Human gut bacteria produce ΤΗ17-modulating bile acid metabolites

Bile acids are steroid-like natural products that are secreted into the gastrointestinal (GI) tract of vertebrate animals after eating — where they act as “detergents” that aid in digestion, as well as ligands for host receptors. In the gut, host-derived primary bile acids are metabolized by resident microbes to form a large group of compounds called secondary bile acids. Both primary and secondary bile acids regulate host metabolism and immune responses. [As ligands for receptors, bile acids represent “extracellular signals,” which then elicit various responses in particular cell-types of the host. This is why the attached article is relevant to gene-environment interactions.] 😉

Bile acids modulate the differentiation and function of T cells, including pro-inflammatory TH17 cells and anti-inflammatory regulatory T (Treg) cells, which help to protect the host against extracellular pathogens and to maintain host immune tolerance, respectively. Specifically, secondary bile acids — such as isoallo-lithocholic acid (isoalloLCA) and iso-deoxycholic acid (isoDCA) — modulate the differentiation of Treg cells. Moreover, 3-oxoLCA inhibits TH17 cell differentiation by blocking the function of the nuclear hormone receptor retinoic-acid-receptor-related orphan nuclear receptor-γt (RORγt).

3-OxoLCA is absent from the caecum of germ-free C57BL/6 mice — suggesting that gut bacteria may synthesize 3-oxoLCA. However, it is not known which commensal [i.e., the relationship between individuals of two species in which one species obtains food or other benefits from the other without either harming or benefiting the latter] bacterial species, and which bacterial enzyme(s) produce(s) 3-oxoLCA, and whether this compound (or additional secondary bile acids) that modulate TH17 cell responses) are implicated in the pathogenesis of inflammatory bowel disease (IBD).

In the attached paper, authors used a screen of human stool isolates to identify the gut bacterial species that produces 3-oxoLCA, as well as an abundant gut metabolite, isolithocholic acid (isoLCA); authors go on to demonstrate these metabolites inhibit TH17 cell differentiation. Multi-omics analyses of two IBD registries revealed that 3-oxoLCA and isoLCA, as well as the bacterial genes responsible for their production, are negatively associated with IBD and TH17-cell-related host gene expression. Taken together, these data suggest that bacterial production of the “3-oxoLCA and isoLCA bile acids” may contribute clinically to gut immune homeostasis in humans.
Recall that: The genetic architecture [i.e., total landscape of genetic contributions to a given phenotype] represents the contribution of: [a] genetics [DNA sequence differences], [b] epigenetics [DNA methylation, RNA-interference, histone modification, and/or chromatin remodeling — all processes that do not alter DNA sequence], [c] environmental factors, [d] endogenous influences, and [e] the interindividual microbiome. This topic [attached paper] suggests that a trait such as “individual risk of IBD” might be affected by at least three, if not all five, of these categories…!! 😊
DwN

Nature 31 Mar 2022; 603: 907-912

COMMENT: This discussion is a great gene-environmental interaction. Hope all is well. JB

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“Completing” the human genome (this time, for real ??)

From: Nebert, Daniel (nebertdw)
Sent: den 9 maj 2022 00:25
Subject: “Completing” the human genome (this time, for real ??) #2

The attached articles accompany the “human genome sequence story” — sent to everyone within the past hour. From left to right: [a] Identification of segmental duplications; [b] Genomic and epigenetic maps of centromeres; [c] The transcriptional and epigenetic state of repeat elements; and [d] Epigenetic patterns throughout the entire completed human genome. 😊DwN

Science, 1 Apr 2022; 376: 55, 56, 57 and 58

Since its initial release in April of 2000, the human reference genome had covered only the euchromatic fraction of the genome [euchromatin is the lightly packed form of chromatin (DNA, RNA, and protein) that is enriched in genes, and is often (but not always) under active transcription].

This leaves the important heterochromatic regions (tightly packed form of chromatin) unfinished. Completing the remaining 8% of the genome [see attached article], the Telomere-to-Telomere (T2T) Consortium now presents the complete 3.055 billion–base pair sequence of a human genome (T2T-CHM13) which: [a] includes gapless assemblies for all chromosomes except Y, [b] corrects errors in the prior references, and [c] introduces nearly 200 million new base pairs (bp) of sequence — containing 1,956 new gene predictions, 99 of which are predicted to be protein-coding.

The completed regions [see attached] include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric (i.e., the centromere is situated so that one chromosomal arm is much shorter than the other arm) chromosomes, unlocking these complex regions of the genome — so that variational and functional studies can now be carried out.

The current human reference genome was released by the Genome Reference Consortium (GRC) in 2013, and most recently patched in 2019 (GRCh38.p13). This reference traces its origin to the publicly-funded Human Genome Project and has been continually improved over the past two decades. Unlike the competing Celera company effort, and most modern sequencing projects based on “shotgun” sequence assembly, the GRC assembly was constructed from sequenced bacterial artificial chromosomes (BACs) that were ordered and oriented along the human genome by means of radiation hybrid, genetic linkage, and fingerprint maps.

However, limitations of BAC cloning have led to an underrepresentation of repetitive sequences, and the opportunistic assembly of BACs derived from multiple individuals resulted in a mosaic of haplotypes. As a result, several GRC assembly gaps are unsolvable — because of incompatible structural polymorphisms on their flanks, and many other repetitive and polymorphic regions were left unfinished, or incorrectly assembled.

To finish the last remaining regions of the genome, authors leveraged the complementary aspects of PacBio HiFi and Oxford Nanopore ultralong-read sequencing to assemble the uniformly homozygous CHM13hTERT cell line (hereafter, CHM13). The resulting T2T-CHM13 reference assembly removes a 20-year-old barrier that had hidden 8% of the genome from sequence-based analysis — including all centromeric regions and the entire short arms of five human acrocentric chromosomes. Authors describe [see attached] the construction, validation, and initial analysis of a truly complete human reference genome and discuss its potential impact on the field. 😊

COMMENT: The BIG question, now, becomes — “Because we have knowledge of ‘this last 8% of the genome’ that has been unavailable until now, do all important GWAS studies need to be repeated?”DwN
COMMENT: Great, many thanks! MI-S
ADDED:
Since its initial release in April of 2000, the human reference genome had covered only the euchromatic fraction of the genome [euchromatin is the lightly packed form of chromatin (DNA, RNA, and protein) that is enriched in genes, and is often (but not always) under active transcription].
This leaves the important heterochromatic regions (tightly packed form of chromatin) unfinished. Completing the remaining 8% of the genome [see attached article], the Telomere-to-Telomere (T2T) Consortium now presents the complete 3.055 billion–base pair sequence of a human genome (T2T-CHM13) which: [a] includes gapless assemblies for all chromosomes except Y, [b] corrects errors in the prior references, and [c] introduces nearly 200 million new base pairs (bp) of sequence — containing 1,956 new gene predictions, 99 of which are predicted to be protein-coding.
The completed regions [see attached] include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric (i.e., the centromere is situated so that one chromosomal arm is much shorter than the other arm) chromosomes, unlocking these complex regions of the genome — so that variational and functional studies can now be carried out.

