UPDATE 19. February 2021: The eccentric scientist behind the ‘gold standard’ COVID-19 test

UPDATE 10. February 2021: Breaking through the unknowns of the human reference genome

UPDATE 20 November 2020: Experts claim they identified human genes that can protect against Covid-19

UPDATE 01. Decmber 2017: New Sequencing Technique Improves Accuracy In Human DNA Analysis

UPDATE 30. November 2017: Artificial life breakthrough after scientists create new living organism using synthetic DNA

UPDATE 02. May 2017: Firestorm brewing as scientists work to create synthetic human DNA

UPDATE 22. February 2017: MATRIX, DOLLY THE SHEEP AND BACTERIA OF THE FUTURE

UPDATE 20. September 2016: Scientists Urge Artificial Human Genome

UPDATE 20. July 2016: The Gloves of Ethics are Off: A biotech startup is expanding the DNA alphabet in hopes of making novel drugs

ICYMI: First Live Organism with Synthetic Genome Created + The HUMAN GENOME PROJECT

Sixty trays can contain the entire human genome as 23,040 different fragments of cloned DNA.
Sixty trays can contain the entire human genome as 23,040 different fragments of cloned DNA. Credit James King-Holmes / Science Source

By Andrew Pollack - 13. May 2016

Scientists are now contemplating the fabrication of a human genome, meaning they would use chemicals to manufacture all the DNA contained in human chromosomes.

The prospect is spurring both intrigue and concern in the life sciences community because it might be possible, such as through cloning, to use a synthetic genome to create human beings without biological parents.

While the project is still in the idea phase, and also involves efforts to improve DNA synthesis in general, it was discussed at a closed-door meeting on Tuesday at Harvard Medical School in Boston. The nearly 150 attendees were told not to contact the news media or to post on Twitter during the meeting.

Organizers said the project could have a big scientific payoff and would be a follow-up to the original Human Genome Project, which was aimed at reading the sequence of the three billion chemical letters in the DNA blueprint of human life. The new project, by contrast, would involve not reading, but rather writing the human genome — synthesizing all three billion units from chemicals.

Dr. Endy, though invited, said he deliberately did not attend the meeting at Harvard because it was not being opened to enough people and was not giving enough thought to the ethical implications of the work.

George Church, a professor of genetics at Harvard Medical School and an organizer of the proposed project, said there had been a misunderstanding. The project was not aimed at creating people, just cells, and would not be restricted to human genomes, he said. Rather it would aim to improve the ability to synthesize DNA in general, which could be applied to various animals, plants and microbes.

“They’re painting a picture which I don’t think represents the project,” Dr. Church said in an interview.

He said the meeting was closed to the news media, and people were asked not to tweet because the project organizers, in an attempt to be transparent, had submitted a paper to a scientific journal. They were therefore not supposed to discuss the idea publicly before publication. He and other organizers said ethical aspects have been amply discussed since the beginning.

The project was initially called HGP2: The Human Genome Synthesis Project, with HGP referring to the Human Genome Project. An invitation to the meeting at Harvard said that the primary goal “would be to synthesize a complete human genome in a cell line within a period of 10 years.”

George Church, one of the organizers of the proposed project, at his lab at Harvard Medical School in 2013.

George Church, one of the organizers of the proposed project, at his lab at Harvard Medical School in 2013. Credit Jessica Rinaldi / Reuters

But by the time the meeting was held, the name had been changed to “HGP-Write: Testing Large Synthetic Genomes in Cells.”

The project does not yet have funding, Dr. Church said, though various companies and foundations would be invited to contribute, and some have indicated interest. The federal government will also be asked. A spokeswoman for the National Institutes of Health declined to comment, saying the project was in too early a stage.

Besides Dr. Church, the organizers include Jef Boeke, director of the institute for systems genetics at NYU Langone Medical Center, and Andrew Hessel, a self-described futurist who works at the Bay Area software company Autodesk and who first proposed such a project in 2012.

Scientists and companies can now change the DNA in cells, for example, by adding foreign genes or changing the letters in the existing genes. This technique is routinely used to make drugs, such as insulin for diabetes, inside genetically modified cells, as well as to make genetically modified crops. And scientists are now debating the ethics of new technology that might allow genetic changes to be made in embryos.

For instance, companies are now using organisms like yeast to make complex chemicals, like flavorings and fragrances. That requires adding not just one gene to the yeast, like to make insulin, but numerous genes in order to create an entire chemical production process within the cell. With that much tinkering needed, it can be easier to synthesize the DNA from scratch.

Right now, synthesizing DNA is difficult and error-prone. Existing techniques can reliably make strands that are only about 200 base pairs long, with the base pairs being the chemical units in DNA. A single gene can be hundreds or thousands of base pairs long. To synthesize one of those, multiple 200-unit segments have to be spliced together.

But the cost and capabilities are rapidly improving. Dr. Endy of Stanford, who is a co-founder of a DNA synthesis company called Gen9, said the cost of synthesizing genes has plummeted from $4 per base pair in 2003 to 3 cents now. But even at that rate, the cost for three billion letters would be $90 million. He said if costs continued to decline at the same pace, that figure could reach $100,000 in 20 years.

J. Craig Venter, the genetic scientist, synthesized a bacterial genome consisting of about a million base pairs. The synthetic genome was inserted into a cell and took control of that cell. While his first synthetic genome was mainly a copy of an existing genome, Dr. Venter and colleagues this year synthesized a more original bacterial genome, about 500,000 base pairs long.

Dr. Boeke is leading an international consortium that is synthesizing the genome of yeast, which consists of about 12 million base pairs. The scientists are making changes, such as deleting stretches of DNA that do not have any function, in an attempt to make a more streamlined and stable genome.

But the human genome is more than 200 times as large as that of yeast and it is not clear if such a synthesis would be feasible.

“Our ability to understand what to build is so far behind what we can build,” said Dr. Minshull, who was invited to the meeting at Harvard but did not attend. “I just don’t think that being able to make more and more and more and cheaper and cheaper and cheaper is going to get us the understanding we need.”

A version of this article appears in print on May 14, 2016, Section A, Page 11 of the New York edition with the headline: Private Talks Are Conducted About a Synthetic Genome.

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Scientists today are trying to play Annunaki against all ethics.

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UPDATES:

 

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The eccentric scientist behind the ‘gold standard’ COVID-19 test

Bombastic biochemist Kary Mullis invented PCR, a tool that redefined genetic science, while driving in 1983. That was only the beginning.

BY FEDOR KOSSAKOVSKI - 19. February 2021

Biochemist Kary Mullis says he was driving from the Bay Area to his cabin in Mendocino in 1983 when suddenly, like a bolt of lightning out of the California sky, he came up with a way to pinpoint a particular stretch of DNA and synthesize an enormous amount of copies.

“The simple technique would make as many copies as I wanted of any DNA sequence I chose, and everybody on Earth who cared about DNA would want to use it,” Mullis recounts in his colorfully titled 1998 memoir Dancing Naked in the Mind Field. “It would spread into every biology lab in the world. I would be famous. I would get the Nobel Prize.”

Mullis did indeed win the 1993 Nobel Prize in chemistry for inventing polymerase chain reaction, or PCR. These three letters have recently shot into the public consciousness because PCR is the basis of the most common, gold standard tests for the SARS-CoV-2 coronavirus. But that’s only the latest game-changing use of PCR. Since its debut, it’s been applied to tasks ranging from helping decode the human genome to saving coral reefs.

“If you're doing any sort of DNA studies, PCR is just the thing you do,” says pioneering genomics researcher Eric Green. “It's almost like saying, How do you use electricity?”

Mullis, who died in August 2019, recounts the origins of PCR in his memoir as the story of a larger-than-life genius who goes it alone and single-handedly invents a tool that kickstarts a new age of biology. But while it’s true Mullis had the original “eureka!” moment, there’s a lot more to the real history of PCR, including the other scientists who helped shape it into a biological powerhouse—sometimes in spite of Mullis’s difficult temperament.

