Young gut, young eyes

I’ll highlight this 2022 rodent study findings of effects on eye health:

“We tested the hypothesis that manipulating intestinal microbiota influences development of major comorbidities associated with aging and, in particular, inflammation affecting the brain and retina. Using fecal microbiota transplantation, we exchanged intestinal microbiota of young (3 months), old (18 months), and aged (24 months) mice.

Transfer of aged donor microbiota into young mice accelerates age-associated central nervous system inflammation, retinal inflammation, and cytokine signaling. It promotes loss of key functional protein in the eye, effects which are coincident with increased intestinal barrier permeability.

These detrimental effects can be reversed by transfer of young donor microbiota.

young and aged fmt

We provide the first direct evidence that aged intestinal microbiota drives retinal inflammation, and regulates expression of the functional visual protein RPE65. RPE65 is vital for maintaining normal photoceptor function via trans-retinol conversion. Mutations or loss of function are associated with retinitis pigmentosa, and are implicated in age-related macular degeneration.

Our finding that age-associated decline in host retinal RPE65 expression is induced by an aged donor microbiota, and conversely is rescued by young donor microbiota transfer, suggests age-associated gut microbiota functions or products regulate visual function.” “Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain”


Exercise substitutes?

Two papers, starting with a 2022 abstract of an ongoing in vitro study with rodent cells:

“Exercise mimetics may target and activate the same mechanisms that are upregulated with exercise administration alone. This is particularly useful under conditions where contractile activity is compromised due to muscle disuse, disease, or aging.

Sulforaphane and Urolithin A represent our preliminary candidates for antioxidation and mitophagy, respectively, for maintaining mitochondrial turnover and homeostasis. Preliminary results suggest that these agents may be suitable candidates as exercise mimetics, and set the stage for an examination of synergistic effects.” “Exercise mimicry: Characterization of nutraceutical agents that may contribute to mitochondrial homeostasis in skeletal muscle” (study not available)

A second 2022 paper reviewed what’s known todate regarding urolithins:

“Urolithins (Uros) are metabolites produced by gut microbiota from the polyphenols ellagitannins (ETs) and ellagic acid (EA). ETs are one of the main groups of hydrolyzable tannins. They can occur in different plant foods, including pomegranates, berries (strawberries, raspberries, blackberries, etc.), walnuts, many tropical fruits, medicinal plants, and herbal teas, including green and black teas.

Bioavailability of ETs and EA is very low. Absorption of these metabolites could be increased by co-ingestion with dietary fructooligosaccharides (FOS).

Effects of other experimental factors: post-intake time, duration of administration, diet type (standard and high-fat), and ET dosage (without, low, and high ET intake) in ETs metabolism were evaluated in blood serum and urine of rats consuming strawberry phenolics. Highest concentrations were obtained after 2–4 days of administration.

Various crucial issues need further research despite significant evolution of urolithin research. Overall, whether in vivo biological activity endorsed to Uros is due to each specific metabolite and(or) physiological circulating mixture of metabolites and(or) gut microbial ecology associated with their production is still poorly understood.

  • Ability of Uros to cross the blood-brain barrier and the nature of metabolites and concentrations reached in brain tissues need to be clarified.
  • Specific in vivo activity for each free and conjugated Uro metabolite is unknown. Studies on different Uro metabolites and their phase-II conjugates are needed to understand their role in human health.
  • Evidence on safety and impact of Uros on human health is still scarce and only partially available for Uro-A.
  • It is unknown whether there are potential common links between gut microbial ecologies of the two unambiguously described metabotypes so far, i.e., equol (isoflavones) and Uros (ellagitannins).
  • Gut microbes responsible for producing different Uros still need to be better identified and characterized, and biochemical pathways and enzymes involved.” “Urolithins: a Comprehensive Update on their Metabolism, Bioactivity, and Associated Gut Microbiota”


Eat broccoli sprouts for stress

This 2022 review subject was aspects of sulforaphane regulating stress:

“Sulforaphane (SFN) shows great versatility in turning on different cellular responses. This isothiocyanate acts as a master regulator of cellular homeostasis due to its antioxidant response and cytoplasmic, mitochondrial, and endoplasmic reticulum (ER) protein modulation. SFN acts as an effective strategy to counteract oxidative stress, apoptosis, and ER stress, among others as seen in different injury models.

The ER is a complex membrane system, involved in several cellular processes including lipid synthesis and distribution, and Ca2+ storage and signaling. The ER is highly dynamic and changes according to cellular demand (e.g., hypoxia, mitochondrial dysfunction, or oxidative stress), leading to accumulation of unfolded or misfolded proteins in ER lumen, known as ER stress.

