Biology subjects

Brookes, P. S.

Publications and source records attributed to Brookes, P. S..

4 recordsLinked to original sources

bioRxiv2018

Cardioprotection by the Mitochondrial Unfolded Protein Response is Mediated by ATF5

The mitochondrial unfolded protein response (UPRmt)1 is a cytoprotective signaling pathway triggered by mitochondrial dysfunction. Activation of the UPRmt upregulates nuclear-encoded mitochondrial genes, including those for chaperones, proteases, and antioxidants, as well as glycolysis, to restore proteostasis and cell energetics. Activating transcription factor 5 (ATF5), a protein with both mitochondrial and nuclear targeting sequences, is proposed to mediate mammalian UPRmt signaling. Since proteostasis and bioenergetics are important in the response of organs such as the heart to injury, we hypothesized that pharmacologic UPRmt activation may be cardioprotective against ischemia-reperfusion (IR) injury and that such protection would require ATF5. Using a perfused heart IR injury model in wild-type and global Atf5-/- mice, we found that in-vivo administration of the UPRmt inducers oligomycin or doxycycline 6 h prior to ex-vivo IR injury was cardioprotective. Such protection was absent in hearts from Atf5-/- mice, and no protection was observed with acute ex-vivo cardiac administration of doxycycline. Loss of ATF5 also did not alter baseline IR injury (without UPRmt induction). Cardiac gene expression analysis by RNA-Seq revealed mild induction of numerous genes in an ATF5-dependent manner, which may be important for cardioprotection. Analysis of hearts by qPCR showed that oligomycin at 6 h significantly induced genes encoding ATF5 and several known UPRmt-linked proteins. We conclude that ATF5 is required for cardioprotection induced by drugs that activate the UPRmt.

cell biology↗

bioRxiv2018

Bioscience-scale automated detection of figure element reuse

Scientists reuse figure elements sometimes appropriately, e.g. when comparing methods, and sometimes inappropriately, e.g. when presenting an old experiment as a new control. To understand such reuse, automatically detecting it would be important. Here we present an analysis of figure element reuse on a large dataset comprising 760 thousand open access articles and 2 million figures. Our algorithm detects figure region reuse, while being robust to rotation, cropping, resizing, and contrast changes, and estimates which of the reuses have biological meaning. Then a three-person panel analyzes how problematic these biological reuses are using contextual information such as captions and full texts. Based on the panel reviews, we estimate that 9% of the biological reuses would be unanimously perceived as at least suspicious. We further estimate that 0.6% of all articles would be unanimously perceived as fraudulent, with inappropriate reuses occurring 43% across articles, 28% within article, and 29% within a figure. Our tool rapidly detects image reuse at scale, promising to be useful to a broad range of people that campaign for scientific integrity. We suggest that a great deal of scientific fraud will be, sooner or later, detectable by automatic methods.

scientific communication and education↗

bioRxiv2017

Nicotinamide mononucleotide (NMN) affords cardioprotection by stimulating glycolysis

Stimulation of the cytosolic NAD+ dependent deacetylase SIRT1 is cardioprotective against ischemia-reperfusion (IR) injury. NAD+ precursors including nicotinamide mononucleotide (NMN) are thought to induce cardioprotection via SIRT1. Herein, while NMN protected perfused hearts against IR (functional recovery: NMN 42{+/-}7% vs. vehicle 11{+/-}3%), this protection was insensitive to the SIRT1 inhibitor splitomicin (recovery 47{+/-}8%). Although NMN-induced cardioprotection was absent in Sirt3-/- hearts (recovery 9{+/-}5%), this was likely due to enhanced baseline injury in Sirt3-/- (recovery 6{+/-}2%), since similar injury levels in WT hearts also blunted the protective efficacy of NMN. Considering alternative cardiac effects of NMN, and the requirement of glycolysis for NAD+, we hypothesized NMN may confer protection via direct stimulation of cardiac glycolysis. In primary cardiomyocytes, NMN induced cytosolic and extracellular acidification and elevated lactate. In addition, [U-13C]glucose tracing in intact hearts revealed that NMN stimulated glycolytic flux. Consistent with a role for glycolysis in NMN-induced protection, hearts perfused without glucose (palmitate as fuel source), or hearts perfused with galactose (no ATP from glycolysis) exhibited no benefit from NMN (recovery 11{+/-}4% and 15{+/-}2% respectively). Acidosis during early reperfusion is known to be cardioprotective (i.e., acid post-conditioning), and we also found that NMN was cardioprotective when delivered acutely at reperfusion (recovery 39{+/-}8%). This effect of NMN was not additive with acidosis, suggesting overlapping mechanisms. We conclude that the acute cardioprotective benefits of NMN are mediated via glycolytic stimulation, with the downstream protective mechanism involving enhanced ATP synthesis during ischemia and/or enhanced acidosis during reperfusion.

biochemistry↗

bioRxiv2017

Evidence for, and Metabolic Consequences of, a Cardiac Mitochondrial KNa1.2 Channel

Controversy surrounds the molecular identity of mitochondrial K+ channels that are important for protection against cardiac ischemia-reperfusion injury. While KNa1.2 (Kcnt2 gene) is necessary for cardioprotection by volatile anesthetics, electrophysiologic evidence for a channel of this type in mitochondria is lacking. The endogenous physiologic role of a potential mito-KNa1.2 channel is also unclear. Herein, single channel patch-clamp of 27 independent cardiac mitochondrial inner membrane (mitoplast) preparations from wild type (WT) mice yielded 6 channels matching the known ion-sensitivity, ion-selectivity, pharmacology and conductance properties of KNa1.2 (slope conductance 138{+/-}1 pS). However, similar experiments on 40 preparations from Kcnt2-/- mice yielded zero such channels. The KNa opener bithionol uncoupled respiration in WT but not Kcnt2-/- cardiomyocytes. Furthermore, when oxidizing only fat as substrate, Kcnt2-/- cardiomyocytes and hearts were less responsive to increases in energetic demand. Kcnt2-/- mice also had elevated body fat, but no baseline differences in the cardiac metabolome. These data support the existence of a cardiac mitochondrial KNa1.2 channel, and a role for cardiac KNa1.2 in regulating metabolism under conditions of high energetic demand.

cell biology↗