Beginnings of a chain reaction

Before PCR, studying DNA was tough. Lots of genetic information is packed into DNA molecules and isolating exactly the right small snippet to study was tricky. Even if a scientist could isolate a section of interest, the amount of material was often so minuscule that there just wasn’t much available for experiments.

To get around this, the state-of-the-art in the 1980s was DNA cloning. In this process, scientists put their desired genetic sequence into the genomes of bacteria, which then divided and replicated both themselves and the introduced genetic code. It’s a powerful but laborious process, which is why something simpler and faster would be such a windfall.

After that fateful weekend in his cabin, Mullis returned to work at Cetus Corporation in Emeryville, California. Cetus was one of the first biotechnology companies in the world, and the culture at the time was closer to what you might find today at a tech startup in Silicon Valley. There, various teams were playing with exciting new tools to clone genes and express proteins that could be used for medical applications.

It was “an unusual group of young scientists, and they tolerated Kary,” says Paul Rabinow, an anthropologist at the University of California, Berkeley, and author of Making PCR: A Story of Biotechnology.

In Rabinow’s telling, Mullis brought the PCR idea to his colleagues. The process was elegant and simple: Heat a DNA molecule to separate the double helix into two strands, and use each strand as a template for making a copy—much like how DNA unspools and copies itself inside our cells. Then you let the sample cool; this would normally cause the two DNA strands to click back into place, but you can hijack the process with lots of short stretches of DNA called primers—just the type of genetic fragments Mullis was working with for other projects.

Easily synthesized in a lab, these primers are designed to click on next to the targeted section of DNA and prevent the two original strands from coming back together. The places on the DNA strands where the primers attach then serve as landing pads for an enzyme called DNA polymerase. It marches down the exposed strand, snapping DNA building blocks known as nucleotides into the correct positions to reconstruct the complementary strands.

If you start with just one piece of DNA, you’ll have two copies of your target sequence after one PCR cycle. Each copy can again be unwound to make more templates. After just 30 cycles, you’ll have over a billion copies—all from one molecule of DNA.

Mullis was known for his eccentric ideas, many of which had basic biology mistakes according to his colleagues, so people initially either didn’t think it would work or didn’t care. But Mullis kept tinkering with the idea, and the following year he was able to bring them some experimental data that seemed to show the chain reaction was working. This caught the attention of several Cetus colleagues, especially biochemist Thomas White.

“I thought, Hmm, it could be bullshit, but he might actually be right,” White says. “And if he is right, it'll transform what we're trying to do here.”

Making PCR work

White had had a soft spot for Mullis ever since they’d became close friends in graduate school at UC Berkeley. Mullis helped White rebuild his car engine and ordained White as a Universal Life minister. White returned the favor by presiding over Mullis’s wedding to his second wife. White had recruited Mullis to work at Cetus and ended up being his boss, helping diffuse tensions when Mullis’s ego would grate on coworkers. 

White asked Mullis to focus exclusively on getting PCR to work. By the end of 1984, White and other company leaders still didn’t think he had enough evidence, so the company kept adding experimental scientists to parallel his efforts. The skilled work of many colleagues—in particular Stephen Scharf, Fred Faloona, and Randall Saiki—finally yielded enough replicable data to declare PCR a success.

With the proof-of-concept demonstrated, getting a publication and, eventually, a patent became top priority. But Mullis kept putting off writing the paper. People had doubted him, White says, and procrastinating on the paper was his revenge. Frustrated by the wait, Saiki co-authored a 1985 paper in the journal Science about a test for sickle cell anemia that included the first published description of PCR. However, that paper only hinted at its power as a standalone technique.

White pleaded with Mullis to finish his paper explaining PCR in detail, and Mullis eventually did and submitted it to Nature. It was rejected. Sciencepassed on it as well. It ended up being published in 1987 in Methods in Enzymology.

By then, Mullis had left Cetus, aggrieved chiefly by the fact he wasn't the first author on the more prestigious Science paper. In parting, Cetus paid Mullis a few months’ salary and a $10,000 bonus, the largest the company had ever doled out to a scientist for an invention. Cetus retained the rights to the technology, and from then on out, Mullis’s contribution to the development of PCR was mostly popularizing it—and himself—at invited speaking and consulting gigs.

In his lifetime, Mullis also denied that HIV causes AIDS, questioned human influence on climate change, gave talks featuring images of nude women, and made sexist remarks to journalists. White still reminisces about his unquestionable creativity, sharp wit, and good humor—but laments how the myth took over the man. “Mullis rejected all of his former friends and colleagues and just disparaged us,” he says. “The Nobel Prize went to his head.”

Unlocking PCR’s potential

Even before Mullis left, other Cetus team members were working to make PCR truly lab-ready. Two problems still made the process clunky to perform. For starters, the heat necessary to perform a cycle was degrading that all-important DNA polymerase, the piece required to construct each DNA copy.

Before leaving, Mullis had proposed a solution: Use a polymerase from the microbes discovered in the boiling-hot pools of Yellowstone National Park. The thinking was that if these organisms can live and replicate at high temperatures, their DNA polymerases must be able to tolerate such extremes. So David Gelfand, another Cetus scientist, flew out to Wisconsin to meet microbiologist Thomas Brock. In the late 1960s, Brock had isolated a species of heat-loving bacteria named Thermus aquaticus from Yellowstone’s thermal pools. That species’ unique DNA polymerase ended up being exactly what was needed.

Meanwhile, Shirley Kwok, a scientist at Cetus, was applying PCR to study HIV but was getting annoyed with the process. Cycling the sample through different temperature regimes by hand was mind-numbingly tedious, and in her case, the work had to be done in a biocontainment facility wearing full personal protective equipment. That’s when a technician named Robert Watson modified a small in-house pipetting robot to manage the thermal cycling. Today, automated thermal cyclers based on the idea are standard in genetics laboratories around the world.

By the late 1980s, PCR was making waves in the scientific community, and in 1991, Cetus sold the PCR rights to what is now the healthcare giant Roche for $300 million. White ended up running the PCR division there, along with over a hundred Cetus scientists he took with him.

Since then, PCR usage has multiplied exponentially, with numerous adaptations for various applications. Medical diagnosis, forensics, food safety, crop development, even the search for the origin of humanity—the boundaries of all these fields and more were busted wide open with the power of PCR.

The chain reaction continues

Genomics researcher Eric Green was finishing up an M.D.-Ph.D. at Washington University in St. Louis in the late 1980s when he first heard of PCR technology. A few years later, he figured out how to use PCR to map the human genome. He was soon tapped to do just that as part of the government-backed Human Genome Project.

“There is just no way the Human Genome Project could have been successful without PCR,” says Green, who is now the head of the National Human Genome Research Institute.

And of course, many of the COVID-19 tests being conducted today use PCR to amplify bits of the genetic code of the SARS-CoV-2 virus from swabbed samples, allowing the tests to detect its presence.

A particularly exciting path forward is simplifying the hardware so PCR can be used outside a laboratory. “These machines, really all they do is heat and cool a sample,” says geneticist and self-professed tinkerer Ezequiel Alvarez Saavedra. “So I figured people don't need to pay three [thousand], five thousand dollars or even more to get this.”

Together with neuroscientist Sebastian Kraves, Alvarez Saavedra started a company called miniPCR bio to create something simpler and cheaper. The key innovation, Alvarez Saavedra says, was switching the heating element from thermoelectric semiconductors to copper wires, similar to the lines that defrost a car windshield. This made the whole construction simpler and more energy efficient. Now you can order a PCR machine housed in a transparent container the size of a tissue box for less than a thousand bucks.

Alvarez Saavedra says that many of his customers are educators wanting to showcase the beauty of biology to students. PCR is “very simple, once someone shows it to you,” he says. “That’s the beauty—it’s very easy to understand.”

