Between 750,000 and 1 million Irish died during the potato famine in the mid-19th century. Now, for the first time, scientists have sequenced the genome, or genetic script, of the pathogen that caused such devastation.

Reporting in the journal eLife, molecular biologists from the U.S. and Europe said they were able to put together the genetic script of the potato blight using dried potato specimens collected during the famine and preserved.

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Sequence-dependent base-pair stepping dynamics in XPD helicase unwinding
Zhi Qi, Robert A Pugh, Maria Spies, Yann R Chemla
Correspondence: Yann R Chemla / University of Illinois at Urbana-Champaign

The ability of an enzyme called XPD helicase to unwind the double helix is influenced by the DNA sequence and the availability of energy.

Decoding the neural mechanisms of human tool use
Jason P Gallivan, D Adam McLean, Kenneth F Valyear, Jody C Culham
Correspondence: Jason P Gallivan / Queen’s University

Imaging experiments reveal that some brain regions do not distinguish between actions performed using tools and those performed using the hands, while others represent these two types of action separately.
See also: Insight by Bradford Mahon

Pharmacological brake-release of mRNA translation enhances cognitive memory
Carmela Sidrauski, Diego Acosta-Alvear, Arkady Khoutorsky, Punitha Vedantham, Brian R Hearn, Han Li, Karine Gamache, Ciara Gallagher, Kenny K-H Ang, Chris Wilson, Voytek Okreglak, Avi Ashkenazi, Byron Hann, Karim Nader, Michelle R Arkin, Adam R Renslo, Nahum Sonenburg, Peter Walter
Correspondence: Peter Walter / Howard Hughes Medical Institute, University of California, San Francisco

A compound that prevents stressors such as UV light and viral infection from downregulating protein synthesis inside cells improves memory performance in mice.
See also: Insight by Graham D Pravitt

TRPM5-mediated calcium uptake regulates mucin secretion from human colon goblet cells
Sandra Mitrovic, Cristina Nogueira, Gerard Cantero-Recasens, Kerstin Kiefer, José M Fernández-Fernández, Jean-François Popoff, Laetita Casano, Frederic A Bard, Raul Gomez, Miguel A Valverde, Vivek Malhotra
Correspondence: Vivek Malhotra / Center for Genomic Regulation

Goblet cells secrete mucins – which are key components of mucus – in a process that is regulated by calcium ions, which enter the goblet cells via a mechanism involving a channel protein called TRPM5.

The rise and fall of the Phytophthora infestans lineage that triggered the Irish potato famine
Kentaro Yoshida, Verena J Schuenemann, Liliana M Cano, Marina Pais, Bagdevi Mishra, Rahul Sharma, Chirsta Lanz, Frank N Martin, Sophien Kamoun, Johannes Krause, Marco Thines, Detlef Weigel, Hernán A Burbano
Correspondence: Hernán A Burbano / Max Planck Institute for Developmental Biology

The late blight pandemic that included the Irish Great Famine in the nineteenth century was caused by a single Phytohpthora infestans genotype, which is distinct but closely related to the most prevalent genotype of the twentieth century.

Article available ahead of publication: http://arxiv.org/abs/1305.4206

Insights

Neuroscience: Watching the brain in action
Bradford Mahon

Cell biology: Less translation, more memory
Graham D Pravitt

Features

Building for the future
Hugh Pelham

An international team of scientists has finally solved one of history’s greatest mysteries: What caused the devastating Irish potato famine of 1845? The research team, which published its findings in the journal eLife this week, used DNA sequencing of plant specimens dating from the mid-19th century to identify the pathogen that led to the death of nearly 1 million people and the mass emigration of another 2 million from Ireland by 1855. The discovery marks the first time scientists have successfully sequenced a plant’s genome from preserved samples and opens the door for further research into the evolution of pathogens and the spread of plant disease around the world.

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They have called the strain HERB-1.

The deadly famine has been linked to a fungal disease called potato blight, which came to Ireland from Mexico.

A team of molecular biologists from Europe and the US reconstructed the spread of the potato blight pathogen from dried plants.

Many of the materials, despite being between 120 to 170 years old, contained intact pieces of DNA, according to the details published in the journal eLife.

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Scientists have used plant samples collected in the mid-19th Century to identify the pathogen that caused the Irish potato famine.

A plant pest that causes potato blight spread to Ireland in 1845 triggering a famine that killed one million people.

DNA extracted from museum specimens shows the strain that changed history is different from modern day epidemics, and is probably now extinct.

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More than 150 researchers and 75 scientific groups issued a declaration on Thursday against the widespread use of journal “impact factors,” blaming the practice for dangerous distortions in financing and hiring in science.

The impact factor “has a number of well-documented deficiencies as a tool for research assessment,” the scientists said in the letter, which had been in preparation since a conference led by publishers and grant-writing agencies last year in San Francisco.

Those deficiencies include the ability of publishers to manipulate the calculations, and the way the metrics encourage university hiring and promotion decisions, as well as grant agencies’ award distributions, that can lack an in-depth understanding of scientific work.

