3 important biological questions about the 2014 Ebola outbreak

Ebola

Ebola virus as viewed on a scanning electron microscope. Source: Charles Humphrey/Examiner

With high fatality rates and disease symptoms that seem to echo scenes from apocalyptic movies, the current Ebola outbreak has managed to capture much debate and controversy this past month. The death toll is now up to 1013 (as of August 11) with West African countries on a high alert. With so much media coverage of the current outbreak, it seems there are some fundamental questions that are consistently left unanswered; I’ve put together three important questions mostly centered around treatment, vaccine and the pathology for the current Ebola outbreak which may be helpful to keep in mind when sifting though the onslaught of news reports:

1. Why is the current outbreak so much worse than previous outbreaks?

In spite of being classified as the worst outbreak in history, the current strain has a mortality rate of about 50%; still high, but significantly lower than previous Ebola strains. To put it in relative terms, the current strain of Ebola is not as highly contagious as influenza; the basic reproductive number R0 (i.e., how many secondary cases each infected person will produce on an average over the period of infection) for Ebola strains from previous outbreaks was ~ 1.3 while influenza can be up to 3. It is possible that the lower mortality rate of the current strain has been advantageous for its transmission; more virulent strains limit their spread by killing off the host faster than lower virulent counterparts. Many believe that the reduced mortality is because patient treatment has significantly improved; but poor healthcare system and cultural factors are playing a role in the rapid spread of this outbreak, summed up here. You might be aware that experimental medicines are currently being considered as an option to treat those who are infected. But many researchers including scientists who have designed the vaccine are not too optimistic about a accelerated or early stage clinical trial for the vaccine.

Ebola Virus Cases and Deaths in West Africa. Source : Fauci, New England Journal of Medicine, as of Aug 13, 2014

Ebola Virus Cases and Deaths in West Africa. Source : Fauci, New England Journal of Medicine, as of Aug 13, 2014

2. How did the Central African Zaire strain end up in West Africa?

The biggest surprise with the outbreak came in April when it was reported that the strain was actually of Central African origin rather than the expected Tai strain of Ivory Coast. This raises the concern that fruit bats are spreading the virus (or if we are encroaching more bat territories) giving a chance for transmission. However, direct bat-human transmission is yet to be documented, despite claims that villagers are eating dead bats and other bush meat, thereby contracting the disease. Why bats? As it turns out, bats have a unique evolutionary history of positive selection on genes that are related to resist oxidative damage and immunity, which lends to their ability to harbor diseases; read more about this in Science and New Scientist. Although it has not been comprehensively tested in experiments, there are several lines of evidence supporting the notion that bats can resist the “cytokine storm” produced by the immune system in response to an acute viral infection making them asymptomatic carriers for a number of viruses including Ebola.While there still is no definitive answer to this question, there are groups currently tracking the bat reservoir in Sub-Saharan Africa and the path of Ebola’s outbreak to get insights into this problem.

3. How old is Ebola?

You may be familiar with the issue that HIV is difficult to prevent because of it’s high mutation rate; this isn’t the case with all viruses. Ebola belongs to the negative sense single-stranded RNA (ssRNA) family filoviridae. Because of RNA polymerase’s lack of a proof-reading mechanism, and because there is no DNA intermediate involved (e.g. HIV), the estimated mutation rate in the virus genome is a million fold higher than it is for HIV. The catch here is that there are no major sequence dissimilarities between the various strains (dating back to 1976). This has led to a thought that the virus has jumped recently from a non-human species (1976) and the outbreaks are essentially its continuation into newer territories (a wave phenomenon). The other school of thought essentially contradicts this idea by saying Ebola has existed for a long time in a reservoir and its mutation rate helps it jump species occasionally into vulnerable populations (some medical researchers have proposed that Ebola could have caused the plague of Athens in 430 B.C). Both groups agree that fruit bats are reservoirs but there could be a third unknown reservoir which we have no idea about. It will be important to keep an eye on studies that answer these questions in coming years based on data from this outbreak. With luck, the vaccines and treatments would protect us then and Ebola would only be studied for its intriguing biology and not due to its potential for devastation.

A death blow for STAP cells? Researchers agree to a retraction.

 

Obokata

Haruko Obokata, lead author of the STAP cell studies.

