

This work was supported by the U.S. Department of Energy (DOE), Office of Biological and Environmental Research.

See the full article here .

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LBNL campus

Berkeley Lab campus Aerial View

Bringing Science Solutions to the World

In the world of science, The Lawrence Berkeley National Laboratory (Berkeley Lab) is synonymous with “excellence.” A number of Nobel prizes are associated with Berkeley Lab. Lab scientists are members of the The National Academy of Sciences, one of the highest honors for a scientist in the United States. A number of our scientists have won the National Medal of Science, our nation’s highest award for lifetime achievement in fields of scientific research. A number of our engineers have been elected to the The National Academy of Engineering, and a number of our scientists have been elected into The Institute of Medicine. In addition, Berkeley Lab has trained thousands of university science and engineering students who are advancing technological innovations across the nation and around the world.

Berkeley Lab is a member of the national laboratory system supported by The DOE through its Office of Science. It is managed by the University of California-Berkeley and is charged with conducting unclassified research across a wide range of scientific disciplines. Located on a 202-acre site in the hills above The University of California-Berkeley campus that offers spectacular views of the San Francisco Bay, Berkeley Lab employs a large number of scientists, engineers and support staff. Technologies developed at Berkeley Lab have generated billions of dollars in revenues, and thousands of jobs. Savings as a result of Berkeley Lab developments in lighting and windows, and other energy-efficient technologies, have also been in the billions of dollars.

Berkeley Lab was founded in 1931 by Ernest Orlando Lawrence, a University of California-Berkeley physicist who won the 1939 Nobel Prize in physics for his invention of the cyclotron, a circular particle accelerator that opened the door to high-energy physics. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab legacy that continues today.

History

1931–1941

The laboratory was founded on August 26, 1931, by Ernest Lawrence, as the Radiation Laboratory of the University of California-Berkeley, associated with the Physics Department. It centered physics research around his new instrument, the cyclotron, a type of particle accelerator for which he was awarded the Nobel Prize in Physics in 1939.

E.O. Lawrence’ first cyclotron.

LBNL 88 inch cyclotron.

LBNL 88 inch cyclotron.

Throughout the 1930s, Lawrence pushed to create larger and larger machines for physics research, courting private philanthropists for funding. He was the first to develop a large team to build big projects to make discoveries in basic research. Eventually these machines grew too large to be held on the university grounds, and in 1940 the lab moved to its current site atop the hill above campus. Part of the team put together during this period includes two other young scientists who went on to establish large laboratories; J. Robert Oppenheimer founded The DOE’s Los Alamos Laboratory, and Robert Wilson founded The DOE’s Fermi National Accelerator Laboratory.

1942–1950

Leslie Groves visited Lawrence’s Radiation Laboratory in late 1942 as he was organizing the Manhattan Project, meeting J. Robert Oppenheimer for the first time. Oppenheimer was tasked with organizing the nuclear bomb development effort and founded today’s DOE Los Alamos National Laboratory to help keep the work secret. At the RadLab, Lawrence and his colleagues developed the technique of electromagnetic enrichment of uranium using their experience with cyclotrons. The “calutrons” (named after the University) became the basic unit of the massive Y-12 facility in Oak Ridge, Tennessee. Lawrence’s lab helped contribute to what have been judged to be the three most valuable technology developments of the war (the atomic bomb, proximity fuse, and radar). The cyclotron, whose construction was stalled during the war, was finished in November 1946. The Manhattan Project shut down two months later.

1951–2018

After the war, the Radiation Laboratory became one of the first laboratories to be incorporated into the Atomic Energy Commission (AEC) (now The Department of Energy . The most highly classified work remained at Los Alamos, but the RadLab remained involved. Edward Teller suggested setting up a second lab similar to Los Alamos to compete with their designs. This led to the creation of an offshoot of the RadLab (now The DOE’s Lawrence Livermore National Laboratory) in 1952. Some of the RadLab’s work was transferred to the new lab, but some classified research continued at Berkeley Lab until the 1970s, when it became a laboratory dedicated only to unclassified scientific research.

Shortly after the death of Lawrence in August 1958, the UC Radiation Laboratory (both branches) was renamed the Lawrence Radiation Laboratory. The Berkeley location became the Lawrence Berkeley Laboratory in 1971, although many continued to call it the RadLab. Gradually, another shortened form came into common usage, LBNL. Its formal name was amended to Ernest Orlando Lawrence Berkeley National Laboratory in 1995, when “National” was added to the names of all DOE labs. “Ernest Orlando” was later dropped to shorten the name. Today, the lab is commonly referred to as “Berkeley Lab”.

The Alvarez Physics Memos are a set of informal working papers of the large group of physicists, engineers, computer programmers, and technicians led by Luis W. Alvarez from the early 1950s until his death in 1988. Over 1700 memos are available on-line, hosted by the Laboratory.

The lab remains owned by the Department of Energy , with management from the University of California-Berkeley. Companies such as Intel were funding the lab’s research into computing chips.

Science mission

From the 1950s through the present, Berkeley Lab has maintained its status as a major international center for physics research, and has also diversified its research program into almost every realm of scientific investigation. Its mission is to solve the most pressing and profound scientific problems facing humanity, conduct basic research for a secure energy future, understand living systems to improve the environment, health, and energy supply, understand matter and energy in the universe, build and safely operate leading scientific facilities for the nation, and train the next generation of scientists and engineers.

The Laboratory’s 20 scientific divisions are organized within six areas of research: Computing Sciences; Physical Sciences; Earth and Environmental Sciences; Biosciences; Energy Sciences; and Energy Technologies. Berkeley Lab has six main science thrusts: advancing integrated fundamental energy science; integrative biological and environmental system science; advanced computing for science impact; discovering the fundamental properties of matter and energy; accelerators for the future; and developing energy technology innovations for a sustainable future. It was Lawrence’s belief that scientific research is best done through teams of individuals with different fields of expertise, working together. His teamwork concept is a Berkeley Lab tradition that continues today.

Berkeley Lab operates five major National User Facilities for the DOE Office of Science:

The Advanced Light Source (ALS) is a synchrotron light source with 41 beam lines providing ultraviolet, soft x-ray, and hard x-ray light to scientific experiments.

The DOE’s Lawrence Berkeley National Laboratory Advanced Light Source.