The current human reference genome was released by the Genome Reference Consortium (GRC) in 2013, and most recently patched in 2019 (GRCh38.p13). This reference traces its origin to the publicly-funded Human Genome Project and has been continually improved over the past two decades. Unlike the competing Celera company effort, and most modern sequencing projects based on “shotgun” sequence assembly, the GRC assembly was constructed from sequenced bacterial artificial chromosomes (BACs) that were ordered and oriented along the human genome by means of radiation hybrid, genetic linkage, and fingerprint maps.

However, limitations of BAC cloning have led to an underrepresentation of repetitive sequences, and the opportunistic assembly of BACs derived from multiple individuals resulted in a mosaic of haplotypes. As a result, several GRC assembly gaps are unsolvable — because of incompatible structural polymorphisms on their flanks, and many other repetitive and polymorphic regions were left unfinished, or incorrectly assembled.

To finish the last remaining regions of the genome, authors leveraged the complementary aspects of PacBio HiFi and Oxford Nanopore ultralong-read sequencing to assemble the uniformly homozygous CHM13hTERT cell line (hereafter, CHM13). The resulting T2T-CHM13 reference assembly removes a 20-year-old barrier that had hidden 8% of the genome from sequence-based analysis — including all centromeric regions and the entire short arms of five human acrocentric chromosomes. Authors describe [see attached] the construction, validation, and initial analysis of a truly complete human reference genome and discuss its potential impact on the field. 😊
Science, 1 Apr 2022; 376: 44-53

ADDED: The attached articles accompany the “human genome sequence story.” From left to right: [a] Identification of segmental duplications; [b] Genomic and epigenetic maps of centromeres; [c] The transcriptional and epigenetic state of repeat elements; and [d] Epigenetic patterns throughout the entire completed human genome. 😊

DwN

Science, 1 Apr 2022; 376: 55, 56, 57 and 58

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“Life” on Earth can be weird (!!!)

Two miles underground, strange bacteria are found thriving
by Chad Boutin
Oct. 20, 2006

A Princeton-led research group has discovered an isolated community of bacteria nearly two miles underground that derives all of its energy from the decay of radioactive rocks rather than from sunlight. According to members of the team, the finding suggests life might exist in similarly extreme conditions even on other worlds.

The self-sustaining bacterial community, which thrives in nutrient-rich groundwater found near a South African gold mine, has been isolated from the Earth’s surface for several million years. It represents the first group of microbes known to depend exclusively on geologically produced hydrogen and sulfur compounds for nourishment. The extreme conditions under which the bacteria live bear a resemblance to those of early Earth, potentially offering insights into the nature of organisms that lived long before our planet had an oxygen atmosphere.

The scientists, who hail from nine collaborating institutions, had to burrow 2.8 kilometers beneath our world’s surface to find these unusual microbes, leading the scientists to their speculations that life could exist in similar circumstances elsewhere in the solar system.

“What really gets my juices flowing is the possibility of life below the surface of Mars,” said Tullis Onstott, a Princeton University professor of geosciences and leader of the research team. “These bacteria have been cut off from the surface of the Earth for many millions of years, but have thrived in conditions most organisms would consider to be inhospitable to life. Could these bacterial communities sustain themselves no matter what happened on the surface? If so, it raises the possibility that organisms could survive — even on planets whose surfaces have long since become lifeless.”

Onstott’s team published its results in the Oct. 20 issue of the journal Science. The research group includes first author Li-Hung Lin, who performed many of the analyses as a doctoral student at Princeton and then as a postdoctoral researcher at the Carnegie Institution.

“These bacteria are truly unique, in the purest sense of the word,” said Lin, now at National Taiwan University. “We know how isolated the bacteria have been because analyses of the water that they live in showed that it’s very old and hasn’t been diluted by surface water. In addition, we found that the hydrocarbons in the environment did not come from living organisms, as is usual, buet rather that the source of the hydrogen needed for their respiration comes from the decomposition of water by radioactive decay of uranium, thorium and potassium.”

Because the groundwater the team sampled to find the bacteria comes from several different sources, it remains difficult to determine specifically how long the bacteria have been isolated. The team estimates the time frame to be somewhere between three and 25 million years, implying that living things are even more adaptable than once thought.

“We know surprisingly little about the origin, evolution and limits for life on Earth,” said biogeochemist Lisa Pratt, who led Indiana University Bloomington’s contribution to the project. “Scientists are just beginning to study the diverse organisms living in the deepest parts of the ocean, and the rocky crust on Earth is virtually unexplored at depths more than half a kilometer below the surface. The organisms we describe in this paper live in a completely different world than the one we know at the surface.”

That subterranean world, Onstott said, is a lightless pool of hot, pressurized salt water that stinks of sulfur and noxious gases humans would find unbreathable. But the newly discovered bacteria, which are distantly related to the Firmicutes division of microbes that exist near undersea hydrothermal vents, flourish there.

“The radiation allows for the production of lots of sulfur compounds that these bacteria can use as a high-energy source of food,” Onstott said. “For them, it’s like eating potato chips.”

But the arrival of the research team brought one substance into the underground world that, though vital to human survival, proved fatal to the microbes — air from the surface.

“These critters seem to have a real problem with being exposed to oxygen,” Onstott said. “We can’t seem to keep them alive after we sample them. But because this environment is so much like the early Earth, it gives us a handle on what kind of creatures might have existed before we had an oxygen atmosphere.”

Onstott said that many hundreds of millions of years ago, some of the first bacteria on the planet may have thrived in similar conditions, and that the newly discovered microbes could shed light on research into the origins of life on Earth.

“These bacteria are probably close to the base of the tree for the bacterial domain of life,” he said. “They might be genealogically quite ancient. To find out, we will need to compare them to other organisms such as Firmicutes and other such heat-loving creatures from deep-sea vents or hot springs.”

The research team is building a small laboratory 3.8 kilometers beneath the surface in the Witwatersrand region of South Africa to conduct further study of the newly discovered ecosystem, said Onstott, who hopes the findings will be of use when future space probes are sent to seek life on other planets.

“A big question for me is, how do these creatures sustain themselves?” Onstott said. “Has this one strain of bacteria evolved to possess all the characteristics it needs to survive on its own, or are they working with other species of bacteria? I’m sure they will have more surprises for us, and they may show us one day how and where to look for microbes elsewhere.”

Other authors of this work include Johanna Lipmann-Pipke of GeoForschungsZentrum, Potsdam, Germany; Erik Boice of Indiana University; Barbara Sherwood Lollar of the University of Toronto; Eoin L. Brodie, Terry C. Hazen, Gary L. Andersen and Todd Z. DeSantis of Lawrence Berkeley National Laboratory, Berkeley, Calif.; Duane P. Moser of the Desert Research Institute, Las Vegas; and Dave Kershaw of the Mponeng Mine, Anglo Gold, Johannesburg, South Africa.

Pratt and Onstott have collaborated for years as part of the Indiana-Princeton-Tennessee Astrobiology Institute (IPTAI), a NASA-funded research center focused on designing instruments and probes for life detection in rocks and deep groundwater on Earth during planning for subsurface exploration of Mars. IPTAI’s recommendations to NASA will draw on findings discussed in the Science report.

This work was also supported by grants from the National Science Foundation, the U.S. Department of Energy, the National Science Council of Taiwan, the Natural Sciences and Engineering Research Council of Canada, Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) and the Killam Fellowships Program.

