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@ketomics

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Sounds pretty (ir)rational!
Hyper dramatic or kinda looks familiar?
And I mean, not just with insulin.
There’s a cult of patients, considering drugs as antidotes or magic pills that will cancel out their metabolic shenanigans.
So, who’s to blame and what do we do?
Because DLK1 is colocalized with insulin in pancreatic β-cells, we examined the role of DLK1 in insulin signaling in OBs and energy metabolism. We show that Glu-OCN specifically stimulates Dlk1 expression by the pancreas. Conversely, Dlk1-deficient (Dlk1−/− ) mice exhibited increased circulating Glu-OCN levels and increased insulin sensitivity, whereas mice overexpressing Dlk1 in OB displayed reduced insulin secretion and sensitivity due to impaired insulin signaling in OB and lowered Glu-OCN serum levels
Proposed model of DLK1 action in regulating the OCN-insulin feed-forward loop.
OB-secreted Glu-OCN stimulates DLK1 production by islet β-cells. DLK1 exerts a negative feedback mechanism that impairs insulin signaling–induced OCN production by OB, thus antagonizing Glu-OCN–induced hypoglycemia. P, phosphorylation.
Ketone Bodies Vs Glucose:
Photo credits to Axona®.
Am I the only one thinking “Less steps, less ROS”?

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Exercise promotes the expression of brain derived neurotrophic factor (BDNF) through the action of the ketone body β-hydroxybutyrate | Exercise induces beneficial responses in the brain, which is accompanied by an increase in BDNF, a trophic factor associated with cognitive improvement and the alleviation of depression and anxiety. However, the exact mechanisms whereby physical exercise produces an induction in brain Bdnf gene expression are not well understood. While pharmacological doses of HDAC inhibitors exert positive effects on Bdnf gene transcription, the inhibitors represent small molecules that do not occur in vivo. Here, we report that an endogenous molecule released after exercise is capable of inducing key promoters of the Mus musculus Bdnf gene. The metabolite β-hydroxybutyrate, which increases after prolonged exercise, induces the activities of Bdnf promoters, particularly promoter I, which is activity-dependent. We have discovered that the action of β-hydroxybutyrate is specifically upon HDAC2 and HDAC3, which act upon selective Bdnf promoters. Moreover, the effects upon hippocampal Bdnf expression were observed after direct ventricular application of β-hydroxybutyrate. Electrophysiological measurements indicate that β-hydroxybutyrate causes an increase in neurotransmitter release, which is dependent upon the TrkB receptor. These results reveal an endogenous mechanism to explain how physical exercise leads to the induction of BDNF.
Author Summary That sugar can be converted into fatty acids in humans is a well-known fact. The question whether the reverse direction, i.e., gluconeogenesis from fatty acids, is also feasible has been a topic of intense debate since the end of the 19 th century. With the discovery of the glyoxylate shunt that allows this conversion in some bacteria, plants, fungi and nematodes it has been considered infeasible in humans since the corresponding enzymes could not be detected. However, by this finding only a single route for gluconeogenesis from fatty acids has been ruled out. To address the question whether there might exist alternative routes in humans we searched for gluconeogenic routes from fatty acids in a metabolic network comprising all reactions known to take place in humans. Thus, we were able to identify several pathways showing that this conversion is indeed feasible. Analyzing evidence concerning the detected pathways lends support to their importance during times of starvation, fasting, carbohydrate reduced and ketogenic diets and other situations in which the nutrition is low on carbohydrates. Moreover, the energetic investment required for this pathway can help to explain the particular efficiency of carbohydrate reduced and ketogenic diets such as the Atkins diet.
First of all, sth I always wanted to address, that A’-nnoys me big time!
I keep hearing how one cannot synthesize glucose from fatty acids.
Well, maybe that’s true (this paper doesn’t think so, but I’ll come back to that later).
So, to set things straight for sth that should be obvious for all the wannabe biochemistry geniouses out there: we do NOT consume free fatty acids!
It’s that simple :) . Dietary fat come in q-ute, very very cute packages; TAGs.
Triacyl + Glycerol = 3FA + 1Glycerol
Yeap, you guessed right. Glycerol is one of glucose’s more or less close relativees.
And DHAP (can always google, remember?) just so happens to a shared intermediate in both gluconeogenesis, glycolysis and glycerol catabolism.
In common words, shared intermediate plus enzymatic repertoire available, undoubtedly denotes the conversion flexibility between macros; mostly of other macro’s flexibility to provide glucose.
