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Researchers develop program to read any genome sequence and decipher its genetic code – Phys.org

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Credit: CC0 Public Domain

Yekaterina “Kate” Shulgina was a first year student in the Graduate School of Arts and Sciences, looking for a short computational biology project so she could check the requirement off her program in systems biology. She wondered how genetic code, once thought to be universal, could evolve and change.

That was 2016 and today Shulgina has come out the other end of that short-term project with a way to decipher this genetic mystery. She describes it in a new paper in the journal eLife with Harvard biologist Sean Eddy.

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The report details a new computer program that can read the of any organism and then determine its genetic code. The program, called Codetta, has the potential to help scientists expand their understanding of how the genetic code evolves and correctly interpret the genetic code of newly sequenced .

“This in it of itself is a very fundamental biology question,” said Shulgina, who does her graduate research in Eddy’s Lab.

The genetic code is the set of rules that tells the cells how to interpret the three-letter combinations of nucleotides into proteins, often referred to as the building blocks of life. Almost every organism, from E. coli to humans, uses the same genetic code. It’s why the code was once thought to be set in stone. But scientists have discovered a handful of outliers—organisms that use alternative genetic codes—exist where the set of instructions are different.

This is where Codetta can shine. The program can help to identify more organisms that use these alternative genetic codes, helping shed new light on how genetic codes can even change in the first place.

“Understanding how this happened would help us reconcile why we originally thought this was impossible… and how these really fundamental processes actually work,” Shulgina said.

Already, Codetta has analyzed the genome sequences of over 250,000 bacteria and other called archaea for alternative genetic codes, and has identified five that have never been seen. In all five cases, the code for the amino acid arginine was reassigned to a different amino acid. It’s believed to mark the first-time scientists have seen this swap in bacteria and could hint at evolutionary forces that go into altering the genetic code.

The researchers say the study marks the largest screening for alternative genetic codes. Codetta essentially analyzed every genome that’s available for bacteria and archaea. The name of the program is a cross between the codons, the sequence of three nucleotides that forms pieces of the genetic code, and the Rosetta Stone, a slab of rock inscribed with three languages.

The work marks a capstone moment for Shulgina, who spent the past five years developing the statistical theory behind Codetta, writing the program, testing it, and then analyzing the genomes. It works by reading the of an organism and then tapping into a database of known proteins to produce a likely . It differs from other similar methods because of the scale at which it can analyze genomes.

Shulgina joined Eddy’s lab, which specializes in comparing genomes, in 2016 after coming to him for advice on the algorithm she was designing to interpret genetic codes.

Until now, no one has done such a broad survey for alternative genetic codes.

“It was great to see new codes, because for all we knew, Kate would do all this work and there wouldn’t turn out to be any new ones to find,” said Eddy, who’s also a Howard Hughes Medical Investigator. He also noted the potential of the system to be used to ensure the accuracy of the many databases that house .

“Many protein sequences in the databases these days are only conceptual translations of genomic DNA sequences,” Eddy said. “People mine these protein sequences for all sorts of useful stuff, like new enzymes or new gene editing tools and whatnot. You’d like for those protein sequences to be accurate, but if the organism is using a nonstandard , they’ll be erroneously translated.”

The researchers say the next step of the work is to use Codetta to search for alternative codes in viruses, eukaryotes, and organellar genomes like mitochondria and chloroplasts.

“There’s still a lot of diversity of life where we haven’t done this systematic screening yet,” Shulgina said.


Explore further

Researchers replace the genes of E. coli bacteria with synthesized genome


More information:
Yekaterina Shulgina et al, A computational screen for alternative genetic codes in over 250,000 genomes, eLife (2021). DOI: 10.7554/eLife.71402

Journal information:
eLife

Citation:
Researchers develop program to read any genome sequence and decipher its genetic code (2021, November 9)
retrieved 9 November 2021
from https://phys.org/news/2021-11-harvard-genome-sequence-decipher-genetic.html

This document is subject to copyright. Apart from any fair dealing for the purpose of private study or research, no
part may be reproduced without the written permission. The content is provided for information purposes only.

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Marine plankton could act as alert in mass extinction event: UVic researcher – Saanich News

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A University of Victoria micropaleontologist found that marine plankton may act as an early alert system before a mass extinction occurs.

With help from collaborators at the University of Bristol and Harvard, Andy Fraass’ newest paper in the Nature journal shows that after an analysis of fossil records showed that plankton community structures change before a mass extinction event.

“One of the major findings of the paper was how communities respond to climate events in the past depends on the previous climate,” Fraass said in a news release. “That means that we need to spend a lot more effort understanding recent communities, prior to industrialization. We need to work out what community structure looked like before human-caused climate change, and what has happened since, to do a better job at predicting what will happen in the future.”