Amy Apprill, a marine microbial ecologist at the Woods Hole Oceanographic Institution, spends a lot of time in the U.S. Virgin Islands studying stony coral tissue loss disease, which leaves behind skeletons that look like bleached coral reefs. This devastating disease was first identified off the coast of Miami in 2014 and has since spread rapidly into the Caribbean. The cause has not been identified, but it could be some kind of bacteria.

“Because we’re looking at bacteria, which make up a really small component by biomass, we really need to rely on PCR,” Apprill says. PCR makes abundance out of scarcity, and scaling down the machine lets Apprill study her microbial harvest at a nearby AirBnB.

“It makes it all portable, and for us that's key,” Apprill says. “You just can’t afford to fly your whole lab to all your different field projects.”

And in 2015, miniPCR bio partnered with Boeing to organize a competitionthat would allow students to perform a DNA experiment in space using the miniaturized PCR machine. Anna-Sophia Boguraev, who was in high school at the time, entered a proposal and won, setting up the first PCR run in space as a proof of concept for future research.

“Since then, it's been used hundreds of times,” says Boguraev, who is currently in the Harvard/MIT M.D.-Ph.D. program. “The age of molecular biology in space has only accelerated.”

Today it’s clear that, despite their contentious relationships, Mullis and his colleagues made an amazing contribution to science—one that will likely inspire generations of researchers for decades to come.

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Breaking through the unknowns of the human reference genome

Since the human genome was published in 2001, many of the gaps in the original sequence have been filled in, offering a more detailed understanding of genome regulation, structure and function.

 PDF version

The release of drafts of the human genome in 2001 was a landmark achievement1,2. Scientists could, for the first time, study long stretches of each human chromosome, base by base. As such, researchers could begin to understand how individual genes were ordered, and how the surrounding non-protein-coding DNA was structured and organized. Despite this amazing progress, the draft genomes were still incomplete, with more than 150 million bases missing3. Technological advances in the intervening years have allowed researchers to add to the draft, with the complete sequencing of a chromosome finally being achieved4,5 in 2020. As a result, new and uncharacterized parts of the human genome are beginning to surface, ushering in another exciting period of biological discovery.

What exactly was included in the draft genomes? The original draft contained many previously unexplored intergenic regions. It also encompassed the vast majority of genes. The International Human Genome Sequencing Consortium1 initially estimated that the genome contained 30,000–40,000 protein-coding genes, although the publication of an updated genome6 in 2004, along with improved gene-prediction approaches7, led the figure to be revised to about 20,000. The 2004 genome gave a high-resolution map of 2.85 billion nucleotides from euchromatin — the more loosely packaged regions of DNA, which are enriched in genes and make up roughly 92% of the human genome.

The reference genome launched the scientific community into an era of genome exploration, shifting the focus from single genes to more-complete, genome-wide studies. However, gaps remained on each of the 23 pairs of human chromosomes, estimated to contain more than 150 megabases of unknown sequence3 (Fig. 1). The largest gaps were at locations enriched with highly repetitive DNA or sequences for which there are many near-identical copies. These sections were originally difficult to clone, sequence and correctly assemble. As a result, the human genome project intentionally under-represented these repetitive sequences. Although researchers had a very basic idea of the nature of sequences in these regions, the regions’ high-resolution genomic organization remained elusive.

Figure 1

Figure 1 | Filling in the missing sequence in the human genome.a, The 2001 draft human genome1,2covered most of the gene-rich DNA, which is loosely packaged in the nucleus. But many gaps remained in tightly packaged regions rich in repetitive DNA sequences, which are often untranscribed (the overall extent of the gaps is exaggerated here, for ease of interpretation). b, Thanks to advances in sequencing and bioinformatics, researchers can now study all of these missing sequences. These include the telomere and subtelomere regions that cap chromosomes; centromere structures that are essential for cell division; and particularly short and highly repetitive chromosome arms known as acrocentric arms. Regions in which DNA is duplicated, either in one location or in a segmented way, can also now be analysed.

Early attempts to close the gaps used long sequence reads to span the repetitive sequences — but such reads were initially highly error-prone. In the 2010s, new opportunities arose, thanks to advances in the ability to read longer stretches of sequence (outlined in refs. 8 and 9, for instance), along with the development of scalable bioinformatic tools. Sequence reads of tens to hundreds of kilobases allowed the study of the genomic organization of many moderately sized gaps. This provided insights into some subtelomeric regions9 — repeat-rich DNA adjacent to the telomere structures that cap the ends of chromosomes. It also enabled the study of the first centromeric satellite array10, in which short sequences are repeated in tandem for about 300 kilobases. A subset of segmental duplications (stretches of sequence that share 90–100% of their bases and are found in multiple locations) was also resolved, many containing genes previously missing from the reference genome9,11. However, many of the largest, multi-megabase-sized repeat-rich regions remained intractable.

Over the past few years, the combination of both ultra-long reads9 and highly accurate long-read data12 has proved a game-changer for resolving these regions13,14, revealing, for the first time, extremely long tracts of tandem repeats and regions enriched in segmental duplications. By breaking down these technological barriers, scientists are now discovering extensive repeat-rich regions that can span millions of bases, and make up the entire short arms of chromosomes.

Researchers do not yet fully understand why parts of the human genome are organized in this way. But gaining such an understanding will undoubtedly be valuable, because these repeat-rich sequences are often positioned at sites that are crucial for life. For example, long tracts of ribosomal DNA (rDNA) repeats encode RNA components of the cell’s protein-synthesizing machinery and have an important role in nuclear organization15. And the repetitive DNA of structures called centromeres is essential for proper chromosome segregation during cell division16.

These large swathes of repetitive DNA come with different sets of rules, in terms of their genomic organization and evolution. They are also subject to different epigenetic regulation (molecular modifications to DNA and associated proteins that do not alter the underlying DNA sequence), which leads repetitive DNA to differ from euchromatin in terms of its organization, replication timing and transcriptional activity1719. Many genome-wide tools and data sets cannot yet fully capture all this information from extremely repetitive DNA regions, and so scientists do not yet have a complete picture of what transcription factors bind to them, how these regions are spatially organized in the nucleus, or how regulation of these parts of our genome changes during development and in disease states. Now, much like the initial release of the genome decades ago, researchers are faced with a new, unexplored functional landscape in the human genome. Access to this information will drive technology and innovation to be inclusive of these repeat regions, once again broadening our understanding of genome biology.

 

In the past year, scientists have used extremely long and highly accurate sequence reads to reconstruct entire human chromosomes from telomere to telomere4,5. Last year also saw the release of a near-complete human reference genome from an effectively ‘haploid’ human cell line, with only five remaining gaps that mark the sites of rDNA arrays (go.nature.com/3rgz93y). In this line, cells have two identical pairs of chromosomes, simplifying the challenge of repeat assembly compared with typical human cells (which are diploid, with different chromosomes inherited from the mother and father). These maps together offer the first high-resolution glimpse of centromeric regions, segmental duplications, subtelomeric repeats and each of the five acrocentric chromosomes, which have very short arms made up almost entirely of highly repetitive DNA at one end.

It is tempting to think scientists are finally approaching the finish line. However, a single genome assembly, even if complete with near-perfect sequence accuracy, is an insufficient reference from which to study the sequence variation that exists across the human population. Existing maps that chart the diversity across the euchromatic parts of the genome must be extended to fully capture repetitive regions, where copy number and repeat organization vary between individuals. Doing so will require the development of strategies for routine production and analysis of complete human diploid genomes. The aspirational goal of reaching a more-complete and comprehensive reference of humanity will undoubtedly improve our understanding of genome structure and its role in human disease, and align with the promise and legacy of the Human Genome Project.

Nature 590, 217-218 (2021)

doi: https://doi.org/10.1038/d41586-021-00293-8

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Download references

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Experts claim they identified human genes that can protect against Covid-19

By Lori Ioannou - 20. November 2020

  • A team of scientists at the New York Genome Center, New York University and Icahn School of Medicine at Mount Sinai say they have identified the genes that can protect human cells against Covid-19.
  • Leading virologist at Mount Sinai, Dr. Benjamin tenOever, developed a series of human lung cell models for coronavirus screening to better understand immune responses to the disease and co-authored the study.
  • The goal was two-fold: to identify the genes that make human cells more resistant to SARS-CoV-2 virus; and test existing drugs on the market that may help stop the spread of the disease.