The ALS is one of the world’s brightest sources of soft x-rays, which are used to characterize the electronic structure of matter and to reveal microscopic structures with elemental and chemical specificity. About 2,500 scientist-users carry out research at ALS every year. Berkeley Lab is proposing an upgrade of ALS which would increase the coherent flux of soft x-rays by two-three orders of magnitude.

Berkeley Lab Laser Accelerator (BELLA) Center

A view of BELLA, the Berkeley Lab Laser Accelerator. Credit: Roy Kaltschmidt-Berkeley Lab.

LBNL FLEXLAB.

The DOE Joint Genome Institute supports genomic research in support of the DOE missions in alternative energy, global carbon cycling, and environmental management. The JGI’s partner laboratories are Berkeley Lab, the DOE’s Lawrence Livermore National Laboratory, the DOE’s Oak Ridge National Laboratory (ORNL), the DOE’s Pacific Northwest National Laboratory (PNNL), and the DOE’s HudsonAlpha Institute for Biotechnology . The JGI’s central role is the development of a diversity of large-scale experimental and computational capabilities to link sequence to biological insights relevant to energy and environmental research. A large number of scientist-users take advantage of JGI’s capabilities for their research every year.

LBNL Molecular Foundry

The LBNL Molecular Foundry is a multidisciplinary nanoscience research facility. Its seven research facilities focus on Imaging and Manipulation of Nanostructures; Nanofabrication; Theory of Nanostructured Materials; Inorganic Nanostructures; Biological Nanostructures; Organic and Macromolecular Synthesis; and Electron Microscopy. Approximately 700 scientist-users make use of these facilities in their research every year.

The DOE’s NERSC National Energy Research Scientific Computing Center is the scientific computing facility that provides large-scale computing for the DOE’s unclassified research programs. Its current systems provide over 3 billion computational hours annually. NERSC supports 6,000 scientific users from universities, national laboratories, and industry.

DOE’s NERSC National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory.

Cray Cori II supercomputer at National Energy Research Scientific Computing Center at DOE’s Lawrence Berkeley National Laboratory, named after Gerty Cori, the first American woman to win a Nobel Prize in science.

Cray Shasta Perlmutter SC18 AMD Epyc Nvidia pre-exascale supercomputer.

NERSC is a DOE Office of Science User Facility.

The DOE’s Energy Science Network is a high-speed network infrastructure optimized for very large scientific data flows. ESNet provides connectivity for all major DOE sites and facilities, and the network transports roughly 35 petabytes of traffic each month.

Berkeley Lab is the lead partner in the DOE’s Joint Bioenergy Institute (JBEI), located in Emeryville, California. Other partners are the DOE’s Sandia National Laboratory, the University of California (UC) campuses of Berkeley and Davis, the Carnegie Institution for Science , and the DOE’s Lawrence Livermore National Laboratory (LLNL). JBEI’s primary scientific mission is to advance the development of the next generation of biofuels – liquid fuels derived from the solar energy stored in plant biomass. JBEI is one of three new U.S. Department of Energy (DOE) Bioenergy Research Centers (BRCs).

Berkeley Lab has a major role in two DOE Energy Innovation Hubs. The mission of the Joint Center for Artificial Photosynthesis (JCAP) is to find a cost-effective method to produce fuels using only sunlight, water, and carbon dioxide. The lead institution for JCAP is the California Institute of Technology and Berkeley Lab is the second institutional center. The mission of the Joint Center for Energy Storage Research (JCESR) is to create next-generation battery technologies that will transform transportation and the electricity grid. The DOE’s Argonne National Laboratory leads JCESR and Berkeley Lab is a major partner.

From The College of Engineering At The University of Miami: “Bio-inspired solutions to tackle a billion-dollar corrosion problem”

From The College of Engineering

At

The University of Miami

1.30.24

A new highly competitive federal grant is helping College of Engineering assistant professor Ali Ghahremaninezhad find solutions for an important challenge: the longevity of the country’s infrastructure.

UMiami.

In a significant stride towards combating corrosion, researchers led by civil and architectural engineering assistant professor Ali Ghahremaninezhad are pioneering a bio-inspired strategy. Their work, funded by a new grant from the United States Department of Transportation, focuses on harnessing genetically engineered biomolecules derived from biomass to tackle corrosion issues.

Metal corrosion stands as a primary problem behind the deterioration of both civil and defense infrastructure, causing substantial economic losses. Estimates suggest that unmitigated corrosion costs $276 billion annually, chipping away at approximately 3.1 percent of the United States’ Gross Domestic Product (GDP). Ghahremaninezhad’s team seeks to change the approach to corrosion prevention by exploring genetically modified biomolecules.

The key innovation lies in combining different biological elements to identify biomolecules that interact with specific metal surfaces under certain environmental conditions. This approach not only seeks to stop corrosion but also offers the ability to tailor and program these biomolecules for a variety of environments.

UMiami.

Beyond the immediate impact on infrastructure protection, the team recognizes the broader environmental implications. The production and use of biobased products, a central focus of Ghahremaninezhad’s research, are known to result in lower greenhouse gas emissions compared to traditional petroleum-based counterparts. This dual-pronged approach not only addresses the immediate corrosion crisis but also aligns with broader goals of mitigating climate change and fostering a sustainable bioeconomy.

See the full article here.

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply” near the bottom of the post.

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Please help promote STEM in your local schools.

Stem Education Coalition

The College of Engineering is focused on educating the next generation of engineers to prepare societal leaders with strong scientific and technical skills combined with an ethical and moral outlook to impact academia, business, government and/or the non-profit sector. Through discovery of new knowledge and its application we tackle global challenge problems, and create opportunities through innovation and entrepreneurship. We do this with a deep commitment to excellence, demonstrated meritocracy, transparency, inclusiveness, and diversity.

The College of Engineering transforms lives by:

Creating new knowledge
Transmitting knowledge through innovative education for facilitating life-long learning
Translating knowledge through innovation and entrepreneurship, and
Applying knowledge to benefit the community

The University of Miami is a private research university in Coral Gables, Florida. The university enrolls over 19,000 students in 12 separate colleges and schools, including the Leonard M. Miller School of Medicine in Miami’s Health District, a law school on the main campus, and the Rosenstiel School of Marine and Atmospheric Science focused on the study of oceanography and atmospheric sciences on Virginia Key, with research facilities at the Richmond Facility in southern Miami-Dade County.

