Genetic factors

Epigenetic clocks and entropy

gettingwell4 4-5 stars Advanced knowledge, Epigenetics, Immune system, Stress , , , ,

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.”

https://elifesciences.org/articles/75244 “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.”

https://onlinelibrary.wiley.com/doi/10.1111/acel.13376 “Genetic associations for two biological age measures point to distinct aging phenotypes”

PXL_20220322_191309272

Selecting broccoli varieties

gettingwell4 5+ stars Premium, Epigenetics

This 2022 study evaluated 14 broccoli varieties grown in the same conditions for their floret compounds:

“Glucosinolate (GSL) profile and content in 11 inbred broccoli lines and three commercial cultivars were analyzed. Hydrolysate content, myrosinase activity, and nitrile formation rate were also determined.

Sulforaphane – an isothiocyanate (ITC) hydrolysate of glucoraphanin – content showed relatively higher value in the following order: 5404 > 5410 > 5407 > 5411, although glucoraphanin content was lower in those lines:

1-s2.0-S0304423822001108-gr3_lrg

No significant relationship was found between myrosinase activity and total hydrolysate content, except in line 5310, which had the lowest myrosinase activity and the lowest total hydrolysate content. There was no significant correlation between myrosinase activities and sulforaphane.

We found a clear difference in selecting functional broccoli by considering only the GSL content or hydrolysates.

  • Even if total GSL content and individual GSL content were high, ITC content could not be produced at a high level.
  • When GSL content is high, if nitrile formation rate was also high, more nitrile than ITC would be produced.

Low nitrile formation rate and higher hydrolysate content should be considered when selecting functional broccoli lines with high GSL content.”

https://www.sciencedirect.com/science/article/pii/S0304423822001108 “Selection of broccoli (Brassica oleracea var. italica) on composition and content of glucosinolates and hydrolysates”

As 3-day-old broccoli sprouts have the optimal yields, Lab analyses of broccoli sprout compounds, Tailoring measurements for broccoli sprouts, and this study found, there weren’t many potential health benefits based solely on broccoli varieties’ glucoraphanin contents. But genotypes had a greater effect than did environmental influences, and seed / sprout / stalk / floret beneficial contents differed.

There are opportunities for vendors to showcase healthier broccoli products. Growing, harvesting, and storage conditions will make that expensive to test and certify, though.

As A follow-on study to 3-day-old broccoli sprouts have the optimal yields, Enhancing sulforaphane content, and Microwave broccoli to increase sulforaphane levels showed, there are ways to improve myrosinase activity and isothiocyanate yield. I do these easy actions every day while growing 3-day-old sprouts from unknown broccoli varieties. Waiting for evidence to compel changing that.

Strange birds

PXL_20220401_193452029

Epigenetic components for evaluating a person’s physical fitness

gettingwell4 4-5 stars Advanced knowledge, Epigenetics ,

This 2022 human study incorporated DNA methylation measures of four physical fitness parameters into a new epigenetic clock:

“Our work introduces new DNAm biomarkers for fitness parameters of gait speed (walking speed), hand grip strength, forced expiratory volume in one second (FEV1), and maximal oxygen uptake (VO2max). These DNAm biomarkers represent new tools for researchers with access to blood samples and interest in epigenetic components to fitness.

Our DNAm biomarker fitness parameter biomarkers are not intended to replace true physical fitness measurements. Instead, these DNAm biomarker estimates provide an epigenetic component to evaluating a person’s physical fitness. This biomarker integrates the established DNAm prediction of mortality risk GrimAge.

DNAmFitAge provides an easily interpretable tool to relate physical fitness to biological age. Adjusting DNAmFitAge for chronological age generates a novel measure of epigenetic age acceleration, FitAgeAcceleration, which is informative for physical activity level, mortality risk, coronary heart disease risk, comorbidities, and disease-free status across several large validation datasets.

ttd

The age-adjusted version FitAgeAcceleration provides a novel measure of epigenetic age acceleration explained through physical fitness. This research demonstrates biological age can be estimated using DNAm fitness parameter biomarkers which are dependent on exercise lifestyle.”

https://www.medrxiv.org/content/10.1101/2022.03.21.22272043v1.full-text “DNAmFitAge: Biological Age Indicator Incorporating Physical Fitness”

I walk quickly on the beach almost every day at > 3 mph. I occasionally see younger people eclipse my gait speed, which makes me try harder. 🙂

Gut microbiota knowledge through 2021

gettingwell4 2-3 stars Required further work, Amygdala, Cortisol, Dopamine, Epigenetics, Glutamate, Hippocampus, Hypothalamus, Immune system, Limbic system, Memory, Neurochemicals, Oxytocin, Serotonin, Stress , , , , , , ,

I’ll curate this 2022 review of what’s known and unknown about our trillions of gut microbiota through its topic headings:

“Most microbial taxa and species of the human microbiome are still unknown. Without revealing the identity of these microbes as a first step, we cannot appreciate their role in human health and diseases.

