Monthly Archives: June 2021

An international team of scientists says it has sequenced and assembled the entirety of the human genome, including parts that were missed in the sequencing of the first human genome two decades ago.

The claim, if confirmed, surpasses the achievement laid out by leaders from the Human Genome Project and Celera Genomics on the White House lawn in 2000, when they announced the sequencing of the first draft human genome. That historic draft, and subsequent human DNA sequences, have all missed about 8% of the genome.

The sequencing of the new genome fills in these gaps using new technology. It has different limitations, however, including the type of cell line that the researchers used in order to speed up their effort.

The work was detailed May 27 in a pre-print, meaning it has not yet been peer-reviewed.

Youre just trying to dig into this final unknown of the human genome, said Karen Miga, a researcher at the University of California, Santa Cruz, who co-led the international consortium that created the sequence. Its just never been done before and the reason it hasnt been done before is because its hard.

Miga emphasized that she wont consider the announcement official until the paper is peer-reviewed and published in a medical journal.

READ MORE: Psst, the human genome was never completely sequenced. Some scientists say it should be

The new genome is a leap forward, researchers say, that was made possible by new DNA sequencing technologies developed by two private sector companies: Pacific Biosciences of Menlo Park, Calif., also known as PacBio, and Oxford Nanopore, of Oxford Science Park, U.K.. Their technologies for reading out DNA have very specific advantages over the tools that have long been considered researchers gold standards.

Ewan Birney, the deputy director general of the European Molecular Biology Laboratory called the result a technical tour de force. The original genome papers were carefully worded because they did not sequence every DNA molecule from one end to the other, he noted. What this group has done is show that they can do it end-to-end. Thats important for future research, he said, because it shows what is possible.

George Church, a Harvard biologist and sequencing pioneer, called the work very important. He said he likes to note in his talks that up until now no one has sequenced the entire genome of a vertebrate something that is no longer true, if the new work is confirmed.

One important and unanswered question: How important are these missing pieces of the human puzzle? The consortium said that it increased the number of DNA bases from 2.92 billion to 3.05 billion, a 4.5% increase. But the count of protein-coding genes increased by just 0.4%, to 19,969. That doesnt mean, researchers emphasized, that the work couldnt also lead to other new insights, including those related to how genes are regulated.

The DNA sequence used was not from a person, but from a hydatidiform mole, a growth in a womans uterus caused when sperm fertilized an egg that did not have a nucleus. This meant that it contained two copies of the same 23 chromosomes, instead of two differing sets of chromosomes, as normal human cells do.

The researchers chose these cells, which had been kept in a lab, because this made the computational effort of creating the DNA sequence simpler. The original draft genome created in 2003 also contained only 23 chromosomes, but as technologies for DNA sequencing have become cheaper and simpler, researchers have tended to sequence all 46 chromosomes.

Elaine Mardis, co-executive director of the Institute for Genomic Medicine at Nationwide Childrens Hospital, worried that because these cell lines were kept in the lab, potentially mutating, the new genetic information may be largely the detritus that accumulates as a cell line is propagated over many years in culture.

Miga said that studies of the cell line had shown it to be similar to human cells, and that the researchers used cells that had been kept frozen, not propagated for many years. We went to great lengths in the preprints to demonstrate that these new sequences serve as biological reference for human genomes, Miga wrote in an email. She agreed the next step was for the group to try to sequence all 46 chromosomes, known as a diploid genome.

Why did it take 20 years for this last 8% of the genome to be sequenced, even as the cost of sequencing the rest of the genome dropped from $300 million to as little as $300? The answer has to do with the way DNA sequencing technologies work.

The current workhorse DNA sequencers, made by Illumina, take little fragments of DNA, decode them, and reassemble the resulting puzzle. This works fine for most of the genome, but not in areas where DNA code is the result of long repeating patterns. If a supercomputer only had small fragments, how could it assemble a DNA sequence that repeated AGAGAGA for bases upon bases? Thats what the missing 8% of the genome looked like.

READ MORE: At Illumina, the era of the genome has arrived. But what role will the company play?

Among these unmappable regions were one of the most recognizable structures in biology. If youve ever looked at chromosomes (think back to high school biology), they look like strings that have been knotted together. Those knots are centromeres, bundles of DNA that hold the chromosomes together. They play a key role in cell division. And they are full of repeats.

It was the centromeres, in fact, that drew Miga to want to see these missing regions.

