From The University of Cambridge (UK): “New route to evolution – how DNA from our mitochondria gets into our genomes”

From The University of Cambridge (UK)

10.5.22
Craig Brierley

Mitochondria surrounded by cytoplasm. Credit: Dr David Furness.

Scientists have shown that in one in every 4,000 births, some of the genetic code from our mitochondria – the ‘batteries’ that power our cells – inserts itself into our DNA, revealing a surprising new insight into how humans evolve.

In a study published today in Nature [below], researchers at the University of Cambridge and Queen Mary University of London show that mitochondrial DNA also appears in some cancer DNA suggesting that it acts as a sticking plaster to try and repair damage to our genetic code.

Mitochondria are tiny ‘organelles’ that sit within our cells, where they act like batteries, providing energy in the form of the molecule ATP to power the cells. Each mitochondrion has its own DNA – mitochondrial DNA – that is distinct to the rest of the human genome which is comprised of nuclear DNA.

Mitochondrial DNA is passed down the maternal line – that is, we inherit it from our mothers, not our fathers. However, a study published in PNAS [below] in 2018 from researchers at the Cincinnati Children’s Hospital Medical Center in the USA reported evidence that suggested some mitochondrial DNA had been passed down the paternal line.

To investigate these claims, the Cambridge team looked at the DNA from over 11,000 families recruited to Genomics England’s 100,000 Genomes Project, searching for patterns that looked like paternal inheritance. The Cambridge team found mitochondrial DNA ‘inserts’ in the nuclear DNA of some children that were not present in that of their parents. This meant that the US team had probably reached the wrong conclusions: what they had observed were not paternally-inherited mitochondrial DNA, but rather these inserts.

Now, extending this work to over 66,000 people, the team showed that the new inserts are actually happening all the time, showing a new way our genome evolves.

Professor Patrick Chinnery, from the Medical Research Council Mitochondrial Biology Unit and Department of Clinical Neurosciences at the University of Cambridge, explained: “Billions of years ago, a primitive animal cell took in a bacterium that became what we now call mitochondria. These supply energy to the cell to allow it to function normally, while removing oxygen, which is toxic at high levels. Over time, bits of these primitive mitochondria have passed into the cell nucleus, allowing their genomes to talk to each other.

“This was all thought to have happened a very long time ago, mostly before we had even formed as a species, but what we’ve discovered is that that’s not true. We can see this happening right now, with bits of our mitochondrial genetic code transferring into the nuclear genome in a measurable way.”

The team estimate that mitochondrial DNA transfers to nuclear DNA in around one in every 4,000 births. If that individual has children of their own, they will pass these inserts on – the team found that most of us carry five of the new inserts, and one in seven of us (14%) carry very recent ones. Once in place, the inserts can occasionally lead to very rare diseases, including a rare genetic form of cancer.

It is not clear exactly how the mitochondrial DNA inserts itself – whether it does so directly or via an intermediary, such as RNA – but Professor Chinnery says it is likely to occur within the mother’s egg cells.

When the team looked at sequences taken from 12,500 tumour samples, they found that mitochondrial DNA was even more common in tumour DNA, arising in around one in 1,000 cancers, and in some cases, the mitochondrial DNA inserts actually causes the cancer.

“Our nuclear genetic code is breaking and being repaired all the time,” said Professor Chinnery. “Mitochondrial DNA appears to act almost like a Band-Aid, a sticking plaster to help the nuclear genetic code repair itself. And sometimes this works, but on rare occasions if might make things worse or even trigger the development of tumours.”

More than half (58%) of the insertions were in regions of the genome that code for proteins. In the majority of cases, the body recognizes the invading mitochondrial DNA and silences it in a process known as methylation, whereby a molecule attaches itself to the insert and switches it off. A similar process occurs when viruses manage to insert themselves into our DNA. However, this method of silencing is not perfect, as some of the mitochondrial DNA inserts go on to be copied and move around the nucleus itself.

The team looked for evidence that the reverse might happen – that mitochondrial DNA absorbs parts of our nuclear DNA – but found none. There are likely to be several reasons why this should be the case.

Firstly, cells only have two copies of nuclear DNA, but thousands of copies of mitochondrial DNA, so the chances of mitochondrial DNA being broken and passing into the nucleus are much greater than the other way around.

Secondly, the DNA in mitochondria is packaged inside two membranes and there are no holes in the membrane, so it would be difficult for nuclear DNA to get in. By contrast, if mitochondrial DNA manages to get out, holes in the membrane surrounding nuclear DNA would allow it pass through with relative ease.

Professor Sir Mark Caulfield, Vice Principal for Health at Queen Mary University of London, said: “I am so delighted that the 100,000 Genomes Project has unlocked the dynamic interplay between mitochondrial DNA and our genome in the cell’s nucleus. This defines a new role in DNA repair, but also one that could occasionally trigger rare disease, or even malignancy.”

The research was mainly funded by the Medical Research Council, Wellcome, and the National Institute for Health Research.

Science papers:
Nature
PNAS 2018
See the science papers for instructive material.

See the full article here .

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The University of Cambridge (UK) [legally The Chancellor, Masters, and Scholars of the University of Cambridge] is a collegiate public research university in Cambridge, England. Founded in 1209 Cambridge is the second-oldest university in the English-speaking world and the world’s fourth-oldest surviving university. It grew out of an association of scholars who left the University of Oxford (UK) after a dispute with townsfolk. The two ancient universities share many common features and are often jointly referred to as “Oxbridge”.

Cambridge is formed from a variety of institutions which include 31 semi-autonomous constituent colleges and over 150 academic departments, faculties and other institutions organized into six schools. All the colleges are self-governing institutions within the university, each controlling its own membership and with its own internal structure and activities. All students are members of a college. Cambridge does not have a main campus and its colleges and central facilities are scattered throughout the city. Undergraduate teaching at Cambridge is organized around weekly small-group supervisions in the colleges – a feature unique to the Oxbridge system. These are complemented by classes, lectures, seminars, laboratory work and occasionally further supervisions provided by the central university faculties and departments. Postgraduate teaching is provided predominantly centrally.

Cambridge University Press a department of the university is the oldest university press in the world and currently the second largest university press in the world. Cambridge Assessment also a department of the university is one of the world’s leading examining bodies and provides assessment to over eight million learners globally every year. The university also operates eight cultural and scientific museums, including the Fitzwilliam Museum, as well as a botanic garden. Cambridge’s libraries – of which there are 116 – hold a total of around 16 million books, around nine million of which are in Cambridge University Library, a legal deposit library. The university is home to – but independent of – the Cambridge Union – the world’s oldest debating society. The university is closely linked to the development of the high-tech business cluster known as “Silicon Fe”. It is the central member of Cambridge University Health Partners, an academic health science centre based around the Cambridge Biomedical Campus.

By both endowment size and consolidated assets Cambridge is the wealthiest university in the United Kingdom. In the fiscal year ending 31 July 2019, the central university – excluding colleges – had a total income of £2.192 billion of which £592.4 million was from research grants and contracts. At the end of the same financial year the central university and colleges together possessed a combined endowment of over £7.1 billion and overall consolidated net assets (excluding “immaterial” historical assets) of over £12.5 billion. It is a member of numerous associations and forms part of the ‘golden triangle’ of English universities.

Cambridge has educated many notable alumni including eminent mathematicians; scientists; politicians; lawyers; philosophers; writers; actors; monarchs and other heads of state. As of October 2020, 121 Nobel laureates; 11 Fields Medalists; 7 Turing Award winners; and 14 British prime ministers have been affiliated with Cambridge as students; alumni; faculty or research staff. University alumni have won 194 Olympic medals.

History

By the late 12th century, the Cambridge area already had a scholarly and ecclesiastical reputation due to monks from the nearby bishopric church of Ely. However, it was an incident at Oxford which is most likely to have led to the establishment of the university: three Oxford scholars were hanged by the town authorities for the death of a woman without consulting the ecclesiastical authorities who would normally take precedence (and pardon the scholars) in such a case; but were at that time in conflict with King John. Fearing more violence from the townsfolk scholars from the University of Oxford started to move away to cities such as Paris; Reading; and Cambridge. Subsequently enough scholars remained in Cambridge to form the nucleus of a new university when it had become safe enough for academia to resume at Oxford. In order to claim precedence, it is common for Cambridge to trace its founding to the 1231 charter from Henry III granting it the right to discipline its own members (ius non-trahi extra) and an exemption from some taxes; Oxford was not granted similar rights until 1248.

A bull in 1233 from Pope Gregory IX gave graduates from Cambridge the right to teach “everywhere in Christendom”. After Cambridge was described as a studium generale in a letter from Pope Nicholas IV in 1290 and confirmed as such in a bull by Pope John XXII in 1318 it became common for researchers from other European medieval universities to visit Cambridge to study or to give lecture courses.

Foundation of the colleges

The colleges at the University of Cambridge were originally an incidental feature of the system. No college is as old as the university itself. The colleges were endowed fellowships of scholars. There were also institutions without endowments called hostels. The hostels were gradually absorbed by the colleges over the centuries; but they have left some traces, such as the name of Garret Hostel Lane.

Hugh Balsham, Bishop of Ely, founded Peterhouse – Cambridge’s first college in 1284. Many colleges were founded during the 14th and 15th centuries but colleges continued to be established until modern times. There was a gap of 204 years between the founding of Sidney Sussex in 1596 and that of Downing in 1800. The most recently established college is Robinson built in the late 1970s. However, Homerton College only achieved full university college status in March 2010 making it the newest full college (it was previously an “Approved Society” affiliated with the university).

In medieval times many colleges were founded so that their members would pray for the souls of the founders and were often associated with chapels or abbeys. The colleges’ focus changed in 1536 with the Dissolution of the Monasteries. Henry VIII ordered the university to disband its Faculty of Canon Law and to stop teaching “scholastic philosophy”. In response, colleges changed their curricula away from canon law and towards the classics; the Bible; and mathematics.

Nearly a century later the university was at the centre of a Protestant schism. Many nobles, intellectuals and even commoners saw the ways of the Church of England as too similar to the Catholic Church and felt that it was used by the Crown to usurp the rightful powers of the counties. East Anglia was the centre of what became the Puritan movement. In Cambridge the movement was particularly strong at Emmanuel; St Catharine’s Hall; Sidney Sussex; and Christ’s College. They produced many “non-conformist” graduates who, greatly influenced by social position or preaching left for New England and especially the Massachusetts Bay Colony during the Great Migration decade of the 1630s. Oliver Cromwell, Parliamentary commander during the English Civil War and head of the English Commonwealth (1649–1660), attended Sidney Sussex.

Modern period

After the Cambridge University Act formalized the organizational structure of the university the study of many new subjects was introduced e.g. theology, history and modern languages. Resources necessary for new courses in the arts architecture and archaeology were donated by Viscount Fitzwilliam of Trinity College who also founded the Fitzwilliam Museum. In 1847 Prince Albert was elected Chancellor of the University of Cambridge after a close contest with the Earl of Powis. Albert used his position as Chancellor to campaign successfully for reformed and more modern university curricula, expanding the subjects taught beyond the traditional mathematics and classics to include modern history and the natural sciences. Between 1896 and 1902 Downing College sold part of its land to build the Downing Site with new scientific laboratories for anatomy, genetics, and Earth sciences. During the same period the New Museums Site was erected including the Cavendish Laboratory which has since moved to the West Cambridge Site and other departments for chemistry and medicine.