A. Understanding the Microbiome Composition and Factors That Shape Its Diversity
Effect of Diet Composition on the Microbiome Diversity

  • Macronutrients and Microbiome Diversity
  • Nutrient and Mineral Supplements and Microbiome Diversity

Stress

Drugs

Race and Host Genetics

Aging

Lifestyle

  • Exercise
  • Smoking
  • Urbanization

B. Understanding the Microbiome Function and Its Association With Onset and Progression of Many Diseases

Microbiome Association With Inflammatory and Metabolic Disorders

  • Chronic Inflammation in GIT and Beyond
  • Development of Malignant Tumors
  • Obesity
  • Coronary Artery Disease
  • Respiratory Diseases

Microbiome Role in Psychiatric, Behavioral, and Emotional Disorders

C. Understanding the Microbiome Function as Mediated by Secreted Molecules

D. Conclusion and Future Directions – A pioneering study aimed to computationally predict functions of microbes on earth estimates the presence of 35.5 million functions in bacteria of which only 0.02% are known. Our knowledge of its functions and how they mediate health and diseases is preliminary.”

https://www.frontiersin.org/articles/10.3389/fmicb.2022.825338 “Recent Advances in Understanding the Structure and Function of the Human Microbiome”

I took another test last month at the 14-month point of treating my gut microbiota better. Compared with the 7-month top level measurements, what stood out was an increase in relative abundance from 1% to 7% in the Verrucomicrophia phylum that pretty much exclusively comprises species Akkermansia muciniphilia in humans:

top 5 phylum 2-2022

This review termed Akkermansia muciniphilia relative increases as beneficial. Go with the Alzheimer’s Disease evidence didn’t.

Preventing human infections with dietary fibers inferred that insufficient dietary fiber may disproportionately increase abundance of this species. But I already eat much more fiber than our human ancestors’ estimated 100 grams of fiber every day, so lack of fiber definitely didn’t cause this relative increase.

Resistant starch therapy observed:

“Relative abundances of smaller keystone communities (e.g. primary degraders) may increase, but appear to decrease simply because cross-feeders increase in relative abundance to a greater extent.”

I’ll wait for further evidence while taking responsibility for my own one precious life.

Didn’t agree with this review’s statements regarding microbial associations with fear. These reviewers framed such associations as if gut microbiota in the present had stronger influences on an individual’s fear responses than did any of the individual’s earlier experiences. No way.

I came across this review by it citing The microbiome: An emerging key player in aging and longevity, which was Reference 25 of Dr. Paul Clayton’s blog post What are You Thinking?

Also didn’t agree with some of the doctor’s post:

  • Heterochronic parabiosis of young and old animals is wildly different from fecal transfer. Can’t really compare them to any level of detail.
  • Using a rodent young-to-old fecal microbiota transplant study to imply the same effects would happen in humans? Humans don’t live in controlled environments, so why would a young human individual’s gut microbiota necessarily have healthier effects than an old individual’s?
  • Another example was the penultimate paragraph: “By adding a mix of prebiotic fibers to your diet and maintaining a more youthful and less inflammatory microbiome you will have less inflammation, less endotoxaemia and less inflammageing. You will therefore live healthier and longer.” I’m okay with the first sentence. Equivalating the first sentence to both healthspan and lifespan increases in the second sentence wasn’t supported by any of the 45 cited references.

Advanced glycation / lipoxidation end products

gettingwell4 4-5 stars Advanced knowledge, Epigenetics, Immune system, Stress , , , ,

Three papers on what can be expected from AGEs, beginning with a 2022 review:

“Carbonyl stress is a condition characterized by an increase in the steady-state levels of reactive carbonyl species (RCS) that leads to accumulation of their irreversible covalent adducts with biological molecules. In addition to causing damage directly, the RCS adducts advanced glycation end-products (AGEs) and advanced lipoxidation end-products (ALEs) elicit chronic inflammation through receptor-mediated mechanisms.

Endogenously formed RCS and AGEs/ALEs accumulation induced by hyperglycemia, hyperlipidemia, and oxidative stress have been long recognized as critical factors in pathogenesis of cardiovascular, renal, and eye complications. The role of dietary glyco/lipotoxins in vascular complications is debated, as the metabolic fate of most ingested AGEs/ALEs and RCS remains unknown, and their contribution to systemic carbonyl stress is uncertain.

rcs ages ales

Plasma glucose spikes after a meal rich in readily absorbable carbohydrates, particularly in association with an unfavorable lipid composition, may promote proinflammatory and pro-oxidant responses by inducing a transient increase in RCS levels and consequent AGE formation. As protein-bound AGEs are not easily eliminated from the body, they can eventually accumulate in vascular and metabolic tissues because of repeated cycles of nutrient-induced carbonyl stress, favoring establishment of systemic low chronic inflammation.

Post-challenge glucose excursions are associated with a transient increase in circulating RCS levels, particularly in diabetic and prediabetic individuals. Diet-induced weight loss is associated with decreases in postprandial carbonyl stress in obese subjects. Data on lean and metabolically healthy individuals are limited.”

https://www.mdpi.com/2072-6643/14/5/1061/htm “Food-Related Carbonyl Stress in Cardiometabolic and Cancer Risk Linked to Unhealthy Modern Diet”

I understand that researchers feel obligated to end papers with suggestions for future research. It’s a little irritating, though, when these are pie-in-the-sky.

People who wait for endogenous vs. exogenous AGE / ALE questions to be answered in their lifetimes are at risk for giving themselves diseases.

