The Illusion of Knowledge: The paradigm shift in aging research that shows the way to human rejuvenation

Dr. Harold Katcher increased interviews to coincide with release of his book this month. Here’s one in four parts that provides highlights of his rejuvenation research progress:


Previously curated papers of his work include:

Epigenetic clocks so far in 2021

2021’s busiest researcher took time out this month to update progress on epigenetic clocks:

Hallmarks of aging aren’t all associated with epigenetic aging.

epigenetic aging vs. hallmarks of aging

Interventions that increase cellular lifespan aren’t all associated with epigenetic aging.

epigenetic aging vs. cellular lifespan

Many of his authored or coauthored 2021 papers developed human / mammalian species relative-age epigenetic clocks.

epigenetic clock mammalian maximum lifespan

Relative-age epigenetic clocks better predict human results from animal testing.

pan-mammalian epigenetic clock


Previously curated papers that were mentioned or relevant included:

Gut microbiota and critical development periods

This 2021 rodent study focused on global histone acetylation as a model to understand roles of microbially produced short-chain fatty acids in liver function:

“Despite the utility of germ-free mice in probing complex interactions between gut microbiota and host physiology, germ-free mice are developmentally, physiologically, and metabolically unique when compared with their conventionally housed counterparts. We sought to determine whether antibiotic-mediated microbiota depletion would affect global hepatic histone acetylation states through SCFA-dependent mechanisms, as previously observed in germ-free mice.

The inability of antibiotic-mediated microbiota depletion to recapitulate findings observed in germ-free mice suggests that the transition from a germ-free to a colonized mouse leads to resilient alterations in hepatic histone acetylation states that cannot be altered by further modulating the microbial environment. This finding is distinct from other germ-free phenotypes that are considered to be partially reversible, with clear alterations in their function observed after antibiotic treatment.

histone acetylation

Comparing antibiotic-treated and untreated mice that both received CCl4 at 24 and 48 hours after injury, there were almost no histone acetylation differences. This demonstrates that hepatic injury leads to a global shift in histone acetylation that is primarily independent of gut microbiota.

Major chromatin reorganization driven by histone acetylation leads to markers of differentiation, and addition of targeted differentiation signals induces events to stabilize these histone acetylation patterns – a key feature of embryonic development and terminal cellular differentiation. Differences in histone acetylation patterns seen between germ-free and conventionally raised mice may be a developmental-like effect of hepatocytes not yet exposed to microbial by-products.

Results suggest that microbial and dietary modifications to the gut microbiome in conventionally raised mice are not a means to modulate global hepatic histone acetylation. Microbiota-dependent landscaping of the hepatic epigenome appears static in nature, while the hepatic transcriptome is responsive to alterations in the gut microbiota, yet independent of global histone acetylation.

Findings underscore significant differences between these model systems that should be taken into account when considering their relevance to human biology.”

https://aasldpubs.onlinelibrary.wiley.com/doi/10.1002/hep.32043 “Global Microbiota-Dependent Histone Acetylation Patterns Are Irreversible and Independent of Short Chain Fatty Acids” (not freely available) Thanks to Dr. Elliot S. Friedman for providing a copy.


1. By describing “a key feature of embryonic development,” this study provided a gut microbiota-liver analogy of critical periods. If developmental events don’t happen when they are required, it’s probable that their window is missed, and won’t reopen later for a second chance at normalizing.

2. Many studies used a germ-free animal model, such as:

This study provided evidence for a limitation of this model, especially when extrapolating germ-free animal results to humans without similarly testing humans.


PXL_20210914_165000840_exported_1399

All about vasopressin

This 2021 review subject was vasopressin:

“Vasopressin is a ubiquitous molecule playing an important role in a wide range of physiological processes, thereby implicated in pathomechanisms of many disorders. The most striking is its central effect in stress-axis regulation, as well as regulating many aspects of our behavior.

Arginine-vasopressin (AVP) is a nonapeptide that is synthesized mainly in the supraoptic, paraventricular (PVN), and suprachiasmatic nucleus of the hypothalamus. AVP cell groups of hypothalamus and midbrain were found to be glutamatergic, whereas those in regions derived from cerebral nuclei were mainly GABAergic.

In the PVN, AVP can be found together with corticotropin-releasing hormone (CRH), the main hypothalamic regulator of the HPA axis. The AVPergic system participates in regulation of several physiological processes, from stress hormone release through memory formation, thermo- and pain regulation, to social behavior.

vasopressin stress axis

AVP determines behavioral responses to environmental stimuli, and participates in development of social interactions, aggression, reproduction, parental behavior, and belonging. Alterations in AVPergic tone may be implicated in pathology of stress-related disorders (anxiety and depression), Alzheimer’s, posttraumatic stress disorder, as well as schizophrenia.