The university offers 132 undergraduate, 148 master’s, and 67 doctoral degree programs, of which 63 are research/scholarship and 4 are professional areas of study. Over the years, the university’s students have represented all 50 states and close to 150 foreign countries. With more than 16,000 full- and part-time faculty and staff, The University of Miami is a top 10 employer in Miami-Dade County. The University of Miami’s main campus in Coral Gables has 239 acres and over 5.7 million square feet of buildings.

The University of Miami is classified among “R1: Doctoral Universities – Very high research activity”. The University of Miami annual research expenditures are over $400 million. The University of Miami offers a large library system with over 3.9 million volumes and exceptional holdings in Cuban heritage and music.

The University of Miami also offers a wide range of student activities, including fraternities and sororities, and hundreds of student organizations. The Miami Hurricane, the student newspaper, and WVUM, the student-run radio station, have won multiple collegiate awards. The University of Miami’s intercollegiate athletic teams, collectively known as the Miami Hurricanes, compete in Division I of the National Collegiate Athletic Association. The University of Miami’s football team has won national championships since and its baseball team has won national championships.

Research

The University of Miami is classified among “R1: Doctoral Universities – Very high research activity”. The University of Miami receives over $200 million in annual federal research funding, including over $131 million from the Department of Health and Human Services and $15 million from the National Science Foundation. Of the $8.2 billion appropriated by Congress in 2009 as a part of the stimulus bill for research priorities of The National Institutes of Health, the Miller School received $40.5 million. In addition to research conducted in the individual academic schools and departments, Miami has the following university-wide research centers:

The Center for Computational Science
The Institute for Cuban and Cuban-American Studies (ICCAS)
Leonard and Jayne Abess Center for Ecosystem Science and Policy
The Miami European Union Center: This group is a consortium with Florida International University established in fall 2001 with a grant from the European Commission through its delegation in Washington, D.C., intended to research economic, social, and political issues of interest to the European Union.
The Sue and Leonard Miller Center for Contemporary Judaic Studies
John P. Hussman Institute for Human Genomics – studies possible causes of Parkinson’s disease, Alzheimer’s disease and macular degeneration.
Center on Research and Education for Aging and Technology Enhancement (CREATE)
Wallace H. Coulter Center for Translational Research

The Miller School of Medicine receives more than $200 million per year in external grants and contracts to fund 1,500 ongoing projects. The medical campus includes more than 500,000 sq ft (46,000 m^2) of research space and the The University of Miami Life Science Park, which has an additional 2,000,000 sq ft (190,000 m^2) of space adjacent to the medical campus. The University of Miami’s Interdisciplinary Stem Cell Institute seeks to understand the biology of stem cells and translate basic research into new regenerative therapies.

The Rosenstiel School of Marine and Atmospheric Science receives over $50 million in annual external research funding. Their laboratories include a salt-water wave tank, a five-tank Conditioning and Spawning System, multi-tank Aplysia Culture Laboratory, Controlled Corals Climate Tanks, and DNA analysis equipment. The campus also houses an invertebrate museum with 400,000 specimens and operates the Bimini Biological Field Station, an array of oceanographic high-frequency radar along the US east coast, and the Bermuda aerosol observatory. The University of Miami also owns the Little Salt Spring, a site on the National Register of Historic Places, in North Port, Florida, where RSMAS performs archaeological and paleontological research.

The University of Miami built a brain imaging annex to the James M. Cox Jr. Science Center within the College of Arts and Sciences. The building includes a human functional magnetic resonance imaging (fMRI) laboratory, where scientists, clinicians, and engineers can study fundamental aspects of brain function. Construction of the lab was funded in part by a $14.8 million in stimulus money grant from the National Institutes of Health.

The university receives over $161 million in science and engineering funding from the U.S. federal government, the largest Hispanic-serving recipient and very high overall. $117 million of the funding was through the Department of Health and Human Services and was used largely for the medical campus.

The University of Miami maintains one of the largest centralized academic cyber infrastructures in the country with numerous assets. The Center for Computational Science High Performance Computing group has been in continuous operation since 2007. Over that time the core has grown from a zero HPC cyberinfrastructure to a regional high-performance computing environment that currently supports more than 1,200 users, 220 TFlops of computational power, and more than 3 Petabytes of disk storage.

From Science Magazine : “Tiny fossils reveal microbes that gave rise to all plants and animals became multicellular 1.6 billion years ago”

From Science Magazine

1.24.24
Elizabeth Pennisi
With reporting by Dennis Normile.

Early eukaryotes found in ancient Chinese rock formation offer a “grand vision of life”.

The 1.635-billion-year-old Chuanlinggou Formation in China yielded microscopic, algalike fossils.Lanyun Miao et al./Chinese Academy of Sciences’s Nanjing Institute of Geology and Palaeontology.

A new study describing a microscopic, algalike fossil dating back more than 1.6 billion years supports the idea that one of the hallmarks of the complex life we see around us—multicellularity— is much older than previously thought. Together with other recent research, the fossil, reported today in Science Advances, suggests the lineage known as eukaryotes— which features compartmentalized cells and includes everything from redwoods to jellies to people—became multicellular some 600 million years earlier than scientists once generally thought [Science Advances].

“It’s a fantastic paper,” says Michael Travisano, an evolutionary ecologist at the University of Minnesota who helped show that yeast can become multicellular in the lab. “This gives us a better idea of the grand vision of life.”

Typically, biologists subdivide that grand vision into two categories: eukaryotes, with their DNA packaged into nuclei, and prokaryotes such as bacteria, which have free-floating DNA. Prokaryotes evolved first, up to 3.9 billion years ago; within a few hundred million years, some of them, the cyanobacteria, began to form chains of cells, considered an advance in life’s complexity. About 2 billion years ago, much larger, single-cell eukaryotes bearing nuclei showed up. For decades, researchers thought eukaryotes didn’t form simple multicellular structures until 1 billion years after they arose, and that once chain structures evolved, more elaborate body plans—animals with organs—appeared soon after. “There was this perception that multicellularity was hard [to evolve],” Travisano says.

Then in 1989, researchers described Qingshania magnifica, a microscopic fossil they suggested was a primitive green alga, a multicellular eukaryote. No one paid the discovery much mind, even though it came from the Chuanlinggou Formation in North China, which includes layers that are 1.6 billion years old. But since 2015, Maoyan Zhu and Lanyun Miao, paleobiologists at the Chinese Academy of Sciences’s Nanjing Institute of Geology and Palaeontology, have collected rocks from the same area, dissolved them, and eventually uncovered 279 microscopic fossils, all but one of them specimens of Q. magnifica.

