From The Perelman School of Medicine At The University of Pennsylvania Folding@home: “Folding@home – How You and Your Computer Can Play Scientist”

From The Perelman School of Medicine

At

The University of Pennsylvania

5.16.23
Alex Gardner

Two heads are better than one. The ethos behind the scientific research project Folding@home is that same idea, multiplied: 50,000 computers are better than one.

Folding@home is a distributed computing project which is used to simulate protein folding, or how protein molecules assemble themselves into 3-D shapes.

Folding@home

Research into protein folding allows scientists to better understand how these molecules function or malfunction inside the human body. Often, mutations in proteins influence the progression of many diseases like Alzheimer’s disease, cancer, and even COVID-19.

Penn is home to both the computer brains and human minds behind the Folding@home project which, with its network, forms the largest supercomputer in the world [disputed below]. All of that computing power continually works together to answer scientific questions such as what areas of specific protein implicated in Parkinson’s disease may be susceptible to medication or other treatment.

Led by Gregory Bowman, a Penn Integrates Knowledge professor of Biochemistry and Biophysics in the Perelman School of Medicine who has joint appointments in the Department of Biochemistry and Biophysics in the Perelman School of Medicine and the Department of Bioengineering in the School of Engineering and Applied Science, Folding@home is open for any individual around the world to participate in and essentially volunteer their computer to join a huge network of computers and do research.

Using the network hub at Penn, Bowman and his team assign experiments to each individual computer which communicates with other computers and feeds info back to Philly. To date, the network is comprised of more than 50,000 computers spread across the world.

“What we do is like drawing a map,” said Bowman, explaining how the networked computers work together in a type of system that experts call Markov state models. “Each computer is like a driver visiting different places and reporting back info on those locations so we can get a sense of the landscape.”

Individuals can participate by signing up and then installing software to their standard personal desktop or laptop. Participants can direct the software to run in the background and limit it to a certain percentage of processing power or have the software run only when the computer is idle.

When the software is at work, it’s conducting unique experiments designed and assigned by Bowman and his team back at Penn. Users can play scientist and watch the results of simulations and monitor the data in real time, or they can simply let their computer do the work while they go about their lives.

Related:
BOINC-Berkeley Infrastructure for Open Network Computing at UC-Berkeley

BOINC computing power
Totals
24-hour average: 15.270 PetaFLOPS.
Active: 44,440 volunteers. 151,719 computers [compare to folding@home’s claim at 50,000 computers to be “the largest supercomputer in the world”.

BOINC-Berkeley Open Infrastructure for Network Computing from University of California-Berkeley

BOINC-Berkeley Open Infrastructure for Network Computing from University of California-Berkeley.

My BOINC stats

BOINC lets you help cutting-edge science research using your computer. The BOINC app, running on your computer, downloads scientific computing jobs and runs them invisibly in the background. It’s easy and safe.

About 30 science projects use BOINC. They investigate diseases, study climate change, discover pulsars, and do many other types of scientific research.

The BOINC and Science United projects are located at the University of California-Berkeley and are supported by the National Science Foundation.

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”.

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About Penn Medicine

Our history of patient care began more than two centuries ago with the founding of the nation’s first hospital, Pennsylvania Hospital, in 1751 and the nation’s first medical school at the University of Pennsylvania in 1765. Penn Medicine has pioneered medical frontiers with a staff comprised of innovators who have dedicated their lives to advancing medicine through excellence in education, research and patient care.

When you choose Penn Medicine, you benefit from more than two centuries of the highest standards in patient care, education and research. The caliber of comfort and individual attention you receive is unmatched by any other hospital in the Mid-Atlantic region.

Nationally Recognized

We are consistently recognized nationally and internationally for excellence in health care. The cornerstone of our reputation is our medical and support staff, who choose to dedicate their careers to serving the needs of our patients and community.

The Hospitals of the University of Pennsylvania — Penn Presbyterian are proud to be ranked #13 in the nation and once again the #1 hospital in Pennsylvania by U.S. News & World Report’s Honor Roll of Best Hospitals.

Providing the Community with Resources

We promote innovation and teaching excellence. We advance medical science through research and create the next generation of leaders in medicine. We’re constantly working towards an even more precise and personalized practice of health care.

The results of these efforts are passed directly onto you, our patients.

Health Equity Initiative at Penn Medicine

At Penn, we strive to provide high quality and family-centered care for our patients and the community, and support an inclusive workforce and clinical learning environment for our employees.

Mission and History

Academic life at University of Pennsylvania is unparalleled, with 100 countries and every U.S. state represented in one of the Ivy League’s most diverse student bodies. Consistently ranked among the top 10 universities in the country, Penn enrolls 10,000 undergraduate students and welcomes an additional 10,000 students to our world-renowned graduate and professional schools.

Penn’s award-winning educators and scholars encourage students to pursue inquiry and discovery, follow their passions, and address the world’s most challenging problems through an interdisciplinary approach.

The University of Pennsylvania is a private Ivy League research university in Philadelphia, Pennsylvania. The university claims a founding date of 1740 and is one of the nine colonial colleges chartered prior to the U.S. Declaration of Independence. Benjamin Franklin, Penn’s founder and first president, advocated an educational program that trained leaders in commerce, government, and public service, similar to a modern liberal arts curriculum.

Penn has four undergraduate schools as well as twelve graduate and professional schools. Schools enrolling undergraduates include the College of Arts and Sciences; the School of Engineering and Applied Science; the Wharton School; and the School of Nursing. Penn’s “One University Policy” allows students to enroll in classes in any of Penn’s twelve schools. Among its highly ranked graduate and professional schools are a law school whose first professor wrote the first draft of the United States Constitution, the first school of medicine in North America (Perelman School of Medicine, 1765), and the first collegiate business school (Wharton School, 1881).

Penn is also home to the first “student union” building and organization (Houston Hall, 1896), the first Catholic student club in North America (Newman Center, 1893), the first double-decker college football stadium (Franklin Field, 1924 when second deck was constructed), and Morris Arboretum, the official arboretum of the Commonwealth of Pennsylvania. The first general-purpose electronic computer (ENIAC) was developed at Penn and formally dedicated in 1946. In 2019, the university had an endowment of $14.65 billion, the sixth-largest endowment of all universities in the United States, as well as a research budget of $1.02 billion. The university’s athletics program, the Quakers, fields varsity teams in 33 sports as a member of the NCAA Division I Ivy League conference.

As of 2018, distinguished alumni and/or Trustees include three U.S. Supreme Court justices; 32 U.S. senators; 46 U.S. governors; 163 members of the U.S. House of Representatives; eight signers of the Declaration of Independence and seven signers of the U.S. Constitution (four of whom signed both representing two-thirds of the six people who signed both); 24 members of the Continental Congress; 14 foreign heads of state and two presidents of the United States, including Donald Trump. As of October 2019, 36 Nobel laureates; 80 members of the American Academy of Arts and Sciences; 64 billionaires; 29 Rhodes Scholars; 15 Marshall Scholars and 16 Pulitzer Prize winners have been affiliated with the university.

History

The University of Pennsylvania considers itself the fourth-oldest institution of higher education in the United States, though this is contested by Princeton University and Columbia University. The university also considers itself as the first university in the United States with both undergraduate and graduate studies.

In 1740, a group of Philadelphians joined together to erect a great preaching hall for the traveling evangelist George Whitefield, who toured the American colonies delivering open-air sermons. The building was designed and built by Edmund Woolley and was the largest building in the city at the time, drawing thousands of people the first time it was preached in. It was initially planned to serve as a charity school as well, but a lack of funds forced plans for the chapel and school to be suspended. According to Franklin’s autobiography, it was in 1743 when he first had the idea to establish an academy, “thinking the Rev. Richard Peters a fit person to superintend such an institution”. However, Peters declined a casual inquiry from Franklin and nothing further was done for another six years. In the fall of 1749, now more eager to create a school to educate future generations, Benjamin Franklin circulated a pamphlet titled Proposals Relating to the Education of Youth in Pensilvania, his vision for what he called a “Public Academy of Philadelphia”. Unlike the other colonial colleges that existed in 1749—Harvard University, William & Mary, Yale Unversity, and The College of New Jersey—Franklin’s new school would not focus merely on education for the clergy. He advocated an innovative concept of higher education, one which would teach both the ornamental knowledge of the arts and the practical skills necessary for making a living and doing public service. The proposed program of study could have become the nation’s first modern liberal arts curriculum, although it was never implemented because Anglican priest William Smith (1727-1803), who became the first provost, and other trustees strongly preferred the traditional curriculum.

Franklin assembled a board of trustees from among the leading citizens of Philadelphia, the first such non-sectarian board in America. At the first meeting of the 24 members of the board of trustees on November 13, 1749, the issue of where to locate the school was a prime concern. Although a lot across Sixth Street from the old Pennsylvania State House (later renamed and famously known since 1776 as “Independence Hall”), was offered without cost by James Logan, its owner, the trustees realized that the building erected in 1740, which was still vacant, would be an even better site. The original sponsors of the dormant building still owed considerable construction debts and asked Franklin’s group to assume their debts and, accordingly, their inactive trusts. On February 1, 1750, the new board took over the building and trusts of the old board. On August 13, 1751, the “Academy of Philadelphia”, using the great hall at 4th and Arch Streets, took in its first secondary students. A charity school also was chartered on July 13, 1753 by the intentions of the original “New Building” donors, although it lasted only a few years. On June 16, 1755, the “College of Philadelphia” was chartered, paving the way for the addition of undergraduate instruction. All three schools shared the same board of trustees and were considered to be part of the same institution. The first commencement exercises were held on May 17, 1757.

The institution of higher learning was known as the College of Philadelphia from 1755 to 1779. In 1779, not trusting then-provost the Reverend William Smith’s “Loyalist” tendencies, the revolutionary State Legislature created a University of the State of Pennsylvania. The result was a schism, with Smith continuing to operate an attenuated version of the College of Philadelphia. In 1791, the legislature issued a new charter, merging the two institutions into a new University of Pennsylvania with twelve men from each institution on the new board of trustees.

Penn has three claims to being the first university in the United States, according to university archives director Mark Frazier Lloyd: the 1765 founding of the first medical school in America made Penn the first institution to offer both “undergraduate” and professional education; the 1779 charter made it the first American institution of higher learning to take the name of “University”; and existing colleges were established as seminaries (although, as detailed earlier, Penn adopted a traditional seminary curriculum as well).

After being located in downtown Philadelphia for more than a century, the campus was moved across the Schuylkill River to property purchased from the Blockley Almshouse in West Philadelphia in 1872, where it has since remained in an area now known as University City. Although Penn began operating as an academy or secondary school in 1751 and obtained its collegiate charter in 1755, it initially designated 1750 as its founding date; this is the year that appears on the first iteration of the university seal. Sometime later in its early history, Penn began to consider 1749 as its founding date and this year was referenced for over a century, including at the centennial celebration in 1849. In 1899, the board of trustees voted to adjust the founding date earlier again, this time to 1740, the date of “the creation of the earliest of the many educational trusts the University has taken upon itself”. The board of trustees voted in response to a three-year campaign by Penn’s General Alumni Society to retroactively revise the university’s founding date to appear older than Princeton University, which had been chartered in 1746.

Research, innovations and discoveries

Penn is classified as an “R1” doctoral university: “Highest research activity.” Its economic impact on the Commonwealth of Pennsylvania for 2015 amounted to $14.3 billion. Penn’s research expenditures in the 2018 fiscal year were $1.442 billion, the fourth largest in the U.S. In fiscal year 2019 Penn received $582.3 million in funding from the National Institutes of Health.

In line with its well-known interdisciplinary tradition, Penn’s research centers often span two or more disciplines. In the 2010–2011 academic year alone, five interdisciplinary research centers were created or substantially expanded; these include the Center for Health-care Financing; the Center for Global Women’s Health at the Nursing School; the $13 million Morris Arboretum’s Horticulture Center; the $15 million Jay H. Baker Retailing Center at Wharton; and the $13 million Translational Research Center at Penn Medicine. With these additions, Penn now counts 165 research centers hosting a research community of over 4,300 faculty and over 1,100 postdoctoral fellows, 5,500 academic support staff and graduate student trainees. To further assist the advancement of interdisciplinary research President Amy Gutmann established the “Penn Integrates Knowledge” title awarded to selected Penn professors “whose research and teaching exemplify the integration of knowledge”. These professors hold endowed professorships and joint appointments between Penn’s schools.

Penn is also among the most prolific producers of doctoral students. With 487 PhDs awarded in 2009, Penn ranks third in the Ivy League, only behind Columbia University and Cornell University (Harvard University did not report data). It also has one of the highest numbers of post-doctoral appointees (933 in number for 2004–2007), ranking third in the Ivy League (behind Harvard and Yale University) and tenth nationally.

In most disciplines Penn professors’ productivity is among the highest in the nation and first in the fields of epidemiology, business, communication studies, comparative literature, languages, information science, criminal justice and criminology, social sciences and sociology. According to the National Research Council nearly three-quarters of Penn’s 41 assessed programs were placed in ranges including the top 10 rankings in their fields, with more than half of these in ranges including the top five rankings in these fields.

Penn’s research tradition has historically been complemented by innovations that shaped higher education. In addition to establishing the first medical school; the first university teaching hospital; the first business school; and the first student union Penn was also the cradle of other significant developments. In 1852, Penn Law was the first law school in the nation to publish a law journal still in existence (then called The American Law Register, now the Penn Law Review, one of the most cited law journals in the world). Under the deanship of William Draper Lewis, the law school was also one of the first schools to emphasize legal teaching by full-time professors instead of practitioners, a system that is still followed today. The Wharton School was home to several pioneering developments in business education. It established the first research center in a business school in 1921 and the first center for entrepreneurship center in 1973 and it regularly introduced novel curricula for which BusinessWeek wrote, “Wharton is on the crest of a wave of reinvention and change in management education”.

Several major scientific discoveries have also taken place at Penn. The university is probably best known as the place where the first general-purpose electronic computer (ENIAC) was born in 1946 at the Moore School of Electrical Engineering.

ENIAC UPenn

It was here also where the world’s first spelling and grammar checkers were created, as well as the popular COBOL programming language. Penn can also boast some of the most important discoveries in the field of medicine. The dialysis machine used as an artificial replacement for lost kidney function was conceived and devised out of a pressure cooker by William Inouye while he was still a student at Penn Med; the Rubella and Hepatitis B vaccines were developed at Penn; the discovery of cancer’s link with genes; cognitive therapy; Retin-A (the cream used to treat acne), Resistin; the Philadelphia gene (linked to chronic myelogenous leukemia) and the technology behind PET Scans were all discovered by Penn Med researchers. More recent gene research has led to the discovery of the genes for fragile X syndrome, the most common form of inherited mental retardation; spinal and bulbar muscular atrophy, a disorder marked by progressive muscle wasting; and Charcot–Marie–Tooth disease, a progressive neurodegenerative disease that affects the hands, feet and limbs.

Conductive polymer was also developed at Penn by Alan J. Heeger, Alan MacDiarmid and Hideki Shirakawa, an invention that earned them the Nobel Prize in Chemistry. On faculty since 1965, Ralph L. Brinster developed the scientific basis for in vitro fertilization and the transgenic mouse at Penn and was awarded the National Medal of Science in 2010. The theory of superconductivity was also partly developed at Penn, by then-faculty member John Robert Schrieffer (along with John Bardeen and Leon Cooper). The university has also contributed major advancements in the fields of economics and management. Among the many discoveries are conjoint analysis, widely used as a predictive tool especially in market research; Simon Kuznets’s method of measuring Gross National Product; the Penn effect (the observation that consumer price levels in richer countries are systematically higher than in poorer ones) and the “Wharton Model” developed by Nobel-laureate Lawrence Klein to measure and forecast economic activity. The idea behind Health Maintenance Organizations also belonged to Penn professor Robert Eilers, who put it into practice during then-President Nixon’s health reform in the 1970s.

International partnerships

Students can study abroad for a semester or a year at partner institutions such as the London School of Economics(UK), University of Barcelona [Universitat de Barcelona](ES), Paris Institute of Political Studies [Institut d’études politiques de Paris](FR), University of Queensland(AU), University College London(UK), King’s College London(UK), Hebrew University of Jerusalem(IL) and University of Warwick(UK).

From The College of Arts and Sciences At Cornell University Via “The Chronicle”: “Picking up good vibrations – of proteins – at CHESS”

From The College of Arts and Sciences

At

Cornell University

Via

“The Chronicle”

5.10.23
Rick Ryan | Cornell Laboratory for Accelerator-Based Sciences and Education

A new method for analyzing protein crystals – developed by Cornell researchers and given a funky two-part name – could open up applications for new drug discovery and other areas of biotechnology and biochemistry.

The development, outlined in a paper published March 3 in Nature Communications [below], provides researchers with the tools to interpret the once-discarded data from X-ray crystallography experiments – an essential method used to study the structures of proteins. This work, which builds on a study released in 2020 [Nature Communications (below)], could lead to a better understanding of a protein’s movement, structure and overall function.

As a structural biologist, Nozomi Ando, M.S. ’04, Ph.D. ’09, assistant professor of chemistry and chemical biology, is interested in charting the motion of proteins, and their internal parts, to better understand protein function. This type of movement is well known but has been difficult to document because the standard technique for imaging proteins is X-ray crystallography, which produces essentially static snapshots.

