DNA Day

Every year in April countries around the world celebrate DNA Days. These national DNA Day are very often used to educate the public about current DNA science. Students, teachers and the public can learn more about genetics and genomics. The day commemorates both the completion of the Human Genome Project in April 2003, and the discovery of DNA's double helix in 1953.

Canada’s DNA Day brings together students and the science community.  Established by Let’s Talk Science and Genome Alberta, it includes live virtual Q&A sessions with Canadian experts. This year the events cover personalized medicine and DNA barcoding. The barcoding part will be broadcasted from of our institute on April 21st and yours truly and two colleagues will give short talks and serve as experts in the Q&A sessions.

Sounds like fun and I am really looking forward to it.

Another round of the intro course

By the way, we are running another round of the DNA barcoding intro course. It will start in a week from now: April 18 to June 10, 2016

Meanwhile I am busy developing two new modules, one on metabarcoding and another on of DNA barcoding in regulatory contexts and forensics

Distribution and diversity of a potato cyst nematode

Image from http://nematode.unl.edu

Potato cyst nematodes (PCN) are small (1 mm) roundworms belonging to the genus Globodera, which comprises 12 species. These worms live on the roots of plants of the Solanaceae family with prominent members such as potatoes and tomatoes. The nematodes cause growth retardation and, at very high population densities, damage to the roots and early senescence of the plants. PCN are thought to be originated in the Andes but are now widespread both in Europe and North America .

These nematodes can cause significant economic damage. Estimated costs due to yield loss and control measures are thought be at the range of billions of US dollars. PCN species are present on both EPPO and USDA quarantine organism lists.

Science and Advice for Scottish Agriculture (SASA) annually undertake national DNA diagnostic tests to determine the presence of PCN in potato seed and ware land by extracting DNA from soil floats. These DNA samples provide a unique resource for monitoring the distribution of PCN and further interrogation of the diversity within species.

In a new study researchers identified a section of cytb (<450bp) descriptive of three main mitotypes of one species (Globodera pallida) present in the UK and used a high throughput sequencing approach to the simultaneous analysis of all SASA samples (>800). By using this approach, the colleagues were able to describe the distribution of Globodera pallida mitotypes across Scotland with field-scale resolution. In addition they could quantify the relative abundance of each mitotype across an order of magnitude.

This study provides a method for accurate, quantitative and high-throughput typing of up to one thousand fields simultaneously, while revealing novel insights into the national genetic variability of an economically important plant parasite.

The future of biodiversity collections

The time for business as usual has passed. Threats to biodiversity are increasing. There is a real concern that the scientific community does not have the resources necessary to answer important questions.

This concern has been reinforced recently as e.g. in the US state and federal agencies have reduced or withdrawn support for biodiversity collections. The biodiversity community has responded to these developments in the usual ways, reactive, but not proactive.

Biological diversity collections leaders, scientists, communications professionals, and scientific organization leaders met last Fall at The Field Museum of Natural History in Chicago for a workshop organized by the Biodiversity Collections Network. They identified poor communication within the biodiversity collections community and between the community and decision-makers as a contributing factor. 

Seven recommendations emerged from this workshop and are outlined in a report. The general recommendations are:

1) The community must articulate a compelling and inclusive long-term vision for natural history collections.

2) The community should work with an existing community-serving organization with links to administrators, policymakers, and communicators to foster greater coordination of targeted messages.

3) The community must engage new stakeholders to increase the sustainability (i.e., new funding, proper institutional support, adequate workforce) of digitization efforts.

4) The community must do a better job of communicating outcomes and benefits of digitization efforts to policymakers, administrators, other scientists, and the public.

5) The community must develop metrics for assessing the impact of current and new communication tools and practices.

6) The community must develop and embrace innovative communication methods and tool kits.

7) The community must support and engage in communications training programs that help all biodiversity collections stakeholders, particularly scientists, become more effective spokespeople for natural history collections.

These developments show how important it is that we do a better job of communicating about both the increased demand for spatial and temporal data on biodiversity and the vitally important research that biodiversity collections enable. The report includes a number of significant recommendations for the Natural Science Collections Alliance and we are eager to begin addressing these in collaboration with our membership and partners.

Hope for cold water species

The great irony is that the cold headwater streams that were believed to be most vulnerable to climate change appear to be the least vulnerable. Equally ironic is that we arrived at that insight simply by amassing, organizing and carefully analyzing large existing databases, rather than collecting new data that would have been far more expensive.