ER stress is buffered by unfolded protein response (UPR) activation, a homeostatic signaling network that orchestrates recovery of ER function by decreasing the burden of misfolded proteins. If stress signals continue it could lead to apoptosis activation.

Studies highlight a close interrelationship between ER stress and oxidative stress, two events driven by the accumulation of reactive oxygen species. Responses to stress inevitably perpetuate, and act as a vicious cycle that triggers development of different pathologies, such as cardiovascular diseases, neurodegenerative diseases, and others.

The PERK/Nrf2 pathway communicates oxidative stress and ER stress:


SFN couples oxidative and ER stress to promote cellular redox homeostasis. Further studies in animal and human models are required to elucidate pathways and proteins involved in differential responses orchestrated by SFN, emphasizing that responses will depend on cell type and kind of pathology, as well as SFN concentration.” “Role of sulforaphane in endoplasmic reticulum homeostasis through regulation of the antioxidant response” (not freely available) Thanks to Dr. Alejandro Silva for providing a copy.

Every hand’s a winner, and every hand’s a loser has more on UPR.

A healthspan improvement

Two 2022 publishments, starting with an excerpt from an informative interview with the Director of one of the three Interventions Testing Program centers:

“A paper submitted this week is one in which we tried a combination of rapamycin plus acarbose. Rapamycin works very well in male and female mice, while acarbose works significantly in both sexes but has a much stronger effect in males.

What we found in males is that when you give rapamycin and acarbose together, you do better than either rapamycin by itself or acarbose by itself. That combination of drugs together gives male survival a 29% boost.

That’s the largest percentage increase we’ve seen in males or females. This combination is the best thing we’ve ever had for either sex.

When you give acarbose and rapamycin together to females, they don’t do any better or any worse than on rapamycin alone. This is not too surprising because acarbose gives only a small effect in females. We expected it wouldn’t have a big boost over rapamycin alone in female animals, and that’s what we found.”

The study mentioned above:

“C57BL/6 mice were fed a cocktail diet containing one-half the dose of each drug compared to full dose cocktail diet and control diet. Half-dose drug cocktail was just as effective as full dose in preventing age-related cognitive impairment, but was less effective in other physical performance tests. Half-dose cocktail also had no effect on reducing pathological lesions.

Rapamycin was the major contributor for the cocktail’s effect on suppressing cognitive impairment. Decreased neuronal activation and impaired cognitive performance during aging occurs in both humans and rodents. Chronic mTOR attenuation by rapamycin has shown benefits of restoring deficits in neurovascular coupling response and cerebrovascular dysfunction in aging rodent models.

C57BL/6 female mice fed chow with acarbose performed equally well in grip strength as females fed chow with cocktail. That this sex-dependent result in strength performance was not seen in cocktail treated mice suggests that rapamycin and phenylbutyrate contributed in some way.

grip strength

HET3 4-way cross is a useful strain to help validate effects of the cocktail on aging parameters in C57BL/6 mice. HET3 mice were tested in the same manner, age, and timing as C57BL/6 mice, but only with the drug cocktail compared to control chow.

grip strength het3 mice

Grip strength force was normalized by body weight measured on the testing date so that peak force was expressed relative to body weight.

The drug cocktail was very effective in delaying progression of age-related pathology in all organs examined. We view this as a vital component of the study since mice were treated for only three months.

Administration of a cocktail has a major advantage over any individual drug tested in this study. A combination of three drugs previously shown to enhance lifespan and health span in mice is able to delay aging phenotypes more effectively and more robustly than any individual drug in the cocktail when started at middle age and given for a short period of time.” “Short term treatment with a cocktail of rapamycin, acarbose and phenylbutyrate delays aging phenotypes in mice”

It makes evolutionary sense for male mice to benefit more from anti-aging treatments than females.  Per How well do single-mother rodent studies inform us about human fathers?

“The Rattus and Mus genera used in almost all rodent research aren’t part of the 6% in which fathers also provide offspring care.”

There probably isn’t an evolutionary advantage for male mice to live much longer after sperm donation. Female mice don’t cache sperm.

It’s similar to studies in which treatments only benefited subjects who started out deficient. This interview hinted at how females’ healthspans and lifespans were already evolutionarily protected, with only male mice benefiting from 17α-estradiol treatment.

Female protection may have limits in humans. For example, most whale species don’t experience menopause. In those that do, like Orca, menopause is thought to be evolutionarily determined in order to keep females’ children from competing for resources with females’ grandchildren and great-grandchildren. That’s a hypothesis, though, as those species’ male lifespans aren’t adequately measured.

Rodent research and development on interventions and doses continues. 37 months is a human equivalent to this study’s 3-month treatment. What will effective anti-aging treatments be for humans?