“Because we’re studying really challenging biological systems, the group often has to pioneer new structural methods as well,” said postdoctoral researcher Steve Meisburger, Ph.D. ’14, the paper’s lead author. “One of the questions that we have been interested in since the beginning is how a protein’s subtle breathing motions direct biochemical function.”

Protein crystallography produces bright spots, known as “Bragg peaks”, from the crystals, providing high-resolution information about the shape and structure of a protein. This process also captures blurry images – patterns and clouds related to the movement and vibrations of the proteins – hidden in the background of the Bragg peaks.

These background images are typically discarded, with priority given to the bright Bragg peak imagery that is more easily analyzed.

“We know that this pattern is related to the motion of the atoms of the protein, but we haven’t been able to use that information,” said lead author Steve Meisburger, Ph.D. ’14, a former postdoctoral researcher in the lab of Nozomi Ando, M.S. ’04, Ph.D. ’09, associate professor of chemistry and chemical biology in the College of Arts and Sciences. “The information is there, but we didn’t know how to use it. Now we do.”

Meisburger worked closely with Ando to develop the robust workflow to decode the weak background signals from crystallography experiments called diffuse scattering. This allows researchers to analyze the total scattering from crystals, which depends on both the protein’s structure and the subtle blur of its movements.

Their two-part method – which the team dubbed GOODVIBES and DISCOBALL – simultaneously provides a high-resolution structure of the protein and information on its correlated atomic movements.

“GOODVIBES” analyzes the X-ray data by separating the movements – subtle vibrations – of the protein from other proteins that might be moving around it. “DISCOBALL” independently validates these movements for certain proteins directly from the data, allowing researchers to trust the results from GOODVIBES and understand what the protein might be doing.

Ando said that while the potential for using diffuse scattering has been recognized for a long time, the act of accurately measuring the subtle signal while processing the data for something useful has been very difficult to do.

“It is much more computationally intensive to analyze than trying to analyze crystallography data alone,” Ando said. “We have a lot more data to deal with in diffuse scattering, because we are looking everywhere all at once, and the signal is also very nuanced.“

The overarching goal, Ando said, is to turn GOODVIBES and DISCOBALL into a genuine structural technique that can be used by researchers at synchrotrons all over the world.

“There is a lot of interest within the structural biology and biochemistry fields to use this signal,” Ando said. “We weren’t satisfied with just understanding what’s contained in the signal; it was really important for us to make the next step of creating the tools, and making GOODVIBES and DISCOBALL available for others to use these tools and test their hypotheses.”

These methods were developed using lysozyme proteins collected at the Cornell High Energy Synchrotron Source (CHESS).

“CHESS” Cornell High Energy Synchrotron Source.

The Ando group will be returning to CHESS this spring to collaborate with Meisburger, now a CHESS staff scientist, on more complex protein structures using their new method.

By isolating the internal motion signals from total scattering data of these complex proteins, researchers can learn more about how proteins move and interact with other important molecules. This information can be used to design new drugs and therapies that target specific proteins.

Experiments were performed at the Center for High Energy X-ray Sciences (CHEXS), which is supported by the National Science Foundation, and the Macromolecular Diffraction at CHESS (MacCHESS) facility, which is supported by the National Institute of General Medical Sciences, the National Institutes of Health (NIH) and New York State’s Empire State Development Corporation. This work was supported by grants from the NIH.

Nature Communications

Fig. 1: Workflow to measure and interpret protein correlated motion using X-ray crystallography.

First, X-ray diffraction images are acquired from protein crystals at room temperature (RT-MX). The Bragg peaks and continuous scattering are processed separately to obtain the protein structure and a three-dimensional map of diffuse scattering on an absolute intensity scale (electron units). The structure includes mean atomic positions and atomic displacement parameters (ADPs or B-factors) that quantify motion, and the pattern of diffuse scattering depends on how motions are correlated. To separate the internal and external (rigid-body) protein motions, a physical model of lattice disorder is refined to the intense diffuse halo features (GOODVIBES), and the lattice contribution to the diffuse map and variance-covariance matrix of rigid-body motion (V-Cov) are simulated. In parallel, a model-free analysis is performed to estimate displacement covariances (DISCOBALL) and validate the off-diagonal elements of the simulated lattice V-Cov (yellow shading). The lattice contribution to the diffuse map is subtracted and the residual diffuse scattering is sorted by inter-atomic vector using a Fourier transform (3D-ΔPDF). Similarly, the internal ADPs are found by subtracting the lattice contribution (diagonal blocks of V-Cov, blue shading). The internal motion signal can be interpreted by various models. To match crystal simulations, a target diffuse map can be created using GOODVIBES to add back external motions that are consistent with the specific supercell used by the simulations.

Nature Communications 2020

Fig. 1: Diffuse scattering map of triclinic lysozyme with intensities on an absolute scale of electron units (Ie).

a) Ribbon diagram of lysozyme (top) and the triclinic unit cell containing one protein (bottom). b) A highly detailed three-dimensional map of diffuse scattering was obtained. The outer sphere is drawn at 2 Å resolution. c) The total scattering is made up of three components: inelastic Compton scattering (lower left), a broad isotropic ring that dominates the diffuse signal (upper left), and variational features in the diffuse scattering (right). Intense halos are visible in the layers containing Bragg peaks (l  = 0 plane, upper right). Cloudy scattering is best visualized in the planes mid-way between the Bragg peaks (l  = 1∕2 plane, lower right).

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”.

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Cornell University College of Arts and Sciences

The College of Arts and Sciences is a division of Cornell University. It has been part of the university since its founding, although its name has changed over time. It grants bachelor’s degrees, and masters and doctorates through affiliation with the Cornell University Graduate School. Its major academic buildings are located on the Arts Quad and include some of the university’s oldest buildings. The college offers courses in many fields of study and is the largest college at Cornell by undergraduate enrollment.

Originally, the university’s faculty was undifferentiated, but with the founding of the Cornell Law School in 1886 and the concomitant self-segregation of the school’s lawyers, different departments and colleges formed.

Initially, the division that would become the College of Arts and Sciences was known as the Academic Department, but it was formally renamed in 1903. The College endowed the first professorships in American history, musicology, and American literature. Currently, the college teaches 4,100 undergraduates, with 600 full-time faculty members (and an unspecified number of lecturers) teaching 2,200 courses.

The Arts Quad is the site of Cornell’s original academic buildings and is home to many of the college’s programs. On the western side of the quad, at the top of Libe Slope, are Morrill Hall (completed in 1866), McGraw Hall (1872) and White Hall (1868). These simple but elegant buildings, built with native Cayuga bluestone, reflect Ezra Cornell’s utilitarianism and are known as Stone Row. The statue of Ezra Cornell, dating back to 1919, stands between Morrill and McGraw Halls. Across from this statue, in front of Goldwin Smith Hall, sits the statue of Andrew Dickson White, Cornell’s other co-founder and its first president.

Lincoln Hall (1888) also stands on the eastern face of the quad next to Goldwin Smith Hall. On the northern face are the domed Sibley Hall and Tjaden Hall (1883). Just off of the quad on the Slope, next to Tjaden, stands the Herbert F. Johnson Museum of Art, designed by I. M. Pei. Stimson Hall (1902), Olin Library (1959) and Uris Library (1892), with Cornell’s landmark clocktower, McGraw Tower, stand on the southern end of the quad.

Olin Library replaced Boardman Hall (1892), the original location of the Cornell Law School. In 1992, an underground addition was made to the quad with Kroch Library, an extension of Olin Library that houses several special collections of the Cornell University Library, including the Division of Rare and Manuscript Collections.

Klarman Hall, the first new humanities building at Cornell in over 100 years, opened in 2016. Klarman houses the offices of Comparative Literature and Romance Studies. The building is connected to, and surrounded on three sides by, Goldwin Smith Hall and fronts East Avenue.

Legends and lore about the Arts Quad and its statues can be found at Cornelliana.

The College of Arts and Sciences offers both undergraduate and graduate (through the Graduate School) degrees. The only undergraduate degree is the Bachelor of Arts. However, students may enroll in the dual-degree program, which allows them to pursue programs of study in two colleges and receive two different degrees. The faculties within the college are:

Africana Studies and Research Center*
American Studies
Anthropology
Archaeology
Asian-American Studies
Asian Studies
Astronomy/Astrophysics
Biology (with the College of Agriculture and Life Sciences)
Biology & Society Major (with the Colleges of Agriculture and Life Sciences and Human Ecology)
Chemistry and Chemical Biology
China and Asia-pacific Studies
Classics
Cognitive Studies
College Scholar Program (frees up to 40 selected students in each class from all degree requirements and allows them to fashion a plan of study conducive to achieving their ultimate intellectual goals; a senior thesis is required)
Comparative Literature
Computer Science (with the College of Engineering)
Earth and Atmospheric Sciences (with the Colleges of Agriculture and Life Sciences and Engineering)
Economics
English
Feminist, Gender, and Sexuality Studies
German Studies
Government
History
History of Art
Human Biology
Independent Major
Information Science (with the College of Agriculture and Life Sciences and College of Engineering)
Jewish Studies
John S. Knight Institute for Writing in the Disciplines
Latin American Studies
Latino Studies
Lesbian, Gay, Bisexual, and Transgender Studies
Linguistics
Mathematics
Medieval Studies
Modern European Studies Concentration
Music
Near Eastern Studies
Philosophy
Physics
Psychology
Religious Studies
Romance Studies
Russian
Science and Technology Studies
Society for the Humanities
Sociology
Theatre, Film, and Dance
Visual Studies Undergraduate Concentration

*Africana Studies was an independent center reporting directly to the Provost until July 1, 2011.

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 nearly 20,000 students representing every state and 120 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. As of January 2021, 61 Nobel laureates, four Turing Award winners and one Fields Medalist have been affiliated with Cornell. Cornell counts more than 250,000 living alumni, and its former and present faculty and alumni include 34 Marshall Scholars, 33 Rhodes Scholars, 29 Truman Scholars, 7 Gates Scholars, 55 Olympic Medalists, 10 current Fortune 500 CEOs, and 35 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 more than 15,000 undergraduate and 9,000 graduate students from all 50 American states and 119 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 fourth in the world in producing the largest number of graduates who go on to pursue PhDs in engineering or the natural sciences at American institutions, and fifth 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; in 2009 Cornell spent $671 million on science and engineering research and development, the 16th highest in the United States.

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

For the 2016–17 fiscal year, the university spent $984.5 million on research. Federal sources constitute the largest source of research funding, with total federal investment of $438.2 million. 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 was on the top-ten list of U.S. universities receiving the most patents in 2003, and was one of the nation’s top five institutions in forming start-up companies. In 2004–05, Cornell received 200 invention disclosures; filed 203 U.S. patent applications; completed 77 commercial license agreements; and distributed royalties of more than $4.1 million to Cornell units and inventors.

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 The California Institute of Technology 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 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.

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. The International Linear Collider(JP), to be completed in the late 2010s, will complement the CERN Large Hadron Collider(CH) and shed light on questions such as the identity of dark matter and the existence of extra dimensions.
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 Yale University: “‘There is no textbook’ – Biochem course confronts the climate challenge”

From Yale University

4.25.23
Kevin Dennehy

Media Contact
Bess Connolly
elizabeth.connolly@yale.edu

A novel course shows Yale undergrads that all climate-related problems can be viewed through the lens of biochemistry — and challenges them to find solutions.

In her course “Biochemistry and Our Changing Climate,” Yale’s Karla Neugebauer introduces case studies related to climate change through the eyes of a biochemist — and challenges the undergraduates to think about how the principles of biochemistry might yield climate solutions. (Photo by Dan Renzetti)

Typically, the students who enroll in Karla Neugebauer’s undergraduate classes are interested in examining life at the molecular level.

But during a recent seminar discussion, Neugebauer, a professor of molecular biophysics and biochemistry and of cell biology at Yale, asked a group of students to think at a larger scale, too, and in multiple dimensions: What are some of the ideal material properties you’d need, she asked, if you were constructing a building?

Specifically, she wanted the group to consider the kinds of materials and processes that would be necessary to create buildings in a way that produces lower carbon emissions — or, for that matter, that might actually remove carbon from the atmosphere, benefitting human and planetary health alike.

During that discussion earlier this semester — part of Neugebauer’s course “Biochemistry and Our Changing Climate” (MB&B 365/565) — she introduced some relevant examples from the world of architecture, including the use of timber-based wood products espoused by Alan Organschi of the Yale School of Architecture. The emerging technology, she told the group, could not only drastically reduce the emissions required to meet the surging global demand for buildings but make the cities of the future “carbon sinks.”

She also reviewed the creation of sturdy, sustainable bricks for construction embedded with living materials — including fungi and Cyanobacteria — that could offer alternatives to concrete, and promising new processes in enzyme engineering that produce more sustainable building materials, such as clear, renewable polymers for windows that store carbon instead of the current carbon-expensive method that makes windows from sand.

Underlying all these advances are the basics of biochemistry.

And that’s, really, the focus of the course, which Neugebauer first offered in the fall of 2021. The course illustrates that while most biochemical research today focuses on human health — and most biochemists see their own work in the context of disease — insights into the building blocks of life can also be harnessed to address the climate challenge, whether it’s protein engineering that can help produce planet-friendly materials, enzymes that help degrade plastics, alternative foods that can replace beef, or chemical modulators that target insects carrying zoonotic diseases.

“At a certain point it occurred to me that every discipline has a role in combating climate change,” said Neugebauer, of Yale’s Faculty of Arts and Sciences and Yale School of Medicine. “Poets and songwriters can help us emotionally to be courageous. And biochemistry offers a way of thinking about biology and the molecules that support the living world that can offer important insights.”

Teaching biochemistry, she says, doesn’t necessarily reveal “translational ways of saving the planet,” the way, say, working in engineering or policy might. It’s a discipline, a way of thinking, with a lot of history and a lot of knowledge one must learn to become an expert.

“But, armed with that expertise, one could conceive of solutions for the planet,” she says. “In each class I’m not telling students how they can save the world. I don’t know!

“My course isn’t for engineers,” she added. “It’s for people who are interested in biochemistry. And it’s for them to see possibilities for themselves.”

Students enrolled in “MB&B 365/565” during a class this semester. “One of the reasons I was so drawn to this class is that not only are we talking about the challenges of climate change, but we’re talking about the solutions,” said one student. (Photo by Dan Renzetti)

“Almost all problems are chemical problems”

During each class session Neugebauer introduces case studies on particular issues related to climate change and asks students to contemplate them through the eyes of a biochemist.

In one session she discussed the novel discovery that cows living in western Canada were found to produce less methane because they’d eaten red algae from the sea, a potentially key insight since beef production generates far greater carbon and methane emissions than any other food. While people in other fields are exploring how one might deliver more of the same red algae to more cows, and thus reduce global methane emissions, a biochemist asks other questions. What’s the molecular mechanism behind this phenomenon? Is there a molecule or set of molecules in the red algae that kills the gut bacteria producing the methane? Or is the molecular compound instead serving as an inhibitor of methanogenesis (a biochemical pathway that generates methane) in that bacterium? Could scientists develop a chemical cocktail that could be delivered broadly and economically to all cows?

On other days the class has explored findings that molecules in smoke promote plant growth (knowledge that might be useful for helping forest systems recover after fires); the amino acid synthesis reactions inhibited by the common pesticide Roundup; and the biochemical factors that cause coral bleaching. (Although most people know that coral bleaching is caused by rising sea temperatures, it is less commonly understood that it’s the algal symbionts inside the coral that experience a stress response and secrete hydrogen peroxide, causing coral tissue to expel them; this starves the coral tissue, which relies on the algal symbionts to produce their food.)

As Neugebauer says, the implications of all these phenomena are easier to understand — and possibly address — once you know which molecules are involved.

“There is no other course like this and there is no textbook,” said Neugebauer, an expert in RNA biology who came to Yale in 2013. “These are tentacles being extended between predicted and observed changes in the living world — like salt pH and temperature, fire, pollution, et cetera — and biochemical principles.”

While these connections might be clear, she’s not aware of any class being offered anywhere that explores climate change through the lens of biochemistry. Other classes Neugebauer teaches include MB&B 301 (the second semester of undergraduate biochemistry for majors) and MB&B 449 (“Medical Impacts of Basic Science”).

For the Yale College students enrolled in the course, the questions it has raised are appealing and inspiring.

“I’ve taken a lot of science classes where there are very, very detailed discussions about the mechanisms of a biochemical molecule or research about a specific way this molecule functions,” said Yaya Guo, a junior who is studying molecular biophysics and biochemistry and economics. “Sometimes you say, ‘OK, that’s cool, but what do you do with that information?’ This class really reminds you that almost all problems are actually chemical problems.”

After learning about the course, editors of the open access journal BBA Advances invited the class to submit a manuscript on the lessons it reveals. So Neugebauer assigned the students to collaborate on an article in which they will address five questions about how principles of biochemistry can be used to combat climate change. All of the students will be listed as co-authors.

“One of the reasons I was so drawn to this class is that not only are we talking about the challenges of climate change, but we’re talking about the solutions,” said Katherine Moon, another Yale junior enrolled in the class. “This makes me feel really hopeful.”

In April, the class visited East Rock Park to collect moss samples containing tardigrades, eight-legged invertebrates also known as water bears. In an experiment, they soaked the moss in water, after which some tardigrades emerged from a desiccated state, Neugebauer said, illustrating how organisms can survive in extreme temperatures. (The students wore t-shirts promoting bird-friendly architecture.)

What role can biochemists play?