In today’s paper, they report that the fossils consist of strings of up to 20 cylindrical cells, with adjoining cell walls, like plants, visible under a microscope as dark rings. Several fossils had spores—with their own cell walls—suggesting the filaments had specialized reproductive structures.

“What’s striking about these fossils is they are really rather enormous for that age, and they are multicellular,” says Jochen Brocks, an organic geochemist at Australian National University. William Ratcliff, an evolutionary biologist at the Georgia Institute of Technology who also works on multicellular yeast, adds that he’s impressed by the level of internal detail revealed in the ancient life. “I got a little dopamine hit seeing those internal sporelike compartments.”

Miao performed chemical tests on the fossils and found the structures of their organic carbon compounds were different from those in cyanobacteria fossils in these rocks. Her team concluded the filaments were most likely green algae, similar to modern eukaryotes such as Urospora wormskioldii.

Some of the microscopic fossils found in China included spores (top image).Lanyun Miao et al./Chinese Academy of Sciences’s Nanjing Institute of Geology and Palaeontology.

“The authors have done a commendable job of interpreting the fossils,” says Stefan Bengtson, paleobiologist emeritus at the Swedish Museum of Natural History. “The hypothesis that these are filamentous green algae is a good start.”

The new findings build on work Bengtson and colleagues reported in 2017 [plosbiology], when they proposed that 1.6-billion-year-old fossils found in India represented red algae. In 2021, another team described “walled microfossils,” which they interpreted as a diverse set of eukaryotes, in deposits from Canada dating back 1.57 billion years . And just last month, Leigh Anne Riedman and Susannah Porter, paleontologists at the University of California-Santa Barbara, and colleagues described what they say are several eukaryotic fossils found in 1.642-billion-year-old rocks from Australia.

The sheer diversity of body plans found in these early forms of multicellular life is astounding, Riedman notes. Some were cylindrical with chambers. Others were spherical. One had a lid that appeared to open, possibly to get rid of the cell’s contents. “Every indication suggests eukaryotes were much more diverse and complex by this time than previously appreciated,” she says.

If simple but diverse multicellular forms appeared so early, then complex multicellularity took a lot longer to evolve than most researchers had thought; the first creatures with organs and cells that did not have direct access to the outside environment didn’t appear until less than 1 billion years ago. Such a delayed timeline makes sense to Shuhai Xiao, a geobiologist and a paleobiologist at the Virginia Polytechnic Institute and State University. Truly complex eukaryotes “have multiple cells that stay together, communicate with each other, and have different sizes, shapes, and functions,” he explains. “It takes time [to make such advances].”

If the recent findings hold up, they are “remarkable” and transformative, says László Nagy, an evolutionary biologist at the Hungarian Research Network’s Biological Research Centre. But he’s cautious about claiming similarities to living algae. “It is challenging to compare a 1.6-billion-year-old organism to extant ones,” Nagy says. “This is such a long time that any resemblance to extant organisms may be due to chance.” And Ratcliff says these organisms may not even be eukaryotes: “It’s possible that [these fossils] are just superweird bacteria that don’t resemble extant species.”

But Harvard University paleontologist Andrew Knoll, a co-author on the Science Advances paper, says the data and the presence of cell walls—which prokaryotes lack—are proof enough. “If this were found in [400-million-year-old] Devonian rocks, people would describe it as algae and no one would bat an eyelash,” he says.

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply” at the bottom of the post.

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Please help promote STEM in your local schools.

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From The Robert R. McCormick School of Engineering At Northwestern University : “Dirt-powered fuel cell runs forever”

From The Robert R. McCormick School of Engineering

At

Northwestern University

1.12.24
Amanda Morris

New tech harvests energy from microbes in soil to power sensors and communications.

Working in the lab, Northwestern alumnus Bill Yen buries the fuel cell in soil.

A Northwestern University-led team of researchers has developed a new fuel cell that harvests energy from microbes living in dirt.

About the size of a standard paperback book, the completely soil-powered technology could fuel underground sensors used in precision agriculture and green infrastructure. This potentially could offer a sustainable, renewable alternative to batteries, which hold toxic, flammable chemicals that leach into the ground, are fraught with conflict-filled supply chains and contribute to the ever-growing problem of electronic waste.

To test the new fuel cell, the researchers used it to power sensors measuring soil moisture and detecting touch, a capability that could be valuable for tracking passing animals. To enable wireless communications, the researchers also equipped the soil-powered sensor with a tiny antenna to transmit data to a neighboring base station by reflecting existing radio frequency signals.

Not only did the fuel cell work in both wet and dry conditions, but its power also outlasted similar technologies by 120%.

The research was published Jan. 12 in the Proceedings of the Association for Computing Machinery on Interactive, Mobile, Wearable and Ubiquitous Technologies. The study authors also are releasing all designs, tutorials and simulation tools to the public, so others may use and build upon the research.

“The number of devices in the Internet of Things (“IoT”) is constantly growing,” said Northwestern alumnus Bill Yen, who led the work. “If we imagine a future with trillions of these devices, we cannot build every one of them out of lithium, heavy metals and toxins that are dangerous to the environment. We need to find alternatives that can provide low amounts of energy to power a decentralized network of devices. In a search for solutions, we looked to soil microbial fuel cells, which use special microbes to break down soil and use that low amount of energy to power sensors. As long as there is organic carbon in the soil for the microbes to break down, the fuel cell can potentially last forever.”

“These microbes are ubiquitous; they already live in soil everywhere,” said Northwestern’s George Wells, a senior author on the study. “We can use very simple engineered systems to capture their electricity. We’re not going to power entire cities with this energy. But we can capture minute amounts of energy to fuel practical, low-power applications.”

Wells is an associate professor of civil and environmental engineering at Northwestern’s McCormick School of Engineering. Now a Ph.D. student at Stanford University, Yen started this project when he was an undergraduate researcher in Wells’ laboratory.

Solutions for a dirty job

In recent years, farmers worldwide increasingly have adopted precision agriculture as a strategy to improve crop yields. The tech-driven approach relies on measuring precise levels of moisture, nutrients and contaminants in soil to make decisions that enhance crop health. This requires a widespread, dispersed network of electronic devices to continuously collect environmental data.

“If you want to put a sensor out in the wild, in a farm or in a wetland, you are constrained to putting a battery in it or harvesting solar energy,” Yen said. “Solar panels don’t work well in dirty environments because they get covered with dirt, do not work when the sun isn’t out and take up a lot of space. Batteries also are challenging because they run out of power. Farmers are not going to go around a 100-acre farm to regularly swap out batteries or dust off solar panels.”