More strange birds


Young immune system, young brain

This 2022 study investigated brain aging:

“We aimed to explore key genes underlying cognitively normal brain aging and its potential molecular mechanisms. Cellular and molecular mechanisms of brain aging are complex and mainly include:

  1. Dysfunction of mitochondria;
  2. Accumulation of oxidatively damaged proteins, nucleic acids, and lipids in brain cells;
  3. Disorders of energy metabolism;
  4. Impaired ‘waste disposal’ mechanism (autophagosome and proteasome functionality);
  5. Impaired signal transduction of adaptive stress response;
  6. Impaired DNA repair;
  7. Abnormal neural network activity;
  8. Imbalance of neuronal Ca2+ processing;
  9. Stem cell exhaustion; and
  10. Increased inflammation.

mrna brain expression

Expression of CD44, CD93, and CD163 mRNA detected by qPCR in hippocampal tissue of cognitively normal aged and young mice.

Underlying molecular mechanisms for maintaining healthy brain aging are related to decline of immune-inflammatory responses. CD44, CD93, and CD 163 are potential biomarkers.” “Identification of Key Biomarkers and Pathways for Maintaining Cognitively Normal Brain Aging Based on Integrated Bioinformatics Analysis”


Estimating bioavailability of oat compounds

Two papers on oat compounds’ bioavailability, starting with a 2022 review:

“There are many nutrients and bioactive chemical compounds exerting beneficial properties in oats. Results indicated that oats and their extracts possessed essential roles in preventing chronic diseases.

However, most studies focused on Avns’ [avenanthramides] functions were performed using cell models. In animal models, one disadvantage of Avns was low bioavailability.

Avns were also metabolized in the gastrointestinal tract in a gut microbiota (especially Faecalibacterium prausnitzii) dependent or independent manner. Administration of Avns usually ranged from 100−300 mg/ kg, which was much higher than that for cell treatment.

After eating cookies with 9.2 mg or 0.4 mg (control) Avns for 8 weeks, plasma level of TNF-α after exercise was significantly reduced in young women (16 women aged 18−30 years). Similar results were obtained in a study enrolling postmenopausal women (16 women aged 50−80 years), and Avns supplementation (9.2 mg in cookies) dramatically reduced plasma levels of IL-1β and C-reactive protein after exercise.

More attention should be given to studying preventative effect of Avns on chronic diseases and underlying molecular mechanisms, and further revealing potential roles of small molecules with powerful regulatory activity, such as miRNAs.” “The Progress of Nomenclature, Structure, Metabolism, and Bioactivities of Oat Novel Phytochemical: Avenanthramides” (not freely available)

This first paper’s Reference 25 was a 2018 paper on oat compounds’ bioaccessibility that used an in vitro digestion system without microbiota:

“Malting was performed for 5 days, from M0 (non-malted oat grains) to M5 (oat grains malted for 5 days), using the following: steeping at 20 °C for 24 h, germination in the dark at 15 °C, and kilning in an air oven at 100 °C for 12 h.

The cookie formulation with lowest phenol concentration showed highest bioaccessibility. This result was surprising, as we expected an increase in SP [soluble phenols] bioaccessibility, in parallel with increasing SP concentration of cookies.

bioavailability avena nuda avn sp

A portion of 5B cookies provides 4.8 mg of AVNs, which is more than double a maximal daily AVN intake in oat consumers.” vitro bioaccessibility of avenanthramides in cookies made with malted oat flours” (not freely available)

Every day I eat Avena nuda oats that start out as 82 grams of seeds, and two servings of 3-day-old Avena sativa oat sprouts that each start out as 20 grams of seeds. Using this second paper’s 50 gram Avena nuda methods to develop estimates:

avena nuda avn sp

  • (82 g / 50 g) x 42 µg = 69 µg total AVNs; and
  • (82 g / 50 g) x 660 µg = 1,082 µg soluble phenols.

My Avena nuda whole oat grain total AVNs and soluble phenol weights aren’t much. They aren’t bioavailability estimates. Their species and growing conditions are different from this second paper, etc.

That’s all okay with me. I eat Avena nuda oats primarily to make my trillion+ gut microbiota partners happy with indigestible-to-me whole grain contents, expecting that they will reciprocate.

Plugging in the study’s 3-day figures to estimate Avena sativa oat sprouts:

  • (40 g / 50 g) x 324 µg = 259 µg total AVNs; and
  • (40 g / 50 g) x 1350 µg = 1,080 µg soluble phenols.

Using the first graphic’s 3-day relative bioaccessibility percentages:

  • 259 µg x .28 = 72 µg total bioavailable AVNs; and
  • 1,080 µg x .41 = 442 µg bioavailable soluble phenols.

Both papers cited studies that found with eccentric exercise, “9.2 mg per day AVNs are sufficient to provide effects on exercise induced inflammation.” I exercise at least 30 minutes every day, but don’t perform eccentric exercises more frequently than every five days per Eat broccoli sprouts for your workouts.