Offering hope and inspiration in the face of a global crisis is the reason Neugebauer started the course. She remembers the devastation and helplessness she felt when, during a vacation in the Australian Outback in 2006, she happened to read an article about the region’s horrific future absent aggressive climate action. A few years later, she remembers, her grown son and his friend tried to convince her that in light of the planet’s ongoing climate catastrophe, the only fields worth pursuing were engineering and policy.

This drove Neugebauer to consider the role biochemists might play in addressing the crisis. At Yale, she realized, she had a platform for exploring possibilities. And she had an opportunity to drive home that the climate fight is one everyone should be part of — and to inspire students to discover solutions.

Young people are terrified by the climate crisis, Neugebauer said, and they are looking for ways to address it, regardless of their primary academic focus. She thinks every department at Yale — whether it’s chemistry, or statistics, or English, or philosophy — should offer similar courses with “climate change” in the title.

“I think that 17-year-olds would be comforted to know that the generation ahead of them has buy-in and is willing to help them rather than hearing, ‘Hey, 17- and 18-year-olds, you figure it out.’ Why don’t we do something to help them imagine how they can participate in the solution? I think that’s a role that education has.”

About half the students enrolled in “Biochemistry and Our Changing Climate” this semester plan to go to medical school.

“As a health professional, it is so valuable to be able to have the knowledge of the chemistry behind so many of the health problems that arise from climate change, and just the overall knowledge of climate change,” said Sasha Wood, a junior enrolled in the class who will attend Icahn School of Medicine at Mount Sinai after graduation.

For Katherine Moon, who also aspires to a career in medicine, studying the planetary costs of climate change has almost felt like studying human biology. “You would think that studying climate and ecology would be so complex, and it would be so hard to tackle it,” she said. “But when you delve into the biochemistry of it, the biochemistry rules apply the same everywhere on Earth. [Addressing the challenges] is almost like developing a pharmaceutical for the world. It feels totally doable.”

One of the benefits of the course, added Deborah Arul, who is studying molecular biophysics & biochemistry and sociology, is that it really gets down to the chemical basics of climate change — whether it’s the causes or potential solutions. Unlike many science classes, she said, there are opportunities to explore social considerations — for instance, why the low cost of producing certain plastics make them ubiquitous in the environment. “But then you get right back to the biochemical solutions,” she said. “You don’t get lost in the debate.”

For Lilijana Oliver, a Yale College senior who enrolled in the course this spring, part of what has stood out during these discussions is just how relevant these molecular truths are to just about every challenge associated with climate change.

“If you keep asking these broad questions, and you keep asking ‘why?’” she said, “you eventually get to biochemistry.”

See the full article here .

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Yale University is a private Ivy League research university in New Haven, Connecticut. Founded in 1701 as the Collegiate School, it is the third-oldest institution of higher education in the United States and one of the nine Colonial Colleges chartered before the American Revolution. The Collegiate School was renamed Yale College in 1718 to honor the school’s largest private benefactor for the first century of its existence, Elihu Yale. Yale University is consistently ranked as one of the top universities and is considered one of the most prestigious in the nation.

Chartered by Connecticut Colony, the Collegiate School was established in 1701 by clergy to educate Congregational ministers before moving to New Haven in 1716. Originally restricted to theology and sacred languages, the curriculum began to incorporate humanities and sciences by the time of the American Revolution. In the 19th century, the college expanded into graduate and professional instruction, awarding the first PhD in the United States in 1861 and organizing as a university in 1887. Yale’s faculty and student populations grew after 1890 with rapid expansion of the physical campus and scientific research.

Yale is organized into fourteen constituent schools: the original undergraduate college, the Yale Graduate School of Arts and Sciences and twelve professional schools. While the university is governed by the Yale Corporation, each school’s faculty oversees its curriculum and degree programs. In addition to a central campus in downtown New Haven, the university owns athletic facilities in western New Haven, a campus in West Haven, Connecticut, and forests and nature preserves throughout New England. As of June 2020, the university’s endowment was valued at $31.1 billion, the second largest of any educational institution. The Yale University Library, serving all constituent schools, holds more than 15 million volumes and is the third-largest academic library in the United States. Students compete in intercollegiate sports as the Yale Bulldogs in the NCAA Division I – Ivy League.

As of October 2020, 65 Nobel laureates, five Fields Medalists, four Abel Prize laureates, and three Turing award winners have been affiliated with Yale University. In addition, Yale has graduated many notable alumni, including five U.S. Presidents, 19 U.S. Supreme Court Justices, 31 living billionaires, and many heads of state. Hundreds of members of Congress and many U.S. diplomats, 78 MacArthur Fellows, 252 Rhodes Scholars, 123 Marshall Scholars, and nine Mitchell Scholars have been affiliated with the university.

Research

Yale is a member of the Association of American Universities (AAU) and is classified among “R1: Doctoral Universities – Very high research activity”. According to the National Science Foundation , Yale spent $990 million on research and development in 2018, ranking it 15th in the nation.

Yale’s faculty include 61 members of the National Academy of Sciences , 7 members of the National Academy of Engineering and 49 members of the American Academy of Arts and Sciences . The college is, after normalization for institution size, the tenth-largest baccalaureate source of doctoral degree recipients in the United States, and the largest such source within the Ivy League.

Yale’s English and Comparative Literature departments were part of the New Criticism movement. Of the New Critics, Robert Penn Warren, W.K. Wimsatt, and Cleanth Brooks were all Yale faculty. Later, the Yale Comparative literature department became a center of American deconstruction. Jacques Derrida, the father of deconstruction, taught at the Department of Comparative Literature from the late seventies to mid-1980s. Several other Yale faculty members were also associated with deconstruction, forming the so-called “Yale School”. These included Paul de Man who taught in the Departments of Comparative Literature and French, J. Hillis Miller, Geoffrey Hartman (both taught in the Departments of English and Comparative Literature), and Harold Bloom (English), whose theoretical position was always somewhat specific, and who ultimately took a very different path from the rest of this group. Yale’s history department has also originated important intellectual trends. Historians C. Vann Woodward and David Brion Davis are credited with beginning in the 1960s and 1970s an important stream of southern historians; likewise, David Montgomery, a labor historian, advised many of the current generation of labor historians in the country. Yale’s Music School and Department fostered the growth of Music Theory in the latter half of the 20th century. The Journal of Music Theory was founded there in 1957; Allen Forte and David Lewin were influential teachers and scholars.

In addition to eminent faculty members, Yale research relies heavily on the presence of roughly 1200 Postdocs from various national and international origin working in the multiple laboratories in the sciences, social sciences, humanities, and professional schools of the university. The university progressively recognized this working force with the recent creation of the Office for Postdoctoral Affairs and the Yale Postdoctoral Association.

Notable alumni

Over its history, Yale has produced many distinguished alumni in a variety of fields, ranging from the public to private sector. According to 2020 data, around 71% of undergraduates join the workforce, while the next largest majority of 16.6% go on to attend graduate or professional schools. Yale graduates have been recipients of 252 Rhodes Scholarships, 123 Marshall Scholarships, 67 Truman Scholarships, 21 Churchill Scholarships, and 9 Mitchell Scholarships. The university is also the second largest producer of Fulbright Scholars, with a total of 1,199 in its history and has produced 89 MacArthur Fellows. The U.S. Department of State Bureau of Educational and Cultural Affairs ranked Yale fifth among research institutions producing the most 2020–2021 Fulbright Scholars. Additionally, 31 living billionaires are Yale alumni.

At Yale, one of the most popular undergraduate majors among Juniors and Seniors is political science, with many students going on to serve careers in government and politics. Former presidents who attended Yale for undergrad include William Howard Taft, George H. W. Bush, and George W. Bush while former presidents Gerald Ford and Bill Clinton attended Yale Law School. Former vice-president and influential antebellum era politician John C. Calhoun also graduated from Yale. Former world leaders include Italian prime minister Mario Monti, Turkish prime minister Tansu Çiller, Mexican president Ernesto Zedillo, German president Karl Carstens, Philippine president José Paciano Laurel, Latvian president Valdis Zatlers, Taiwanese premier Jiang Yi-huah, and Malawian president Peter Mutharika, among others. Prominent royals who graduated are Crown Princess Victoria of Sweden, and Olympia Bonaparte, Princess Napoléon.

Yale alumni have had considerable presence in U.S. government in all three branches. On the U.S. Supreme Court, 19 justices have been Yale alumni, including current Associate Justices Sonia Sotomayor, Samuel Alito, Clarence Thomas, and Brett Kavanaugh. Numerous Yale alumni have been U.S. Senators, including current Senators Michael Bennet, Richard Blumenthal, Cory Booker, Sherrod Brown, Chris Coons, Amy Klobuchar, Ben Sasse, and Sheldon Whitehouse. Current and former cabinet members include Secretaries of State John Kerry, Hillary Clinton, Cyrus Vance, and Dean Acheson; U.S. Secretaries of the Treasury Oliver Wolcott, Robert Rubin, Nicholas F. Brady, Steven Mnuchin, and Janet Yellen; U.S. Attorneys General Nicholas Katzenbach, John Ashcroft, and Edward H. Levi; and many others. Peace Corps founder and American diplomat Sargent Shriver and public official and urban planner Robert Moses are Yale alumni.

Yale has produced numerous award-winning authors and influential writers, like Nobel Prize in Literature laureate Sinclair Lewis and Pulitzer Prize winners Stephen Vincent Benét, Thornton Wilder, Doug Wright, and David McCullough. Academy Award winning actors, actresses, and directors include Jodie Foster, Paul Newman, Meryl Streep, Elia Kazan, George Roy Hill, Lupita Nyong’o, Oliver Stone, and Frances McDormand. Alumni from Yale have also made notable contributions to both music and the arts. Leading American composer from the 20th century Charles Ives, Broadway composer Cole Porter, Grammy award winner David Lang, and award-winning jazz pianist and composer Vijay Iyer all hail from Yale. Hugo Boss Prize winner Matthew Barney, famed American sculptor Richard Serra, President Barack Obama presidential portrait painter Kehinde Wiley, MacArthur Fellow and contemporary artist Sarah Sze, Pulitzer Prize winning cartoonist Garry Trudeau, and National Medal of Arts photorealist painter Chuck Close all graduated from Yale. Additional alumni include architect and Presidential Medal of Freedom winner Maya Lin, Pritzker Prize winner Norman Foster, and Gateway Arch designer Eero Saarinen. Journalists and pundits include Dick Cavett, Chris Cuomo, Anderson Cooper, William F. Buckley, Jr., and Fareed Zakaria.

In business, Yale has had numerous alumni and former students go on to become founders of influential business, like William Boeing (Boeing, United Airlines), Briton Hadden and Henry Luce (Time Magazine), Stephen A. Schwarzman (Blackstone Group), Frederick W. Smith (FedEx), Juan Trippe (Pan Am), Harold Stanley (Morgan Stanley), Bing Gordon (Electronic Arts), and Ben Silbermann (Pinterest). Other business people from Yale include former chairman and CEO of Sears Holdings Edward Lampert, former Time Warner president Jeffrey Bewkes, former PepsiCo chairperson and CEO Indra Nooyi, sports agent Donald Dell, and investor/philanthropist Sir John Templeton.

Yale alumni distinguished in academia include literary critic and historian Henry Louis Gates, economists Irving Fischer, Mahbub ul Haq, and Nobel Prize laureate Paul Krugman; Nobel Prize in Physics laureates Ernest Lawrence and Murray Gell-Mann; Fields Medalist John G. Thompson; Human Genome Project leader and National Institutes of Health director Francis S. Collins; brain surgery pioneer Harvey Cushing; pioneering computer scientist Grace Hopper; influential mathematician and chemist Josiah Willard Gibbs; National Women’s Hall of Fame inductee and biochemist Florence B. Seibert; Turing Award recipient Ron Rivest; inventors Samuel F.B. Morse and Eli Whitney; Nobel Prize in Chemistry laureate John B. Goodenough; lexicographer Noah Webster; and theologians Jonathan Edwards and Reinhold Niebuhr.

In the sporting arena, Yale alumni include baseball players Ron Darling and Craig Breslow and baseball executives Theo Epstein and George Weiss; football players Calvin Hill, Gary Fenick, Amos Alonzo Stagg, and “the Father of American Football” Walter Camp; ice hockey players Chris Higgins and Olympian Helen Resor; Olympic figure skaters Sarah Hughes and Nathan Chen; nine-time U.S. Squash men’s champion Julian Illingworth; Olympic swimmer Don Schollander; Olympic rowers Josh West and Rusty Wailes; Olympic sailor Stuart McNay; Olympic runner Frank Shorter; and others.

From “Science Magazine” : “An ancient gene stolen from bacteria set the stage for human sight”

From “Science Magazine”

4.10.23
Elizabeth Pennisi

A bacterial gene helps make vertebrate vision possible.Ingo Arndt/NaturePL/Science Source.

The eye is so complex that even Charles Darwin was at a loss to explain how it could have arisen. Now, it turns out that the evolution of the vertebrate eye got an unexpected boost—from bacteria, which contributed a key gene involved in the retina’s response to light. The work, reported today in the PNAS [below], drives home the evolutionary importance of genes borrowed from other species.

“Their findings demonstrate how complex structures like the vertebrate eye can evolve, not only by modifying existing genetic material but also by acquiring and integrating foreign genes,” says Ling Zhu, a retinal biologist at the University of Sydney’s Save Sight Institute who was not involved with the work. “It’s incredible.”

Bacteria are known to readily swap genes packaged in viruses or mobile pieces of DNA called “transposons” or even as free-floating DNA. But vertebrates, too, can incorporate microbial genes. When the human genome was first sequenced in 2001, scientists thought it contained about 200 bacteria-derived genes, though the microbial origins of many did not hold up.

Hoping to improve on those earlier efforts, Matthew Daugherty, a biochemist at the University of California-San Diego, and colleagues used sophisticated computer software to trace the evolution of hundreds of human genes by searching for similar sequences in hundreds of other species. Genes that seemed to have appeared first in vertebrates and had no predecessors in earlier animals were good candidates for having jumped across from bacteria, particularly if they had counterparts in modern microbes. Among the dozens of potentially alien genes, one “blew me away,” Daugherty recalls.

The gene called IRBP (for interphotoreceptor retinoid-binding protein), was already known to be important for seeing. The protein it encodes resides in the space between the retina and the retinal pigment epithelium, a thin layer of cells overlying the retina. In the vertebrate eye, when light hits a light-sensitive photoreceptor in the retina, vitamin A complexes become kinked, setting off an electrical pulse that activates the optic nerve. IRBP then shifts these molecules to the epithelium to be unkinked. Finally, it shuttles the restored molecules back to the photoreceptor. “IRBP,” Zhu explains, “is essential for the vision of all vertebrates.”

Vertebrate IRBP most closely resembles a class of bacterial genes called pepsidases whose proteins recycle other proteins. Since IRBP is found in all vertebrates but generally not in their closest invertebrate relatives, Daugherty and his colleagues propose that more than 500 million years ago microbes transferred a pepsidase gene into an ancestor of all living vertebrates. Once the gene was in place, the protein’s recycling function was lost and the gene duplicated itself twice, explaining why IRBP has four copies of the original pepsidase DNA. Even in its microbial forebears, this protein may have had some ability to bind to light-sensing molecules, Daugherty suggests. Other mutations then completed its transformation into a molecule that could escape from cells and serve as a shuttle.

Not everyone agrees that the evolution of IRBP was crucial for vertebrate vision. “I don’t think it had to happen” in order for vertebrates to see well, says Sönke Johnsen, a biologist at Duke University. Invertebrate eyes make do without IRBP, he notes. Instead of shuttling back and forth, the vitamin A complex stays put in the retina, where one wavelength of light bends the light-sensing molecule, while another unbends it. Some researchers have speculated that mechanism hampers invertebrates’ night vision. Yet “there are plenty of extremely good invertebrate eyes,” Johnsen says.

Daugherty agrees that vertebrates’ reliance on IRBP could simply be a historical accident. “We are sort of stuck with it,” Daugherty says.

Either way, the work supports the idea that horizontal gene transfer can help to endow organisms with new functions, says Julie Dunning Hotopp, a genome biologist at the University of Maryland School of Medicine’s Institute for Genome Sciences. Once these genes take root in a new species, evolution can tinker with them to produce totally new abilities or enhance existing ones. “It is the biological equivalent of upcycling that happens in my Buy Nothing Group.”

PNAS
See the science paper for instructive material with images.

Fig. 1.

Discontinuous distribution of IRBP homologs across the tree of life. (A) Schematic of the vertebrate visual cycle indicating the physical separation of retinoid-mediated sensing of light in photoreceptor (PR) cells and retinoid regeneration in retinal pigment epithelium (RPE) cells. Interphotoreceptor retinoid-binding protein (IRBP, also known as retinol-binding protein, RBP3) is required to shuttle retinoids between the two cell types. (B) Histogram of BLASTp e-values obtained after searching the RefSeq protein database for IRBP homologs (Dataset S1 and SI Appendix, Extended Methods). Single-domain homologs in nonvertebrate eukaryotes are labeled and colored by species name or species group. Above is a species tree of eukaryotes whose genomes were queried in this study. Species with branches colored gray lack detectable IRBP homologs in their genomes. The e-values of the 10 closest bacterial homologs to IRBP are shown to the left. (C) Sequence comparison between the individual domains of human IRBP and the top scoring bacterial homolog (complete alignment in SI Appendix, Fig. S1). (D) Structural comparison of D4 from bovine IRBP (PDB: 7JTI) (4) and a predicted structure of a bacterial homolog that was generated by AlphaFold2 (5).