To overcome these challenges, Wells, Yen and their collaborators wondered if they could instead harvest energy from the existing environment. “We could harvest energy from the soil that farmers are monitoring anyway,” Yen said.

‘Stymied efforts’

Making their first appearance in 1911, soil-based microbial fuel cells (MFCs) operate like a battery — with an anode, cathode and electrolyte. But instead of using chemicals to generate electricity, MFCs harvest electricity from bacteria that naturally donate electrons to nearby conductors. When these electrons flow from the anode to the cathode, it creates an electric circuit.

But in order for microbial fuel cells to operate without disruption, they need to stay hydrated and oxygenated — which is tricky when buried underground within dry dirt.

“Although MFCs have existed as a concept for more than a century, their unreliable performance and low output power have stymied efforts to make practical use of them, especially in low-moisture conditions,” Yen said.

Winning geometry

With these challenges in mind, Yen and his team embarked on a two-year journey to develop a practical, reliable soil-based MFC. His expedition included creating — and comparing — four different versions. First, the researchers collected a combined nine months of data on the performance of each design. Then, they tested their final version in an outdoor garden.

The best-performing prototype worked well in dry conditions as well as within a water-logged environment. The secret behind its success: Its geometry. Instead of using a traditional design, in which the anode and cathode are parallel to one another, the winning fuel cell leveraged a perpendicular design.

Made of carbon felt (an inexpensive, abundant conductor to capture the microbes’ electrons), the anode is horizontal to the ground’s surface. Made of an inert, conductive metal, the cathode sits vertically atop the anode.

Although the entire device is buried, the vertical design ensures that the top end is flush with the ground’s surface. A 3D-printed cap rests on top of the device to prevent debris from falling inside. And a hole on top and an empty air chamber running alongside the cathode enable consistent airflow.

The lower end of the cathode remains nestled deep beneath the surface ensuring that it stays hydrated from the moist, surrounding soil — even when the surface soil dries out in the sunlight. The researchers also coated part of the cathode with waterproofing material to allow it to breathe during a flood. And, after a potential flood, the vertical design enables the cathode to dry out gradually rather than all at once.

On average, the resulting fuel cell generated 68 times more power than needed to operate its sensors. It also was robust enough to withstand large changes in soil moisture — from somewhat dry (41% water by volume) to completely underwater.

The researchers say all components for their soil-based MFC can be purchased at a local hardware store. Next, they plan to develop a soil-based MFC made from fully biodegradable materials. Both designs bypass complicated supply chains and avoid using conflict minerals.

“With the COVID-19 pandemic, we all became familiar with how a crisis can disrupt the global supply chain for electronics,” said study co-author Josiah Hester, a former Northwestern faculty member who is now at the Georgia Institute of Technology. “We want to build devices that use local supply chains and low-cost materials so that computing is accessible for all communities.”

See the full article here .

Comments are invited and will be appreciated, especially if the reader finds any errors which I can correct. Use “Reply” at the bottom of the post.

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Please help promote STEM in your local schools.

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Established in 1909, the The Robert R.McCormick School of Engineering is one of twelve constituent schools at Northwestern University. Most engineering classes are held in the Technological Institute (1942), which students commonly refer to as “Tech.” In October 2005, another building affiliated with the School, the Ford Motor Company Engineering Design Center, opened.

The trustees of Northwestern University founded a College of Technology in June 1873, but in his report for 1876-77, President Oliver Marcy announced that the new college had failed for lack of financial resources to develop the faculty and facilities.

In 1891, President Henry Wade Rogers called for the founding of a new Engineering School, stating that universities in general were “not performing the work necessary to prepare men for the various activities of modern life, so different from the life their fathers lived half a century ago.” This was realized in 1909, when the new College of Engineering was opened in Swift Hall. Operationally, the Engineering School until the mid-1920s was a department of the College of Liberal Arts. The major emphasis was on a broad general education with a particular stress on mathematics and science. In 1937, the Engineering School ran into difficulties with the American Engineers’ Council for Professional Development, which denied the School accreditation. In response, a four-year curriculum satisfying the ECPD was put into place.

In 1939, Walter Patton Murphy (1873–1942), a wealthy inventor of railroad equipment, donated $6.735 million to the School of Engineering. Murphy meant for the Institute to offer a “cooperative” education, whereby academic courses and practical application in industrial settings were closely integrated. In 1942, Northwestern received an additional bequest of $28 million from Murphy’s estate to provide for an engineering school “second to none.” A cooperative education program was designed in the late 1930s by Charles F. Kettering, former research head of General Motors, and Herman Schneider, dean of the engineering school at the University of Cincinnati. The program required undergraduates to work outside the classroom in technical positions for several terms over the course of their college years.

South Campus

Northwestern is recognized nationally and internationally for its educational programs.

On May 31, 1850, nine men gathered to begin planning a university that would serve the Northwest Territory.

Given that they had little money, no land and limited higher education experience, their vision was ambitious. But through a combination of creative financing, shrewd politicking, religious inspiration and an abundance of hard work, the founders of Northwestern University were able to make that dream a reality.

In 1853, the founders purchased a 379-acre tract of land on the shore of Lake Michigan 12 miles north of Chicago. They established a campus and developed the land near it, naming the surrounding town Evanston in honor of one of the University’s founders, John Evans. After completing its first building in 1855, Northwestern began classes that fall with two faculty members and 10 students.
Twenty-one presidents have presided over Northwestern in the years since. The University has grown to include 12 schools and colleges, with additional campuses in Chicago and Doha, Qatar.

From EOS: “Modern Microbial Mats Offer Glimpses of Other Times and Places”

From EOS

At

AGU

1.12.24
Bopaiah A. Biddanda
biddandb@gvsu.edu
Anthony D. Weinke
Ian P. Stone
Steven A. Ruberg
Phil A. Hartmeyer

This late-afternoon underwater image displays the dynamic tapestry of colors making up a microbial mat at the bottom of Middle Island Sinkhole in Lake Huron at about 23 meters deep in July 2021. These mats are composed of photosynthetic cyanobacteria (purple) that migrate to the surface during the day and chemosynthetic microbes (white) that migrate to the surface at night, shifting the mat color from mostly purple during the day to mostly white at night. Credit: Phil Hartmeyer, NOAA Thunder Bay National Marine Sanctuary.