Advantages of 3-day-old oat sprouts over oat grains provided methods comparable to my Avena sativa 3-day-old oat sprouts intake, although it didn’t assess bioavailability. Sprouts’ beneficial effects compared with seeds “were mainly related to their high content of avenanthramides A (2p), B (2f), and C (2c), quercetin 3-O-rutinoside [rutin], kaempferol, sinapoylquinic acid, and apigenin and luteolin derivatives.”

Couldn’t say whether I benefit more from bioavailability of 3-day-old oat sprouts’ directly soluble phenols, or from bioavailability of their phenolic breakdown byproducts provided by gut microbiota. For example, regarding oat sprouts rutin content, a 2019 review pointed out:

“Humans lack the enzyme needed to hydrolyze this bond. Consequently, microorganisms in the colon mediate hydrolysis of this rutinoside, resulting in minimal intestinal absorption, and production of phenolic acid metabolites in the colon.”

Osprey below a bird-like cloud


All about AGEs

My 900th curation is a 2022 review by the lead author of Reversibility of AGEs concentrations that fleshed out details of advanced glycation end products (AGEs) topics:

“This review aims to provide a state-of-the-art overview of the toxicokinetics and toxicodynamics of endogenously formed and exogenous dietary AGEs and their precursors. AGEs are a heterogenous group of:

  • Low molecular mass (LMM) glycation products formed by reaction with a free amino acid residue and/or to dicarbonyl precursors; and
  • High molecular mass (HMM) glycation products formed by reaction with a protein-bound amino acid residue, including cross-linked products (i.e. when two amino acid residues are involved instead of one).

Cross-linking of body proteins results in:

  • Altered structure and function of the proteins;
  • Proteins are less easily degraded;
  • An increase in stiffness in tissues that are rich in these proteins, including arterial, lung tissue, joints, and extracellular matrix. Stiffness in these tissues has been associated with diseases including hypertension, cataracts, dementia, atherosclerosis, glomerulosclerosis, emphysema, and joint pain.

In endogenous formation of AGEs and their precursors, the same pathways as exogenous proceed via non-enzymatic reactions, although they occur at lower rates due to the lower physiological temperatures. In addition, specific endogenous AGE formation pathways include glycolysis and the polyol pathway active under hyperglycemic conditions.

Considering heterogeneity of glycation products, as also reflected in different ADME outcomes, AGEs and their precursors cannot be grouped together. Specific, individual information is required for a proper evaluation, especially considering ADME properties.


The role of exogenous HMM AGEs and precursors seems to be restricted by limited bioavailability to local effects on the intestine including its microbiota, unless being degraded to their LMM form. An important role is probably left for reactive (endogenously formed) dicarbonyl AGE precursors and as a consequence the endogenously formed AGEs.

The direct contribution of reactive dicarbonyl precursors to dicarbonyl stress and their indirect contribution to endogenous HMM AGE formation and subsequent AGE receptor activation remain to be further studied.” “Differences in kinetics and dynamics of endogenous versus exogenous advanced glycation end products (AGEs) and their precursors”

Recent glucosamine research

Prompted by a conversation in Year Two of Changing to a youthful phenotype with sprouts, here are sixteen 2022 papers published in the last 45 days involving glucosamine. There are more researchers alive today than in the sum of human history, and they are compelled to publish.

Human research “The efficacy and safety of Jinwu Gutong capsule in the treatment of knee osteoarthritis: A meta-analysis of randomized controlled trials”

“The Jinwu Gutong (JWGT) capsule is a Chinese patent medicine that is widely used in the treatment of knee osteoarthritis (KOA) and osteoporosis in China and is considered to have the potential for good clinical efficacy. The application of JWGT combined with NSAIDs, hyaluronic acid, or glucosamine can significantly improve the clinical efficacy of the latter agents in KOA treatment.”

1-s2.0-S0378874122002860-ga1_lrg “Breast cancer imaging with glucosamine CEST (chemical exchange saturation transfer) MRI: first human experience” (not freely available)

“This study aims to evaluate the feasibility of imaging breast cancer with glucosamine (GlcN) CEST MRI technique to distinguish between tumor and surrounding tissue, compared to the conventional MRI method. The results of this initial feasibility study indicate the potential of GlcN CEST MRI to diagnose breast cancer in a clinical setup.” “The comparison of curcuminoid formulations or its combination with conventional therapies versus conventional therapies alone for knee osteoarthritis” (not freely available)

“Curcuminoid formulations or its combination with conventional therapies has been used for the treatment of knee osteoarthritis. Evidence is limited due to small-sized clinical trials. This study aims to evaluate the efficacy of curcuminoid formulations or its combination with conventional therapies for KOA.”

