Category Archives: Transhuman News

Download PDF Sequence search: A DNA-editing tool helps scientists find functions for the more than 98 percent of the genome that doesn't include genes.

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Tweaks to the CRISPR gene-editing system allow researchers to identify stretches of DNA that regulate gene expression1. Researchers could use the method to find sequences that control genes tied to autism.

The CRISPR system uses RNA guides to direct the DNA-cleaving enzyme CAS9 to specific spots in the genome. Scientists have used the system to edit, activate and disable genes. But regions that control these genes are hidden in the vast expanse of poorly understood DNA dubbed the dark genome.

The new method, described in the April issue of Nature Biotechnology, involves the use of chemical tags for DNA that activate or deactivate certain sections of the genome. Researchers engineered one version of CAS9 to add an activating tag, and another to add a deactivating tag.

They created two libraries that each contain thousands of guide RNAs. Each of the RNAs targets a DNA segment thought to regulate the expression of a gene or group of related genes. One library is specific for the beta-globin region, which contains genes involved in the production of hemoglobin. The other targets the breast cancer gene HER2.

The researchers loaded each of the guide RNAs into a virus and injected the virus into cultured human cells.

After 14 days in culture, the researchers gauged the expression of HER2 and beta-globin genes in the cells using fluorescent markers on the genes. They used a specialized instrument to sort out the brightest 10 percent and the darkest 10 percent of cells.

The researchers then identified where in the genome the guides had attached, revealing the sequences that regulate the expression of HER2 or beta-globin genes.

The study confirmed known regulatory segments for beta-globin genes and revealed new ones for HER2.

The regulatory segments generally produce subtle changes in gene expression, those that differ from baseline by less than twofold. But several of them working together might produce more dramatic changes, the researchers say.

They also say the method can be scaled up to enable screening of the entire genome, rather than just selected regions.

Original post:
CRISPR hack unearths gems buried in 'dark genome' - Spectrum

Matthew Cabe Staff Writer @DP_MatthewCabe

Significant news for the Mojave Desert in recent weeks emanated from separate sections of the scientific world.

Out in Mojave, California, on May 31, the worlds largest all-composite plane ever built rolled out of its Mojave Air and Space Port hangar for the first time.

Dubbed Stratolaunch, the dual-fuselage plane weighs approximately 250 tons unfueled, stands 50 feet tall and boasts a record-setting wingspan (385 feet) thats 25 feet longer than a football field. Its powered by six Boeing 747 engines.

Before Stratolaunchs gargantuan reveal, several weeks were spent removing the fabrication infrastructure and three-story scaffolding around the plane. Crews then rested the planes full weight on 28 wheels.

Stratolaunch belongs to billionaire Paul Allen, the Microsoft co-founder who owns the Seattle Seahawks and is currently Forbes' 42nd richest person in the world. In 2011, Allen founded Stratolaunch Systems with the goal of making access to space more convenient, reliable and routine.

The purpose of Stratolaunch the plane, then, is to launch satellite-carrying rockets into space at a reduced cost. Allens company partnered with the Virginia-based Orbital ATK, which will provide the rockets capable of carrying the 1,000-pound satellites. Stratolaunch will drop the rockets from about 35,000 feet.

The main cost-effective benefit of an air launch such as this, the company said, is an ability to avoid the limitations of fixed launch sites that can be impacted by weather, air traffic and ship traffic on ocean ranges.

According to the Associated Press, all this will translate into new ways to beam the Internet all across the globe, which in turn will provide better communication.

In the interim, Stratolaunch CEO Jean Floyd said the company will conduct numerous tests in the coming weeks at the Mojave hangar while keeping the plane on track for a launch demonstration in 2019.

On the same day Stratolaunch rolled out of its hangar, researchers from Arizona State Universitys School of Life Sciences made headlines by decoding the Mojave Desert tortoises genome. Their findings were published in the scientific journal PLOS ONE.

Such a breakthrough could help our reptilian neighbor survive an increasing number of threats, according to Science Daily.

Those threats include natural predators, invasive grasses also a threat to the beloved Joshua tree an upper respiratory disease and human activity. All have contributed to the decline of the Mojave Desert tortoise.