Why are the regions that are so fundamental to life, so fundamental to how the cell operates, positioned over parts of our genome that are these giant seas of tandem repeats? she remembers asking as a grad student.

It was that question that led her, in discussion with Adam Phillippy, a researcher at the National Institutes of Health, to propose starting their current initiative, called the Telomere 2 Telomere Consortium, after the telomeres, which are the ends of the chromosome, in 2019. They signed on Evan Eichler, a University of Washington biologist who had been worried about the missing parts of the genome for years, as a co-author.

The work was possible because the Oxford Nanopore and PacBio technologies do not cut the DNA up into tiny puzzle pieces. The Oxford Nanopore technology runs a DNA molecule through a tiny hole, resulting in a very long sequence. The PacBio tech uses lasers to examine the same sequence of DNA again and again, creating a readout that can be highly accurate. Both are more expensive than the existing Illumina technology.

The companies are in a heated race. For this project, the researchers say, the PacBio technologys accuracy proved invaluable, and they used Oxford Nanopore to finish up some areas. But Oxford Nanopore has already been promising new, more usable tech. In the here and now, PacBio has the advantage but its not clear how long theyll be able to keep it, said Michael Schatz, an associate professor at Johns Hopkins University.

All the researchers spoke of a vision of the future where instead of using a single reference genome, they would assemble hundreds of different, complete genomes that are interlinked and ethnically diverse, and can be used as references. Miga is helping lead that work, as well. And this is just a step in that direction.

But until now, Schatz says, there have always been questions about what was missing. Now finally we have the right data, he said. We have the right technology.

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Researchers may have sequenced the final unknown of the human genome - PBS NewsHour

In the earliest stages of domestication, managed goats looked identical to their wild counterparts, the bezoar (pictured here).

By Michael PriceJun. 7, 2021 , 3:45 PM

Ancient hunters and farmers living in the foothills and valleys of western Irans verdant highlands may have been among the first people to domesticate livestock. Now, a new studywhich includes the oldest livestock genome yet sequencedbolsters that notion, appearing to capture genetic and archaeological evidence of a transitional stage between wild-hunted goats and their domesticated descendants.

The study has captured the ground zero for goat domestication, or close to it, says David MacHugh, an animal geneticist at University College Dublin. And because the advent of livestock domestication helped pave the way for larger populations and complex societies, he says, it is really one of the pivotal moments in prehistory.

Since the 1950s, archaeologists have unearthed ancient livestock bones near Irans Zagros Mountains. The area lies at the eastern end of the Fertile Crescent, the region considered the cradle of agriculture and several early civilizations. Animal remainssome of which date to about 10,000 years agoshow signs of domestication, such as smaller bodies and shorter horns. Evidence of early pig and sheep domestication has been found in the region, as well.

Researchers analyzed bones, like this leg bone, and ancient DNA from goats unearthed at two sites in western Iran.

Much of the archaeological research in the area halted because of the Iranian Revolution in the late 1970s, and the Iran-Iraq War, which began in 1980. This region sort of fell into a dark abyss for quite a while, says Melinda Zeder, an emeritus archaeologist at the Smithsonian Institutions National Museum of Natural History. Its now seeing a recent resurgence of interest in all sorts of domestication issues, with goats being a primary one.

To learn about the process of early animal domestication, Zeder and othersincluding several Iranian archaeologistsanalyzed goat bones excavated in the 1960s and 70s from two sites in the Zagros Mountains, Ganj Dareh and Tepe Abdul Hosein. People lived, hunted, and grew crops in these fertile valleys from about 8200 to 7600 B.C.E. The wild ancestor of todays domestic goat (Capra aegagrus hircus), the bezoar (C. aegagrus), was their primary prey.

The pattern of male and female goat remains at these sites was the first clue that people were likely managing herds, not just hunting them. Hunters and herders target different kinds of animals, Zeder explains. Hunters are after the bang for your buck fast return, so they go for big adults. Herders, meanwhile, care less about individual size, focusing instead on keeping females alive to sustain and grow the herd, she says. As a result, herders tend to cull most young males and keep lots of older females.

Thats exactly the pattern the researchers saw at Ganj Dareh and Tepe Abdul Hosein: relatively few males and lots of older females. Hoof impressions imprinted in mud bricks at Ganj Dareh further strengthened the case that people here were managing goats, as wild goats probably werent tromping through the village. Strangely, though, these seemingly herded goats looked exactly like wild bezoars, with large bodies and horns. So, the researchers turned to ancient DNA.

