Our new lab space!

Well, new to us at least.

Over the past couple of months, we’ve been lucky enough to absorb an adjacent lab’. Up to now, our main lab’ was 7420, at the bottom center on the plan shown below, with a small cell culture room in the back (20A). We also used the lab’ next door (7424) on the same corridor, but this was problematic because there’s no connecting door. For security reasons the adjacent lab had to be locked when unoccupied, so to get there meant removing gloves and fiddling with keys while carrying an ice bucket. Another problem – we were using the back room (20A) for animal work, but because it’s a dedicated cell culture room, it has positive air pressure. So, all the dander and allergens and other gunk would float out into the main lab. Not good when you’re allergic to mice!

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The cost to open a doorway between the 2 big labs was prohibitive, but for a while we’d been aware there was an old connecting door to the lab behind us (7512 on the plan). That room was used by Alan Smrcka ‘s group as a student office and general storage room, and the door was simply blocked on both sides with drywall and a few wooden shelves/cabinets. The lab’ once belonged to a former Dept. chair, but was never officially decommissioned when he retired a few years ago, so the cupboards were full of old supplies, chemicals and defunct equipment. So, we approached Alan and he very generously agreed to a swap – room 7512 in exchange for 7424. After a few weeks of construction dust, we now have a new lab, and finally 3 rooms of contiguous space. It wasn’t quite like this but you get the idea…

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The new space is nothing short of a revelation for the way we work. We now have a simple arrangement with in-vivo stuff in the new room (7512), cell stuff in the middle, and biochemistry in the main lab at the front. The great thing is there’s a fume hood in the new room, so we can keep allergen exposures to a minimum elsewhere in the lab. Also now the cell culture room (20A) with positive air pressure can finally serve its intended purpose.

Here’s what’s left of the connecting door, looking through from the new lab’ into the cell culture room. On the right is our cardiomyocyte preparation rig, making it easy to transfer the freshly prepared cells into the cell culture hood and incubator. There’s still some finish work to be done on the floor and the bench-edges.

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This is now our perfusion bench. On the left is the surgical area with dissecting scope, ventilator, EKG, thermal pad etc.  Then on the right are two separate Langendorff heart perfusion rigs. There’s a third rig out of view, on the opposite side of the new lab. Due to fire regulations we’re not allowed to use the top shelves near the ceiling for storage, so those are blocked off.

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We also relocated our HPLC to the new lab. Here it is next to the fume hood…

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In the cell culture room we now have our 2 seahorses – XF24 and XF96.  This used to be the bench where all our perfusion gear was. You can also see the gas perfusion system mounted on the shelf – we do some fun things involving flooding the plates inside the seahorse with argon gas, as reported here.

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Here’s another view of the cell culture room showing the hood, with the seahorse bench on the left…

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During the reshuffle we were able to divest some old equipment that was broken no longer being used.  A key piece was our Aviv Model 14 spectrophotometer, which Jack Aviv himself came to collect. It had served us well, and was the source of several publications, but had sat unused for many years and took up a lot of space. Here it is in the back of Jack’s van…

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The other thing this move allowed us to do, was consolidate our refrigeration in the front lab’, so now we have 4C, -20C and -80C all in one place.

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Most of the demo’ work was done by UR facilities, plus moving electrical panels, putting in new floor tiles to bridge the gap, some HVAC work to balance out the flows, removal of old telephone lines, replacing all the fluorescent light tubes etc. Some things we did ourselves – for example we used the opportunity to do some paint touch-up throughout the lab (the drywall was pretty beaten up in places). Here’s our technician Bill hard at work – this is how we roll!

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Environmental Health Sciences also helped us to dispose of the various chemicals through the hazardous waste program. We managed to fill 3 dumpsters with old equipment and supplies from the cupboards of the 7512 lab – a bonus for the Department is the lab is now clean and no longer a hazard liability.

Like all moves this one was pretty disruptive, but the new space really works well. The 3 Langendorff rigs are already cranking out data. Having all the cell culture stuff in one room means less contamination. No more messing with gloves and keys to get between labs.  The new lab has a door leading out to the elevator lobby, which gives us another fire escape route, plus that’s where the bathrooms are located so it’s easier to go answer the call of nature during experiments!  All in all a very worthwhile process.

Retraction? No problem just send it to Frontiers!

A while ago I documented some data problems in a JBC paper, including a failed attempt by the authors to correct the paper, followed ultimately by its retraction.