Japanese media reports that co-authors of one of the two STAP stem cell papers published in Nature in January agree to a retraction. The introduction of induced stemness in cultured cells by the STAP procedure showed promise as a revolutionary method for obtaining multi-potent cell types for biomedical research, until researchers called for an investigation of the methods and ethics in the publication in the face of irreproducible results. As it turns out, the investigation performed by the RIKEN institute did indeed find research misconduct in the papers, even while the researchers stood by their results. While Obokata, the lead author on the study, says that the mistakes were non-malicious, RIKEN concluded that data was falsified or fabricated. Indeed, figures that were claimed as separate mice turned out to be to images of the same animal.

Currently, only the Letters paper is being considered for retraction while the methods paper will remain published. However, researchers deeply entrenched in the fight against the use or consideration of the STAP methodology are calling for an immediate editorial retraction of both articles. Paul Knoepfler, an associate professor at the UC Davis School of Medicine says, “Whatever the reason, it is well past time for Nature to editorially retract these tainted papers. There is nothing more to be learned that could save the papers and every day that passes with them still in the Nature portfolio is a shame.”

Read more coverage at ScienceInsider.

Time to edit the textbooks: DNA Ligase I not essential for cell viability

A DNA Ligase I-null B cell line produced an almost completely normal diploid karyotype (a single, non-dangerous rearrangement occurred)  , showing it is capable of normal DNA synthesis. Han et al, Cell Reports 2014

A DNA Ligase I-null B cell line produced an almost completely normal diploid karyotype (a single, non-dangerous rearrangement occurred) , showing it is capable of normal DNA synthesis. Han et al, Cell Reports 2014

For decades it was universally acknowledged that the expression of DNA Ligase I was essential for cell viability, as it was thought to play a unique and critical role in the ligation of Okazaki fragments during DNA replication as well as a critical role in the repair of damaged DNA. A recent Cell Reports paper by researchers from Michigan State University and USC show that B cells completely deficient in expression for DNA Ligase I are not only capable of proliferating at a normal rate, but they are capable of producing functional immunoglobulin recombination and show similar survival curves when challenged with DNA damaging chemicals.

The paper is short (only 4 figures), but the experiments are elegant and the findings are profound. This discovery literally redefines the composition of the family of proteins responsible for piecing our DNA together during replication. This seminal paper will undoubtedly be reflected in textbook revisions to our understanding of DNA synthesis and repair as well as potentially influencing our understanding of how cancer cells might circumvent our targeted assassination by DNA damaging drugs.

Reference

1. Han, L., Masani, S., Hsieh, C.-L. & Yu, K. DNA ligase I is not essential for Mammalian cell viability. Cell Rep. 7, 316–20 (2014).

Don’t STAP Believing: When Scientific Breathroughs Really Are Too Good To Be True

The following is a guest post returning to the topic of STAP cells by Keith Jacobs, a PhD student at Washington University in St. Louis studying radiosensitivity in stem cells. You can read more of Keith’s thoughts on science at The Blabbering Biologist, or follow him on Twitter and Google+.

Haruko Obokata, the scientist who first reported the STAP cell methodology, defends her discovery.

Haruko Obokata, the scientist who first reported the STAP cell methodology, defends her discovery.

Stem cell biology has stimulated intense scientific and clinical interest since the first successful isolation and culture of human embryonic stem cells in 1998.  Unfortunately, as a result of legal restrictions on the use of embryonic stem cells put into place under the Bush administration, research during the mid-2000s was forced to focus on developing novel methods for obtaining pluripotent stem cells without the use of embryonic tissue.  The first major breakthrough occurred in 2006 when scientists collaborated on Nobel Prize-winning research that successfully created pluripotent stem cells from differentiated fibroblasts, labeled as induced pluripotent stem cells (iPSCs).  While there have been numerous recent improvements upon the original discovery of iPSCs, including transdifferentiation which can bypass the stem cell state entirely when converting one cell type to another, all of these techniques remain relatively inefficient.

In January of 2014, scientists from Harvard University and the

Centre for Developmental Biology in Japan published a pair of papers in Nature describing a technique for obtaining pluripotent stem cells from any other cell type, simply by incubating cells in an acidic buffer for 30 minutes, known as stimulus-triggered acquisition of pluripotency (STAP).  In addition to its simplicity and the ability to work with cells from any origin, this technique also demonstrated a greatly increased efficiency over previous methods.  These findings were considered to be ground-breaking and expected to revolutionize the stem cell field, resulting in international media coverage.  Due to the simplicity of the assay, it was surprising to many that the method had not been previously discovered.  Additionally, many labs struggled to reproduce the results, albeit often with somewhat different methods.  While inability to reproduce a technique does not on its own suggest any major flaws in a publication, this raised suspicions about the validity of the data.