So, please think again if a) you think you cannot live without exogenous supply of sugar(s) - of any kind, that is, and yes fruit I’m looking straight at you! ; we do not need to consume sugar in order to have glucose to spend/spare. We can certainly make some. And b) ketone bodies. Yeap, verbless sentences.
Ketone bodies are the prefered substrate for the synthesis of Acetyl-CoA, but thtat’s another cool story.
Now, off I go! Got some PubMed catch up to do! So eager to read on his one!
During early fasting, increases in skeletal muscle proteolysis liberate free amino acids for hepatic gluconeogenesis in response to pancreatic glucagon. Hepatic glucose output diminishes during the late protein-sparing phase of fasting, when ketone body ...
ABSTRACT:
Early stages of fasting: Free amino acids from muscle tissue catabolism serve as substrate for gluconeogenesis; cells still utilise glucose for energy
[..] ”During early fasting, increases in skeletal muscle proteolysis liberate free amino acids for hepatic gluconeogenesis in response to pancreatic glucagon.
Later stages after fasting for some time: No need for production of glucose by catabolizing muscle tissue. Ketone body production kicks off and spplies ample energy to the cells. In fact, ketone bodies are prefered to glucose as a substrate for Acetyl-CoA production
[..] “Hepatic glucose output diminishes during the late protein-sparing phase of fasting, when ketone body production by the liver supplies compensatory fuel for glucose-dependent tissues 1–4.
↑ ↑ ↑ TORC2 , ↓↓ ↓ Insulin = FOXO1 de-activation
“Glucagon stimulates the gluconeogenic program by triggering the dephosphorylation and nuclear translocation of the CREB regulated transcription coactivator 2 (CRTC2; also known as TORC2),
“while parallel decreases in insulin signaling augment gluconeogenic gene expression through the de-phosphorylation and nuclear shuttling of Forkhead Box O1 (FOXO1) 5–7.”
[..] “a fasting-inducible switch, consisting of the histone acetyl-transferase (HAT) P300 and the nutrient-sensing deacetylase Sirtuin 1 (SIRT1), maintains energy balance through the sequential induction of CRTC2 and FOXO1. Following glucagon induction, CRTC2 stimulated gluconeogenic gene expression through an association with P300, which we show here is also activated by de-phosphorylation at Ser89 during fasting. In turn, P300 increased hepatic CRTC2 activity by acetylating it at Lys628, a site that also targets CRTC2 for degradation following its ubiquitination by the E3 ligase Constitutive Photomorphogenic Protein (COP1) 8″”
“Glucagon effects were attenuated during late fasting, when CRTC2 was down-regulated due to SIRT1-mediated deacetylation and when FOXO1 supported expression of the gluconeogenic program.
“Disrupting SIRT1 activity, by liver-specific knockout of the SIRT1 gene or by administration of SIRT1 antagonist, increased CRTC2 activity and glucose output, while exposure to SIRT1 agonists reduced them.
In view of the reciprocal activation of FOXO1 and its coactivator peroxisome proliferator activated receptor gamma coactivator 1 alpha (PGC-1α) by SIRT1 activators 9–12, our results illustrate how the exchange of two gluconeogenic regulators during fasting maintains energy balance.”
Take-home notes:
Transcription levels don’t always count as an activity marker. Both FOXO and CREB’s activity is regulated by phospho/dephosphorylation.
Transcription levels are a good start but if we have a doubt bout our results, in context of course, maybe we should check out western blot data as well.
ABSTRACT HIGHLIGHTS:
“a role for mTORC1 activity in promoting the ageing of the liver.”
“PPARα , the master transcriptional activator of ketogenic genes2″
“The multi-component mechanistic target of rapamycin complex 1 (mTORC1) kinase is the central node of a mammalian pathway that coordinates cell growth with the availability of nutrients, energy and growth factors1.
Progress has been made in the identification of mTORC1 pathway components and in understanding their functions in cells, but there is relatively little known about the role of the pathway in vivo.
Specifically, we have little knowledge regarding the role mTOCR1 has in liver physiology.
In fasted animals, the liver performs numerous functions that maintain whole-body homeostasis, including:
the production of ketone bodies for peripheral tissues to use as energy sources.
“Here we show that mTORC1 controls ketogenesis in mice in response to fasting. “
We find that liver-specific loss of TSC1 (tuberous sclerosis 1), an mTORC1 inhibitor1, leads to a fasting-resistant increase in liver size, and to a pronounced defect in ketone body production and ketogenic gene expression on fasting.