Animal, chemical, and microbiota research “Regulation of the urea cycle by CPS1 O-GlcNAcylation in response to dietary restriction and aging”

“O-linked N-acetyl-glucosamine glycosylation (O-GlcNAcylation) of intracellular proteins is a dynamic process broadly implicated in age-related disease, yet it remains uncharacterized whether and how O-GlcNAcylation contributes to the natural aging process. Our results identify CPS1 O-GlcNAcylation as a key nutrient-sensing regulatory step in the urea cycle during aging and dietary restriction, implying a role for mitochondrial O-GlcNAcylation in nutritional regulation of longevity.” “Laccase-Catalyzed Derivatization of Aminoglycoside Antibiotics and Glucosamine”

“The increasing demand for new and effective antibiotics requires intelligent strategies to obtain a wide range of potential candidates. The products protected mice against infection with Staphylococcus aureus, which was lethal to the control animals. The results underline the great potential of laccases in obtaining new biologically active compounds, in this case new antibiotic candidates from the class of aminoglycosides.” “Gelatin-glucosamine hydrochloride/crosslinked-cyclodextrin metal-organic frameworks@IBU composite hydrogel long-term sustained drug delivery system for osteoarthritis treatment” (not freely available)

“Osteoarthritis (OA) is a disease of articular cartilage degradation and inflammation of the joint capsule. Combining anti-inflammatory therapy with nutritional supplement is an effective means for the treatment of OA. Mechanical properties, sustained drug release behavior, and good biocompatibility of G-GH/CL-CD-MOF@IBU composite hydrogel showed that it has potential application in OA treatment of long-term sustained nutritional supplement and anti-inflammatory synchronously.” “Glucosamine enhances proliferation, barrier, and anti-oxidative functions in porcine trophectoderm cells”

“Trophectoderm (TE) is the first epithelium that appears during mammalian embryogenesis, and is a polarized transporting single cell layer that comprises the wall of the blastocyst. Previous studies have revealed the functional roles of glucose (Gluc), fructose (Fruc), and glutamine (Gln), which play a positive role in porcine trophectoderm (pTr) cell proliferation and migration, suggesting the importance of nutrients for normal development of the conceptus and implantation.

This work was conducted to test the hypothesis that glucosamine (GlcN), which is synthesized from Gln and Fruc-6-phosphate through the hexosamine biosynthesis pathway, can stimulate proliferation and sustain the barrier and anti-oxidative functions of pTr cells. GlcN plays an important role in promoting proliferation and stimulating the mTOR cell signaling pathway, as well as ameliorating oxidative stress and augmenting barrier functions in pTr cells.” “O-GlcNAcase Inhibitor ASN90 is a Multimodal Drug Candidate for Tau and α-Synuclein Proteinopathies”

“Neurodegenerative proteinopathies are characterized by the intracellular formation of insoluble and toxic protein aggregates in the brain that are closely linked to disease progression. O-GlcNAcase prevents the removal of O-linked N-acetyl-d-glucosamine moieties from intracellular proteins and has emerged as an attractive therapeutic approach to prevent the formation of tau pathology.” “Glucosamine facilitates cardiac ischemic recovery via recruiting Ly6Clow monocytes in a STAT1 and O-GlcNAcylation-dependent fashion”

“Glucosamine (GlcN, 2-amino-2-deoxy-d-glucose) is a freely available and commonly used dietary supplement for human cartilage health, which hexosamine biosynthesis pathway and induces protein O-GlcNAcylation. GlcN early therapy (GlcN/E), which initiated 1 day before myocardial infarction (MI), effectively facilitated cardiac ischemic recovery. More importantly, short-term GlcN therapy initiated even 3 days post-MI (GlcN/L) was also sufficient to induce clear cardiac protection, suggesting that both GlcN/E and GlcN/L therapies effectively ameliorate post-MI cardiac dysfunction and scar formation.” “Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics”

“For many microbes, we know little about them beyond their genome sequences. We built an automated tool to identify gaps: transporters or enzymes that should be present, to explain how a bacterium uses a carbon source, but could not be found in the genome. By comparing these gaps to large-scale genetic data for 29 bacteria, we identified hundreds of novel transporters and enzymes, and a new metabolic pathway for consuming glucosamine.” “Ingadosides A-C, acacic acid-type saponins from Inga sapindoides with potent inhibitory activity against downy mildew”

“As part of a project aiming at the discovery of environmentally friendly alternatives to copper in organic agriculture, a 96% ethanolic extract from the leaves of Inga sapindoides showed potent inhibitory activity against grapevine downy mildew. I. sapindoides, a tree which is often cultivated for shading coffee plantations in Central America, may represent a sustainable source of fungicidal products to be used in the replacement of copper.”

