Yersinia pestis, Ghost of Plagues Past

Skeleton Blog2

Who’s afraid of the big bad plague? Bet you the owners of the bones above were. This Halloween, we’re highlighting the work of researchers who tested (extremely carefully) for the presence of the pathogen Yersinia (Y.) pestis (a.k.a., the “Bubonic Plague”) in human skeletal remains from three sites in Germany and Switzerland.  Thought to be victims of the Black Death, these individuals died alongside an estimated 75-200 million other Europeans affected by this outbreak of the plague, which diminished Europe’s population during the 14th century by one third.

The specialized protocol the researchers used in this study was carefully created to be in line with modern plague diagnostic procedures and to address the unique challenge of working with ancient DNA (aDNA), which varies in quality from sample to sample and is easily contaminated with modern DNA. Contamination is common and can be hard to identify, often resulting from poor handling practices at excavation or during preparatory procedures. The researchers  did their best to avoid the possibility by thoroughly cleaning the surfaces of the bones and teeth that samples were drawn from, and using multiple controls to highlight any points of contamination from the laboratory that occurred during the experiments. At a time when the results from testing of aDNA samples can be highly contested, a validated  DNA replication process was used to ensure authenticity of the tests and to prevent misinterpretation of the results by the scientific community.

Bones and teeth from 29 individuals, ranging from 300-600 years old, were collected from sites in Manching-Pichl and Brandenburg in Germany and Basel, Switzerland and housed at the State Collection for Anthropology and Palaeoanatomy  in Munich. Selected samples were then moved to newly constructed labs at the ArcheoBio Center of the Ludwig Maximilian University  Munich for preparation and aDNA extraction. Researchers followed a strict protocol to prevent any sample contamination at this stage. The new facility contains three air-locked and pressurized rooms, each meant to provide a contamination-free workplace for processing aDNA samples for replication. Before admittance to the three-room complex, staff were required to shower, wash their hair, and enter a gowning room to replace their freshly laundered clothes with two pairs of gloves, a hairnet, hooded overalls, and a screened facemask. A second gowning room required the addition of another set of hooded overalls. Scientists then moved through the rooms sequentially, preparing the aDNA samples and negative controls (meant to test for contamination in the replication process) for analysis.

Once preparatory procedures were complete, sealed tubes containing the negative controls and aDNA were transferred to the Bundeswehr Institute of Microbiology for the addition of positive controls (tubes containing DNA from Y. pestis), DNA replication and analysis. Of the 29 samples tested, seven contained fragments of a Y. pestis gene after an initial round of replication, and four additional samples tested positive for Y. pestis after further rounds of testing.

Although the skeletons above are not, Y. pestis is still alive and well in parts of the world. Now called the “Modern Plague” to differentiate it from previous plagues caused by the same pathogen, such as Justinian’s plague and the Black Death, the disease affects 1,000-3,000 people per year. Modern treatments have thankfully limited the number of deaths that result from these cases, leaving us less likely to end up in the ground after getting sick, like these poor individuals. Nevertheless, research on the presence of the pathogen in ancient samples remains crucial for our continued understanding of how this disease affected our population in the past.

So, in case you need a scary costume idea for tonight’s festivities, why not draw some inspiration from our friends above? A skeletal Black Death victim and a masked, double-overalled plague researcher sound like great costume ideas to us.

Happy Halloween from PLOS ONE!

Citation: Seifert L, Harbeck M, Thomas A, Hoke N, Zöller L, et al. (2013) Strategy for Sensitive and Specific Detection of Yersinia pestis in Skeletons of the Black Death Pandemic. PLoS ONE 8(9): e75742. doi:10.1371/journal.pone.0075742

Image Credit: Courtesy of the authors and the Bavarian State Department of Historical Monuments


Beta SHERPA/FACT Applications Programmer’s Interface Announced

SHERPA Services is pleased to announce the launch of a beta version of an application programmers’ interface (API) for SHERPA/FACT, the funders and authors compliance tool. This is available for beta testing during November 2013.

Potential Applications

SHERPA/FACT is a tool that helps authors check if a journal’s open access policies complies with the requirements of the open access policies of the research funders Research Councils UK (RCUK) and Wellcome Trust. The data on journal policies is drawn from SHERPA/RoMEO and the funders’ policies from SHERPA/JULIET. Matching the two sets of policies is quite a complex process.