See the full article here .

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From The DOE’s Brookhaven National Laboratory: “Structure of ‘Oil-Eating’ Enzyme Opens Door to Bioengineered Catalysts”

From The DOE’s Brookhaven National Laboratory

3.30.23
Karen McNulty Walsh
kmcnulty@bnl.gov
(631) 344-8350

Peter Genzer
genzer@bnl.gov
(631) 344-3174

Atomic level details reveal how enzyme selectively breaks hydrocarbon bonds suggesting bioengineering strategies for making useful chemicals.

Long-sought structure of oil-eating enzyme complex: A high-resolution cryo-EM map of the transmembrane two-protein complex (left) allows researchers to determine the locations of individual amino acids that make up the two proteins (right). AlkG (gray) serves and an electron carrier, transporting electrons from its single iron atom (red sphere) to the two iron atoms (red spheres) at the active site of the AlkB enzyme (colorful ribbon structure). The magenta structure below the active site is the substrate (see close-up views). Credit: BNL.

Scientists at the U.S. Department of Energy’s Brookhaven National Laboratory have produced the first atomic-level structure of an enzyme that selectively cuts carbon-hydrogen bonds—the first and most challenging step in turning simple hydrocarbons into more useful chemicals. As described in a paper just published in Nature Structural & Molecular Biology [below], the detailed atomic level “blueprint” suggests ways to engineer the enzyme to produce desired products.

“We want to create a diverse pool of biocatalysts where you can specifically select the desired substrate to produce wanted and unique products from abundant hydrocarbons,” said study co-lead Qun Liu, a Brookhaven Lab structural biologist. “The approach would give us a controllable way to convert cheap and abundant alkanes—simple carbon-hydrogen compounds that make up 20-50 percent of crude oil—into more valuable bioproducts or chemical precursors, including alcohols, aldehydes, carboxylates, and epoxides.”

The idea is particularly attractive because most industrial catalytic processes used for alkane conversions produce unwanted byproducts and heat-trapping carbon dioxide (CO2) gas. They also contain costly materials and require high temperatures and pressure. The biological enzyme, known as AlkB, operates under more ordinary conditions and with very high specificity. It uses inexpensive earth-abundant iron to initiate the chemistry while producing few unwanted byproducts.

“Nature has figured out how to do this kind of chemistry with an inexpensive abundant metal and at ambient temperature and pressures,” said John Shanklin, chair of Brookhaven Lab’s Biology Department and a senior author on the paper. “As a result, there’s been massive interest in this enzyme, but a complete lack of understanding of its architecture and how it works—which is necessary to re-engineer it for new purposes. With this structure, we have now overcome this obstacle.”

From rancid oil to sweet success

Research team: Brookhaven Lab scientists Jin Chai, Qun Liu, John Shanklin, and Sean McSweeney stand in front of the cryo-electron microscope (cryo-EM) used to decipher the long-sought structure of an enzyme that selectively cleaves hydrocarbon bonds. Credit: BNL.

AlkB was discovered 50 years ago in a machine shop where bacteria were digesting cooling oil making it smell rancid. Biochemists discovered the bacterial enzyme AlkB as the factor enabling the microbes’ unusual appetite. Scientists have been interested in harnessing AlkB’s hydrocarbon-chomping ability ever since.

Over the years, studies revealed that the enzyme sits partially embedded in the bacteria’s membranes, and that it operates in conjunction with two other proteins. Shanklin and Liu—and scientists elsewhere—tried solving the enzyme’s structure using x-ray crystallography. That method bounces high-intensity x-rays off a crystallized version of a protein to identify where the atoms are. But membrane proteins like AlkB are notoriously difficult to crystallize—especially when they are part of a multi-protein complex.

“We couldn’t get high enough resolution,” Liu said.

Then in early 2021, Brookhaven opened its new cryo-electron microscope (cryo-EM) facility, the Laboratory for BioMolecular Structure (LBMS). The scientists used a cryo-EM, which does not require a crystallized sample, to take pictures of a few million individual frozen protein molecules from many different angles. Computational tools then sorted through the images, identified and averaged the common features—and ultimately generated a high-resolution, three-dimensional map of the enzyme complex. Using this map, the scientists then pieced together the known atomic-level structures of the individual amino acids that make up the protein complex to fill in the details in three dimensions.

Identifying the right conditions to stabilize the transmembrane region of the enzyme and maintain the structural details was a challenge that required a good deal of trial and error. Shanklin credits Jin Chai, one of the researchers in his lab, “for his commitment and determination to solving this puzzle.”

Structure reveals how enzyme works

The detailed structure shows exactly how AlkB and one of the two associated proteins (AlkG) work together to cleave carbon-hydrogen bonds. In fact, the solved structure contained an unexpected bonus: a substrate alkane molecule that was trapped in the enzyme’s active site cavity.

Active site: These closeups of the AlkB active site show how nine histidine amino acids (denoted as “H” in the left image) form a cavity (gray shaded region, right). This cavity guides the substrate (magenta) to the active site (near the two iron, Fe, atoms) in a single orientation, where only the terminal carbon-hydrogen bond can be cleaved. Modifying the enzyme to change the shape of this cavity could allow the enzyme to attack different C-H bonds. Credit: BNL.

“Our structure shows how the amino acids that make up this enzyme form a cavity that orients the hydrocarbon substrate so that just one specific carbon-hydrogen bond can approach the active site,” Liu said. “It also shows how electrons move from the carrier protein (AlkG) to the di-iron center at the enzyme’s active site, allowing it to activate a molecule of oxygen to attack this bond.”

Shanklin suggests thinking of the enzyme as a bond-cutting machine like a circular saw: “How you hold the alkane with respect to the enzyme’s di-iron center determines how the activated oxygen interacts with the hydrocarbon. If you guide the end of the alkane against the activated oxygen, it’s going to initiate some chemistry on that last carbon.

“The engineering we want to do is to change the shape of the active site cavity so we can have the substrate (or a different substrate) approach the activated oxygen at different angles and in different C-H bond locations to perform different reactions.”

In nature, the scientists noted, a third protein not included in this structure (AlkT) provides the electrons to AlkG, the carrier protein. The carrier protein then transports the electrons to the two iron atoms that activate oxygen at AlkB’s active site. Replacing that electron donating protein with an electrode to supply electrons would be simpler and less costly than using the biological electron donor, they suggest.

DOE just funded the team’s proposal to develop such ‘Transformative Biohybrid Diiron Catalysts for C-H Bond Functionalization,’ based in part on this preliminary structural work.

“This structure and our knowledge of how the AlkG/AlkB complex works, puts us in a great position to bioengineer this enzyme to select which carbon-hydrogen bond gets activated in a variety of substrates and to control the electrons and oxygen to re-engineer its selectivity,” Liu said.

This work was supported by the DOE Office of Science (BES) and by Laboratory Directed Research and Development funds at Brookhaven Lab. LBMS is supported by the DOE Office of Science (BER). This research also used resources of Brookhaven Lab’s Center for Functional Nanomaterials (CFN), which is a U.S. Department of Energy Office of Science (BES) User Facility.

Nature Structural & Molecular Biology
See the science paper for instructive material with images.

See the full article here .

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Brookhaven Campus. Credit: BNL.

One of ten national laboratories overseen and primarily funded by the The DOE Office of Science, The DOE’s Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.

Research at BNL specializes in nuclear and high energy physics, energy science and technology, environmental and bioscience, nanoscience and national security. The 5300 acre campus contains several large research facilities, including the Relativistic Heavy Ion Collider [below] and National Synchrotron Light Source II [below]. Seven Nobel prizes have been awarded for work conducted at Brookhaven lab.

BNL is staffed by approximately 2,750 scientists, engineers, technicians, and support personnel, and hosts 4,000 guest investigators every year. The laboratory has its own police station, fire department, and ZIP code (11973). In total, the lab spans a 5,265-acre (21 km^2) area that is mostly coterminous with the hamlet of Upton, New York. BNL is served by a rail spur operated as-needed by the New York and Atlantic Railway. Co-located with the laboratory is the Upton, New York, forecast office of the National Weather Service.

Major programs

Although originally conceived as a nuclear research facility, Brookhaven Lab’s mission has greatly expanded. Its foci are now:

Nuclear and high-energy physics
Physics and chemistry of materials
Environmental and climate research
Nanomaterials
Energy research
Nonproliferation
Structural biology
Accelerator physics

Operation

Brookhaven National Lab was originally owned by the Atomic Energy Commission and is now owned by that agency’s successor, the United States Department of Energy (DOE). DOE subcontracts the research and operation to universities and research organizations. It is currently operated by Brookhaven Science Associates LLC, which is an equal partnership of Stony Brook University and Battelle Memorial Institute. From 1947 to 1998, it was operated by Associated Universities, Inc. (AUI), but AUI lost its contract in the wake of two incidents: a 1994 fire at the facility’s high-beam flux reactor that exposed several workers to radiation and reports in 1997 of a tritium leak into the groundwater of the Long Island Central Pine Barrens on which the facility sits.

Foundations

Following World War II, the US Atomic Energy Commission was created to support government-sponsored peacetime research on atomic energy. The effort to build a nuclear reactor in the American northeast was fostered largely by physicists Isidor Isaac Rabi and Norman Foster Ramsey Jr., who during the war witnessed many of their colleagues at Columbia University leave for new remote research sites following the departure of the Manhattan Project from its campus. Their effort to house this reactor near New York City was rivalled by a similar effort at the Massachusetts Institute of Technology to have a facility near Boston, Massachusetts. Involvement was quickly solicited from representatives of northeastern universities to the south and west of New York City such that this city would be at their geographic center. In March 1946 a nonprofit corporation was established that consisted of representatives from nine major research universities — Columbia University, Cornell University, Harvard University, Johns Hopkins University, Massachusetts Institute of Technology, Princeton University, University of Pennsylvania, University of Rochester, and Yale University.

Out of 17 considered sites in the Boston-Washington corridor, Camp Upton on Long Island was eventually chosen as the most suitable in consideration of space, transportation, and availability. The camp had been a training center from the US Army during both World War I and World War II. After the latter war, Camp Upton was deemed no longer necessary and became available for reuse. A plan was conceived to convert the military camp into a research facility.

On March 21, 1947, the Camp Upton site was officially transferred from the U.S. War Department to the new U.S. Atomic Energy Commission (AEC), predecessor to the U.S. Department of Energy (DOE).

Research and facilities

Reactor history

In 1947 construction began on the first nuclear reactor at Brookhaven, the Brookhaven Graphite Research Reactor. This reactor, which opened in 1950, was the first reactor to be constructed in the United States after World War II. The High Flux Beam Reactor operated from 1965 to 1999. In 1959 Brookhaven built the first US reactor specifically tailored to medical research, the Brookhaven Medical Research Reactor, which operated until 2000.

Accelerator history

In 1952 Brookhaven began using its first particle accelerator, the Cosmotron. At the time the Cosmotron was the world’s highest energy accelerator, being the first to impart more than 1 GeV of energy to a particle.

BNL Cosmotron 1952-1966.

The Cosmotron was retired in 1966, after it was superseded in 1960 by the new Alternating Gradient Synchrotron (AGS).

BNL Alternating Gradient Synchrotron (AGS).

The AGS was used in research that resulted in 3 Nobel prizes, including the discovery of the muon neutrino, the charm quark, and CP violation.

In 1970 in BNL started the ISABELLE project to develop and build two proton intersecting storage rings.

The groundbreaking for the project was in October 1978. In 1981, with the tunnel for the accelerator already excavated, problems with the superconducting magnets needed for the ISABELLE accelerator brought the project to a halt, and the project was eventually cancelled in 1983.

The National Synchrotron Light Source operated from 1982 to 2014 and was involved with two Nobel Prize-winning discoveries. It has since been replaced by the National Synchrotron Light Source II. [below].

BNL National Synchrotron Light Source.

After ISABELLE’S cancellation, physicist at BNL proposed that the excavated tunnel and parts of the magnet assembly be used in another accelerator. In 1984 the first proposal for the accelerator now known as the Relativistic Heavy Ion Collider (RHIC)[below] was put forward. The construction got funded in 1991 and RHIC has been operational since 2000. One of the world’s only two operating heavy-ion colliders, RHIC is as of 2010 the second-highest-energy collider after the Large Hadron Collider (CH). RHIC is housed in a tunnel 2.4 miles (3.9 km) long and is visible from space.

On January 9, 2020, it was announced by Paul Dabbar, undersecretary of the US Department of Energy Office of Science, that the BNL eRHIC design has been selected over the conceptual design put forward by DOE’s Thomas Jefferson National Accelerator Facility [Jlab] as the future Electron–ion collider (EIC) in the United States.

Electron-Ion Collider (EIC) at DOE’s Brookhaven National Laboratory to be built inside the tunnel that currently houses the Relativistic Heavy Ion Collider [RHIC]. Credit: BNL.

In addition to the site selection, it was announced that the BNL EIC had acquired CD-0 from the Department of Energy. BNL’s eRHIC design proposes upgrading the existing Relativistic Heavy Ion Collider, which collides beams light to heavy ions including polarized protons, with a polarized electron facility, to be housed in the same tunnel.

Other discoveries

In 1958, Brookhaven scientists created one of the world’s first video games, Tennis for Two. In 1968 Brookhaven scientists patented Maglev, a transportation technology that utilizes magnetic levitation.

Major facilities

Relativistic Heavy Ion Collider (RHIC), which was designed to research quark–gluon plasma and the sources of proton spin. Until 2009 it was the world’s most powerful heavy ion collider. It is the only collider of spin-polarized protons.

Center for Functional Nanomaterials (CFN), used for the study of nanoscale materials.

BNL National Synchrotron Light Source II, Brookhaven’s newest user facility, opened in 2015 to replace the National Synchrotron Light Source (NSLS), which had operated for 30 years. NSLS was involved in the work that won the 2003 and 2009 Nobel Prize in Chemistry.

Alternating Gradient Synchrotron, a particle accelerator that was used in three of the lab’s Nobel prizes.
Accelerator Test Facility, generates, accelerates and monitors particle beams.
Tandem Van de Graaff, once the world’s largest electrostatic accelerator.

Computational Science resources, including access to a massively parallel Blue Gene series supercomputer that is among the fastest in the world for scientific research, run jointly by Brookhaven National Laboratory and Stony Brook University-SUNY.

Interdisciplinary Science Building, with unique laboratories for studying high-temperature superconductors and other materials important for addressing energy challenges.
NASA Space Radiation Laboratory, where scientists use beams of ions to simulate cosmic rays and assess the risks of space radiation to human space travelers and equipment.

Off-site contributions

It is a contributing partner to the ATLAS experiment, one of the four detectors located at 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(LHC). Credit: CERN.

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] map. Credit: CERN.

The European Organization for Nuclear Research [La Organización Europea para la Investigación Nuclear][ Organization européenne pour la recherche nucléaire] [Europäische Organization für Kernforschung] By now iconic image of (CH)[CERN] ATLAS. Credit: CERN.

It is currently operating at 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] near Geneva, Switzerland.

Brookhaven was also responsible for the design of the Spallation Neutron Source at DOE’s Oak Ridge National Laboratory, Tennessee.

DOE’s Oak Ridge National Laboratory Spallation Neutron Source annotated.

Brookhaven plays a role in a range of neutrino research projects around the world, including the Daya Bay Neutrino Experiment (CN) nuclear power plant, approximately 52 kilometers northeast of Hong Kong and 45 kilometers east of Shenzhen, China.

Daya Bay Neutrino Experiment (CN) nuclear power plant, approximately 52 kilometers northeast of Hong Kong and 45 kilometers east of Shenzhen, China .

DOE’s Fermi National Accelerator Laboratory DUNE LBNF from FNAL to Sanford Underground Research Facility, Lead, South Dakota.

BNL Center for Functional Nanomaterials. Credit: BNL.

DOE’s Brookhaven National Laboratory NSLS II. Interior. Credit: BNL.

DOE’s Brookhaven National Laboratory NSLS II. Credit: BNL.

DOE’s Brookhaven National Laboratory(US) RHIC Campus. Credit: BNL.

BNL RHIC’s newly enhanced STAR detector. The house-size STAR detector at the Relativistic Heavy Ion Collider (RHIC) acts like a giant 3D digital camera to track particles emerging from particle collisions at the center of the detector.

DOE’s Brookhaven National Laboratory(US)/RHIC Phenix detector. Credit: BNL..

Brookhaven sPhenix Assembly. Credit: BNL.

BNL RHIC Schematic view of the proposed sPHENIX detector. Credit: BNL.

BNL RHIC inner hadronic calorimeter being installed in the sPHENIX Detector. Credit: BNL.

From The Johns Hopkins University Via The “HUB” : “Ancient proteins offer new clues about origins of life on Earth”

From The Johns Hopkins University

Via

The “HUB”

2.27.23
Roberto Molar Candanosa

Our Planet Earth

In early Earth simulation co-led by researchers at Johns Hopkins, scientists gain insights into how amino acids shaped the genetic code of ancient microorganisms

By simulating early Earth conditions in the lab, researchers have found that without specific amino acids, ancient proteins would not have known how to evolve into everything alive on the planet today—including plants, animals, and humans.

The findings, which detail how amino acids shaped the genetic code of ancient microorganisms, shed light on the mystery of how life began on Earth.