A second paper is a 2021 human cell study:

“Sulforaphane (SFN) found in cruciferous vegetables is a potent activator of the Nrf2 transcription factor, the master regulator of redox biology in mammalian cells. Nrf2 modulates expression of several antioxidant enzymes, such as γ-glutamylcysteine ligase (γ-GCL). This is the rate-limiting step in synthesis of the major non-enzymatic antioxidant glutathione (GSH). Silencing of Nrf2 or inhibition of GSH synthesis abolished SFN-promoted mitochondrial protection in cells exposed to methylglyoxal (MG), a pro-oxidant agent whose levels are high in several human diseases.

sfn vs mg

MG is a reactive dicarbonyl presenting both endogenous (e.g. glycolysis) and exogenous (e.g. food cooking) sources. MG induces neurotoxicity, at least in part, by affecting mitochondrial function, including a decline in oxidative phosphorylation (OXPHOS) system activity, bioenergetics failure, and redox disturbances.

We found that SFN prevented MG-induced OXPHOS dysfunction and mitochondrial redox impairment. SFN protected mitochondria of MG-challenged cells by a mechanism involving the Nrf2/γ-GCL/GSH axis.”

https://link.springer.com/article/10.1007/s11064-020-03204-x “The Isothiocyanate Sulforaphane Depends on the Nrf2/γ‑GCL/GSH Axis to Prevent Mitochondrial Dysfunction in Cells Exposed to Methylglyoxal” (not freely available)

Although this study’s 5 µM sulforaphane treatment is achievable in human plasma, that level isn’t sustainable for 24 hours as the study did in vitro. Would sulforaphane’s in vivo effects likewise prevent methylglyoxal from inducing AGEs?

A third paper is a 2022 human study:

“AGEs have been widely reported to play an important role in osteoporosis (OP). We investigated the effect of AGEs on osteoblast function and underlying mechanisms.

op lumbar vertebrae

Levels of bone mineral density (BMD), serum AGEs, and fasting blood glucose (FBG) were measured in patients with OP and healthy individuals:

  • Patients with OP had a higher level of serum AGEs and FBG compared with healthy individuals.
  • The level of serum AGEs in patients with OP was negatively correlated with BMD, but was positively correlated with FBG.
  • AGEs and serum from patients with OP markedly inhibited hFOB1.19 osteoblast cell proliferation, alkaline phosphatase production, and mineralized nodule formation.
  • Apoptosis and ferroptosis were significantly promoted by AGEs and serum from patients with OP.
  • Serum from OP patients with T2DM caused stronger effect than that from OP patients with normal FBG.

Collectively, AGEs could disrupt functions of osteoblasts by inducing cell ferroptosis, thus contributing to OP.”

https://www.spandidos-publications.com/10.3892/mmr.2022.12656 “Advanced glycation end products promote osteoporosis by inducing ferroptosis in osteoblasts”

Nanoencapsulating Brassica bioactives with Brassica membrane vesicles

gettingwell4 4-5 stars Advanced knowledge, Epigenetics, Immune system ,

Two 2022 in vitro studies from the group that published Red cabbage effects on gut microbiota, with the first nanoencapsulating sulforaphane:

“Sulforaphane (SFN) loaded into membrane vesicles derived from broccoli plants was studied to determine anti-inflammatory potential in a human-macrophage-like in vitro cell model under both normal and inflammatory conditions.

LPS increased IL-6 levels 1.86-fold. All compounds (free SFN, unloaded broccoli membrane (BM)-vesicles, and encapsulated SFN) mediated a dose-dependent reduction in IL-6, both in basal conditions [left] and simulated inflammatory conditions [right]. Encapsulated SFN had the greatest power.

Il-6 nanoencapsulated sulforaphane

These results showed that membrane vesicles by themselves had anti-inflammatory properties. Possible routes of administration of BM-vesicles loaded with SFN are parenteral, transdermal, and oral.”

https://www.mdpi.com/1422-0067/23/4/1940/htm “Membrane Vesicles for Nanoencapsulated Sulforaphane Increased Their Anti-Inflammatory Role on an In Vitro Human Macrophage Model”

A second study nanoencapsulated Bimi®, a crossbreed between broccoli and green Chinese kale:

“The aim of this work was to increase stability of isothiocyanates (ITCs) present in extracts of Bimi® edible parts by nanoencapsulation using cauliflower-derived plasma membrane vesicles.

Bimi® has emerged as a mild-flavoured option to pungent broccoli. As a raw gourmet material, Bimi® is highly and carefully selected, with part of edible production discarded.

Indole glucosinolates (GSLs) represented 81% of total GSL content. The only aliphatic GSL detected in a quantifiable amount was glucoraphanin, accounting for 19% of total GSLs.

1-s2.0-S0308814622006422-gr1_lrg

Comparisons between concentrations of ITCs in gastric and intestinal digestions:

A) 3,3-diindolylmethane (DIM);

  • Bimi® extract increased 2 times, and no differences in nanoencapsulated treatment after intestinal digestion.
  • Concentrations were 4- and 2-fold higher in the nanoencapsulated form than extract between gastric and intestinal digestions, respectively.

