Category Archives: Transhuman News

Genomic changes in individual cells can eventually lead to cancer or other diseases. So scientists would like to be able to sequence the genome in a single cell. But the methods to do so can be plagued by the preferential amplification of some regions of the genome over others, leading to incomplete sequence coverage.

A team led by X. Sunney Xie of Harvard University and Peking University has developed a whole-genome amplification method that reduces such bias and errors (Science 2017, DOI: 10.1126/science.aak9787).

In the method, called LIANTI, researchers fragment genomic DNA from a single cell by inserting pieces of DNA called transposons. The transposons tag the DNA fragments so that they get amplified linearly instead of exponentially. The amplified DNA is then used to generate a library for subsequent DNA sequencing.

Compared with other whole-genome amplification methods, LIANTI has more uniform amplification and higher sequence coverage. The method enabled the detection of a type of mutation called copy-number variation, which involves the gain or loss of regions of the genome, which is hard to detect with high resolution using other amplification methods. The researchers were even able to characterize so-called micro-copy-number variations, which are smaller than 100,000 bases, with a resolution of about 10,000 bases.

Xie and coworkers used this ability to detect gains and losses of sequences to show that initiation of DNA replication is random and differs from cell to cell. They also showed that many single-nucleotide variations detected in previous single-cell sequencing are artifacts caused by instability of the DNA bases.

Originally posted here:
Method improves single-cell genome analysis - Chemical & Engineering News (subscription)

The researchers made the announcement in Nature Communications.

UC Davis researchers have announced in Nature Communications that they have unlocked a treasure-trove of genetic information about lettuce and related plants, releasing the first comprehensive genome assembly for lettuce and the huge Compositae plant family, according to a press release.

Garden lettuce, or Lactuca sativa, is the plant species that includes a salad bars worth of lettuce types, ranging from iceberg to romaine. With an annual on-farm value of more than $2.4 billion, it is the most valuable fresh vegetable and one of the 10 most valuable crops, overall, in the United States.

Lettuce is a member of the huge Compositae family, which includes the good, the bad, and the ugly of the plant world, from the daisy and sunflower to ragweed and the dreaded star thistle.

The genome assembly a compilation of millions of DNA sequences into a useful genetic portrait provides researchers with a valuable tool for exploring Compositae familys many related plant species.

This genome assembly provides the foundation for numerous further genetic, evolutionary and functional studies of this whole family of plants, said Reyes-Chin-Wo, the lead author and graduate student in the laboratory of plant geneticist Richard Michelmore.

This is particularly significant because Compositae is the most successful family of flowering plants on earth in terms of the number of species and environments inhabited, said Richard Michelmore, who directs the UC Davis Genome Center.

Triplicate genes may explain success

The researchers found that specific genes in the lettuce genome were consistent with certain physical traits like the production of a rubber-containing milky sap that have also been found in taxonomically distinct species, such as the rubber tree.

The study also provided evidence that somewhere during the evolution of lettuce about 45 million years ago, its genome was triplicated. As a result, one-fourth of the genome appears in multiple related regions. Because such genomic duplications may give plant species an advantage in colonizing new environments, the ancient triplication event might, in part, explain the success of the Compositae plant family.

New technology yields more precise information

Michelmore noted that this is the first reported genome assembly of a plant species resulting from use of a new technology which gives information information about the physical proximity of the DNA sequences to which proteins are bound.

The new approach, developed by Dovetail Genomics, a company spun out from UC Santa Cruz, resulted in a more contiguous and accurate genome assembly, even though lettuce has one of the larger plant genomes sequenced to date, he said.

The sequencing was done in collaboration with the genomics firm BGI. Funding was provided by 10 plant breeding companies through the Lettuce Genomics Sequencing Consortium, UC Davis Genome Center, National Science Foundation and U.S. Department of Agriculture.

Go here to see the original:
University of California, Davis researchers publish lettuce genome assembly - Produce Grower (press release)

D.R. Venema and Scot McKnight, Adam and the Genome, (Brazos, 2017).

On first blush the title of this book suggests an Indie rock band. But seriously, this is a very well researched book on genetics, and Biblical interpretation vis a vis the origins of human life, and whether or not Adam (and Eve) were historical persons. The genetics part of the book by D.R. Venema is a difficult read for those not familiar with genetics, even at the lay persons level, whereas, Scot McKnights half of the book (beginning at p. 93) is quite clear, but in some ways more problematic, from my point of view. Nonetheless, it is written with the sort of style and grace and honesty that we have come to expect in Scots books.

If we ask what prompted the book, all is made clearer by statements late in the study on pp. 172-73. The concern is about people losing their faith due to an encounter with science, particularly evolutionary theory, especially perhaps those who have come from more fundamentalist Protestant backgrounds. Scot deals regularly with such students and frames the matter this way: Here is what is vital for this book: [a] persons faith was challenged by his realization about evolution and he was forced to make a choice about whether the Bible or evolution was the truest description and understanding of the world. He chose science because the understanding of the Bible was in his view demonstrably wrong. Dennis and I are proposing another alternative: accepting the reality of genetic evidence supporting a theory of evolution along with an understanding of Adam and Eve that is more in turn with the historical context of Genesis.

