Monthly Archives: July 2017

Achieving the genomics dream could make a huge difference to the 3.5 million adults and children with one of the 7,000 recognised rare diseases that could be treated far more quickly and more effective with genome testing.

Every persons genome contains 3.2 billion letters of genetic code, amounting to two terabytes of data. If it was printed your genome would fill a stack of books 61 metres high. Although officials now talk about personalised medicine, what they are trying to deliver is diagnosis and treatment related to the genomic signature of a particular patient.

It would be a disservice to patients if the UK were slow to respond to innovations in this area.

Sir Harpal Kumar, Chief Executive, Cancer Research UK

This means giving the most effective drugs against cancer, using drugs which will cause fewer side effects, seeking new drugs and treatments and moving to personalised prevention. There will also be other applications, many of which we are not yet aware of, the report says.

In the case of cancer, tumour cells develop a different genome to normal cells. Comparing a patients normal and cancerous DNA can provide valuable clues about the best form of treatment, although this information is not set in stone. Cancers evolve rapidly and alter their DNA, which can make them resistant to treatments.

This is still much more to learn about genomes and their relation with treatment response, but once that knowledge base expands there should be much faster diagnosis of rare diseases which currently take on average four years to diagnose.

The average patient sees five different doctors and is misdiagnosed three times before the nature of his or her illness is finally known.

As Dame Sally Davies the nations top doctor pointed out when launching her Generation Genome report, the true benefits of genomic medicine will only be realised if all clinical staff, managers and the Government work together to make wider use of revolutionary genetics techniques in the battle to improve cancer survival rates and identify rare diseases faster so patients can get the right care at the earliest opportunity.

Sir Harpal Kumar, Cancer Research UKs chief executive, said: It would be a disservice to patients if the UK were slow to respond to innovations in this area.

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How your genome could make cancer treatment more effective - iNews

July 3, 2017

The genome sequences of two "false" corals offer a window into the evolution of calcification, which may help their reef-building cousins.

Mushroom polyps. Elephant ear corals. Disc anemones. Whatever you want to call themscientists prefer corallimorphsthese aquarium invertebrates are among the closest known relatives to reef-building corals. A team led by researchers from the Red Sea Research Center at KAUST has now sequenced the entire genomes of two such "naked" coral species, so-called because they don't lay down calcium carbonate skeletons.

DNA maps offer a window into the evolution of calcification and could help scientists save the world's coral reefs from extinction.

"These are the first genomes to be published from this group of organisms," said Manuel Aranda, an Assistant Professor of Marine Science at KAUST who led the genome project. "The resources and analysis we provide are the foundation for future studies aimed at understanding how corals evolved the ability to build one of the most productive and biodiverse ecosystems on our planet."

Aranda teamed up with researchers at the Scientific Centre of Monaco to extract DNA from tissue samples of Amplexidiscus fenestrafer and Discosoma sp., two corallimorphs with a shape like that of terrestrial mushrooms. Xin Wang, a Ph.D. student in Aranda's lab, then worked with technicians at the KAUST Bioscience Core Facility to sequence, assemble and annotate both species' genomes. They pinpointed all the genes in the corallimorph genomes by looking for sequence similarity to known genes found in other species' genomes, including those of two sea anemones and a coral.

In this way, they confirmed that corallimorphs are the closest living relatives of reef-building corals, providing a much-needed genomic resource to fill the evolutionary gap between sea anemones and corals. They also showed that the A. fenestrafer genome is approximately 370-million DNA letters long with 21,372 genes and that the genome of A. Discosoma is 445-million nucleotides in length with 23,199 genes. These sizes are in between those for sea anemones and corals, consistent with the evolutionary history and complexity of this taxonomic grouping.

Scientists everywhere can now freely access and browse both new corallimorph genome maps though an online platform available at corallimorpharia.reefgenomics.org.

Aranda hopes the research community will use the genome sequences to better understand the evolutionary origin of the genes that allowed corals to become the ecosystem builders they are today. In his lab, for example, Aranda and his team are exploring the evolutionary innovations that corals had to make to acquire the ability to calcify. "So far," said Wang, "we have found several genes involved in calcification that have been uniquely duplicated in corals."

Explore further: Gene sequences reveal secrets of symbiosis

Advances in genomic research are helping scientists to reveal how corals and algae cooperate to combat environmental stresses. KAUST researchers have sequenced and compared the genomes of three strains of Symbiodinium, a ...

Single-celled plankton known as dinoflagellates are shown to cope with stress using an unexpected strategy of editing their RNA rather than changing gene expression levels.

Sequencing the genome of an organism allows scientists to investigate its unique genetic make-up, its evolutionary links to other creatures, and how it has adapted to its environment. Researchers at King Abdullah University ...