The FACT website (http://www.sherpa.ac.uk/fact/) is designed for general use. However, some users may wish to customise SHERPA/FACT for their institutions, which can be achieved using the FACT API. For instance, the API would enable them to:

  • Embed FACT within their own branded web pages
  • Link to local information on open access funds, guides, policies, and advisors
  • Reformat the FACT data, for example to highlight local policies and preferences

The FACT API could also be used for statistical studies, such as checking the potential compliance of lists of journals or articles. E.g. see:

http://www.sherpa.ac.uk/documents/FACT-OR2013-2013-07-09.pptx, slides 20 to 23.

Main Features

Having specified the required funder(s), the API can be queried by journal titles or ISSNs.

The API returns FACT data for Gold (Paid OA), Green (self-archiving) and Overall compliance. There is a choice of XML (default), JSON, and PHP array output formats. In general, all computable information is returned as arguments and displayable information is returned as data. E.g.

<goldcompliance goldcompliancecode="yes" goldcompliancereport="paidoa">You can publish your article compliantly with open access</goldcompliance>

See: http://www.sherpa.ac.uk/fact/apimanual for more information and examples.

Beta Testing Invitation

We invite developers and researchers to participate in the beta testing of the FACT API. You need to register for a free SHERPA/RoMEO API Key, which you can do at:

http://www.sherpa.ac.uk/romeo/apiregistry

There is a short presentation on how to register and how to use the API key at:

http://www.sherpa.ac.uk/romeo/RoMEO-API-Keys-2011-10-04.pdf.

Feedback

Testers will be able to send us comments and report issues at any time using the FACT Feedback form. They will, however, also be asked to complete a questionnaire at the end of the testing period. All feedback will help towards getting the API ready for production release.

Production Version

We are currently investigating sustainability options for the development and support of the FACT service, including the API. We therefore do not have a date for releasing the production version. Please note that we may need to charge a subscription for use of the API production version.

We would be happy to extend SHERPA/FACT and its API to cover further research funders anywhere in the world. Interested funding bodies are invited to contact us.

Contact Details

Peter Millington – peter.millington@nottingham.ac.uk – Technical queries

Azhar Hussain – azhar.hussain@nottinham.ac.uk – SHERPA/FACT service queries

Read issue 1.5 of Physiological Reports

Physiological ReportsThe latest issue of Physiological Reports has now closed. The journal is a collaboration between The Physiological Society and the American Physiological Society, and is therefore in a unique position to serve the international physiology community through quick time to publication while upholding a quality standard of sound research that constitutes a useful contribution to the field. 

Below are the ‘editor’s choice’ articles for this issue:

purple_lock_open The spontaneous electrical activity of neurons in leech ganglia
Majid Moshtagh-Khorasani, Evan W. Miller and Vincent Torre
Summary: Using the newly developed voltage-sensitive dye VF2.1.Cl, we monitored simultaneously the spontaneous electrical activity, which is segregated in three main groups: neurons comprising Retzius cells, Anterior Pagoda, and Annulus Erector motoneurons firing almost periodically, a group of neurons firing sparsely and randomly, and a group of neurons firing bursts of spikes of varying durations. These three groups interact and influence each other only weakly.

purple_lock_open The manipulation of strain, when stress is controlled, modulates in vivo tendon mechanical properties but not systemic TGF-?1 levels
Gerard E. McMahon, Christopher I. Morse, Adrian Burden, Keith Winwood and Gladys L. Onambélé-Pearson
Summary: This study describes the manner in which tendon strain during chronic loading/unloading affects tendon dimensional and mechanical properties, as well as muscle function. We also determine the degree of association of these adaptations with a growth factor that has pleiotropic effects on muscle and tendon transforming growth factor beta (TGF-?1). We demonstrate that the impact of strain on the muscle–tendon complex (over and above the absolute stress imposed on this unit) optimizes the magnitude of improvement in both tendon and muscular functional characteristics.