A team of scientists say they have identified the genes that can protect human cells against Covid-19. The scientists from the New York Genome Center, New York University and Icahn School of Medicine at Mount Sinai used CRISPR, a technology that allows them to alter DNA sequences, to make their discoveries.

The discovery comes after an eight-month screen of all 20,000 genes in the human genome led by Dr. Neville Sanjana at the New York Genome Center. Leading virologist at Mount Sinai, Dr. Benjamin tenOever, developed a series of human lung cell models for the coronavirus screening to better understand immune responses to the disease and co-authored the study.

Their study, published online last month by Cellwill appear in the scientific peer-reviewed journal's Jan. 7 print issue.

The goal was two-fold: to identify the genes that make human cells more resistant to SARS-CoV-2 virus; and test existing drugs on the market that may help stop the spread of the disease.

The breakthrough comes at a time when drug makers such as Pfizer, Oxford-AstraZeneca and Moderna are fast-forwarding vaccine and therapeutics to treat Covid-19. On Friday, Pfizer and BioNTech requested emergency authorization from the FDA for their Covid vaccine that contains genetic material called messenger RNA, which scientists expect provokes the immune system to fight the virus.

According to a press release from NYU and the New York Genome Center, the team employed a broad range of scientific techniques to analyze genetic dependencies between viruses and their human hosts.

After intensive research, the scientists and doctors claim they have found 30 genes that block the virus from infecting human cells including RAB7A, a gene that seems to regulate the ACE-2 receptorthat the virus binds to and uses to enter the cell. The spike protein's first contact with a human cell is through ACE-2 receptor.

"Our findings confirmed what scientists believe to be true about ACE-2 receptor's role in infection; it holds the key to unlocking the virus," said tenOever. "It also revealed the virus needs a toolbox of components to infect human cells. Everything must be in alignment for the virus to enter human cells."

The team researchers discovered that the genes most likely to be responsible for aiding the virus' ability to replicate were clustered in several specific protein groups that are involved in moving proteins to and from cell membranes.

Cholesterol and the virus

The research team also identified drugs that are currently on the market for different diseases that they claim block the entry of Covid-19 into human cells by increasing cellular cholesterol. In particular, they found three drugs currently on the market were more than 100-fold more effective in stopping viral entry in human lung cells:

  • Amlodipine, brand name Norvasc, by Pfizer, to treat high blood pressure and angina.
  • Tamoxifen, brand name Soltamox by Fortovia Therapeutics, an estrogen modulator, to treat breast cancer.
  • Ilomastat, brand name Galardin, it's a matrix metalloprotease inhibitor, that now being manufactured by many companies; a chemotherapy agent, with applications for skincare and anti-aging products.

The other five drugs that were tested — called PIK-111, Compound 19, SAR 405, Autophinib, ALLN --  are used in research but are not yet branded and used in clinical trials for existing diseases.

Overall, the findings offer insight into novel therapies that may be effective in treating Covid-19 and reveal the underlying molecular targets of those therapies.

The bioengineers in New York were working on other projects with gene-editing technology from CRISPR but quickly pivoted to studying the coronavirus when it swept through the metropolitan area last March. "Seeing the tragic impact of Covid-19 here in New York and across the world, we felt that we could use the high-throughput CRISPR gene editing tools that we have applied to other diseases to understand what are the key human genes required by the SARS-CoV-2 virus," said Sanjana in the press release.

a person standing in front of a computer: Dr. Neville Sanjana and his team at the New York Genome Center used CRISPR to identify the genes that can protect human cells against Covid-19.

Dr. Neville Sanjana and his team at the New York Genome Center used CRISPR to identify the genes that can protect human cells against Covid-19. © Provided by CNBC

As he explained further to CNBC, "current treatments for SARS-CoV-2 infection currently go after the virus itself, but this study offers a better understanding of how host genes influence viral entry and will enable new avenues for therapeutic discovery."

Previously, Sanjana has used the CRISPR technology screens to identify a wide array of diseases, from muscular dystrophy to several types of cancer.

"The hope is that the data from this study— which pinpoints required genes for SARS-CoV-2 infection — could in the future work be combined with human genome sequencing data to identify individuals that might be either more susceptible or more resistant to Covid-19," Sanjana said.

The New York team is not the first to use CRISPR gene editing techniques to fight Covid-19. Other bioengineering groups at MIT and Stanford have been using CRISPR to develop ways to fight the SARS-CoV-2 and develop diagnostic tools for Covid-19.

The potential for using CRISPR to eliminate viruses has already generated some enthusiasm in the research community. Last year, for example, Excision BioTherapeutics licensed a technology from Temple University that uses CRISPR, combined with antiretroviral therapy, to eliminate HIV, the virus that causes AIDS. 

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New Sequencing Technique Improves Accuracy In Human DNA Analysis

By Deirdre O’Donnell - 01. December 2017

Conventional DNA sequencing is getting more powerful and time-effective. However, it is still based on amplification, which involves using a DNA polymerase such as Taq to produce numerous copies of the sequence to be analysed. The problem with amplification is that it can increase the risk of false-positive results in terms of pertinent mutations.

New Sequencing Technique Improves Accuracy in Human DNA Analysis

Other methods, such as short-sequence high-throughput screening, are also very accurate, but are not applicable to scans of larger portions of DNA, such as haplotyping. A new sequencing technique, developed at UCSD, can sequence strands that encompass haplotypes with greater accuracy than PCR, according to the team behind it.

Haplotype analysis

Modern-day DNA sequencing methods, such as those based on the polymerase chain reaction (PCR) are accurate enough to detect single-nucleotide polymorphisms (SNPs), which are among the finest variations the human genome can present. However, they can be associated with ‘false calls’, which are erroneous SNP detections that can considerably exaggerate the actual risk of a somatic mutation.

‘False calls’ can occur in relatively high numbers (e.g. in five figures) per sequencing analysis. In addition, clinical medicine also benefits from the study of genetic features at the larger scale. These include haplotypes, which are varying numbers of alleles often closely related by chromosomal location and the functions of the proteins they express. For example, the HLA haplotype, which spans about five thousand base-pairs on chromosome 6, codes for important immune-system proteins and plays a role in organ donor compatibility. Haplotype analysis may require whole-genome sequencing (WGS), in which all chromosomal DNA in a cell is amplified and scanned for anomalies. However, this increases the risk of false calls.

Therefore, a team from the Departments of Bioengineering, Computer Science & Engineering, Electrical & Computer Engineering and Paediatrics at the University of California (San Diego) proposed a new DNA sequencing system, involving the use of a microfluidic processor. This device has multiple compartments, one of which isolates a single cell for DNA extraction. Other chambers extract the genome from the cell, and separate the twin strands of DNA. One of these strands is then broken down into 24 fragments, each of which is sent into its own individual container. They are then amplified using the multiple deflection technique (or MDA).

New amplification technique

The team behind this new amplification technique call it SISSOR, or single-stranded sequencing using microfluidic reactors. They claim that it results in a considerably reduced error rate (of about 1x10-8compared to about 1x10-5 following conventional MDA) due to a number of factors and optimisations. These include the reduced risk of DNA contamination and the fine-tuning of the steps involved in DNA purification and amplification. Examples of these were fine-tuning the concentrations of alkaline solution and temperatures in the strand-separation chamber; optimising the MDA process with the high-accuracy Phi-29 polymerase, and longer primers (short strands of custom-generated DNA that start the amplification process).

