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 ( 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:, 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: 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:

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


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 – – Technical queries

Azhar Hussain – – 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.

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.

Do developing countries profit from free books?: Discovery and online usage in developed and developing countries compared

For years, Open Access has been seen as a way to remove barriers to research in developing countries. In order to test this, an experiment was conducted to measure whether publishing academic books in Open Access has a positive effect on developing countries. During a period of nine months the usage data of 180 books was recorded. Of those, a set of 43 titles was used as control group with restricted access. The rest was made fully accessible.The data shows the digital divide between developing countries and developed countries: 70 percent of the discovery data and 73 percent of online usage data come from developed countries. Using statistical analysis, the experiment confirms that Open Access publishing enhances discovery and online usage in developing countries. This strengthens the claims of the advocates of Open Access: researchers from the developing countries do benefit from free academic books.

Rice University Press: Nascentis fame

Rice University Press (RUP), which began full operation in February 2007, proved a short-lived experiment. After three years of supporting one paid staff position and modest additional funding for contracted book design work, office expenses, and travel, Rice closed the press down as part of a larger, campuswide, budget-cutting effort. Faced with a choice between investing more financial and human capital in its press as a condition for gaining substantial foundation support or opting out of the experiment altogether, university administration chose the latter. Short-lived as the RUP experience was, it nevertheless offers some important lessons for people pondering the future of academic publishing and its inexorable move in a digital direction. There is no question that traditional printed-on-paper publishing is dying out and that it will be replaced by digital academic discourse distributed on a different economic model. There are, however, substantial questions about when and how this paradigm shift will come about, and the Rice University Press story may offer some answers.

Editor’s Note [16.1]

I’m delighted to hand over the reins of The Journal of Electronic Publishing to Maria Bonn (Editor) and Jonathan McGlone (Managing Editor). We at Michigan Publishing are excited to see the journal continue to feature new scholarship and create new opportunities for exploring and improving professional practice in the years to come.

Join Jack Andraka in making publicly funded research available to all!

Watch Jack ›› Learn about FASTR ›› Take Action!


Jack Andraka perfectly illustrates the power of free, online access to scientific and scholarly research articles, a concept called Open Access. Yet, even though taxpayers fund much of the published research, most scientific papers are locked behind expensive paywalls that can cost $30 per article or thousands of dollars per journal subscription. These prices are so high that students like Jack — and even top researchers — often have to go without the benefit of cutting edge information in their field.

Fortunately, Jack and others are advocating for a solution, called the Fair Access to Science and Technology Research Act (or FASTR).  FASTR is a bipartisan bill that would require research articles funded by taxpayers to be made freely available online within six months.  This bill would help both students like Jack and established researchers alike to gain access to the articles they need to discover the next breakthrough, accelerate scientific advancement, and improve the lives of people all around the world, while generating economic and job growth.

Fill in the form below to send a letter to your legislators in Congress urging them to pass FASTR and help gifted researchers like Jack get access to the articles they’ll need to make the next big discovery!

Note: after you click take action, you will have the chance to review the letters before they are sent.

If the form below does appear properly on your device, follow this link directly to our action center


Mandate Open Access (OA) Says L.J.Haravu of Open Source ILMS-NewGenLib Fame

As a part of Open Access Week-2013 was organized the special lecture by Mysore Librarians and Information Scientists Association (MyLISA). Mr. L.J. Haravu, UNESCO Expert on implementation of technology base library services in South East Asia and Arab Countries, gave a special lecture on this occasion on the theme of “Open Access: The Philosophy and Trends” at the SBRR Mahajana First Grade College, Mysore, India on 26th October 2013.

Haravu started his lecture by citing some of the historical, cultural and social movements that have influenced the human civilization in the past. He pointed out that these movements have started because of some fundamental causes that hindered the human freedom and aspirations of common people. These movements have resulted in new legislations, regulations and reforms, he said. Continuing his lecture he said that movements have by-products or spin-offs.
During 1950s and 60s India witnessed a library movement in a big way, as a part of this there were movements in the areas of classification and indexing, thesaurus building. Now we have been witnessing a new kind of movements in the field of library automation, digitization, open source software adaptation, etc. 

While speaking on the philosophy behind OA movements, Haravu highlighted some of the major breakthrough in scholarly publishing domain which played crucial role in spreading OA movements. Some of the major changes in scholarly publishing domain that led to OA movements were: increased emphasis for publishing research papers (publish or perish syndrome), rapid increase in scholarly publications, rise in subscription cost of scholarly journals (200% to 250% of increase in the last 25 years), dwindling library budget, deprived of access to research materials, publishers monopoly and so on. Because of some of these reasons, stakeholders involved in scholarly publications – academicians, scientists, librarians, activists – launched OA movement.