The loss of raptor (regulatory associated protein of mTOR, complex 1) an essential mTORC1 component1, has the opposite effects.
[Q: Raptor levels on keto diet ever measured??]
[UPDATE: Nope, they are co-mentioned only in this paper]
In addition, we find that the inhibition of mTORC1 is required for the fasting-induced activation of
PPARα , the master transcriptional activator of ketogenic genes2,
and that suppression of NCoR1 (nuclear receptor co-repressor 1), a co-repressor of PPARα3, reactivates ketogenesis in cells and livers with hyperactive mTORC1 signalling.
Like livers with activated mTORC1, livers from aged mice have a defect in ketogenesis4, 5, which correlates with an increase in mTORC1 signalling.
<!--Ring a bell?? All conditions with hyperactive mTORC1? A list anyone?!-->
Moreover, we show that the suppressive effects of mTORC1 activation and ageing on PPARα activity and ketone production are not additive,
and that mTORC1 inhibition is sufficient to prevent the ageing-induced defect in ketogenesis.
Thus, our findings reveal that mTORC1 is a key regulator of PPARα function and hepatic ketogenesis and
suggest a role for mTORC1 activity in promoting the ageing of the liver.”
“Abstract
The effects of ketone body metabolism suggests that mild ketosis may offer therapeutic potential in a variety of different common and rare disease states. These inferences follow directly from the metabolic effects of ketosis and the higher inherent energy present in d-β-hydroxybutyrate relative to pyruvate, the normal mitochondrial fuel produced by glycolysis leading to an increase in the ΔG′ of ATP hydrolysis. The large categories of disease for which ketones may have therapeutic effects are:
(1) diseases of substrate insufficiency or insulin resistance,
(2) diseases resulting from free radical damage,
(3) disease resulting from hypoxia.
Current ketogenic diets are all characterized by elevations of free fatty acids, which may lead to metabolic inefficiency by activation of the PPAR system and its associated uncoupling mitochondrial uncoupling proteins. New diets comprised of ketone bodies themselves or their esters may obviate this present difficulty.“

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Worth of note, the MCT modified ketogenic diet, which allows for aslightly more flexible diet, with regards to protein/carbohydrate allowed thresholds.
Although, still, if thinking about autophagy and related benefits, would probably opt for the classical, low(er) -CHO, lower protein version of the diet.
(Author may have to report some conflict of interest, due to AED patent)
Med Hypotheses. 2015 Nov;85(5):690-3. doi: 10.1016/j.mehy.2015.08.013. Epub 2015 Aug 21.
And strangely enough, open access!
ABSTRACT:
“DEP-domain containing 5 (DEPDC5), encoding a repressor of the mechanistic target of rapamycin complex 1 (mTORC1) signaling pathway, has recently emerged as a major gene mutated in familial focal epilepsies and focal cortical dysplasia.
Here we established a global knockout rat using TALEN technology to investigate in vivo the impact of Depdc5-deficiency.
Homozygous Depdc5−/− embryos died from embryonic day 14.5 due to a global growth delay.
Constitutive mTORC1 hyperactivation was evidenced in the brains and in cultured fibroblasts of Depdc5−/− embryos, as reflected by enhanced phosphorylation of its downstream effectors S6K1 and rpS6.
Consistently, prenatal treatment with mTORC1 inhibitor rapamycin rescued the phenotype of Depdc5−/− embryos.
Heterozygous Depdc5+/− rats developed normally and exhibited no spontaneous electroclinical seizures, but had altered cortical neuron excitability and firing patterns.
Depdc5+/− rats displayed cortical cytomegalic dysmorphic neurons and balloon-like cells
strongly expressing phosphorylated rpS6, indicative of mTORC1 upregulation,
and not observed after prenatal rapamycin treatment.
These neuropathological abnormalities are reminiscent of the hallmark brain pathology of human focal cortical dysplasia.
Altogether, Depdc5 knockout rats exhibit multiple features of rodent models of mTORopathies, and thus, stand as a relevant model to study their underlying pathogenic mechanisms “
Intermittent fasting (IF) can decrease the levels of pro-inflammatory cytokines in the periphery and brain. Here we investigated the impact of IF (16 h of food deprivation daily) for 4 months on NLRP1 and NLRP3 inflammasome activities following cerebral ischemia. Ischemic stroke was induced in C57BL/6J mice by middle cerebral artery occlusion, followed by reperfusion (I/R). IF decreased the activation of NF-κB and MAPK signaling pathways, the expression of NLRP1 and NLRP3 inflammasome proteins, and both IL-1β and IL-18 in the ischemic brain tissue.