Comparing the ancient goat DNA with that of modern wild goats from the region, the scientists found distinct genetic clusters indicating the apparently managed goats were being bred with one another, they report today in the Proceedings of the National Academy of Sciences. This confirms the herders maintained a goat population largely separate from the regions wild goats, Zeder says. The earliest of the goat remains date to about 8200 B.C.E., making the DNA in the study the oldest livestock genomes yet sequenced.

Within these early managed goats, the researchers identified the six major mitochondrial haplotypes, or sets of genes inherited along the female line, that are present in modern domestic goat populations. That find suggests todays goats are direct descendants of those that lived 10,000 years ago, Zeder says. Within the genomes of these ancient goats, the researchers also identified a genetic variant called STIM1-RRM1 that is known in other domestic animals to help reduce anxiety and promote learning.

The upshot, Zeder says, is that these ancient goats appear to represent a critical moment in domestication in which people were managing herds but hadnt yet selected for the physical traits that youd recognize at the petting zoo.

This is a fascinating study, says Cheryl Makarewicz, an archaeozoologist at the University of Kiel who wasnt involved with the work. The results suggest the earliest livestock herders tinkered with management strategies before they succeeded in domesticating their animals, she adds. There was a lot of experimentation going on.

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Oldest livestock genome reveals origin of today's goats - Science Magazine

A team of researchers from Columbia University has found that eusocial snapping shrimp possess larger genomes compared to their less-social relatives. The larger genome comprises an accumulation of transposable elements moving DNA sequences providing new insights on the relationship between social and genome evolution. The research is published in PNAS.1

Rubenstein, a professor of ecology, evolution and environmental biology, is particularly interested in the Synalpheus genus of snapping shrimp, as it contains the only known aquatic eusocial species.

If an organism is eusocial, it demonstrates advanced social behaviors including: living together in groups, cooperating to take care of offspring, division of labor and overlap of generations such that younger populations can assist older generations. It is a phenomenon that is well recognized and studied in certain species of insects, such as ants.

Rubenstein and team serendipitously discovered that the shrimp possess another interesting characteristic: the size of their genome varies dramatically and appears to be related to their social organization. This contradicts what is known about eusociality in the insect world. Genomic studies have demonstrated that eusocial insects typically have smaller genomes than their less-social relatives.

Transposable elements are sometimes referred to as "jumping genes" they are DNA sequences that move within the genome. This movement can create and/or reverse mutations that alter a cell's genetic identity, thereby contributing to evolution.

"We developed a method for extracting information about transposable elements from low coverage sequencing data. This approach allowed us to compare large numbers of shrimp species in an efficient and cost-effective manner without first having to sequence and assemble the genomes of every species," Rubenstein told Technology Networks.

"We found that eusocial species had more transposable elements in their genomes than non-eusocial species," he added. "We used evolutionary modeling to explore why such a relationship exists and found that they seem to accumulate in the genomes of eusocial species."

The researchers hypothesize that the increased transposable elements in the genome are due to the unique social organization of the shrimp. Being a eusocial species, the majority of the shrimp will never reproduce in their lifetime. The reduced effective population size means that it is difficult to "purge" transposable elements from the genome; consequently, they accumulate over time. "Interestingly, each eusocial species seems to accumulate a different type of transposable element in their genome," Rubenstein added.

The incredible size of the shrimp genomes posed a challenge for the researchers it precluded them from applying next-generation sequencing techniques to the entire shrimp genome, a method known as whole-genome sequencing, or WGS. "We developed a novel way to study transposable elements from limited amounts of sequence data," Rubenstein explained. As a next step, the team hope to go back and sequence the whole genome to gather even more data and learn as much as possible about the relationship between social evolution and genome evolution. They also intend to analyze in greater detail where the transposons occur to determine if they play a role in the evolution of eusociality. "We also hope to look at transposable elements in other social organisms, like birds and mammals, to see whether these same relationships hold in vertebrates," Rubenstein concluded.

Dustin Rubenstein was speaking to Molly Campbell, Science Writer for Technology Networks.

Reference: Chak STC, Harris SE, Hultgren KM, Jeffery NW, Rubenstein DR. Eusociality in snapping shrimps is associated with larger genomes and an accumulation of transposable elements. Proc Natl Acad Sci USA. 2021;118(24):e2025051118. doi: 10.1073/pnas.2025051118.