An increasing body of evidence confirms epigenetic contribution to changes in AVP or AVP receptor mRNA level, not only during the early perinatal period, but also in adulthood:

  • DNA methylation is more targeted on a single gene; and it is better characterized in relation to AVP;
  • Some hint for bidirectional interaction with histone acetylation was also described; and
  • miRNAs are implicated in the hormonal, peripheral role of AVP, and less is known about their interaction regarding behavioral alteration.”

https://www.mdpi.com/1422-0067/22/17/9415/htm “Epigenetic Modulation of Vasopressin Expression in Health and Disease”


Find your way, regardless of what the herd does.

PXL_20210911_103344386

Choosing your gut immune response

This 2021 paper reviewed evidence for immune system effects associated with specific gut areas:

“The intestinal immune system must not only contend with continuous exposure to food, commensal microbiota, and pathogens, but respond appropriately according to intestinal tissue differences. The entire intestine, inclusive of its lymph nodes, is considered a immunosuppressive organ overall compared to most other tissues, indicating that a state of tolerance to food and commensals – yet vigilance toward pathogens – was an evolutionarily stable strategy.

By operating in compartments, the immune system may generate multiple immune outcomes, even with simultaneous opposite goals e.g., tolerance or inflammation. Generation of unique immunologic niches within the intestine is influenced by a combination of tissue intrinsic properties, extrinsic environmental factors, and regionalized immune populations.

intestinal immune compartmentalization

Complexity of intrinsic and extrinsic driving forces shaping an intestinal niche makes it very challenging to determine causality in disease development and predicting effective therapeutic approaches. We really only stand at the beginning of understanding this interplay.”

https://www.nature.com/articles/s41385-021-00420-8 “Intestinal immune compartmentalization: implications of tissue specific determinants in health and disease”


I patterned this post after Choosing your future with β-glucan:

“So where do you choose to be? In an 80% survival group who were administered β-glucan before they encountered a serious infection? Or in a < 20% survival group who didn’t take β-glucan?”

and Long-lasting benefits of a common vaccine:

“As inferred by “induction of trained immunity by both Bacillus Calmette-Guerin tuberculosis vaccine and β-glucan” many of these findings also apply to yeast cell wall β-glucan treatments.”

This paper’s food allergy references were interesting. It’s an area that personally requires further work, although avoidance has historically been effective.

This paper briefly mentioned broccoli’s effects in the proximal small intestine. It wasn’t informative per gut compartment with this year’s focus on making my gut microbiota happy, such as what our colonic microbiota can do to reciprocate their host giving them what they want.

This review’s human studies referenced what could be done post-disease like surgery etc. in different gut compartments. Very little concerned an individual taking responsibility for their own one precious life to prevent such diseases in the first place. Its Conclusions section claim was a fallacy:

“..very challenging to determine causality in disease development and predicting effective therapeutic approaches.”

PXL_20210911_104042916

Don’t count on broccoli compounds bailing out a high-fat diet’s effects on gut microbiota

Two rodent studies of mature broccoli and broccoli sprouts’ effects on a high-fat diet, with the first from 2021 investigating broccoli florets and stalks:

“Addition of broccoli florets to a HFD ameliorated insulin sensitivity. Florets further promoted gut microbiota diversity and low-grade inflammatory-associated strains.

Stalk supplementation also altered gut microbiota, leading to increased Bacteroidetes/Firmicutes ratio and levels of communities that preserve mucus layer and gut integrity while simultaneously decreasing levels of potentially harmful species.

Addition of broccoli to a HFD did not ameliorate body and tissues weight gain or food intake. Both broccoli stalks and florets did not affect fat accumulation, carbohydrate, or lipid metabolism-related parameters.”

https://www.frontiersin.org/articles/10.3389/fnut.2021.680241/full “Broccoli Florets Supplementation Improves Insulin Sensitivity and Alters Gut Microbiome Population – A Steatosis Mice Model Induced by High-Fat Diet”


A 2020 study cited by this first study investigated compounds extracted from 1-day-old broccoli sprouts:

Bioaccessibility of aliphatic glucosinolates was shown to 76.2 ± 0.6%:

aliphatic glucosinolate bioavailability

Glucoraphanin was the predominant glucosinolate with the highest bioaccessibility in broccoli, and could effectively prevent HFD-induced body weight gain in mice, especially increases in liver weight and the accumulation of lipids in adipocytes. Furthermore, supplementation with glucoraphanin reduced the level of oxidative stress, regulated genes of FAS, PPARα, CPT1 and ACOX associated with lipid metabolism, and might be associated with changes in composition of gut microbiota.”

https://www.frontiersin.org/articles/10.3389/fnut.2021.680241/full “Effect of glucoraphanin from broccoli seeds on lipid levels and gut microbiota in high-fat diet-fed mice”

This study’s title was “Effect of glucoraphanin from broccoli seeds..” although its Materials and methods section disclosed:

“1 day after germination from broccoli seeds, sprouts were boiled in water for 30 min. The resulting aqueous extract was processed by liquid solid separation and condensation and was subsequently spray-dried to yield an extract powder containing 249 mg glucoraphanin.”