purple_lock_open Effects of dipeptidyl peptidase-4 inhibition in an animal model of experimental asthma: a matter of dose, route, and time
Michael Stephan, Hendrik Suhling, Jutta Schade, Mareike Wittlake, Tihana Tasic, Christian Klemann, Reinhard Pabst, Marie-Charlot Jurawitz, Kerstin A. Raber, Heinz G. Hoymann, Armin Braun, Thomas Glaab, Torsten Hoffmann, Andreas Schmiedl and Stephan von Hörsten
Summary: This article focuses on alteration of asthmatic allergic reaction using a CD26/DPP4 (dipeptidyl peptidase-4) inhibitor in a rat model of asthmatic inflammation. This study proves different effects on clinical signs and cellular inflammation depending on the route of drug administration (chronic via drinking water or inhaled). Aerosolization of the DPP4 inhibitor simultaneously with the allergen significantly reduced airway hyperresponsiveness and ameliorated histopathological signs compared to controls.

purple_lock_open Renal angiotensin II type 1 receptor expression and associated hypertension in rats with minimal SHR nuclear genome
Jason A. Collett, Anne K. Hart, Elaine Patterson, Julie Kretzer and Jeffrey L. Osborn
Summary: Angiotensin II (AII) and its receptors play a major role in the physiology and pathophysiology of blood pressure control. Analysis of different components of the renin–angiotensin system and their heritability was evaluated in a “conplastic” rodent model. AII type 1 receptors, but not other aspects of renin–angiotensin system (RAS) were elevated in the kidneys of hypertensive animals, suggesting a heritable influence of RAS contributing significantly to hypertension.

The jouranl recently published its 100th article. Find out more about the first 100 articles here.

You can submit your article to Physiological Reports using the online submission site. We look forward to hearing from you soon.

Latest Article Alert from Child and Adolescent Psychiatry and Mental Health

The following new articles have just been published in Child and Adolescent Psychiatry and Mental Health

For articles using Author Version-first publication you will see a provisional PDF corresponding to the accepted manuscript. In these instances, the fully formatted Final Version PDF and full text (HTML) versions will follow in due course.

Research
A school based study of psychological

Latest Article Alert from International Breastfeeding Journal

The following new articles have just been published in International Breastfeeding Journal

For articles using Author Version-first publication you will see a provisional PDF corresponding to the accepted manuscript. In these instances, the fully formatted Final Version PDF and full text (HTML) versions will follow in due course.

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Prevalence of Exclusive Breastfeeding Practices and

Latest Article Alert from Journal of Occupational Medicine and Toxicology

The following new articles have just been published in Journal of Occupational Medicine and Toxicology

For articles using Author Version-first publication you will see a provisional PDF corresponding to the accepted manuscript. In these instances, the fully formatted Final Version PDF and full text (HTML) versions will follow in due course.

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Novel method using hybrid markers:

Latest Article Alert from BMC Infectious Diseases

The following new articles have just been published in BMC Infectious Diseases

For articles using Author Version-first publication you will see a provisional PDF corresponding to the accepted manuscript. In these instances, the fully formatted Final Version PDF and full text (HTML) versions will follow in due course.

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Local phylogenetic analysis identifies distinct trends in

Latest Article Alert from BMC Cardiovascular Disorders

The following new articles have just been published in BMC Cardiovascular Disorders

For articles using Author Version-first publication you will see a provisional PDF corresponding to the accepted manuscript. In these instances, the fully formatted Final Version PDF and full text (HTML) versions will follow in due course.

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Association between winter season and risk of death

The Legacy of the Vanity Press and Digital Transitions

As its name suggests, “vanity publishing” did not acquire a stellar reputation in the twentieth century. Although some vanity publishers have served authors with niche audiences, others ran such notorious scams that they helped stigmatize the business of author-subsidized books. But fraud was only one reason for the stigma against vanity publishers. They were also criticized for producing low-quality books and failing to act as gatekeepers. By the late twentieth century, the stigma had received limited attention in scholarly literature, but among professional authors, publishers, and librarians, avoiding vanity presses was mostly common sense. Aspiring authors were warned that publishing with a vanity press could be a career-killer, and commentary in articles and trade journals suggested publishers and librarians were exasperated with the quality of the books that rolled from vanity presses and the treatment of authors who used them.