Imagine you could go back in time to see what life was like in the sulfur-rich, oxygen-poor seas of Earth’s Proterozoic eon (~2.5–0.6 billion years ago). No one knows exactly what ecosystems of the distant past looked like, but there is a good chance that you’d see thin veils of microbial life clinging to shallow sunlit sediments or thriving around deep-sea hydrothermal vents.

As it happens, geology, water, and time have converged to paint colorful microbial mats across underwater landscapes in North America’s Great Lakes (and elsewhere) that are thought to resemble the planet’s early biosphere. Similar mat communities may also exist and mark the beginnings of life on other habitable planets or moons.

Around the world, isolated aquatic environments with low oxygen and high sulfur levels provide refugia that enable such modern-day mats to thrive. These communities of “extremophiles”, such as those in sinkholes at the bottom of Lake Huron, contribute greatly to our understanding of the origins of life on Earth. They also add to Earth’s biodiversity, provide relatively easy to access analogues of deep marine vents, and can serve as test beds in our search for alien life.

Recent research has continued to reveal fascinating and vital aspects of microbial mats that survive under extreme environmental conditions. For example, findings have indicated that Lake Huron’s sinkholes are carbon sinks, that mat microbes may optimize oxygen production through daily migrations of less than a millimeter, and that more submerged sinkholes are present across the Great Lakes basin than previously thought.

These unique ecosystems have many more secrets to reveal and insights to offer about past, present, and maybe future life on Earth, as well as about the conditions under which life might survive on habitable extraterrestrial worlds. However, they are also vulnerable to damage from natural and anthropogenic pressures, suggesting an important need not only to further study them but also to conserve them.

Mats of the Great Lakes

Today, microbial mats find refugia in globally distributed extreme environments such as cold seeps, thermal springs, permanently ice covered lakes in the dry valleys of Antarctica, submarine blue holes, and deep-sea vents.

In 2001, maritime archaeologists exploring Thunder Bay National Marine Sanctuary in Lake Huron made a serendipitous finding of what appeared to be limestone karst features. This was the first of many discoveries of submerged sinkholes in the lake, in everywhere from sunlit shallows to its deep, dark bottom waters. Further studies have revealed that these groundwater-fed sinkholes contain relatively dense, salty, acidic, and cold water compared with the typical fresh lake water above [Biddanda et al., 2012]. This venting groundwater spreads over the lake bottom, fueling growth of vibrantly colored microbial mats.

All four lower Great Lakes (from west to east: Michigan, Huron, Erie, and Ontario) have foundations of roughly 400-million-year-old Paleozoic limestone karst. Groundwater in their aquifers washes through marine evaporites, gaining sulfates and losing oxygen during its transit underground to springs and sinkholes. Over time, this water has eroded the limestone underneath the Great Lakes to form submerged sinkholes.

Divers float over the wall of a sinkhole covered with purple microbial mats clinging to rocks and white microbial strings that waft in the relatively dense groundwater current that is falling over a sill. Here high-sulfur, low-oxygen groundwater streaming through ancient Paleozoic marine evaporites fuels the filamentous, purple-pigmented photosynthetic cyanobacteria and nonpigmented sulfur-oxidizing chemosynthetic bacteria that form the microbial mats. Credit: Phil Hartmeyer, NOAA Thunder Bay National Marine Sanctuary.

These Great Lakes sinkholes are hard to find because they are relatively small—ranging from the size of a coffee table to a soccer field—and far apart (meters to kilometers) and because there are no signatures of their presence on the lakes’ surfaces. Yet they may be abundant in all four lower Great Lakes given their similar bedrock. Indeed, multibeam acoustic surveys by our team in the past 6 years have revealed more than 2 dozen previously unmapped sinkholes in offshore Lake Huron at depths greater than 120 meters. We also recently explored the Great Sulphur Spring, a sinkhole about half the size of a soccer field in the Lake Erie basin containing cyanobacterial mats similar to those in Lake Huron sinkholes.

Meanwhile, colleagues at Wisconsin Shipwreck Coast National Marine Sanctuary have recently reported numerous lake bottom anomalies in western Lake Michigan that are hallmarks of sinkholes. And sport divers have made many reports of mat sightings in Lake Ontario and Lake Erie, although these reports have not yet been investigated scientifically.

Clues to the Biosphere’s Beginnings

Microbial life in many of these sinkholes is characterized by a textbook redox tower, a series of oxidation-reduction reactions extending from organisms on the mat surface that make their own food in oxygen-free as well as oxygen-rich water (anoxygenic and oxygenic autotrophs, respectively) down to methane-generating microbes in the oxygen-free sediments below (methanogenic chemoautotrophs) [Biddanda et al., 2012]. Photosynthetic and chemosynthetic mats colonize shallow, sunlit sinkholes. In deeper water, where sunlight cannot penetrate, sinkholes are inhabited by chemosynthetic mats similar to those found around submarine seeps in the ocean where sulfur-rich water is venting.

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Knowledge of the rate and timing of photosynthesis through Earth’s deep past is critical to understanding how the planet’s atmosphere became oxygenated. Infant Earth’s atmosphere contained essentially zero oxygen, but geologic evidence suggests that beginning about 2.5 billion years ago, oxygen slowly accumulated to concentrations that allow us to live and breathe today [Klatt et al., 2021].

Many theories have been proposed to explain the slow pace of oxygenation from about 1.8 billion to 0.8 billion years ago—the so-called Boring Billion—when seemingly little changed in the planet’s climate, chemistry, and biology. One theory, for example, posits that the younger Earth’s short day length (resulting from its faster rotation) limited the amount of photosynthesis that could occur over a continuous period of sunlight. As the tidal pull of the Moon slowed the planet’s spinning and day length increased, eventually to the 24 hours we experience now, the daily duration of photosynthesis also likely increased, resulting in net oxygenation of the water as well as the air.

Today, slow rates of oxygen production reminiscent of the Proterozoic are exemplified in shallow sinkholes where photosynthesis is closely balanced by respiration. Only late in the day does oxygen production outpace its consumption in these environments. Models suggest that such meager, but measurable, net oxygen production would have oxygenated the atmosphere over eons as Earth’s day length increased [Klatt et al., 2021].