Well, guess what showed up at Frontiers this week… the exact same paper. The title is almost the same, huge blocks of the text are the same, and the majority of the data and figures (minus the mistakes during figure preparation) are the same. Without making any comments on the reliability of the data in the new paper, which I haven’t examined in detail yet, the following questions come to mind….

  • Did the editors at Frontiers know the paper had been retracted from another journal?  If so (or not), how would this have influenced the peer review process?
  • The authors listed on the retracted paper and the new one are identical. I don’t know how other people run their labs, but if my lab had a paper retracted for questionable data integrity, the person responsible for those problems would be out the door faster than you can say “Committee on Publication Ethics”. Keeping the same authors suggests that either Dr. Donmez is an extremely forgiving employer and chose not to fire the subordinate responsible for this mess, or that she was personally responsible for the problem data so there is no subordinate to fire.**
  • What about copyright? The original version of the paper is still up at the JBC site for all the world to see. Does Frontiers have the right to publish the same information, in clear in breach of JBC’s copyright?  How does copyright work on a retracted paper?
  • How should episodes such as this inform how we deal with retracted papers in the future?

Regarding the last point, perhaps a good starting point would be a check-box on the intake form for journals, stating whether the work is a republication of a previously retracted work. Perhaps such papers could then be accompanied by a statement with assurances that the original data have been scrutinized to ensure their integrity.

** I’ve run into this problem before – seeing a paper in the review stages with creative data presentation, and then seeing it appear elsewhere with the exact same list of authors. How many more papers are out there, where authors dodged a bullet in the review stages but made it to press somewhere else?

UPDATE (4pm 9/2/2014) – I just learned via PubPeer that a paper from Rui Curi (favorite South American dood who threatened to sue me) was re-published in an open access journal OmicsOnline, which is on Beall’s list of predatory (pay-4-glam) journals. Incidentally, the original paper was in J Lipid Res, also an ASBMB journal (like JBC), and so the original full-text is still up there on the JLR website. Again, the copyright question arises – does omicsonline own the paper now?  Has anyone done an analysis to see how much of the content of these new predatory open access journals is comprised of stuff retracted from other places?

UPDATE 2 (9am 9/3/2014) – Following an email last night, I have now heard back from the Frontiers in Aging Neuroscience EiC, Gemma Casadesus Smith. They were “unaware of this issue and will look closely into it”.  Hopefully that’s not a euphemism for try to forget about it until all washes over, as frequently seems to happen at other journals.  Now we play the waiting game…

2 years for a retraction at Cell

About 6 months ago I wrote this post, about the trouble I was having in getting 3 problem papers by a single author dealt with by journals. The author in question was Gizem Donmez of Tufts University, who in 2013 threatened to sue me for defamation based on the things I had written about her science. The papers were:

J. Biol. Chem. 2012;287;32307-32311; PMID22898818 – Retracted July 2013
Cell 2010;142;320-332; PMID20655472 - Retracted this week
J. Neurosci. 2012;32;124-32; PMID22219275 – Still intact

As you can see from the 2nd entry there, the Cell paper has now been retracted. While this is indeed good news, it is by no means indicative that all is well in the world.  In-fact, the story of how this played out indicates deep problems at Cell. Here’s the time-line…

August 2012 – Original email by me to Cell using a pseudonym. The anonymous contact who sent me details of these papers to blog about also indicated they had contacted the journal. No responses were received despite multiple emails. Attempts to contact Dr. Donmez’s Institutional Research Integrity Officer and Department Chair were also ignored.

September 2012 – Papers were blogged about on my now defunct site-that-must-not-be-named. Numerous emails with links to the blog post were sent to all interested parties, including the Ellison Medical Foundation which had just awarded Dr. Donmez a prestigious “New Scholar in Aging” award, largely on the basis of work published in these papers. To date, Ellison has refused to engage in any conversation regarding the integrity of data used in her award application. The ORI was also informed, and to the best of my knowledge their investigation is ongoing.

September 2013 – I contacted Cell again using my real name, reiterating my concerns. Cell responded 2 months later, saying this..Despite some apparent superficial similarities, upon extensive examination we were unable to find any compelling evidence for manipulation or duplication in those panels and therefore are not taking any further action at this time.” The email came from Sri Devi Narasimhan, an editor at Cell who trained with Heidi Tissenbaum at UMass, who in-turn trained in the lab’ of the paper’s senior author (who also happens to be on Cell‘s editorial board).