The University of Cambridge began to award PhD degrees in the first third of the 20th century. The first Cambridge PhD in mathematics was awarded in 1924.

In the First World War 13,878 members of the university served and 2,470 were killed. Teaching and the fees it earned came almost to a stop and severe financial difficulties followed. As a consequence, the university first received systematic state support in 1919 and a Royal Commission appointed in 1920 recommended that the university (but not the colleges) should receive an annual grant. Following the Second World War the university saw a rapid expansion of student numbers and available places; this was partly due to the success and popularity gained by many Cambridge scientists.

From The Harvard Medical School: “Old Mysteries and New Insights”

From The Harvard Medical School

at

Harvard University
News & Research

Ancient DNA illuminates 15000 years of history at Europe-Asia crossroads.

Fresco of a horse from the ancient kingdom of Urartu in what is now Armenia and Turkey. The new DNA analyses included several individuals associated with the kingdom. Image: EvgenyGenkin/CC BY-SA 3.0

Growing up in Greece, Iosif Lazaridis shared his compatriots’ appreciation that they lived in “the crossroads of Europe and Asia,” past and present.

To the east lay Turkey and Armenia, gateways to the Near East and Asia. To the north were the Balkans, leading the way into central Europe.

Lazaridis wondered how people in these regions were related to one another. Who shared long-ago ancestry with whom? How might those forebears have moved around this part of the world and had children with one another throughout millennia? How deeply connected were their modern descendants despite national borders and political conflicts?

Many people moved to Greece from the Balkans after the collapse of the Soviet Union, and many Greeks descend from refugees who came from Turkey in the early 20th century, Lazaridis knew. “Surely these changes that happened as I was growing up and that I heard about from old people were just the tip of the iceberg of what had happened in the centuries before,” he said.

The questions simmered at the back of Lazaridis’ mind as he moved to California to earn a PhD in information and computer science. They followed him to Boston, where he joined the lab of geneticist David Reich at Harvard Medical School.

There, he and colleagues around the world began to unearth answers through the study of ancient DNA.

Now, Lazaridis is co-first author of a trio of papers, published Aug. 25 in the journal Science [below], that tell the most complete story yet of ancestry in this pivotal part of the world.

The studies describe 15,000 years of genetic history in what the team has dubbed the Southern Arc: the lands sweeping from southeastern Europe into the Middle East, encompassing more than a dozen countries from Romania and Serbia through Greece and Turkey into Armenia, Azerbaijan, Iran, Lebanon, and Israel.

Featuring the genomes of more than 1,300 ancient people, 727 of them sequenced for the first time, the work represents one of the largest analyses to date of ancient human DNA.

“Often there’s an artificial distinction between Europe and Asia that people make,” said Lazaridis, research fellow in genetics at HMS who serves as a staff scientist in the Reich lab. “For these studies, we said, we have a bunch of people who are neighbors; let’s forget about such preconceptions and try to figure out how they’re all related and who moved where across time.”

Map of the intersection between Europe and the Middle East shows many yellow dots interspersed with pink and gray dots connected by black lines to create more than one dozen defined regionsThe geography of the Southern Arc as described in the new trio of papers. The colored circles and squares mark sites where ancient individuals whose DNA was analyzed in the studies were found. Yellow dots indicate genomes studied for the first time. Image: Lazaridis, Alpaslan-Roodenberg, et al., Science

In addition to illuminating shifts in different populations’ genetic makeup across the centuries, the analyses provide fresh genetic insights into old mysteries such as the identities of Minoan and Mycenaean peoples and the geographic origin of Indo-European languages.

“This is a major leap forward in the field and a milestone in terms of richness of data from this complex region,” said co-senior author Reich, professor of genetics at HMS and professor of human evolutionary biology at Harvard University. “Some very striking stories emerge thanks to the power of ancient DNA in large sample sizes.”

No easy feat

The results were made possible by collaboration across borders and specialties. The Reich lab partnered with researchers at the University of Vienna to lead a 206-person team based in more than 30 countries.

“These studies were accomplished through a huge amount of raw human effort,” said Lazaridis.

Lazaridis shares first authorship of the papers with Songül Alpaslan-Roodenberg, a physical anthropologist from Turkey who is affiliated with the Reich lab and the University of Vienna. Reich shares senior authorship with Ron Pinhasi, a physical anthropologist and geneticist at the University of Vienna.

“One amazing thing about these papers is they represent cooperation between countries where it’s historically been difficult to get along, such as Greece, Turkey, Armenia, Albania, Bulgaria, and North Macedonia,” said Reich. “Navigating that was a complex issue.”

The team also overcame climatic challenges.

Until a few years ago, it was difficult or impossible to recover DNA from ancient people buried in regions like the Middle East because heat degrades the delicate material. The discovery in 2015 that an inner-ear bone does an exceptional job of preserving DNA and the development of new sequencing and analytic techniques threw open the doors to studying large collections of ancient DNA from previously inaccessible environments.

Co-authors in different fields worked together to interpret the findings in light of what was already known through archaeological evidence, ancient texts, and other materials. Some of the discoveries add detail to existing histories. Others fill in gaps. Still others challenge conventional theories.

“Once you look at this many individuals across space and time in an expansive view, you start seeing connections you couldn’t if you focused on only one site or period,” said Lazaridis.

The findings

“These findings are another example of how archaeogenetic results can provide a missing layer of information that cannot be obtained from other sources,” said Alpaslan-Roodenberg.

Science papers:
Science
The genetic history of the Southern Arc: A bridge between West Asia and Europe

Ancient DNA from Mesopotamia suggests distinct Pre-Pottery and Pottery Neolithic migrations into Anatolia

A genetic probe into the ancient and medieval history of Southern Europe and West Asia

See the full article here .

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Please help promote STEM in your local schools.

Stem Education Coalition

The The Harvard Medical School community is dedicated to excellence and leadership in medicine, education, research and clinical care. To achieve our highest aspirations, and to ensure the success of all members of our community, we value and promote common ideals that center on collaboration and service, diversity, respect, integrity and accountability, lifelong learning, and wellness and balance. To be a citizen of this community means embracing a collegial spirit that fosters inclusion and promotes achievement.

From Harvard University

8.25.22
STEPHANIE DUTCHEN

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

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

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

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

Harvard University has more alumni, faculty, and researchers who have won Nobel Prizes (161) and Fields Medals (18) than any other university in the world and more alumni who have been members of the U.S. Congress, MacArthur Fellows, Rhodes Scholars (375), and Marshall Scholars (255) than any other university in the United States. Its alumni also include eight U.S. presidents and 188 living billionaires, the most of any university. Fourteen Turing Award laureates have been Harvard affiliates. Students and alumni have also won 10 Academy Awards, 48 Pulitzer Prizes, and 108 Olympic medals (46 gold), and they have founded many notable companies.

Colonial

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

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

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

19th century

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

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

20th century

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

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

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

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

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

21st century

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

From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH): “Making CRISPR hype more of a reality”

From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH)

7.6.22
Dr. Eric Aird

This year we celebrate 10 years of genome editing with CRISPR.

Scientific American/ Credit: Getty Images

The system is often referred to as molecular scissors, and this designation is quite accurate for its first applications. These short 10 years were marked by stunningly swift development and a great promise to cure thousands of genetic diseases with relative ease – with a single treatment dose that specifically corrects disease-​causing DNA mutations in the body’s cells. Sickle cell anemia and muscular dystrophy are two such diseases. And indeed, a decade later, we are now delivering on that promise in the form of many therapies currently being tested in human clinical trials.

Parallel to the development of the first such therapies, scientists have further evolved genome editing technologies. Recently developed molecular CRISPR tools have little in common with molecular scissors and are poised to make medical applications even safer.

Let’s take a brief look back: “first generation” CRISPR genetic scissors dock at specific sites in the genome and cut the DNA molecule. The cell generates short, arbitrary mutations at the break site to, for example, disrupt gene function. However, unintended genetic alterations to the cell are possible, and the scope of diseases treatable with this methodology are relatively small. An ill-​intended cut in the genome might manifest itself as a trigger for cancer decades later. Additionally, these scissors cause DNA damage, and such damage is inherently toxic and potentially lethal for cells. Stem cells, a primary target for clinical uses of CRISPR, react particularly sensitively to DNA damage.

A broad application of this first generation of CRISPR in humans is therefore not entirely risk-​free. This is also a major reason why scientists have developed molecular tools to generate genomic modifications without using scissors.

In the past few years, researchers across the globe have developed a host of such “next generation” CRISPR technologies. A more appropriate analogy for these innovative systems would that be of a molecular taxi. Such platforms can be used to shuttle, for example, specialized proteins to specific destinations in the genome. These proteins can directly change the DNA code without the same deleterious consequences caused by scissors.

Reduced toxicity

Not only does this approach reduce toxicity for cells, but it also vastly expands the range of treatable genetic diseases. Instead of simply cutting a gene to render it non-​functional, these CRISPR genome editors1 can be used to correct individual genetic mutations to restore gene function. It is estimated that more than 100,000 DNA mutations in our genome cause disease, a vast majority of which could be treated with such new technologies.

Next generation genome editing systems are expected to be used in human trials for the first time later this year. An American biotech company recently received approval to begin human trials to cure sickle cell disease and beta-​thalassemia.2 Treatments for high cholesterol and a form of blindness are also on the verge of moving into humans as well, not to mention the plethora of projects to treat a range of genetic disorders that are currently being tested in animals and could one day benefit humans. In all cases, these diseases can be cured by reverting the mutated genetic code back to the “normal” sequence, reversions which were not possible with the traditional CRISPR scissor-​based approach.

One-​time therapy

CRISPR-​based technologies have an enormous upside. Today, patients suffering from hemophilia need multiple infusions per week. A CRISPR treatment, on the other hand, would ideally take place once, and the cells modified with CRISPR would persist for the rest of the patient’s life.

This also means, however, that once the treatment has been started, it can no longer be discontinued. But would you choose a treatment where you can never stop taking the drug? This question arises with CRISPR-​based therapies.

Safety concerns about unintended editing have mostly, but not entirely, been alleviated with next generation CRISPR molecular taxis. It must be stressed that the first generation treatments currently being clinically tested have underwent extensive studies to determine and limit detrimental effects. Nevertheless, the safety of CRISPR-​based systems must be kept in mind. It is important that the long-​term safety profiles of CRISPR technologies are established, and therefore I expect the first CRISPR-​treated patients will be monitored for life.

A cure for previously incurable diseases

Given all the safety considerations, one must also consider the therapeutic alternatives. Take progeria for example, a genetic disease in which children rapidly age and medication only exists to marginally extend lifespan. A next generation CRISPR technology currently under development has the potential to revolutionize progeria therapy: it doubled the lifespan in mouse models. For a fatal disease like progeria, for which there is no or inadequate therapy, many patients are likely to opt for a CRISPR treatment, even if there is some residual risk of potentially negative outcomes in the long term.

The speed at which CRISPR technologies have advanced over the past decade has been tremendous. Regulatory agencies, which are required to assess the safety of these technologies, have sometimes failed to keep up with this pace. Urgently needed guidelines for the approval of the new technologies are not yet mature. This must change. There is a great need for action on the part of the regulatory authorities.

