From The University of California-San Diego (US) via Science Alert (AU) : “Scientists Spot Eerily Sophisticated Patterns in ‘Simple’ Bacteria Colonies”

From The University of California-San Diego (US)

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ScienceAlert

Science Alert (AU)

7 JANUARY 2022
CLARE WATSON

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Bacillus subtilis, a bacterium found in soil, creates concentric rings as it grows. Credit:Kwang-Tao Chou/The University of California-San Diego (US).

Bacterial colonies can organize themselves into complex ring-like patterns which have an “intriguing similarity” to developing embryos and were thought to be unique to plants and animals, new research suggests.

Bacterial cells band together in clumps to form tightly packed colonies called biofilms that have a growing reputation [Nature Reviews Microbiology] for acting strangely like multicellular organisms. These biofilms can be found almost anywhere, from boat hulls, crops and hot springs, to the sticky, stubborn plaque that builds up on our teeth.

But as we’ve come to learn, biofilms should not be mistaken for slimy globs of cells – they can form sophisticated patterns that resemble how plants and animals develop segments as they grow, as this new research shows.

“We are seeing that biofilms are much more sophisticated than we thought,” says molecular biologist and study author Gürol Süel of The University of California-San Diego (US) whose previous research suggested biofilms share a collective memory similar to neurons in the brain (though not all scientists were convinced).

What’s more, biofilms also seem to be capable of recruiting other bacterial species to join their communities using long-range electrical signals.

In this latest study, Süel and colleagues have observed bacterial biofilms grown in the lab forming ring-like structures that are reminiscent of developmental ‘stripes’ seen in plants and animals.

In multicellular organisms, this cellular patterning known as segmentation gives rise to different types of tissues and complex body forms, whereas biofilm communities, which are essentially clumps of single-cell bacterium, were thought to form only the most primitive structures.

“Our discovery demonstrates that bacterial biofilms employ a developmental patterning mechanism hitherto believed to be exclusive to vertebrates and plant systems,” the researchers write.

In the lab, the team grew Bacillus subtilis, a rod-shaped bacterium that is found in soil and humans and forms wrinkly biofilms.

When starved of nitrogen, the growing biofilms organized themselves into clear circular bands, resembling tree rings and the sort of segmentation seen in developing embryos. Take a look at the video below, which captures one colony growing over two days.


Bacterial segmentation

This ring-like patterning, the researchers think, is generated by an underlying genetic circuitry in the bacterial cells which responds to extreme stress when nutrients such as vital nitrogen are in short supply.

Mathematical modelling and experiments revealed that as the biofilms grew outward and gobbled up nutrients, a ‘wave’ of nutrient depletion moved across the bacterial cells, essentially ‘freezing’ each cell in place with the stress-mitigating genes they were using at the time.

This pulsing, on-again off-again stress response created repeating segments of different cell types in the circular biofilm, the researchers found and is consistent with a ‘clock and waveform’ mechanism, which has only been seen in highly evolved organisms before this.

“In an expanding biofilm,” the researchers write, “this ‘freezing’ mechanism might naturally occur during development: replicating cells at the leading edge of biofilm grow, leaving behind daughter cells that become embedded within the biofilm and thus have less nutrient access.”

Süel and colleagues go on to speculate that this patterning mechanism might be another way biofilms cope with unpredictable conditions, hedging their bets so to speak, “as not all spores are formed at the same time and the same region of the biofilm.”

This is not the first time that scientists have spied bacterial communities mimicking multicellular organisms, and there are undoubtedly marked differences between the two, as the researchers note.

In 2020, scientists showed how biofilm growth mirrors embryonic development, with expanding colonies following a tightly orchestrated sequence of gene expression over several months [Molecular Biology and Evolution].

At the time that study was published, geneticist Tomislav Domazet-Lošo from The Catholic University of Croatia [Hrvatsko katoličko sveučilište](HRV) said: “Considering that the oldest known fossils are bacterial biofilms, it is quite likely that the first life was also multicellular, and not a single-celled creature as considered so far.”

