Category Archives: Transhuman News

UC Santa Cruz Banana Slug Genome Project
Learn more at crowdfund.ucsc.edu/sluggenome!

By: UCSantaCruz

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UC Santa Cruz Banana Slug Genome Project - Video

PUBLIC RELEASE DATE:

27-Oct-2014

Contact: Craig Brierley craig.brierley@admin.cam.ac.uk 44-012-237-66205 University of Cambridge @Cambridge_Uni

The team of researchers, led by Dr Rafael Carazo Salas from the Department of Genetics, combined high-resolution 3D confocal microscopy and computer-automated analysis of the images to survey the fission yeast genome with respect to three key cellular processes simultaneously: cell shape, microtubule organisation and cell cycle progression. Microtubules are small, tube-like structures which help cells divide and give them their structure.

Of the 262 genes whose functions the team report in a study published today in the journal Developmental Cell, two-thirds are linked to these processes for the first time and a third are implicated in multiple processes.

"More than ten years since the publication of the human genome, the so-called 'Book of Life', we still have no direct evidence of the function played by half the genes across all species whose genomes have been sequenced," explains Dr Carazo Salas. "We have no 'catalogue' of genes involved in cellular processes and their functions, yet these processes are fundamental to life. Understanding them better could eventually open up new avenues of research for medicines which target these processes, such as chemotherapy drugs."

Using a multi-disciplinary strategy that took the team over four years to develop, the researchers were able to manipulate a single gene at a time in the fission yeast genome and see simultaneously how this affected the three cellular processes. Fission yeast is used as a model organism as it is a unicellular organism in other words, it consists of just one cell whereas most organisms are multicellular, yet many of its most fundamental genes carry out the same function in humans, for example in cell development.

The technique enabled the researchers not only to identify the functions of hundreds of genes across the genome, but also, for the first time, to systematically ask how the processes might be linked. For example, they found in the yeast and, importantly, validated in human cells a previously unknown link between control of microtubule stability and the machinery that repairs damage to DNA. Many conventional cancer therapies target microtubular stability or DNA damage, and whilst there is evidence in the scientific literature that drugs targeting both processes might interact, the reason why has been unclear.

"Both the technique and the data it produces are likely to be a very valuable resource to the scientific community in the future," adds Dr Carazo Salas. "It allows us to shine a light into the black box of the genome and learn exciting new information about the basic building blocks of life and the complex ways in which they interact."

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Imaging the genome: Cataloguing the fundamental processes of life

PUBLIC RELEASE DATE:

27-Oct-2014

Contact: Susan Brown sdbrown@ucsd.edu 858-246-0161 University of California - San Diego @UCSanDiego

A hinge in the RNA genome of the virus that causes hepatitis C works like a switch that can be flipped to prevent it from replicating in infected cells. Scientists have discovered that this shape is shared by several other virusesamong them one that kills cancer cells.

That's Seneca Valley virus, which seems harmless to healthy human cells but lethal to cancer stem cells.

"Clearly we'd like to understand it better," said Thomas Hermann, professor of chemistry and biochemistry at the University of California, San Diego.

Hermann's research group has determined the molecular structure of this critical switch in the Seneca Valley virus and found that it matches the L-shaped switch in hepatitis C virus, which his group had previously described.

The similarity was a surprise.

"It wasn't immediately apparent to us from the genome sequence alone," said Mark Boerneke, a graduate student in chemistry and lead author of the report in the Proceedings of the National Academy of Sciences online the week of October 27. "This is a different virus that regulates protein production in a similar fashion."

This kind of viral on-off switch is part of an IRES, for internal ribosome entry site. Ribosomes are the structures inside cells that make proteins. Lacking their own protein-making machinery, viruses use the IRES to hijack the ribosomes of cells they've infected to produce proteins they need to replicate.

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Viral switches share a shape

The Genome Analysis Centre (TGAC) in Norwich will lead research into the development of bioinformatics to support the identification and characterisation of viruses through metagenomics.

The BBSRC-funded research, led by TGACs Dr Richard Leggett, aims to develop computational algorithms that can accurately assemble viral genomes contained within metagenomic samples. These microbial samples pose a challenge to researchers as, not only do they contain numerous different viral species, it is also difficult to locate precisely which species are present.

As a currently under-explored area, the research is vital to improve our ability to identify viruses. Beneficial to researchers involved in the study of animal-to-human transmitted viruses, disease diagnostics and epidemiology, the three-year project will demonstrate the practical value of the developed bioinformatics tool by testing it against real datasets taken from species expected to host a variety of viruses, including a set of African rodent samples.

Samples are being provided by collaborators led by Pablo Murcia at the MRC-University of Glasgow Centre for Virus Research.

Metagenomics is broadly defined as environmental genomics, allowing the study of microbial communities of our living world. While the sequencing of metagenomic samples follows the same process as that for sequencing a single genome, it becomes more complex at the assembly stage where the short sequenced fragments of DNA must be correctly arranged into the genomes of multiple species.

This intricacy is compounded by the currently limited bioinformatics tools available to conduct the assembly for metagenomic samples, particularly for those containing viruses. Having demonstrated the possibility and feasibility of such a tool by the Institutes previous MetaCortex project, the new research will create the algorithms required to address this gap in metagenomic capabilities.

Dr Richard Leggett, project leader at TGAC, said: This is an exciting project and we hope the work will equip researchers who are looking at a wide range of viral infections, including those affecting humans and agriculturally important livestock.

The project, titled: Development of computational strategies for identification and characterisation of viruses in metagenomic samples is funded by the BBSRC Responsive Mode Award.

The Genome Analysis Centre (TGAC) is a world-class research institute focusing on the development of genomics and computational biology.

TGAC is based within the Norwich Research Park and receives strategic funding from the Biotechnology and Biological Science Research Council (BBSRC) 7.4 million in 2013/14 as well as support from other research funders.

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TGAC leads research to identify animal-human transmitted diseases