Author Summary: The tight control of cellular metabolism and energy production plays a crucial role during embryonic development, cancer and neurodegenerative disorders. We show that mitochondrial pyruvate carrier deficiency in mice causes metabolic alterations that result in lactic acidosis, neurotransmitter imbalance, energy deficit, brain damage and embryonic lethality. Feeding the pregnant dams a ketogenic diet allowed the survival of affected embryos until birth. Our results demonstrate the importance of the mitochondrial pyruvate carrier in maintaining the metabolic program necessary to sustain normal mammalian development.
Impressive at least. Both on the wet/dry front.
But allow me to laser-beam (yeap, just used it as a verb!) on the off-target metabolomics approach.
Sounds interesting. Wish more papers about keto had that kind of willingness to search likewise.
Quoting straight from ze paper:
“ MPC deficiency alters the metabolic and neurotransmitter balance in the embryonic brainIn an attempt to understand the metabolic changes that could explain the survival ofMPC1gt/gt embryos until the end of gestation, we performed non-targeted metabolomic analyses on telencenphalic brain extracts from E13.5 embryos maintained on a normal or a ketogenic diet. Upon processing and annotation, a total of 222 metabolite ions could be detected (S3 Table). A principal component analysis of these data revealed that the most prominent metabolic changes were specific to the MPC1gt/gt brain samples from animals maintained on normal diet, while MPC1gt/gt ketogenic diet samples clustered with theMPC1+/+ samples (Fig 6A). Moreover, the predominant changes were all indicative of abnormal TCA cycle activity (Fig 6B).”
Pin pointing or what?
“A ketogenic diet is commonly used to treat the lactic acidosis resulting from PDH deficiency in humans [26,27], and has been shown to have similar effects in experiments with zebrafish ♥ embryos [34].
Used therapeutically, the ketogenic diet reduces lactic acidosis probably by decreasing glucose uptake and aerobic glycolysis, the main pathway induced in mammalian cells to compensate for a deficiency in OXPHOS.
The beneficial effects of the ketogenic diet may be:
immediate, through fueling the TCA cycle with acetyl-CoA, or
delayed, through an epigenetic regulation of gene expression [35] in the embryos.
In addition, the beneficial effects of the ketogenic diet may also be mediated through changes in the maternal metabolism thus changing the supply of metabolites and/or growth factors to the embryo.
In our experiments, maintaining the pregnant dams on a ketogenic diet from E8.5 onwards reduced lactate accumulation allowing the MPC1gt/gt embryos to complete normal gestation (Fig 5).
We suggest that this is because the diet is able to sustain efficient oxidative metabolism, which is required during the later stages of embryogenesis for cell and tissue differentiation [1,3,4].
In agreement with this is the fact that the ketogenic diet rescued the energy deficit observed in vivo in the brains of E13.5 MPC1gt/gt embryos (S3 Fig).
Moreover, in addition to the effects on lactic acid and energy balance, we observed that the ketogenic diet also normalized other metabolic parameters in the brain, including:
glutaminolysis which seemed abnormally elevated in untreated MPC1gt/gt embryos as evidenced by reduced glutamine and glutamate levels (Fig 6C and 6D).
Under the ketogenic diet,
glutamine
glutamate, and
GABA
levels were increased compared to untreated MPC1gt/gt embryos (Fig 6C and 6D) whereas the level of NAAG was decreased (Fig 6C).
It was recently shown that GABAergic transmission in neonatal mice is essential for cortical neuron development and the establishment of a proper balance between excitation and inhibition in the adult cortex [36].
Together our results allow us to hypothesize that during embryogenesis, MPC activity is required not only for adapting energy metabolism to the needs of the developing embryo, but also in maintaining a balanced pool of major neurotransmitters and ensuring normal brain development.
It is already established that pyruvate dehydrogenase (PDH) deficiency is associated with severe neurological phenotypes such as :
developmental defects
ataxia
cognitive delay and
epilepsy [24–27],
the latter being caused by impaired energetic status and abnormal neurotransmitter metabolism [26].
