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).

New tool in the cellular repair kit: ESCRT machinery described as critical component of plasma membrane repair

Jimenez et al, Science 2014

Jimenez et al, Science 2014

Researchers from Institut Curie and Le Centre National de la Recherche Scientifique in France describe in a new paper in Science magazine this week the role of endosomal sorting complex required for transport (ESCRT) in the rapid repair of plasma membrane damage, which is commonly caused by things such as pore-forming toxins or mechanical stress. ESCRT is most well known for its role in vesicle budding and fission.

The researchers elucidated the spatial and temporal kinetics of ESCRT activity in plasma membrane repair with a series of elegant experiments utilizing the membrane impermeable DNA stain propidium iodide as well as a variety of membrane damaging techniques (micropipette tearing, two-photon laser ablation, toxin exposure and detergents). In the case of ESCRT machinery, the repair of plasma membrane sections did not involve the in situ patching of the membrane, but rather the isolation of the damaged segments followed by a pinching-off, shedding and closure of the membrane. Further, while shedding of damaged membrane segments was halted by energy depletion, accumulation of ESCRT to the membrane increased, suggesting a passive, or alternatively motivated, mechanism for ESCRT recruitment to the site of membrane damage.

Membrane damage repair, or lack thereof, is critical in a variety of normal and pathological conditions. This expansion of the basic understanding of membrane repair is an important piece of the puzzle for understanding this universal cellular processed essential for maintaining homeostasis and mediating stress response.

The paper contains some really beautifully performed experiments and the data are gorgeous. Check out the paper in the reference below:

A. Jimenez et al., ESCRT Machinery Is Required for Plasma Membrane Repair, Science. 343 (2014), doi:10.1126/science.1247136.

Happy Birthday, Charles Darwin

A man who dares to waste one hour of time has not discovered the value of life. – Charles Darwin

Without fail, there is not a single biologist alive today who is not in some way affected by or influenced by the work of Charles Darwin. His insights into the possibility of adaptation by reproductive fitness and natural selection, often simplified as “the survival of the fittest” is as important today as it ever was. While it was original identified in larger organisms, adaptive evolution is both a boon and a hindrance upon society. We use adaptive evolution to develop new therapeutics by processes such as selective enrichment (SELEX), for clonal microbiology, even for machine learning. Yet, at the same time, we are affected by antibiotic resistant microbes and diseases which evolve so quickly we can’t get a foothold in treatment.

Darwin did not only work on organic evolution, however. His studies into human behavior and globally relevant emotional responses provided critical insights still used in the social and behavioral sciences. Though his work in botany was a bit less successful, Darwin was clearly a man whose thirst for knowledge drove his life, which I take to heart and find quite noble.

The quote above, which is quite unrelated to his scientific work, I think is a great one to embrace no matter what your career, position or age. Particularly in science (since that is what I know best), it’s painfully clear that a stagnant work bench is a dreaded waste. So, I think we can all take a page from Darwin’s book (to place beside all of the other pages from his scientific wisdom), and hit the bench!

Happy Birthday, Darwin.

Happy 2014! Celebrate with a new inspirational science wallpaper!

To my surprise and delight, one of the most popular posts from this past year turned out to be the 2013 New Year chromosomes wallpaper. To continue the tradition, I’ve updated the wallpaper to include chromosomes 20 and 14 from the Alu FISH (Fluorescence In-situ Hybridization) karyotype produced by Dr. C. Michael Gibson.

Last year I included a favorite science quote from the ever-popular science communicator, the late Carl Sagan:

“Science is a way of thinking much more than it is a body of knowledge.”

This year’s wallpaper features a quote from Isaac Asimov, the beloved science fiction/popular science author and biochemistry professor whose work continues to inspire young scientists:

“There is a single light of science, and to brighten it anywhere is to brighten it everywhere.”

2014_chromosomes_wallpaper_1280x800

I hope that this wallpaper (the downloads are available below), for those of you who decide to use it, becomes a daily reminder of the importance of not just a single field of science, nor just the science done by scientists, but rather the global support and awareness of the scientific endeavor and all of the wonderful benefits we gain from its progress.

Best wishes to everyone for a safe and happy New Year!

 

“A-POP-TOSIS”

We all have pet-peeves; those little things in life that get under your skin. They don’t ruin your day, but they are conspicuous enough that you always notice them… and maybe you cringe a little.

Those who know me personally know that the quickest way to make me cringe is to mispronounce the word “apoptosis.” Even first year biology students have very likely heard variations in the pronunciation of this very, very important term. This past week’s experience at the ASCB 2013 conference has really emphasized to me that there is a need to set things straight. Continue reading