On the Move

68 Pages·2016·10.74 MB·English

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CELL SIGNALING TECHNOLOGY 2/
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Deciphering Cancer
Antibodies to evaluate key signaling
networks in cell death and survival.
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Editorial 2-2016 Lab Times page 3

Slow Food, Slow Cinema,
Slow Living…
…our lives have becomes so fast, we occasionally need some- meeting, held in February in Washington. Amongst others, No-
one to tell us to stop and relax. The Slow movement has even spilt belists Harold Varmus, Randy Schekman and EMBO director,
over to scientific realms, in which a number of researchers des- Maria Leptin, convened at the HHMI headquarters to talk about
perately demand more time to think and read (if you have some whether and how preprints can serve the life science community.
extra time, there’s more about Slow Science in LT 2-2012 pg 20- Twenty-four hours later, “It seemed like nearly everyone in at-
27). But there’s one thing in the life sciences research business tendance was sold on the idea that biomedical researchers should
that needs a little bit of speeding up – the publication and in par- all post pre-prints of their work, and had already turned their at-
ticular the reviewing process. What has been the longest you have tention to questions about how to do it,” blogged Michael Eisen,
had to wait for a paper to be published? Half a year, two years, or cell bio logist at the University of California, Berkeley, and co-
even more? founder of PLoS.
Quite a few scientists claim that it takes much longer, nowa- It might be a little harder to convince the rest of the scientif-
days, to publish a study than it took a decade or so ago. Can this ic community, though. There are many reasons for preprint reluc-
be? With all the technology available, you’d think that the time tance. From the obvious (scooping) to the administrative (some
between submission of a manuscript and journals don’t allow manuscripts to be
publication of a paper in a print or online published anywhere else), to the prac-
journal would shrink to virtually zero. tical (in a job application, a paper looks
Alright, that’s pushing it a bit but a re- better than a non-reviewed preprint).
cent paper analysis commissioned by Na- But besides many other benefits, pre-
ture revealed that although the time for prints have the advantage of so-called
reviewing a paper has not changed over gro ‘priority’. With all changes date stamped,
oi
the last 30 years – it takes about 100 days a/ it’s easy to follow who got the idea for
from submission to acceptance – the time otoli an experiment and hypothesis first. This
to publish the accepted manuscript has o: F could become important for filing pat-
ot
halved (approx. 25 days) since the early Ph ents, for instance (life science patents
2000s (10 February, 2016). are also highlighted in one of our back-
Tallying up the numbers, it still takes 125 days or four months ground stories, pg 20-25). But priority can also be detrimental to
to finally get that study out there and that’s the best case scenar- science, finds blogger drugmonkey.
io. In a survey conducted by Nature, 36.8 per cent of the respond- “The pursuit of priority holds back the progress of science in
ents, the majority, answered that it took them one or two years to many ways. It keeps people from working on a topic because they
publish a research paper. For a few researchers, the publication figure that some other lab is way ahead of them and will beat
odyssey lasted more than five years. For a PhD student, trying to them to the punch (science always can use a different take, no
graduate, this can be a serious cliffhanger. two labs come up with the exact same constellation of evidence).
Following the submission-to-publication time of his own arti- It unfairly keeps people from being able to get rewarded for their
cles, cell biologist Steve Royle at the University of Warwick draws work (in a multi-year, multi-person, expensive pursuit of the same
interesting comparisons in his blog quantixed. On average, it took thing, does it make sense that a two-week difference in when a
him nine months to publish a research paper – “the same amount manuscript is submitted is all-critical to the credit?). It keeps peo-
of time to have a baby” and 121 days for reviews – “equivalent to ple from collaborating or sharing their ideas lest someone else
four lunar cycles”. “The irony in all this is that, even though we swoops in and scores the credit by publishing first. It can fuel the
are working at the absolute bleeding edge of science with all of inability to replicate findings (what if the group with priority was
this technology at our disposal, our methods for reporting sci- wrong and nobody else bothered to put the effort in because they
ence are badly out of date,” he comments. “In my opinion, wast- couldn’t get enough credit?),” the researcher points out.