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According to the release, the fossil record is the most complete and extensive archive of biological changes available to science and by applying advanced computational analyses to the archive, researchers were able to detail the global community structure of the oceans dating back millions of years.

A key finding of the study was that during the “early eocene climatic optimum,” a geological era with sustained high global temperatures equivalent to today’s worst case global warming scenarios, marine plankton communities moved to higher latitudes and only the most specialized plankton remained near the equator, suggesting that the tropical temperatures prevented higher amounts of biodiversity.

“Considering that three billion people live in the tropics, the lack of biodiversity at higher temperatures is not great news,” paper co-leader Adam Woodhouse said in the release.

Next, the team plans to apply similar research methods to other marine plankton groups.

Read More: Global study, UVic researcher analyze how mammals responded during pandemic

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The largest marine reptile ever could match blue whales in size – Ars Technica

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Blue whales have been considered the largest creatures to ever live on Earth. With a maximum length of nearly 30 meters and weighing nearly 200 tons, they are the all-time undisputed heavyweight champions of the animal kingdom.

Now, digging on a beach in Somerset, UK, a team of British paleontologists found the remains of an ichthyosaur, a marine reptile that could give the whales some competition. “It is quite remarkable to think that gigantic, blue-whale-sized ichthyosaurs were swimming in the oceans around what was the UK during the Triassic Period,” said Dean Lomax, a paleontologist at the University of Manchester who led the study.

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Giant jawbones

Ichthyosaurs were found in the seas through much of the Mesozoic era, appearing as early as 250 million years ago. They had four limbs that looked like paddles, vertical tail fins that extended downward in most species, and generally looked like large, reptilian dolphins with elongated narrow jaws lined with teeth. And some of them were really huge. The largest ichthyosaur skeleton so far was found in British Columbia, Canada, measured 21 meters, and belonged to a particularly massive ichthyosaur called Shonisaurus sikanniensis. But it seems they could get even larger than that.

What Lomax’s team found in Somerset was a surangular, a long, curved bone that all reptiles have at the top of the lower jaw, behind the teeth. The bone measured 2.3 meters—compared to the surangular found in the Shonisaurus sikanniensis skeleton, it was 25 percent larger. Using simple scaling and assuming the same body proportions, Lomax’s team estimated the size of this newly found ichthyosaur at somewhere between 22 and 26 meters, which would make it the largest marine reptile ever. But there was one more thing.

Examining the surangular, the team did not find signs of the external fundamental system (EFS), which is a band of tissue present in the outermost cortex of the bone. Its formation marks a slowdown in bone growth, indicating skeletal maturity. In other words, the giant ichthyosaur was most likely young and still growing when it died.

Correcting the past

In 1846, five large bones were found at the Aust Cliff near Bristol in southwestern England. Dug out from the upper Triassic rock formation, they were dubbed “dinosaurian limb bone shafts” and were exhibited in the Bristol Museum, where one of them was destroyed by bombing during World War II.

But in 2005, Peter M. Galton, a British paleontologist then working at the University of Bridgeport, noticed something strange in one of the remaining Aust Cliff bones. He described it as an “unusual foramen” and suggested it was a nutrient passage. Later studies generally kept attributing those bones to dinosaurs but pointed out things like an unusual microstructure that was difficult to explain.

According to Lomax, all this confusion was because the Aust Cliff bones did not belong to dinosaurs and were not parts of limbs. He pointed out that the nutrient foramen morphology, shape, and microstructure matched with the ichthyosaur’s bone found in Somerset. The difference was that the EFS—the mark of mature bones—was present on the Aust Cliff bones. If Lomax is correct and they really were parts of ichthyosaurs’ surangular, they belonged to a grown individual.

And using the same scaling technique applied to the Somerset surangular, Lomax estimated this grown individual to be over 30 meters long—slightly larger than the biggest confirmed blue whale.

Looming extinction

“Late Triassic ichthyosaurs likely reached the known biological limits of vertebrates in terms of size. So much about these giants is still shrouded by mystery, but one fossil at a time, we will be able to unravel their secrets,” said Marcello Perillo, a member of the Lomax team responsible for examining the internal structure of the bones.

This mystery beast didn’t last long, though. The surangular bone found in Somerset was buried just beneath a layer full of seismite and tsunamite rocks that indicate the onset of the end-Triassic mass extinction event, one of the five mass extinctions in Earth’s history. The Ichthyotian severnensis, as Lomax and his team named the species, probably managed to reach an unbelievable size but was wiped out soon after.

The end-Triassic mass extinction was not the end of all ichthyosaurs, though. They survived but never reached similar sizes again. They faced competition from plesiosaurs and sharks that were more agile and swam much faster, and they likely competed for the same habitats and food sources. The last known ichthyosaurs went extinct roughly 90 million years ago.

