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New computer program can read any genome sequence and decipher its genetic code – News-Medical.net

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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 genome sequence 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 organisms.

“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.”

Yekaterina “Kate” Shulgina

Already, Codetta has analyzed the genome sequences of over 250,000 bacteria and other single-celled organisms 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 genome of an organism and then tapping into a database of known proteins to produce a likely genetic code. 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 protein sequences.

“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 code, 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.

Journal reference:

Shulgina, Y & Eddy, S.R., (2021) A computational screen for alternative genetic codes in over 250,000 genomes. eLife. doi.org/10.7554/eLife.71402.

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Hubble Looks at Spiral Galaxy NCG 7329 – Sci-News.com

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The NASA/ESA Hubble Space Telescope has captured an amazing photo of the spiral galaxy NCG 7329.

This Hubble image shows NCG 7329, a spiral galaxy located some 149 million light-years away in the constellation of Tucana. Image credit: NASA / ESA / Hubble / Riess et al.

NCG 7329 was first discovered by the English astronomer John Herschel on July 20, 1835.

Otherwise known as ESO 109-12, IRAS 22369-6644 and LEDA 69453, it resides 149 million light-years away in the constellation of Tucana.

The galaxy is a member of the NGC 7329 group (LGG 462), an assembly of more than 10 galaxies bound together by gravity.

This new image of NCG 7329 is made up of observations from Hubble’s Wide Field Camera 3 (WFC3) in the infrared and optical parts of the spectrum.

“Creating a colorful image such as this one using a telescope such as Hubble is not as straightforward as pointing and clicking a camera,” Hubble astronomers said.

“Commercial cameras will typically try to collect as much light of all visible wavelengths as they can, in order to create the most vibrant images possible.”

“In contrast, raw images collected by Hubble are always monochromatic, because astronomers typically want to capture very specific ranges of wavelengths of light at any time, in order to do the best, most accurate science possible.”

“In order to control which wavelengths of light will be collected, Hubble’s cameras are equipped with a wide variety of filters, which only allow certain wavelengths of light to reach the cameras’ CCDs (a CCD is a camera’s light sensor — phone cameras also have CCDs).”

“How are the colorful Hubble images possible given that the raw Hubble images are monochromatic? This is accomplished by combining multiple different observations of the same object, obtained using different filters,” they added.

“This image of NCG 7329, for example, was processed from Hubble observations made using four different filters, each of which spans a different region of the light spectrum.”

“Specialized image processors and artists can make informed judgements about which optical colors best correspond to each filter used.”

“They can then color the images taken using that filter accordingly.”

“Finally, the images taken with different filters are stacked together, and voila!”

“The colorful image of a distant galaxy is complete, with colors as representative of reality as possible.”

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SpaceX Tapped For 3 More Possible Commercial Crew Flights To Space – Forbes

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SpaceX’s Crew Dragon is just going to get busier shuttling astronauts in the coming years.

NASA announced it intends to issue a sole-source modification to SpaceX’s long-term contract to send astronauts to the International Space Station. This follows an agency call for proposals back in October for more flight options to send people to space.

Boeing’s Starliner spacecraft, which is the other major system, is not quite yet ready for humans following a difficult uncrewed test flight in 2019 that never saw the spacecraft reach the ISS. Starliner has spent some time fixing computer glitches and other issues (including a valve problem that delayed an expected 2021 launch) and is now expecting a second uncrewed test flight by 2022.

The October solicitation, NASA noted, confirms SpaceX is the only viable choice for the time being, given the agency’s safety requirements and the need to keep the space station staffed continuously in the coming years.

“It’s critical we begin to secure additional flights to the space station now so we are ready as these missions are needed to maintain a U.S. presence on station,” Kathy Lueders, associate administrator of NASA’s space 0perations mission directorate, said in a blog post. “Our U.S. human launch capability is essential to our continued safe operations in orbit and to building our low-Earth orbit economy.”

NASA stated it would use these new flights “as early as 2023”, and that the contract (in securing flights and allowing the agency to task personnel elsewhere) will help them get Boeing’s Starliner system ready to fly astronauts once it’s been certified.

“NASA and Boeing will provide additional updates on the status of Starliner’s next mission as we work through the investigation and verification efforts to determine root cause and effective vehicle remediation,” said Phil McAlister, director of commercial spaceflight at NASA, in the same statement.

The latest issue holding up the flight was an oxidizer isolation valve that was found in August, and NASA and Boeing together elected to pull the spacecraft back to the hanger to figure out how to fix the issue before sending the spacecraft aloft.

Another pressing issue for NASA’s future will be extending the planned retirement of the ISS from 2024 to at least 2028, which the agency has said for years it wants to do. It is in negotiations with Congress and with its international partners to do this, and in the meantime, last week the agency also announced it has secured three early-stage contracts for future private space stations to fly late in the 2020s.

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See what food challenges astronauts face in space – CGTN America

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For the first time ever, NASA and the Canadian Space Agency hosted the Deep Space Food Challenge. 

The competition brought universities and companies together to propose solutions on how to feed astronauts on a long mission. Last month, NASA announced that the winners and one of the international winners of the Phase 1 competition came from a group of students in a university in South America. 

CGTN’s Michelle Begue reports Colombia.

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