B) Indole-3-carbinol (I3C);

  • Bimi® extract increased 1.5 times, and nanoencapsulated treatment decreased 23% after intestinal digestion.
  • Concentrations were 3 times higher and 2 times higher in the nanoencapsulated form than extract between gastric and intestinal digestions, respectively.

C) SFN

  • Bimi® extract increased almost 10 times, and 100 times in nanoencapsulated treatment after intestinal digestion.
  • No differences between treatments after gastric digestion, but concentrations were 6 times higher in the nanoencapsulated form than extract after intestinal digestion.

Cauliflower-derived plasma membrane vesicles are able to enhance stability of ITCs through in vitro gastrointestinal digestion, improving their bioaccessibility and potential bioavailability.”

https://www.sciencedirect.com/science/article/pii/S0308814622006422 “Nanoencapsulation of Bimi® extracts increases its bioaccessibility after in vitro digestion and evaluation of its activity in hepatocyte metabolism”

Reversing hair greying

gettingwell4 4-5 stars Advanced knowledge, Epigenetics, Hypothalamus, Immune system, Limbic system, Memory, Stress, Telomeres ,

I’ll highlight this 2021 human study’s findings regarding stress:

“We profiled hair pigmentation patterns (HPPs) along individual human hair shafts, producing quantifiable physical timescales of rapid greying transitions. White/grey hairs that naturally regain pigmentation across sex, ethnicities, ages, and body regions, quantitatively define reversibility of greying in humans.

A systematic survey of two-colored hairs on the scalp of a 35-year-old Caucasian male with auburn hair color over a 2-day period yielded five two-colored hair shafts (HSs) from the frontal and temporal scalp regions. Unexpectedly, all HSs exhibited reversal. HPP analysis further showed that all HSs underwent reversal of greying around the same time period.

A retrospective assessment of psychosocial stress levels using a time-anchored visual analog scale (participants rate and link specific life events with start and end dates) was then compared to HPPs. Reversal of greying for all hairs coincided closely with decline in stress and a 1-month period of lowest stress over the past year (0 on a scale of 0–10) following a 2-week vacation.

vacay

We were also able to examine a two-colored hair characterized by an unusual pattern of complete HS greying followed by rapid and complete reversal plucked from the scalp of a 30-year-old Asian female participant with black hair. HPP analysis of this HS showed a white segment representing approximately 2 cm.

Quantitative life stress assessment revealed a specific 2-month period associated with an objective life stressor (marital conflict and separation, concluded with relocation) where the participant rated her perceived stress as highest (9–10 out of 10) over the past year. The increase in stress corresponded in time with complete but reversible hair greying.

separation

We document a complete switch-on/off phenomena during a single anagen cycle. Proteomic features of hair greying directly implicate multiple metabolic pathways that are both reversible in nature and sensitive to stress-related neuroendocrine factors.

This new method to quantitatively map recent life history in HPPs provides an opportunity to longitudinally examine the influence of recent life exposures on human biology. Additional prospective studies with larger sample sizes are needed to confirm robust reproducibility and generalizability of our findings.”

https://elifesciences.org/articles/67437 “Quantitative mapping of human hair greying and reversal in relation to life stress”

See Reversing hair greying, Part 2 for selected papers through 2024 that cited this study.

Vitamin K2 and hypertension

gettingwell4 2-3 stars Required further work, Epigenetics, Immune system ,

This 2021 rodent study investigated effects of Vitamin K2 on salt-sensitive hypertension:

“Mice were supplemented with VK2 and gut bacteria were detected by 16S rRNA. Common signaling pathway-related proteins were detected to further verify signaling pathways before validation of clinical samples.

Diets for 4 weeks were:

  • Normal group diet containing 0.5% NaCl;
  • High salt group (HS) diet containing 8% NaCl;
  • High salt diet plus VK2 supplementation group (HS_VK2) diet containing 8% NaCl and additional 0.025% VK2.

VK2 supplementation protected blood pressure and aortic vessels in salt-induced mice:

mk-4 salt

VK2 treated salt-sensitive hypertension by inhibiting the renin–angiotensin system.

fnut-08-639467-g009

Possible mechanisms of VK2 for salt-sensitive hypertension.”

https://www.frontiersin.org/articles/10.3389/fnut.2021.639467/full “Network and 16S rRNA Sequencing-Combined Approach Provides Insightal Evidence of Vitamin K2 for Salt-Sensitive Hypertension”

The form of Vitamin K2 was MK-4 per its C31H40O2 molecular formula. Data wasn’t provided to calculate a human-equivalent dose for 0.025% MK-4.

This study was part of a 2022 Gut Microbial Response to Host Metabolic Phenotypes collection which included animal studies investigating gut microbiota in contexts of β-carotene and β-sitosterol supplementation. I found this collection by it citing the 2018 rodent study GLP-1 release and vagal afferent activation mediate the beneficial metabolic and chronotherapeutic effects of D-allulose which was Reference 27 of Dr. Paul Clayton’s blog post Sweet Nothing.

Signaling pathways and disordered proteins

gettingwell4 2-3 stars Required further work, Cortisol, Epigenetics, Glutamate, Immune system, Memory, Neurochemicals, Stress , , ,

This 2022 review explored the title subject:

“Cell signaling imposes many demands on proteins that comprise these pathways, including abilities to form active and inactive states, and to engage in multiple protein interactions. Signaling often requires amplifying signals, regulating or tuning responses to signals, combining information sourced from multiple pathways, all while ensuring process fidelity.