The first decade of CRISPR has brought immense potential, rapid technological development, and the first patients treated. As we look to the next 10 years, both first and next generation CRISPR systems are poised to deliver on its potential and provide life-​long cures to patients of both rare and more common genetic disorders.

See the full article here .

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Please help promote STEM in your local schools.

Stem Education Coalition

The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH) is a public research university in the city of Zürich, Switzerland. Founded by the Swiss Federal Government in 1854 with the stated mission to educate engineers and scientists, the school focuses exclusively on science, technology, engineering and mathematics. Like its sister institution The Swiss Federal Institute of Technology in Lausanne [EPFL-École Polytechnique Fédérale de Lausanne](CH) , it is part of The Swiss Federal Institutes of Technology Domain (ETH Domain)) , part of the The Swiss Federal Department of Economic Affairs, Education and Research [EAER][Eidgenössisches Departement für Wirtschaft, Bildung und Forschung] [Département fédéral de l’économie, de la formation et de la recherche] (CH).

The university is an attractive destination for international students thanks to low tuition fees of 809 CHF per semester, PhD and graduate salaries that are amongst the world’s highest, and a world-class reputation in academia and industry. There are currently 22,200 students from over 120 countries, of which 4,180 are pursuing doctoral degrees. In the 2021 edition of the QS World University Rankings ETH Zürich is ranked 6th in the world and 8th by the Times Higher Education World Rankings 2020. In the 2020 QS World University Rankings by subject it is ranked 4th in the world for engineering and technology (2nd in Europe) and 1st for earth & marine science.

As of November 2019, 21 Nobel laureates, 2 Fields Medalists, 2 Pritzker Prize winners, and 1 Turing Award winner have been affiliated with the Institute, including Albert Einstein. Other notable alumni include John von Neumann and Santiago Calatrava. It is a founding member of the IDEA League and the International Alliance of Research Universities (IARU) and a member of the CESAER network.

ETH Zürich was founded on 7 February 1854 by the Swiss Confederation and began giving its first lectures on 16 October 1855 as a polytechnic institute (eidgenössische polytechnische schule) at various sites throughout the city of Zurich. It was initially composed of six faculties: architecture, civil engineering, mechanical engineering, chemistry, forestry, and an integrated department for the fields of mathematics, natural sciences, literature, and social and political sciences.

It is locally still known as Polytechnikum, or simply as Poly, derived from the original name eidgenössische polytechnische schule, which translates to “federal polytechnic school”.

ETH Zürich is a federal institute (i.e., under direct administration by the Swiss government), whereas The University of Zürich [Universität Zürich ] (CH) is a cantonal institution. The decision for a new federal university was heavily disputed at the time; the liberals pressed for a “federal university”, while the conservative forces wanted all universities to remain under cantonal control, worried that the liberals would gain more political power than they already had. In the beginning, both universities were co-located in the buildings of the University of Zürich.

From 1905 to 1908, under the presidency of Jérôme Franel, the course program of ETH Zürich was restructured to that of a real university and ETH Zürich was granted the right to award doctorates. In 1909 the first doctorates were awarded. In 1911, it was given its current name, Eidgenössische Technische Hochschule. In 1924, another reorganization structured the university in 12 departments. However, it now has 16 departments.

ETH Zürich, EPFL (Swiss Federal Institute of Technology in Lausanne) [École polytechnique fédérale de Lausanne](CH), and four associated research institutes form The Domain of the Swiss Federal Institutes of Technology (ETH Domain) [ETH-Bereich; Domaine des Écoles polytechniques fédérales] (CH) with the aim of collaborating on scientific projects.

Reputation and ranking

ETH Zürich is ranked among the top universities in the world. Typically, popular rankings place the institution as the best university in continental Europe and ETH Zürich is consistently ranked among the top 1-5 universities in Europe, and among the top 3-10 best universities of the world.

Historically, ETH Zürich has achieved its reputation particularly in the fields of chemistry, mathematics and physics. There are 32 Nobel laureates who are associated with ETH Zürich, the most recent of whom is Richard F. Heck, awarded the Nobel Prize in chemistry in 2010. Albert Einstein is perhaps its most famous alumnus.

In 2018, the QS World University Rankings placed ETH Zürich at 7th overall in the world. In 2015, ETH Zürich was ranked 5th in the world in Engineering, Science and Technology, just behind the Massachusetts Institute of Technology, Stanford University and University of Cambridge (UK). In 2015, ETH Zürich also ranked 6th in the world in Natural Sciences, and in 2016 ranked 1st in the world for Earth & Marine Sciences for the second consecutive year.

In 2016, Times Higher Education World University Rankings ranked ETH Zürich 9th overall in the world and 8th in the world in the field of Engineering & Technology, just behind the Massachusetts Institute of Technology, Stanford University, California Institute of Technology, Princeton University, University of Cambridge(UK), Imperial College London(UK) and University of Oxford(UK) .

In a comparison of Swiss universities by swissUP Ranking and in rankings published by CHE comparing the universities of German-speaking countries, ETH Zürich traditionally is ranked first in natural sciences, computer science and engineering sciences.

In the survey CHE Excellence Ranking on the quality of Western European graduate school programs in the fields of biology, chemistry, physics and mathematics, ETH Zürich was assessed as one of the three institutions to have excellent programs in all the considered fields, the other two being Imperial College London (UK) and the University of Cambridge (UK), respectively.

From “The New York Times” : “CRISPR 10 Years On:: Learning to Rewrite the Code of Life”

From “The New York Times”

June 30, 2022
Carl Zimmer

The gene-editing technology has led to innovations in medicine, evolution and agriculture — and raised profound ethical questions about altering human DNA.

Ten years ago this week, Jennifer Doudna and her colleagues published the results of a test-tube experiment on bacterial genes. When the study came out in the journal Science on June 28, 2012, it did not make headline news. In fact, over the next few weeks, it did not make any news at all.

Looking back, Dr. Doudna wondered if the oversight had something to do with the wonky title she and her colleagues had chosen for the study: “A Programmable Dual RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity.”

“I suppose if I were writing the paper today, I would have chosen a different title,” Dr. Doudna, a biochemist at the University of California-Berkeley, said in an interview.

Far from an esoteric finding, the discovery pointed to a new method for editing DNA, one that might even make it possible to change human genes.

“I remember thinking very clearly, when we publish this paper, it’s like firing the starting gun at a race,” she said.

In just a decade, CRISPR has become one of the most celebrated inventions in modern biology. It is swiftly changing how medical researchers study diseases: Cancer biologists are using the method to discover hidden vulnerabilities of tumor cells. Doctors are using CRISPR to edit genes that cause hereditary diseases.

Editing the genome with CRISPR

Editing the genome with CRISPR Credit Nature

“The era of human gene editing isn’t coming,” said David Liu, a biologist at Harvard University. “It’s here.”

But CRISPR’s influence extends far beyond medicine. Evolutionary biologists are using the technology to study Neanderthal brains and to investigate how our ape ancestors lost their tails. Plant biologists have edited seeds to produce crops with new vitamins or with the ability to withstand diseases. Some of them may reach supermarket shelves in the next few years.

CRISPR has had such a quick impact that Dr. Doudna and her collaborator, Emmanuelle Charpentier of the Max Planck Unit for the Science of Pathogens in Berlin, won the 2020 Nobel Prize for chemistry. The award committee hailed their 2012 study as “an epoch-making experiment.”

Jennifer Doudna shared the 2020 Nobel Prize for chemistry for her work on CRISPR. Credit: Anastasiia Sapon for The New York Times.

Emmanuelle Charpentier via Relaxnews
Emmanuelle Charpentier, a French microbiologist with the Max Planck Unit for the Science of Pathogens in Berlin, who shared the Nobel Prize for Chemistry in 2020 with Dr. Doudna. Credit: Karsten Moran for The New York Times.

Dr. Doudna recognized early on that CRISPR would pose a number of thorny ethical questions, and after a decade of its development, those questions are more urgent than ever.

Will the coming wave of CRISPR-altered crops feed the world and help poor farmers or only enrich agribusiness giants that invest in the technology? Will CRISPR-based medicine improve health for vulnerable people across the world, or come with a million-dollar price tag?

The most profound ethical question about CRISPR is how future generations might use the technology to alter human embryos. This notion was simply a thought experiment until 2018, when He Jiankui, a biophysicist in China, edited a gene in human embryos to confer resistance to H.I.V. Three of the modified embryos were implanted in women in the Chinese city of Shenzhen.

In 2019, a court sentenced Dr. He to prison for “illegal medical practices.” MIT Technology Review reported in April that he had recently been released. Little is known about the health of the three children, who are now toddlers.

Scientists don’t know of anyone else who has followed Dr. He’s example — yet. But as CRISPR continues to improve, editing human embryos may eventually become a safe and effective treatment for a variety of diseases.

Will it then become acceptable, or even routine, to repair disease-causing genes in an embryo in the lab? What if parents wanted to insert traits that they found more desirable — like those related to height, eye color or intelligence?

Françoise Baylis, a bioethicist at Dalhousie University in Nova Scotia, worries that the public is still not ready to grapple with such questions.

“I’m skeptical about the depth of understanding about what’s at issue there,” she said. “There’s a difference between making people better and making better people.”

Making the cut

Dr. Doudna and Dr. Charpentier did not invent their gene-editing method from scratch. They borrowed their molecular tools from bacteria.

In the 1980s, microbiologists discovered puzzling stretches of DNA in bacteria, later called Clustered Regularly Interspaced Short Palindromic Repeats. Further research revealed that bacteria used these CRISPR sequences as weapons against invading viruses.

The bacteria turned these sequences into genetic material, called RNA, that could stick precisely to a short stretch of an invading virus’s genes. These RNA molecules carry proteins with them that act like molecular scissors, slicing the viral genes and halting the infection.

As Dr. Doudna and Dr. Charpentier investigated CRISPR, they realized that the system might allow them to cut a sequence of DNA of their own choosing. All they needed to do was make a matching piece of RNA.

To test this revolutionary idea, they created a batch of identical pieces of DNA. They then crafted another batch of RNA molecules, programming all of them to home in on the same spot on the DNA. Finally, they mixed the DNA, the RNA and molecular scissors together in test tubes. They discovered that many of the DNA molecules had been cut at precisely the right spot.

For months Dr. Doudna oversaw a series of round-the-clock experiments to see if CRISPR might work not only in a test tube, but also in living cells. She pushed her team hard, suspecting that many other scientists were also on the chase. That hunch soon proved correct.

In January 2013, five teams of scientists published studies in which they successfully used CRISPR in living animal or human cells. Dr. Doudna did not win that race; the first two published papers came from two labs in Cambridge, Mass. — one at the Broad Institute of M.I.T. and Harvard, and the other at Harvard.

“Did you CRISPR that?”

Lukas Dow, a cancer biologist at Weill Cornell Medicine, vividly remembers learning about CRISPR’s potential. “Reading the papers, it looked amazing,” he recalled.

Dr. Dow and his colleagues soon found that the method reliably snipped out pieces of DNA in human cancer cells.

“It became a verb to drop,” Dr. Dow said. “A lot of people would say, ‘Did you CRISPR that?’”