More information about this discovery can be found at http://newsinfo.iu.edu/news/page/normal/4229.html and http://www.carnegieinstitution.org/news_releases/news_2006_1019.html

Abstract:

Long-Term Sustainability of a High-Energy, Low-Diversity Crustal Biome

By Li-Hung Lin, Pei-Ling Wang, Douglas Rumble, Johanna Lippmann-Pipke, Erik Boice, Lisa M. Pratt, Barbara Sherwood Lollar, Eoin L. Brodie, Terry C. Hazen, Gary L. Andersen, Todd Z. DeSantis, Duane P. Moser, Dave Kershaw, and T. C. Onstott

Geochemical, microbiological, and molecular analyses of alkaline saline groundwater at 2.8 kilometers depth in Archaean metabasalt revealed a microbial biome dominated by a single phylotype affiliated with thermophilic sulfate reducers belonging to Firmicutes. These sulfate reducers were sustained by geologically-produced sulfate and hydrogen at concentrations sufficient to maintain activities for millions of years with no apparent reliance on photosynthetically-derived substrates.

https://www.princeton.edu/news/2006/10/20/two-miles-underground-strange-bacteria-are-found-thriving

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Microbes deep beneath seafloor survive on byproducts of radioactive process
Results have implications for life on Mars
NARRAGANSETT, R.I. – February 26, 2021 – A team of researchers from the University of Rhode Island’s Graduate School of Oceanography and their collaborators have revealed that the abundant microbes living in ancient sediment below the seafloor are sustained primarily by chemicals created by the natural irradiation of water molecules.

The team discovered that the creation of these chemicals is amplified significantly by minerals in marine sediment. In contrast to the conventional view that life in sediment is fueled by products of photosynthesis, an ecosystem fueled by irradiation of water begins just meters below the seafloor in much of the open ocean. This radiation-fueled world is one of Earth’s volumetrically largest ecosystems.

The research was published today in the journal Nature Communications.

“This work provides an important new perspective on the availability of resources that subsurface microbial communities can use to sustain themselves. This is fundamental to understand life on Earth and to constrain the habitability of other planetary bodies, such as Mars,” said Justine Sauvage, the study’s lead author and a postdoctoral fellow at the University of Gothenburg who conducted the research as a doctoral student at URI.

The process driving the research team’s findings is radiolysis of water – the splitting of water molecules into hydrogen and oxidants as a result of being exposed to naturally occurring radiation. Steven D’Hondt, URI professor of oceanography and a co-author of the study, said the resulting molecules become the primary source of food and energy for the microbes living in the sediment.

“The marine sediment actually amplifies the production of these usable chemicals,” he said. “If you have the same amount of irradiation in pure water and in wet sediment, you get a lot more hydrogen from wet sediment. The sediment makes the production of hydrogen much more effective.”

Why the process is amplified in wet sediment is unclear, but D’Hondt speculates that minerals in the sediment may “behave like a semiconductor, making the process more efficient.”

The discoveries resulted from a series of laboratory experiments conducted in the Rhode Island Nuclear Science Center. Sauvage irradiated vials of wet sediment from various locations in the Pacific and Atlantic Oceans, collected by the Integrated Ocean Drilling Program and by U.S. research vessels. She compared the production of hydrogen to similarly irradiated vials of seawater and distilled water. The sediment amplified the results by as much as a factor of 30.

“This study is a unique combination of sophisticated laboratory experiments integrated into a global biological context,” said co-author Arthur Spivack, URI professor of oceanography.

The implications of the findings are significant.

“If you can support life in subsurface marine sediment and other subsurface environments from natural radioactive splitting of water, then maybe you can support life the same way in other worlds,” said D’Hondt. “Some of the same minerals are present on Mars, and as long as you have those wet catalytic minerals, you’re going to have this process. If you can catalyze production of radiolytic chemicals at high rates in the wet Martian subsurface, you could potentially sustain life at the same levels that it’s sustained in Earth’s marine sediment.”

Sauvage added, “This is especially relevant — given that the Perseverance Rover has just landed on Mars, with its mission to collect Martian rocks and to characterize its habitable environments.”

D’Hondt said the research team’s findings also have implications for the nuclear industry, including for how nuclear waste is stored and how nuclear accidents are managed. “If you store nuclear waste in sediment or rock, it may generate hydrogen and oxidants faster than in pure water. That natural catalysis may make those storage systems more corrosive than is generally realized,” he said.

The next steps for the research team will be to explore the effect of hydrogen production through radiolysis in other environments on Earth and beyond, including oceanic crust, continental crust and subsurface Mars. They also will seek to advance the understanding of how subsurface microbial communities live, interact and evolve — when their primary energy source is derived from the natural radiolytic splitting of water.

This study was supported by the U.S. National Science Foundation and the U.S. National Aeronautics and Space Administration. The project is also affiliated with the Center for Dark Energy Biosphere Investigations.

URI researchers: Microbes deep beneath seafloor survive on byproducts of radioactive process

COMMENT: In discussions with evolutionary biologists, we learned recently that “not all animals and fungi use oxygen and give off carbon dioxide”; and, on the other hand, “not all plants use carbon dioxide and give off oxygen.” It turns out there are exceptions — if one includes deviations seen in bacteria.

The first article below (posted in 2006) noted that “some baceria live off radioactive decay in rocks” — which were discovered deep in South African gold mines. The second article below (posted in 2021) noted that “some microbes that live in the marine sediment use chemicals that are made from the irradiation of water — hydrogen and oxidants created when naturally-occurring radiation splits apart water molecules.”

It had been thought that “most marine-sediment microbes lived off the products of photosynthesis” — but it looks like these types of indirectly-radiation-fed microbes are extremely common — and may even be dominant in the seafloor. Time to change the biology textbooks. Life is getting more complicated, and weird. ☹ ☹ 😊 😊

DwN

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The SOLVAY Prize recognizes the mRNA pioneer whose findings led to the mRNA COVID vaccines

This brief story, published in Nature — represents the follow-up of Dr. Katalin Karikó, an obscure scientist quietly working alone in the lab, who first designed an mRNA construct that was successful in having intact messenger RNA (mRNA) enter living cells, without getting quickly degraded by RNase enzymes; following successful entry into the cell, the new mRNA construct could then be successfully translated into the protein product by the cell’s own machinery.

As GEITP has discussed in earlier emails over the past 2 years, many labs (including my own, between 1976 and 1984) had repeatedly attempted to insert RNA into live cells and have it function normally — before it was very rapidly degraded by RNases. No one was successful — until Dr. Karikó thought up a clever way to avoid RNase degradation. 😊

It’s good to see that her creative work has now been recognized and rewarded. 😊😊
DwN
CHEMISTRY PRIZE RECOGNIZES mRNA PIONEER
THE SOLVAY PRIZE acknowledges innovative work that has a major social impact. Her ground-breaking work on RNA led to an entirely new type of vaccine — yet Katalin Karikó spent most of her career in obscurity, searching for funding to support her research. Without a faculty position or a lab group, she had to do most of the benchwork herself, including even defrosting the lab freezer!
However, she describes those times of quietly getting on with work as a joy. “It was only from the outside that it seems like a struggle,” she says.“I have had a lot of fun in the lab.”
Now an adjunct professor at the University of Pennsylvania — and Senior Vice President at BioNTech — Karikó is feted as one of the heroes of the COVID-19 pandemic. Her decades of research into messenger RNA (mRNA) paved the way for the vaccines developed by BioNTech, Pfizer and Moderna.
Karikó’s contribution has now been recognized by her being awarded the 2022 Solvay Prize. The prize is awarded every two years for major scientific discoveries — those with the potential to shape tomorrow’s chemistry and enhance human progress. Past winners include the biochemist Carolyn Bertozzi, for inventing ‘bioorthogonal’ chemical reactions that can be performed in living cells, and Nobel laureate Ben Feringa, for creating molecular motors that could power nanorobots. “When I look at the people who previously won the Solvay Prize, I feel very humbled,” says Karikó.
A QUIET BREAKTHROUGH
In vitro-transcribed (IVT) mRNA encoding therapeutic proteins, or viral antigens, has had great potential for treating or preventing various diseases, but for years the body’s inflammatory response to mRNA hampered its medical use. In 2005, while collaborating with Drew Weissman, also at U Penn, Karikó discovered that swapping out uridine for pseudouridine, a nucleoside naturally found in RNA, not only thwarted the immune reaction to mRNA, but also improved its translational efficiency, opening the door for future therapeutics.