But the researchers, led by Marc Tollis, believe the tortoises now decoded genome i.e. a complete set of its DNA will provide a launchpad for further study into areas like disease resistance.

Tollis, as quoted in Science Daily: We don't know how the tortoise is handling the fact that it's also being threatened by an upper respiratory disease," said Tollis. "Decoding this genome will help us catalog which tortoise genes are evolving quickly enough to help them overcome this threat.

Other advantages include deeper dives into how the Mojave tortoise is adapting to its changing desert environment and the diversity of its hybridization with its sister species, the Sonoran Desert tortoise.

The goal is to increase conservation efforts for the Mojave tortoise, which is listed as threatened under the U.S. Endangered Species Act, by posing new questions in light of the decoded genome.

Inevitably, though, the simplest answer already exists. It came up during a chat I had in 2016 with Ed LaRue, a former U.S. Bureau of Land Management biologist and tortoise counter with nearly 30 years experience.

I asked Ed what can be done to combat the significant population reductions numbers decreased 50 percent between 2004 and 2012 alone among Mojave tortoises.

(People) go out to the desert and see a tortoise and think it would be cool in their backyard, Ed said. So to encourage people to understand that they are wild and endangered and don't belong in backyards.

Interpretation: leave the tortoises alone. Maybe look toward the desert skies instead.

You might just spot a giant in two years' time.

Matthew Cabe can be reached at MCabe@VVDailyPress.com or at 760-951-6254. Follow him on Twitter @DP_MatthewCabe.

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This Desert Life: A massive plane, a decoded genome - VVdailypress.com

June 6, 2017 Apple with apple scab. Credit: Wageningen University

A high quality genome sequence of apple is published in this week's Nature Genetics by an international team of scientists, among which researchers of Wageningen University & Research in the Netherlands. The publication of the sequence facilitates faster and more targeted breeding of new apple varieties with increased disease resistance, improved production traits, and better fruit quality. With this the results support a more sustainable production of apple fruit, both from an environmental and a financial perspective.

The genome sequence was assembled by an international consortium of research institutions from France, Italy, Germany, the Netherlands and South Africa. The high quality of the genome data, indicating over 42 thousand putative genes, is the result of the use of latest sequencing technologies, which generate long stretches of DNA sequences, a very specific apple variety, and the most informative genetic linkage map in apple developed in earlier research.

The genome sequence gives new insights into the organization of the apple genome. Already 93 percent of the 42,000 putative genes have been validated through RNA sequencing. This knowledge is useful for the identification of genes that control a trait of interest and for the development of DNA-based diagnostic tests that can accelerate breeding of new varieties.

The use of a so-called di-haploid apple variety was critical for the success of this study. Apple is an outcrossing species, making its genome heterozygous. Also, apple originated from a hybridization between two different species, which was coupled with a whole genome duplication. As a result, each regular apple variety has up to four variants for each of its DNA sequences. The di-haploid variety used in this study is special as it has only up to two variants of every sequence. This leads to a dramatic complexity reduction, which made it possible to generate a very high quality genome sequence.

The new insights in the apple genome include a clear view on the duplication patterns among the 17 chromosomes of apple. This facilitates the identification of gene copies with similar function. Next, so called 'repetitive regions' have been assembled. These thus far uncharacterized regions of the apple genome may be involved in regulating gene expression. Finally, a new type of repeat sequence was found that may be specific for centromeres, which may lead to new insights in chromosome division and replication.

The research was coordinated by Etienne Bucher of INRA-Angers. Researchers of Wageningen University & Research contributed to the genome sequencing, genome mapping and assembly, applying their experience and skills in bioinformatics and by giving early access to a high quality reference genetic linkage map in apple.

Wageningen University & Research itself develops new apple varieties, which resulted in the top-variety 'Elstar', 'Santana' and the recently released 'Natyra'. The latter two are suited for biological production since these varieties have disease resistances. Additionally, 'Santana' is suitable for consumption by most individuals with a mild apple allergy.

Wageningen will use the new insights in the DNA of the apple in the targeted breeding of new varieties.

Explore further: Sunflower genome sequence to provide roadmap for more resilient crops

More information: High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development, Nature Genetics (2017). nature.com/articles/doi:10.1038/ng.3886

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Apple genome sequence helpful to breeding of new varieties ... - Phys.Org