Microsoft PowerPoint - graphical abstract_revised “Aerobic exercise combined with glucosamine hydrochloride capsules inhibited the apoptosis of chondrocytes in rabbit knee osteoarthritis by affecting TRPV5 expression”

“This study aimed to investigate the effect of aerobic exercise combined with glucosamine on the apoptosis of chondrocytes of rabbit knee osteoarthritis by affecting the expression of TRPV5. Aerobic exercise combined with glucosamine hydrochloride capsules inhibited the apoptosis of chondrocytes in rabbit KOA by affecting the expression of TRPV5.” “Smart erythrocyte-hitchhiking insulin delivery system for prolonged automatic blood glucose control”

“Long and automatic control of blood glucose levels in diabetic patients could solve the problems caused by frequent insulin injections. Herein, we exploited the protection potential of erythrocytes by a ‘hitchhiking’ strategy to significantly prolong the blood circulation time of a specifically-designed smart hitchhiking insulin delivery system (SHIDS). In the SHIDS, insulin, glucose oxidase, and catalase were co-loaded into nanoparticles formed by modified chitosan. The free glucosamines in chitosan anchor glucose transporters on the surface of erythrocytes, allowing erythrocyte-hitchhiking in the blood flow.” “Maillard-reacted peptides from glucosamine-induced glycation exhibit a pronounced salt taste-enhancing effect” (not freely available)

“Reducing salt intake, as one of the most cost-effective approaches, is congruent with improved population health. Maillard-reacted peptides exhibited a significant salt taste-enhancing effect, which may be attributed to the glucosamine-induced glycation. The current study provides a theoretical basis for preparation of salt taste-enhancing peptides and their future application to reduce salt content of formulated foods.” “Peptidoglycan from Akkermansia muciniphila Muc T: chemical structure and immunostimulatory properties of muropeptides” (not freely available)

“Akkermansia muciniphila is an intestinal symbiont known to improve the gut barrier function in mice and humans. Our results provide new insights into the diversity of cell envelope structures of key gut microbiota members and their role in steering host-microbiome interactions.”

Reviews “Ruminal bacteria lipopolysaccharides: an immunological and microbial outlook”

“Lipopolysaccharides (LPS) are outer membrane components of Gram-negative bacteria made of three regions: the O-antigen; the core oligosaccharide; and a glucosamine disaccharide linked to hydroxy fatty acids, which is named lipid A. this review identifies numerous areas for future research, including setting the basis for future modeling and simulation of host microbiome interactions in ruminants.”


Reversibility of AGEs concentrations

This 2021 rodent study investigated dietary advanced glycation end products (AGEs):

“There is increasing evidence in humans and animals that consumption of dietary AGEs contribute to AGEs measured in plasma and organs and that a diet high in dietary AGEs in humans has negative biological effects, such as low-grade inflammation, endothelial dysfunction, and insulin resistance. However:

  • It is currently unknown whether AGE accumulation in tissues and the negative biological effects associated with a high AGE diet are reversible; and
  • How dietary AGEs are involved in the aforementioned biological effects remains poorly understood.

We hypothesized that mice fed a high dietary AGE diet for 10 weeks would show increased blood and tissue AGEs, increased inflammatory markers, and different microbiota composition as compared to mice fed a standard dietary AGE diet. In addition, we studied whether changes following the high dietary AGE diet were reversible by implementing a switch after 5-weeks of high dietary AGE diet to the standard dietary AGE diet for 5 subsequent weeks.


To obtain a high AGE diet, a standard rodent chow was baked at 160 C for two hours. Free- and protein-bound AGEs Nε-(carboxymethyl)lysine (CML), Nε-(1-carboxyethyl)lysine (CEL), and Nδ-(5-hydro-5-methyl-4-imidazolon-2-yl)-ornithine (MG-H1) were analyzed in plasma, liver, and kidney. Additionally, free-, protein-bound AGEs, and AGE precursor oxoaldehydes methylglyoxal (MGO), glyoxal (GO), and 3-deoxyglucosone (3DG) were analysed in animal diets.

Inflammatory z-score consists of TNF-α, IFN-γ, KC/GRO, IL-6, and IL-10:

inflammatory z scores

A high AGE-diet led to an increase of AGEs in plasma, kidney, and liver, and to more inflammation, and modification of gut microbiota. These effects were reversed or discontinued by a diet lower in AGEs.

Our observations of reversible AGE accumulation in kidney and liver may not be extrapolated to other organs. Likewise, our findings in mice cannot be directly extrapolated to humans, as species differences exist in for example metabolic rate and dietary habits, as also in gut microbiota composition.” “Dietary advanced glycation end products (AGEs) increase their concentration in plasma and tissues, result in inflammation and modulate gut microbial composition in mice; evidence for reversibility” (not freely available)

This study started with 9-week-old mice and lasted eleven weeks, the human equivalents of which are ages 20 to 30 years. Study measurements weren’t intended to detect all potential symptoms of high-AGE diets. The lead author followed up with All about AGEs.