Despite the importance that this discovery would later have, there was initially little response from other scientists. “Nobody really contacted us; I had two invitations to give lectures, but that was about it,” Karikó recalls. Over time, RNA became increasingly popular for vaccine developers, building on Karikó’s research. Although no RNAvaccines had been approved when COVID-19 first struck, candidates based on the viral sequence were ready within weeks and were quickly produced for clinical trials.

‘MY HOBBY IS SCIENCE’
This year’s prize coincides with the 100th anniversary of the first Solvay Conference for Chemistry, which brought together many leading figures to discuss the key problems of the day. The conference — along with its counterpart in physics — was created by Ernest Solvay, who wanted to support fundamental science after making his fortune through industrial production of sodium carbonate for use in glass manufacturing. He created Solvay in 1863, and the company continues to develop and support innovative science for solving some of the world’s most pressing challenges. “With the Solvay Prize, we want to highlight the originality of the chemistry and its potential impact,” says Patrick Maestro, Scientific Director of Solvay. “Karikó’s work has already had a significant impact, and there is even more to come in other areas of medicine.” Karikó says that she will spend the €300,000 prize money on furthering research into mRNA therapeutics: “I am 67 years old; I won’t start changing my hobbies now. My hobby is science.”

Nature 21 Apr 2002; 604: i (first page of journal avertisements)

COMMENT: Dan,
It is my understanding that Dr. Katalin Karikó was demoted at the University of Pennsylvania, because she had repeatedly failed to get her own research grant money. The study sections told her that “her ideas (her research proposals) were not possible.”
By the way, Dr. Karikó’s daughter competed in The World Olympics Games two times, four years apart, as a member of the U.S. Women’s Rowing Team, and they won gold medals both times!

COMMENT: Nancy,

You make a good point/comment (and it’s worth an informative, educational reply). 😉 I’m sure a lot of our GEITP’ers do not know the “chemical structure of pseudouridine.” Pseudouridine (abbreviated by the Greek letter psi, Ψ) is an isomer of the nucleoside uridine in which the uracil is attached via a carbon-carbon instead of a nitrogen-carbon glycosidic bond. (In this configuration, uracil is sometimes referred to as “pseudouracil.”)
Frontiers | The Critical Contribution of Pseudouridine to mRNA COVID-19 Vaccines | Cell and Developmental Biology

As Dr. Karikó stated in her recent invited review [Nature Reviews Immunology 2021; volume 21, page 619], “In the 1990s, we started to investigate mRNA as a platform for protein replacement therapy. Because these mRNAs encoded self-proteins, we did not think that mRNA transfection would generate any adverse immune effects. However, we found that transfecting human dendritic cells (DCs) with mRNA, or even with non-coding ribonucleotide homopolymers, induced inflammatory cytokines (Ni, H. et al., 2002).

“At the time, we knew that DNA activates Toll-like receptor 9 (TLR9) and that double-stranded RNA can activate TLR3 and induce type I interferon. We hypothesized that one of the remaining TLR family members might sense single-stranded RNA. We also started to explore the activation of human DCs by different types of RNA to determine whether they all induce inflammatory cytokines. Natural RNAs are synthesized from the four basic nucleotides, but some of the nucleosides can be post-transcriptionally modified. We found that tRNA, which is known to be enriched in modified nucleosides, was non-inflammatory, and that the TLR7 and TLR8 receptors can sense single-stranded RNA. We set out to generate RNA with modified nucleosides by in vitro synthesis. Surprisingly, the replacement of uridine with pseudouridine rendered the RNAs non-immunogenic (Karikó, K. et al., 2005).

“In subsequent studies we demonstrated that mRNA containing pseudouridine was an ideal molecule for protein replacement therapy because it was efficiently translated and, unlike its unmodified counterpart, did not induce interferon in mice. Indeed, the injection of a small amount of mRNA was sufficient for the encoded protein to exert its therapeutic effect (Karikó, K. et al., 2008; Karikó, K. et al., 2012).”

So, there you have it — in a nutshell. 😊—DwN

COMMENT: From: NK
Sent: Tuesday, April 26, 2022 5:30 PM
What a great story!! I had never heard of pseudouridine!

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LNT History documentary

Over the years, GEITP has repeatedly covered all of Ed Calabrese’s articles — as he slowly unraveled the entire fraudulent story of how the Linear No-Threshold (LNT) Model was arrived at in the mid 1950s, how it was based on erroneously interpreted Drosophila (fruit fly) studies by Hermann Joseph Muller (and others) in the 1930s and 1940s, and how the Nobel Prize in Physiology or Medicine in 1946 was awarded (nevertheless) to Muller “for discovery of the production of mutations by means of x-ray irradiation” — when the mutations were, in fact, irradiation-induced DNA damage (breaks) and not mutations at all. ☹

Online [click on URL below] one can follow 22 Episodes [interviews of Professor Calabrese by the Health Physics Society (HPS)] of this fraudulent story, which was discovered by sleuth Calabrese. These 22 interviews could conveniently provide the basis for a Term Course in any college or university — on how the second-ranked most expensive duplicitous pseudoscience has cost taxpayers of the Western World billions of dollars, how it is still supported today ( !! ) by government agencies such as the U.S. Environmental ‘Protection’ Agency (USEPA), and how it continues in thousands of labs worldwide even today — more than 60 years later. ☹

What is the first-ranked most expensive duplicitous pseudoscience costing taxpayers of the Western World trillions of dollars? Answer: the “Global Warming” scam [which began as a political movement in the early 1980s, and then changed its name to “Climate Change” in 2009, because the brief warming period of 1980-97 had ‘unfortunately’ appeared to reach a plateau in the late ’90s]. Also, the warming period of 1928-45 was actually hotter, worldwide, than the late-20th-century warming period. In between (1945-78) was (you guessed it) the 20th-century worldwide cooling period. ☹

DwN

The History of the LNT Episode Guide (hps.org)

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Possible association between glyphosate exposure and autism spectrum disorder (ASD)

Human complex diseases represent a phenotype (trait) that reflects the combination of: [a] genetics (e.g., DNA sequence variants); [b] epigenetics (chromosomal changes other than DNA sequence alterations); [c] environmental factors (pesticides, chemical pollutants); [d] endogenous influences (diabetes, heart disease); and [e] differences in one’s microbiome. Autism spectrum disorder (ASD) is a great example of a very complex disease trait that is certainly polygenic, plus influenced by epigenetic and environmental factors, and perhaps even by variability in the microbiome. Many genome-wide association studies (GWAS) have identified a number of low-effect genes, noncoding DNA loci, repetitive DNA sequences, and changes in DNA methylation that show correlations with ASD. Clinically, ASD is a developmental disorder that presents as severe social and communication impairment, combined with limited or focused interests and repetitive-type behaviors.