The developments in contemporary technologies (Internet) provided them a great platform to provide access to information easily like never before. OA movement was formally launched in three international meetings in 2002-03, in Budapest, Bethesda and Berlin, he said. He said that there were two major rubrics of OA publishing models. One is OAJs (Open Access Journals) and another model is OAA (Open Access Archiving). He cited some of the examples for OAJs: Public Library of Science (PLoS), Directory of Open Access Journals (DOAJ). For open access archiving major institutional repositories and OAIster. Because of OA movement, today we have, open courseware (MIT Open Courseware), open educational resources, open theses, open data and open source films, he said.


Haravu mentioned some of the barriers for open access, such as business model of OAJ publishers, emergence of predatory OA journals, authors’ reluctance for publishing their research papers in OA journals, etc.
 He urged the librarians to play an active role in creating awareness and educate academicians/executives about the importance of OA. He also urged the librarians to play crucial role in establishing institutional repositories in their respective intuitions and adopting OA mandate.

The New PLOS ONE Collection on “Sauropod Gigantism – A Cross-Disciplinary Approach”

Sauropod-Collection-600x600 (3) (2)The exceptional gigantism of sauropod dinosaurs has long been recognized as an important stage in the evolution of vertebrates, the presence of which raises questions as to why no other land-based lineage has ever reached this size, how these dinosaurs functioned as living animals, and how they were able to maintain stable populations over distinct geological periods.

We are pleased to announce the publication of a PLOS Collection featuring new research on the complex Evolutionary Cascade Theory that attempts to answer  these questions and  explain how the unique gigantism of sauropod dinosaurs was possible. The fourteen papers that make up the collection address sauropod gigantism from a number of varied disciplinary viewpoints, including ecology, engineering, functional morphology, animal nutrition, evolutionary biology, and paleontology.

Sauropod dinosaurs were the largest terrestrial animals to roam the earth, exceeding all other land-dwelling vertebrates in both mean and maximal body size. While convergently evolving many features seen in large terrestrial mammals, such as upright, columnar limbs and barrel-shaped trunks, sauropods evolved some unique features, such as the extremely long necks and diminutive heads they are famous for. Dr Martin Sander, Professor of Paleontology at Universität Bonn and coordinating author for this series of 14 papers, said of the collection:

“This new collection brings together the latest research on the biology of sauropod dinosaurs, the largest animals to ever walk on Earth. Having been extinct for 65 million years, reconstructing sauropod biology represents a particular challenge. Using a wide array of scientific expertise, often from seemingly unlikely fields, has led to some amazing insights. For example, principles of soil mechanics have been used to ‘weigh a dinosaur’ based on its trackways, whilst the latest in computer modeling can make a dinosaur walk again.

The ultimate question underlying this research is how sauropods were able to evolve their uniquely gigantic body size. The wide-ranging disciplines covered in the collection means that there is a -broad, multi-disciplinary audience for the research, as well as general interest in dinosaurs; therefore, we felt that it was essential to publish such a volume in a leading open-access journal such as PLOS ONE to ensure the widest possible dissemination of our work.”

Readers are able to download “Sauropod Gigantism: A Cross-Disciplinary Approach” not only as a PDF but also as an ebook (.mobi and .epub formats) from the collection page. It will also be available on Flipboard (search “PLOS Collections”).

Image credits:
Collection Image: Kent A. Stevens, University of Oregon

Make my collection open access!

I just sent this message to my library to tell them how much I want to support Knowledge Unlatched – let’s make open access to scholarly monographs a reality!

I would like to dedicate up to the remainder of my new faculty start-up fund to support this project (capped maximum of US $1,680). For the future, I would wholly support dropping the big deals of every large publisher and re-directing funding to support works like this.

As a bit of context, at the University of Ottawa we new faculty members have the good fortune of having a $2,000 start-up fund to build the collection.

International Open Access Week: Wiley’s participation

oaweekLast week (Oct 21-25) was International Open Access Week.  We spent the week particpating in discussion and sharing information. In cased you  missed anything, here is a summary of our week.

The results of  Wiley’s open access survey of 8000+ authors were published.  You can read a summary of the results on our Exchanges blog site.

We created a data visualization tool so that users can drill into the data by research experience, region, and subject area.

We also produced this infographic which shows key results from our author survey alongside OA results from our librarian survey (conducted in May) as well as Wiley’s own experiences of where authors who choose to publish OA are coming from.

We wrote about the effect that funder mandates are having on the take-up of Wiley’s OA offerings.

Also, during this International Open Access week, we announced the transition of four leading journals from the subscription model to Gold OA from January 2014, bringing the total number of Wiley’s open access titles to 28.

You can also read a comment here from Helen Bray about the role of open communications from publishers in the open science movement.

More about Wiley Open Access can be found on this blog, or here:  And lastly, don’t forget you can follow us at or tweet us at  @WileyOpenAccess

Immunity, Inflammation and Disease Publishes Issue 1.1

LSJ-12-45832-WOAI-NW-Immunology-Cover-101x131pxWe are pleased to announce that Immunity, Inflammation and Disease has now launched with the publication of its inaugural issue. Immunity, Inflammation and Disease is a peer-reviewed, open access, interdisciplinary journal, providing rapid publication of cutting-edge research across the broad field of immunology.