Eat broccoli sprouts every day and its predecessor study demonstrated that broccoli intake every day had beneficial effects during shorter periods than either of these studies.

Both studies had many “may”, “could”, and “might” statements. Not sure that broccoli compounds / gut microbiota relationships are adequately investigated by choosing a few out of tens of thousands of gut microbiota species as both studies attempted to do.

There are too many additive / antagonistic / synergistic combinations to analyze even before reaching twenty gut microbiota species. But researchers aren’t often sponsored for studies unless they conform to existing research.


I haven’t made headway in understanding my top 10 of 42,156 gut microbiota species’ exact causes, effects, and interactions. The top three by themselves are considered beneficial:

top 1-10 species

Uncertainty is fine for now, though, with a 40-hour work week interfering. Finding out what my gut microbiota generally want and giving that to them has been a productive approach this year.

Improving gut barriers

Three papers on gut barriers, with the first a 2020 review of four intestinal barrier layers:

“The epithelial cell layer and outer/inner mucin layer constitute the physical barrier. Intestinal alkaline phosphatase (IAP) produced by epithelial cells and antibacterial proteins secreted by Panneth cells represent the functional barrier.

Multiple layers of this barrier, from intestinal lumen to systemic circulation, include:

  1. Luminal intestinal alkaline phosphatase (IAP) that dephosphorylates bacterial endotoxin lipopolysaccharide (LPS) to detoxify it;
  2. Mucus layer that provides a physical barrier preventing interactions between gut bacteria and intestinal epithelial cells;
  3. Tight junctions between epithelial cells that limit paracellular transport of bacteria and/or bacterial products to systemic circulation; and
  4. Antibacterial proteins secreted by specialized intestinal epithelial cells or Paneth cells, and IgA [immunoglobulin A] secreted by immune cells present in lamina propria underlying the epithelial cell layer.

m_bvz039f0001

The presence of LPS in systemic circulation is identified as a causal or complicating factor in diverse diseases such as:

  • Diet-induced metabolic diseases;
  • Autism;
  • Alzheimer’s disease;
  • Parkinson’s disease;
  • Arthritis;
  • Obesity-induced osteoarthritis;
  • Asthma; and
  • Several autoimmune diseases.

Causal relationships between circulating LPS levels and development of multiple diseases underscore the importance of changes in intestinal barrier layers associated with disease development.

Correcting intestinal barrier dysfunction to modulate multiple diseases can be envisioned as a viable therapeutic option. Identifying precise defects by use of specific biomarkers would facilitate targeted interventions.”

https://academic.oup.com/jes/article/4/2/bvz039/5741771 “Intestinal Barrier Dysfunction, LPS Translocation, and Disease Development”


A second 2020 review focused on IAP:

“IAP plays a vital role in intestinal barrier function, affecting bicarbonate secretion, duodenal surface pH, nutrient resorption, local intestinal inflammation, and gut microbiota. Disturbances of IAP functions are associated with persistent inflammatory diseases associated with aging (i.e.,inflammageing), inflammatory bowel diseases, type 2 diabetes mellitus, obesity, metabolic syndrome, and chronic kidney disease (CKD).

Expression and activity of IAP are directly affected by food intake, i.e., quantity and type of macro- and micronutrients including vitamins and other bioactive nutrients, or by absence of food, as well as indirectly by composition of gut microbiota that in turn are highly dependent on food intake. Increased IAP gene expression and activity promoting detoxification of LPS may lead to improvement of both intestinal and systemic inflammation, reduced bacteria translocation, and maintaining gut barrier function.

IAP could be used as an inflammatory marker together with other markers, such as interleukins, to predict inflammation and diseases that are based on chronic inflammatory processes.”

https://doi.org/10.1007/s13167-020-00228-9 “Intestinal alkaline phosphatase modulation by food components: predictive, preventive, and personalized strategies for novel treatment options in chronic kidney disease” (not freely available)


A third paper was a 2021 rodent study by coauthors of the first paper:

“We developed intestine-specific IAP transgenic mice (IAPTg) overexpressing human chimeric IAP to examine direct effects of increased IAP expression on barrier function and development of metabolic diseases. We evaluated effects of intestine-specific IAP overexpression in hyperlipidemic Ldlr−/− mice. The data presented demonstrated significant attenuation of Western-type diet (WD)-induced LPS translocation in Ldlr−/−IAPTg mice, with significant reduction in intestinal lipid absorption, hyperlipidemia, hepatic lipids, and development of atherosclerotic lesions.

circresaha.120.317144.fig09

IAP is produced by enterocytes, and catalyzes removal of 1 of the 2 phosphate groups from the toxic lipid A moiety of LPS. This produces monophosphoryl-LPS, and results in attenuation of the downstream TLR (Toll-like receptor)-4–dependent inflammatory cascade.