The prevalence of ASD has been exploding since the mid-1960s, rising from about one case of autism per 20,000 patients (in ~1960) to one case of ASD in 44 children today (~460 per 20,000(!!). One important caveat is that diagnosis of ASD is MUCH broader than it was, 60+ years ago. Throughout my clinical pediatrics training in the 1960s, I can remember only one ASD patient among the thousands of patients I was in contact with during those years.

The attached paper focuses on a possibly significant contribution of an environmental factor during pregnancy in ASD etiology. Proposed environmental chemicals that might cause ASD include: selective serotonin reuptake inhibitors (SSRIs), pesticides, herbicides, phthalates, polychlorinated biphenyls, solvents, air pollutants, fragrances, and heavy metals. For example, increases in the widely-used chemical, glyphosate [N-(phosphonomethyl)glycine], the active ingredient in the herbicide Roundup, were reported to be associated with increases in ASD rates over the same period — reported in the US public school system. Authors cite a population-based case-control study in California, showing the risk of ASD was associated with use of glyphosate (odds ratio = 1.16). For ASD children with intellectual disability, estimated odds ratios were higher with prenatal exposure to glyphosate (odds ratio = 1.33). These reports suggest that possible relationships between glyphosate and ASD should be explored in animal models.

Epidemiological studies implicate in utero maternal immune activation (MIA), playing a key role in the etiology of developmental disorders such as ASD; also, there are a number of positive associations between maternal infections or inflammatory biomarkers and ASD. Collectively, it is suggested that MIA during pregnancy can increase the risk of developmental disorders such as ASD in offspring. Authors [in the attached paper] show that soluble epoxide hydrolase (sEH), participating in metabolism of polyunsaturated

fatty acids (PFAs) might be involved in genesis of ASD in mouse offspring, following MIA; authors also found ASD-like behavioral abnormalities in juvenile offspring after maternal exposure to high levels of formulated glyphosate. [Authors state the dose of glyphosate is “0.098% in drinking water,” but authors should report what that computes to, in mg per kg per day]

Authors found higher levels of sEH in the prefrontal cortex (PFC), hippocampus, and striatum of juvenile offspring; in addition, they discovered decreased levels of epoxy-fatty acids [e.g., 8,9-EpETrE] in the blood, PFC, hippocampus, and striatum of juvenile offspring after maternal glyphosate exposure — which would be consistent with increased activity of sEH in the offspring. Moreover, authors found abnormal composition of gut microbiota and short-chain fatty acids in fecal samples of juvenile offspring after maternal glyphosate exposure. Interestingly, oral administration of TPPU (an sEH inhibitor) during pregnancy from embryonic day-5 (E5) to postnatal day 21 (P21) prevented ASD-like behaviors (e.g., social interaction deficits and increased grooming time) in the juvenile offspring after maternal glyphosate exposure.

These findings suggest that maternal “exposure to high levels of glyphosate” — causes ASD-like behavioral abnormalities and abnormal composition of gut microbiota in juvenile offspring mice, and that increased activity of sEH might play a role in ASD-like behaviors in offspring due to maternal glyphosate exposure. Authors suggest that “sEH might therefore be considered as a target for ASD in offspring,” following maternal stress from environmental exposure to contaminants. This study is a good example of gene-environment interactions, the recurrent theme of these GEITP blogs. 😊
DwN

COMMENTS:Hi Dan, Thanks for sending this around. There are several strong candidates which may play a role in the horrendous increase in ASD. And I agree that improved diagnosis is only a small part of the puzzle. Air pollution and other environmental pollution might play some role.

Much of the research has been conducted using PURE glyphosate (i.e., the active ingredient which is what is required for pesticide testing). The problem is that it may be the formulations that are part of the problem. Anyhow, lots of interesting work happening now on glyphosate — demonstrating that it is NOT innocuous to humans. LSB

COMMENT: Dan, I just did a back-of-the-envelope calculation on doses of glyphosate used in this ASD study:

They used ~1,000 ppm (million) in drinking water. The levels in tap water range from 85-330 ppt (trillion) — which means the dose they used is 3- to 12-million times higher than the average level found in tap water.

The difference with respect to food is more reasonable and that is likely the major glyphosate exposure clinically. The acceptable daily intake (ADI) for glyphosate is 0.5 ppm; therefore, the dose they used in mice (without allometric correction) is 2,000 times the human ADI.

Is this study relevant to toxicology? It irritates me that the authors use descriptors in the Abstract such as “…suggest that maternal exposure…” whereas in the title, the authors state: “Maternal glyphosate exposure CAUSES autism-like…” Association is NOT causation — even if this paper gets published in Proc Natl Acad Sci USA !! DW

COMMENT: This is GREAT, Dave. I saw the authors described in the text their treatment as “0.008% in drinking water” — where did you find all the additional details about the regimen used? DWN
COMMENT: Dan: I was going by the information in their Supplemental Materials section — “In this study, we used commercially available RoundupⓇ Maxload [48% (w/v) glyphosate (N-phosphonomethylglycine) potassium salt, having 52% other ingredients such as water and surfactant. [Lot #11946898. Nissan Chemical Corporation, Tokyo, Japan]. Previous studies used drinking water containing 0.38% (w/v) glyphosate (expressed as free base: 1% RoundupⓇ), during pregnancy and lactation, equivalent to 50 mg/kg/day of glyphosate (1,2). This corresponds to 1/20th of the glyphosate no-observed-adverse-effect level, as described previously (3). Therefore, water or formulated glyphosate [or 0.1, 0.25, 0.50, 0.75, 1.0 % RoundupⓇ] was given to the pregnant mice from E5 to P21 (weaning).”

“Measurement of glyphosate in the blood. Water or 0.098% (w/v) formulated glyphosate was given to pregnant mice from E5 to P21, as described above.”

The glyphosate dose of 0.1% would be 1000 ppm, and that is what I used, to compare with the reported levels in tap water (85-330 ppt). If mice drink 4 mL water/day at 0.1%, that would be 4 mg/day or 160 mg/kg for a 25 g mouse.

If the doses were between 0.1% and 1% of a formula containing 48% glyphosate, that would be about 2 mg/day (80 mg/kg), i.e., 20 mg/day (800 mg/kg).

The acceptable daily intake (ADI) for humans in food is 0.5 ppm or 0.5 x 10-7 g/g food. If a human eats 1,800 g food/day, that works out to 0.9 mg/day glyphosate, or 0.013 mg /kg for a 70-kg human. So, whatever the dose they actually used, it is many orders of magnitude higher than the human ADI. If my math is off, I will blame it on being quarantined in this pandemic, going on now, for more than 2 years. ☹ DW

COMMENT: I had intended to emphasize the authors’ use of the word “causes” in the title of their article (notice in the subject line of this email, it more conservatively says “possible association,” which is much more scientifically accurate thing to say). Kudos to Professor David Williams for bringing this topic up. Far too often, authors see a correlation — and immediately assume it is the cause-and-effect. “Possible association” is the much more accurate way to describe any observed correlation.