Cancer biologists began systematically altering every gene in cancer cells to see which ones mattered to the disease. Researchers at KSQ Therapeutics, also in Cambridge, used CRISPR to discover a gene that is essential for the growth of certain tumors, for example, and last year, they began a clinical trial of a drug that blocks the gene.

Caribou Biosciences, co-founded by Dr. Doudna, and CRISPR Therapeutics, co-founded by Dr. Charpentier, are both running clinical trials for CRISPR treatments that fight cancer in another way: by editing immune cells to more aggressively attack tumors.

Those companies and several others are also using CRISPR to try to reverse hereditary diseases. On June 12, researchers from CRISPR Therapeutics and Vertex, a Boston-based biotech firm, presented at a scientific meeting new results from their clinical trial involving 75 volunteers who had sickle-cell anemia or beta thalassemia. These diseases impair hemoglobin, a protein in red blood cells that carries oxygen.

The researchers took advantage of the fact that humans have more than one hemoglobin gene. One copy, called fetal hemoglobin, is typically active only in fetuses, shutting down within a few months after birth.

The researchers extracted immature blood cells from the bone marrow of the volunteers. They then used CRISPR to snip out the switch that would typically turn off the fetal hemoglobin gene. When the edited cells were returned to patients, they could develop into red blood cells rife with hemoglobin.

Speaking at a hematology conference, the researchers reported that out of 44 treated patients with beta thalassemia, 42 no longer needed regular blood transfusions. None of the 31 sickle cell patients experienced painful drops in oxygen that would have normally sent them to the hospital.

CRISPR Therapeutics and Vertex expect to ask government regulators by the end of year to approve the treatment.

Other companies are injecting CRISPR molecules directly into the body. Intellia Therapeutics, based in Cambridge and also co-founded by Dr. Doudna, has teamed up with Regeneron, based in Westchester County, N.Y., to begin a clinical trial to treat transthyretin amyloidosis, a rare disease in which a damaged liver protein becomes lethal as it builds up in the blood.

Equipment in the lab of Feng Zhang, a leading CRISPR researcher with the Broad Institute in Cambridge, Mass. Credit: Tony Luong for The New York Times.

Doctors injected CRISPR molecules into the volunteers’ livers to shut down the defective gene. Speaking at a scientific conference last Friday, Intellia researchers reported that a single dose of the treatment produced a significant drop in the protein level in volunteers’ blood for as long as a year thus far.

The same technology that allows medical researchers to tinker with human cells is letting agricultural scientists alter crop genes. When the first wave of CRISPR studies came out, Catherine Feuillet, an expert on wheat, who was then at the French National Institute for Agricultural Research, immediately saw its potential for her own work.

“I said, ‘Oh my God, we have a tool,’” she said. “We can put breeding on steroids.”

At Inari Agriculture, a company in Cambridge, Dr. Feuillet is overseeing efforts to use CRISPR to make breeds of soybeans and other crops that use less water and fertilizer. Outside of the United States, British researchers have used CRISPR to breed a tomato that can produce vitamin D.

Kevin Pixley, a plant scientist at the International Maize and Wheat Improvement Center in Mexico City, said that CRISPR is important to plant breeding not only because it’s powerful, but because it’s relatively cheap. Even small labs can create disease-resistant cassavas or drought-resistant bananas, which could benefit poor nations but would not interest companies looking for hefty financial returns.

Because of CRISPR’s use for so many different industries, its patent has been the subject of a long-running dispute. Groups led by the Broad Institute and the University of California both filed patents for the original version of gene editing based on CRISPR-Cas9 in living cells. The Broad Institute won a patent in 2014, and the University of California responded with a court challenge.

In February of this year, the U.S. Patent Trial and Appeal Board issued what is most likely the final word on this dispute. They ruled in favor of the Broad Institute.

Jacob Sherkow, an expert on biotech patents at the University of Illinois College of Law, predicted that companies that have licensed the CRISPR technology from the University of California will need to honor the Broad Institute patent.

“The big-ticket CRISPR companies, the ones that are farthest along in clinical trials, are almost certainly going to need to write the Broad Institute a really big check,” he said.

Dr. Zhang of the Broad Institute, which recently won a major patent dispute over Crispr technology.Credit: Tony Luong for The New York Times.

Prime CRISPR

The original CRISPR system, known as CRISPR-Cas9, leaves plenty of room for improvement. The molecules are good at snipping out DNA, but they’re not as good at inserting new pieces in their place. Sometimes CRISPR-Cas9 misses its target, cutting DNA in the wrong place. And even when the molecules do their jobs correctly, cells can make mistakes as they repair the loose ends of DNA left behind.

A number of scientists have invented new versions of CRISPR that overcome some of these shortcomings. At Harvard, for example, Dr. Liu and his colleagues have used CRISPR to make a nick in one of DNA’s two strands, rather than breaking them entirely. This process, known as base editing, lets them precisely change a single genetic letter of DNA with much less risk of genetic damage.

Dr. Liu has co-founded a company called Beam Therapeutics to create base-editing drugs. Later this year, the company will test its first drug on people with sickle cell anemia.

Dr. Liu and his colleagues have also attached CRISPR molecules to a protein that viruses use to insert their genes into their host’s DNA. This new method, called prime editing, could enable CRISPR to alter longer stretches of genetic material.

“Prime editors are kind of like DNA word processors,” Dr. Liu said. “They actually perform a search and replace function on DNA.”

Rodolphe Barrangou, a CRISPR expert at North Carolina State University and a founder of Intellia Therapeutics, predicted that prime editing would eventually become a part of the standard CRISPR toolbox. But for now, he said, the technique was still too complex to become widely used. “It’s not quite ready for prime time, pun intended,” he said.

Gene-edited babies

Dr. He claimed to have created the first genetically edited twin babies at the University of Hong Kong in 2018. Credit: Alex Hofford/EPA, via Shutterstock.

Advances like prime editing didn’t yet exist in 2018, when Dr. He set out to edit human embryos in Shenzen. He used the standard CRISPR-Cas9 system that Dr. Doudna and others had developed years before.

Dr. He hoped to endow babies with resistance to H.I.V. by snipping a piece of a gene called CCR5 from the DNA of embryos. People who naturally carry the same mutation rarely get infected by H.I.V.

In November 2018, Dr. He announced that a pair of twin girls had been born with his gene edits. The announcement took many scientists like Dr. Doudna by surprise, and they roundly condemned him for putting the health of the babies in jeopardy with untested procedures.

Dr. Baylis of Dalhousie University criticized Dr. He for the way he reportedly presented the procedure to the parents, downplaying the radical experiment they were about to undertake. “You could not get an informed consent, unless you were saying, ‘This is pie in the sky. Nobody’s ever done it,’” she said.

In the nearly four years since Dr. He’s announcement, scientists have continued to use CRISPR on human embryos. But they have studied embryos only when they’re tiny clumps of cells to find clues about the earliest stages of development. These studies could potentially lead to new treatments for infertility.

Bieke Bekaert, a graduate student in reproductive biology at Ghent University in Belgium, said that CRISPR remains challenging to use in human embryos. Breaking DNA in these cells can lead to drastic rearrangements in the chromosomes. “It’s more difficult than we thought,” said Ms. Bekaert, the lead author of a recent review of the subject. “We don’t really know what is happening.”

Still, Ms. Bekaert held out hope that prime editing and other improvements on CRISPR could allow scientists to make reliably precise changes to human embryos. “Five years is way too early, but I think in my lifetime it may happen,” she said.

See the full article here .

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From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH): “The beauty and benefits of biodiversity”

From The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH)

01.07.2022
Peter Rüegg

Biodiversity is beautiful, but it’s also vitally important. ETH researchers are getting to the heart of how species diversity and genetic diversity evolve – and why we must fight to preserve them.

Spring is synonymous with bright yellow dandelions, lush green fields and cloudless blue skies, a captivating combination of colours that sends many people into raptures of delight. Yet biodiversity researchers such as Alex Widmer, Professor of Plant Ecological Genetics in the Department of Environmental Systems Science, take a rather different view: “I know too much about ecosystems to take any pleasure in something so monotonous,” he says. His notion of beauty tends more towards dry grasslands and natural meadows rich in different species. “A far cry,” he says, “from the picture-​postcard idyll.” He argues that such areas are beautiful in much less obvious ways. Unfertilized, minimally cultivated meadows and dry grasslands are incredibly diverse, he says, which makes them not just beautiful, but essential.

“Species diversity makes ecosystems resilient,” says Widmer, “and at the core of that resilience is genetic diversity.” Without genetic diversity, he explains, species and organisms cannot adapt to existing and evolving environmental conditions. And it’s this adaptability that lies at the very heart of speciation.

Natural meadows exhibit high levels of diversity. (Photograph: Peter Rüegg)

Loïc Pellissier, Professor of Ecosystems and Landscape Evolution in the Department of Environmental Systems Science, agrees that much of the beauty of biodiversity is hidden from view. One of the most beautiful aspects of biodiversity, he says, is how species co-​evolve and exist together. “All organisms have evolved to interact with each other, as anyone who works in species diversity will tell you. To me, ecosystems are like huge jigsaw puzzles, in which all the pieces fit together more or less perfectly.” His research focuses on how species diversity arises and evolves. Because this occurs over the course of millions of years, Pellissier relies on computer models to simulate geological processes and the evolutionary forces that lead to the formation of new species.

Genetic diversity

Pellissier also conducts numerous field projects to unlock the secrets of species diversity. He favours a new and increasingly popular method that enables ecologists to detect species and organisms from the DNA they leave behind in the environment – known for short as environmental DNA, or eDNA. Researchers simply collect water and soil samples and analyse them to see what genetic material they contain. They then match whatever DNA they find to the corresponding organisms, provided a reference is available for this. This method provides a relatively quick way to determine whether a species is present in an ecosystem or not – and it works for a wide variety of organisms. “eDNA gives us a new insight into an ecosystem’s diversity,” he says.

Recently, Pellissier co-​authored a study on the diversity of reef fish worldwide. Researchers collected over 200 seawater samples from various tropical coral reefs and then “fished out” whatever fish DNA they could find. Using the eDNA method it took the researchers less than two years to confirm the presence of more fish species and families than experts had managed to identify during 13 years of reef dives.

Yet species diversity is only one aspect of biodiversity, the others being habitat diversity and genetic diversity. “Of the three, genetic diversity is the one that has been most neglected,” says Widmer. “Studying and monitoring genetic diversity is much more difficult and time-​consuming than monitoring habitats or species numbers.” Hence the numerous inventories of Swiss plants, animals and habitats – from forests and wetlands to dry grasslands. “Yet there isn’t a single monitoring project in Switzerland that focuses on the genetic diversity of living things,” says Widmer, “This is despite the fact that genetic diversity is fundamental for species diversity and adaptability.”

To fill this gap, Widmer has joined forces with the Swiss Federal Institute for Forest, Snow and Landscape Research WSL on a project that aims to add this crucial element to Switzerland’s existing biodiversity monitoring systems. With the support of the Swiss Federal Office for the Environment (FOEN), Widmer and his colleagues have already launched a pilot study of five different species, including two plant species, a butterfly and a toad. The fifth species in their study is the yellowhammer, a songbird commonly found in cultivated areas of Switzerland. The researchers have already sequenced the genomes of one hundred individual yellowhammers from right across the country.