“You see the same amino acids in every organism, from humans to bacteria to archaea, and that’s because all things on Earth are connected through this tree of life that has an origin, an organism that was the ancestor to all living things,” said Stephen Fried, a Johns Hopkins chemist who co-led the research with scientists at Charles University in the Czech Republic. “We’re describing the events that shaped why that ancestor got the amino acids that it did.”

The findings are newly published in the Journal of the American Chemical Society [below] .

In the lab, the researchers mimicked primordial protein synthesis of 4 billion years ago by using an alternative set of amino acids that were highly abundant before life arose on Earth.

They found ancient organic compounds integrated the amino acids best suited for protein folding into their biochemistry. In other words, life thrived on Earth not just because some amino acids were available and easy to make in ancient habitats but also because some of them were especially good at helping proteins adopt specific shapes to perform crucial functions.

“Protein folding was basically allowing us to do evolution before there was even life on our planet,” Fried said. “You could have evolution before you had biology, you could have natural selection for the chemicals that are useful for life even before there was DNA.”

Even though the primordial Earth had hundreds of amino acids, all living things use the same 20 of these compounds. Fried calls those compounds “canonical.” But science has struggled to pinpoint what’s so special—if anything—about those 20 amino acids.

In its first billion years, Earth’s atmosphere consisted of an assortment of gases like ammonia and carbon dioxide that reacted with high levels of ultraviolet radiation to concoct some of the simpler canonical amino acids. Others arrived via special delivery by meteorites, which introduced a mixed bag of ingredients that helped life on Earth complete a set of 10 “early” amino acids.

How the rest came to be is an open question that Fried’s team is trying to answer with the new research, especially because those space rocks brought much more than the “modern” amino acids.

“We’re trying to find out what was so special about our canonical amino acids,” Fried said. “Were they selected for any particular reason?”

Scientists estimate Earth is 4.6 billion years old, and that DNA, proteins, and other molecules didn’t begin to form simple organisms until 3.8 billion years ago. The new research offers new clues into the mystery of what happened during the time in between.

“To have evolution in the Darwinian sense, you need to have this whole sophisticated way of turning genetic molecules like DNA and RNA into proteins. But replicating DNA also requires proteins, so we have a chicken-and-egg problem,” Fried said. “Our research shows that nature could have selected for building blocks with useful properties before Darwinian evolution.”

Scientists have spotted amino acids in asteroids far from Earth, suggesting those compounds are ubiquitous in other corners of the universe. That’s why Fried thinks the new research could also have implications for the possibility of finding life beyond Earth.

“The universe seems to love amino acids,” Fried said. “Maybe if we found life on a different planet, it wouldn’t be that different.”

This research is supported by the Human Frontier Science Program grant HFSP-RGY0074/2019 and the NIH Director’s New Innovator Award (DP2-GM140926).

The study’s authors include Anneliese M. Faustino, of Johns Hopkins; Mikhail Makarov, Alma C. Sanchez Rocha, Ivan Cherepashuk, Robin Krystufek, and Klara Hlouchova, of Charles University; Volha Dzmitruk, Tatsiana Charnavets, and Michal Lebl, of the Czech Academy of Sciences; and Kosuke Fujishima, of Tokyo Institute of Technology.

Journal of the American Chemical Society

Abstract
Whereas modern proteins rely on a quasi-universal repertoire of 20 canonical amino acids (AAs), numerous lines of evidence suggest that ancient proteins relied on a limited alphabet of 10 “early” AAs and that the 10 “late” AAs were products of biosynthetic pathways. However, many nonproteinogenic AAs were also prebiotically available, which begs two fundamental questions: Why do we have the current modern amino acid alphabet and would proteins be able to fold into globular structures as well if different amino acids comprised the genetic code? Here, we experimentally evaluate the solubility and secondary structure propensities of several prebiotically relevant amino acids in the context of synthetic combinatorial 25-mer peptide libraries. The most prebiotically abundant linear aliphatic and basic residues were incorporated along with or in place of other early amino acids to explore these alternative sequence spaces. The results show that foldability was likely a critical factor in the selection of the canonical alphabet. Unbranched aliphatic amino acids were purged from the proteinogenic alphabet despite their high prebiotic abundance because they generate polypeptides that are oversolubilized and have low packing efficiency. Surprisingly, we find that the inclusion of a short-chain basic amino acid also decreases polypeptides’ secondary structure potential, for which we suggest a biophysical model. Our results support the view that, despite lacking basic residues, the early canonical alphabet was remarkably adaptive at supporting protein folding and explain why basic residues were only incorporated at a later stage of protein evolution.

See the full article here .

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Johns Hopkins University campus

Johns Hopkins University opened in 1876, with the inauguration of its first president, Daniel Coit Gilman. “What are we aiming at?” Gilman asked in his installation address. “The encouragement of research … and the advancement of individual scholars, who by their excellence will advance the sciences they pursue, and the society where they dwell.”

The mission laid out by Gilman remains the university’s mission today, summed up in a simple but powerful restatement of Gilman’s own words: “Knowledge for the world.”

What Gilman created was a research university, dedicated to advancing both students’ knowledge and the state of human knowledge through research and scholarship. Gilman believed that teaching and research are interdependent, that success in one depends on success in the other. A modern university, he believed, must do both well. The realization of Gilman’s philosophy at Johns Hopkins, and at other institutions that later attracted Johns Hopkins-trained scholars, revolutionized higher education in America, leading to the research university system as it exists today.

The Johns Hopkins University is a private research university in Baltimore, Maryland. Founded in 1876, the university was named for its first benefactor, the American entrepreneur and philanthropist Johns Hopkins. His $7 million bequest (approximately $147.5 million in today’s currency)—of which half financed the establishment of the Johns Hopkins Hospital—was the largest philanthropic gift in the history of the United States up to that time. Daniel Coit Gilman, who was inaugurated as the institution’s first president on February 22, 1876, led the university to revolutionize higher education in the U.S. by integrating teaching and research. Adopting the concept of a graduate school from Germany’s historic Ruprecht Karl University of Heidelberg, [Ruprecht-Karls-Universität Heidelberg] (DE), Johns Hopkins University is considered the first research university in the United States. Over the course of several decades, the university has led all U.S. universities in annual research and development expenditures. In fiscal year 2016, Johns Hopkins spent nearly $2.5 billion on research. The university has graduate campuses in Italy, China, and Washington, D.C., in addition to its main campus in Baltimore.

Johns Hopkins is organized into 10 divisions on campuses in Maryland and Washington, D.C., with international centers in Italy and China. The two undergraduate divisions, the Zanvyl Krieger School of Arts and Sciences and the Whiting School of Engineering, are located on the Homewood campus in Baltimore’s Charles Village neighborhood. The medical school, nursing school, and Bloomberg School of Public Health, and Johns Hopkins Children’s Center are located on the Medical Institutions campus in East Baltimore. The university also consists of the Peabody Institute, Applied Physics Laboratory, Paul H. Nitze School of Advanced International Studies, School of Education, Carey Business School, and various other facilities.

Johns Hopkins was a founding member of the American Association of Universities. As of October 2019, 39 Nobel laureates and 1 Fields Medalist have been affiliated with Johns Hopkins. Founded in 1883, the Blue Jays men’s lacrosse team has captured 44 national titles and plays in the Big Ten Conference as an affiliate member as of 2014.

Research

The opportunity to participate in important research is one of the distinguishing characteristics of Hopkins’ undergraduate education. About 80 percent of undergraduates perform independent research, often alongside top researchers. In FY 2013, Johns Hopkins received $2.2 billion in federal research grants—more than any other U.S. university for the 35th consecutive year. Johns Hopkins has had seventy-seven members of the Institute of Medicine, forty-three Howard Hughes Medical Institute Investigators, seventeen members of the National Academy of Engineering, and sixty-two members of the National Academy of Sciences. As of October 2019, 39 Nobel Prize winners have been affiliated with the university as alumni, faculty members or researchers, with the most recent winners being Gregg Semenza and William G. Kaelin.

Between 1999 and 2009, The Johns Hopkins University was among the most cited institutions in the world. It attracted nearly 1,222,166 citations and produced 54,022 papers under its name, ranking No. 3 globally [after Harvard University and the Max Planck Society (DE)] in the number of total citations published in Thomson Reuters-indexed journals over 22 fields in America.

In FY 2000, Johns Hopkins received $95.4 million in research grants from the National Aeronautics and Space Administration, making it the leading recipient of NASA research and development funding. In FY 2002, Hopkins became the first university to cross the $1 billion threshold on either list, recording $1.14 billion in total research and $1.023 billion in federally sponsored research. In FY 2008, Johns Hopkins University performed $1.68 billion in science, medical and engineering research, making it the leading U.S. academic institution in total R&D spending for the 30th year in a row, according to a National Science Foundation ranking. These totals include grants and expenditures of JHU’s Applied Physics Laboratory in Laurel, Maryland.

The Johns Hopkins University also offers the “Center for Talented Youth” program—a nonprofit organization dedicated to identifying and developing the talents of the most promising K-12 grade students worldwide. As part of the Johns Hopkins University, the “Center for Talented Youth” or CTY helps fulfill the university’s mission of preparing students to make significant future contributions to the world. The Johns Hopkins Digital Media Center (DMC) is a multimedia lab space as well as an equipment, technology and knowledge resource for students interested in exploring creative uses of emerging media and use of technology.

In 2013, the Bloomberg Distinguished Professorships program was established by a $250 million gift from Michael Bloomberg. This program enables the university to recruit fifty researchers from around the world to joint appointments throughout the nine divisions and research centers. For The American Academy of Arts and Sciences each professor must be a leader in interdisciplinary research and be active in undergraduate education. Directed by Vice Provost for Research Denis Wirtz, there are currently thirty-two Bloomberg Distinguished Professors at the university, including three Nobel Laureates, eight fellows of the American Association for the Advancement of Science, ten members of the American Academy of Arts and Sciences, and thirteen members of the National Academies.

From The University of California-Santa Cruz: “RNA Rescue challenge invites players to solve puzzles and advance RNA therapeutics”

From The University of California-Santa Cruz

2.21.23
Tim Stephens
stephens@ucsc.edu

Researchers at The University of California-Santa Cruz have developed a new puzzle challenge for the online game Eterna, enlisting players to help design a novel RNA drug to treat hemophilia A.

Introducing “OpenASO: RNA Rescue”

Researchers at The University of California-Santa Cruz working to develop novel RNA-based medicines are teaming up with a new group of collaborators—players of the online game Eterna. The game’s new “OpenASO: RNA Rescue” challenge will tap into the collective intelligence of Eterna’s 250,000 registered users to help design an RNA drug for the treatment of hemophilia A.

An antisense oligonucleotide (ASO) can bind to a messenger RNA molecule, as shown in this illustration, and, in some cases, can correct defects in RNA splicing caused by genetic mutations. (Image credit: Sharif Ezzat/Eterna)

“The Eterna player community may be able to come up with designs that we wouldn’t get using traditional screening methodologies for drug development,” said Michael Stone, professor of chemistry and biochemistry at The University of California-Santa Cruz.

Eterna is an open science platform that has been engaging citizen scientists in RNA-related puzzles for over 10 years. Previous challenges have included “OpenVaccine”, to design a more stable mRNA vaccine against COVID-19, and “OpenTB”, to develop a new diagnostic device to detect tuberculosis.

Stone and his colleagues at The University of California-Santa Cruz—including molecular biologist Jeremy Sanford and geneticist Olena Vaske, both faculty in the Department of Molecular, Cell and Developmental Biology—have been working to develop therapies for diseases caused by genetic mutations that disrupt the processing of RNA in the cell. One approach that has shown promise in treating this type of disease is called antisense oligonucleotide (ASO) therapy.

In all cells RNA molecules copy information from DNA and direct the synthesis of proteins. ASOs are short segments of RNA designed to bind to specific cellular RNA molecules. They can modify gene expression or RNA processing and, in some cases, correct defects caused by genetic mutations. But developing an ASO that has the desired effect typically requires “brute force” screening efforts that can take many years to yield positive results.

“One of the goals of our project is to accelerate that discovery process,” Stone said. “That’s where Eterna comes in.”

Rhiju Das, who leads Eterna and is a Howard Hughes Medical Institute investigator at Stanford University School of Medicine, said Eterna players have come up with RNA design solutions that out-performed the results of supercomputers and expert research teams.

When Stone told Das about his team’s work on developing an RNA-based therapy for hemophilia A, Das said he thought the Eterna community might be able to help.

“The community of Eterna players has discovered unusual principles for designing new kinds of RNA diagnostics and stabilizing mRNA vaccines, resulting in dozens of scientific papers. It will be exciting to see what they can now do in ASO therapeutics with experimental feedback from experts at The University of California-Santa Cruz,” Das said.

Hemophilia A is caused by mutations in the gene for the blood clotting factor 8 (F8), a protein required for the normal clotting of blood to control bleeding. When a protein-coding gene like F8 is activated, its DNA code is copied into RNA molecules called messenger RNAs. Before these messenger RNAs can direct protein synthesis, however, they undergo a modification process called RNA splicing that involves removing certain sections of the sequence. This RNA splicing process can be derailed by genetic mutations.

“It turns out that many genetic diseases involve splicing defects,” Stone said. “Jeremy Sanford’s research team has identified hemophilia-causing mutations in the factor 8 gene that lead to RNA-splicing defects, and we want to target this ‘toxic RNA’ with ASOs.”

In the OpenASO: RNA Rescue challenge, Eterna players are tasked with designing an RNA oligonucleotide that can bind to the F8 messenger RNA in a way that will correct the splicing defect. “Our idea is to design an oligonucleotide to disrupt a certain tract of the RNA that modulates splicing,” Stone explained. “But as players start to dig in, they’ll come up with solutions based on their own criteria, which may have nothing to do with biology but which might actually work.”

Winning solutions are determined by the votes of the player community. The University of California-Santa Cruz researchers will then synthesize the top candidates and test them in laboratory experiments, reporting the results back to the players.

“We’re all very excited to see how this goes,” Stone said. “There is a long list of mutations that appear to cause RNA splicing defects and a lot of interest in exploring the potential for ASO therapies.”

The University of California-Santa Cruz team’s preliminary work on Factor 8 mutations was funded by a seed grant from The University of California-Santa Cruz Office of Research. In addition, critical contributions to the investigation of RNA splicing defects in F8 were made by undergraduates in Sanford’s lab, funded by a National Science Foundation grant to support course-based undergraduate research experience (CURE) labs at The University of California-Santa Cruz.

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UC Santa Cruz campus.

The University of California-Santa Cruz, opened in 1965 and grew, one college at a time, to its current (2008-09) enrollment of more than 16,000 students. Undergraduates pursue more than 60 majors supervised by divisional deans of humanities, physical & biological sciences, social sciences, and arts. Graduate students work toward graduate certificates, master’s degrees, or doctoral degrees in more than 30 academic fields under the supervision of the divisional and graduate deans. The dean of the Jack Baskin School of Engineering oversees the campus’s undergraduate and graduate engineering programs.

The University of California-Santa Cruz is a public land-grant research university in Santa Cruz, California. It is one of the ten campuses in the University of California system. Located on Monterey Bay, on the edge of the coastal community of Santa Cruz, the campus lies on 2,001 acres (810 ha) of rolling, forested hills overlooking the Pacific Ocean.

Founded in 1965, The University of California-Santa Cruz began with the intention to showcase progressive, cross-disciplinary undergraduate education, innovative teaching methods and contemporary architecture. The residential college system consists of ten small colleges that were established as a variation of the Oxbridge collegiate university system.

Among the Faculty is 1 Nobel Prize Laureate, 1 Breakthrough Prize in Life Sciences recipient, 12 members from the National Academy of Sciences, 28 members of the American Academy of Arts and Sciences, and 40 members of the American Association for the Advancement of Science. Eight University of California-Santa Cruz alumni are winners of 10 Pulitzer Prizes. The University of California-Santa Cruz is classified among “R1: Doctoral Universities – Very high research activity”. It is a member of the Association of American Universities, an alliance of elite research universities in the United States and Canada.

The university has five academic divisions: Arts, Engineering, Humanities, Physical & Biological Sciences, and Social Sciences. Together, they offer 65 graduate programs, 64 undergraduate majors, and 41 minors.

Popular undergraduate majors include Art, Business Management Economics, Chemistry, Molecular and Cell Biology, Physics, and Psychology. Interdisciplinary programs, such as Computational Media, Feminist Studies, Environmental Studies, Visual Studies, Digital Arts and New Media, Critical Race & Ethnic Studies, and the History of Consciousness Department are also hosted alongside UCSC’s more traditional academic departments.

A joint program with The University of California-Hastings enables University of California-Santa Cruz students to earn a bachelor’s degree and Juris Doctor degree in six years instead of the usual seven. The “3+3 BA/JD” Program between University of California-Santa Cruz and The University of California-Hastings College of the Law in San Francisco accepted its first applicants in fall 2014. University of California-Santa Cruz students who declare their intent in their freshman or early sophomore year will complete three years at The University of California-Santa Cruz and then move on to The University of California-Hastings to begin the three-year law curriculum. Credits from the first year of law school will count toward a student’s bachelor’s degree. Students who successfully complete the first-year law course work will receive their bachelor’s degree and be able to graduate with their University of California-Santa Cruz class, then continue at The University of California-Hastings afterwards for two years.

According to the National Science Foundation, The University of California-Santa Cruz spent $127.5 million on research and development in 2018, ranking it 144th in the nation.