As with >90% (or probably >99%) of all toxicological studies, authors choose a dose WAY beyond “environmental reality,” in order to find “an effect.” This paper is a great example of this. In My Humble Opinion, this paper should never have been published — at least not in the high-visibility prestigious Proc Natl Acad Sci USA journal. ☹

What are the likely causes of ASD? Clearly, it must be a polygenic disease — with dozens if not hundreds of genes, each contributing a “small-effect” to the phenotype. In addition, to explain the incredible increase in frequency of this disease in the Western World since 1970, there must be epigenetic effects (the time for this increase to appear, i.e., <50 years, is way too short for DNA mutations to be involved). Environmental factors, lifestyle suspects, include things around us today — that were not there 50-60 years ago: e.g., [a] steady and excessive exposure of TV, electronic games and fast-moving videos to children almost from birth; [b] dietary changes (today there is so much “fast foods,” excessive sugar, and lack of a nutritious well-balanced diet); and [c] tendency of teachers, school counselors and parents diagnosing every transient behavioral defect in every school kid as “likely having ASD.” DwN COMMENT: Wow, this discussion is very harsh on the authors. I think the authors mentioned that their results in animals are “not readily translated into human populations,” because the concentration they used here was way higher than environmental levels. The purpose of this study was to demonstrate that glyphosate (at some level of exposure) could cause behavioral disorders that are similar to an ASD-like phenotype (for example, “arsenic causes cancers”). Based on their study, I believe it is safe to say glyphosate "is associated with" ASD-like symptoms in mice — at the concentrations at which the authors chose to use. ZL COMMENT: Findings in a mouse model, or any other nonhuman model for that matter, means nothing more than a hypothesis — unless the model has been validated in clinical studies with human patients. We at P & G lost many millions of dollars, trying to develop new drugs for humans, based on animal preclinical work. We saw many more failures, compared to successes. Academicians who publish these preclinical studies are only interested in getting their names in lights. And, of course, their University PR departments trump up the potential value. R D'A COMMENT: All of this is an interesting discussion — especially because the renewal assessment report of glyphosate is now on the board of the European Food Safety Authority (EFSA). Their license should be either renewed or discarded in the EU by the end of this year. Evaluation by the EFSA is a huge effort; we have thousands of pages and public opinions comprising more than 2,000 comments. ☹ OP **[Read emails from oldest to newest]** This email-chain just keeps going and going. Maybe there is lots to ventilate about? Here are two more of the latest comments. One from the Editor of Critical Reviews in Toxicology. And this last one is from Dr,, Jim Adams, who has a sobering message from “someone in the trenches” — a general practitioner for 40+ years. 😊 I hope everyone enjoys his frankness, honesty and humor as much as I do. 😊 —DwN COMMENT: J A I’ve been saving the Roundup emails and now I feel that I am at a point where I can attempt to sound off — which is the point of my reply to this, and other, related trends in modern problem-solving that crosses many fields of interest. (I’ll try not to ramble too much.) Every day in my practice, I see people who haven’t been diagnosed — even after thousands of dollars of tests, or they have had their problems solved by thousands of dollars of medications. If it’s a broken bone, no problem. If it’s fatigue or one of the myriad chronic pain or even more obvious illnesses almost always based on obesity — not so easy. Medicine has become compartmentalized. If you take “fatigue” to a cardiologist, you get thousands of dollars of cardiac tests. If you send “fatigue” to an internist, you get another set of tests, and a CAT scan or two. If you send “fatigue” to one of the “second-tier practitioners,” you get a repeat of some of the above — plus a sleep study and more and more pills that are like throwing darts in the darkness of failed knee-jerk approaches to complex problems. So finally, for all our deviations from normal hard work and the struggles over the millennia that kept us from becoming walking eggplants or other vegetables, the “alternate” problem-solvers get a shot: psychiatry, functional medicine, dietary guides, and a whole host of herbal incantations, etc. Then, maybe watching TV before bed — turns out to be the “real cause." This mirrors, in a sense, the Roundup studies, wherein the millions of chemicals floating around become targets, “searches for causality,” — especially if a company like Monsanto with deep pockets is involved. Let’s consider all the food additives, chemicals in cosmetics, herbicides and pesticides. Why not add PVC pipe, residuals of all food processing, and, more realistically, every new and old drug or potion on the market? For example, take psychostimulants for children who can’t do well in school. The adverse effect studies extend at best two years…!! We're talking about habit-forming drugs that alter brain structure, and there is no feasible way to look at subtle, or not-so-subtle, mental or physical effects 20 years from now. Now, add in statins, etc. How can one account for possible drug effects and combination-drug long-term effects from something as minute as the amount of Roundup sprayed on weeds…?? Then, I have this problem with all pesticide and herbicide fears. I live in the Mississippi Delta — where airplanes have sprayed every imaginable chemical directly in the air, since I was 10 years old. You smell them all spring, summer and fall while riding down the highways. When I was age 10, I stood in my T-shirt and marked the rows for airplanes flying over my head, smearing my glasses with 2-4-D (remember dioxin?) and every chemical, except Paraquat, a chemical we all knew “was toxic.” (My brother uses Paraquat in spray rigs every year to spray the stuff on the ground, as if that’s safer.) What’s my obvious point? If chemicals for bugs and weeds are truly toxic, it would seem to me that those of us in the Mississippi Delta with 60 years of intense, yearly exposure, second only to the crop-dusters and spray-rig-tractor drivers, should be more valid study subjects than rats. My friends and I rode our bikes in the DDT fog sprayers as children. But then, this returns to paragraph one. We know nothing. We have science groomed by ulterior motives…money mostly…and hysteria. None of us is as brilliant as a Cray Computer, and we are simply throwing darts in darkness to invent answers — using clever tools and tests — all depending on our particular fields of interest. Yet, from another viewpoint, are we all like the doctors, including myself years ago, who are more like college kids smoking pot…”I’ve done it, and it’s hasn’t killed me yet?” We assume safety if there aren’t visible or palpable immediate adverse effects. There is a pill for everything. And by the way, despite the use of an incredible array of pesticides, some sprayed over the entire city overhead by airplanes at night during summer, when our mosquitoes are horrid. Right now, at 6 am in Cleveland, Mississippi, it sounds like a songbird sanctuary, and by sunrise, the air will be literally filled with insects flying or crawling over every square inch of territory in my back yard. I don’t know if the Joni Mitchell lyric “Give me spots on my apples, but leave the birds and the bees” is an intelligent assessment of reality or not. I, by the way, keep bees in my back yard, and they’re buzzing around and surviving just fine. In summary, I’m 72 years old, and I have been breathing high doses of every evil chemical imaginable, and it’s done no harm that I can see. (This is an old photo below…well, I did have to have a few plastic surgeries over the years.) From: RM Subject: Fw: California regulators changing language on glyphosate and cancer risk Dan: I have followed the recent exchanges on your blog. I have stayed on the sidelines — because I received a lot of flak — related to articles by Willliams et al. on “glyphosate's potential carcinogenicity,” which I chose to accept for publication and it got published in Critical Reviews in Toxicology; and I refused to retract them in response to requests from IARC and others. You will find the attached article of interest. I am sure you recognize Carey Gillam has a vested position. Keep up the great work that you do — in communicating and discussing these high-profile issues(!!) Best regards, RM COMMENT: Let me add to the firestorm…As a proud member of the National Academy of Schmoozers, I could not agree more with Fred. I’m continually dismayed by the number of so-called toxicology studies that draw ‘disconcerting’ conclusions for human health — based on in vitro (and sometines in vivo) studies that use doses/concentrations that are 1,000 times to, sometimes, 10s-of-thousands of times, higher than could ever conceivably be achieved from ‘environmental’ exposures. Imagine if drug safety assessment were based on observed effects on in vitro studies that required doses thousands of times higher than physiological-based pharmacokinetic modeling and simulation (PBPK) therapeutic concentrations. We would have no new drugs….the Glyphosate ‘controversy’ is just the tip of this toxicology iceberg…. ☹ COMMENT: [Read emails from oldest to newest]** Lastly, to bring this email-chain into perspective and full-circle, the short video clip [attached] of a small toddler on a farm shows an example of a child who is completely aware of his surroundings and acts appropriately when challenged by a cow. No doubt the child’s parents have been using glyphosate on their farm, and their entire family has been exposed. Even during her pregnancy with this child, the toddler was likely exposed to this herbicide in utero. But, as you can see here — he does NOT show any evidence of ASD. 😊😉😉 DwN Nebert, Daniel (nebertdw) Sent: Wednesday, April 13, 2022 5:22 PM The raging firestorm of GLYPHOSATE — continueth, including claims of an association and possible causation not only to ASD but also to cancer. For many years, I’ve been aware of this political battle and fraudulent (glyphosate-cancer) “scientific” studies and claims. Sound science (following The Scientific Method *) continues to be replaced by government opinion and policy, and this trend seems to be accelerating during these past 2-3 decades. Why? Perhaps this has to do with the internet? or social media? or incompetent teaching of the latest generation of students? I just don’t know. DwN *The six steps of The Scientific Method include: 1) ask a question; 2) learn what is already known about the topic; 3) construct a hypothesis; 4) experiment to test the hypothesis (including repeat experiments to confirm the same result); 5) analyze data from the experiments and draw conclusions; 6) communicate the results to others. [Repeat Steps 1 through 6 again and again.] From: GeK Dear Dr. Nebert, Jim Enstrom included me on the correspondence involving you, David Williams, and others regarding the PNAS paper linking glyphosate exposure and ASD. Since there was no direct mention of cancer in the email exchange, I wanted to make you aware – if you are not already aware – of the unfortunate controversy that has been raging for seven years regarding the claim of carcinogenicity of glyphosate. The controversy stems from IARC’s 2015 determination that glyphosate is a “probable carcinogen.” (This initial publication was followed several years later by IARC Monograph 112, which reached the same conclusion.) IARC based its conclusion of probable carcinogenicity solely on animal (rodent) studies, which it judged to constitute sufficient evidence (whereas the epidemiologic evidence was judged to be insufficient). However, the Agency’s evaluation of the rodent studies has been criticized on the grounds that the wrong statistical test was used to assess dose-response trends, erroneously declaring certain positive trends statistically significant. In addition, where comparable inverse trends occurred, these were ignored. Other irregularities have been documented by Reuters reporter, Kate Kelland, who found that non-carcinogenic findings were edited out in successive drafts. There is also the appearance of a serious conflict of interest on the part of Christopher Portier, who served as an invited guest on the Working Group but, who was also influential in IARC’s 2014 decision to evaluate glyphosate. Within days of the publication of IARC's conclusion in March, 2015, Portier signed a lucrative contract to act as a litigation consultant for two law firms that were preparing to sue Monsanto on behalf of glyphosate cancer victims. Regarding the epidemiology, most studies have been case-control studies of occupational groups exposed to glyphosate. Many of these were conducted when glyphosate was less widely used and exposure would have been low. An association of glyphosate with non-Hodgkin’s lymphoma (NHL) was found in some of these studies. It is noteworthy that IARC ignored the results of the large prospective cohort study, the Agricultural Health Study [AHS], conducted by NCI among 54,000 pesticide applicators. Although the latest results regarding glyphosate were not published until 2018, the results of the analyses involving glyphosate had circulated far earlier, and, furthermore, the head of the Working Group that evaluated glyphosate, Aaron Blair, was one of the lead researchers on the AHS, who would have been intimately aware of the results. The overall conclusion from the AHS analysis was as follows: “In this large, prospective cohort study, no association was apparent between glyphosate and any solid tumors or lymphoid malignancies overall, including NHL and its subtypes.” Recently, together with two colleagues, I published an updated meta-analysis of epidemiologic studies of glyphosate exposure and NHL. Using updated information from the case-control studies, where available, and examining the five different latency conditions considered in the AHS analyses, we found no association of glyphosate exposure with risk of NHL. Given your interest in carcinogenesis and your comments on the toxicology of glyphosate, I wanted to draw your attention to the situation regarding glyphosate and cancer. This question has serious implications for agriculture, where glyphosate has been enormously useful to farmers, providing an environmentally benign means of controlling weeds and increasing yields, enabling no-till cultivation. Activists, litigators, and politicians have taken IARC’s glyphosate determination as gospel, and this has provided the basis for four (by my count) successful lawsuits in California against Monsanto and its successor company, Bayer. In addition, local jurisdictions and states (such as the state of Maine) are considering banning glyphosate, based on IARC’s verdict. In this juggernaut, the judgment of 17 other national and international health/regulatory agencies, which have found glyphosate to be non-carcinogenic and to not pose a risk to the general population, is blithely ignored. In other words, carefully-conducted reviews, including those of the U.S. EPA, Health Canada, and the European Food Safety Authority, among others, are simply deemed to be of no weight — when counterpoised to IARC’s seriously flawed (some would say, fraudulent) conclusion.