January 2014 – I complained to Cell about this rather obvious appearance of conflict-of-interest, and blogged about it here. Over the course of the next month, several attempts were made to contact Cell, including numerous promises from Editor-in-Chief Emilie Marcus’ assistant that she would get back to me. That never happened. To date I have received no communication whatsoever from Dr. Marcus regarding these issues.

February 2014 – I decided to involve the Committee on Publication Ethics, COPE. There ensued many emails to establish correct procedures for raising a formal complaint (TL/DR – one must ensure all avenues at the journal have been exhausted before COPE will take on a case. This is easy – when a journal’s EiC goes incommunicado, all avenues are exhausted). The full text of my complaint about Cell is here, (minus all the attachments) but it really boils down to the following…

In refusing to initially respond to an anonymous correspondent, and then further refusing to respond to emails and follow up requests for more information using my real identity, the journal breached Code Section 15.1 “Editors should respond promptly to complaints and should ensure there is a way for dissatisfied complainants to take complaints further”.
In assigning a misconduct investigation to a staff member who is a trainee of a trainee of the lead author of the paper in question, the journal breached Code Sections 2.1 “Duties include informing readers about steps taken to ensure that submissions from members of the journal’s staff or editorial board receive an objective and unbiased evaluation” and 17.1 “Editors should have systems for managing their own conflicts of interest as well as those of their staff, authors, reviewers and editorial board members”.

March to July 2014 - I made numerous attempts over the past few months to find out what’s going on at COPE and at Cell. While I don’t wish to reproduce all the emails at least 26 of them over the course of 6 months), the gist of the conversation is as follows:

Me: What’s going on?
COPE: We contacted the publisher
Me: Why the publisher? It’s the editor I’m complaining about.
COPE: Although the editors looked into your case, the publishers had not yet completed an investigation. Elsevier told us they’re still looking into it. We’ve been pushing hard on this for the past few weeks.
COPE: The editors are now investigating the 2nd round of concerns you raised in your blog post.
Me: So let me get this straight. There are actually 4 investigations – one each for the editors and the publishers, and one for each round of allegations. So far after 2 years, only 1 of these 4 is complete and the outcome was “unable to find any compelling evidence”.?
COPE: Yes. We’ll keep you posted.

August 2014 – Someone (not me) recently revived the PubPeer thread on this paper, independently “rediscovering” the various image problems within it.

August 12 (yesterday) – Finally, the paper has been retracted, with a rather detailed retraction notice indicating a LOT of image problems. I want to compare and contrast the statement from the Cell editor further up the page with the retraction notice…

Cell editor Jan’ 14. “Despite some apparent superficial similarities, upon extensive examination we were unable to find any compelling evidence for manipulation or duplication”.

Cell editors Aug’ 14. “It has come to our attention that several figures in the paper contain images in which gel lanes were spliced together without appropriate indication. There are also instances of image duplication”.

Given the first statement, you really have to ask if the Cell editorial team is living in an alternate universe, where the term “extensive” means half-assed? It’s also somewhat troubling that there’s been no formal contact from the journal to the person who actually raised the complaints. Although there’s no precedent or requirement for such, you’d think as a matter of courtesy that a journal would formally notify a correspondent of an impending retraction, rather than just have them learn about it via social media. But, we already know basic manners aren’t a strong suit at Cell, so no big surprise there.

What next?
At this point, I have not been contacted at all by COPE, so I’m assuming their investigation into potential breach of code-of-conduct at Cell is still ongoing. Given that Cell and Elsevier are two of COPE’s biggest customers/subscribers, I can imagine there’s rather a lot of pressure on COPE to make this story go away. Let’s hope that doesn’t happen – Cell screwed up really badly here and if heads don’t roll then this case becomes yet another indicator of how corrupt the academic publication system really is.

 

α-Ketoglutarate & Lifespan, Really?

So this paper came across my desk this weekend (yes it was published a month ago so I’m a bit late to the game here, shoot me). I’m having a hard time believing the central result isn’t due to a simple artifact.