The team tested the SISSOR method on the well-known PGP1 human cell line. They isolated three single cells, amplified them as described, and then converted the resulting 24 fragments for each cell into barcoded sequence-data libraries, which were then converted into full DNA sequences using the conventional Illumina method. These were mapped onto a human reference genome, which generated up to 98 percent homology in terms of mappable bases (or ‘reads’). The combined reads from all three cells resulted in 94.9 percent coverage of the reference genome. However, each individual cell generated approximately 63 percent coverage, indicating that certain fragments were lost in the course of each individual SISSOR process.

The human DNA

The human DNA (CC BY-SA 4.0)

The team analysed the PGP1 genome by reconstructing the fragments into a whole genome in the analysis stage, using the Hidden Markov model (HMM). This resulted in the consistent detection of fragment boundaries, which in turn allowed the team to detect one or more alleles in a haplotype with high accuracy. The team were able to assemble haplotypes at a rate of about 500 kilobases at a time, which is a length of about tenfold compared to those achieved using conventional assembly methods. The team’s analysis method improved the chances that each allele is only ‘called’ once, regardless of how many separate chambers across multiple cells it is found in. On the other hand, variations within these same alleles could be called with greater confidence than variations within an allele analysed using conventional sequencing processes.

The SISSOR technique may produce multiple copies of the same allele (especially if a number of cells are used, as in this study) to compare for each variation detected. In other words, if the variation is found in all copies of the same allele from three identical cells, this improves the real picture of its statistical power and significance. The team developed an algorithm for variant-calling that reflected this and also corrected for potential errors such as those caused by MDA. The allele sequences were assembled into those for full haplotypes using the popular algorithm for this purpose, HapCUT2, which generated contiguous haplotype sequences of an average of 7 megabases (Mb) in length (compared to about 3Mb for pre-existing PGP1 haplotypes). In all, the team detected 1.2 million SNPs in their genome, which were found to have a 99.3 percent rate of agreement across all fragments. This compares well with those associated with pre-existing PGP1 sequencing data.

SISSOR, as described in an advance publication of the journal PNAS, is a novel sequencing technique that takes a strand of chromosomal DNA and breaks it down into 24 relatively large fragments, which are then amplified separately using an optimised microfluidic processor for high-fidelity sequencing using conventional techniques. This allows for the re-assembly of this data into ultra-long haplotype sequences that possess highly accurate information on the location of SNPs and how likely they are to cause a dangerous mutation in living cells. Therefore, the SISSOR method need not rely on existing sequencing libraries of the haplotype or genome to be analysed, but instead has the option of comparing multiple copies of the same allele from a small number of donor cells. The team of UCSD researchers behind this new sequencing technique believe it may have a role in applications such as IVF, in which the cells available for testing are severely limited.

Top image: Human DNA Analysis. (Public Domain)

References:

Chu WK, Edge P, Lee HS, Bansal V, Bafna V, Huang X, et al. Ultraaccurate genome sequencing and haplotyping of single human cells. Proceedings of the National Academy of Sciences. 2017. Available at: https://www.pnas.org/content/early/2017/10/23/1707609114.full.pdf

Ramsey D. UC San Diego Scientists Create Device for Ultra-Accurate Genome Sequencing of Single Human Cells. UCSD News Center. 2017. Available at: https://ucsdnews.ucsd.edu/pressrelease/uc_san_diego_scientists_create_device_for_ultra_accurate_genome_sequencing

Author:

Deirdre's picture

DEIRDRE O’DONNELL received her MSc. from the National University of Ireland, Galway in 2007. She has been a professional writer for several years. Deirdre is also an experienced journalist and editor with particular expertise in writing on many areas of medical science. She is also interested in the latest technology, gadgets and innovations.

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Artificial life breakthrough after scientists create new living organism using synthetic DNA

The organism can store and retrieve man-made genetic information

By Julie Steenhuysen - 30. November 2017
The researches say the step forward shows that synthetic organisms can reinvent the most basic facets of life

The researches say the step forward shows that synthetic organisms can reinvent the most basic facets of life (DANIEL LEAL-OLIVAS/AFP/Getty Images)

In a major step toward creating artificial life, US researchers have developed a living organism that incorporates both natural and artificial DNA and is capable of creating entirely new, synthetic proteins.

The work, published in the journal Nature, brings scientists closer to the development of designer proteins made to order in a laboratory.

Previous work by Floyd Romesberg, a chemical biologist at the Scripps Research Institute in La Jolla, California, showed that it was possible to expand the genetic alphabet of natural DNA beyond its current four letters: adenine(A), cytosine(C), guanine (G) and thymine(T).

In 2014, Romesberg and colleagues created a strain of E. coli bacteria that contained two unnatural letters, X and Y.

In the latest work, Romesberg’s team has shown that this partially synthetic form of E. coli can take instructions from this hybrid genetic alphabet to make new proteins.

“This is the first time ever a cell has translated a protein using something other than G, C, A or T,” Romesberg said.

Although the actual changes to the organism were small, the feat is significant, he said in a telephone interview. “It’s the first change to life ever made.”

It’s a goal Romesberg has been working toward for the past 20 years. Creating new forms of life, however, is not the main point. Romesberg is interested in using this expanded genetic alphabet to create new types of proteins that can be used to treat disease.

In 2014, he formed a company called Synthorx Inc, which is working on developing new protein-based treatments.

“A lot of proteins that you want to use as drugs get cleared in the kidney very quickly,” Romesberg said. The new system would allow scientists to attach fat molecules to drugs to keep them in the body longer.

Romesberg is aware that the creation of semi-synthetic organisms might raise concerns of hybrid life forms spreading beyond the lab, but the system they used makes such an escape unlikely.

For example, in natural DNA, base pairs are attracted to each other through the bonding of hydrogen atoms. Romesberg’s X and Y bases are attracted through an entirely different process, which prevents them from accidentally bonding with natural bases.

And because cells cannot make their own X and Y without the addition of certain chemicals, the semi-synthetic organisms cannot live outside of a laboratory. [N.B.: ... this statement is disputed !!!]

“They can’t escape,” Romesberg said. “There’s no ‘Jurassic Park’ scenario.”

Read more

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Firestorm brewing as scientists work to create synthetic human DNA

By Alex Ossola - 02. May 2017

See the source imageKEY POINTS

  • The Human Genome Project (HGP) took 13 years and $3 billion to complete.
  • Scientists planning to synthesize human DNA think it is as little as 5 years away.
  • They are seeking $100 million, and believe it will in total cost less than HGP.
  • Their aim is to get the cost of making a DNA base pair down to one cent.

As synthetic DNA is being researched, ethical questions are coming to surface

Last May a seemingly commonplace meeting kicked off a firestorm of controversy. More than 100 experts in genetics and bioengineering convened at Harvard Medical School for a meeting that was closed to the public — attendees were asked not to contact news media or to post about the meeting on social media.

The same group is getting back together in New York City next week.

To the meeting organizers, last year’s secretive measures were, counterintuitively, to make sure as many people heard about the project as possible. They were submitting a paper about the project to a scientific journal and were discouraged from sharing the information publicly before it was published.

But there’s another reason why this group of scientists, while encouraging debate and public involvement, would be wary of attracting too much attention. Their project is an effort to synthesize DNA, including human DNA. Researchers will start with simpler organisms, such as microbes and plants, but hope to ultimately create strands of human genetic code. One of the group’s organizers, Jef Boeke, director of the Institute for Systems Genetics at NYU School of Medicine, told CNBC that incorporating synthesized DNA into mammalian (or even human) cells could happen in four to five years.

This project follows in the footsteps of the Human Genome Project (HGP), the 13-year$2.7 billion project that enabled scientists to first decode the human genome. “HGP allowed us to read the genome, but we still don’t completely understand it,” said Nancy Kelley, the coordinator of the new effort, dubbed GP-write.

Harvard geneticist George Church poses for a portrait inside his lab at Harvard Medical School.

