Papers, Graduations & More

Lots of recent happenings in the lab to report…

(1) Congratulations to Owen Smith, who successfully defended his PhD thesis in March!  Owen’s final paper from his thesis work is currently in revision, but you can see the pre-print at BioRxiv here.  Owen is going on to do a post-doc in the lab of Roman Eliseev in the Center for Musculoskeletal Research.

(2) On April 11th we have another graduation – Jimmy Zhang is finishing up the PhD part of his MD/PhD and returning to medical school.  Jimmy’s last paper on his thesis work is also in revision, but no pre-print yet as per journal policy (boo!)  The short version – not everything in this paper appears to be 100% correct.

(3) We have a new post-doc’ in the lab. Chaitanya Kulkarni (Chaitu) came from Bob Kern‘s lab in the Medicinal Chemistry program at the University of Iowa, with a strong background in developing mito-targeted drugs.

(4) Our paper on the metabolic effects of NMN is also in revision, but the BioRxiv pre-print is here.

(5) Some work on metabolomics of the developing embryonic heart, performed with our collaborators Steve Ebert at UCF and George Porter here in Rochester was published in J Biol Chem.

With another paper about to be submitted, all being well we should be looking at hlf a dozen primary science manuscripts in press by late summer, plus a couple of reviews. Publish or perish…

Latest Paper – Mito’ KNa1.2 Channel

Our paper on a mitochondrial KNa1.2 channel is now out as a pre-print at BioRxiv. It describes about 4 years of work by Owen Smith, a (hopefully soon to be graduated) student in the lab.

This new report builds off our paper last year showing that KNa1.2** is required for cardioprotection by volatile anesthetic preconditioning (APC). In that paper, we kind-of showed that there’s a mitochondrial KNa1.2 channel, but the gold standard is patch-clamp of isolated mito’ inner membranes (mitoplasts) and, to put it mildly, this is not a simple technique! With the help of Liz Jonas at Yale and Casey Kinally at NYU (now retired), Owen finally cracked it and we now have solid evidence the channel exists in mitochondria.

The next question was “OK, if this channel exists, it didn’t evolve over millions of years waiting for volatile anesthetics to be invented in the 20th century, so what’s its endogenous physiologic role?”  What we found is that the hearts of channel knockouts have a rather odd metabolic phenotype – they can’t exhibit maximal respiratory or work capacity, BUT this is only true when they’re burning fat as a fuel. They’re perfectly OK on glucose, and they’re fine at baseline, they just can’t go full-speed when burning fat.

This finding has some interesting implications…. First, it implies a mechanistic link between a mitochondrial potassium channel and the regulation of cardiac metabolism. To the best of our knowledge this is the first such reported link.  Second, we found that activating mito’ KNa1.2 uncouples mitochondria, and it was reported in 2014 that Niclosamide, a KNa activator, is beneficial in a high fat diet model of diabetes. Ergo, this mito’ channel could be an important (and so far overlooked) drug target for regulating metabolism, with potential importance for obesity, diabetes, metabolic syndrome etc.

Anyway, while the paper is being reviewed at a “regular” journal (fingers crossed), the pre-print hopefully gets the story out there for critique by the field at large. If you have something to say  – have at it in the BioRxiv comments, or Tweet/E-mail me. Our previous pre-prints have benefitted enormously from incorporation of comments on BioRxiv at the journal revision stage.

**For those confused by the naming, KNa1.2 is the new name for “Slo2.1”, which is also known as “Slick”, and is encoded by the Kcnt2 gene. We used to call it by the Slo nomenclature, since Slo2.1 is part of a larger family of channels related to the Drosophila slow-poke allele, which is Slo1. Slo1 is a KCa channel, whereas Slo2.1 and its sibling Slo2.2 (aka KNa1.1, Slack) are KNa channels.

New grant, new toys, conferences, and we’re hiring!

Some exciting recent developments in the lab…

GRANTS!  Our long-running NIH R01 project (R01-HL-071158) was competitively renewed for its 4th cycle (through June 2021).  The current iteration of the project aims to understand the role of acidic pH in remodeling of cardiac metabolism that occurs in ischemia. Here’s the project description on NIH RePorter.

RESULTS!  Our paper on the role (or not!) of sirtuin-dependent deacetylation in regulating 2-hydroxyglutarate generation was published in Biochem J.  We have another paper in the pipeline on the regulation of metabolism by sirtuins, to be submitted this fall.

TOYS!  The financial stars aligned, and we were fortunate to get the opportunity to acquire a new (well, refurbished) mass-spec’ for the lab.

It‘s a Thermo TSQ Quantum Access Max, which is their work-horse triple-quad. It’s plumbed in next to our HPLC, and will enable us to perform metabolomic analyses in-house (although our colleague Josh Munger remains an important collaborator, having gotten us into this field to begin with!)   Our new lab Tech’ Mary is currently developing a custom SRM library for targeted metabolomics (aka making us bankrupt by purchasing the entire Sigma catalog!)