The paper describes the ability of α-ketoglurate, an intermediate in the Krebs’ cycle, to extend lifespan in C. elegans. The authors let the worms swim around in a solution of 8 mM α-KG and they lived longer.  There are some interesting knockout experiments showing the importance of various downstream mediators (mTOR, ATPsynthase) in the effects, but the key problem here seems to be that the authors may have overlooked a potential alternative mechanism…

α-KETOGLUTARATE IS AN ANTIOXIDANT

Yeah, so side-stepping the issue that just about every small molecule has at some point in the past few years been tagged as an antioxidant, there might actually be some decent proof here, in the form of a chemical mechanism. You see, a few years ago I reviewed (and was subsequently asked to write an editorial on) a paper in Free Radical Biology & Medicine, showing that α-keto acids (e.g., α-KG, pyruvate, oxaloacetate) can be non-enzymatically decarboxylated in free solution by reaction with hydrogen peroxide.  The reaction is as follows:

α-KG + H2O2 → succinate + CO2

As outlined in our editorial, what this amounts to is a short-cut in the TCA cycle… you can get from α-KG to succinate without α-KGDH, so if the enzyme is inhibited (coincidentally this may occur due to oxidative stress such as H2O2), there’s a way to bypass the inhibition and allow the cycle to keep turning. Furthermore, this property of α-keto acids is well known in experimental circles… if you’ve ever made up a solution of pyruvate you know it goes off pretty quickly. That’s oxidative decarboxylation in action (the product in this case would be acetate). We even showed that this reaction (oxaloacetate → malonate) could occur in perfused hearts and may play a role in ischemic preconditioning. So, it happens in real mammalian tissues and is not just a theoretical test-tube reaction of the type often wheeled out to show that something is a biologically relevant antioxidant.

So, overall it just strikes me as not a very big deal that adding 8 mM of a known antioxidant to a plate of worms has an effect on lifespan.

The dose response shows an effect on lifespan in the 1-10 mM range with an EC50 of ~3 mM, which is right in line with a generic non-enzymatic effect, and not really compatible with the KM values for most of the enzymes that handle these metabolites (typical KM for α-KGDH is 150 μM in the presence of Ca2+, only going into the mM range in the complete absence of Ca2+ which never happens in-vivo). Moreover, Fig. 2 of the paper shows that many of the effects which are proposed to account for the lifespan phenotype at the whole organism level occur at concentrations of α-KG in the 100-200 μM range, i.e. 5-fold lower than the level used in live worms). Oh, and it’s probably worth mentioning that some of the proposed downstream mechanisms might be sensitive to oxidative stress.

Given all the kerfuffle in recent years about TCA cycle intermediates as hot sexy new signaling molecules, it’s hardly surprising that this study made it into Nature. However, it’s frustrating that some simple controls were not included… (i) Do other α-keto acids prolong lifespan? (ii) Does adding α-KG to media and letting it sit for a few days at room temp’ on the shelf diminish the effect? (ii) Are lifespan-extending effects of other antioxidants additive to the effect of α-KG? (iv) Are effects of α-KG greater in worms known to generate more H2O2?

I left a comment on this at PubMedCommons, and also at PubPeer. The latter notifies the authors automatically, so hopefully we can get some feedback on this.

Summer Happenings

It’s been a while since I updated the lab blog, so here’s a run-down of what’s new in the past few months…

  • Marcin Karcz, a resident in the Department of Anesthesiology, got his fellowship grant funded by FAER (The Foundation for Anesthesia Education and Research), and will start in the lab shortly.
  • Our paper with Michael O’Reilly on mitochondrial DNA double strand breaks and ATM activation was finally published in FRBM.
  • The publications page is finally updated to include our 2013 and YTD 2014 papers.
  • We have a summer undergraduate intern, Ling Yang from biomedical engineering, who is designing/making circuits for electrical stimulation of isolated cardiomyoyctes.
  • Our dual-PI R01 application with Keith Nehrke on the mitochondrial unfolded protein response received a 13th percentile score. Not fundable (NHLBI payline is 11%) but hopefully close enough to fly on the next cycle.
  • Chad Galloway got an impact score of 30 for his K01 application. No percentiles given, so it’s fingers crossed for the October council meeting at NIDDK.
  • Chad also got his paper on mito’ morphology in NASH published in AJP Endo (accepted but not online yet).
  • AHA Grants have been flying out the door… pre-doc’ from Owen Smith, and lots of letters/references for pre-doc’, post-doc’, grant-in-aid and others. It looks like their fall review cycle is going to be packed!
  • Andrew and Sergiy went to the AHA Basic Cardiovascular Sciences meeting in Las Vegas NV, where allegedly Sergiy won a whole 5 dollars (and promptly lost it again).  Oh, and Andrew won a travel award.

Outside the lab’ there’s plenty happening too.  Summer vacations being taken, home improvement projects being done, happenings in the world of PPPR such as this great editorial at PubPeer, trying to get letters/paperwork together for my promotion, playing with my 3D printer, and of course the usual shenanigans over on Twitter.