Although designed as a liberal arts-oriented university, The University of California-Santa Cruz quickly acquired a graduate-level natural science research component with the appointment of plant physiologist Kenneth V. Thimann as the first provost of Crown College. Thimann developed The University of California-Santa Cruz’s early Division of Natural Sciences and recruited other well-known science faculty and graduate students to the fledgling campus. Immediately upon its founding, The University of California-Santa Cruz was also granted administrative responsibility for the Lick Observatory, which established the campus as a major center for Astronomy research. Founding members of the Social Science and Humanities faculty created the unique History of Consciousness graduate program in The University of California-Santa Cruz’s first year of operation.

Famous former University of California-Santa Cruz faculty members include Judith Butler and Angela Davis.

The University of California-Santa Cruz’s organic farm and garden program is the oldest in the country, and pioneered organic horticulture techniques internationally.

As of 2015, The University of California-Santa Cruz’s faculty include 13 members of the National Academy of Sciences, 24 fellows of the American Academy of Arts and Sciences, and 33 fellows of the American Association for the Advancement of Science. The Baskin School of Engineering, founded in 1997, is The University of California-Santa Cruz’s first and only professional school. Baskin Engineering is home to several research centers, including the Center for Biomolecular Science and Engineering and Cyberphysical Systems Research Center, which are gaining recognition, as has the work that UCSC researchers David Haussler and Jim Kent have done on the Human Genome Project, including the widely used University of California-Santa Cruz Genome Browser. The University of California-Santa Cruz administers the National Science Foundation’s Center for Adaptive Optics.

Off-campus research facilities maintained by The University of California-Santa Cruz include the Lick and The W. M. Keck Observatory, Mauna Kea, Hawai’i and the Long Marine Laboratory. From September 2003 to July 2016, The University of California-Santa Cruz managed a University Affiliated Research System (UARC) for the NASA Ames Research Center under a task order contract valued at more than $330 million.

The University of California-Santa Cruz was tied for 58th in the list of Best Global Universities and tied for 97th in the list of Best National Universities in the United States by U.S. News & World Report’s 2021 rankings. In 2017 Kiplinger ranked The University of California-Santa Cruz 50th out of the top 100 best-value public colleges and universities in the nation, and 3rd in California. Money Magazine ranked The University of California-Santa Cruz 41st in the country out of the nearly 1500 schools it evaluated for its 2016 Best Colleges ranking. In 2016–2017, The University of California-Santa Cruz Santa Cruz was rated 146th in the world by Times Higher Education World University Rankings. In 2016 it was ranked 83rd in the world by the Academic Ranking of World Universities and 296th worldwide in 2016 by the QS World University Rankings.

In 2009, RePEc, an online database of research economics articles, ranked the The University of California-Santa Cruz Economics Department sixth in the world in the field of international finance. In 2007, High Times magazine placed The University of California-Santa Cruz as first among US universities as a “counterculture college.” In 2009, The Princeton Review (with Gamepro magazine) ranked The University of California-Santa Cruz’s Game Design major among the top 50 in the country. In 2011, The Princeton Review and Gamepro Media ranked The University of California-Santa Cruz’s graduate programs in Game Design as seventh in the nation. In 2012, The University of California-Santa Cruz was ranked No. 3 in the Most Beautiful Campus list of Princeton Review.

The University of California-Santa Cruz is the home base for the Lick Observatory.

UCO Lick Observatory’s 36-inch Great Refractor telescope housed in the South (large) Dome of main building.

The University of California-Santa Cruz Lick Observatory Since 1888 Mt Hamilton, in San Jose, California, Altitude 1,283 m (4,209 ft)

UC Observatories Lick Automated Planet Finder fully robotic 2.4-meter optical telescope at Lick Observatory, situated on the summit of Mount Hamilton, east of San Jose, California, USA.

The UCO Lick C. Donald Shane telescope is a 120-inch (3.0-meter) reflecting telescope located at the Lick Observatory, Mt Hamilton, in San Jose, California, Altitude 1,283 m (4,209 ft).

Search for extraterrestrial intelligence expands at Lick Observatory

New instrument scans the sky for pulses of infrared light

March 23, 2015
By Hilary Lebow
Astronomers are expanding the search for extraterrestrial intelligence into a new realm with detectors tuned to infrared light at The University of California-Santa Cruz’s Lick Observatory. A new instrument, called NIROSETI, will soon scour the sky for messages from other worlds.

“Infrared light would be an excellent means of interstellar communication,” said Shelley Wright, an assistant professor of physics at The University of California-San Diego who led the development of the new instrument while at The University of Toronto (CA)’s Dunlap Institute for Astronomy and Astrophysics (CA).

Infrared light would be a good way for extraterrestrials to get our attention here on Earth, since pulses from a powerful infrared laser could outshine a star, if only for a billionth of a second. Interstellar gas and dust is almost transparent to near infrared, so these signals can be seen from great distances. It also takes less energy to send information using infrared signals than with visible light.

The NIROSETI instrument saw first light on the Nickel 1-meter Telescope at Lick Observatory on March 15, 2015. (Photo by Laurie Hatch.)

Astronomers are expanding the search for extraterrestrial intelligence into a new realm with detectors tuned to infrared light at University of California’s Lick Observatory. A new instrument, called NIROSETI, will soon scour the sky for messages from other worlds.

Alumna Shelley Wright, now an assistant professor of physics at The University of California- San Diego, discusses the dichroic filter of the NIROSETI instrument, developed at the University of Toronto Dunlap Institute for Astronomy and Astrophysics (CA) and brought to The University of California-San Diego and installed at the UC Santa Cruz Lick Observatory Nickel Telescope (Photo by Laurie Hatch).

“Infrared light would be an excellent means of interstellar communication,” said Shelley Wright, an assistant professor of physics at The University of California-San Diego who led the development of the new instrument while at the University of Toronto’s Dunlap Institute for Astronomy and Astrophysics (CA).

NIROSETI team from left to right Rem Stone UCO Lick Observatory Dan Werthimer, UC Berkeley; Jérôme Maire, U Toronto; Shelley Wright, The University of California-San Diego Patrick Dorval, U Toronto; Richard Treffers, Starman Systems. (Image by Laurie Hatch).

Wright worked on an earlier SETI project at Lick Observatory as a University of California-Santa Cruz undergraduate, when she built an optical instrument designed by University of California-Berkeley researchers. The infrared project takes advantage of new technology not available for that first optical search.

Infrared light would be a good way for extraterrestrials to get our attention here on Earth, since pulses from a powerful infrared laser could outshine a star, if only for a billionth of a second. Interstellar gas and dust is almost transparent to near infrared, so these signals can be seen from great distances. It also takes less energy to send information using infrared signals than with visible light.

Frank Drake, professor emeritus of astronomy and astrophysics at The University of California-Santa Cruz and director emeritus of the SETI Institute, said there are several additional advantages to a search in the infrared realm.

Frank Drake with his Drake Equation. Credit Frank Drake.

Drake Equation, Frank Drake, Seti Institute.

“The signals are so strong that we only need a small telescope to receive them. Smaller telescopes can offer more observational time, and that is good because we need to search many stars for a chance of success,” said Drake.

The only downside is that extraterrestrials would need to be transmitting their signals in our direction, Drake said, though he sees this as a positive side to that limitation. “If we get a signal from someone who’s aiming for us, it could mean there’s altruism in the universe. I like that idea. If they want to be friendly, that’s who we will find.”

Scientists have searched the skies for radio signals for more than 50 years and expanded their search into the optical realm more than a decade ago. The idea of searching in the infrared is not a new one, but instruments capable of capturing pulses of infrared light only recently became available.

“We had to wait,” Wright said. “I spent eight years waiting and watching as new technology emerged.”

Now that technology has caught up, the search will extend to stars thousands of light years away, rather than just hundreds. NIROSETI, or Near-Infrared Optical Search for Extraterrestrial Intelligence, could also uncover new information about the physical universe.

From The Department of Materials Science and Engineering At The Massachusetts Institute of Technology: “Making nanoparticle building blocks for new materials” Associate Professor Robert Macfarlane

From The Department of Materials Science and Engineering

At

The Massachusetts Institute of Technology

2.17.23
Zach Winn

“I like to make things,” Macfarlane says. “I want to make materials that can be functional and useful, and I want to do so by figuring out the basic principles that go into making new structures at many different size ranges.” Photo: Adam Glanzman.

Some researchers are driven by the quest to improve a specific product, like a battery or a semiconductor. Others are motivated by tackling questions faced by a given industry. Rob Macfarlane, MIT’s Paul M. Cook Associate Professor in Materials Science and Engineering, is driven by a more fundamental desire.

“I like to make things,” Macfarlane says. “I want to make materials that can be functional and useful, and I want to do so by figuring out the basic principles that go into making new structures at many different size ranges.”

He adds, “For a lot of industries or types of engineering, materials synthesis is treated as a solved problem — making a new device is about using the materials we already have in new ways. In our lab’s research efforts, we often have to educate people that the reason we can’t do X, Y, or Z right now is because we don’t have the materials needed to enable those technological advances. In many cases, we simply don’t know how to make them yet. This is the goal of our research: Our lab is about enabling the materials needed to develop new technologies rather than focusing on just the end products.”

By uncovering design principles for nanocomposites, which are materials made from mixtures of polymers and nanoparticles, Macfarlane’s career has gradually evolved from designing specks of novel materials to building functional objects you can hold in your hand. Eventually, he believes his research will lead to new ways of making products with fine-tuned and predetermined combinations of desired electrical, mechanical, optical, and magnetic properties.

Along the way Macfarlane, who earned tenure last year, has also committed himself t mentoring students. He’s taught three undergraduate chemistry courses at MIT, including his current course, 3.010 (Synthesis and Design of Materials), which introduces sophomores to the fundamental concepts necessary for designing and making their own new structures in the future. He also recently redesigned a course in which he teaches graduate students how to be educators by learning how to do things like write a syllabus, communicate with and mentor students, and design homework assignments.

Ultimately, Macfarlane believes mentoring the next generation of researchers is as important as publishing papers.

“I’m fortunate. I’ve been successful, and I have the opportunity to pursue research I’m passionate about,” he says. “Now I view a major component of my job as enabling my students to be successful. The real product and output of what I do here is not just the science and tech advancements and patents, it’s the students that go on to industry or academia or wherever else they choose, and then change the world in their own ways.”

From nanometers to millimeters

Macfarlane was born and raised on a small farm in Palmer, Alaska, a suburban community about 45 minutes north of Anchorage. When he was in high school, the town announced budget cuts that would force the school to scale back a number of classes. In response, Macfarlane’s mother, a former school teacher, encouraged him to enroll in the science education classes that would be offered to students a year older than him, so he wouldn’t miss the chance to take them.

“She knew education was paramount, so she said ‘We’re going to get you into these last classes before they get watered down,’” Macfarlane recalls.

Macfarlane didn’t know any of the students in his new classes, but he had a passionate chemistry teacher that helped him discover a love for the subject. As a result, when he decided to attend Willamette University in Oregon as an undergraduate, he immediately declared himself a chemistry major (which he later adjusted to biochemistry).

Macfarlane attended Yale University for his master’s degree and initially began a PhD there before moving to Northwestern University, where a PhD student’s seminar set Macfarlane on a path he’d follow for the rest of his career.

“[The PhD student] was doing exactly what I was interested in,” says Macfarlane, who asked the student’s PhD advisor, Professor Chad Mirkin, to be his advisor as well. “I was very fortunate when I joined Mirkin’s lab, because the project I worked on had been initiated by a sixth-year grad student and a postdoc that published a big paper and then immediately left. So, there was this wide-open field nobody was working on. It was like being given a blank canvas with a thousand different things to do.”

The work revolved around a precise way to bind particles together using synthetic DNA strands that act like Velcro.

Researchers have known for decades that certain materials exhibit unique properties when assembled at the scale of 1 to 100 nanometers. It was also believed that building things out of those precisely organized assemblies could give objects unique properties. The problem was finding a way to get the particles to bind in a predictable way.

With the DNA-based approach, Macfarlane had a starting point.

“[The researchers] had said, ‘Okay, we’ve shown we can make a thing, but can we make all the things with DNA?’” Macfarlane says. “My PhD thesis was about developing design rules so that if you use a specific set of building blocks, you get a known set of nanostructures as a result. Those rules allowed us to make hundreds of different crystal structures with different sizes, compositions, shapes, lattice structures, etc.”

After completing his PhD, Macfarlane knew he wanted to go into academia, but his biggest priority had nothing to do with work.

“I wanted to go somewhere warm,” Macfarlane says. “I had lived in Alaska for 18 years. I did a PhD in Chicago for six years. I just wanted to go somewhere warm for a while.”

Macfarlane ended up at Caltech in Pasadena, California, working in the labs of Harry Atwater and Nobel laureate Bob Grubbs. Researchers in those labs were studying self-assembly using a new type of polymer, which Macfarlane says required a “completely different” skillset compared to his PhD work.

In 2015, after two years of learning to build materials using polymers and soaking up the sun, Macfarlane plunged back into the cold and joined MIT’s faculty. In Cambridge, Macfarlane has focused on merging the assembly techniques he’s developed for both polymers, DNA, and inorganic nanoparticles to make new materials at larger scales.

That work led Macfarlane and a group of researchers to create a new type of self-assembling building blocks that his lab has dubbed “nanocomposite tectons” (NCTs). NCTs use polymers and molecules that can mimic the ability of DNA to direct the self-organization of nanoscale objects, but with far more scalablility — meaning these materials could be used to build macroscopic objects that can a person can hold in their hand.

“[The objects] had controlled composition at the polymer and nanoparticle level; they had controlled grain sizes and microstructural features; and they had a controlled macroscopic three-dimensional form; and that’s never been done before,” Macfarlane says. “It opened up a huge number of possibilities by saying all those properties that people have been studying for decades on these nanoparticles and their assemblies, now we can actually make them into something functional and useful.”

A world of possibilities

As Macfarlane continues working to make NCTs more scalable, he’s excited about a number of potential applications.

One involves programming objects to transfer energy in specific ways. In the case of mechanical energy, if you hit the object with a hammer or it were involved in a car crash, the resulting energy could dissipate in a way that protects what’s on the other side. In the case of photons or electrons, you could design a precise path for the energy or ions to travel through, which could improve the efficiency of energy storage, computing, and transportation components.

The truth is that such precise design of materials has too many potential applications to count.

Working on such fundamental problems excites Macfarlane, and the possibilities coming from his work will only grow as his team continues to make advances.

“In the end, NCTs open up many new possibilities for materials design, but what might be especially industrially relevant is not so much the NCTs themselves, but what we’ve learned along the way,” Macfarlane says. “We’ve learned how to develop new syntheses and processing methods, so one of the things I’m most excited about is making materials with these methods that have compositions that were previously inaccessible.”

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”.

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MIT Department of Materials Science and Engineering campus – The Engineering Oval on Centennial Campus includes the new Fitts-Woolard Building, next to the Hunt Library. Photo by Becky Kirkland.

What is MSE?

Engineering disciplines focus on addressing human problems by constructing tools and shaping solutions. Materials science and engineering (MSE) does so by studying, understanding, designing, and producing the materials those tools and solutions are made of — and on creating new materials that serve human needs.

MSE combines the power of intellectual curiosity and scientific discovery with the tangible impact of engineering disciplines. By integrating approaches from diverse academic and engineering specialties that range from physics and biology to metallurgy and ceramics, MSE addresses complex problems through a materials-focused approach. This deeply interdisciplinary field encompasses nearly every form of matter — from the atom-by-atom construction of nanomaterials and the directed growth of biological substances to the forging of heat-treated steel.

USPS “Forever” postage stamps celebrating Innovation at MIT.

The Massachusetts Institute of Technology is a private land-grant research university in Cambridge, Massachusetts. The institute has an urban campus that extends more than a mile (1.6 km) alongside the Charles River. The institute also encompasses a number of major off-campus facilities such as the MIT Lincoln Laboratory , the MIT Bates Research and Engineering Center , and the Haystack Observatory , as well as affiliated laboratories such as the Broad Institute of MIT and Harvard and Whitehead Institute.

MIT AeroAstro campus

MIT Lincoln Laboratory campus

Massachusettes Institute of Technology-Haystack Observatory Westford, Massachusetts, USA, Altitude 131 m (430 ft).

The Computer Science and Artificial Intelligence Laboratory (CSAIL)

MIT-IBM Watson AI Lab, 314 Main St. in the Kendall Square technology center of Cambridge, Massachusetts.

The Kavli Institute For Astrophysics and Space Research

MIT’s Institute for Medical Engineering and Science is a research institute at the Massachusetts Institute of Technology

The MIT Laboratory for Nuclear Science

The MIT Media Lab

MIT PLasma Science and Fusion Center

The MIT School of Engineering

The MIT Sloan School of Management

Spectrum

MIT School of Architecture and Planning campus.

MIT Electrical Engineering & Computer Science campus.

Founded in 1861 in response to the increasing industrialization of the United States, Massachusetts Institute of Technology adopted a European polytechnic university model and stressed laboratory instruction in applied science and engineering. It has since played a key role in the development of many aspects of modern science, engineering, mathematics, and technology, and is widely known for its innovation and academic strength. It is frequently regarded as one of the most prestigious universities in the world.

As of December 2020, 97 Nobel laureates, 26 Turing Award winners, and 8 Fields Medalists have been affiliated with MIT as alumni, faculty members, or researchers. In addition, 58 National Medal of Science recipients, 29 National Medals of Technology and Innovation recipients, 50 MacArthur Fellows, 80 Marshall Scholars, 3 Mitchell Scholars, 22 Schwarzman Scholars, 41 astronauts, and 16 Chief Scientists of the U.S. Air Force have been affiliated with The Massachusetts Institute of Technology. The university also has a strong entrepreneurial culture and MIT alumni have founded or co-founded many notable companies. Massachusetts Institute of Technology is a member of the Association of American Universities.