Harvard geneticist George Church poses for a portrait inside his lab at Harvard Medical School. Jessica Rinaldi | Reuters

High school biology covers the basic building blocks for DNA, called nucleotides — adenine (A), cytosine (C), guanine (G) and thymine (T). Humans’ 3 billion pairs provide the blueprints for how to build our cells. The intention of GP-write is to provide a better fundamental understanding of how these pieces work together. Using synthesized genomes has both pragmatic and theoretical implications — it could lead to lower cost and higher quality of DNA synthesis, discoveries about DNA assembly in cells and the ability to test many DNA variations.

“If you do that, you gain a much deeper understanding of how a complicated apparatus goes,” Boeke said. Boeke likens the genome to a bicycle — you can only fully understand something once you take it apart and put it back together. “Really, a synthetic genome is an engine for learning new information.”

Boeke is particularly excited about what he calls an “ultrasafe cell line.” Certain types of mammalian cells intended to produce certain types of large molecule drugs, called biologics.

″[Cell lines] have been cultured in dishes in labs for decades. But you can’t engineer the genomes — the tools for doing that are quite crude, relatively speaking,” Boeke said. Sometimes these cells get infected with a virus, and it completely shuts down drug production. A synthetic cell that lacked unnecessary genetic material could, evidence suggests, be virus-resistant, consistently producing useful drugs to treat disease.

The results of GP-write could also lead to stem cell therapy that doesn’t run the risk of infecting the patient with another disease, which appears to be what happened to one patient who received stem cell treatment in Mexico. Or they could create a line of microorganisms that could help humans generate some of their own amino acids — nutrients we usually get from food.

We have a four- to five-year period where there can be plenty of time for debate. ... Whenever it’s human, everyone has an opinion and wants their voice to be heard. We want to hear what people have to say.

Jef Boeke

GP-WRITE ORGANIZER AND DIRECTOR OF THE INSTITUTE FOR SYSTEMS GENETICS AT NYU SCHOOL OF MEDICINE

These outcomes, of course, won’t happen overnight. Boeke, who has spent years synthesizing yeast DNA, knows there will be plenty of technical hurdles. “Getting big pieces of DNA efficiently into mammalian cells, engineering them rapidly, these will be major challenges,” he said.

Scientists will also have to do that without breaking the bank. Right now, Kelley estimates that it costs 10 cents to synthesize every base pair, the bonded molecules that make up the double helix of DNA (start-up GenScript advertises even higher prices, at 23 cents for “economy”). Considering that humans have 3 billion base pairs. “If we can get that [cost] down to one cent per base pair, it would really make a difference,” Kelley said.

Since last May’s meeting, Kelley, Boeke and their collaborators have published an article in Science about the project, as well as a white paper outlining its timeline. Close to 200 researchers and collaborators around the world have expressed interest in participating, Kelley says, ranging from institutional researchers to corporate scientists. Preliminary experiments are already underway, and the project organizers are discussing the project with companies as well as federal and state agencies that might help them reach their goal of raising $100 million this year. They estimate GP-write should cost less, in total, than the $3 billion Human Genome Project, though they have not provided more specific cost projections.

It might not be so bad if these advances took some time. Afternews broke of the May meeting, some criticized the way the rollout was handled. “Given that human genome synthesis is a technology that can completely redefine the core of what now joins all of humanity together as a species, we argue that discussions of making such capacities real ... should not take place without open and advance consideration of whether it is morally right to proceed,” read one op-ed, published in Cosmos.

Boeke says a public and scientific discussion is exactly what the GP-write organizers intend to have. “I think articulation of our plan not to start right off synthesizing a full human genome tomorrow was helpful. We have a four- to five-year period where there can be plenty of time for debate about the wisdom of that, whether resources should be put in that direction or in another. Whenever it’s human, everyone has an opinion and wants their voice to be heard. We want to hear what people have to say,” Boeke said.

Up to 250 people are expected at the New York Genome Center meeting, which will include discuss of applications, ethics and logistics behind the GP-write project.

Author:

Alex Ossola, special to CNBC.com

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MATRIX, DOLLY THE SHEEP AND BACTERIA OF THE FUTURE

I make an effort to stay abreast of the latest developments in science, especially where biological research combines with information technology. Some ideas in particular prove to be quite an intellectual adventure.

By Norbert Biedrzycki - 22. February 2017

Norbert Biedrzycki Matrix Dolly bakteria

One field which has drawn my attention for quite a while now is synthetic biology. To this day I remember newspaper headlines a dozen plus years ago announcing the successful cloning of Dolly the Sheep. Those euphoric and promising statements intertwined with pure hysteria: “We have crossed a red line. We are well on our way to cloning humans!”, claimed some ethicists and journalists. As we know, no human has been cloned yet, and I don’t think one will be. (Although there is no telling what goes on in the secret laboratories of the most powerful armies).

Are we living in a Matrix?

The outrage that broke out at the time reminds me of a recent statement made by Bank of America. Its report contained a sensational hypothesis suggesting we may all be living in a Matrix similar to the one depicted in the famous movie by the Wachowski brothers. The degree of digitization we have achieved and the “virtual” nature of our reality make it conceivable that we too may be a “simulation” of a complex and incredibly developed computer program. I see an analogy between the two events separated by a dozen plus years. It concerns general ethical and philosophical questions. In our civilizational development, we have reached a point where “artificial worlds” – laboratory-produced living organisms and artificial intelligence – may play a critical role in all of our lives. What can we expect? To what end will we use the achievements of today’s science and information technologies? Are people under threat from artificial organisms and AI systems?

What is synthetic biology?

To go back to synthetic biology – what is it? In a nutshell, synthetic biology is a field of science concerned with developing artificial biological systems capable of processing information from the outside. Such information may then be used to produce chemical compounds or energy. Synthetic biology has the potential to program new DNA to build new forms of life, which may be engineered by means of gene sequencing and DNA synthesis. Such forms of life are designed and simulated using computers. Microorganisms and specifically bacteria created in this manner may be applied in a variety of fields. One of them is medicine.

Catastrophic visions

I would like to state my view on the popular opinion that such research may breed abuse. It is difficult to refute these sorts of statements. I realize that humans today already have the capacity to produce viruses that can harm people. I also know that it is possible to combine bacteria with electronic systems into single organisms, which appeals to the imagination of military engineers. I am aware of the Human Genome Project, which has mapped the entire human genome with a view to, as some claims go, creating human-like creatures. Personally, I compare these ominous musings to the arguments of people who at the time the Internet was first created (note that it was born in military laboratories) prophesied that the world wide web would be used primarily to spy on people. Just as today’s Internet can be used for terrorist attacks, so the potential of synthetic medicine may pose theoretical threats. Note one thing however: a number of safeguards are in place in research on genetically-modified bacteria. There is actually a “kill switch” designed to destroy any organisms that breach the perimeters of their designated environments.

And optimistic prospects

Recently, Kickstarter, a platform used to raise funds to finance visionary projects, featured an interesting proposal. Its authors were appealing for money to develop a technology that would make plants glow. This is only one example of the products of synthetic biology being commercialized. I expect a proliferation of initiatives that rely on synthetic biology within the next few years. Importantly, many of them are likely to come from academia. The prestigious Massachusetts Institute of Technology has for years held a contest for new ideas that utilize science.

The International Genetically Engineered Machine Competition attracts many young students with brilliant ideas. For instance, in 2013 students from Poland submitted the FluoSafe project for enhancing bacteria with a protein that glows in the presence of carcinogenic acrylamide, which is present in e.g. chips and fried meat. Acrylamide was detected by two bacterial sensors. Another example is that of young scientists from Hong Kong who used genetically modified bacteria as an alternative means of storing data. Bacterial disks could be developed to store text, photographs and even videos.

Fashionable science

I am confident that the most interesting developments still lie ahead. Synthetic biology is gaining popularity. From a niche field of science, it is evolving into one that draws much attention from industry and business. What fascinates me is how inventions in this field combine with information technology. Perhaps our computer hard drives will soon assume a completely different form.