IAP also:

  • Dephosphorylates other proinflammatory molecules such as flagellin and ATP, resulting in their detoxification;
  • Regulates expression of key gap junction proteins (zonula occludens, claudin, and occludin) and their cellular localization, which directly modulates intestinal barrier function;
  • Promotes growth of various commensal bacteria in the gut by decreasing luminal concentrations of nucleotide triphosphates via dephosphorylation; and
  • Translocates from the apical surface of enterocytes during fat absorption. Increased serum IAP accompanies fat absorption, which is consistent with observed increased levels of circulating LPS in WD-fed mice, providing one more likely mechanism by which WD affects intestinal barrier function via IAP.

Nutrients and food components/supplements that increase IAP include galacto- or chito- oligosaccharides, glucomannan, and vitamin D3. These provide a novel opportunity to develop simple strategies for modulation of diet/nutrition to target metabolic diseases including diabetes, fatty liver disease, atherosclerosis, and heart disease.”

https://www.ahajournals.org/doi/10.1161/CIRCRESAHA.120.317144 “Over-Expression of Intestinal Alkaline Phosphatase Attenuates Atherosclerosis”


Previously curated IAP studies were:

PXL_20210710_093310161.NIGHT

Take acetyl-L-carnitine for early-life trauma

This 2021 rodent study traumatized female mice during their last 20% of pregnancy, with effects that included:

  • Prenatally stressed pups raised by stressed mothers had normal cognitive function, but depressive-like behavior and social impairment;
  • Prenatally stressed pups raised by control mothers did not reverse behavioral deficits; and
  • Control pups raised by stressed mothers displayed prenatally stressed pups’ behavioral phenotypes.

Acetyl-L-carnitine (ALCAR) protected against and reversed depressive-like behavior induced by prenatal trauma:

alcar regime

ALCAR was supplemented in drinking water of s → S mice either from weaning to adulthood (3–8 weeks), or for one week in adulthood (7–8 weeks). ALCAR supplementation from weaning rendered s → S mice resistant to developing depressive-like behavior.

ALCAR supplementation for 1 week during adulthood rescued depressive-like behavior. One week after ALCAR cessation, however, the anti-depressant effect of ALCAR was diminished.

Intergenerational trauma induces social deficits and depressive-like behavior through divergent and convergent mechanisms of both in utero and early-life parenting environments:

  • We establish 2-HG [2-hydroxyglutaric acid, a hypoxia and mitochondrial dysfunction marker, and an epigenetic modifier] as an early predictive biomarker for trauma-induced behavioral deficits; and
  • Demonstrate that early pharmacological correction of mitochondria metabolism dysfunction by ALCAR can permanently reverse behavioral deficits.”

https://www.nature.com/articles/s42003-021-02255-2 “Intergenerational trauma transmission is associated with brain metabotranscriptome remodeling and mitochondrial dysfunction”


Previously curated studies cited were:

This study had an effusive endorsement of acetyl-L-carnitine in its Discussion section, ending with:

“This has the potential to change lives of millions of people who suffer from major depression or have risk of developing this disabling disorder, particularly those in which depression arose from prenatal traumatic stress.”

I take a gram daily. Don’t know about prenatal trauma, but I’m certain what happened during my early childhood.

I asked both these researchers and those of Reference 70 for their estimates of a human equivalent to “0.3% ALCAR in drinking water.” Will update with their replies.


PXL_20210704_095621886

Vitamin K-dependent proteins

This 2020 review focused on three Vitamin K-dependent proteins (VKDPs):

“We summarize three important emerging VKDPs: Growth arrest‑specific protein 6 (Gas 6), Gla‑rich protein (GRP) and periostin in terms of their functions in physiological and pathological conditions. As examples:

  • Carboxylated Gas 6 and GRP effectively protect blood vessels from calcification;
  • Gas 6 protects from acute kidney injury and is involved in chronic kidney disease;
  • GRP contributes to bone homeostasis and delays progression of osteoarthritis; and
  • Periostin is involved in all phases of fracture healing and assists myocardial regeneration in the early stages of myocardial infarction.

IJMM-47-03-4835-g00

The ‘+’ refers to promotion and ‘-‘ refers to inhibition. Green represents Gas 6 physiological effects and red represents its pathological effects.