Süel and colleagues also point out that biofilms don’t exhibit clear-cut boundaries between cell types in the same way that embryos develop distinct cell layers so any apparent similarities are just conceptual at this stage.

Still, these recent observations are reigniting some big questions about what defines a multicellular organism when ‘simple’ single-celled organisms appear to be far more advanced than we first thought.

“That debate will be rekindled by this [latest] study,” The University of Oxford (UK) cell biologist Tanmay Bharat told New Scientist. “From an evolutionary cell biology perspective, it would be interesting to study where the differences lie.”

The study was published in Cell.

See the full article here .

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The University of California- San Diego (US), is a public research university located in the La Jolla area of San Diego, California, in the United States. The university occupies 2,141 acres (866 ha) near the coast of the Pacific Ocean with the main campus resting on approximately 1,152 acres (466 ha). Established in 1960 near the pre-existing Scripps Institution of Oceanography, University of California, San Diego is the seventh oldest of the 10 University of California campuses and offers over 200 undergraduate and graduate degree programs, enrolling about 22,700 undergraduate and 6,300 graduate students. The University of California-San Diego is one of America’s “Public Ivy” universities, which recognizes top public research universities in the United States. The University of California-San Diego was ranked 8th among public universities and 37th among all universities in the United States, and rated the 18th Top World University by U.S. News & World Report’s 2015 rankings.

The University of California-San Diego is organized into seven undergraduate residential colleges (Revelle; John Muir; Thurgood Marshall; Earl Warren; Eleanor Roosevelt; Sixth; and Seventh), four academic divisions (Arts and Humanities; Biological Sciences; Physical Sciences; and Social Sciences), and seven graduate and professional schools (Jacobs School of Engineering; Rady School of Management; Scripps Institution of Oceanography; School of Global Policy and Strategy; School of Medicine; Skaggs School of Pharmacy and Pharmaceutical Sciences; and the newly established Wertheim School of Public Health and Human Longevity Science). University of California-San Diego Health, the region’s only academic health system, provides patient care; conducts medical research; and educates future health care professionals at the University of California-San Diego Medical Center, Hillcrest; Jacobs Medical Center; Moores Cancer Center; Sulpizio Cardiovascular Center; Shiley Eye Institute; Institute for Genomic Medicine; Koman Family Outpatient Pavilion and various express care and urgent care clinics throughout San Diego.

The university operates 19 organized research units (ORUs), including the Center for Energy Research; Qualcomm Institute (a branch of the California Institute for Telecommunications and Information Technology); San Diego Supercomputer Center; and the Kavli Institute for Brain and Mind, as well as eight School of Medicine research units, six research centers at Scripps Institution of Oceanography and two multi-campus initiatives, including the Institute on Global Conflict and Cooperation. The University of California-San Diego is also closely affiliated with several regional research centers, such as the Salk Institute; the Sanford Burnham Prebys Medical Discovery Institute; the Sanford Consortium for Regenerative Medicine; and the Scripps Research Institute. It is classified among “R1: Doctoral Universities – Very high research activity”. According to the National Science Foundation(US), UC San Diego spent $1.265 billion on research and development in fiscal year 2018, ranking it 7th in the nation.

The University of California-San Diego is considered one of the country’s “Public Ivies”. As of February 2021, The University of California-San Diego faculty, researchers and alumni have won 27 Nobel Prizes and three Fields Medals, eight National Medals of Science, eight MacArthur Fellowships, and three Pulitzer Prizes. Additionally, of the current faculty, 29 have been elected to the National Academy of Engineering, 70 to the National Academy of Sciences(US), 45 to the National Academy of Medicine(US) and 110 to the American Academy of Arts and Sciences.

History

When the Regents of the University of California originally authorized the San Diego campus in 1956, it was planned to be a graduate and research institution, providing instruction in the sciences, mathematics, and engineering. Local citizens supported the idea, voting the same year to transfer to the university 59 acres (24 ha) of mesa land on the coast near the preexisting Scripps Institution of Oceanography(US). The Regents requested an additional gift of 550 acres (220 ha) of undeveloped mesa land northeast of Scripps, as well as 500 acres (200 ha) on the former site of Camp Matthews from the federal government, but Roger Revelle, then director of Scripps Institution and main advocate for establishing the new campus, jeopardized the site selection by exposing the La Jolla community’s exclusive real estate business practices, which were antagonistic to minority racial and religious groups. This outraged local conservatives, as well as Regent Edwin W. Pauley.