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The More Social the Shrimp, the Larger Its Genome - Technology Networks

At its 18th plenary meeting (1-4 June 2021), the Committee on Bioethics of the Council of Europe adopted the following conclusions regarding genome editing technologies:

In accordance with itsStatement on genome editing technologiesadopted in December 2015 and itsStrategic Action Plan on Human Rights and Technologies in Biomedicine (2020-2025); the Committee on Bioethics (DH-BIO) examined Article 13 of the Oviedo Convention in the light of developments in human genome editing.

Taking into account the technical and scientific aspects of these developments as well as the ethical issues they raise, it considered that the conditions were not met for a modification of the provisions of Article 13.

However, it agreed on the need to provide clarifications, in particular on the terms preventive, diagnostic and therapeutic and to avoid misinterpretation of the applicability of this provision to research.

As underlined by the DH-BIO in November 2018, ethics and human rights must guide any use of genome editing technologies in human beings in accordance with the Convention on Human Rights and Biomedicine (theOviedo Convention, 1997) - the only international legally binding instrument addressing human rights in the biomedical field which provides a unique reference framework to that end. The Oviedo Convention represents the outcome of an in-depth discussion at European level, on developments in the biomedical field, including in the field of genetics.

Article 13 of the Convention addresses these concerns about genetic enhancement or germline genetic engineering by limiting the purposes of any intervention on the human genome, including in the field of research, to prevention, diagnosis or therapy. Furthermore, it prohibits any intervention with the aim of introducing a modification in the genome of any descendants. This Article was guided by the acknowledgement of the positive perspectives of genetic modification with the development of knowledge of the human genome; but also by the greater possibility to intervene on and control genetic characteristics of human beings, raising concern about possible misuse and abuses.

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Genome editing technologies: some clarifications but no revision of the Oviedo Convention - Council of Europe

Scientists including experts at Trinity College Dublin on ancient DNA have revealed the genetic make-up of the earliest goat livestock herds who inhabited the once lush landscape of western Iran, in the oldest livestock genome yet sequenced.

The findings, assimilated from DNA taken from remains of 32 goats that died some 10,000 years ago, provide clues to how early agricultural practices shaped the evolution of goats and in turn the lifestyle of humans over following centuries.

The latest findings follow on from archaeological evidence that had previously pointed to the Zagros Mountains as providing the earliest evidence of goat management by ancient hunters and farmers.At Ganj Dareh, bone remains indicate deliberate slaughtering of male goats once they were fully grown.

In contrast, female goats were allowed to reach older ages, meaning early goat-keepers maximised the number of breeding female animals similar to practices by herders in the area today.

A close relationship between early herders and goats is seen in the foundations of the Ganj Dareh settlement, with bricks bearing the imprint of cloven goat hooves. However, their goats resembled the wild bezoar, with a larger body size and scimitar horn shape.

Dr Kevin G Daly of TCDs school of genetics and microbiology, who was involved in the new research, said: Our study shows how archaeology and genetics can address highly important questions by building off ideas and results from both fields. Our genetic results point to the Zagros region as being a major source of ancestry of domestic goats and that herded, morphologically wild goats were genetically on the path to domestication by about 10,200 years ago.

Genetic analyses indicated to the researchers that the ancient goats in question fell at the very base of the domestic goat lineage, suggesting they were closely related to the animals first recruited during domestication.

A surprising find, however, was the discovery from the 32 remains of a small number of goats whose genomes appeared more like their wild relatives the bezoar ibex. This suggests these early goat herders continued to hunt goats from wild herds.

Professor of population genetics at TCD Dan Bradley underlined how techniques involving ancient DNA are providing insights into how modern agriculture emerged.

Ancient DNA continues to allow us to plumb the depths of ancient prehistory and examine the origins of the worlds first livestock herds. Over 10,000 years ago, early animal farmers were practising husbandry with a genetic legacy that continues today, he added.

The study has captured the ground zero for goat domestication, or close to it, David MacHugh, an animal geneticist at University College Dublin, told Science magazine. And because the advent of livestock domestication helped pave the way for larger populations and complex societies, it is really one of the pivotal moments in prehistory, he believed.

Since the 1950s, archaeologists have unearthed ancient livestock bones near the Zagros Mountains. The area lies east of the Fertile Crescent, the region considered the cradle of agriculture and some early civilisations. Animal remains from the area show signs of domestication, such as smaller bodies and shorter horns. Evidence of early pig and sheep domestication has also been found in the region.

The latest collaboration included researchers at the US Smithsonian Institution and other scientists in Denmark, France and Iran. Funded by the European Research Council, the researchers findings are published in Proceedings of the National Academy of Sciences of the US.