  • Gas 6 resists vascular calcification: i) Gas 6 promotes proliferation and migration of endothelial progenitor cells (EPCs); ii) Gas 6 inhibits apoptosis and senescence of vascular smooth muscle cells (VSMCs) by binding Tyro3, Axl and Mer (TAM) receptors; iii) Gas 6 decreases expression of inflammatory factors, including TNF-α and ICAM-1.
  • Gas 6 protects from acute kidney injury: i) Gas 6 significantly reduces creatinine and blood urea nitrogen; ii) Gas 6 enhances macrophages to uptake apoptotic cells; iii) Gas 6 reduces the expression of pro-inflammatory cytokines, such as IL-1β.
  • Gas 6 assists tumor progression: i) Gas 6 is necessary for survival, proliferation and growth of tumor cells; ii) Gas 6 contributes to drug resistance and tumor angiogenesis; iii) Gas 6 negatively regulates tumor immunity.

Numerous physiological benefits of vitamin K2 have been identified, such as anti-vascular calcification, glycemic control, and lipid-lowering effects. However, some questions about relationships between vitamin K2 and cancers remain unsolved. VKDPs are expected to be biomarkers for many diseases.”

https://www.spandidos-publications.com/10.3892/ijmm.2020.4835?text=fulltext “Role of emerging vitamin K‑dependent proteins: Growth arrest‑specific protein 6, Gla‑rich protein and periostin (Review)”


This review’s VKPD biomarkers included:

  • Vascular calcification;
  • Asthma;
  • Bronchial obstruction;
  • Diabetic nephropathy; and
  • Fracture risk.

Elaborating on this last item:

“In a cohort of 607 postmenopausal women from France that were followed up for 7 years, a positive correlation between serum periostin and fracture risk was observed. The association was independent of bone mineral density and prior fractures, indicating that periostin is an independent predictive marker of fracture risk.”

As pointed out in Chronological age by itself is an outdated clinical measurement, bone mineral density is one of several historical measurements that were selected for their relative convenience instead of chosen for their efficacy. We’re in a different century now.

PXL_20210628_094545802

Basal cognition

To follow up Electroceuticals, a 2021 article by Dr. Michael Levin:

“A key philosophical idea, borrowed from computer science, is substrate independence. Components of a living system can carry out appropriate, clearly specified cognitive functions.

Cognitive processes in embryogenesis and regeneration:

rstb20200458f01

    • (a) An egg will reliably give rise to a species-specific anatomical outcome.
    • (b) This process is usually described as a feed-forward system where activity of gene-regulatory networks (GRNs) within cells results in expression of effector proteins that, via structural properties of proteins and physical forces, will result in the emergence of complex shape. This class of models (bottom-up process driven by self-organization and parallel activity of large numbers of local agents) is difficult to apply to several biological phenomena. Regulative development can alter subsequent steps to reach the correct anatomical goal state despite drastic deviations of the starting state.
    • (c) For example, mammalian embryos can be divided in half, giving rise to perfectly normal monozygotic twins, each of which has regenerated the missing cell mass.
    • (d) Mammalian embryos can also be combined, giving rise to a normal embryo in which no parts are duplicated.
    • (e) Such capabilities suggest that pattern control is fundamentally a homeostatic process—a closed-loop system using feedback to minimize error (distance) between a current shape and a target morphology. Although these kinds of decision-making models are commonplace in engineering, they are only recently beginning to be employed in biology. This kind of pattern-homeostatic process must store a setpoint that serves as a stop condition; however, as with most types of memory, it can be specifically modified by experience.
    • (f) In the phenomenon of trophic memory, damage created at a specific point on the branched structure of deer antlers is recalled as ectopic branch points in subsequent years’ antler regeneration. This reveals ability of cells at the scalp to remember spatial location of specific damage events and alter cell behaviour to adjust the resulting pattern appropriately—a pattern memory that stretches across months of time and considerable spatial distance and is able to modify low-level (cellular) growth rules to construct a pre-determined stored pattern that differs from genome-default for this species.
    • (g) A similar capability was recently shown in a molecularly tractable model system, in which genetically normal planarian flatworms were bioelectrically reprogrammed to regenerate two-headed animals when cut in subsequent rounds of asexual reproduction in plain water.
    • (h) The decision making revealed by cells, tissues and organs in these examples of dynamic remodelling toward specific target states could be implemented by cybernetic processes at various positions along a scale of proto-cognitive complexity.

A challenge for the field of basal cognition is to reveal gradualism of cellular properties underwriting this critical biological function to leverage an understanding of clear phase transitions observed in cognitive capacities. The origin and development of nervous systems is so far the most dramatic example.”

https://royalsocietypublishing.org/doi/10.1098/rstb.2020.0458 “Uncovering cognitive similarities and differences, conservation and innovation”


Why aren’t more resources being directed toward these research efforts? Glad to see that at least one co-founder of Microsoft, Paul Allen, posthumously used his billions to sponsor science for human good.