The beauty of the world’s coral reefs never fails to amaze. Yet behind such splendour, there lies much more – namely, a diverse habitat for a host of marine life. (Photograph: Stocksy)

As well as working with living organisms, the researchers also study the genetic material of specimens held in collections. “This tells us whether populations from over 100 years ago were as diverse as today’s, or whether some of that genetic diversity has been lost,” says Widmer. Research into biodiversity in Switzerland has already revealed a sharp decline in species diversity, he notes: “We’d like to find out whether the same applies to genetic diversity.” Once the pilot study is complete, Widmer’s goal is to set up a large-​scale monitoring project encompassing up to 50 species. These would be examined at regular intervals to detect changes in their genetic diversity. However, it is still unclear whether this complex and ambitious project will receive the necessary funding.

Fragile and endangered beauty

Time is of the essence because biodiversity is under threat and declining rapidly. It is only by firmly fitting together the many different pieces of the biodiversity puzzle that we can slow the extinction of individual species. Reduce this network by half, and species will die out a thousand times faster – and when external pressures such as climate change are factored in, species extinction will occur a thousand times faster again.

“Biodiversity is essential to our lives,” says Widmer. “It impacts everything from our mental well-​being to whether we have food on the table.” Diverse ecosystems are much more stable and better geared for the future than monotonous, species-​poor habitats. Pellissier nods in agreement: “Biodiversity is like classical art in the sense that it can’t be replaced. If the earth loses its biological riches, it will lose its magic.”

See the full article here .

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Please help promote STEM in your local schools.

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The Swiss Federal Institute of Technology in Zürich [ETH Zürich] [Eidgenössische Technische Hochschule Zürich] (CH) is a public research university in the city of Zürich, Switzerland. Founded by the Swiss Federal Government in 1854 with the stated mission to educate engineers and scientists, the school focuses exclusively on science, technology, engineering and mathematics. Like its sister institution The Swiss Federal Institute of Technology in Lausanne [EPFL-École Polytechnique Fédérale de Lausanne](CH) , it is part of The Swiss Federal Institutes of Technology Domain (ETH Domain)) , part of the The Swiss Federal Department of Economic Affairs, Education and Research [EAER][Eidgenössisches Departement für Wirtschaft, Bildung und Forschung] [Département fédéral de l’économie, de la formation et de la recherche] (CH).

The university is an attractive destination for international students thanks to low tuition fees of 809 CHF per semester, PhD and graduate salaries that are amongst the world’s highest, and a world-class reputation in academia and industry. There are currently 22,200 students from over 120 countries, of which 4,180 are pursuing doctoral degrees. In the 2021 edition of the QS World University Rankings ETH Zürich is ranked 6th in the world and 8th by the Times Higher Education World Rankings 2020. In the 2020 QS World University Rankings by subject it is ranked 4th in the world for engineering and technology (2nd in Europe) and 1st for earth & marine science.

As of November 2019, 21 Nobel laureates, 2 Fields Medalists, 2 Pritzker Prize winners, and 1 Turing Award winner have been affiliated with the Institute, including Albert Einstein. Other notable alumni include John von Neumann and Santiago Calatrava. It is a founding member of the IDEA League and the International Alliance of Research Universities (IARU) and a member of the CESAER network.

ETH Zürich was founded on 7 February 1854 by the Swiss Confederation and began giving its first lectures on 16 October 1855 as a polytechnic institute (eidgenössische polytechnische schule) at various sites throughout the city of Zurich. It was initially composed of six faculties: architecture, civil engineering, mechanical engineering, chemistry, forestry, and an integrated department for the fields of mathematics, natural sciences, literature, and social and political sciences.

It is locally still known as Polytechnikum, or simply as Poly, derived from the original name eidgenössische polytechnische schule, which translates to “federal polytechnic school”.

ETH Zürich is a federal institute (i.e., under direct administration by the Swiss government), whereas The University of Zürich [Universität Zürich ] (CH) is a cantonal institution. The decision for a new federal university was heavily disputed at the time; the liberals pressed for a “federal university”, while the conservative forces wanted all universities to remain under cantonal control, worried that the liberals would gain more political power than they already had. In the beginning, both universities were co-located in the buildings of the University of Zürich.

From 1905 to 1908, under the presidency of Jérôme Franel, the course program of ETH Zürich was restructured to that of a real university and ETH Zürich was granted the right to award doctorates. In 1909 the first doctorates were awarded. In 1911, it was given its current name, Eidgenössische Technische Hochschule. In 1924, another reorganization structured the university in 12 departments. However, it now has 16 departments.

ETH Zürich, EPFL (Swiss Federal Institute of Technology in Lausanne) [École polytechnique fédérale de Lausanne](CH), and four associated research institutes form The Domain of the Swiss Federal Institutes of Technology (ETH Domain) [ETH-Bereich; Domaine des Écoles polytechniques fédérales] (CH) with the aim of collaborating on scientific projects.

Reputation and ranking

ETH Zürich is ranked among the top universities in the world. Typically, popular rankings place the institution as the best university in continental Europe and ETH Zürich is consistently ranked among the top 1-5 universities in Europe, and among the top 3-10 best universities of the world.

Historically, ETH Zürich has achieved its reputation particularly in the fields of chemistry, mathematics and physics. There are 32 Nobel laureates who are associated with ETH Zürich, the most recent of whom is Richard F. Heck, awarded the Nobel Prize in chemistry in 2010. Albert Einstein is perhaps its most famous alumnus.

In 2018, the QS World University Rankings placed ETH Zürich at 7th overall in the world. In 2015, ETH Zürich was ranked 5th in the world in Engineering, Science and Technology, just behind the Massachusetts Institute of Technology, Stanford University and University of Cambridge (UK). In 2015, ETH Zürich also ranked 6th in the world in Natural Sciences, and in 2016 ranked 1st in the world for Earth & Marine Sciences for the second consecutive year.

In 2016, Times Higher Education World University Rankings ranked ETH Zürich 9th overall in the world and 8th in the world in the field of Engineering & Technology, just behind the Massachusetts Institute of Technology, Stanford University, California Institute of Technology, Princeton University, University of Cambridge(UK), Imperial College London(UK) and University of Oxford(UK) .

In a comparison of Swiss universities by swissUP Ranking and in rankings published by CHE comparing the universities of German-speaking countries, ETH Zürich traditionally is ranked first in natural sciences, computer science and engineering sciences.

In the survey CHE Excellence Ranking on the quality of Western European graduate school programs in the fields of biology, chemistry, physics and mathematics, ETH Zürich was assessed as one of the three institutions to have excellent programs in all the considered fields, the other two being Imperial College London (UK) and the University of Cambridge (UK), respectively.

From The University of Bath (UK) via “The Conversation (AU)” and “Science Alert (AU)” : “New DNA Technology Is Shaking Up The Branches of The Evolutionary Tree”

From The University of Bath (UK)

via

“The Conversation (AU)”

and

“Science Alert (AU)”

25 JUNE 2022
MATTHEW WILLS

A portion of Ernst Haeckel’s ‘tree of life’ sketch. (Ernst Haeckel)

If you look different to your close relatives, you may have felt separate from your family. As a child, during particularly stormy fall outs you might have even hoped it was a sign that you were adopted.
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As our new research shows, appearances can be deceptive when it comes to family. New DNA technology is shaking up the family trees of many plants and animals.

The primates, to which humans belong, were once thought to be close relatives of bats because of some similarities in our skeletons and brains. However, DNA data now places us in a group that includes rodents (rats and mice) and rabbits. Astonishingly, bats turn out to be more closely related to cows, horses, and even rhinoceroses than they are to us.

Scientists in Darwin’s time and through most of the 20th century could only work out the branches of the evolutionary tree of life by looking at the structure and appearance of animals and plants. Life forms were grouped according to similarities thought to have evolved together.

About three decades ago, scientists started using DNA data to build “molecular trees”. Many of the first trees based on DNA data were at odds with the classical ones.

Sloths and anteaters, armadillos, pangolins (scaly anteaters), and aardvarks were once thought to belong together in a group called edentates (“no teeth”), since they share aspects of their anatomy.

Molecular trees showed that these traits evolved independently in different branches of the mammal tree. It turns out that aardvarks are more closely related to elephants while pangolins are more closely related to cats and dogs.

Coming together

There is another important line of evidence that was familiar to Darwin and his contemporaries. Darwin noted that animals and plants that appeared to share the closest common ancestry were often found close together geographically. The location of species is another strong indicator they are related: species that live near each other are more likely to share a family tree.

For the first time, our recent paper [Communications Biology] cross-referenced location, DNA data, and appearance for a range of animals and plants. We looked at evolutionary trees based on appearance or on molecules for 48 groups of animals and plants, including bats, dogs, monkeys, lizards, and pine trees.

Evolutionary trees based on DNA data were two-thirds more likely to match with the location of the species compared with traditional evolution maps. In other words, previous trees showed several species were related based on appearance.

Our research showed they were far less likely to live near each other compared to species linked by DNA data.

It may appear that evolution endlessly invents new solutions, almost without limits. But it has fewer tricks up its sleeve than you might think.

Animals can look amazingly alike because they have evolved to do a similar job [National Library of Medicine] or live in a similar way. Birds, bats and the extinct pterosaurs have, or had, bony wings for flying, but their ancestors all had front legs for walking on the ground instead.

The color wheels and key indicate where members of each order are found geographically. The molecular tree has these colors grouped together better than the morphological tree, indicating closer agreement of the molecules to biogeography.(Oyston et al., Communication Biology, 2022)

Similar wing shapes and muscles evolved in different groups because the physics of generating thrust and lift in air are always the same. It is much the same with eyes, which may have evolved 40 times in animals, and with only a few basic “designs”.

Our eyes are similar to squid’s eyes, with a crystalline lens, iris, retina, and visual pigments. Squid are more closely related to snails, slugs, and clams than us. But many of their mollusk relatives have only the simplest of eyes.

Moles evolved as blind, burrowing creatures at least four times, on different continents, on different branches of the mammal tree. The Australian marsupial pouched moles (more closely related to kangaroos), African golden moles (more closely related to aardvarks), African mole rats (rodents), and the Eurasian and North American talpid moles (beloved of gardeners, and more closely related to hedgehogs than these other “moles”) all evolved down a similar path.

Evolution’s roots

Until the advent of cheap and efficient gene sequencing technology in the 21st century, appearance was usually all evolutionary biologists had to go on.

While Darwin (1859) showed that all life on Earth is related in a single evolutionary tree, he did little to map out its branches. The anatomist Ernst Haeckel (1834-1919) was one of the first people to draw evolutionary trees that tried to show how major groups of life forms are related.

(Ernest Haeckel)

Haeckel’s drawings made brilliant observations of living things that influenced art and design in the 19th and 20th centuries. His family trees were based almost entirely on how those organisms looked and developed as embryos. Many of his ideas about evolutionary relationships were held until recently.

As it becomes easier and cheaper to obtain and analyze large volumes of molecular data, there will be many more surprises in store.

See the full article here.

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The University of Bath (UK) is a public research university located in Bath, Somerset, United Kingdom. It received its royal charter in 1966, along with a number of other institutions following the Robbins Report. Like the University of Bristol (UK) and University of the West of England-Bristol (UK), Bath can trace its roots to the Merchant Venturers’ Technical College, established in Bristol as a school in 1595 by the Society of Merchant Venturers. The university’s main campus is located on Claverton Down, a site overlooking the city of Bath, and was purpose-built, constructed from 1964 in the modernist style of the time.