The Editor-in-Chief, Marc Veldhoen has selected these papers to highlight from the issue:

purple_lock_open Relative contribution of IL-1?, IL-1? and TNF to the host response to Mycobacterium tuberculosis and attenuated M. bovis BCG by Marie-Laure Bourigault, Noria Segueni, Stéphanie Rose, Nathalie Court, Rachel Vacher, Virginie Vasseur, François Erard, Marc Le Bert, Irene Garcia, Yoichiro Iwakura, Muazzam Jacobs, Bernhard Ryffel and Valerie F. J. Quesniaux
Summary: Here, we confirm that both TNF and IL-1 pathways are required to control M. tuberculosis infection since absence of both IL-1a and IL-1ß recapitulated the dramatic defect seen in the absence of IL-1R1 or TNF. However, presence of either IL-1a or IL-1ß allows some control of acute M. tuberculosis infection. Further, although TNF is essential for the early control of infection by either virulent or attenuated mycobacteria, IL-1 pathway is dispensable for controlling less virulent infection by M. bovis BCG.

purple_lock_open Human pre-B cell receptor signal transduction: evidence for distinct roles of PI3kinase and MAP-kinase signalling pathways by Kolandaswamy Anbazhagan, Amrathlal Rabbind Singh, Piec Isabelle, Ibata Stella, Alleaume-De Martel Céline, Eliane Bissac, Brassart Bertrand, Nyga Rémy, Taylor Naomi, Fuentes Vincent, Jacques Rochette and Kaïss Lassoued
Summary: PI3K and MAPK exerted opposing effects on the pre-BCR-induced activation of the canonical NF-?B and c-Fos/AP1 pathways. In addition, pre-BCR-induced down-regulation of Rag1, Rag2, E2A and Pax5 transcripts occurred in a PI3K-dependent manner.

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We would like to invite you to submit your immunology paper to the journal. All authors retain copyright in their articles and benefit from high visibility on Wiley Online Library. All articles are fully open access on publication.

submit to IID

Moonlit Rendezvous: The Box Jellyfish’s Monthly Meet-up in Waikiki

Box Jellyfish

When you think about tropical paradise, Hawaii is often at the top of the list. Waikiki is one of the most iconic Hawaiian beaches on Oahu and is a popular swimming and surfing spot. However, it is also a popular stop for the box jellyfish, one of the most venomous animals in the world. Once a month, about 8 to 12 days after the full moon, the shallow waters of Waikiki beach are temporarily flooded with box jellyfish. They are not coming in for a mai tai under the waning moon; rather, scientists believe that jellyfish reproduce in these waters. This monthly influx creates a hazard to swimmers due to the jellyfish’s painful—and even lethal—stings.

The environmental factors that affect these influxes are not well understood, and learning more about them may help us predict and mitigate the risk that box jellyfish pose to swimmers. Several scientists from Hawaiian institutions published the first long-term (14-year) assessment of the environmental conditions that potentially correlate with box jellyfish population changes in the North Pacific Sub-tropical Gyre.

The researchers surveyed a 400-m section of Waikiki beach during the days jellyfish were present. They counted more than 66,000 jellyfish over 14 years and compared the data to 3 measures of how the climate changes over time, called climate indices; 13 physical and biological variables, such as sea surface temperature and plankton; and seven weather measurements, including wind speed, air temperature, and rainfall.

They confirmed that box jellyfish arrive at Waikiki monthly after each full moon and stay for 2- 4 days. They counted on average 400 jellyfish each month, but the range was quite wide at 5-2,365 individuals. Rather than seeing a net population change over 14 years, researchers observed approximately 4-year periods of increased population count followed by 4-year periods of decreased population count, which coincided with fluctuations in three main environmental factors: oceanic changes in salinity and nutrient availability, called the North Pacific Gyre Oscillation, small organisms’ ability to access nutrients, called primary production, and abundance of small zooplankton.

The researchers suggest that the relationship between environmental fluctuations and jellyfish population changes at Waikiki may result from changes in the availability of food for jellyfish in the ocean around Hawaii, brought about by the North Pacific Gyre Oscillation. During an increase in nutrient availability, phytoplankton populations also increase, meaning more food for jellyfish, allowing them to grow faster and increase their rate of reproduction.

Previous studies have shown that jellyfish populations change due to human-caused disturbances, but this is one of the first long-term studies showing that large-scale climate patterns may also impact box jellyfish populations. Understanding long-term climate and oceanic trends and their effects on jellyfish populations may provide information to develop strategies for avoiding mass stinging events and beach closures at Waikiki and other popular recreation sites in the Pacific.


Citation: Chiaverano LM, Holland BS, Crow GL, Blair L, Yanagihara AA (2013) Long-Term Fluctuations in Circalunar Beach Aggregations of the Box Jellyfish Alatina moseri in Hawaii, with Links to Environmental Variability. PLoS ONE 8(10): e77039. doi:10.1371/journal.pone.0077039

Image Credit: Jellyfish by James Brennan Molokai Hawaii