The amino acid ergothioneine

A trio of papers on ergothioneine starts with a 2019 human study. 3,236 people without cardiovascular disease and diabetes mellitus ages 57.4 ± 6.0 were measured for 112 metabolites, then followed-up after 20+ years:

“We identified that higher ergothioneine was an independent marker of lower risk of cardiometabolic disease and mortality, which potentially can be induced by a specific healthy dietary intake.

overall mortality and ergothioneine

Ergothioneine exists in many dietary sources and has especially high levels in mushrooms, tempeh, and garlic. Ergothioneine has previously been associated with a higher intake of vegetables, seafood and with a lower intake of solid fats and added sugar as well as associated with healthy food patterns.”

https://heart.bmj.com/content/106/9/691 “Ergothioneine is associated with reduced mortality and decreased risk of cardiovascular disease”


I came across this study by its citation in a 2021 review:

“The body has evolved to rely on highly abundant low molecular weight thiols such as glutathione to maintain redox homeostasis but also play other important roles including xenobiotic detoxification and signalling. Some of these thiols may also be derived from diet, such as the trimethyl-betaine derivative of histidine, ergothioneine (ET).

image description

ET can be found in most (if not all) tissues, with differential rates of accumulation, owing to differing expression of the transporter. High expression of the transporter, and hence high levels of ET, is observed in certain cells (e.g. blood cells, bone marrow, ocular tissues, brain) that are likely predisposed to oxidative stress, although other tissues can accumulate high levels of ET with sustained administration. This has been suggested to be an adaptive physiological response to elevate ET in the damaged tissue and thereby limit further injury.”

https://www.sciencedirect.com/science/article/pii/S2213231721000161 “Ergothioneine, recent developments”


The coauthors of this review were also coauthors of a 2018 review:

“Ergothioneine is avidly taken up from the diet by humans and other animals through a transporter, OCTN1. Ergothioneine is not rapidly metabolised, or excreted in urine, and has powerful antioxidant and cytoprotective properties.

ergothioneine in foods

Effects of dietary ET supplementation on oxidative damage in young healthy adults found a trend to a decrease in oxidative damage, as detected in plasma and urine using several established biomarkers of oxidative damage, but no major decreases. This could arguably be a useful property of ET: not interfering with important roles of ROS/RNS in healthy tissues, but coming into play when oxidative damage becomes excessive due to tissue injury, toxin exposure or disease, and ET is then accumulated.”

https://febs.onlinelibrary.wiley.com/doi/full/10.1002/1873-3468.13123 “Ergothioneine – a diet-derived antioxidant with therapeutic potential”


I’m upping a half-pound of mushrooms every day to 3/4 lb. (340 g). Don’t think I could eat more garlic than the current six cloves.

PXL_20210606_095517049

I came across this subject in today’s video:

Gut microbiota topics

Here are thirty 2019 and 2020 papers related to Switch on your Nrf2 signaling pathway topics. Started gathering research on this particular theme three months ago.

There are more researchers alive today than in the sum of all history, and they’re publishing. I can’t keep up with the torrent of interesting papers.

on

2020 A prebiotic fructo-oligosaccharide promotes tight junction assembly in intestinal epithelial cells via an AMPK-dependent pathway

2019 Polyphenols and Intestinal Permeability: Rationale and Future Perspectives

2020 Prebiotic effect of dietary polyphenols: A systematic review

2019 Protease‐activated receptor signaling in intestinal permeability regulation

2020 Intestinal vitamin D receptor signaling ameliorates dextran sulfate sodium‐induced colitis by suppressing necroptosis of intestinal epithelial cells

2019 Intestinal epithelial cells: at the interface of the microbiota and mucosal immunity

2020 The Immature Gut Barrier and Its Importance in Establishing Immunity in Newborn Mammals

2019 Prebiotics and the Modulation on the Microbiota-GALT-Brain Axis

2019 Prebiotics, Probiotics, and Bacterial Infections

2020 Vitamin D Modulates Intestinal Microbiota in Inflammatory Bowel Diseases

2020 Microbial tryptophan metabolites regulate gut barrier function via the aryl hydrocarbon receptor

2019 Involvement of Astrocytes in the Process of Metabolic Syndrome

2020 Intestinal Bacteria Maintain Adult Enteric Nervous System and Nitrergic Neurons via Toll-like Receptor 2-induced Neurogenesis in Mice (not freely available)

2019 Akkermansia muciniphila ameliorates the age-related decline in colonic mucus thickness and attenuates immune activation in accelerated aging Ercc1−/Δ7 mice

2020 Plasticity of Paneth cells and their ability to regulate intestinal stem cells

2020 Coagulopathy associated with COVID-19 – Perspectives & Preventive strategies using a biological response modifier Glucan

2020 Synergy between Cell Surface Glycosidases and Glycan-Binding Proteins Dictates the Utilization of Specific Beta(1,3)-Glucans by Human Gut Bacteroides