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A Paleolithic Raw Bar, and a Human ‘Brush with Extinction’

This article from Medscape, just received today, is about “evolution” and had such an intriguing title — that I had to begin reading it. And once I began reading it (it’s written very breezily and it’s enjoyable to read), I could not stop. And I think this is worthwhile information to share with all of GEITP. The topic includes climate, diet, and human gene evolution. In fact, at one point, I wondered about a possible relationship between this topic — and autism spectrum disorder (i.e., the Western World diet of today versus that of 50-70 years ago). 😊

DwN

A Paleolithic Raw Bar, and a Human ‘Brush with Extinction’

Bret S. Stetka, MD
March 25, 2021

This essay is adapted from the newly released book A History of the Human Brain: From the Sea Sponge to CRISPR, How Our Brain Evolved.

“He was a bold man that first ate an oyster.”

—Jonathan Swift

That man or, just as likely, that woman may have done so out of necessity. It was either eat this glistening, gray blob of briny goo. Or perish.

Beginning 190,000 years ago, a glacial age we identify today as Marine Isotope Stage 6, or MIS6, had set in, cooling and drying out much of the planet. There was widespread drought, leaving the African plains a harsher, more barren substrate for survival — an arena of competition, desperation, and starvation for many species, including Homo sapiens. Some estimates have the Sapien population dipping to just a few hundred people during MIS6. Like other apes today, we were an endangered species. But through some nexus of intelligence, ecological exploitation, and luck, we managed. Anthropologists argue over what part of Africa would’ve been hospitable enough to rescue Homo sapiens from Darwinian oblivion. Arizona State University archeologist Curtis Marean believes the continent’s southern shore is a good candidate.

