Thursday, 26 March 2015

Mobile DNA Sequencer Shows Potential for Disease Surveillance

A pocket-sized device that can rapidly determine the sequence of an organism's DNA has shown its potential in disease detection, according to a study published in the open access, open data journal GigaScience
Thursday, 26 March 2015

This is a close up of MinION.
Credit: Andrew Kilianski.
A pocket-sized device that can rapidly determine the sequence of an organism's DNA has shown its potential in disease detection, according to a study published in the open access, open data journal GigaScience.

In the first analysis of its kind, researchers were able to use the device to accurately identify a range of closely-related bacteria and viruses within six hours, demonstrating the potential for this technology to be used as a mobile diagnostic clinic during outbreaks.

The MinION™ 'Nanopore sequencer' is a low-cost palm-sized sequencing device from Oxford Nanopore Technologies that has been made available to some research groups for testing. It is powered and operated via a USB connection plugged into a laptop, which means that it could potentially be used for on-site clinical analyses in remote locations, negating the need for samples to be sent off to laboratories.

Lead author Andrew Kilianski from Edgewood Chemical Biological Center, USA, whose team tested the device in joint collaboration with Signature Science, LLC, said:

"Our findings are important because we have for the first time communicated to the community that this technology can be incredibly useful in its current state.”

"Being able to accurately identify and characterize strains of viruses and bacteria using a mobile platform is attractive to anyone collecting biological samples in the field. And we expect that as the technology improves, the sequencing will generally become cheaper, faster and more accurate, and could have further clinical applications."

This image shows MinIONs and 
laptops. Credit: Scott Edmunds.
The researchers were able to use the MinION™ to accurately identify and differentiate viral and bacterial species from samples. Within six hours, the device generated sufficient data to identify an E. coli sample down to species level, and three poxviruses (cowpox, vaccinia-MVA, and vaccinia-Lister) down to strain level. The device was able to distinguish between the two vaccinia strains despite them being closely related and over 98% similar to each other.

The technology relies on protein 'nanopores' to determine the sequence of a strand of DNA. At the core of the protein is a hollow tube only a few nanometres in diameter, through which a single DNA strands can pass. As the DNA strand passes through the nanopore, it causes characteristic electrical signatures, from which bases can be identified, and the sequence of the strand determined.

Despite MinION™'s observed read error rate of 30%, which is higher than that of other DNA sequencing methods, the team was able to overcome some of the current limitations by utilizing an approach based on amplified DNA (an 'amplicon' approach). This allowed them to confidently differentiate between closely-related strains.

The amplicon approach allows for the analysis of more complex mixed samples containing a range of organisms in a short runtime. For whole genome sequencing approaches in less pure samples, they note that improvements will need to be made as the technology matures.

The authors state it would be difficult to accurately characterize pathogens within a complex sample in six hours without applying the amplicon methodology.

Contact: Joel Winston

Reference:
Bacterial and viral identification and differentiation by amplicon sequencing on the MinION nanopore sequencer
Andy Kilianski, Jamie L Haas, Elizabeth J Corriveau, Alvin T Liem, Kristen L Willis, Dana R Kadavy, C Nicole Rosenzweig and Samuel S Minot
GigaScience 2015, DOI: 10.1186/s13742-015-0051-z
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Wednesday, 25 March 2015

Stem Cells Make Similar Decisions to Humans

Stem Cells Make Similar Decisions to Humans
Wednesday, 25 March 2015

Pancreas explant. 
Scientists at the University of Copenhagen have captured thousands of progenitor cells of the pancreas on video. They have filmed the cells making decisions to both divide and expand the organ or to specialize into the endocrine cells that regulate our blood sugar levels.

The new study reveals that stem cells behave as people in a society, making individual choices but with enough interactions to bring them to their end-goal. The results could eventually lead to a better control over the production of insulin-producing endocrine cells for diabetes therapy.

The research is published in the scientific journal PLOS Biology.

Why one cell matters
In a joint collaboration between the University of Copenhagen and University of Cambridge, Professor Anne Grapin- Botton and a team of researchers including Assistant Professor Yung Hae Kim from DanStem focused on marking the progenitor of the embryonic pancreas, commonly referred to as ‘mothers’, and their ‘daughters’ in different fluorescent colours and then captured them on video to analyse how they make decisions.