In the 2014 Research Excellence Framework, 32% of Bath’s submitted research activity achieved the highest possible classification of 4*, defined as world-leading in terms of originality, significance and rigour. 87% was graded 4*/3*, defined as world-leading/internationally excellent. The annual income of the institution for 2017–18 was £287.9 million of which £37.0 million was from research grants and contracts, with an expenditure of £283.1 million.

The university is a member of the Association of Commonwealth Universities (UK), the Association of MBAs, the European Quality Improvement System, the European University Association (EU), Universities UK and GW4 (UK).

From The Massachusetts Institute of Technology: “Convenience-sized RNA editing”

From The Massachusetts Institute of Technology

May 31, 2022
Sarah CP Williams | McGovern Institute for Brain Research

MIT neuroscientists expand CRISPR toolkit with new compact Cas7-11 enzyme.

Artistic rendering of the CRISPR Cas 7-11S enzyme. Image: Steve Dixon.

Last year, researchers at MIT’s McGovern Institute for Brain Research discovered and characterized Cas7-11, the first CRISPR enzyme capable of making precise, guided cuts to strands of RNA without harming cells in the process. Now, working with collaborators at the University of Tokyo, the same team has revealed that Cas7-11 can be shrunk to a more compact version, making it an even more viable option for editing the RNA inside living cells. The new, compact Cas7-11 was described May 27 in the journal Cell along with a detailed structural analysis of the original enzyme.

“When we looked at the structure, it was clear there were some pieces that weren’t needed, which we could actually remove,” says Research Scientist and McGovern Fellow Omar Abudayyeh, who led the new work with Research Scientist and McGovern Fellow Jonathan Gootenberg and collaborator Hiroshi Nishimasu from the University of Tokyo. “This makes the enzyme small enough that it fits into a single viral vector for therapeutic applications.”

The authors, who also include former McGovern Institute postdoc Nathan Zhou and Kazuki Kato from the University Tokyo, see the new three-dimensional structure of Cas7-11 as a rich resource to answer questions about the basic biology of the enzymes and reveal other ways to tweak its function in the future.

Targeting RNA

Over the past decade, the CRISPR-Cas9 genome editing technology has given researchers the ability to modify the genes inside human cells — a boon for both basic research and the development of therapeutics to reverse disease-causing genetic mutations. But CRISPR-Cas9 only works to alter DNA, and for some research and clinical purposes, editing RNA is more effective or useful.

A cell retains its DNA for life, and passes an identical copy to daughter cells as it duplicates, so any changes to DNA are relatively permanent. However, RNA is a more transient molecule, transcribed from DNA and degraded not long after.

“There are lots of positives about being able to permanently change DNA especially when it comes to treating an inherited genetic disease,” Gootenberg says. “But for an infection, an injury, or some other temporary disease, being able to temporarily modify a gene through RNA targeting makes more sense.”

Until Abudayyeh, Gootenberg, and their colleagues discovered and characterized Cas7-11, the only enzyme that could target RNA had a messy side effect; when it recognized a particular gene, the enzyme — Cas13 — began cutting up all the RNA around it. This property makes Cas13 effective for diagnostic tests, where it is used to detect the presence of a piece of RNA, but not very useful for therapeutics, where targeted cuts are required.

The discovery of Cas7-11 opened the doors to a more precise form of RNA editing analogous to the Cas9 enzyme for DNA. However, the massive Cas7-11 protein was too big to fit inside a single viral vector — the empty shell of a virus that researchers typically use to deliver gene editing machinery into patient’s cells.

Structural insight

To determine the overall structure of Cas7-11, Abudayyeh, Gootenberg, and Nishimasu used cryo-electron microscopy, which shines beams of electrons on frozen protein samples and measures how the beams are transmitted. The researchers knew that Cas7-11 was like an amalgamation of five separate Cas enzymes, fused into one single gene, but were not sure exactly how those parts folded and fit together.

“The really fascinating thing about Cas7-11, from a fundamental biology perspective, is that it should be all these separate pieces that come together, but instead you have a fusion into one gene,” Gootenberg says. “We really didn’t know what that would look like.”

The structure of Cas7-11, caught in the act of binding both its target tRNA strand and the guide RNA, which directs that binding, revealed how the pieces assembled and which parts of the protein were critical to recognizing and cutting RNA. This kind of structural insight is critical to figuring out how to make Cas7-11 carry out targeted jobs inside human cells.

The structure also illuminated a section of the protein that wasn’t serving any apparent functional role. This finding suggested the researchers could remove it, re-engineering Cas7-11 to make it smaller without taking away its ability to target RNA. Abudayyeh and Gootenberg tested the impact of removing different bits of this section, resulting in a new compact version of the protein, dubbed Cas7-11S. With Cas7-11S in hand, they packaged the system inside a single viral vector, delivered it into mammalian cells, and efficiently targeted RNA.

The team is now planning future studies on other proteins that interact with Cas7-11 in the bacteria from which it originates, and also hopes to continue working towards the use of Cas7-11 for therapeutic applications.

“Imagine you could have an RNA gene therapy, and when you take it, it modifies your RNA, but when you stop taking it, that modification stops,” Abudayyeh says. “This is really just the beginning of enabling that tool set.”

This research was funded, in part, by the McGovern Institute Neurotechnology Program, K. Lisa Yang and Hock E. Tan Center for Molecular Therapeutics in Neuroscience, G. Harold and Leila Y. Mathers Charitable Foundation, MIT John W. Jarve (1978) Seed Fund for Science Innovation, FastGrants, Basis for Supporting Innovative Drug Discovery and Life Science Research Program, JSPS KAKENHI, Takeda Medical Research Foundation, and Inamori Research Institute for Science.

See the full article here .

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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.

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

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 (AAU).

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 Cold Spring Harbor Laboratory: “Decoding how a protein on the move keeps cells healthy”

From Cold Spring Harbor Laboratory

31 May 2022

Nick Wurm,
Communications Specialist
wurm@cshl.edu
516-367-8455

The protein Argonaute, which helps cells control protein production in a process called RNA interference. Image: In conjunction with Scripps Research.

Cells produce proteins like little factories. But if they make too much at the wrong times it can lead to diseases like cancer, so they control production with a process called RNA interference (RNAi). As of July 2021, several drugs already take advantage of RNAi to treat painful kidney and liver diseases—with another seven in clinical trials. There is a lot of potential for RNAi therapeutics, and Cold Spring Harbor Laboratory (CSHL) researchers are working hard to paint a complete picture of the process, to improve therapies today and make better ones tomorrow.

CSHL Professor & HHMI Investigator Leemor Joshua-Tor and recent CSHL School of Biological Sciences graduate Brianna Bibel are filling in some of the blanks. They recently discovered how RNAi’s workhorse protein Argonaute (Ago) leverages limited resources to keep protein production on track.

It’s important to understand exactly how RNAi works because it’s such a basic and heavily used process, Joshua-Tor said. It also offers a kind of safety net for therapeutics because it doesn’t make permanent changes to cells and can be reversed. Joshua-Tor says:

“For therapeutics, you would maybe not want to mess around with the genome so much. In all these kinds of things, you want to know exactly what’s happening, and if something isn’t working, then you know what to do and where to look. The more information you have, the better it is—you get a complete picture of what’s happening.”

Ago helps cut off protein production by finding, binding, and destroying molecules called mRNA—which tell cells to make proteins. But the amount of Ago in the body pales in comparison to the amount of mRNA it must target. After destroying one, the protein is still capable of finding another but it can’t move on without help. Bibel discovered how cells use a process called phosphorylation to break Ago’s grip on a mRNA target, allowing it to commute to the next. Bibel explains:

“Our theory is that having phosphorylation promote release is a way that you could free up Argonaute because when the target gets released, the guide’s still there and it’s super duper stable. So our thinking is that by phosphorylating it, you’re going to free it to go repress other targets—because it’s still totally capable of doing that work.”

Bibel hopes her discovery will come in handy as research into RNAi continues. “A lot of great advances in science come from just doing basic research,” she said. “And this is one of those basic research questions, trying to figure out how this is working.”

Science paper:
eLife

See the full article here.

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Advancing the frontiers of biology through research & education

Founded in 1890, Cold Spring Harbor Laboratory has shaped contemporary biomedical research and education with programs in cancer, neuroscience, plant biology and quantitative biology. Home to eight Nobel Prize winners, the private, not-for-profit Laboratory employs 1,100 people including 600 scientists, students and technicians. The Meetings & Courses Program hosts more than 12,000 scientists from around the world each year on its campuses in Long Island and in Suzhou, China. The Laboratory’s education arm also includes an academic publishing house, a graduate school and programs for middle and high school students and teachers.

From The MPG Institute for Plant Breeding Research[MPG Institut für Pflanzenzüchtungsforschung](DE): “A two-step adaptive walk in the wild”

From The MPG Institute for Plant Breeding Research[MPG Institut für Pflanzenzüchtungsforschung](DE)

May 18, 2022

Angela Hancock
Max Planck Research Group Leader
hancock@mpipz.mpg.de

Dr Mia von Scheven
Head of Public Relations and Outreach
+49 221 5062-670
pr@mpipz.mpg.de

New research in plants that colonized the base of an active stratovolcano reveals that two simple molecular steps rewired nutrient transport, enabling adaptation.

An international team led by Angela Hancock at The MPG Institute for Plant Breeding Research[MPG Institut für Pflanzenzüchtungsforschung](DE) and including scientists from The Victory Project[Associação Projecto Vitó](CV) and Fogo Natural Park (Cape Verde), The University of Nottingham (UK), and The Ruhr-University Bochum [Ruhr-Universität Bochum,](DE) studied a wild thale cress (Arabidopsis thaliana) population that colonized the base of an active stratovolcano. They found that a two-step molecular process rewired nutrient transport in the population. The findings, published today in the journal Science Advances, reveal an exceptionally clear case of an adaptive walk in a wild population. The discovery has broader implications for evolutionary biology and crop improvement.

Adapting to a novel soil environment

Nutrient homeostasis is crucial for proper plant growth and thus central to crop productivity. Pinpointing the genetic changes that allow plants to thrive in novel soil conditions provides insights into this important process. However, given the immense size of a genome, it is challenging to identify the specific functional variants that enable adaptation.

Members of the research team previously found that wild populations of the molecular model plant, Arabidopsis thaliana, commonly referred to as thale cress, colonized the Cape Verde Islands from North Africa and adapted using new mutations that arose after the colonization of the islands. Here, the scientists focus on the thale cress population from Fogo Island, which grows at the base of Pico de Fogo, an active stratovolcano. “We wanted to know: What does it take to live at the base of an active volcano? How did the plants adapt to the volcanic soil of Fogo?”, said Hancock.

“What we found was surprising,” said Emmanuel Tergemina, first author of the study. “While the plants from Fogo appeared to be healthy in their natural environment, they grew poorly on standard potting soil.” Chemical analysis of Fogo soils showed they were severely depauperate of manganese, an element that is crucial for energy production and proper plant growth. In contrast, leaves from Fogo plants grown on standard potting soil contained high levels of manganese, suggesting the plants had evolved a mechanism to increase manganese uptake.