Foundation and vision

In 1859, a proposal was submitted to the Massachusetts General Court to use newly filled lands in Back Bay, Boston for a “Conservatory of Art and Science”, but the proposal failed. A charter for the incorporation of the Massachusetts Institute of Technology, proposed by William Barton Rogers, was signed by John Albion Andrew, the governor of Massachusetts, on April 10, 1861.

Rogers, a professor from the University of Virginia , wanted to establish an institution to address rapid scientific and technological advances. He did not wish to found a professional school, but a combination with elements of both professional and liberal education, proposing that:

“The true and only practicable object of a polytechnic school is, as I conceive, the teaching, not of the minute details and manipulations of the arts, which can be done only in the workshop, but the inculcation of those scientific principles which form the basis and explanation of them, and along with this, a full and methodical review of all their leading processes and operations in connection with physical laws.”

The Rogers Plan reflected the German research university model, emphasizing an independent faculty engaged in research, as well as instruction oriented around seminars and laboratories.

Early developments

Two days after The Massachusetts Institute of Technology was chartered, the first battle of the Civil War broke out. After a long delay through the war years, MIT’s first classes were held in the Mercantile Building in Boston in 1865. The new institute was founded as part of the Morrill Land-Grant Colleges Act to fund institutions “to promote the liberal and practical education of the industrial classes” and was a land-grant school. In 1863 under the same act, the Commonwealth of Massachusetts founded the Massachusetts Agricultural College, which developed as the University of Massachusetts Amherst ). In 1866, the proceeds from land sales went toward new buildings in the Back Bay.

The Massachusetts Institute of Technology was informally called “Boston Tech”. The institute adopted the European polytechnic university model and emphasized laboratory instruction from an early date. Despite chronic financial problems, the institute saw growth in the last two decades of the 19th century under President Francis Amasa Walker. Programs in electrical, chemical, marine, and sanitary engineering were introduced, new buildings were built, and the size of the student body increased to more than one thousand.

The curriculum drifted to a vocational emphasis, with less focus on theoretical science. The fledgling school still suffered from chronic financial shortages which diverted the attention of the MIT leadership. During these “Boston Tech” years, Massachusetts Institute of Technology faculty and alumni rebuffed Harvard University president (and former MIT faculty) Charles W. Eliot’s repeated attempts to merge MIT with Harvard College’s Lawrence Scientific School. There would be at least six attempts to absorb MIT into Harvard. In its cramped Back Bay location, MIT could not afford to expand its overcrowded facilities, driving a desperate search for a new campus and funding. Eventually, the MIT Corporation approved a formal agreement to merge with Harvard, over the vehement objections of MIT faculty, students, and alumni. However, a 1917 decision by the Massachusetts Supreme Judicial Court effectively put an end to the merger scheme.

In 1916, The Massachusetts Institute of Technology administration and the MIT charter crossed the Charles River on the ceremonial barge Bucentaur built for the occasion, to signify MIT’s move to a spacious new campus largely consisting of filled land on a one-mile-long (1.6 km) tract along the Cambridge side of the Charles River. The neoclassical “New Technology” campus was designed by William W. Bosworth and had been funded largely by anonymous donations from a mysterious “Mr. Smith”, starting in 1912. In January 1920, the donor was revealed to be the industrialist George Eastman of Rochester, New York, who had invented methods of film production and processing, and founded Eastman Kodak. Between 1912 and 1920, Eastman donated $20 million ($236.6 million in 2015 dollars) in cash and Kodak stock to MIT.

Curricular reforms

In the 1930s, President Karl Taylor Compton and Vice-President (effectively Provost) Vannevar Bush emphasized the importance of pure sciences like physics and chemistry and reduced the vocational practice required in shops and drafting studios. The Compton reforms “renewed confidence in the ability of the Institute to develop leadership in science as well as in engineering”. Unlike Ivy League schools, Massachusetts Institute of Technology catered more to middle-class families, and depended more on tuition than on endowments or grants for its funding. The school was elected to the Association of American Universities in 1934.

Still, as late as 1949, the Lewis Committee lamented in its report on the state of education at The Massachusetts Institute of Technology that “the Institute is widely conceived as basically a vocational school”, a “partly unjustified” perception the committee sought to change. The report comprehensively reviewed the undergraduate curriculum, recommended offering a broader education, and warned against letting engineering and government-sponsored research detract from the sciences and humanities. The School of Humanities, Arts, and Social Sciences and the MIT Sloan School of Management were formed in 1950 to compete with the powerful Schools of Science and Engineering. Previously marginalized faculties in the areas of economics, management, political science, and linguistics emerged into cohesive and assertive departments by attracting respected professors and launching competitive graduate programs. The School of Humanities, Arts, and Social Sciences continued to develop under the successive terms of the more humanistically oriented presidents Howard W. Johnson and Jerome Wiesner between 1966 and 1980.

The Massachusetts Institute of Technology‘s involvement in military science surged during World War II. In 1941, Vannevar Bush was appointed head of the federal Office of Scientific Research and Development and directed funding to only a select group of universities, including MIT. Engineers and scientists from across the country gathered at Massachusetts Institute of Technology ‘s Radiation Laboratory, established in 1940 to assist the British military in developing microwave radar. The work done there significantly affected both the war and subsequent research in the area. Other defense projects included gyroscope-based and other complex control systems for gunsight, bombsight, and inertial navigation under Charles Stark Draper’s Instrumentation Laboratory; the development of a digital computer for flight simulations under Project Whirlwind; and high-speed and high-altitude photography under Harold Edgerton. By the end of the war, The Massachusetts Institute of Technology became the nation’s largest wartime R&D contractor (attracting some criticism of Bush), employing nearly 4000 in the Radiation Laboratory alone and receiving in excess of $100 million ($1.2 billion in 2015 dollars) before 1946. Work on defense projects continued even after then. Post-war government-sponsored research at MIT included SAGE and guidance systems for ballistic missiles and Project Apollo.

These activities affected The Massachusetts Institute of Technology profoundly. A 1949 report noted the lack of “any great slackening in the pace of life at the Institute” to match the return to peacetime, remembering the “academic tranquility of the prewar years”, though acknowledging the significant contributions of military research to the increased emphasis on graduate education and rapid growth of personnel and facilities. The faculty doubled and the graduate student body quintupled during the terms of Karl Taylor Compton, president of The Massachusetts Institute of Technology between 1930 and 1948; James Rhyne Killian, president from 1948 to 1957; and Julius Adams Stratton, chancellor from 1952 to 1957, whose institution-building strategies shaped the expanding university. By the 1950s, The Massachusetts Institute of Technology no longer simply benefited the industries with which it had worked for three decades, and it had developed closer working relationships with new patrons, philanthropic foundations and the federal government.

In late 1960s and early 1970s, student and faculty activists protested against the Vietnam War and The Massachusetts Institute of Technology ‘s defense research. In this period Massachusetts Institute of Technology’s various departments were researching helicopters, smart bombs and counterinsurgency techniques for the war in Vietnam as well as guidance systems for nuclear missiles. The Union of Concerned Scientists was founded on March 4, 1969 during a meeting of faculty members and students seeking to shift the emphasis on military research toward environmental and social problems. The Massachusetts Institute of Technology ultimately divested itself from the Instrumentation Laboratory and moved all classified research off-campus to the MIT Lincoln Laboratory facility in 1973 in response to the protests. The student body, faculty, and administration remained comparatively unpolarized during what was a tumultuous time for many other universities. Johnson was seen to be highly successful in leading his institution to “greater strength and unity” after these times of turmoil. However, six Massachusetts Institute of Technology students were sentenced to prison terms at this time and some former student leaders, such as Michael Albert and George Katsiaficas, are still indignant about MIT’s role in military research and its suppression of these protests. (Richard Leacock’s film, November Actions, records some of these tumultuous events.)

In the 1980s, there was more controversy at The Massachusetts Institute of Technology over its involvement in SDI (space weaponry) and CBW (chemical and biological warfare) research. More recently, The Massachusetts Institute of Technology’s research for the military has included work on robots, drones and ‘battle suits’.

Recent history

The Massachusetts Institute of Technology has kept pace with and helped to advance the digital age. In addition to developing the predecessors to modern computing and networking technologies, students, staff, and faculty members at Project MAC, the Artificial Intelligence Laboratory, and the Tech Model Railroad Club wrote some of the earliest interactive computer video games like Spacewar! and created much of modern hacker slang and culture. Several major computer-related organizations have originated at MIT since the 1980s: Richard Stallman’s GNU Project and the subsequent Free Software Foundation were founded in the mid-1980s at the AI Lab; the MIT Media Lab was founded in 1985 by Nicholas Negroponte and Jerome Wiesner to promote research into novel uses of computer technology; the World Wide Web Consortium standards organization was founded at the Laboratory for Computer Science in 1994 by Tim Berners-Lee; the MIT OpenCourseWare project has made course materials for over 2,000 Massachusetts Institute of Technology classes available online free of charge since 2002; and the One Laptop per Child initiative to expand computer education and connectivity to children worldwide was launched in 2005.

The Massachusetts Institute of Technology was named a sea-grant college in 1976 to support its programs in oceanography and marine sciences and was named a space-grant college in 1989 to support its aeronautics and astronautics programs. Despite diminishing government financial support over the past quarter century, MIT launched several successful development campaigns to significantly expand the campus: new dormitories and athletics buildings on west campus; the Tang Center for Management Education; several buildings in the northeast corner of campus supporting research into biology, brain and cognitive sciences, genomics, biotechnology, and cancer research; and a number of new “backlot” buildings on Vassar Street including the Stata Center. Construction on campus in the 2000s included expansions of the Media Lab, the Sloan School’s eastern campus, and graduate residences in the northwest. In 2006, President Hockfield launched the MIT Energy Research Council to investigate the interdisciplinary challenges posed by increasing global energy consumption.

In 2001, inspired by the open source and open access movements, The Massachusetts Institute of Technology launched OpenCourseWare to make the lecture notes, problem sets, syllabi, exams, and lectures from the great majority of its courses available online for no charge, though without any formal accreditation for coursework completed. While the cost of supporting and hosting the project is high, OCW expanded in 2005 to include other universities as a part of the OpenCourseWare Consortium, which currently includes more than 250 academic institutions with content available in at least six languages. In 2011, The Massachusetts Institute of Technology announced it would offer formal certification (but not credits or degrees) to online participants completing coursework in its “MITx” program, for a modest fee. The “edX” online platform supporting MITx was initially developed in partnership with Harvard and its analogous “Harvardx” initiative. The courseware platform is open source, and other universities have already joined and added their own course content. In March 2009 the Massachusetts Institute of Technology faculty adopted an open-access policy to make its scholarship publicly accessible online.

The Massachusetts Institute of Technology has its own police force. Three days after the Boston Marathon bombing of April 2013, MIT Police patrol officer Sean Collier was fatally shot by the suspects Dzhokhar and Tamerlan Tsarnaev, setting off a violent manhunt that shut down the campus and much of the Boston metropolitan area for a day. One week later, Collier’s memorial service was attended by more than 10,000 people, in a ceremony hosted by the Massachusetts Institute of Technology community with thousands of police officers from the New England region and Canada. On November 25, 2013, The Massachusetts Institute of Technology announced the creation of the Collier Medal, to be awarded annually to “an individual or group that embodies the character and qualities that Officer Collier exhibited as a member of The Massachusetts Institute of Technology community and in all aspects of his life”. The announcement further stated that “Future recipients of the award will include those whose contributions exceed the boundaries of their profession, those who have contributed to building bridges across the community, and those who consistently and selflessly perform acts of kindness”.

In September 2017, the school announced the creation of an artificial intelligence research lab called the MIT-IBM Watson AI Lab. IBM will spend $240 million over the next decade, and the lab will be staffed by MIT and IBM scientists. In October 2018 MIT announced that it would open a new Schwarzman College of Computing dedicated to the study of artificial intelligence, named after lead donor and The Blackstone Group CEO Stephen Schwarzman. The focus of the new college is to study not just AI, but interdisciplinary AI education, and how AI can be used in fields as diverse as history and biology. The cost of buildings and new faculty for the new college is expected to be $1 billion upon completion.

The Caltech/MIT Advanced aLIGO was designed and constructed by a team of scientists from California Institute of Technology , Massachusetts Institute of Technology, and industrial contractors, and funded by the National Science Foundation .

Caltech /MIT Advanced aLigo

It was designed to open the field of gravitational-wave astronomy through the detection of gravitational waves predicted by general relativity. Gravitational waves were detected for the first time by the LIGO detector in 2015. For contributions to the LIGO detector and the observation of gravitational waves, two Caltech physicists, Kip Thorne and Barry Barish, and Massachusetts Institute of Technology physicist Rainer Weiss won the Nobel Prize in physics in 2017. Weiss, who is also a Massachusetts Institute of Technology graduate, designed the laser interferometric technique, which served as the essential blueprint for the LIGO.

The mission of The Massachusetts Institute of Technology is to advance knowledge and educate students in science, technology, and other areas of scholarship that will best serve the nation and the world in the twenty-first century. We seek to develop in each member of The Massachusetts Institute of Technology community the ability and passion to work wisely, creatively, and effectively for the betterment of humankind.

From The DOE’s Brookhaven National Laboratory: “Study Identifies New Levers for Controlling Plant Biochemistry”

From The DOE’s Brookhaven National Laboratory

1.11.23
Karen McNulty Walsh,
kmcnulty@bnl.gov
(631) 344-8350, or

Peter Genzer,
genzer@bnl.gov
(631) 344-3174

1.11.23

Research reveals new tools for tailoring plants for range of applications including carbon-neutral utilization of plant biomass for agro-industrial applications.

Fluorescent visualization of proteins in leaf cells. In addition to performing genetic and biochemical studies, the scientists used a green fluorescent protein (GFP) “tag” and microscope facilities at Brookhaven Lab’s Center for Functional Nanomaterials to visualize the proteins they were studying in leaf cells. Left: Localization of a GFP-labeled electron donor protein along the endoplasmic reticulum (inner network of membranes) in leaf cells. Right: A GFP-labeled complex of the P450 enzyme interacting with the electron donor. In this case the scientists attached half of the GFP tag to each of these proteins; the fluorescent glow occurs only when the two halves come together as the proteins interact. (In both images the red signal comes from chlorophyl.)Credit: BNL.

Plant biochemists at the U.S. Department of Energy’s Brookhaven National Laboratory have discovered a new level of regulation in the biochemical “machinery” that plants use to convert organic carbon derived from photosynthesis into a range of ring-shaped aromatic molecules. The research, just published in the journal Science Advances [below], suggests new strategies for controlling plant biochemistry for agricultural and industrial applications. 

“Our study reveals the long-overlooked complexity and versatility of a key set of enzymes known as cytochrome P450 monooxygenases,” said study lead author Chang-Jun Liu of Brookhaven Lab’s biology department. “These enzymes operate as a synthetic machine to produce a wide range of aromatic compounds in plants—including compounds that build plants’ waterproof skeleton and vasculature, and others that provide defense from insect invasions and ultraviolet (UV) radiation.”

Uncovering the complexity of how these enzymes are regulated provides a new set of genetic tools scientists can use to precisely control which compounds get produced in different parts of a plant. The work could help facilitate long-term carbon storage and the carbon-neutral utilization of plant biomass for energy applications, improve plants’ nutritional properties, or increase their resistance to disease and harsh environmental conditions.

Postdoctoral researcher Xianhai Zhao and biochemist Chang-Jun Liu with Arabidopsis plants used in this study. Credit: BNL.

Molecular machinery

Scientists have long known that P450 enzymes do not work alone to determine the structural and biological features of aromatic compounds.

“To make P450 machines run they need partner molecules to deliver electrons. These electrons act as a power source to fuel the machine,” Liu explained.

Conventionally, scientists thought that the P450s primarily interact with a general electron donor called cytochrome P450 reductase to produce a variety of aromatic compounds. But the new study shows that different P450s selectively partner with different electron donors (and electron transport chains) to drive their activities. Moreover, the researchers found that the same P450 enzyme can make use of distinct electron donors and electron transport chains in different parts of a plant—stems, leaves, and seeds—to produce different classes of aromatics.

The scientists made these discoveries by analyzing the aromatic compounds that accumulated in different parts of plants in which the genes for different electron donors had been selectively deleted.

“By knocking out these genes, we were able to determine the contributions of distinct electron donors, identifying which ones drive the production of different aromatics in different parts of the plant,” Liu said. “Then, in yeast cells, we re-assembled different electron transport chains in combination with plant P450 enzymes to mimic the reactions in plants. Those studies helped us verify the contributions of individual electron donors and transport chains in supporting P450 activity.”

The experimental work was primarily conducted by postdoctoral researcher Xianhai Zhao under Liu’s guidance.

“Plants have evolved a number of homologous genes for electron donors,” Zhao explained, “so we needed to create plants with deletions of single genes and combinations of genes. We then examined the changes in the product distribution of aromatics over the course of plant development.”

“We also conducted a comprehensive comparative analysis of electron-donor gene expression and the abundance of electron source molecules in different parts of the plant and measured the electron transfer rates of different transport chains,” Zhao added.