The Human Genome Project, Projekt opracowania ludzkiego genotypu – Genetics and Public Policy Center at John Hopkins University

Dolly the Sheep cloning process – Encyclopedia Britannica

 

Synthetic biology: process of artificial design and engineering biological systems and living organism. Single cell example – drawing by Enrigueta Chrisco

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Scientists Urge Artificial Human Genome

#By RAŞIT GÜRDILEK - 20. September 2016

Genetic code “read” 12 years ago, to be “written” now!

Assembling at Harvard Medical School, 25 leading geneticists issued a call to science community for cooperative efforts for the artificial synthesis of the entire human genome.

The initiative, dubbed Human Genome Project – Write, or HPG-write for short, was published online at the website of Science.  

The project envisages the synthesis from their chemical components of 3 billion base pairs which form the double helix of DNA which contains some 20.000 genes which determine our biological traits and liabilities and govern the systems and mechanisms our bodies depend  on, and then to insert the artificial genome into a cell.

As the method for the undertaking, the proponents suggest chemical synthesis of stretches of DNA strands several million base pairs long and their insertion into the strand in place of the natural piece.   

As factors fueling optimism about the success of the project, researchers cite, among others,  the progress attained so far in the synthesis of the whole yeast genome expected to be completed next year, other advances in the field and the extraordinary power of the CRISPR/Cas-9 genetic manipulation technique  (See: KURIOUS).

Way stations

Addressing the criticism caused by the issue of the call by a limited number of geneticists meeting behind closed doors, as well as articulated fears about such applications as “designer humans” and likely objections on ethical, social and legal grounds, the statement listed a number of applications concerning human health as “pilot projects”.

Foreseen as way stations on the road to the realization of the project, these include the synthesis of specific chromosomes and cancer genotypes to model human disease, construction of “ultra-safe cell lines” made resistant to viral contamination, making stem cells immune to cancer-causing mutations and the synthesis of a pig genome purged of viral genes and those triggering immune response for harvesting organs to be safely transplanted to humans.  

Despite these potential benefits, however, the authors of the statement expectedly drew some flak from critics objecting to the issue of the call without first subjecting it to a wider scientific preview and public debate as well as doubts expressed by some scientists who wondered aloud how a totally synthetic genome, even if it’s made, could be implanted into a mammal cell.

These grumblings seemingly have not discouraged the proponents who point to similar objections to the initiative for “reading”  the human genome when it was launched 25 years ago, saying it’s high time now to write the human genetic code.

Twenty-five geneticists who signed the call addressed to international research institutions, universities and laboratories, said the initiative would be officially launched later this year with a starting budged of 100 million dollars to be collected from existing project funds. 

REFERENCES

  • 1. “The Genome Project – Write”, ScienceOnline, 2 June 2016
  • 2. “Scientists reveal proposal to build huuman genome frm scratch”, ScienceOnline, 2 June 2016

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The Gloves of Ethics are Off:

A biotech startup is expanding the DNA alphabet in hopes of making novel drugs

By Meghana Keshavan - 20. July 2016

A digital representation of the human genome.

MARIO TAMA/GETTY

San Diego synthetic biology company Synthorx is entering the drug discovery game with a couple extra base pairs up its sleeve: It’s developing new biologic drugs with an expanded DNA alphabet, adding synthetic nucleotides X and Y to the standard lineup of A, C, G, and T.

The company just raised $10 million, on top of $6 million in investment it collected back in 2014.

CEO Court Turner spoke with STAT about the company’s technology — and its plans for developing drugs for diabetes and other conditions with that loaded-up DNA.

How does your technology work?

If you go back to the beginning of time, all nature around you is coded based around four nucleotides: A, G, C, and T. After 16 years of research, we’ve added X and Y. So instead of having two base pairs, we’ve got three — which basically translates to having a larger hard drive on a computer. These unnatural base pairs are replicated and transcribed exactly the same as A, C, G, and T.

What can you do with that expanded genetic alphabet?

The four natural nucleotides combine to make 64 codons, and 20 natural amino acids. With six nucleotides, we now have access to 216 codons, which theoretically incorporate into well over 100 amino acids.

We’re using whole cells to work as a natural factory for producing our compounds. We feed the synthetic DNA into a bacterial cell line normally used to produce protein therapeutics — except the resulting protein now has one or more synthetic amino acids.

We want to impart some characteristics in these new protein therapeutics — whether it means extending the half-life, or improving the pharmacokinetics, attaching more things onto a protein to give it a better drug property.

What’s the rationale behind developing these synthetic amino acids?

The idea of putting a synthetic amino acid into a protein has been thought about for a while, but it’s been hard to do it at scale.

So we’re going after targets that have been in the eye of pharma companies for many years, but haven’t been addressable by traditional methods — mostly because they could only make these compounds in small amounts, and couldn’t scale them for drug development.

We’ll do partnered deals, but also internally develop drugs. We’re looking at metabolic disease — for example, diabetes — and infectious disease. We’re looking to build antibiotics.

An expanded genetic code sounds promising and futuristic, but $10 million doesn’t seem like a lot in the biotech world. What gives?

It’s a little cheaper to run a biotech company in San Diego, when compared to Boston. We’re going to double the size of the company with this raise — go up to 16 people —and get a CSO [chief scientific officer] and a CBO [chief business officer]. It’ll give us years of runway to go after a number of these programs.

 

Author:

Meghana Keshavan

Meghana Keshavan - Biotech Correspondent - Meghana covers biotech and contributes to The Readout newsletter.

   @megkesh

Related: 

‘Game of Genomes’ Season 1: An epic quest to crack the mysteries of our DNA

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ICYMI:

First Live Organism with Synthetic Genome Created

By  - 20. May 

After almost 15 years of work and $40 million, a team of scientists at the J. Craig Venter Institute says they have succeeded in creating the first living organism with a completely synthetic genome. This advance could be proof that genomes designed in a computer and assembled in a lab can function in a donor cell, eventually reproducing fully functional living creatures, that is, artificial life.

As described today in the journal Science, the study scientists constructed the genome of the bacterium Mycoplasma mycoides from more than 1,000 sections of preassembled units of DNA. Researchers then transplanted the artificially assembled genome into a M. capricolum cell that had been emptied of its own genome. Once the DNA "booted up," the bacteria began to function and reproduce in the same manner as naturally occurring M. mycoides.

To boot up, the DNA utilized elements of the M. capricolum recipient cells, according to study team member Carole Lartigue of the Venter Institute. The bacterial cells still contained certain "machinery" that let them carry out the process of expressing a gene, or taking the genetic code and using it to build proteins – called transcription. When the artificial genome entered the cell, the cellular machines that run DNA transcription recognized the DNA, and began doing their job, Lartigue said.

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"This cell's lineage is the computer, it's not any other genetic code," said Daniel Gibson, lead author of the Science paper, also of Venter Institute.

 

To create the genomes, Gibson and his colleagues used yeast to glue together thousands of DNA snippets, each containing 1,080 base pairs, which they ordered from another lab. To assist in assembly, each section of DNA contained 80 base pairs at every end that instructed the yeast where to join the two strands.

Slowly, the DNA strands came together in runs of tens of thousands of base pairs, and then hundreds of thousands, until the yeast produced a complete 1,080,000-base-pair synthetic genome.

The scientists then compared the completed genome with two previously sequenced, natural M. mycoides genomes that served as road maps. The two road maps differed slightly, forcing the Venter scientists to commit to following one or the other, without knowing which genome was more accurate.

Even a tiny inaccuracy could prevent the inert DNA from activating into a live bacterium, making accuracy paramount. At one point, a single base pair mistake set the entire program back three months. But DNA sequencing accuracy has become so advanced that at least finding the mistakes took only days, not the months needed a decade ago during the infancy of genetic engineering.

However, the synthesis process still introduced some mutations into the M. mycoides genome. The researchers deliberately inserted four sequences of DNA that serve as watermarks so they could distinguish between the naturally occurring and synthetic bacteria.