PEOPLE! Our GEBS summer student Irma Ruiz finished up and is now back at Tulane.

Irma worked on optimizing and running blue-native and clear-native gels, for the study of mitochondrial respiratory super-complexes, making some interesting findings in the various knockout mouse lines we maintain.



MEETINGS!  Lab members will be presenting at a few upcoming conferences…

JOIN US!  Coupled to the grant competing renewal, we’re looking to hire a new post-doctoral fellow to work on cardiac metabolomics. Here is a copy of the job ad’, which will be posted at the various meetings listed above. If you’re interested, feel free to talk with any of us during these meetings, or call or email for more details.

New Tech, Student & Papers in the pipeline

We have a new lab’ tech – Mary Day – who joined us from SUNY Oswego via the UR clinical labs). Mary will be taking over the management of our mouse colonies, among other things.

We also have a student in the GEBS summer scholar’s program – Irma Ruiz-Concepcion, from Tulane University in New Orleans, who will be looking at respiratory super-complexes in mouse hearts.

Our latest paper on the the role (or not!) of acetylation as a regulator of 2-hydroxyglutarate generation, is now up as a pre-print on BioRxiv.  Also our collaborator Paul Trippier’s paper on novel complex II inhibitors was accepted. We also have a number of other papers in the pipeline this summer, from colaborations with Michael O’Reilly, Xin Li, Gail Johnson, Vadim Ten, and Daniel Acuna. Plus a chapter on mitochondria and nitric oxide in the upcoming 3rd edition of Ignarro’s “NO Bible“, co-authored with Sruti Shiva and Laura Castro.  The Biochem. J. review on mito’ K+ channels should be out any day now.

May 2017 Update

Lots of things happening in the lab this spring…

(1) We hired a new technician who will be starting after Memorial Day.

(2) Congratulations to Jimmy Zhang (MSTP student), who got an F30 fellowship funded. Now begins the fun process of divesting from an AHA fellowship that he got funded late last year. That in itself involved extrication from his inclusion on a training grant beforehand. First world problems.

(3) Congrat’s also to Dr. Sergiy Nadtochiy, who has been promoted to Assistant Professor (tenure track) in the Department of Neurology. Sergiy is now a qualified anatomy instructor in the medical school and a key teacher in the HSF (human structure and function) physiology course. Luckily for us he still gets to hang out in the lab’ and do experiments 20% of the time.

(4) The competing renewal application for R01-HL-071158 received a 12th percentile score. Current NHLBI payline is 15%, so assuming nothing crazy happens* between now and the end of the fiscal year, we’ll hopefully be receiving a notice-of-award later this summer. (*not guaranteed given the current state of affairs in Washington DC).

(5) Due to the above, the money we had been planning to use for a no-cost-extension, is now planned to be used for the purchase of a refurbished mass-spec’. We’re hoping to take delivery soon of a ThermoScientific TSQ Quantum Access Max, which will be hooked up to or existing Shimadzu LC rig to give us an in-house LC-MS/MS capabilities, for metabolomics and other small molecule analysis.

(6) Our review on mitochondrial K+ channels is still not out yet. Apparently Biochemical Journal doesn’t publish review articles, even on-line, until they’re given page numbers in the print version of the journal.

(7) Our paper in JBC last year was essentially vindicated by a new paper in Nature Chemical Biology, but the authors chose not to cite us, which is kind of not nice.

(8) We’re getting a GEBS summer scholar student for this year, for June and July.

(9) Paul gave a talk at the Biopysical Society annual meeting in New Orleans in February, and at Medical College of Wisconsin in April. Additionally I had a very enjoyable visit to the Biological Sciences Department at LeMoyne University in Syracuse, to discuss our research and PhD programs with their really bright undergrads.

(10) Several members of the lab’ will be attending/presenting at the APS Physiological Bioenergetics meeting in San Diego this August.

(11) Lots of progress (retractions etc.) on various scientific misconduct cases I’m involved with (Saad, Aggarwal, Lee). Sadly, many other cases reported on PubPeer (such as this one) have yet to be dealt with by the journals despite multiple attempts at badgering them to do the right thing.

(12) Paul may or may not have been involved in discussions with various reporters who’ve published some critical pieces about certain scientists this spring. There’s more to come on some prominent players in this area!

(13) After some procrastination and a original idea to go on hiatus, UMDF decided that, after all, they were going to have a grant program this year. So, instead of the usual cycle spread over 6 months (letters-of-intent, triage, review, invite full applications, triage, review, in-person meeting, council, awards), we’re doing a condensed format (<2 months total) with a targeted RFA.  So far it’s been going well despite the short time-line. Hopefully will reap rewards down the line for mito’ patients.

(14) Papers to come this summer… Owen’s paper on the Slo2.1-/- mouse. Yves’ paper on mitoUPR and cardioprotection. Jimmy’s paper on succinate in cardiac ischemia. Sergiy’s paper on lysine acetylation and hydroxyglutarate. I should stop updating this post and go do some writing!