These experiments helped the scientists identify the underlying reasons certain P450 enzymes partnered with different electron transport chains in different parts of the plant.

Next steps

The knowledge gained provides scientists with a new set of genetic tools they can manipulate to control aromatic production.

“We can manipulate particular electron donors—instead of the P450s—to suppress a distinct set of aromatics and achieve a desired outcome,” Liu said.

For example, reducing an aromatic compound known as lignin in stems could make plants easier to break down and convert to biofuels. Reducing levels of certain aromatics in seeds could improve their nutritional value.

“The detailed knowledge presented in this study allows us to make selected changes in one part of a plant without affecting another—like the accumulation of aromatic compounds that provide UV sunscreen in leaves,” Liu said.

The Brookhaven team plans to test these genetic manipulation strategies to optimize bioenergy crops. They’ll also conduct further studies using cryo-electron microscopes at Brookhaven’s Laboratory for BioMolecular Structure to understand the atomic-level details that drive the selective partnerships between P450 enzymes and specific electron donors.

“Exploring the molecular basis for the selective P450-electron donor association will help us further understand how the P450 system operates,” Liu said. “That, in turn, will allow us to potentially create more efficient enzyme systems to produce desired bioproducts and to enhance the conversion and storage of carbon taken in through photosynthesis.”

This work was funded by the DOE Office of Science (BES). This research used a confocal microscope at Brookhaven Lab’s Center for Functional Nanomaterials, a U.S. DOE Office of Science user facility.

Science paper:
Science Advances
See the science paper for instructive material with images and graphs.

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”.

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Please help promote STEM in your local schools.

Stem Education Coalition

Brookhaven Campus. Credit: BNL.

One of ten national laboratories overseen and primarily funded by the The DOE Office of Science, The DOE’s Brookhaven National Laboratory conducts research in the physical, biomedical, and environmental sciences, as well as in energy technologies and national security. Brookhaven Lab also builds and operates major scientific facilities available to university, industry and government researchers. The Laboratory’s almost 3,000 scientists, engineers, and support staff are joined each year by more than 5,000 visiting researchers from around the world. Brookhaven is operated and managed for DOE’s Office of Science by Brookhaven Science Associates, a limited-liability company founded by Stony Brook University the largest academic user of Laboratory facilities, and Battelle, a nonprofit, applied science and technology organization.

Research at BNL specializes in nuclear and high energy physics, energy science and technology, environmental and bioscience, nanoscience and national security. The 5300 acre campus contains several large research facilities, including the Relativistic Heavy Ion Collider [below] and National Synchrotron Light Source II [below]. Seven Nobel prizes have been awarded for work conducted at Brookhaven lab.

BNL is staffed by approximately 2,750 scientists, engineers, technicians, and support personnel, and hosts 4,000 guest investigators every year. The laboratory has its own police station, fire department, and ZIP code (11973). In total, the lab spans a 5,265-acre (21 km^2) area that is mostly coterminous with the hamlet of Upton, New York. BNL is served by a rail spur operated as-needed by the New York and Atlantic Railway. Co-located with the laboratory is the Upton, New York, forecast office of the National Weather Service.

Major programs

Although originally conceived as a nuclear research facility, Brookhaven Lab’s mission has greatly expanded. Its foci are now:

Nuclear and high-energy physics
Physics and chemistry of materials
Environmental and climate research
Nanomaterials
Energy research
Nonproliferation
Structural biology
Accelerator physics

Operation

Brookhaven National Lab was originally owned by the Atomic Energy Commission and is now owned by that agency’s successor, the United States Department of Energy (DOE). DOE subcontracts the research and operation to universities and research organizations. It is currently operated by Brookhaven Science Associates LLC, which is an equal partnership of Stony Brook University and Battelle Memorial Institute. From 1947 to 1998, it was operated by Associated Universities, Inc. (AUI), but AUI lost its contract in the wake of two incidents: a 1994 fire at the facility’s high-beam flux reactor that exposed several workers to radiation and reports in 1997 of a tritium leak into the groundwater of the Long Island Central Pine Barrens on which the facility sits.

Foundations

Following World War II, the US Atomic Energy Commission was created to support government-sponsored peacetime research on atomic energy. The effort to build a nuclear reactor in the American northeast was fostered largely by physicists Isidor Isaac Rabi and Norman Foster Ramsey Jr., who during the war witnessed many of their colleagues at Columbia University leave for new remote research sites following the departure of the Manhattan Project from its campus. Their effort to house this reactor near New York City was rivalled by a similar effort at the Massachusetts Institute of Technology to have a facility near Boston, Massachusetts. Involvement was quickly solicited from representatives of northeastern universities to the south and west of New York City such that this city would be at their geographic center. In March 1946 a nonprofit corporation was established that consisted of representatives from nine major research universities — Columbia University, Cornell University, Harvard University, Johns Hopkins University, Massachusetts Institute of Technology, Princeton University, University of Pennsylvania, University of Rochester, and Yale University.

Out of 17 considered sites in the Boston-Washington corridor, Camp Upton on Long Island was eventually chosen as the most suitable in consideration of space, transportation, and availability. The camp had been a training center from the US Army during both World War I and World War II. After the latter war, Camp Upton was deemed no longer necessary and became available for reuse. A plan was conceived to convert the military camp into a research facility.

On March 21, 1947, the Camp Upton site was officially transferred from the U.S. War Department to the new U.S. Atomic Energy Commission (AEC), predecessor to the U.S. Department of Energy (DOE).

Research and facilities

Reactor history

In 1947 construction began on the first nuclear reactor at Brookhaven, the Brookhaven Graphite Research Reactor. This reactor, which opened in 1950, was the first reactor to be constructed in the United States after World War II. The High Flux Beam Reactor operated from 1965 to 1999. In 1959 Brookhaven built the first US reactor specifically tailored to medical research, the Brookhaven Medical Research Reactor, which operated until 2000.

Accelerator history

In 1952 Brookhaven began using its first particle accelerator, the Cosmotron. At the time the Cosmotron was the world’s highest energy accelerator, being the first to impart more than 1 GeV of energy to a particle.

BNL Cosmotron 1952-1966.

The Cosmotron was retired in 1966, after it was superseded in 1960 by the new Alternating Gradient Synchrotron (AGS).

BNL Alternating Gradient Synchrotron (AGS).

The AGS was used in research that resulted in 3 Nobel prizes, including the discovery of the muon neutrino, the charm quark, and CP violation.

In 1970 in BNL started the ISABELLE project to develop and build two proton intersecting storage rings.

The groundbreaking for the project was in October 1978. In 1981, with the tunnel for the accelerator already excavated, problems with the superconducting magnets needed for the ISABELLE accelerator brought the project to a halt, and the project was eventually cancelled in 1983.

The National Synchrotron Light Source operated from 1982 to 2014 and was involved with two Nobel Prize-winning discoveries. It has since been replaced by the National Synchrotron Light Source II. [below].

BNL National Synchrotron Light Source.

After ISABELLE’S cancellation, physicist at BNL proposed that the excavated tunnel and parts of the magnet assembly be used in another accelerator. In 1984 the first proposal for the accelerator now known as the Relativistic Heavy Ion Collider (RHIC)[below] was put forward. The construction got funded in 1991 and RHIC has been operational since 2000. One of the world’s only two operating heavy-ion colliders, RHIC is as of 2010 the second-highest-energy collider after the Large Hadron Collider (CH). RHIC is housed in a tunnel 2.4 miles (3.9 km) long and is visible from space.

On January 9, 2020, it was announced by Paul Dabbar, undersecretary of the US Department of Energy Office of Science, that the BNL eRHIC design has been selected over the conceptual design put forward by DOE’s Thomas Jefferson National Accelerator Facility [Jlab] as the future Electron–ion collider (EIC) in the United States.

Electron-Ion Collider (EIC) at DOE’s Brookhaven National Laboratory to be built inside the tunnel that currently houses the Relativistic Heavy Ion Collider [RHIC]. Credit: BNL.

In addition to the site selection, it was announced that the BNL EIC had acquired CD-0 from the Department of Energy. BNL’s eRHIC design proposes upgrading the existing Relativistic Heavy Ion Collider, which collides beams light to heavy ions including polarized protons, with a polarized electron facility, to be housed in the same tunnel.

Other discoveries

In 1958, Brookhaven scientists created one of the world’s first video games, Tennis for Two. In 1968 Brookhaven scientists patented Maglev, a transportation technology that utilizes magnetic levitation.

Major facilities

Relativistic Heavy Ion Collider (RHIC), which was designed to research quark–gluon plasma and the sources of proton spin. Until 2009 it was the world’s most powerful heavy ion collider. It is the only collider of spin-polarized protons.

Center for Functional Nanomaterials (CFN), used for the study of nanoscale materials.

BNL National Synchrotron Light Source II, Brookhaven’s newest user facility, opened in 2015 to replace the National Synchrotron Light Source (NSLS), which had operated for 30 years. NSLS was involved in the work that won the 2003 and 2009 Nobel Prize in Chemistry.

Alternating Gradient Synchrotron, a particle accelerator that was used in three of the lab’s Nobel prizes.
Accelerator Test Facility, generates, accelerates and monitors particle beams.
Tandem Van de Graaff, once the world’s largest electrostatic accelerator.

Computational Science resources, including access to a massively parallel Blue Gene series supercomputer that is among the fastest in the world for scientific research, run jointly by Brookhaven National Laboratory and Stony Brook University-SUNY.

Interdisciplinary Science Building, with unique laboratories for studying high-temperature superconductors and other materials important for addressing energy challenges.
NASA Space Radiation Laboratory, where scientists use beams of ions to simulate cosmic rays and assess the risks of space radiation to human space travelers and equipment.

Off-site contributions

It is a contributing partner to the ATLAS experiment, one of the four detectors located at 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(LHC). Credit: CERN.

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] map. Credit: CERN.

The European Organization for Nuclear Research [La Organización Europea para la Investigación Nuclear][ Organization européenne pour la recherche nucléaire] [Europäische Organization für Kernforschung]By now iconic image of (CH)[CERN] ATLAS. Credit: CERN.

It is currently operating at 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] near Geneva, Switzerland.

Brookhaven was also responsible for the design of the Spallation Neutron Source at DOE’s Oak Ridge National Laboratory, Tennessee.

DOE’s Oak Ridge National Laboratory Spallation Neutron Source annotated.

Brookhaven plays a role in a range of neutrino research projects around the world, including the Daya Bay Neutrino Experiment (CN) nuclear power plant, approximately 52 kilometers northeast of Hong Kong and 45 kilometers east of Shenzhen, China.

Daya Bay Neutrino Experiment (CN) nuclear power plant, approximately 52 kilometers northeast of Hong Kong and 45 kilometers east of Shenzhen, China .

DOE’s Fermi National Accelerator Laboratory DUNE LBNF from FNAL to Sanford Underground Research Facility, Lead, South Dakota.

BNL Center for Functional Nanomaterials. Credit: BNL.

DOE’s Brookhaven National Laboratory NSLS II. Interior. Credit: BNL.

DOE’s Brookhaven National Laboratory NSLS II. Credit: BNL.

DOE’s Brookhaven National Laboratory(US) RHIC Campus. Credit: BNL.

BNL RHIC’s newly enhanced STAR detector. The house-size STAR detector at the Relativistic Heavy Ion Collider (RHIC) acts like a giant 3D digital camera to track particles emerging from particle collisions at the center of the detector.

DOE’s Brookhaven National Laboratory(US)/RHIC Phenix detector. Credit: BNL..

Brookhaven sPhenix Assembly. Credit: BNL.

BNL RHIC Schematic view of the proposed sPHENIX detector. Credit: BNL.

BNL RHIC inner hadronic calorimeter being installed in the sPHENIX Detector. Credit: BNL.

From The University of Pittsburgh Via “The Conversation (AU)” : “Visualizing the inside of cells at previously impossible resolutions provides vivid insights into how they work”

From The University of Pittsburgh

Via

“The Conversation (AU)”

1.6.23
Jeremy Berg

Cryo-electron tomography shows what molecules look like in high-resolution – in this case, the virus that causes COVID-19. Nanographics, CC BY-SA.

“All life is made up of cells several magnitudes smaller than a grain of salt. Their seemingly simple-looking structures mask the intricate and complex molecular activity that enables them to carry out the functions that sustain life. Researchers are beginning to be able to visualize this activity to a level of detail they haven’t been able to before.

Biological structures can be visualized by either starting at the level of the whole organism and working down, or starting at the level of single atoms and working up. However, there has been a resolution gap between a cell’s smallest structures, such as the cytoskeleton that supports the cell’s shape, and its largest structures, such as the ribosomes that make proteins in cells.

By analogy of Google Maps, while scientists have been able to see entire cities and individual houses, they did not have the tools to see how the houses came together to make up neighborhoods. Seeing these neighborhood-level details is essential to being able to understand how individual components work together in the environment of a cell.

New tools are steadily bridging this gap. And ongoing development of one particular technique, cryo-electron tomography, or cryo-ET, has the potential to deepen how researchers study and understand how cells function in health and disease.

Cryo-EM won the 2017 Nobel Prize in chemistry: Cryo-electron microscopy explained.

As the former editor-in-chief of Science magazine and as a researcher who has studied hard-to-visualize large protein structures for decades, I have witnessed astounding progress in the development of tools that can determine biological structures in detail. Just as it becomes easier to understand how complicated systems work when you know what they look like, understanding how biological structures fit together in a cell is key to understanding how organisms function.

A brief history of Microscopy

In the 17th century, “light microscopy” first revealed the existence of cells. In the 20th century, “electron microscopy” offered even greater detail, revealing the elaborate structures within cells, including organelles like the endoplasmic reticulum, a complex network of membranes that play key roles in protein synthesis and transport.

From the 1940s to 1960s, biochemists worked to separate cells into their molecular components and learn how to determine the 3D structures of proteins and other macromolecules at or near atomic resolution. This was first done using “X-ray crystallography” to visualize the structure of myoglobin, a protein that supplies oxygen to muscles.

Over the past decade, techniques based on nuclear magnetic resonance, which produces images based on how atoms interact in a magnetic field, and cryo-electron microscopy have rapidly increased the number and complexity of the structures scientists can visualize.

What is cryo-EM and cryo-ET?

Cryo-electron microscopy, or cryo-EM, uses a camera to detect how a beam of electrons is deflected as the electrons pass through a sample to visualize structures at the molecular level. Samples are rapidly frozen to protect them from radiation damage. Detailed models of the structure of interest are made by taking multiple images of individual molecules and averaging them into a 3D structure.

Cryo-ET shares similar components with cryo-EM but uses different methods. Because most cells are too thick to be imaged clearly, a region of interest in a cell is first thinned by using an ion beam. The sample is then tilted to take multiple pictures of it at different angles, analogous to a CT scan of a body part – although in this case the imaging system itself is tilted, rather than the patient. These images are then combined by a computer to produce a 3D image of a portion of the cell.

This is a cryo-ET image of the chloroplast of an algal cell. Engel et al. (2015), CC BY.

The resolution of this image is high enough that researchers – or computer programs – can identify the individual components of different structures in a cell. Researchers have used this approach, for example, to show how proteins move and are degraded inside an algal cell.

Many of the steps researchers once had to do manually to determine the structures of cells are becoming automated, allowing scientists to identify new structures at vastly higher speeds. For example, combining cryo-EM with artificial intelligence programs like AlphaFold [see Nature paper below] [Nature (below)] can facilitate image interpretation by predicting protein structures that have not yet been characterized.

Understanding cell structure and function

As imaging methods and workflows improve, researchers will be able to tackle some key questions in cell biology with different strategies.

The first step is to decide what cells and which regions within those cells to study. Another visualization technique called correlated light and electron microscopy, or CLEM [FEBSLetters (below)], uses fluorescent tags to help locate regions where interesting processes are taking place in living cells.

This is a cryo-EM image of a human T-cell leukemia virus type-1 (HTLV-1). vdvornyk/iStock via Getty Images Plus.

Comparing the genetic difference between cells [iScience (below)] can provide additional insight. Scientists can look at cells that are unable to carry out particular functions and see how this is reflected in their structure. This approach can also help researchers study how cells interact with each other.

Cryo-ET is likely to remain a specialized tool for some time. But further technological developments and increasing accessibility will allow the scientific community to examine the link between cellular structure and function at previously inaccessible levels of detail. I anticipate seeing new theories on how we understand cells, moving from disorganized bags of molecules to intricately organized and dynamic systems.”

Science papers:
Nature 2021
FEBSLetters 2022
iScience 2018
See the science papers for instructive material with images.

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”.

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Please help promote STEM in your local schools.

Stem Education Coalition

The University of Pittsburgh is a state-related research university, founded as the Pittsburgh Academy in 1787. Pitt is a member of The Association of American Universities, which comprises 62 preeminent doctorate-granting research institutions in North America.

From research achievements to the quality of its academic programs, the University of Pittsburgh ranks among the best in higher education.

Faculty members have expanded knowledge in the humanities and sciences, earning such prestigious honors as the National Medal of Science, the MacArthur Foundation’s “genius” grant, the Lasker-DeBakey Clinical Medical Research Award, and election to The National Academy of Sciences and The Institute of Medicine.
Pitt students have earned Rhodes, Goldwater, Marshall, and Truman Scholarships, among other highly competitive national and international scholarship

Alumni have pioneered MRI and TV, won Nobels and Pulitzers, led corporations and universities, served in government and the military, conquered Hollywood and The New York Times bestsellers list, and won Super Bowls and NBA championships.