The watermarks contain a code that translates DNA into English letters with punctuation, allowing the scientists to literally write messages with the genes. When translated, the watermarks spell out the names of the 46 researchers who helped with the project, quotations from James Joyce, physicist Richard Feynman and J. Robert Oppenheimer, and a URL that anyone who deciphers the code can e-mail.

Synthetic bacteria have tantalized scientists for years with the promise of bacterial cultures with computer designed genomes producing custom enzymes, fuels and medications cheaply and efficiently.

 

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from WorldMysteries Website

To suppose that earth is the only populated world in infinite space is as absurd as to believe that in an entire field sown with millet,

only one grain will grow.

Metrodorus of Chios
4th century B.C.

 

A DNA molecule consists of a ladder, formed of sugars and phosphates, and four nucleotide bases:

  • adenine  (A)

  • thymine  (T)

  • cytosine (C)

  • guanine  (G)

The genetic code is specified by the order of the nucleotide bases, and each gene possesses a unique sequence of base pairs.

Scientists use these base sequences to locate the position of genes on chromosomes and to construct a map of the entire human genome.

The Human Genome Project (HGP) is an international research program designed to construct detailed genetic and physical maps of the human genome, to determine the complete nucleotide sequence of human DNA, to localize the estimated 50,000-100,000 genes within the human genome, and to perform similar analyses on the genomes of several other organisms used extensively in research laboratories as model systems.

The scientific products of the HGP will comprise a resource of detailed information about the structure, organization and function of human DNA, information that constitutes the basic set of inherited "instructions" for the development and functioning of a human being. Successfully accomplishing these ambitious goals will demand the development of a variety of new technologies.

It will also necessitate advanced means of making the information widely available to scientists, physicians, and others in order that the results may be rapidly used for the public good. Improved technology for biomedical research will thus be another important product of the HGP.

From the inception of the HGP, it was clearly recognized that acquisition and use of such genetic knowledge would have momentous implications for both individuals and society and would pose a number of policy choices for public and professional deliberation.

Analysis of the ethical, legal, and social implications of genetic knowledge, and the development of policy options for public consideration are therefore yet another major component of the human genome research effort.

The Human Genome project revealed that human beings have 30,000-40,000 genes. That number is much lower than expected. For example, fruit fly has 13,300 genes, roundworm - 18,300 genes, mustard weed - 25,700 genes.

According to genetic analysis, though, more than 98% of human DNA is identical to chimpanzee DNA.

In fact, chimpanzees are more closely related to humans than orangutans and gorillas.

"Humans are simply odd looking apes," psychologist Roger Fouts of Central Washington University in Ellensburg, Washington, writes in his 1997 book, Next of Kin: My Conversations With Chimpanzees.

"A traveler from an antique land... lives within us all," claims Sykes, a professor of genetics at Oxford.

This unique traveler is mitochondrial DNA, and, as this provocative account illustrates, it can help scientists and archeologists piece together the history of the human race.

Find out more by reading this book: The Seven Daughters of Eve: The Science That Reveals Our Genetic Ancestry by Bryan Sykes.


Controversial Discoveries

A 3.5-million-year-old fossil, flat-faced human from Kenya - Kenyanthropus platy-ops, suggests the human family tree is a lot more complicated than we knew. Implication is clear: More than one species of pre-human was wandering around Africa a few million years ago, and it's anyone's guess which of them evolved into human race.

Fred Spoor

University College, London

 

Several years ago, spearpoints and other tools of modern man were found under a layer of volcanic ash.

When Dr. McIntyre, a member of the U.S. Geological Survey, was invited to date the overlying ash, the archaeologists thought it could be as old as 20,000 years old, pushing the arrival of man in the New World back around 5,000 years.

No one was prepared when uranium series dating and fission tracking methods provided the astounding age of 250,000 years.

Dr. McIntyre shares what happened next:

"I thought, okay, we got something big here but I'm going to stick with the dates. I didn't realize it was going to ruin my whole career."

Tree of Life
 

Mesopotamian "Tree of Life"
 


The Olmec "Tree of Life" (Mesoamerican Cosmology).
The lineage founder, 2 Grass, is being born from a twisting World Tree.

Detail from Selden Codex page 2. Source: FAMSI
 

 


DNA - our modern "Tree of Life"
 

The Human Genome Project
Summary of the Initial Sequencing and Analysis of the Human Genome

from WhiteHeadInstitute Website

recovered through WayBackMachine Website

Over the last decade, genomes have been sequenced for more than 40 species, mostly bacteria.

The human genome sequence is 8 times larger than all the previously sequenced genomes put together. In 1990, the Human Genome Project (HGP) began as an international collaboration propelled by the hope that global views of entire genomes would allow researchers to attack scientific problems in systematic and unbiased ways.

In its early years, the HGP produced maps of the human and mouse genomes and sequenced the genomes of yeast and nematode worm.

Now, it has produced a 94%-complete working draft of the human genome sequence, the totality of human DNA, where each letter in the draft has been read an average of 5 times. About 30% of the human genome has been sequenced with more than twice this redundancy, resulting in highly accurate "finished" sequence.

For example, the whole of chromosomes 21 and 22 have been sequenced to a finished state. No later than 2003, all the human chromosomes will be sequenced to a finished state.

The Human Genome Project first separated the genome into large "clones" - segments of DNA each representing about 0.005% of the whole genome — before chopping the clones and sequencing small fragments. Using such clones whose positions are known added to the confidence that the genome sequence would be assembled properly and allowed effective international collaboration.

All collaborators in the project made sequence data publicly available without restriction within 24 hours.

Large blocks of highly repetitive sequence, for example at the tips of chromosome arms and at the centromeres (the portions of chromosomes that appear as pinched centers when chromosomes are condensed) have been avoided, because current technology cannot yet sequence these regions. 

The total human genome, contained in a set of 23 chromosomes, is now estimated to contain 3,164.7 million letters (or nucleotides).

Genome size does not always correlate with the apparent complexity of a species because of the large amounts of repetitive sequence in many genomes. In humans the actual part of the genome that codes for proteins makes up less than 2% of the genome while repeated sequences make up at least 50% of the genome.

Repetitive sequences are thought to have no direct functions, but they shed light on chromosome structure and dynamics. They hold important clues about evolutionary events, help chart mutation rates, and by seeding DNA rearrangements, they can modify genes and create new ones. They also serve as tools for genetic studies. 

The vast majority of repeated sequences in the human genome are derived from transposable elements — sequences like those that form viral genomes — that propagate by inserting fresh copies of themselves in random places in the genome.

A full 45% of the human genome derives from such transposons.

A major surprise of this new global analysis of the human genome is that many components in this diverse array of repeated sequences, traditionally considered to be "junk," appear to have played a beneficial role over the course of human evolution.

Genes are sprawled over much larger regions in humans compared with fruit fly and nematode worm. Genes remain difficult to identify in humans because they form such a small portion of the genome and are so spread out, but it appears that the total number of genes is 30,000-35,000, close to the number originally estimated some 20 years ago, but much smaller than more recent estimates.

Apparently, humans have only twice as many genes as the fly or worm, but they have on average three times as many kinds of proteins because of "alternative splicing," a process that can yield different protein products from the same gene. 

Compared with the organisms whose genomes have been sequenced before, humans have a particular abundance of proteins involved in cell structure, defense and immunity, DNA copying, the synthesis of RNA and proteins, and communication between cells. Humans have an unusually high number of complex proteins that fit into more than one functional category and many proteins that are embedded in the surface of cells. 

Since the genome sequence has been released as it was generated over the last four years, a large number of discoveries have already been spawned by the sequence data.

At least 30 different disease genes have been identified by directly using sequence produced by the HGP. In the coming years, the human genome should be sequenced to a finished state, where all gaps are closed and the sequence is at least 99.99% accurate.

Genome sequence from other species will provide crucial insights about genes and the regions that regulate their activity.

There will be a pressing need for improved methods to analyze the abundance of information being generated. And genetics will become an increasingly important part of the medical mainstream.

The pressure will grow to encourage educated use of genetic information and to set thoughtful limits on its use.

 

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