ing even more time chasing publication is crazy, counter-produc- Scientific publishing, it seems, is still stuck in the slow lane
tive and demotivating for the people in the lab.” but one toe is already on the accelerator. How many lunar cycles
So, what’s the best way to speed up publication of scientific will pass or babies will be born before the speed of publication
papers? That’s exactly the question Nature asked in another sur- can keep up with the speed of data generation?
vey. Here, the majority (41.8 per cent) of respondents answered
that reviewers should stop asking for unnecessary revisions, and
that editors should make quicker and clearer decisions (22.1 per
cent). Only a small number of respondents (14.4 per cent) want
to put the pedal to the metal themselves, so-to-speak, and publish
preprints.
Heralded as a good, perhaps the best, way to accelerate sci-
entific publishing, preprints have been the subjects of discussion
at the ASAPbio (Accelerating Science and Publication in Biology)
LT_216_03_03.indd 3 04/04/2016 14:00
page 4 Lab Times 2-2016 Contents
News
Picture of the issue / Citizen science project in Spain yields first results / EMBO withdraws Installation
Grant / Recently awarded / FASEB issues recommendations to improve research reproducibility /
Data sharing debate between pharma company and scientists / Proposed budget cuts in Switzerland /
Swedish researchers find a new clue to hibernation in bear droppings __________________ 6-12
Photo: Fotolia/Sielan OROOevbpessieren atrhviroaceht niL olienntest ?eor f ( f2Troh6me): . OC..w oSll lp(e5aa9ign)u:: e LL-aoeboe kjCi tSo f_hfea_er_p _P.._a. y_as_n __d__ S__e__e__!________________________________________________________________________________________________111453
Several attempts to get a plagiarised paper
Analysis
retracted, has resulted in nothing but frustra-
tion for two taxonomists. Why does it take so Plagiarism at Elsevier
long to correct the scientific record? (p. 16) Scientists inform the editor-in-chief about a fraudulent paper but nothing happens. __________16
Patents in the Life Sciences
Is there any point in patenting life science discoveries and inventions? ___________________20
Cover Story
Relocation of an entire lab can be a daunting task. Experienced scientists share their advice to
simplify your move. ________________________________________________________26
Journal Club
Photo: Juha Haikola TOHraeosinrsadeshl/te/PiBmoer/tlNuggoiuarmwl Va Fiysou lElaoxlwpislioinnrggin htgho tewh cemo gnicetrnaoecbtte ibcs e srteewcaerceettn to offa gtteh cneee lcltsoic ma mnmdoo dnnief icucuaroctkinoosno s ’_s o _bf _ltuh_ee_ ie_r g_hg_os_s t__ p__l__a__nt__ _________333042
Cuckoos are master deceivers, their eggs in- Publication Statistics
distinguishable from their hosts. Frode Fos-
Clinical Neuroscience in Europe _______________________________________________36
søy and Bård Stokke revealed how the com-
mon cuckoo inherits egg colour trait. (p. 32)
Biobusiness
News
Austrian cancer vaccine induces immune response / Belgium’s Tigenix heads for IPO _________39
Scientists in Court
Two GlaxoSmithKline researchers allegedly used the stolen property of their long term employer
to benefit their own business. Fact or fiction? ______________________________________40
Research Antibodies
Did one of the world’s largest suppliers of antibodies ignore livestock farming protocols? ______42
Further News
Affymetrix becomes part of Thermo Fisher / Sweden’s Aprea raises millions for anticancer drug _47
Service
You always thought that the research anti-
body manufacturing industry was squeaky Product Survey: Genome editing kits __________________________________________48
clean? You could be wrong, given the incidents New products ____________________________________________________________56
at a US antibody supplier’s facility. (p. 42) Methods
Tips and tricks of the trade: 3D-printed microscope _________________________________53
Bench philosophy: Deep learning applications in biology _____________________________54
Book Reviews
Development and Reproduction in Humans and Animal Model Species. By Werner Müller et al. _57
Washington Careers
University of CAna riendeer pSetnradteengt ieexsp efortr g Yroouupn gev Eauluraotpede athne S EcUie’sn FtPis7t sp r(oLgIrXa)mme. What did they learn? _______58
Photo: Jobs / Calendar __________________________________________________________61
Deep learning algorithms enable machines to
Humour
“think” in a similar way to the human brain.