2020 Shaping the Innate Immune Response by Dietary Glucans: Any Role in the Control of Cancer?

2020 Systemic microbial TLR2 agonists induce neurodegeneration in Alzheimer’s disease mice

2019 Prebiotic supplementation in frail older people affects specific gut microbiota taxa but not global diversity

2020 Effectiveness of probiotics, prebiotics, and prebiotic‐like components in common functional foods

2020 Postbiotics-A Step Beyond Pre- and Probiotics

2019 Pain regulation by gut microbiota: molecular mechanisms and therapeutic potential

2020 Postbiotics: Metabolites and mechanisms involved in microbiota-host interactions

2020 Postbiotics against Pathogens Commonly Involved in Pediatric Infectious Diseases

2019 Glutamatergic Signaling Along The Microbiota-Gut-Brain Axis

2019 Lipoteichoic acid from the cell wall of a heat killed Lactobacillus paracasei D3-5 ameliorates aging-related leaky gut, inflammation and improves physical and cognitive functions: from C. elegans to mice

2020 Live and heat-killed cells of Lactobacillus plantarum Zhang-LL ease symptoms of chronic ulcerative colitis induced by dextran sulfate sodium in rats

2019 Health Benefits of Heat-Killed (Tyndallized) Probiotics: An Overview

2020 New Horizons in Microbiota and Metabolic Health Research (not freely available)

Oat species comparisons of the good stuff

This 2020 study compared and contrasted distributional compositions of two oat species’ seeds:

“Oat grains of one hulless variety (Lamont) with low avenanthramide (AVA) contents and one hulled variety (Reins) with high AVA contents were sequentially abraded. Contents of nutrients (protein, oil, starch, β-glucan, ash, and other carbohydrates) and AVAs were measured.

A relationship between content of a constituent in the surface layer abraded off (termed pearling fine, or PF) at each cycle of pearling and the cumulative level of surface removal could be established. This relationship essentially describes true distribution or localization of individual constituents across an oat kernel.

AVAs provide health benefits in mammals, including anti-oxidation, anti-inflammation, anti-atherosclerosis, and anti-cancer properties. Relationships between contents of four AVAs and total AVAs in pearling fines (A) and corresponding pearled kernels (B) of hulless Lamont oat [top] and hulled Rein [bottom] with cumulative surface removal levels achieved by sequential pearling:

For Lamont oat, AVAs 2c, 2f, 2p, 5p, and total AVAs all showed decreasing concentrations with increasing levels of surface removal. The first PF (4% surface removal) contained the highest amounts for all four AVAs, with 2p near ten times higher than in whole grain.

Hulled Reins oat differed significantly from hulless Lamont oat in not only amounts of AVAs but also their distribution patterns within kernels. Dehulling caused reduction in total AVA content.

Pearled oats contained less protein, oil, ash, and other carbohydrates and AVAs, but more starch than whole grain. In contrast, oat bran contained more AVAs, protein, oil, ash and other carbohydrates but less β-glucan and starch as compared to whole grain.”

https://www.sciencedirect.com/science/article/abs/pii/S0308814620315302 “Distributions of nutrients and avenanthramides within oat grain and effects on pearled kernel composition” (not freely available)


There were higher AVA contents in hulls of the top graphic’s species (Avena nuda) compared with its next ten seed layers. Humans require the bottom graphic’s oat species’ (Avena sativa) hull, which is “about 25% total grain mass,” to be milled off before we eat it. So AVA data points on the bottom graph A start around 25% surface removal.

As mentioned in Eat oats to prevent diabetes, I replaced steel-cut Avena sativa oats with whole Avena nuda oats for breakfast. I don’t know how well Avena nuda hulls are digested, but gut microbiota ferment similar indigestibles into beneficial compounds.

The first study of Eat oat sprouts for AVAs found “up to 25-fold increase” in AVAs with 7-day-old Avena sativa sprouts. I expect 3-day-old hulled Avena sativa sprouts I eat also increase AVAs as they germinate.

Our first 1000 days

This 2021 review subject was a measurable aspect of our early lives:

“The first 1000 days from conception are a sensitive period for human development programming. During this period, environmental exposures may result in long-lasting epigenetic imprints that contribute to future developmental trajectories.

The present review reports on effects of adverse and protective environmental conditions occurring on glucocorticoid receptor gene (NR3C1) regulation in humans. Thirty-four studies were included.

The hypothalamic-pituitary-adrenal (HPA) axis is key in regulating mobilization of energy. It is involved in stress reactivity and regulation, and it supports development of behavioral, cognitive, and socio-emotional domains.

The NR3C1 gene encodes for specific glucocorticoid receptors (GRs) in the mammalian brain, and it is epigenetically regulated by environmental exposures.