PLOS ONE, 2024.  DOI: 10.1371/journal.pone.0300289

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Jeremy Hansen – The Canadian Encyclopedia

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Early Life and Education

Jeremy Hansen grew up on a farm near the community of Ailsa Craig, Ontario, where he attended elementary school. His family moved to Ingersoll,
Ontario, where he attended Ingersoll District Collegiate Institute. At age 12 he joined the 614 Royal Canadian Air Cadet Squadron in London, Ontario. At 16 he earned his Air Cadet
glider pilot wings and at 17 he earned his private pilot licence and wings. After graduating from high school and Air Cadets, Hansen was accepted for officer training in the Canadian Armed Forces (CAF). He was trained at Chilliwack, British Columbia, and the Royal Military College at Saint-Jean-sur-Richelieu,
Quebec. Hansen then enrolled in the Royal Military College of Canada in Kingston,
Ontario. In 1999, he completed a Bachelor of Science in space science with First Class Honours and was a Top Air Force Graduate from the Royal Military College. In 2000, he completed his Master of Science in physics with a focus on wide field of view satellite tracking.   

CAF Pilot

In 2003, Jeremy Hansen completed training as a CF-18 fighter pilot with the 410 Tactical Fighter Operational Training Squadron at Cold Lake, Alberta.
From 2004 to 2009, he served by flying CF-18s with the 441 Tactical Fighter Squadron and the 409 Tactical Fighter Squadron. He also flew as Combat Operations Officer at 4 Wing Cold Lake. Hansen’s responsibilities included NORAD operations effectiveness,
Arctic flying operations and deployed exercises. He was promoted to the rank of colonel in 2017. (See also Royal Canadian Air Force.)

Career as an Astronaut

In May 2009, Jeremy Hansen and David Saint-Jacques were chosen out of 5,351 applicants in the Canadian Space Agency’s
(CSA) third Canadian Astronaut Recruitment Campaign. He graduated from Astronaut Candidate Training in 2011 and began working at the Mission Control Center in Houston, Texas, as capsule communicator (capcom, the person in Mission Control who speaks directly
to the astronauts in space.

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David Saint-Jacques (left) and Jeremy Hansen (right) during a robotics familiarization session, 25 July 2009.

As a CSA astronaut, Hansen continues to develop his skills. In 2013, he underwent training in the High Arctic and learned how to conduct geological fieldwork (see Arctic Archipelago;
Geology). That same year, he participated in the European Space Agency’s CAVES program in Sardinia, Italy. In that human performance experiment Hansen lived underground for six days.
In 2014, Hansen was a member of the crew of NASA Extreme Environment Mission Operations (NEEMO) 19. He spent seven days off Key Largo, Florida, living in the Aquarius habitat on the ocean floor, which is used to simulate conditions of the International
Space Station and different gravity fields. In 2017, Hansen became the first Canadian to lead a NASA astronaut class, in which he trained astronaut candidates from Canada and the United States.  

Did you know?

Hansen has been instrumental in encouraging young people to become part of the STEM (Science, Technology,
Engineering, Mathematics) workforce with the aim of encouraging future generations of space explorers.
His inspirational work in Canada includes flying a historical “Hawk One” F-86 Sabre jet.

Artemis II

In April 2023, Hansen was chosen along with Americans Christina Koch, Victor Glover and Reid Wiseman to crew NASA’s Artemis II mission to the moon. The mission, scheduled for no earlier
than September 2025 after a delay due to technical problems, marks NASA’s first manned moon voyage since Apollo 17 in 1972. The Artemis II astronauts will not land on the lunar
surface, but will orbit the moon in an Orion spacecraft. They will conduct tests in preparation for future manned moon landings, the establishment of an orbiting space station called Lunar Gateway, or Gateway, and a base on the moon’s surface where astronauts
can live and work for extended periods. The path taken by Orion will carry the astronauts farther from Earth than any humans have previously travelled. Hansen’s participation in Artemis II is a direct result of Canada’s contribution of Canadarm3
to Lunar Gateway. (See also Canadarm; Canadian Space Agency.)

“Being part of the Artemis II crew is both exciting and humbling. I’m excited to leverage my experience, training and knowledge to take on this challenging mission on behalf of Canada. I’m humbled by the incredible contributions and hard work of so many
Canadians that have made this opportunity a reality. I am proud and honoured to represent my country on this historic mission.” – Jeremy Hansen (Canadian Space Agency, 2023)

Did you know?

On his Artemis II trip, Hansen will wear an Indigenous-designed mission patch created for him by Anishinaabe artist Henry Guimond.

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Honours and Awards

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