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The Wellcome Trust and the Higher Education Funding Council for England are among the bodies calling for the use of the journal impact factor in funding, appointment and promotion decisions to be scrapped.

The metric – which ranks journals by the average number of citations their articles attract in a set period, usually the preceding two years – has become “an obsession in world science”, says a coalition of academics, editors, publishers and research funders, in a declaration published on 16 May.

“The Journal Impact Factor was developed to help librarians make subscription decisions, but it’s become a proxy for the quality of research,” said Stefano Bertuzzi, executive director of the American Society for Cell Biology (ASCB).

“The ‘high-impact’ obsession is warping our scientific judgement, damaging careers, and wasting time and valuable work.”

Read more (Please note that this article is not open-access.  You may be prompted to pay a fee to view complete text.)

Mark Ware recently asked me some questions about the state of web scale annotation, based on my impressions from the recent iannotate conference (at which I gave a short talk on the idea of research threads)

What is the eLife view of annotation systems?

We like the fact that there is now a W3C standard for Open Annotations (OA). We are encouraged that so many projects out there are looking to make their annotations interoperable with this standard.

Are you planning to support open annotation on the eLife site?

We implemented discussion using Disqus, and we are happy with that so far, but we are looking at (OA) for some other potential products. If there were a way to make other annotations from other sources apparent to our readers on our article pages we would definitely look into supporting that. We have been looking at some of the work of the open citations project , and my understanding is that there is a move to make data from this project available under the OA framework.

If so, which platform would you use, Hypothes.is or something else?

We would probably use Hypothes.is, Domeo or annotator, but it would come down to the pros and cons when it got to the point of implementation. We need to look at all of these tools more closely, but all three of these tools are excellent.

Do you see open annotation as offering something distinctively different from earlier commenting approaches, which (I think) have had rather limited success?

Yes. Two things mainly:

1) many tools are looking to make their data cross functional through the OA W3C spec, that could be huge if many academic players adopt tools that support this. Think of like being RSS for scientific assertions, that would just be huge. It opens the door to all sorts of applications that simple RSS of comments don’t support.

2) the ability to tie an activity to a specific location in the text. Though frequency of annotation may not be higher than commenting, location specific activity is intrinsically more valuable, being able to see quickly, for example, the location of a paper that has interested the most people. In addition this framework is ideally suited to making machine learning runs over the literature connect well to the human reading experience.

How critical is the reputation management part? Hypothes.is have made a big deal of this, with a workshop last year and a lot of reputation experts in their advisers, but I wonder if it will add unnecessary complexity for STM annotation? I think Hypothes.is seen as an important part of ensuring quality though?

This was not the focus of the recent workshop, which was far more about implementing the underlying infrastructure of annotation. That said I personally think you can look at three broad use cases around annotation.

Personal annotation (public or private). In this case reputation is not a concern.

Public annotation as a signifier of activity. In this case you are looking that there is annotation, rather than looking at what the annotation says. In this case reputation is required only at the level of determining whether the annotation is span or not. We have a reasonable handle on how to deal with this in other web scale systems.

Annotation as a guide to insight. In this case reputation is critically important, and it seems that the key is going to be making annotation systems interoperable, so that karma can flow from one system to another. It’s a subtle issue, and one that we will need to address going forward. John Perry Barlow made the great point that information is not the same as knowledge and not the same as insight, and it is knowledge systems that we should be striving to create.

Do you have any concern about pseudonymous commenting at eLife?

We do. We allow anonymous comments on eLife, but only where the commenter has explained who they are, and justified why their comment should be anonymous. In terms of pseudonymous commenting, this is something I am less worried about in the academic sphere, as name, identity reputation and prestige are so deeply linked. Were one academic to impersonate another I feel that this would be uncovered very quickly. In the few cases where there has been high profile sock puppetry there is usually a fairly clear smell around the topic area.

Are there any concerns about long term preservation of annotations alongside the original article, i.e. is there any danger of them not being as robustly preserved as journal content (e.g. with dark archives etc.) and/or getting separated from the content?

This is a subtle question. It’s not clear that you want all comments available all the time. A new student might be better served by the text being presented as a blank slate (something that rapgenius is not yet able to do). On the other end, were we to be able to see every annotation that had ever been made on the the bible, the annotation corpus would significantly outweigh the underlying corpus. Perhaps our systems will need to be able to selectively forget, or fumble the information? I’m not sure.

In terms of preservation, this is something that came up in the talk and was mooted as one of the fundamental “Hilbert problems” for the annotation community. Other people felt that the majority use cases were going to be personal. I think it is fair to say that there are indeed concerns, but how those concerns break down is not clear, and what we do about them is also not clear.

One of the deep insights in the conference was that we have not created a web, but rather a directed graph. The architecture of the internet does not allow resources to know what other resources are saying about them, or what other resources are pointing at them. Perhaps this is the problem that annotation can solve?