Within weeks however, a myriad of allegations threatened the integrity of the publication.  First, online commenters noticed apparent duplications of figures from previous publications.  The Wall Street Journal then posted evidence that the lead author had plagiarized part of her PhD thesis.  While all authors continued to support the overall claims of the paper despite admitting some “mistakes”, the increasing questions about the study soon caused one of the co-authors to request retraction of the paper.  The Riken Centre began an internal investigation into several questionable figures and on April 1st officially declared that research misconduct occurred due to falsification of data.  They reported two specific instances of misconduct, in addition to multiple other inconsistencies.  Currently the two STAP papers have not been retracted and the lead author continues to stand by her findings.  While the story is even more complicated by the recent resignation of the chairman of the investigative panel over accusations of fabricated images in his own publications, it appears that these publications have all but met their ultimate demise.

Personally, I believe that the overall phenomenon is likely true, however in order to sell the paper to a top journal, the authors needed a large amount of confirmatory evidence and controls that were too difficult to obtain.  When this paper was first published, both myself and other members of my department thought how beautifully the phenomenon of stress-induced de-differentiation would explain many previously unexplained experimental observations.  However, even when you strongly believe that the results of a novel discovery must be true based on all the numerous little observations and associated phenomena you have noticed, it can be very difficult to obtain enough clean, believable confirmatory evidence in order to appease reviewers.  It is therefore easy to understand the temptation to fabricate some controls, and this explains why the author in question adamantly stands by her work despite the declaration of fraud.  The existence of clear and evident research misconduct does not completely discount the discovery, however it does promote a strong lack of credibility, and it will need to be successfully repeated by multiple other labs before it will be accepted by the scientific community ever again.

STAP the madness: Japanese stem cell researchers call for retraction of acid bath-based technique

The shockingly simple proposed method for pluripotent transition from somatic cells. From Obokata et al, Nature 2014.

The shockingly simple proposed method for pluripotent transition from somatic cells. From Obokata et al, Nature 2014.

Former and current researchers out of the RIKEN Center for Developmental Biology in Kobe, Japan call for the retraction of a pair of Nature papers by  (here and here; full citations below) published earlier this year out of the same institute describing a simple and potentially powerful new method for producing stem cells. The original papers described the sudden transition from differentiated cells into cells displaying stemness by inducing stress in a sightly acidic bath composed simply of HBSS (a simple salt solution) titrated to pH 5.7 for only 25 minutes. They call this method STAP, for stimulis-triggered aquisition of pluripotency. This is a shockingly simple method that, if supported, could change the way stem cell research is conducted. Therein lies the problem – researchers listed as authors on the paper publicly announced their disapproval of some of the methods and data contained in the papers, stirring an international call for reassessment of this supposed discovery.

Haruko Obokata on Jan. 28.  Image: Agence France-Presse/Getty Images

Haruko Obokata on Jan. 28. Image: Agence France-Presse/Getty Images

Teruhiko Wakayama, one of the co-authors on the paper, says “I have lost faith in the paper. Overall there are now just too many uncertainties about it. I think we have to wait for some confirmation… To check the legitimacy of the paper, we should retract it, prepare proper data and images, and then use those to demonstrate, with confidence, that the paper is correct.” The RIKEN institute says they are currently investigating potential academic misconduct.

One of the most redeeming aspects of this controversy, in my opinion, is the level of self-checking we are seeing from the science community at large; my favorite example is the Knoepfler Lab Stem Cell blog. The blog is written by Paul Knoepfler, an associate professor at the UC Davis Medical School, who is following the story by aggregating data from other labs (including his own) which are trying to reproduce the data published in the original papers. This is exactly the idea behind the peer-reviewed nature of science; it isn’t just about the quality of the reported literature and if the words make sense… the science has to work. While no group has had success yet, time will tell what is in store for this potentially paradigm-shifting method.

Read more excellent coverage at Nature News Blog and The Wall Street Journal.

References

  1. Obokata, H. et al. Stimulus-triggered fate conversion of somatic cells into pluripotency. Nature 505, 641–7 (2014).
  2.  Obokata, H. et al. Bidirectional developmental potential in reprogrammed cells with acquired pluripotency. Nature 505, 676–680 (2014).