Paul the Postdoc __________________________________________________________06
So why not use deep learning tools to solve
Contact _________________________________________________________________49
biological questions? (p. 54)
Laboratory Tales ___________________________________________________________67
LT_216_04_05.indd 4 04.04.16 16:56
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page 6 Lab Times 2-2016 News
Picture of the issue
Excellent Images Wel(l)come!
There’s always a good reason to celebrate and especially to “cele-
brate science, medicine and life”. The Wellcome Trust gets in the fes-
tive mood by selecting the “most informative, striking and techni-
cally excellent” images, recently added to their collection. Now in their 15th
year, the Wellcome Image Awards honour 20 scientists, physicians and art-
ists from Europe and the USA. Among
them, Fernán Federici from the Univer-
sity of Cambridge. His image of develop-
ing maize leaves, taken by confocal mi-
croscopy (bottom, left), is reminiscent of
Roman floor mosaics. And it was exact-
ly this intricate pattern that ultimately
caught the jury’s eye. “It reminds us how
complex even relatively simple organisms
are when seen on this scale,” jury mem-
ber, James Cutmore, commented. Optical
coherence tomography, a non-invasive
imaging technique that uses laser light, is
used to diagnose glaucoma, diabetes and
age-related macular degeneration. But
it can also be used to create a lasting im-
pression on contest judges. This is what
Peter Maloca from the University of Basel did with his 3D image “Inside the
Human Eye” (middle, right), revealing the tunnel-like structure of blood ves-
sels in a healthy human choroid in the centre of the retina. Speaking about
eyes… The image from Sílvia A. Ferreira, Cristina Lopo and Eileen Gentle-
man (King’s College London) of something that looks like a human pupil is
actually a single human stem cell, embedded in a porous hydrogel matrix
(top, left). Although the jury rather saw “a nebula frozen in time”, they were
wowed by the image’s sharpness, a characteristic of the technique employed,
cryo genic scanning electron microscopy. -KG-
Paul the Postdoc
by Rafael Florés
Stupid research! Some days I really think
about quitting it all and looking for a
completely different job...
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page 8 Lab Times 2-2016 News
Microbial map of the mouth
file of the young Spanish population”. Fur-
Recently Awarded Spit it Out! ther analysis, which is still in the prelimi-
nary phase, revealed some interesting dif-
When children stick out their tongue, par- ferences, depending on where in Spain
For his contributions to genetics in the ents tell them to stop and behave. But sci- the students live, what type of water they
last 15 years, Detlef Weigel (MPI for entists at the Centre for Genomic Regula- drink, whether they smoke, or whether
Developmental Biology, Tübingen) has tion in Barcelona encourage that behav- they share their home with a pet. Ultimate-
been awarded the 2016 GSA Medal iour. Their Saca la Lengua or Stick out your ly, the knowledge gained through this pro-
Tongue project is meant to not only “study ject could be used to come up with ideas for
from the Genetics Society of America.
the mouth’s microbiome and its possible re- better oral health.
Praised for his “deep rooted understand-
lationship with our environmental charac- As is right and proper, students and oth-
ing of genetics and his technological
teristics and lifestyle”, it is also aimed at er participants, who have significantly con-
creativity”, Weigel has greatly advanced
bringing life sciences, and in particular bio- tributed to the project, will become co-au-
the knowledge of plant flowering, the
informatics, closer to young people, inspir- thors of future publications. “It was a per-
prize committee said. His studies re-
ing the next generation of researchers and fect combination of ‘boot’ and ‘lab coat’ bio-
vealed, for instance, early events in
scientists. logy, which often seem so remote from one
flower development, the molecular basis “We’re very happy with the experience another,” Bejarano concludes.