Sensitivity, adaptability, and tunability are possible, in part, due to inclusion of intrinsically disordered regions in many proteins involved in cell signaling.  This review highlights the critical role of intrinsically disordered proteins for signaling:

  • In widely diverse organisms (animals, plants, bacteria, fungi);
  • In every category of cell signaling pathway (autocrine, juxtacrine, intracrine, paracrine, and endocrine); and
  • At each stage (ligand, receptor, transducer, effector, terminator) in the cell signaling process.

Function of the glucocorticoid receptor is regulated in part by its intrinsically disordered C-terminal tail. Prior to activation, the glucocorticoid receptor resides in cytosol:

glucocorticoid receptor

Intrinsic disorder in the glucocorticoid receptor not only enables multiple allosteric regulatory interactions to impact function, but also allows deployment of different surfaces of the protein to enable binding to many different sets of macromolecules, and regulation of these interactions via mRNA splicing and phosphorylation.

Combinations of alternative translation initiation and alternative mRNA splicing result in production of multiple glucocorticoid receptor isoforms from one gene. Various isoforms exhibit distinctive tissue distribution patterns and altered transcriptional regulatory profiles.

Greater than 90% of transcription factors either contain intrinsically disordered regions of proteins or are entirely intrinsically disordered. The many advantages conferred by disorder to cell signaling cascades means that:

  1. Understanding signaling required definition of roles disorder plays in each pathway;
  2. Many more examples of disordered proteins in cell signaling pathways are likely to be discovered; and
  3. More mechanisms by which disorder functions remain to be elucidated.”

https://biosignaling.biomedcentral.com/articles/10.1186/s12964-022-00821-7 “Intrinsically disordered proteins play diverse roles in cell signaling”

Cells in vivo seldom act on their own impetus. I would have liked discussion – or at least mention – of bidirectional signals between genes / cells / tissues / organs / organism / environment. This review’s topic of cell signaling pathways excluded “interactions of complex, interconnected systems spanning hierarchical levels” as explored in An environmental signaling paradigm of aging.

Vitamin K forms

gettingwell4 4-5 stars Advanced knowledge, Epigenetics, Immune system, Stress , , ,

Two papers on Vitamin K, beginning with a 2021 review:

“Vitamin K is involved in many biological processes. Menaquinones (MK) [Vitamin K2] and phylloquinone [Vitamin K1] vary in biological activity, showing different bioavailability, half-life, and transport mechanisms.

The effective dose to decrease uncarboxylated osteocalcin was six times lower for MK-7 than for MK-4. Similarly, MK-7 affected blood coagulation system at dose three to four times lower than vitamin K1.

Both vitamin K1 and MK-7 inhibited decline in bone mineral density. However, benefits for occurrence of cardiovascular diseases have been observed only for long-chain menaquinones. There are currently no guidelines for recommended doses and forms of vitamin K in prevention of osteoporosis, atherosclerosis, and other cardiovascular disorders.”

https://www.mdpi.com/2304-8158/10/12/3136/htm “Relationship between Structure and Biological Activity of Various Vitamin K Forms”

This first paper cited a 2019 meta-analysis for:

“Vitamin K2 supplementation is a preventative measure rather than an osteoporosis treatment.

Meta-analysis of various interventions for improving BMD revealed that vitamin K2 can increase lumbar spine BMD. It ranked sixth among eighteen different single or combined interventions including Ca, vitamin D, estrogen, isoflavone and exercise.

Effect size for change in bone mineral density (BMD) using forest plots. LS, lumbar spine; D, vitamin D; Est, oestrogen; Ex, exercise; K, vitamin K; Iso, isoflavone; FN, femoral neck.

urn cambridge.org id binary-alt 20211204100437-73338-optimisedImage-S0007114519002290_fig3g

Lumbar spine:

  • Ca, vitamin D, vitamin K, oestrogen, exercise, Ca + vitamin D, vitamin D + vitamin K, and vitamin D + oestrogen were associated with significantly beneficial effects relative to no treatment.
  • Ca, vitamin D, oestrogen, and Ca + vitamin D were associated with beneficial effects compared with placebo.
  • Vitamin D + vitamin K was associated with positive effect with Ca.
  • Oestrogen, vitamin D + vitamin K, and vitamin D + oestrogen were associated with beneficial effect compared with vitamin D.
  • Ca + vitamin D + exercise had a beneficial effect compared with Ca + vitamin D.
  • Ca + oestrogen, and isoflavone + exercise were related to negative effects relative to oestrogen.

Femoral neck:

  • Ca, exercise, and vitamin D + oestrogen were associated with significant beneficial intervention effects relative to no treatment.

The present study demonstrated that many interventions were valuable for improving BMD in the LS and FN of postmenopausal women. It confirmed the need for postmenopausal women to improve BMD through preventive measures such as nutrients or oestrogen.