A research team led by the U.S. Forest Service drew information from huge stream-temperature and biological databases contributed by over 100 agencies and a USGS-run regional climate model to describe warming trends throughout 222,000 km of streams in the northwestern United States.

The colleagues found that over the last 40 years, stream temperatures warmed at the average rate of 0.10°C per decade. This translates to thermal habitats shifting upstream at a rate of  300-500 meters per decade in headwater mountain streams where many sensitive cold-water species currently live. The authors are quick to point out that climate change is still detrimentally affecting the habitats of those species, but at a much slower rate than earlier studies forecast. This indicates that many populations of cold-water species will continue to persist this century and mountain landscapes will play an increasingly important role in that preservation by becoming climate refugia. This also means that resource managers will have more time than previously thought to complete extensive biological surveys of ecological communities in mountain streams so that conservation planning strategies can adequately address all species.

One of the great complexities of restoring trout and salmon under a rapidly changing climate is understanding how this change plays out across the landscape. Dr. Isaak and his colleagues show that many mountain streams may be more resistant to temperature change than our models suggest and that is very good news. This provides us more time to effect the changes we need for long-term persistence of these populations.

A DNA diode

It looks as if this week will become my "what-else-is-happening-in-DNA-research" week. Yesterday the alternate use of stop codons in some bacteria and today the fascinating research by colleagues from the US and Israel - a nanoscale diode made out of DNA.

Continuous demand for more computing power is pushing the limitations of present day methods. This need is driving researchers to look for molecules with promising properties and find ways to establish reliable contacts between molecular components and bulk materials in an electrode, in order to mimic conventional electronic elements at the molecular scale.

An example for such an element is the nanoscale diode (or molecular rectifier). A diode operates like a valve to facilitate electronic current flow in one direction. Researchers envision that a collection of these nanoscale diodes, that are essentially molecules, has properties that resemble traditional electronic components such as a wire, transistor or rectifier. The emerging field of single molecule electronics hopes to find ways to overcome Moore's Law - the observation that over the history of computing hardware the number of transistors in a dense integrated circuit has doubled approximately every two years - beyond the limits of conventional silicon integrated circuits.

The researchers took a single DNA molecule constructed from just 11 base pairs and connected it to an electronic circuit only a few nanometers in size. When they measured the current through the molecule, it did not show any special behavior. However, when layers of a coralyne were inserted between layers of DNA, the behavior of the circuit changed drastically. Coralyne is a small crescent-shaped molecule that is among a group of molecules known to preferentially intercalate DNA triplexes over duplexes and to increase the thermal stability of triplex DNA . In the case of the diode experiment the current jumped to 15 times larger negative vs. positive voltages--a necessary feature for a nano diode.

In summary, we have constructed a molecular rectifier based on intercalating specific, small molecules into designed DNA strands. Not only do these results offer a new method for studying the DNA–molecule interaction, they also suggest a novel strategy for engineering molecular electronic elements based on a specifically designed functional DNA complex.

Stop doesn't always mean stop

This illustrates the ease by which the genetic code may evolve new coding schemes, possibly aiding organisms to adapt to changing environments, and show the genetic code is much more flexible than previously thought.

In 2014 researchers from the Joint Genome Institute and Yale University found out that some organisms interpret the one of three "stop" codons which terminate translation to mean anything but. In a computational study they scanned several trillion base pairs of metagenomic data and revealed a large number of stop codon reassignments in bacteria and bacteriophages. In some of those organisms, the three-letter codon UGA, which normally signals the end of a protein-coding gene, is hijacked to code for a the rarely encoded amino acid called selenocysteine.

The same team now discovered that some microorganisms actually recognize more than one codon for selenocysteine. From approximately 6.4 trillion bases of metagenomic sequences and 25,000 microbial genomes, the team identified several species that recognize the stop codons UAG and UAA, in addition to 10 sense codons, as acceptable variants for the selenocysteine codon UGA.

What about eukaryotic organisms? Although we found nine tRNASec variants of algal origin, they need further validation, because they are almost identical to canonical tRNASec species. A similar search of 92 mammalian genomes (215 Gbp) and of the Drosophila melanogaster genome (139 Mbp) showed no exception to the use of UGA as the Sec codon. Whether this is related to the necessity of selenoproteins in high-level redox signaling pathways or due to the sophisticated backup systems remains to be investigated. However, in the lower eukaryote Euplotes crassus UGA serves both as a Cys and also as a SECIS-dependent Sec codon