for floral patterns and mechanisms for and with meeting the challenge of a citizen
natural flowering time. science project in biomedicine. We have in-
EMBO grant withdrawn
volved society in most phases of the project:
Her “boundless energy and enthusi- from the establishment of initial hypotheses Cash Return
asm” not only made Fiona Watt (King’s to the bioinformatic and statistical analysis,
College London) one of Europe’s top including the collection of samples,” said Once again, PubPeer eyes have seen dou-
stem cell experts, it also earned her a Luis Serrano, director of the CRG. ble. Duplicated images to be exact, in a Na-
very special recognition, the 2016 FEBS ture Genetics paper by Portuguese research-
er Sonia Melo et al. The post-publication
| EMBO Women in Science Award.
peer review platform is famous for reveal-
Throughout her career, Watt has discov-
ing violations of Good Scientific Practice; it
ered more and more clues to unravel
was them, who got the ball rolling, causing
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Two European researchers are among Photo: w pplaipeder f oorn atnh eE MreBfeOre Inncseta llilsatt,i oMne Glor ahnatd. Sahpe-
the winners of this year’s Protein So- won the grant, which would have given her
ciety Awards. Andreas Plückthun At the heart of the project, launched a an annual award of €50,000 for up to five
year ago, is the microbial analysis of more years and access to EMBL core facilities, as
(University of Zürich) won the Christian
than 1,000 saliva samples from high school well as ample opportunity to set up a net-
B. Anfinsen Award that recognises
students from all over Spain. Besides the sa- work of collaborators.
technological advancements in protein
liva sample, the study set-up also included Needless to say, EMBO immediately
research and Jane Clarke (University
a questionnaire with more than 50 ques- started an investigation into Melo’s case.
of Cambridge) was honoured with the
tions about the student’s eating and drink- On Retraction Watch, the Portuguese re-
Stein and Moore Award, given to protein
ing habits, for instance. CRG researcher Luis searcher explained how the duplicated im-
scientists who consistently make valu-
Bejarano insisted on collecting the samples ages ended up in the now retracted paper:
able contributions to the field. Regarded himself. Travelling over 7,000 km, with his “The first version of the submitted man-
as a pioneer in protein engineering, hand centrifuge and a battery-powered uscript shows that the figures were accu-
Plückthun developed methods to create freezer, he thinks it was a very good idea to rate without the duplication that appeared
new proteins and protein variants. One involve the public. “For example, in some in the final version. The published correc-
of his achievements is the engineering villages, students asked us what they should tion (2010) to the manuscript happened
of Designed Ankyrin Repeat Proteins or write in the questionnaire if they drink wa- because one of these mistakes was identi-
DARPins, novel scaffolds for selective ter from a well – we hadn’t even thought fied soon after the original publication. At
protein binding. Clarke uses a multidis- about that!” that time point this was taken as an isolat-
ciplinary approach to study protein fold- The carefully collected and analysed ed error, which happened during final fig-
samples allowed the scientists to draw up ure assembly of the images. Unfortunately,
ing, misfolding and assembly. -KG-
a “high-resolution, oral microbiome pro- I failed to see the other duplicated imag-
LT_216_06_12.indd 8 04/04/2016 13:57
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page 10 Lab Times 2-2016 News
es in the manuscript.” The researcher, who the “ability to duplicate (i.e., repeat) a pri- HES infusions for critically ill patients or
stands by her data, takes on responsibility or result using the same source materials patients with sepsis or burns. The restrict-
for the “embarrassing error” and now has and methodologies”. Reproducibility is the ed usage meant a drastic drop of Fresenius
to bear the consequences. “ability to achieve similar or nearly identi- Kabi’s sales figures for Voluven, their HES
After careful consideration, EMBO re- cal results using comparable materials and product.