Microbial Choreography

The everyday lifestyle of today’s sinkhole microbes offers clues to how the early biosphere might have worked to bury organic carbon and emit oxygen. In what might be a modern incarnation of the first synchronized movement ever choreographed, photosynthetic and chemosynthetic microbes alternately migrate hundreds of micrometers daily at speeds of 50–200 micrometers per minute toward the mat surfaces. There, they take turns harvesting sunlight and hydrogen sulfide during the day and oxygen at night, turning the mats distinctly purple during the day and white at night [Biddanda et al., 2023].

Evidence so far suggests that sinkholes are, indeed, sinks for carbon, with mat microbes’ daily migrations amplifying the biological pump’s removal of surface carbon into sediments. Nold et al. [2013] revealed that the huge repository of organic matter–rich sediments underlying sinkhole mats were primarily composed of planktonic carbon. Each day, vertically migrating phototactic (i.e., moving toward light) mat filaments climbed over settling organic carbon debris from above (such as dead plankton) and subducted it into the anaerobic layer below, where it was preserved.

Bright-field microscopy of motile microbes in the upper 1–2 millimeters of a mat reveals the dominant presence of photosynthetic cyanobacteria (purple in true color) and chemosynthetic sulfur-oxidizing microbes containing dark sulfur granules in Middle Island Sinkhole, Lake Huron. In a well-choreographed daily tango, these two groups of filamentous microbes take turns migrating vertically to the surface and then back down again during dawn and dusk. Watch time-lapse videos via the Open Science Framework here and here. Credit: Tony Weinke and Bopi Biddanda, Robert B. Annis Water Resources Institute, Grand Valley State University.

In another study, pebbles and shells placed atop mats were covered by mat filaments climbing over them within hours, and they were completely buried out of sight beneath sediments within days [Biddanda et al., 2015]. Biomarker studies in sulfur spring-fed Lake Cadagno in Switzerland also have shown evidence for high rates of organic carbon accumulation under microbial mats [Hebting et al., 2006].

Contributions to Modern-Day Biodiversity

Microbial mats in Lake Huron’s sinkholes comprise a diverse assemblage of bacteria, archaea, and viruses. A small number of protists and even low-oxygen-tolerant invertebrates such as tardigrades and nematodes live at the periphery of sinkholes where groundwater mixes with lake water. Primary producers in the mats include motile filamentous cyanobacteria that carry out both anoxygenic and oxygenic photosynthesis, as well as microbes that chemosynthesize by oxidizing sulfur. Sediment layers below the mats provide niches for sulfate-reducing bacteria, methanogens, and a variety of other organisms.

Consortium-lifestyle microbial mats offer ideal contexts for studying ecological, biogeochemical, and evolutionary interactions. For example, researchers have probed the long and intimate relationship between mat cyanobacteria and their viruses. Voorhies et al. [2015] directly linked an abundant virus to its cyanobacterial host in a modern-day mat ecosystem. Such interactions between the organisms may reenact some of the very first microscopic biologial warfare, which might have had profound outcomes for life over its long geobiologic history.

The mats also enable robust testing of the effects of biodiversity on ecosystem stability and of concepts like evenness–functional redundancy relationships. Indeed, omics studies (e.g., genomic, metabolomic, and, especially, proteomic) of mat community compositions suggest that these communities are functionally diverse and versatile [Voorhies et al., 2012; Grim et al., 2021; McGovern et al., 2023].

Mat organisms’ ability to thrive in extreme environments, including below winter ice cover in Great Lakes sinkholes, makes these mats practical analogues and test sites in our search for life in extraterrestrial hydrospheres [Biddanda et al., 2021]. In addition, they could harbor secondary metabolites of considerable pharmacological potential.

Another fascinating feature of these mats is distinctive conical protrusions filled with sedimentary gases such as methane that form near the peak growing season in summer. In the field, we have observed that these protrusions frequently tear off and float to the surface during late summer, where water and wind currents may disperse them. And in very recent laboratory studies, we have observed nonmotile filaments (of both cyanobacteria and sulfur-oxidizing microbes) in dehydrated mats become motile again within minutes of rehydration by groundwater. This observation, if confirmed, hints that transport by water and air could be a mechanism by which mat microbes have colonized refugia from the tropics to the poles.

A fingerlike protrusion rises from a microbial mat in the Middle Island Sinkhole. These features, which form as sedimentary gases such as methane rise from below the mat, often tear apart from the mat and float away, suggesting a possible means for mat microbes to disperse and colonize other refugia. Credit: Phil Hartmeyer, NOAA Thunder Bay National Marine Sanctuary.

The collective contribution of groundwater-fed sinkholes to the biodiversity and physiologies of the Great Lakes, as well as to the lakes’ water quality and even water levels, makes them important features. But the roles and significance of extant microbial mats thriving under extreme environmental conditions around the world remain largely unnoticed—and their vulnerability to environmental perturbations remains unquantified.

The potential for these environments to harbor clues to our evolutionary past and the fact that many basic scientific questions about their present-day structure and function remain unanswered support the need for their conservation.

The Vulnerability and Value of Mats

Mat ecosystems require protection because of their relative isolation, rarity, biological uniqueness and diversity, and likely outsized role in shaping the biosphere’s past and present—and possibly its future because it’s not inconceivable that Earth’s biosphere could someday be dominated by mats again if conditions for nonmicrobial life become untenable. Today these ecosystems are vulnerable to climate change and anthropogenic pressures from hydroengineering of watersheds and paving of on-land areas that recharge offshore sinkholes, for example. Holistic and sustainable conservation of submerged, mat-hosting sinkholes should involve protection of both terrestrial and aquatic domains that influence them.

Several anthropogenic perturbations may affect these systems in unknown ways, whereas others pose more obvious threats. We already know, for example, about the negative impacts of herbicides on photosynthetic communities of lakes and coastal ocean habitats such as corals, but we don’t know how sensitive isolated sinkhole microbial communities may be to such pollution. We also don’t know the age of groundwater entering Great Lakes sinkholes; the younger the water is, the greater the concern is that effects of terrestrial perturbations on mat ecosystems may be more immediate.

Other direct threats to these ecosystems emerge from potential industrial activities such as exploration for lake bed oil, gas, or minerals as well as offshore wind turbine siting, among others. Although sinkholes like those within Thunder Bay National Marine Sanctuary are relatively protected from such direct threats, sinkholes elsewhere across the lower Great Lakes are not afforded the same assurance.

In addition to more direct hazards, climate change may cause indirect threats because of its effects on everything from water temperatures and ice cover to wind and rainfall. Thus, it raises many conservation-related questions: How might climate change affect the survival of isolated and widely dispersed sinkhole communities? How might rapidly rising surface temperatures affect the currently stable groundwater temperature regime?