AGEs’ reversibility in older humans is one of my operative hypotheses:

  • I haven’t cooked or eaten high AGE precursor or AGEs food at home in the past three years.
  • The highest AGE item I’ve eaten at restaurants has been fish tacos.
  • I’m not hyperglycemic, and don’t expect that further AGE accumulation from either exogenous or endogenous sources has occurred.


State-dependent memory

This 2021 review by two coauthors of What can cause memories that are accessible only when returning to the original brain state? provided evidence for alternative interpretations of memory experiments:

“Memory consolidation hypotheses postulate a long series of various and time consuming elaborate processes that come to protect memory from disruption after various periods of time. For more than fifty years, consolidation hypotheses led to the idea that:

  1. Memories are fragile and can easily be disrupted; and
  2. Memories require several hours to be encoded (Cellular Consolidation), and extensive periods of time (days to weeks and even months and years), to be definitely stabilized (Systems Consolidation).

Although these views rely on well substantiated findings, their interpretation can be called into question.

An alternative position is that amnesia reflects retrieval difficulties due to contextual changes. This simple explanation is able to account for most, if not all, results obtained in consolidation studies.

memory state dependency

Systems Consolidation can be explained in terms of a form of state-dependency.

Recent memory remains detailed, context-specific (in animals), and vivid (in humans) and very susceptible to contextual changes. With the passage of time, memories become less precise, and retention performance less and less affected by contextual changes.” “Revisiting systems consolidation and the concept of consolidation” (not freely available)

I came across this review while trying to understand why a 2022 rodent study felt wrong. That study followed the standard memory paradigm, and I appreciate its lead author providing a copy since it wasn’t otherwise available.

But those researchers boxed themselves in with consolidation explanations for findings. They used drugs to change subjects’ memories’ contexts between training and testing. They didn’t see that tested memories were dependent on subjects’ initial brain states.

This review cited a paper abstracted in Resiliency in stress responses, namely Neurobiological mechanisms of state-dependent learning.

Crab for lunch


Biological age and zinc

This 2022 human study investigated zinc’s influence in modulating DNA methylation patterns:

“The purpose of this study was to identify epigenetic variables related to serum Zn (ZnS) levels and Zn daily ingestion (ZnDI) in a case-control cohort. Individuals were selected and classified according to their body mass index into two groups: control group of 11 women without obesity, and study group composed of 10 women with obesity. Inclusion criteria were women aged 18–50 years with stable body weight for at least 6 months.

Novel Zinc-Related Differentially Methylated Regions in Leukocyt

A negative correlation of ZnS with epigenetic age acceleration residual suggested that the higher the ZnS levels, the lower the aging rate:

serum zinc

Our results regarding Zn homeostasis in women with obesity suggested regulation by other mechanisms besides ingestion:

  • Zn-associated differentially methylated regions may exert downstream effects on inflammation, macronutrient metabolism, and DNA/cellular process repair.
  • Hypomethylation of the PM20D1 gene could interconnect DNA methylation and nutritional status.” “Novel Zinc-Related Differentially Methylated Regions in Leukocytes of Women With and Without Obesity”

This study emphasized that nutrients aren’t the whole story on health. We also have to be in metabolic zones where our diet and nutrient choices can achieve desired effects.

Subjects’ selection criteria (BMI) was more than double the control group’s. Sometimes people’s lives show others what not to do with their own.

Epigenetic clocks and entropy

Two epigenetic clock papers, starting with a 2022 rodent study:

“We tested performance of new pan-tissue and liver-specific epigenetic mouse clocks, evaluating how these related to metabolic states, genotype-dependent life expectancy, and methylome entropy.

Entropy, a measure of noise and information loss, increases as a function of time and age. In context of the methylome, higher entropy represents a tendency for the highly organized hypo- and hypermethylated landscape to erode towards a more hemi-methylated [discordant] state.

This increase in disorder, particularly across CpGs that are highly conserved, could have important functional consequences. Entropy of age-gain CpGs was increased by high fat diet, and predicted strain lifespan.

Overall, we find that mice belonging to longer-lived BXD strains had a more youthful methylome with lower entropy at age-gain CpGs. Entropy of age-loss CpGs on the other hand, was related to body weight.

entropy associations

(h) Residual plot (adjusted for age, diet, BWF [final body weight], glucose, cholesterol, and batch) shows an inverse association between entropy at age-gain sites, and lifespan. (i) A similar residual plot shows the association between BWF and age-loss entropy.