versed its funding decision. Not because methodologies”. Scientists, policy makers However, the pharmaceutical compa-
Melo had worked in an unethical manner and journalists should make sure to remem- ny, which had supported the CHEST tri-
but because her work lacked diligence. An ber the differences. al with €3.5 million, detected some incon-
EMBO spokesperson told Retraction Watch: It’s similarly important to remember and sistencies in the NEJM article. “We have
“(…) The committee concluded that the be aware of a few other things that could af- many specific concerns about the publi-
body of work, upon which the selection for fect research reproducibility/replicability. cation”, Fresenius Kabi’s senior vice presi-
an installation grant was made, contained Scientists working with mice, for instance, dent, Hrishikesh Kulkarni, told The British
evidence of a level of negligence in handling are recommended to not only discuss an ex- Medical Journal (BMJ,) which tried to me-
and presenting data that would have pre- periment with their research group but also diate between the opposing parties. They
cluded a recommendation for an award. with staff at the animal facility as the “or- could be easily solved if the company could
The committee therefore decided that So- ganisation, daily operation, environment, get access to the raw data and initiate an in-
nia Melo should not become a member of and staffing of an animal facility can affect dependent analysis. But Myburgh has res-
the EMBO network of Young Investigators the outcomes of experiments”. ervations. “We have no issue with the con-
and Installation Grantees, and that the in- Experiments with antibodies can also cept of data sharing (…) The concerns we
stallation grant will be revoked. This has make one or the other scientist tear his or
been communicated to Sonia Melo and her her hair out. Therefore, FASEB “strongly rec-
home institution on February 29.” ofumnmdienngd asg” etnhcaite sr epsueta rtchheeirr sh,e jaodusr ntoaglse tahnedr Kathy Zinn
RGecoomomden dAatidonvs oinc reeproducibility tivcnoaeg trca yoal olmnegtaeiubs euto, p dnt hiuweemsi .tc bhoTe mhar,i psst tlhseaehtne oda upnalrrtdoidb d iofnuodccryltmu ntdayaetpm ,ef oae, rt,v ttechhintee-- mainpictures.net/
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ence can move on? For the US Food and Although the recommendations have
Drug Administration, for instance, two been devised by the Federation of Ameri-
positive randomised control trials are suf- can Societies, they are certainly also good
ficient to prove a new drug’s effectiveness. advice for European scientists.
But, there’s no definitive answer for all re-
search disciplines, yet.
Data sharing with Big Pharma?
Also, the Federation of American So-
cieties for Experimental Biology (FASEB), No Trust Starch or saline – that’s the question
which published a set of recommenda- that splits intensive care specialists.
tions to “promote the reproducibility and Sharing data has become natural to many
transparency of biomedical and biologi- scientists but should researchers aban- have, come down to the people with ulteri-
cal research” in January, didn’t comment don this ideal, if they suspect re-analys- or motives, which contradict or do not ad-
on that issue. The Federation does have a ers to have a hidden agenda? That’s the here to the scientific principles we adhere
lot of other advice, particularly addressing current debate in intensive care medi- to. That’s the danger.”
the two factors that are regularly involved cine. In the leading roles: German phar- The CHEST investigators also refused
with irreproducible experiments: antibod- maceutical company, Fresenius Kabi, and the offer to release the data for re-analysis
ies and mouse models (http://tinyurl.com/ John Myburgh (George Institute for Global to the Yale Open Data Access (YODA) pro-
zbtvrwp). Health, Sydney, Australia), principal inves- ject. That’s because, again, Fresenius prom-
“What began as a thought-provoking tigator of the CHEST trial, comparing sa- ised to sponsor the re-analysis. “The con-
discussion of some very real challenges fac- line and modified starch solution (HES) for clusion is that we cannot provide data for
ing our community resulted in practical rec- fluid replacement in critically ill patients. an analysis funded or otherwise supported
ommendations to help scientists begin to In a 2012 paper, published in the New by Fresenius, given their conflict of interest
move the needle in their own labs and insti- England Journal of Medicine, Myburgh and and repeated efforts to discredit the CHEST
tutions (…) We cannot take for granted the colleagues found that although there was trial in an effort to protect their commer-
public’s trust in science. It is time to enact no difference between patients receiving cial interests. (…) we cannot agree to pro-
policies and procedures that emphasise the saline or the starch solution regarding mor- vide data in these circumstances,” Vlado
tradition of rigor in research,” FASEB Presi- tality, “HES was associated with signifi- Perkovic, executive director of the George
dent, Parker Antin, stated in a press release. cantly more adverse events”. Thereupon, Institute, wrote in an email to the BMJ. “We
First of all, it’s important to know your regulatory authorities, like the European want restrictions on who could do the anal-
basic terms. Replicability, FASEB defines, is Medicines Agency, recommended against yses,” Myburgh added.
LT_216_06_12.indd 10 04/04/2016 13:57