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

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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.

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.


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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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Here's what the only total solar eclipse of 2021 was like from a cruise ship near Antarctica – Space.com

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Editor’s note: The only total solar eclipse of 2021 occurred Saturday, Dec. 4, over Antarctica, where few people could see it. Some intrepid explorers, like our columnist Joe Rao, attempted to see the eclipse from cruise ships near Antarctica. Here’s what Joe and his ship saw.

FROM THE LE COMMANDANT CHARCOT IN THE SOUTHERN OCEAN OFF OF ANTARCTICA — Approximately 200 passengers on board this exploration cruise ship, owned by the French cruise line, Ponant, sadly suffered a complete cloud out of this total solar eclipse, which swept across a part of the frozen Antarctic continent on Saturday.

Late Friday evening, Captain Etienne Garcia, Master of the Le Commandant Charcot, reversed the course of the ship. It had been previously heading on a southeast trajectory just to the east of the center-line of the eclipse track, but based on a check of satellite imagery, Captain Garcia decided to turn and head on a northwest trajectory and maneuver the ship closer to the eclipse center line. The satellite images had shown a more-or-less general cloud cover, but the search was on for some thin spots which might have provided some partial visibility.

Photos: Amazing 2021 total solar eclipse views from Antarctica

Image 1 of 1

A view from the stern of Le Commandant Charcot looking up toward the ship’s bridge under overcast skies prior to the start of the total solar eclipse of 2021. (Image credit: Joe Rao)

Solar Eclipse Photography Guide

Unfortunately, during the overnight hours as the temperatures cooled the overcast only became thicker. And the passengers and crew who gathered at the stern of the ship after 3 a.m. (“Chilean Summer Time”) only saw gray skies.

At the time it encountered the moon’s dark umbral shadow, the 30,000-ton exploration vessel was located near 57.72 degrees south and 44.02 degrees west, to the northeast of the South Orkney Islands. About 20 minutes before second contact, the start of the total phase of the eclipse, passengers began to notice a subtle diminution of the light levels and it really began accelerating toward darkening in the final couple of minutes before totality as the moon’s shadow raced toward us from the northeast at 3,100 mph.

Related: The 8 most famous solar eclipses in history

The moment of totality of the total solar eclipse of 2021 from the deck of the  Le Commandant Charcot in the sea near the coast of Antarctica on Dec. 4, 2021. The sky was clouded out, but is considerably darker and lights can be seen shining on the ship’s bridge. (Image credit: Joe Rao)

A number of petrels — tube-nosed seabirds indiginous to this part of the world —were flying and swooping around the ship as the darkness was coming on and we also caught sight of two whales that breached the sea surface alongside our ship. Whether they were all reacting to the darkening sky is debatable, but certainly a possibility.

Totality lasted 97 seconds. No distinct shadow or cone of darkness was noted. Rather, just an amorphous darkening of the sky — like someone turning down a rheostat or dimmer switch. No colors were seen and the end of totality seemed more pronounced as the light seemed to come back quicker than it when it faded away.

During totality, it actually began to drizzle very lightly and a few minutes after third contact it actually started to snow lightly. The air temperature hovered at around 0C (32F), but factoring in the winds made it feel noticeably colder.

Related: The stages of the 2021 total solar eclipse explained

Captain Etienne Garcia, Master of the Le Commandant Charcot, making last-minute course corrections in an attempt to locate a break in the clouds for a view of the total eclipse. (Image credit: Joe Rao)

Well … we gave it our best shot, but unfortunately came up empty. Those who had never experienced a total solar eclipse, were impressed by the dramatic darkening of the sky, but for those like myself, who knew what was hidden from our view behind the cloud deck, it was quite disappointing.

I knew when I accepted this assignment to work with Captain Garcia and his staff, that the weather odds were long for success based on long-term climate records for this part of the world. It is nonetheless hard to take, considering how brilliantly sunny our skies were in the two days prior to the eclipse.

This was eclipse number 13 for me . . . the very first dating back to July 1972; only my second cloud-out (the first was 44 years ago in Colombia, October 1977). My batting average for eclipse success is 84.7%, so I really have little to complain about — but a bitter defeat nonetheless.

On a bright note, with today’s 97 seconds, I have now spent over 30 minutes “basking” in the shadow of the moon. 

Back in 1973, I was at a gathering of eclipse chasers at the Hayden Planetarium where Dr. Charles Hugh Smiley of Brown University was attending. The Director at Hayden, Mark Chartrand said that Dr. Smiley had spent more than 30 minutes in the Moon’s umbra, “An unprecedented total!” gushed Dr. Chartrand. I thought to myself at that time that I would never come remotely close to Dr. Smiley’s record, but with today’s eclipse I have. 

Dr. Smiley (who passed away in 1977), ended his career having observed 14 eclipses. Today, many veteran eclipse chasers have seen more than 20 total eclipses and a few individuals, such as solar physicist, Dr. Jay Pasachoff of Williams College in Massachusetts and Dr. Glenn Schneider of the University of Arizona’s Steward Observatory, have seen more than 30!