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10,000-year-old goat remains used to create oldest livetock genome yet sequenced - The Irish Times

Sometimes amusing and always amazing, to me, is when the intelligent elite instructs the citizenry to follow the science while ignoring science! In doing so they wish to impose their beliefs and not science as a political weapon in order to divide us. The latest edition is named Critical Race Theory, a politically acceptable guise for what is, in effect, both racist and Marxist.

I find this amazing because our children have been taught racism for many years, disguised as science, which in fact is the state sponsored religion and cult, Darwinism. Let me be clear, race is a political construct designed to divide the populace. Christians who read the Bible have been aware of this fact for years as it is written, From one man He made every nation living on the entire surface of the earth, and He fixed the limits of their territories and the periods when they will flourish. (Acts 17:26) So to all you educated elitists understand this truth, those of us uneducated Walmart shoppers are relatives of yours! Well, at least that is preferable to having a Monkey's Uncle isn't it?

Noted racists who support molecule to man fantasy including the racist himself, Charles Darwin, as well as Hitler, Sanger and the good doctor Joseph Mengle. Doubters about race, gender or science claim the Bible is a fairy tale.

If they only studied science they would know that the secular Human Genome Project proved there is but one race.

' + this.content + '

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LETTER: Human Genome Project proved there is one race - yoursun.com

The study on New Genomic Techniques (NGTs), which alter the genome of an organism in plant and animal breeding, concluded that the technology has the potential to contribute to a more sustainable food system under the European Green Deal and Farm to Fork Strategy.

It also finds that the current GMO legislation, adopted in 2001, is not fit for purpose for these innovative technologies and is hampering research in the EU, with most development taking place outside the EU.

The Commission will now start a wide and open consultation process to discuss the design of a new legal framework for these biotechnologies.

NPA senior policy adviser Rebecca Veale said: "This could be a really positive step forward because European legislation on this is the most restrictive by far with the UK and other countries also looking at the policy around genetic technologies we hope that well be able to take advantage of the opportunities these technologies offer and there will be more cohesion globally.

"The big question is, however, whether, at EU and UK level, they can agree on a sensible new regulation.

Genome editing has the potential to deliver a range of benefits in plant and animal breeding and for wider society, the NPA highlighted.

The technology, it noted, has already been used at research level to breed pigs with resistance to porcine reproductive and respiratory syndrome (PRRS) and African swine fever (ASF).

Research institutes, companies, cooperatives and associations of EFFAB and FABRE TP that are working in animal breeding and reproduction in Europe are all convinced that novel animal breeding techniques (NABTs) like genome editing can provide efficient additional tools to increase the sustainability of the animal breeding sector.

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UK pig industry backs EU genome editing report: 'This is a positive step forward' - FeedNavigator.com

By sequencing the genomes of 11 individuals with a severe form of childhood amyotrophic lateral sclerosis (ALS), a team led by National Institutes of Health researchers has identified a set of rare mutations that cause the disease. In these patients, they discovered variants in the gene SPTLC1, which is involved in lipid metabolism, and found that these mutations disrupt the production of an enzyme called serine palmitoyltransferase (SPT), leading to unrestrained sphingolipid production and accumulation in the motor neurons affected in ALS. "Alterations in SPT activity have been linked to neurodegeneration, the study's authors write this week in Nature Medicine. "Nevertheless, no human disease has been linked to SPT overactivity." The study's authors also developed small interfering RNAs that target the ALS-causing SPTLC1 allele for degradation while leaving the normal allele intact and normalize sphingolipid levels in vitro as a proof-of-concept for a precision medicine approach for treating this form of ALS.

Genetic variation is commonly used to improve crop yield and quality, but hexaploid wheat one of the world's most important crop plants remains intractable to selective breeding given the narrow diversity of its genome. To address this, a group led by Henan University scientists developed an approach that takes advantage of the genomic variations in the grass species Aegilops tauschii. As described in Nature Plants last week, they developed a platform to rapidly introduce genetic variations from A. tauschii into wheat through a combination of introgression technology, speed breeding, and high-throughput genotyping and phenotyping. The investigators assembled four new reference genomes and resequenced 278 accessions of A. tauschii, revealing "extensive untapped variations" in the plant and introduce improvements in preharvest sprouting resistance and grain weight of new wheat lines.

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Nature Papers Find Variants Behind Childhood ALS, Present Approach to Introduce Variation into Wheat Genome - GenomeWeb