Groundwater flow into the sinkholes is fueled by hydrostatic pressure from rainfall over land. But what are the current rates of groundwater flows to the sinkholes, and what might happen to the composition of the mats if flow rates change? Anthropogenic warming is likely to amplify the water cycle and make it more variable. How might precipitation changes affect life in the sinkholes over the short and long terms?

Clearly, many unknowns exist regarding how microbial mats will respond to human disturbances and climate change in the future. As we work to reveal these unknowns, mat ecosystems provide fascinating, dynamic, and biodiverse theaters of life for exploration.

Author Information

Bopaiah A. Biddanda (biddandb@gvsu.edu) and Anthony D. Weinke, Robert B. Annis Water Resources Institute, Grand Valley State University, Muskegon, Mich.; Ian P. Stone, School for Environment and Sustainability, University of Michigan, Ann Arbor; Steven A. Ruberg, NOAA Great Lakes Environmental Research Laboratory, Ann Arbor, Mich.; and Phil A. Hartmeyer, NOAA Thunder Bay National Marine Sanctuary, Alpena, Mich.; now at NOAA Ocean Exploration and University Corporation for Atmospheric Research, Alpena, Mich.
Citation: Biddanda, B. A., A. D. Weinke, I. P. Stone, S. A. Ruberg, and P. A. Hartmeyer (2024), Modern microbial mats offer glimpses of other times and places, Eos, 105, https://doi.org/10.1029/2024EO240019. Published on 12 January 2024.

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“Eos” is the leading source for trustworthy news and perspectives about the Earth and space sciences and their impact. Its namesake is Eos, the Greek goddess of the dawn, who represents the light shed on understanding our planet and its environment in space by the Earth and space sciences.

From The University of Delaware : “New insights into microbial evolution”

From The University of Delaware

1.12.24
Erica K. Brockmeier
Photos by Evan Krape and courtesy of Terry Papoutsakis and John Hill
Photo illustration by Joy Smoker

University of Delaware engineers uncover new mechanism for gene transfer with implications for fields ranging from ecology to biotechnology and medicine.

Unidel Eugene du Pont Chair Professor Eleftherios “Terry” Papoutsakis (left) and doctoral candidate John Hill discovered a new mechanism for bacterial evolution. Their study, which was recently published in the journal mBio, has implications for a range of fields, from ecology to biotechnology and medicine.

If you still remember that “Dear King Phillip Came Over For Good Spaghetti,” you’ll likely also recall the corresponding taxonomic ranks of biology: Domain, Kingdom, Phylum, Class, Order, Family, Genus and Species. The two domains include prokaryotes, single-celled organisms such as bacteria and archaea, and eukaryotes, which include fungi, plants and animals.

Eukaryotes undergo evolution when mutations are passed down from parent to offspring, known as vertical gene transfer. For prokaryotes, evolution can take place through horizontal gene transfer (HGT for short), where genetic information is directly shared between bacteria. This process allows individual organisms, and even entire species, to quickly gain new genes, including potentially dangerous ones like those that confer antibiotic resistance.

At the University of Delaware, in the lab of Eleftherios “Terry” Papoutsakis, Unidel Eugene du Pont Chair Professor in the College of Engineering’s Department of Chemical and Biomolecular Engineering, the Department of Biological Sciences and the Delaware Biotechnology Institute, researchers recently discovered a new mechanism by which HGT can occur in bacteria. The findings in this study, led by doctoral alumnus Kamil Charubin and doctoral candidate John Hill, expand on the current understanding of evolution and survival strategies for complex microbiomes, with implications for fields ranging from ecology to biotechnology and medicine. The study was published in mBio.

The research for the group’s latest paper began after Charubin observed that two species of bacteria (Clostridium acetobutylicum and C. ljungdahlii) were exchanging nutrients, metabolites and cellular material at high rates when they were in close proximity to one another. They found that the cells were using a mechanism called heterologous cell fusion to transfer materials and wanted to see if bacteria could also transfer genetic information through this mechanism.

“This wasn’t just a few proteins but actually encompassed most of the materials in the cytoplasm,” Hill said. “These findings prompted us to determine whether or not genetic material, including plasmids, could be exchanged as well.”

The researchers found that two species of bacteria (Clostridium acetobutylicum and C. ljungdahlii) can share genetic information via heterologous cell fusion, a mechanism for horizontal gene transfer “that has not been previously contemplated or observed before,” Papoutsakis said.

To see if gene transfer was also occurring when the bacterial cells were in close contact, Hill adapted the group’s laboratory techniques so they could track the movement of the bacteria’s genome and plasmids (circular pieces of DNA used by bacteria that are separate from their genome). The researchers also used selective subculturing techniques, isolating C. acetobutylicum cells after they had taken up plasmids from C. ljungdahlii, then confirmed gene transfer using PacBio Single-Molecule Real Time (SMRT) sequencing data.

The results of this research show that the two species of Clostridium can indeed share genetic information via heterologous cell fusion, a mechanism for HGT “that has not been previously contemplated or observed before,” Papoutsakis said. “Through heterologous cell fusion, we found that there is exchange of DNA between the microbes and that the resulting hybrid cells contain large amounts of genomic DNA from both organisms.”

The researchers said that the group’s latest paper provides new insights into the processes and drivers of bacterial evolution.

“We know that microbial life has evolved in naturally occurring communities, and if there is a large number of interspecies interactions, including gene exchange, that would reveal another aspect of microbial evolution,” Hill said. “These results could implicate that microbes are not evolving independently from one another but rather that there exists a multiplicity of evolutionary trajectories within local environments which are motivated by a variety of external pressures, including HGT.”

Papoutsakis added that this study could also have implications in other fields as well, especially if it’s another way that bacteria can confer traits such as antibiotic resistance to one another.

“There’s a lot more complexity and interaction between microbes in natural microbiomes, such as those in the environment or the human gut, for example,” Papoutsakis said. “This kind of mechanism for HGT can really have important physiological and medical implications.”

This research was supported by a grant from the Army Research Office (W911NF-19-1-0274), the ARPA-E project under contract (AR0001505) and a U.S. Department of Education Graduate Assistance in Areas of National Need (GAANN) Fellowship to John Hill (P200A210065).

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Please help promote STEM in your local schools.

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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 (US)’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. In 2020 [needs an update], University of Delaware expects to open 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)