Two evolutionary steps to a new adaptive peak

The scientists used a combination of genetic mapping and evolutionary analysis to discover the molecular steps that allowed the plants to colonize Fogo’s manganese-limited soil.

In a first evolutionary step, a mutation disrupted the primary iron transport gene (IRT1), eliminating its function. Disruption of this gene in a natural population was striking because this key gene exists intact in all other worldwide populations of the thale cress species – no such disruptions are found elsewhere. Further, the patterns of genetic variation in the IRT1 genomic region suggest that the disrupted version of IRT1 was important in adaptation. Evolutionary reconstruction shows that the mutation swept quickly to fixation across the entire Fogo population so that all Fogo thale cress plants now carry this mutation. Using gene-editing technology (CRISPR-Cas9), the researchers examined the functional effects of IRT1 disruption in Fogo and found that it increases leaf manganese accumulation, which could explain its role in adaptation. However, the loss of the IRT1 transporter came with a cost: it severely reduced leaf iron.

In a second evolutionary step, the metal transporter gene NRAMP1 was duplicated in multiple parallel events. These duplications spread rapidly so that now nearly all thale cress plants in Fogo carry multiple copies of NRAMP1 in their genomes. These duplications amplify NRAMP1 gene function, increasing iron transport and compensating for the iron deficiency induced by IRT1 disruption. Moreover, the amplification occurred by several independent duplication events across the island population. This was unexpected given the short time since colonization (around 5000 years) and the lack of similar events in other worldwide populations. “The rapid rise in frequency of these duplications together with their beneficial effect on nutrient homeostasis indicates these were important in adaptation”, explained Hancock. “Overall, our results provide an exceptionally clear example of how simple genetic changes can rewire nutrient processing in plants, enabling adaptation to a novel soil environment.”

Implications for crop improvement

These results also provide some encouraging news for crop breeding. Traditionally, information about gene function has come from studies of individual mutant lines. However, by using variation that exists in nature, it is possible to uncover more complex multi-step processes that can lead to changes in agriculturally-relevant traits. “The discovery that a simple two-step process alters nutrient transport in this case may offer clues for approaches to improve crops to better fit local soil environments. Moreover, gene disruption and gene amplification, as in the case of IRT1 and NRAMP1 in Fogo, are some of the simplest genetic changes to engineer, which makes them especially exciting because it means that they could be readily transferable to other species,” concluded Tergemina.

See the full article here.

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The MPG Institute for Plant Breeding Research was founded in Müncheberg, Germany in 1928 as part of the Kaiser-Wilhelm-Gesellschaft. The founding director, Erwin Baur, initiated breeding programmes with fruits and berries, and basic research on Antirrhinum majus and the domestication of lupins. After the Second World War, the institute moved west to Voldagsen, and was relocated to new buildings on the present site in Cologne in 1955.

The modern era of the Institute began in 1978 with the appointment of Jeff Schell and the development of plant transformation technologies and plant molecular genetics. The focus on molecular genetics was extended in 1980 with the appointment of Heinz Saedler. The appointment in 1983 of Klaus Hahlbrock broadened the expertise of the Institute in the area of plant biochemistry, and the arrival of Francesco Salamini in 1985 added a focus on crop genetics. During the period 1978-1990, the Institute was greatly expanded and new buildings were constructed for the departments led by Schell, Hahlbrock and Salamini, in addition to a new lecture hall and the Max Delbrück Laboratory building that housed independent research groups over a period of 10 years.

A new generation of directors was appointed from 2000 with the approaching retirements of Klaus Hahlbrock and Jeff Schell. Paul Schulze-Lefert and George Coupland were appointed in 2000 and 2001, respectively, and Maarten Koornneef arrived three years later upon the retirement of Francesco Salamini. The new scientific departments brought a strong focus on utilising model species to understand the regulatory principles and molecular mechanisms underlying selected traits. The longer-term aim is to translate these discoveries to breeding programmes through the development of rational breeding concepts. The arrival of a new generation of Directors also required modernization of the infrastructure. So far, this has involved complete refurbishment of the building that houses the Plant Developmental Biology laboratory (2004), construction of a new guesthouse and library (2005), planning of new buildings for the administration and technical workshops (2009), and a new laboratory building completed in May 2012. The new laboratory building includes a section that links the three scientific departments, offices and the Bioinformatics Research Group.

Departments

Department of Plant Developmental Biology
Department of Plant Microbe Interactions
Department of Comparative Development and Genetics
Department of Chromosome Biology

MPG Society for the Advancement of Science [MPG Gesellschaft zur Förderung der Wissenschaften e. V.] is a formally independent non-governmental and non-profit association of German research institutes founded in 1911 as the Kaiser Wilhelm Society and renamed the Max Planck Society in 1948 in honor of its former president, theoretical physicist Max Planck. The society is funded by the federal and state governments of Germany as well as other sources.

According to its primary goal, the MPG Society supports fundamental research in the natural, life and social sciences, the arts and humanities in its 83 (as of January 2014) MPG Institutes. The society has a total staff of approximately 17,000 permanent employees, including 5,470 scientists, plus around 4,600 non-tenured scientists and guests. Society budget for 2015 was about €1.7 billion.

The MPG Institutes focus on excellence in research. The MPG Society has a world-leading reputation as a science and technology research organization, with 33 Nobel Prizes awarded to their scientists, and is generally regarded as the foremost basic research organization in Europe and the world. In 2013, the Nature Publishing Index placed the MPG institutes fifth worldwide in terms of research published in Nature journals (after Harvard University, The Massachusetts Institute of Technology, Stanford University and The National Institutes of Health). In terms of total research volume (unweighted by citations or impact), the Max Planck Society is only outranked by The Chinese Academy of Sciences [中国科学院](CN), The Russian Academy of Sciences [Росси́йская акаде́мия нау́к](RU) and Harvard University. The Thomson Reuters-Science Watch website placed the MPG Society as the second leading research organization worldwide following Harvard University, in terms of the impact of the produced research over science fields.

The MPG Society and its predecessor Kaiser Wilhelm Society hosted several renowned scientists in their fields, including Otto Hahn, Werner Heisenberg, and Albert Einstein.

History

The organization was established in 1911 as the Kaiser Wilhelm Society, or Kaiser-Wilhelm-Gesellschaft (KWG), a non-governmental research organization named for the then German emperor. The KWG was one of the world’s leading research organizations; its board of directors included scientists like Walther Bothe, Peter Debye, Albert Einstein, and Fritz Haber. In 1946, Otto Hahn assumed the position of President of KWG, and in 1948, the society was renamed the Max Planck Society (MPG) after its former President (1930–37) Max Planck, who died in 1947.

The MPG Society has a world-leading reputation as a science and technology research organization. In 2006, the Times Higher Education Supplement rankings of non-university research institutions (based on international peer review by academics) placed the MPG Society as No.1 in the world for science research, and No.3 in technology research (behind AT&T Corporation and The DOE’s Argonne National Laboratory.

The domain mpg.de attracted at least 1.7 million visitors annually by 2008 according to a Compete.com study.

MPG Institutes and research groups

The MPG Society consists of over 80 research institutes. In addition, the society funds a number of Max Planck Research Groups (MPRG) and International Max Planck Research Schools (IMPRS). The purpose of establishing independent research groups at various universities is to strengthen the required networking between universities and institutes of the Max Planck Society.
The research units are primarily located across Europe with a few in South Korea and the U.S. In 2007, the Society established its first non-European centre, with an institute on the Jupiter campus of Florida Atlantic University (US) focusing on neuroscience.
The MPG Institutes operate independently from, though in close cooperation with, the universities, and focus on innovative research which does not fit into the university structure due to their interdisciplinary or transdisciplinary nature or which require resources that cannot be met by the state universities.

Internally, MPG Institutes are organized into research departments headed by directors such that each MPI has several directors, a position roughly comparable to anything from full professor to department head at a university. Other core members include Junior and Senior Research Fellows.

In addition, there are several associated institutes:

International Max Planck Research Schools

Together with the Association of Universities and other Education Institutions in Germany, the Max Planck Society established numerous International Max Planck Research Schools (IMPRS) to promote junior scientists:

• Cologne Graduate School of Ageing Research, Cologne
• International Max Planck Research School for Intelligent Systems, at the Max Planck Institute for Intelligent Systems located in Tübingen and Stuttgart
• International Max Planck Research School on Adapting Behavior in a Fundamentally Uncertain World (Uncertainty School), at the Max Planck Institutes for Economics, for Human Development, and/or Research on Collective Goods
• International Max Planck Research School for Analysis, Design and Optimization in Chemical and Biochemical Process Engineering, Magdeburg
• International Max Planck Research School for Astronomy and Cosmic Physics, Heidelberg at the MPI for Astronomy
• International Max Planck Research School for Astrophysics, Garching at the MPI for Astrophysics
• International Max Planck Research School for Complex Surfaces in Material Sciences, Berlin
• International Max Planck Research School for Computer Science, Saarbrücken
• International Max Planck Research School for Earth System Modeling, Hamburg
• International Max Planck Research School for Elementary Particle Physics, Munich, at the MPI for Physics
• International Max Planck Research School for Environmental, Cellular and Molecular Microbiology, Marburg at the Max Planck Institute for Terrestrial Microbiology
• International Max Planck Research School for Evolutionary Biology, Plön at the Max Planck Institute for Evolutionary Biology
• International Max Planck Research School “From Molecules to Organisms”, Tübingen at the Max Planck Institute for Developmental Biology
• International Max Planck Research School for Global Biogeochemical Cycles, Jena at the Max Planck Institute for Biogeochemistry
• International Max Planck Research School on Gravitational Wave Astronomy, Hannover and Potsdam MPI for Gravitational Physics
• International Max Planck Research School for Heart and Lung Research, Bad Nauheim at the Max Planck Institute for Heart and Lung Research
• International Max Planck Research School for Infectious Diseases and Immunity, Berlin at the Max Planck Institute for Infection Biology
• International Max Planck Research School for Language Sciences, Nijmegen
• International Max Planck Research School for Neurosciences, Göttingen
• International Max Planck Research School for Cognitive and Systems Neuroscience, Tübingen
• International Max Planck Research School for Marine Microbiology (MarMic), joint program of the Max Planck Institute for Marine Microbiology in Bremen, the University of Bremen, the Alfred Wegener Institute for Polar and Marine Research in Bremerhaven, and the Jacobs University Bremen
• International Max Planck Research School for Maritime Affairs, Hamburg
• International Max Planck Research School for Molecular and Cellular Biology, Freiburg
• International Max Planck Research School for Molecular and Cellular Life Sciences, Munich
• International Max Planck Research School for Molecular Biology, Göttingen
• International Max Planck Research School for Molecular Cell Biology and Bioengineering, Dresden
• International Max Planck Research School Molecular Biomedicine, program combined with the ‘Graduate Programm Cell Dynamics And Disease’ at the University of Münster and the Max Planck Institute for Molecular Biomedicine
• International Max Planck Research School on Multiscale Bio-Systems, Potsdam
• International Max Planck Research School for Organismal Biology, at the University of Konstanz and the Max Planck Institute for Ornithology
• International Max Planck Research School on Reactive Structure Analysis for Chemical Reactions (IMPRS RECHARGE), Mülheim an der Ruhr, at the Max Planck Institute for Chemical Energy Conversion
• International Max Planck Research School for Science and Technology of Nano-Systems, Halle at Max Planck Institute of Microstructure Physics
• International Max Planck Research School for Solar System Science at the University of Göttingen hosted by MPI for Solar System Research
• International Max Planck Research School for Astronomy and Astrophysics, Bonn, at the MPI for Radio Astronomy (formerly the International Max Planck Research School for Radio and Infrared Astronomy)
• International Max Planck Research School for the Social and Political Constitution of the Economy, Cologne
• International Max Planck Research School for Surface and Interface Engineering in Advanced Materials, Düsseldorf at Max Planck Institute for Iron Research GmbH
• International Max Planck Research School for Ultrafast Imaging and Structural Dynamics, Hamburg