UH Mnoa scientists at the John A. Burns School of Medicineand the Hawaii Institute of Marine Biology have published new research showing that corals share many of the genes humans possess, especially those that can ...

New genome-sequence data show that Caribbean corals that have survived mass-extinction events caused by environmental change can rebound and expand their populations.

Unique sections of coral DNA can indicate a higher tolerance to environmental stress, researchers have revealed for the first time.

Beech trees should be considered native to Scotland - despite a long-running debate over their national identity, researchers at the University of Stirling and Science and Advice for Scottish Agriculture (SASA) report.

Purdue University scientists released research findings that indicate corn management processes contributing to optimal levels of plant nitrogen uptake could result in fewer nitrous oxide emissions, long identified as one ...

Arizona State University geoscientist Everett Shock has collaborated with a team of life scientists from Montana State University to discover a puzzle at the junction of geochemistry and biology.

Researchers from James Cook University and the Universit catholique de Louvain, Louvain-la-Neuve, Belgium say unprecedented oceanographic conditions in 2016 produced the perfect storm of factors that lead to a mass coral ...

Half a degree Celsius of global warming has been enough to increase heat waves and heavy rains in many regions of the planet, researchers reported Friday.

Oklahomans are no strangers to Mother Nature's whims. From tornadoes and floods to wildfires and winter storms, the state sees more than its share of natural hazards. But prior to 2009, "terra firma" in Oklahoma meant just ...

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Mushroom-like corals get their genomes mapped - Phys.Org

Our genomes are minefields, studded with potentially damaging DNA sequences over which hundreds of thousands of sentries stand guard. These sentries, called epigenetic marks, attach to the double helix at such spots and prevent the underlying DNA sequences from springing into destructive action.

About half the human genome is composed of these damaging sequences. They are places where ancient viruses and parasitic elements called transposons and retrotransposons have incorporated themselves over the long course of evolution. It's astonishing, then, to consider that during two of the most crucial processes in the life cycle, the sentries are removed, leaving the genome naked. The defenders are quickly welcomed back, but only after an interval in which the epigenetic slate is wiped clean.

Today in Cell, a team from Cold Spring Harbor Laboratory (CSHL) describes its discovery of what might be considered emergency replacements for the sentries, shock troops pressed into service across the genome only during these curiously undefended moments. Specifically, these defenders are protecting the genome in mammalian embryos, at the very early point in their development before they are implanted in the wall of the maternal uterus.

The preimplantation embryo is one of two normal settings in which epigenetic marks are wiped clean before being reinscribed. The other setting is a step in the formation of germline cells - sperm and eggs -- which have temporary defenders already known to biology, so-called piwi-interacting RNAs (piRNAs). The research published today, led by first author Andrea Schorn, a postdoctoral investigator in the lab of Rob Martienssen, demonstrates that another species of small RNA performs an analogous genome-defending role in preimplantation embryos during an interval of epigenetic reprogramming. Dr. Martienssen is a CSHL Professor and HHMI-Gordon and Betty Moore Foundation investigator.

The newly identified defenders come in two varieties - RNA fragments consisting of 18 and 22 nucleotides. These RNA fragments, Dr. Schorn discovered, are perfect complements of sequences in retrotransposons that must be engaged in order for the genomic parasites to be activated.

This fact led to the discovery. Schorn scrutinized the contents of mouse embryonic stem cells and found many free-floating RNA fragments 18 nucleotides in length. Computer analysis revealed that their sequences perfectly matched sequences within transfer RNAs. tRNAs are ubiquitous, and are involved in the synthesis of proteins. It has been known for decades that tRNAs are hijacked by long terminal repeat (LTR)-retrotransposons, a portion of their sequence docking at a primer binding site (PBS) and initiating a process that activates the genomic parasite.

"Knowing that LTR retrotransposons need tRNAs to replicate, it was very tempting to believe that these 18-nucleotide tRNA fragments we were seeing in preimplantation embryonic stem cells could interfere with that process," says Schorn. "We think the cell is deliberately chopping up full-length tRNAs into smaller fragments precisely because both tRNAs and the fragments cut from them recognize the PBS. This means the small, tRNA-derived fragments would be able to occupy that site and inhibit retrotransposon replication and mobility," Martienssen explains.

The implications, Martienssen says, are potentially profound. This appears to tell us one way in which the genomes of mammals have tolerated vast numbers of transposons and other parasitic elements, even during periods when the genome is wiped clean of repressive epigenetic marks. "It's plausible that this is a very ancient mechanism that cells have found to not only inhibit retrotransposons but help in protection against viruses as well," Martienssen says.

Read more from the original source:
Newly Identified Small RNA Fragments Defend the Genome When It's 'Naked' - Bioscience Technology