University of California President Clark Kerr satisfied San Diego city donors by changing the proposed name from University of California, La Jolla, to University of California-San Diego. The city voted in agreement to its part in 1958, and the University of California approved construction of the new campus in 1960. Because of the clash with Pauley, Revelle was not made chancellor. Herbert York, first director of DOE’s Lawrence Livermore National Laboratory, was designated instead. York planned the main campus according to the “Oxbridge” model, relying on many of Revelle’s ideas.

According to Kerr, “San Diego always asked for the best,” though this created much friction throughout the University of California system, including with Kerr himself, because University of California-San Diego often seemed to be “asking for too much and too fast.” Kerr attributed University of California-San Diego’s “special personality” to Scripps, which for over five decades had been the most isolated University of California unit in every sense: geographically, financially, and institutionally. It was a great shock to the Scripps community to learn that Scripps was now expected to become the nucleus of a new University of California campus and would now be the object of far more attention from both the university administration in Berkeley and the state government in Sacramento.

The University of California-San Diego was the first general campus of the University of California to be designed “from the top down” in terms of research emphasis. Local leaders disagreed on whether the new school should be a technical research institute or a more broadly based school that included undergraduates as well. John Jay Hopkins of General Dynamics Corporation pledged one million dollars for the former while the City Council offered free land for the latter. The original authorization for the University of California-San Diego campus given by the University of California Regents in 1956 approved a “graduate program in science and technology” that included undergraduate programs, a compromise that won both the support of General Dynamics and the city voters’ approval.

Nobel laureate Harold Urey, a physicist from the University of Chicago(US), and Hans Suess, who had published the first paper on the greenhouse effect with Revelle in the previous year, were early recruits to the faculty in 1958. Maria Goeppert-Mayer, later the second female Nobel laureate in physics, was appointed professor of physics in 1960. The graduate division of the school opened in 1960 with 20 faculty in residence, with instruction offered in the fields of physics, biology, chemistry, and earth science. Before the main campus completed construction, classes were held in the Scripps Institution of Oceanography.

By 1963, new facilities on the mesa had been finished for the School of Science and Engineering, and new buildings were under construction for Social Sciences and Humanities. Ten additional faculty in those disciplines were hired, and the whole site was designated the First College, later renamed after Roger Revelle, of the new campus. York resigned as chancellor that year and was replaced by John Semple Galbraith. The undergraduate program accepted its first class of 181 freshman at Revelle College in 1964. Second College was founded in 1964, on the land deeded by the federal government, and named after environmentalist John Muir two years later. The University of California-San Diego School of Medicine also accepted its first students in 1966.

Political theorist Herbert Marcuse joined the faculty in 1965. A champion of the New Left, he reportedly was the first protester to occupy the administration building in a demonstration organized by his student, political activist Angela Davis. The American Legion offered to buy out the remainder of Marcuse’s contract for $20,000; the Regents censured Chancellor William J. McGill for defending Marcuse on the basis of academic freedom, but further action was averted after local leaders expressed support for Marcuse. Further student unrest was felt at the university, as the United States increased its involvement in the Vietnam War during the mid-1960s, when a student raised a Viet Minh flag over the campus. Protests escalated as the war continued and were only exacerbated after the National Guard fired on student protesters at Kent State University in 1970. Over 200 students occupied Urey Hall, with one student setting himself on fire in protest of the war.

Early research activity and faculty quality, notably in the sciences, was integral to shaping the focus and culture of the university. Even before The University of California-San Diego had its own campus, faculty recruits had already made significant research breakthroughs, such as the Keeling Curve, a graph that plots rapidly increasing carbon dioxide levels in the atmosphere and was the first significant evidence for global climate change; the Kohn–Sham equations, used to investigate particular atoms and molecules in quantum chemistry; and the Miller–Urey experiment, which gave birth to the field of prebiotic chemistry.