It also confirmed that different single or combined preventions can affect BMD at different sites in different orders. This reveals to medical and health workers and postmenopausal women which methods can be selected preferentially to prevent bone loss.”

https://doi.org/10.1017/S0007114519002290 “Impact of calcium, vitamin D, vitamin K, oestrogen, isoflavone and exercise on bone mineral density for osteoporosis prevention in postmenopausal women: a network meta-analysis”

Amazingly oblivious that this freely-available second 2019 paper has been cited only by this first paper. What recent literature is more relevant to postmenopausal women’s health?

Eat broccoli sprouts for depression, Part 2

gettingwell4 4-5 stars Advanced knowledge, Acetylcholine, Amygdala, Anterior cingulate cortex, Cerebrum, Cortisol, Dopamine, Epigenetics, Glutamate, Hippocampus, Hypothalamus, Immune system, Limbic system, Memory, Neurochemicals, Serotonin, Stress , , , , ,

Here are three papers that cited last year’s Part 1. First is a 2021 rodent study investigating a microRNA’s pro-depressive effects:

“Depressive rat models were established via chronic unpredicted mild stress (CUMS) treatment. Cognitive function of rats was assessed by a series of behavioral tests.

Nrf2 CUMS

Nrf2 was weakly expressed in CUMS-treated rats, whereas Nrf2 upregulation alleviated cognitive dysfunction and brain inflammatory injury.

Nrf2 inhibited miR-17-5p expression via binding to the miR-17-5p promoter. miR-17-5p was also found to limit wolfram syndrome 1 (Wfs1) transcription.

We found that Nrf2 inhibited miR-17-5p expression and promoted Wfs1 transcription, thereby alleviating cognitive dysfunction and inflammatory injury in rats with depression-like behaviors. We didn’t investigate the role of Nrf2 in other depression models (chronic social stress model and chronic restraint stress model) and important brain regions other than hippocampus, such as prefrontal cortex and nucleus accumbens. Accordingly, other depression models and brain regions need to be designed and explored to further validate the role of Nrf2 in depression in future studies.”

https://link.springer.com/article/10.1007/s10753-021-01554-4 “Nrf2 Alleviates Cognitive Dysfunction and Brain Inflammatory Injury via Mediating Wfs1 in Rats with Depression‑Like Behaviors” (not freely available)

This study demonstrated that activating the Nrf2 pathway inhibited brain inflammation, cognitive dysfunction, and depression. Would modulating one microRNA and one gene in vivo without Nrf2 activation achieve similar results?

A 2021 review focused on the immune system’s role in depression:

“Major depressive disorder is one of the most common psychiatric illnesses. The mean age of patients with this disorder is 30.4 years, and the prevalence is twice higher in women than in men.

Activation of inflammatory pathways in the brain is considered to be an important producer of excitotoxicity and oxidative stress inducer that contributes to neuronal damage seen in the disorder. This activation is mainly due to pro-inflammatory cytokines activating the tryptophan-kynurenine (KP) pathway in microglial cells and astrocytes.

Elevated levels of cortisol exert an inhibitory feedback mechanism on its receptors in the hippocampus and hypothalamus, stopping stimulation of these structures to restore balance. When this balance is disrupted, hypercortisolemia directly stimulates extrahepatic enzyme 2,3-indolimine dioxygenase (IDO) located in various tissues (intestine, placenta, liver, and brain) and immune system macrophages and dendritic cells.

Elevation of IDO activities causes metabolism of 99% of available tryptophan in the KP pathway, substantially reducing serotonin synthesis, and producing reactive oxygen species and nitrogen radicals. The excitotoxicity generated produces tissue lesions, and activates the inflammatory response.”

https://academic.oup.com/ijnp/article/25/1/46/6415265 “Inflammatory Process and Immune System in Major Depressive Disorder”

This review highlighted that stress via cortisol and IDO may affect the brain and other parts of the body.

A 2022 review elaborated on Part 1’s findings of MeCP2 as a BDNF inhibitor:

“Methyl-CpG-binding protein 2 (MeCP2) is a transcriptional regulator that is highly abundant in the brain. It binds to methylated genomic DNA to regulate a range of physiological functions implicated in neuronal development and adult synaptic plasticity.

Ability to cope with stressors relies upon activation of the hypothalamic–pituitary–adrenal (HPA) axis. MeCP2 has been shown to contribute to early life stress-dependent epigenetic programming of genes that enhance HPA-axis activity.

We describe known functions of MeCP2 as an epigenetic regulator, and provide evidence for its role in modulating synaptic plasticity via transcriptional regulation of BDNF or other proteins involved in synaptogenesis and synaptic strength like reelin. We conclude that MeCP2 is a promising target for development of novel, more efficacious therapeutics for treatment of stress-related disorders such as depression.”

https://www.mdpi.com/2073-4409/11/4/748/htm “The Role of MeCP2 in Regulating Synaptic Plasticity in the Context of Stress and Depression”

Osprey lunch

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Beneficially stressing sprouts with light

gettingwell4 4-5 stars Advanced knowledge, Epigenetics, Stress ,

This 2021 study investigated effects of light on red cabbage sprouts and microgreens. I’ll highlight its 3-day-old sprout findings:

“Periodic ultraviolet UV-B (280–320 nm) pulses at low doses improved morphological development of red cabbage sprouts, and probably will have the same effect on other sprouts. Similarly, total phenolic content, total flavonoid content, and total antioxidant capacity presented a UV-B dose-dependence response.