Max Planck Schools

• Max Planck School of Cognition
• Max Planck School Matter to Life
• Max Planck School of Photonics

Max Planck Center

• The Max Planck Centre for Attosecond Science (MPC-AS), POSTECH Pohang
• The Max Planck POSTECH Center for Complex Phase Materials, POSTECH Pohang

Max Planck Institutes

Among others:
• Max Planck Institute for Neurobiology of Behavior – caesar, Bonn
• Max Planck Institute for Aeronomics in Katlenburg-Lindau was renamed to Max Planck Institute for Solar System Research in 2004;
• Max Planck Institute for Biology in Tübingen was closed in 2005;
• Max Planck Institute for Cell Biology in Ladenburg b. Heidelberg was closed in 2003;
• Max Planck Institute for Economics in Jena was renamed to the Max Planck Institute for the Science of Human History in 2014;
• Max Planck Institute for Ionospheric Research in Katlenburg-Lindau was renamed to Max Planck Institute for Aeronomics in 1958;
• Max Planck Institute for Metals Research, Stuttgart
• Max Planck Institute of Oceanic Biology in Wilhelmshaven was renamed to Max Planck Institute of Cell Biology in 1968 and moved to Ladenburg 1977;
• Max Planck Institute for Psychological Research in Munich merged into the Max Planck Institute for Human Cognitive and Brain Sciences in 2004;
• Max Planck Institute for Protein and Leather Research in Regensburg moved to Munich 1957 and was united with the Max Planck Institute for Biochemistry in 1977;
• Max Planck Institute for Virus Research in Tübingen was renamed as Max Planck Institute for Developmental Biology in 1985;
• Max Planck Institute for the Study of the Scientific-Technical World in Starnberg (from 1970 until 1981 (closed)) directed by Carl Friedrich von Weizsäcker and Jürgen Habermas.
• Max Planck Institute for Behavioral Physiology
• Max Planck Institute of Experimental Endocrinology
• Max Planck Institute for Foreign and International Social Law
• Max Planck Institute for Physics and Astrophysics
• Max Planck Research Unit for Enzymology of Protein Folding
• Max Planck Institute for Biology of Ageing

From Ludwig Maximilian University of Munich [Ludwig-Maximilians-Universität München] (DE) : “The origin of life- a paradigm shift”

From Ludwig Maximilian University of Munich [Ludwig-Maximilians-Universität München] (DE)

11 May 2022

According to a new concept by LMU chemists led by Thomas Carell it was a novel molecular species composed out of RNA and peptides that set in motion the evolution of life into more complex forms.

LMU-chemists Felix Müller (left) and Luis Escobar discussing a new prebiotic molecular design | © Markus Müller / LMU.

Investigating the question as to how life could emerge long ago on the early Earth is one of the most fascinating challenges for science. Which conditions must have prevailed for the basic building blocks of more complex life to form? One of the main answers is based upon the so-called RNA world idea, which molecular biology pioneer Walter Gilbert formulated in 1986. The hypothesis holds that nucleotides – the basic building blocks of the nucleic acids A, C, G, and U – emerged out of the primordial soup, and that short RNA molecules then formed out of the nucleotides. These so-called oligonucleotides were already capable of encoding small amounts of genetic information.

As such single-stranded RNA molecules could also combine into double strands, however, this gave rise to the theoretical possibility that the molecules could replicate themselves – i.e. reproduce. Only two nucleotides fit together in each case, meaning that one strand is the exact counterpart of another and thus forms the template for another strand.

In the course of evolution, this replication could have improved and at some stage yielded more complex life. “The RNA world idea has the big advantage that it sketches out a pathway whereby complex biomolecules such as nucleic acids with optimized catalytic and, at the same time, information-coding properties can emerge,” says LMU chemist Thomas Carell. Genetic material, as we understand it today, is made up of double strands of DNA, a slightly modified, durable form of macromolecule composed of nucleotides.

However, the hypothesis is not without its issues. For example, RNS is a very fragile molecule, especially when it gets longer. Furthermore, it is not clear how the linking of RNA molecules with the world of proteins could have come about, for which the genetic material, as we know, supplies the blueprints. As laid out in a new paper published in Nature, Carell’s working group has discovered a way in which this linking could have occurred.

Luis Escobar from the Carell Group in his laboratory. | © Markus Müller / LMU.

To understand, we must take another, closer look at RNA. In itself, RNA is a complicated macromolecule. In addition to the four canonical bases A, C, G, and U, which encode genetic information, it also contains non-canonical bases, some of which have very unusual structures. These non-information-coding nucleotides are very important for the functioning of RNA molecules. We currently have knowledge of more than 120 such modified RNA nucleosides, which nature incorporates into RNA molecules. It is highly probable that they are relicts of the former RNA world.

The Carell group has now discovered that these non-canonical nucleosides are the key ingredient, as it were, that allows the RNA world to link up with the world of proteins. Some of these molecular fossils can, when located in RNA, “adorn” themselves with individual amino acids or even small chains of them (peptides), according to Carell. This results in small chimeric RNA-peptide structures when amino acids or peptides happen to be present in a solution simultaneously alongside the RNA. In such structures, the amino acids and peptides linked to the RNA then even react with each other to form ever larger and more complex peptides. “In this way, we created RNA-peptide particles in the lab that could encode genetic information and even formed lengthening peptides,” says Carell.

The ancient fossil nucleosides are therefore somewhat akin to nuclei in RNA, forming a core upon which long peptide chains can grow. On some strands of RNA, the peptides were even growing at several points. “That was a very surprising discovery,” says Carell. “It’s possible that there never was a pure RNA world, but that RNA and peptides co-existed from the beginning in a common molecule.” As such, we should expand the concept of an RNA world to that of an RNA-peptide world. The peptides and the RNA mutually supported each other in their evolution, the new idea proposes.

According to the new theory, a decisive element at the beginning was the presence of RNA molecules that could adorn themselves with amino acids and peptides and so join them into larger peptide structures. “RNA developed slowly into a constantly improving amino acid linking catalyst,” says Carell. This relationship between RNA and peptides or proteins has remained to this day. The most important RNA catalyst is the ribosome, which still links amino acids into long peptide chains today. One of the most complicated RNA machines, it is responsible in every cell for translating genetic information into functional proteins. “The RNA-peptide world thus solves the chicken-and-egg problem,” says Carell. “The new idea creates a foundation upon which the origin of life gradually becomes explicable.”

See the full article here.

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Welcome to Ludwig Maximilian University of Munich [Ludwig-Maximilians-Universität München] (DE) – the University in the heart of Munich. LMU is recognized as one of Europe’s premier academic and research institutions. Since our founding in 1472, LMU has attracted inspired scholars and talented students from all over the world, keeping the University at the nexus of ideas that challenge and change our complex world.

Ludwig Maximilian University of Munich [Ludwig-Maximilians-Universität München] (DE) is a public research university located in Munich, Germany.

The University of Munich is Germany’s sixth-oldest university in continuous operation. Originally established in Ingolstadt in 1472 by Duke Ludwig IX of Bavaria-Landshut, the university was moved in 1800 to Landshut by King Maximilian I of Bavaria when Ingolstadt was threatened by the French, before being relocated to its present-day location in Munich in 1826 by King Ludwig I of Bavaria. In 1802, the university was officially named Ludwig-Maximilians-Universität by King Maximilian I of Bavaria in his as well as the university’s original founder’s honour.

The University of Munich is associated with 43 Nobel laureates (as of October 2020). Among these were Wilhelm Röntgen, Max Planck, Werner Heisenberg, Otto Hahn and Thomas Mann. Pope Benedict XVI was also a student and professor at the university. Among its notable alumni, faculty and researchers are inter alia Rudolf Peierls, Josef Mengele, Richard Strauss, Walter Benjamin, Joseph Campbell, Muhammad Iqbal, Marie Stopes, Wolfgang Pauli, Bertolt Brecht, Max Horkheimer, Karl Loewenstein, Carl Schmitt, Gustav Radbruch, Ernst Cassirer, Ernst Bloch, Konrad Adenauer. The LMU has recently been conferred the title of “University of Excellence” under the German Universities Excellence Initiative.

LMU is currently the second-largest university in Germany in terms of student population; in the winter semester of 2018/2019, the university had a total of 51,606 matriculated students. Of these, 9,424 were freshmen while international students totalled 8,875 or approximately 17% of the student population. As for operating budget, the university records in 2018 a total of 734,9 million euros in funding without the university hospital; with the university hospital, the university has a total funding amounting to approximately 1.94 billion euros.

Faculties

LMU’s Institute of Systematic Botany is located at Botanischer Garten München-Nymphenburg
Faculty of chemistry buildings at the Martinsried campus of LMU Munich

The university consists of 18 faculties which oversee various departments and institutes. The official numbering of the faculties and the missing numbers 06 and 14 are the result of breakups and mergers of faculties in the past. The Faculty of Forestry Operations with number 06 has been integrated into the Technical University of Munich [Technische Universität München] (DE) in 1999 and faculty number 14 has been merged with faculty number 13.

01 Faculty of Catholic Theology
02 Faculty of Protestant Theology
03 Faculty of Law
04 Faculty of Business Administration
05 Faculty of Economics
07 Faculty of Medicine
08 Faculty of Veterinary Medicine
09 Faculty for History and the Arts
10 Faculty of Philosophy, Philosophy of Science and Study of Religion
11 Faculty of Psychology and Educational Sciences
12 Faculty for the Study of Culture
13 Faculty for Languages and Literatures
15 Faculty of Social Sciences
16 Faculty of Mathematics, Computer Science and Statistics
17 Faculty of Physics
18 Faculty of Chemistry and Pharmacy
19 Faculty of Biology
20 Faculty of Geosciences and Environmental Sciences

Research centres

In addition to its 18 faculties, the University of Munich also maintains numerous research centres involved in numerous cross-faculty and transdisciplinary projects to complement its various academic programmes. Some of these research centres were a result of cooperation between the university and renowned external partners from academia and industry; the Rachel Carson Center for Environment and Society, for example, was established through a joint initiative between LMU Munich and the Deutsches Museum, while the Parmenides Center for the Study of Thinking resulted from the collaboration between the Parmenides Foundation and LMU Munich’s Human Science Center.

Some of the research centres which have been established include:

Center for Integrated Protein Science Munich (CIPSM)
Graduate School of Systemic Neurosciences (GSN)
Helmholtz Zentrum München – German Research Center for Environmental Health
Nanosystems Initiative Munich (NIM)
Parmenides Center for the Study of Thinking
Rachel Carson Center for Environment and Society