Sadly ironic that on the day before the eclipse, the skies were brilliantly sunny.  Here is Renate Rao (my wife), enjoying the cold Antarctic sunshine.  Note the large iceberg in the Southern Ocean behind her.  (Image credit: Joe Rao)

At least one cruise ship did get a view of the totally eclipsed sun. Word reached us that National Geographic’s ship “Endurance” managed to sight the sun’s corona between clouds at a position near the beginning of today’s totality path. There were also chartered flights that took observers about 33,000-feet above the cloud cover for airborne views of this morning’s celestial spectacle.

In all, it is estimated that fewer than 3000 people attended observation of today’s total eclipse. 

Another member of the Ponant cruise ships, the Le Boreal, passed our ship on its way north to position itself along the totality path.  A wayward petral photobombed it in this view. (Image credit: Joe Rao)

Related stories:

The next total eclipse on April 20, 2023, will actually be an unusual annular-total, or “hybrid” eclipse, in which along part of the eclipse path an annular or ring eclipse is seen, while along other parts of the eclipse path the eclipse is total. Most eclipse watchers are likely to converge on Cape Range National Park in Western Australia, where totality will last for 62 seconds.

On April 8, 2024, a total eclipse will cross parts of Northern Mexico and the Southern and Eastern United States and Eastern Canada. About 35 million people live in the totality path of this eclipse with the total phase in some cases exceeding 4 minutes.

Editor’s Note: If you snap an amazing solar eclipse photo and would like to share it with Space.com’s readers, send your photo(s), comments, and your name and location to spacephotos@space.com.

Joe Rao serves as an instructor and guest lecturer at New York’s Hayden Planetarium. He writes about astronomy for Natural History magazine, the Farmers’ Almanac and other publications. Follow us on Twitter @Spacedotcom and on Facebook

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Scientists observe total solar eclipse in Antarctica – Global Times

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Scientists from the Chilean Union Glacier Station observe a total solar eclipse in Antarctica, Dec. 4, 2021.Photo:Xinhua

 
Scientists from the Chilean Union Glacier Station observe a total solar eclipse in Antarctica, Dec. 4, 2021.Photo:Xinhua

Scientists from the Chilean Union Glacier Station observe a total solar eclipse in Antarctica, Dec. 4, 2021.Photo:Xinhua

 

Scientists from the Chilean Union Glacier Station observe a total solar eclipse in Antarctica, Dec. 4, 2021.Photo:Xinhua

Scientists from the Chilean Union Glacier Station observe a total solar eclipse in Antarctica, Dec. 4, 2021.Photo:Xinhua

 

Photo taken from Chilean Union Glacier Station in Antarctica on Dec. 4, 2021 shows a total solar eclipse.Photo:Xinhua

Photo taken from Chilean Union Glacier Station in Antarctica on Dec. 4, 2021 shows a total solar eclipse.Photo:Xinhua

 

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Dinosaur Tail Found In Chile Could Point To Discovery Of New Species – NDTV

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Paleontologists have discovered 80 percent of the dinosaur’s skeleton.

Santiago:

Chilean paleontologists on Wednesday presented their findings on a dinosaur discovered three years ago in Patagonia which they said had a highly unusual tail that has stumped researchers.

The remains of the Stegouros elengassen were discovered during excavations in 2018 at Cerro Guido, a site known to harbor numerous fossils, by a team who believed they were dealing with an already known species of dinosaur until they examined its tail.

“That was the main surprise,” said Alexander Vargas, one of the paleontologists. “This structure is absolutely amazing.”

“The tail was covered with seven pairs of osteoderms … producing a weapon absolutely different from anything we know in any dinosaur,” added the researcher during a presentation of the discovery at the University of Chile.

The osteoderms — structures of bony plaques located in the dermal layers of the skin – were aligned on either side of the tail, making it resemble a large fern.

Paleontologists have discovered 80 percent of the dinosaur’s skeleton and estimate that the animal lived in the area 71 to 74.9 million years ago. It was about two meters (almost seven feet) long, weighed 150 kilograms (330 pounds) and was a herbivore.

According to the scientists, who published their research in the journal Nature, the animal could represent a hitherto unknown lineage of armored dinosaur never seen in the southern hemisphere but already identified in the northern part of the continent.

“We don’t know why (the tail) evolved. We do know that within armored dinosaur groups there seems to be a tendency to independently develop different osteoderm-based defense mechanisms,” said Sergio Soto, another member of the team.

The Cerro Guido area, in the Las Chinas valley 3,000 km (1,800 miles) south of Santiago, stretches for 15 kilometers. Various rock outcrops contain numerous fossils.

The finds there allowed the scientists to surmise that present-day America and Antarctica were close to each other millions of years ago.

“There is strong evidence that there is a biogeographic link with other parts of the planet, in this case Antarctica and Australia, because we have two armored dinosaurs there closely related” to the Stegouros, said Soto.

(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)

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