Although UV-B radiation may cause damage to plant tissues, an optimum dose can promote accumulation of antioxidant and UV-protective molecules that enhance nutraceutical biosynthesis in plant foods without altering sensory quality. Such an increase in concentration of bioactive compounds is mainly due to environmental stress generated by UV-B light, which leads to changes in morphology, physiology, and molecular conformation of DNA, RNA, and proteins.

red cabbage sprout phenolics

Total phenolic content of control (0, CTRL) or UV-B-treated (5, 10, and 15 kJ m−2) red cabbage sprouts after 10 days growth at 20 °C. Different capital letters indicate significant differences among treatments at < 0.05. Different lowercase letters indicate significant differences among time of analysis of the same treatment at p < 0.05.

Our results demonstrated that application of UV-B light during germination induces a positive effect on growth of red cabbage sprouts, as well as on secondary metabolite content related to nutritional quality. Analysed bioactive compounds (phenolics, flavonoids, and carotenoids) increased during germination, and tended to remain constant throughout a refrigerated shelf life.”

https://www.mdpi.com/2311-7524/7/12/567/htm “UV-B Radiation as Abiotic Elicitor to Enhance Phytochemicals and Development of Red Cabbage Sprouts”

I came across this study after lead author Dr. Lorena Martínez-Zamora provided an earlier study, Postharvest UV-B and UV-C radiation enhanced the biosynthesis of glucosinolates and isothiocyanates in Brassicaceae sprouts (not freely available). Its focus was also a worthwhile commercialization of cruciferous microgreens.

Nearby researchers also published studies such as Red cabbage effects on gut microbiota and Sprout bioaccessibility last year. Let’s hope a push for cruciferous sprouts and microgreens continues, although consumer acceptance is limited by products not being sweet.

I think these research efforts will succeed. Take a look at oat milk’s quick rise, for example. I had trouble getting delivery of Avena sativa seeds last month because oat milk producers bought up last year’s supplies and futures on this year’s crops.

For me, it’s been 98 weeks of spending at least 45 minutes a day growing 3-day-old broccoli, red cabbage, mustard, and oat sprouts at home. I’m satisfied with results, and won’t turn my kitchen into a laboratory to eke out extra effects with light and other elicitors.

Here’s a photo of this study’s sponsoring institution’s harbor from the latest of two visits:

IMG_20170611_125837

I’d like to return whenever we individually stop being herded and recover our sanity.

Your thymus and calories

gettingwell4 4-5 stars Advanced knowledge, Epigenetics, Immune system, Stress ,

This 2022 paper studied caloric restriction in humans followed up by rodent experiments:

“Extension of lifespan driven by 40% caloric restriction (CR) in rodents causes trade-offs in growth, reproduction, and immune defense that make it difficult to identify therapeutically relevant CR-mimetic targets. We report that about 14% CR for 2 years in healthy humans improved thymopoiesis.

thymus cr

Expression of the gene PLA2G7 is inhibited in humans undergoing CR. Deletion of Pla2g7 in mice showed decreased thymic lipoatrophy, protection against age-related inflammation, lowered NLRP3 inflammasome activation, and improved metabolic health.

Twenty-four-month-old PLA2G7-deficient mice (analogous to ~70-year-old humans) had larger thymi and higher thymocyte abundance, and were protected from age-related thymic involution.

thymus mice

We propose that reduction of PLA2G7 caused by CR in humans might contribute to better adipose tissue metabolism, lower inflammation, and reduced thymic lipoatrophy.”

https://www.science.org/doi/10.1126/science.abg7292 “Caloric restriction in humans reveals immunometabolic regulators of health span” (not freely available). Thanks to Dr. Alexander Predeus for providing a copy.

I would have liked rodent experiments to continue another year or so to determine the control group’s and PLA2G7-deficient group’s healthspans and lifespans. These researchers could have strengthened their findings if increased healthspans also increased lifespans.

CD38 and balance

gettingwell4 4-5 stars Advanced knowledge, Cerebellum, Cerebrum, Epigenetics, Glutamate, Hippocampus, Hypothalamus, Immune system, Limbic system, Lower brain, Neurochemicals, Stress, Telomeres , , ,

I’ll highlight this 2022 review’s relationships between inflammation and cluster of differentiation 38:

“We review the nicotinamide adenine dinucleotide (NAD) catabolizing enzyme CD38, which plays critical roles in pathogenesis of diseases related to infection, inflammation, fibrosis, metabolism, and aging.

NAD is a cofactor of paramount importance for an array of cellular processes related to mitochondrial function and metabolism, redox reactions, signaling, cell division, inflammation, and DNA repair. Dysregulation of NAD is associated with multiple diseases. Since CD38 is the main NADase in mammalian tissues, its contribution to pathological processes has been explored in multiple disease models.

CD38 is upregulated in a cell-dependent manner by several stimuli in the presence of pro-inflammatory or secreted senescence factors or in response to a bacterial infection, retinoic acid, or gonadal steroids. CD38 is stimulated in a cell-specific manner by lipopolysaccharide, tumor necrosis factor alpha, interleukin-6, and interferon-γ.

dysregulated inflammation

CD38 plays a critical role in inflammation, migration, and immunometabolism, but equally important is resolution of the inflammatory response which left unchecked leads to loss of self-tolerance, tissue infiltration of lymphocytes, and circulation of autoantibodies.