The rate of noise accumulation, an aspect of epigenomic aging, can vary between individuals. Resilience or susceptibility to higher noise may be partly modulated by diet as well as genetic factors.

Convergence of evidence from genetic and gene expression analyses indicates that genes involved in metabolism and energy balance contribute to age-dependent restructuring of the methylome, which in turn forms the basis of epigenetic clocks.” “Genetic loci and metabolic states associated with murine epigenetic aging”

Reference 28 was a 2021 human study cited for “identified the APOE locus as the strongest GWAS hit for two measures of biological age acceleration”

“We observed inverse APOE e2 and e4 associations and unique pathway enrichments when comparing two biological age measures. Genes associated with BioAgeAccel were enriched in lipid related pathways, while genes associated with PhenoAgeAccel showed enrichment for immune system, cell function, and carbohydrate homeostasis pathways, suggesting the two measures capture different aging domains.

Our study reaffirms that aging patterns are heterogeneous across individuals, and the manner in which a person ages may be partly attributed to genetic predisposition. Understanding personalized aging susceptibility phenotypes has important implications for primary and secondary disease interventions.” “Genetic associations for two biological age measures point to distinct aging phenotypes”


Vascular memory

This 2022 rodent study investigated effects of inducing hypertension for two weeks:

“Hypertension is conventionally associated with a neurohormonal activation from the sympathetic nervous and the renin-angiotensin-aldosterone systems. Angiotensin II (AngII) is a potent regulator of blood pressure, and is also a key player in hypertension development.

An initial 2-week exposure to AngII induced profound changes in cardiac and vascular remodeling, including endothelial activation, vascular inflammation and oxidant stress, all of which were maintained up to 3 weeks after AngII withdrawal. This phenotype was sustained despite early normalization of blood pressure after AngII withdrawal.

Our RNAseq pathway analysis suggests involvement of epigenetic regulators involved in methylation, such as PRC2. PCR2 complex catalyzes trimethylation of histone H3 on lysine 27 (H3K27me3), a histone mark necessary for maintaining transcriptional repression during multicellular development.

H3K27me3 AngII

Cell type-specific patterns of H3K27me3 are crucial for preserving cell identity. Consistent with this analysis, we observed a significant increase in H3K27me3 epigenetic mark in aortic tissue, intriguingly, only in both memory conditions.

Transient exposure to Ang II produces prolonged vascular remodeling with robust ACTA2 downregulation, associated with epigenetic imprinting, supporting a memory effect despite stimulus withdrawal. Future characterization of underlying AngII-dependent signaling might unveil new targets for its therapeutic modulation and reversal of this adverse legacy effect.” “Sustained Downregulation of Vascular Smooth Muscle Acta2 After Transient Angiotensin II Infusion: A New Model of Vascular Memory”

These subjects’ ages were equivalent to a 20-year-old human:

  • How much earlier could our vascular system retain events we experienced such as epigenetic H3K27me3 increases? Teenaged, late childhood, early childhood, infancy, fetal parts of our lives?
  • How long would these vascular system memories and their continued signaling linger?
  • What experiences could change these long-lasting memories?

Icy fire


Year Two of Changing to a youthful phenotype with sprouts

1. I’ve eaten clinically-relevant doses of sulforaphane every day for 104 weeks now with microwaved 3-day-old broccoli, red cabbage, and mustard sprouts. That’s 8+ times longer than any sulforaphane clinical trial.

I continue to:

  • Eat Avena nuda oats for breakfast;
  • Eat 3-day-old hulled Avena sativa oat sprouts twice a day;
  • Eat AGE-less chicken vegetable soup twice a day;
  • Take supplements that promote healthspan twice a day;
  • Exercise at least 30 minutes daily;
  • Take yeast cell wall β-glucan daily, with nothing else an hour before or after; and
  • Avoid undue stress by working from home 40 hours a week in my 25th year as a professional software developer.

I’ve experienced many positive effects described in studies. Researchers keep exploring new aspects of their fields, and I look forward to more evidence on youthening during Year Three.

2. I’m not especially scientific or maniacal about the above practices, other than weighing sprouting seeds. I pay attention to people who measure everything, but won’t turn my life into a series of unfeeling experiments. As Dr. Arthur Janov said:

“What is the point of life if we cannot feel and love others? Without feeling, life becomes empty and sterile. It, above all, loses its meaning.”

3. Beginning last month, our world was subjected to yet another wave of propaganda, with predictable oppression of those who reported obvious lies and distortions. Previously exposed agendas took a back seat to regain their venom, as their effects waned in herding people toward personally devastating cliffs.

Meme perpetrators don’t care about you or me. Spending our time on their ideas, beliefs, and behaviors takes us further away from dealing with our individually motivating causes and individual truths, with real consequences: a wasted life.

Value your own one precious life. Winter is over, spring is here.