When mixed stressful conditions were not differentiated for their effects on NR3C1 methylation, no significant results were obtained, which speaks in favor of specificity of epigenetic vestiges of different adverse conditions. Specific maternal behaviors and caregiving actions – such as breastfeeding, sensitive and contingent interactive behavior, and gentle touch – consistently correlated with decreased NR3C1 methylation.

If the neuroendocrine system of a developing fetus and infant is particularly sensitive to environmental stimulations, this model may provide the epigenetic basis to inform promotion of family-centered prevention, treatment, and supportive interventions for at-risk conditions. A more ambiguous picture emerged for later effects of NR3C1 methylation on developmental outcomes during infancy and childhood, suggesting that future research should favor epigenome-wide approaches to long-term epigenetic programming in humans.”

https://www.sciencedirect.com/science/article/abs/pii/S0149763421001081 “Glucocorticoid receptor gene (NR3C1) methylation during the first thousand days: Environmental exposures and developmental outcomes” (not freely available). Thanks to Dr. Livio Provenci for providing a copy.


I respectfully disagree with recommendations for an EWAS approach during infancy and childhood. What happened to each of us wasn’t necessarily applicable to a group. Group statistics may make interesting research topics, but they won’t change anything for each individual.

Regarding treatment, our individual experiences and needs during our first 1000 days should be repeatedly sensed and felt in order to be therapeutic. Those memories are embedded in our needs because cognitive aspects of our brains weren’t developed then.

To become curative, we first sense and feel early needs and experiences. Later, we understand their contributions and continuations in our emotions, behavior, and thinking.

And then we can start to change who we were made into.

Don’t brew oat sprouts – eat them!

This 2020 study chemically analyzed four grains and their brew-processing products:

“Side-stream products of malting, particularly rootlet, are currently treated as animal feed. Instead of ending up in final products (e.g., malt and beer), a substantial portion of phytochemicals end up in side streams.

Rootlets are being increasingly investigated to overcome their bitter taste and to unleash their potential. Adding the fact that side-stream products produced in high quantity are also rich in protein, their nutritional value may be too high to justify usage as feed rather than food.

Grains were steeped for 26 to 30 h with a wet–dry–wet steeping program. Oats were wet steeped for 4 h at 13 °C before and after 18 h of dry steeping at 15 °C.

All grains were germinated for 6 days at 15 °C, after which they were dried with a gentle kilning program to a final temperature of 83 °C and moisture of 4%. Rootlets were separated from malt after drying.

Statistically significant changes occurred in abundance of all 285 annotated phytochemicals during malting, when comparing whole grain with malted grain or rootlet. In oats, cumulative levels of avenanthramides increased by 2.6-fold in the malted grain compared to intact whole grain. Up to 25-fold increase has been reported previously after a slightly longer germination.

Phenolamides cumulative levels in oats increased in both malted grain (11-fold) and rootlet (50-fold). Cumulative flavonoid levels were nearly 3-fold higher in malted grain and rootlet compared to whole grain.

Avenanthramides and phenolamides had much lower extractability into the water extract and wort.

To our knowledge, this is the first time avenanthramides are reported from any other species than oats, suggesting that the synthesis pathway for avenanthramides evolved before oats diverged from the other cereals. Furthermore, benzoxazinoids are herein reported for the first time in oats.

Several previously uncharacterized saponins were found in oats in addition to the previously known avenacins and avenacosides. However, because of limited reference data currently available, their identity could not be determined beyond compound class and molecular formula in this study.

Plants can synthetize up to hundreds of thousands of secondary metabolites, and current spectral databases only contain a fraction of them to allow identification. Compounds found in this study do not represent the complete range of phytochemicals existing in cereals.”

https://www.nature.com/articles/s41538-020-00081-0 “Side-stream products of malting: a neglected source of phytochemicals”


Twice a day for six weeks I’ve eaten oat sprouts 3-to-6-days old from two species and three varieties. I’ve never noticed any “bitter taste” of rootlets mentioned.

Maybe “a final temperature of 83 °C and moisture of 4%” had something to do with it? Oat sprouts I ate never got above 25°C, and I doubt their moisture content was < 80%.

Maybe “Oats were wet steeped for 4 h at 13 °C before and after 18 h of dry steeping at 15 °C” gave oat sprouts a bitter taste? I process oat sprout batches the same way I do broccoli sprout batches. A new batch soaks to start germination every 12 hours, then is rinsed three times every 24 hours on a 6 hours – 6 hours – 12 hours cycle. Temperature in my kitchen is 21°C (70°F) because it’s winter outside.

The above graphic is a heat map of 29 studied C-type avenanthramides. Don’t know why 26 known A-type avenanthramides described in Eat oats today! weren’t analyzed. The second study of Sprouting oats stated:

“There is a higher concentration of A-type AVAs [avenanthramides] than C-type AVAs in sprouted oats.”

Reference 33’s “up to 25-fold increase” is curated in Eat oat sprouts for AVAs.