Despite the ability of the ketogenic diet to restore normal metabolism and gestation of theMPC1gt/gt embryos (Figs 5 and 6 and S2 Fig), the newborn pups survive for only a few minutes post-delivery. This suggests that without nutritional support from the dam, which provides a continuous source of glucose and ketone bodies, MPC1gt/gt pups were not able independently to meet their energetic needs during the post-natal starvation state. Loss of pyruvate oxidation and ketogenic supply in the MPC1gt/gt pups may be further exacerbated by the fact that
autophagy-driven gluconeogenesis,
an important source of energy during the post-natal period [37], is probably impaired in these newborn animals.
Indeed, recent reports indicate that liver-specific ablation of MPC activity diminishes the gluconeogenic flux because of the relatively low efficiency of compensatory pathways such as:
glutaminolysis and
pyruvate/alanine cycling in liver [18,19].
Our results show that global loss of MPC activity is incompatible with embryonic development and neonatal survival in mammals.”
So, highlights for me:
Non-carbohydrate substrates for gluconeonenesis pathways: amino acids (sans pyruvate, that is)
Change in neurotransmitters levels and/or ratios
Readily available Acetyl-Coa from ketone bodies
Question:
Could the
BONUS: TCA 101
“Introduction:
Pyruvate is a pivotal component in intermediary metabolism, lying at the crossroads between (←♥!) cytosolic and mitochondrial metabolism.
The main intracellular source of pyruvate is glycolysis in the cytosol, which generates two molecules of pyruvate per molecule of glucose.
Glycolysis-derived pyruvate then follows one of two major routes for energy production: conversion into lactate by lactate dehydrogenase (LDH) in a reaction that replenishes the cytosolic NAD+ cofactor pool, allowing maintenance of the glycolytic flux;
or :
cytosolic pyruvate can enter the mitochondria to be oxidized to acetyl-CoA by the pyruvate dehydrogenase complex (PDH), fueling the TCA cycle and oxidative phosphorylation (OXPHOS).
Alternatively,
mitochondrial pyruvate can be used in an
anaplerotic pathway
through conversion to oxaloacetate by pyruvate carboxylase.
In most differentiated cells, decarboxylation of pyruvate by PDH is used in order to meet the high energetic demands associated with specialized cellular processes such as the transmission of neuronal signals or muscle contraction [1].
In contrast, the strong anabolic requirements of proliferating cells are better met by (←♥ ) high glycolytic rates, since several intermediates in this pathway serve as precursors for biomass production, <!--aka: fast depletion-->
including nucleotides and proteins synthesis [1,2].
This marked reliance on high glycolytic flux is a hallmark of highly proliferating cells, including many cancer cells in which a shift from oxidative phosphorylation to aerobic glycolysis (the Warburg effect) is frequently observed [2]. ”
“In order to fuel the TCA cycle and drive oxidative phosphorylation, glucose-derived pyruvate must enter the mitochondrial matrix.
To do so, it is believed to
diffuse non-specifically through the outer mitochondrial membrane via porins [5],
before being taken up by a specific carrier to cross the impermeable inner mitochondrial membrane.
The existence of a specific transporter has been postulated since the 1970s [6], and its biochemical properties have been extensively studied, including its specific inhibition by chemical compounds [7,8].
However, the molecular and genetic identity of the mitochondrial pyruvate carrier (MPC) were revealed only recently by us and by others [9,10].”

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Results
The study illustrates the genetic and clinical heterogeneity of GLUT-1 DS. Analysis of the SLC2A1 gene disclosed a variety of mutation types. The time between onset of symptoms and diagnosis was more than 11 years on average. The outcome in those with early diagnosis and intervention was surprisingly good. All but one patient with the classic phenotype became seizure free after treatment with the classic ketogenic or modified Atkins diet. Acetazolamide was effective in one patient with paroxysmal exercise-induced dyskinesia. A point prevalence of GLUT-1 DS in Norway was estimated as 2.6 per 1 000 000 inhabitants.
Interpretation
Although the long-term prognosis in patients with GLUT-1 DS partly depends on the underlying genetics, our study supports the assumption that early initiation of treatment with a ketogenic diet may positively affect the outcome.
Bumped into this cool map thing. You choose a keyword and you get an interactive map with relevant keywords and color coded (eg “sort by date”) bubbbles around them. Bubbles represent the original paper and are clickable.
Would like some extra search filters though, maybe similar to PubMed’s advanced search (”AND , ”OR”, “NOT”).
In this search for example, I would like to exclude “patients” or “diet”; make room for more specific terms. Or to be able to sort for molecules, genes, PTM’s, pathways.
Oh, and a sharable link to hold the modifications/additional sorting applied, kinda like Biovista’s Vizit tool. That would be nice.
Still cool though!