In other words, the interpretation of the Word should be adjusted on the basis of the assumed fait accompli of science to demonstrate it has the facts on its side. Neither side of these assumptions, the science or the Biblical interpretation assumptions are without their problems. But I absolutely agree that we need to have a good discussion about this because science is one thing and pseudo-science that denies the geological and genetic evidence for an old earth and ancient human race needs to countered.

See the original post:
Adam and the Genome Part One - Patheos (blog)

April 12, 2017 by Pat Bailey Richard Michelmore, director of the UC Davis Genome Center, and colleagues have released the first comprehensive genome assembly for lettuce and the huge Compositae plant family, which includes diverse plants ranging from the sunflower to star thistle. Credit: Gregory Urquiaga/UC Davis

Today (April 12), UC Davis researchers announced in Nature Communications that they have unlocked a treasure-trove of genetic information about lettuce and related plants, releasing the first comprehensive genome assembly for lettuce and the huge Compositae plant family.

Garden lettuce, or Lactuca sativa, is the plant species that includes a salad bar's worth of lettuce types, ranging from iceberg to romaine. With an annual on-farm value of more than $2.4 billion, it is the most valuable fresh vegetable and one of the 10 most valuable crops, overall, in the United States.

Lettuce is a member of the huge Compositae family, which includes the good, the bad, and the ugly of the plant world, from the daisy and sunflower to ragweed and the dreaded star thistle.

The genome assemblya compilation of millions of DNA sequences into a useful genetic portraitprovides researchers with a valuable tool for exploring the Compositae family's many related plant species.

"This genome assembly provides the foundation for numerous further genetic, evolutionary and functional studies of this whole family of plants," said Sebastian Reyes-Chin-Wo, the lead author and a graduate student in the laboratory of plant geneticist Richard Michelmore.

"This is particularly significant because Compositae is the most successful family of flowering plants on earth in terms of the number of species and environments inhabited," said Richard Michelmore, who directs the UC Davis Genome Center.

Triplicate genes may explain success:

The researchers found that specific genes in the lettuce genome were consistent with certain physical traitslike the production of a rubber-containing milky sapthat have also been found in taxonomically distinct species, such as the rubber tree.

The study also provided evidence that somewhere during the evolution of lettuce about 45 million years ago, its genome was "triplicated." As a result, one-fourth of the genomeincluding about 30 percent of all of its identified genesnow appears in multiple related regions. Because such genomic duplications may give plant species an advantage in colonizing new environments, the ancient triplication event might, in part, explain the success of the Compositae plant family.

New technology yields more precise information:

Michelmore noted that this is the first reported genome assembly of a plant species resulting from use of a new technology that gives information about the physical proximity of the DNA sequences to which proteins are bound.

The new approach, developed by Dovetail Genomics, a company spun out from UC Santa Cruz, resulted in a more contiguous and accurate genome assembly, even though lettuce has one of the larger plant genomes sequenced to date, he said.

Explore further: Sequencing hundreds of nuclear genes in the sunflower family now possible

More information: Sebastian Reyes-Chin-Wo et al, Genome assembly with in vitro proximity ligation data and whole-genome triplication in lettuce, Nature Communications (2017). DOI: 10.1038/ncomms14953

Journal reference: Nature Communications

Provided by: UC Davis

Advances in DNA sequencing technologies have enormous potential for the plant sciences. With genome-scale data sets obtained from these new technologies, researchers are able to greatly improve our understanding of evolutionary ...

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Researchers from the University of Bristol have uncovered one of the reasons for the evolutionary success of flowering plants.

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Scientists at the University of California, Davis have discovered that DNA sequences thought to be essential for gene activity can be expendable. Sequences once called junk sometimes call the shots instead.

The hot springs of Yellowstone National Park may be extreme environments, but they are host to a diversity of microbes that could shed light on the evolution of life on Earth and, perhaps, what lurks on distant planets.

Breaks in DNA can wreak havoc in the body, giving rise to cancer and other health problems. Yet sometimes cells rupture their own DNA for a good reason.

How some industrial pollutants or abnormal levels of cellular metabolites contribute to diverse human diseases is now more clearly understood, based on a new study from the University of Wisconsin Carbone Cancer Center (UWCCC) ...

Cocaine, nicotine, capsaicin. These are just three familiar examples of the hundreds of thousands of small molecules (also called specialized or secondary metabolites) that plants use as chemical ammunition to protect themselves ...

A Florida Museum of Natural History study provides new insights into the complex, shared history between blood-sucking lice and the vitamin-producing bacterial sidekicks that enable them to parasitize mammals, including primates ...

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See the original post here:
Gene salad: Lettuce genome assembly published - Phys.Org