  • Depending upon context, CD38 can either promote or protect against an autoimmune response.
  • Chronic mucosal inflammation and tissue damage characteristic of inflammatory bowel disease predisposes IBD patients to development of colorectal cancer, and the risks increase with duration, extent, and severity of inflammation.
  • Pulmonary fibrosis occurs in the presence of unresolved inflammation and dysregulated tissue repair, and results from an array of injurious stimuli including infection, toxicant exposure, adverse effects of drugs, and autoimmune response.
  • Modulating CD38 and NAD levels in kidney disease may provide therapeutic approaches for prevention of inflammatory conditions of the kidney.
  • Inflammation as well as evidence of senescence are present in pathophysiology of chronic liver diseases that progress to cirrhosis.
  • Inflammation-associated metabolic diseases impair vascular function. Chronic inflammation can lead to vascular senescence and dysfunction.

One cause of NAD decline during aging is due to increase of NAD breakdown in the presence of increased CD38 expression and activity on immune cells, thus linking inflammaging with tissue NAD decline. Other sources of NAD decline include increased DNA-damage requiring PARP1 activation, and decreased NAMPT levels leading to diminished NAD synthesis through the salvage pathway.

Inflammation is among the major risk factors that predispose organisms to age-associated diseases. During aging, accumulation of senescent cells creates an environment rich in proinflammatory signals, leading to ‘inflammaging.’ Metabolically active cells lose their replicative capacity by entering an irreversible quiescent state, and are considered both a cause and a consequence of inflammaging.

Recent findings uncover a major role of CD38 in inflammation and senescence, showing that age-related NAD+ decline and the sterile inflammation of aging are partially mediated by a senescence / senescence associated secretory phenotype (SASP)-induced accumulation of CD38+ inflammatory cells in tissues. Given the clear association between the phenomenon of inflammaging, senescence, and CD38, as well as the impact of CD38 on degradation of NAD and the NAD precursor NMN, future studies should focus on CD38 as a druggable target in viral illnesses.”

https://journals.physiology.org/doi/abs/10.1152/ajpcell.00451.2021 “The CD38 glycohydrolase and the NAD sink: implications for pathological conditions”

We extend good-vs.-bad thinking to nature. Does that paradigm explain much, though?

All pieces of a puzzle are important. Otherwise, evolution would have eliminated what wasn’t necessary for its purposes.

Restoring balance to an earlier phenotype suits my purposes. Don’t want to eliminate inflammatory responses, but instead, calm them down so that they’re evoked appropriately.

Studying AGEs and neurodegeneration

gettingwell4 4-5 stars Advanced knowledge, Epigenetics, Immune system, Memory, Stress , , , , ,

This 2022 review suggested more effective ways to conduct in vitro studies of advanced glycation end products (AGEs) and neurodegenerative diseases:

“The main goal of this review was to present and discuss in vitro models that were applied or have the potential to be used in research on AGEs and ND.

  • We introduced and explained current knowledge on AGEs regarding their formation and accumulation in humans.
  • We presented existing evidence linking involvement of AGEs in ND and explained basic concepts of brain physiology and immunology affected by AGEs.
  • We presented and discussed available in vitro models to study AGE-mediated neurodegeneration by dividing them into sections from simple models. These have been applied to more complex models that have not been yet applied in the field of AGEs, but offer opportunities.
  • We gathered advisable in vitro tools based on their relevance to three primary endpoints that AGEs can impact brain pathophysiology and their characteristics and suitability to mimic ND pathophysiology.

nutrients-14-00363-g002

Several studies have indicated intracellular formation of AGEs by microglia or neurons, but identification of intracellular AGEs in those cases is made by immunoassays, which have received much criticism regarding their reliability to identify and quantify AGEs. Concerns about these techniques are mostly related to undefined specificity and affinity of anti-AGE antibodies.

The source of observed AGE accumulation in the brain of patients (dietary or endogenous) is not yet fully understood. For that reason, studies on AGE digestion and absorption (i.e., in vitro digestion models) are crucial to understanding the type of dietary AGEs that will circulate and cross the BBB to reach the brain.

On the other hand, endogenous AGEs can also be formed due to increased glucose levels derived from a high glycemic diet. Highly reactive molecules in the brain can contribute to locally produced AGEs extracellularly or intracellularly.

Clinical studies mainly focus on the fate and metabolism of dietary AGEs. Exposure based on consumption of certain foods is difficult to translate to a concentration that cells are going to be exposed to. The complexity and multiple sources of protein glycation require application of in vitro models to understand potential contribution to neurodegeneration.”

https://www.mdpi.com/2072-6643/14/2/363/htm “In Vitro Methodologies to Study the Role of Advanced Glycation End Products (AGEs) in Neurodegeneration”

While we’re waiting for research to catch up, we can hedge neurodegenerative disease bets by:

  • Not spiking our blood glucose levels;
  • Avoiding foods with medium and high levels of AGEs;
  • Giving our gut microbiota the intake they need instead of what our unconscious programming dictates; and
  • Maintaining youthful activities.

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