Prior to this work, there were methods to predict how specific types of pancreas cells would evolve as the embryo develops. However, by looking at individual cells, the scientists found that even within one group of cells presumed to be of the same type, some will divide many times to make the organ bigger while others will become specialized and will stop dividing.

The scientists witnessed interesting occurrences where the ‘mother’ of two ‘daughters’ made a decision and passed it on to the two ‘daughters’ who then acquired their specialization in synchrony. By observing enough cells, they were able to extract logic rules of decision-making, and with the help of Dr Pau Rué, a mathematician from the University of Cambridge, they developed a mathematical model to make long-term predictions over multiple generations of cells.

Stem cell movies
"It is the first time we have made movies of a quality that is high enough to follow thousands of individual cells in this organ, for periods of time that are long enough for us to follow the slow decision process. The task seemed daunting and technically challenging, but fascinating,” says Professor Grapin-Botton. 

"With these movies we can see and quantify the dynamics of decisions in each cell in the context of the organ, in a way that will inspire the study of many other organs," says Assistant Professor Yung Hae Kim.

"To complement the movies, which are done on isolated pancreas, we developed a method to visualize the family tree of cells in the untouched organ. We initially focused on one generation but now we are also observing their descendants over multiple generations," Kim elaborates.

Next steps in diabetes therapy
The project has been focused on basic research and is highly theoretical, but it now provides tools to control whether a cell should expand or specialize into an endocrine cell on its way to producing insulin.

“It is a worldwide quest to produce such insulin-producing cells from stem cells, for their transplantation in diabetic patients. In the future, this could be done by increasing the probability of specialization or by pushing ‘mother’ cells to pass on the decision to specialize to their two daughters”, Grapin-Botton concludes.

Contact: Yung Hae Kim

Reference:
Cell Cycle–Dependent Differentiation Dynamics Balances Growth and Endocrine Differentiation in the Pancreas
Yung Hae Kim , Hjalte List Larsen, Pau Rué, Laurence A. Lemaire, Jorge Ferrer and Anne Grapin-Botton 
PLOS Biology, March 18, 2015, DOI: 10.1371/journal.pbio.1002111
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Sunday, 22 March 2015

The ISSCR Issues Statement on Human Germ Line Genome Modification

The International Society for Stem Cell Research has released a statement calling for a moratorium on attempts to apply nuclear genome editing of the human germ line in clinical practice
Sunday, 22 March 2015

In a statement released on Thursday, the International Society for Stem Cell Research called for a moratorium on attempts at clinical application of nuclear genome editing of the human germ line to enable more extensive scientific analysis of the potential risks of genome editing and broader public discussion of the societal and ethical implications.

Technologies used to introduce changes into the DNA sequence of cells have advanced rapidly, making genome editing increasingly simple. Genome editing is feasible, not just in the somatic cells of an adult organism, but also in early embryos, as well as the gametes (sperm and egg) that carry the inheritable, germ line DNA. Research involving germ line nuclear genome editing has been performed to date in many organisms, including mice and monkeys, and applications to human embryos are possible.

The ISSCR statement raises significant ethical, societal and safety considerations related to the application of nuclear genome editing to the human germ line in clinical practice. Current genome editing technologies carry risks of unintended genome damage, in addition to unknown consequences. Moreover, consensus is lacking on what, if any, therapeutic applications of germ line genome modification might be permissible.

The statement calls for a moratorium on attempts to apply nuclear genome editing of the human germ line in clinical practice, as scientists currently lack an adequate understanding of the safety and potential long term risks of germ line genome modification. Moreover, the ISSCR asserts that a deeper and more rigorous deliberation on the ethical, legal and societal implications of any attempts at modifying the human germ line is essential if its clinical practice is ever to be sanctioned.

In calling for the above moratorium, the ISSCR is not taking a position on the clinical testing of mitochondrial replacement therapy, a form of germ line modification that entails replacing the mitochondria (found outside the nucleus) in the eggs of women at risk of transmitting certain devastating diseases to their children.

Contact: Michelle Quivey
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