Engineering, particularly computer science, became an important part of the university’s academics as it matured. University researchers helped develop University of California-San Diego Pascal, an early machine-independent programming language that later heavily influenced Java; the National Science Foundation Network, a precursor to the Internet; and the Network News Transfer Protocol during the late 1970s to 1980s. In economics, the methods for analyzing economic time series with time-varying volatility (ARCH), and with common trends (cointegration) were developed. The University of California-San Diego maintained its research intense character after its founding, racking up 25 Nobel Laureates affiliated within 50 years of history; a rate of five per decade.

Under Richard C. Atkinson’s leadership as chancellor from 1980 to 1995, the university strengthened its ties with the city of San Diego by encouraging technology transfer with developing companies, transforming San Diego into a world leader in technology-based industries. He oversaw a rapid expansion of the School of Engineering, later renamed after Qualcomm founder Irwin M. Jacobs, with the construction of the San Diego Supercomputer Center(US) and establishment of the computer science, electrical engineering, and bioengineering departments. Private donations increased from $15 million to nearly $50 million annually, faculty expanded by nearly 50%, and enrollment doubled to about 18,000 students during his administration. By the end of his chancellorship, the quality of The University of California-San Diego graduate programs was ranked 10th in the nation by the National Research Council.

The university continued to undergo further expansion during the first decade of the new millennium with the establishment and construction of two new professional schools — the Skaggs School of Pharmacy and Rady School of Management—and the California Institute for Telecommunications and Information Technology, a research institute run jointly with University of California Irvine(US). The University of California-San Diego also reached two financial milestones during this time, becoming the first university in the western region to raise over $1 billion in its eight-year fundraising campaign in 2007 and also obtaining an additional $1 billion through research contracts and grants in a single fiscal year for the first time in 2010. Despite this, due to the California budget crisis, the university loaned $40 million against its own assets in 2009 to offset a significant reduction in state educational appropriations. The salary of Pradeep Khosla, who became chancellor in 2012, has been the subject of controversy amidst continued budget cuts and tuition increases.

On November 27, 2017, the university announced it would leave its longtime athletic home of the California Collegiate Athletic Association, an NCAA Division II league, to begin a transition to Division I in 2020. At that time, it will join the Big West Conference, already home to four other UC campuses (Davis, Irvine, Riverside, Santa Barbara). The transition period will run through the 2023–24 school year. The university prepares to transition to NCAA Division I competition on July 1, 2020.

Research

Applied Physics and Mathematics

The Nature Index lists The University of California-San Diego as 6th in the United States for research output by article count in 2019. In 2017, The University of California-San Diego spent $1.13 billion on research, the 7th highest expenditure among academic institutions in the U.S. The university operates several organized research units, including the Center for Astrophysics and Space Sciences (CASS), the Center for Drug Discovery Innovation, and the Institute for Neural Computation. The University of California-San Diego also maintains close ties to the nearby Scripps Research Institute(US) and Salk Institute for Biological Studies(US). In 1977, The University of California-San Diego developed and released the The University of California-San Diego Pascal programming language. The university was designated as one of the original national Alzheimer’s disease research centers in 1984 by the National Institute on Aging. In 2018, The University of California-San Diego received $10.5 million from the DOE National Nuclear Security Administration(US) to establish the Center for Matters under Extreme Pressure (CMEC).

The university founded the San Diego Supercomputer Center (SDSC) in 1985, which provides high performance computing for research in various scientific disciplines. In 2000, The University of California-San Diego partnered with The University of California-Irvine (US) to create the Qualcomm Institute – University of California-San Diego, which integrates research in photonics, nanotechnology, and wireless telecommunication to develop solutions to problems in energy, health, and the environment.

The University of California-San Diegoalso operates the Scripps Institution of Oceanography (SIO)(US), one of the largest centers of research in earth science in the world, which predates the university itself. Together, SDSC and SIO, along with funding partner universities California Institute of Technology(US), San Diego State University(US), and The University of California-Santa Barbara (US), manage the High Performance Wireless Research and Education Network.