For two decades, Marean has overseen excavations at a site called Pinnacle Point on the South African coast. The region has over 9000 plant species, including the world’s most diverse population of geophytes, plants with underground energy-storage organs like bulbs, tubers, and rhizomes. These subterranean stores are rich in calories and carbohydrates, and, by virtue of being buried, are protected from most other species (save the occasional tool-wielding chimpanzee). They are also adapted to cold climates and, when cooked, easily digested. All in all, a coup for hunter-gatherers.

The other enticement at Pinnacle Point could be found with a few easy steps toward the sea. Mollusks. Geological samples from MIS6 show South Africa’s shores were packed with mussels, oysters, clams, and a variety of sea snails. We almost certainly turned to them for nutrition.

Marean’s research suggests that, sometime around 160,000 years ago, at least one group of Homo sapiens began supplementing their terrestrial diet by exploiting the region’s rich shellfish beds. This is the oldest evidence to date of humans consistently feasting on seafood — easy, predictable, immobile calories. No hunting required. As inland Africa dried up, learning to shuck mussels and oysters was a key adaptation to coastal living, one that supported our later migration out of the continent.

Marean believes the change in behavior was possible thanks to our already keen brains, which supported an ability to track tides, especially spring tides. Spring tides occur twice a month with each new and full moon and result in the greatest difference between high and low tidewaters. The people of Pinnacle Point learned to exploit this cycle. “By tracking tides, we would have had easy, reliable access to high-quality proteins and fats from shellfish every two weeks as the ocean receded,” he says. “Whereas you can’t rely on land animals to always be in the same place at the same time.” Work by Jan De Vynck, a professor at Nelson Mandela University in South Africa, supports this idea, showing that foraging shellfish beds under optimal tidal conditions can yield a staggering 3500 calories per hour!

“I don’t know if we owe our existence to seafood, but it was certainly important for the population that Curtis studies. That place is full of mussels,” says Ian Tattersall, curator emeritus with the American Museum of Natural History in New York City, New York.

“And I like the idea that during a population bottleneck, we got creative and learned how to focus on marine resources.” Innovations, Tattersall explains, typically occur in small, fixed populations. Large populations have too much genetic inertia to support radical innovation; the status quo is enough to survive. “If you’re looking for evolutionary innovation, you have to look at smaller groups.”

MIS6 wasn’t the only near-extinction in our past. During the Pleistocene epoch, roughly 2.5 million to 12,000 years ago, humans tended to maintain a small population, hovering around a million and later growing to maybe eight million at most. Periodically, our numbers dipped as climate shifts, natural disasters, and food shortages brought us dangerously close to extinction. Modern humans are descended from the hardy survivors of these bottlenecks.

One especially dire stretch occurred around one million years ago. Our effective population (the number of breeding individuals) shriveled to around 18,000, smaller than that of other apes at the time. Worse, our genetic diversity — the insurance policy on evolutionary success and the ability to adapt — plummeted. A similar near-extinction may have occurred around 75,000 years ago, the result of a massive volcanic eruption in Sumatra.

Our smarts and adaptability helped us endure these tough times — omnivorism helped us survive scarcity.
A Sea of Vitamins

Both Marean and Tattersall agree that the Homo sapiens hanging on in southern Africa couldn’t have lived entirely on shellfish. Most likely they also spent time hunting and foraging roots inland, making pilgrimages to the sea during spring tides. Marean believes coastal cuisine may have allowed a paltry human population to hang on until climate change led to more hospitable terrain. He’s not entirely sold on the idea that marine life was necessarily a driver of human brain evolution.

By the time we incorporated seafood into our diets, we were already smart, our brains shaped through millennia of selection for intelligence. “Being a marine forager requires a certain degree of sophisticated smarts,” he says. It requires tracking the lunar cycle and planning excursions to the coast at the right times. Shellfish were simply another source of calories.

Unless you ask Michael Crawford.

Crawford is a professor at Imperial College London and a strident believer that our brains are those of sea creatures. Sort of.

In 1972, he co-published a paper concluding that the brain is structurally and functionally dependent on an omega-3 fatty acid called docosahexaenoic acid, or DHA. The human brain is composed of nearly 60% fat, so it’s not surprising that certain fats are important to brain health. Nearly 50 years after Crawford’s study, omega-3 supplements are now a multi-billion-dollar business.

Omega-3’s, or more formally, omega-3 polyunsaturated fatty acids (PUFAs), are essential fats, meaning they aren’t produced by the body and must be obtained through diet. We get them from vegetable oils, nuts, seeds, and animals that eat such things. But take an informal poll, and you’ll find most people probably associate omega-fatty acids with fish and other seafood.

The animal brain evolved ~600 million years ago in the ocean and was dependent on DHA…

In the 1970s and 1980s, scientists took notice of the low rates of heart disease in Eskimo communities. Research linked their cardiovascular health to a high-fish diet (though fish cannot produce omega-3’s, they source them from algae), and eventually the medical and scientific communities began to rethink fat. Study after study found omega-3 fatty acids to be healthy. They were linked with a lower risk for heart disease and overall mortality. All those decades of parents forcing various fish oils on their grimacing children now had some science behind them. There is such a thing as a good fat.

Recent studies show that some of omega-3s’ purported health benefits were exaggerated, but they do appear to benefit the brain — especially DHA and eicosapentaenoic acid, or EPA. Omega fats provide structure to neuronal cell membranes and are crucial in neuron-to-neuron communication. They increase levels of a protein called brain-derived neurotrophic factor (BDNF), which supports neuronal growth and survival. A growing body of evidence shows omega-3 supplementation may slow down the process of neurodegeneration, the gradual deterioration of the brain that results in Alzheimer disease and other forms of dementia.

Popping a daily omega-3 supplement or, better still, eating a seafood-rich diet, may increase blood flow to the brain. In 2019, the International Society for Nutritional Psychiatry Research recommended omega-3’s as an adjunct therapy for major depressive disorder. PUFAs appear to reduce the risk for, and severity of, mood disorders such as depression and to boost attention in children with ADHD as effectively as drug therapies.

Many researchers claim there would’ve been plenty of DHA available on land to support early humans, and marine foods were just one of many sources.

Not Crawford.

He believes that brain development and function are not only dependent on DHA but, in fact, DHA sourced from the sea was critical to mammalian brain evolution. “The animal brain evolved 600 million years ago in the ocean and was dependent on DHA, as well as compounds such as iodine, which is also in short supply on land,” he says. “To build a brain, you need these building blocks, which were rich at sea and on rocky shores.”

Crawford cites his early biochemical work showing DHA isn’t readily accessible from the muscle tissue of land animals. Using DHA tagged with a radioactive isotope, he and his colleagues in the 1970s found that “ready-made” DHA, like that found in shellfish, is incorporated into the developing rat brain with 10-fold greater efficiency than plant- and land animal–sourced DHA, where it exists as its metabolic precursor, alpha-linoleic acid. “I’m afraid the idea that ample DHA was available from the fats of animals on the savanna is just not true,” he disputes. According to Crawford, our tiny, wormlike ancestors were able to evolve primitive nervous systems and flit through the silt thanks to the abundance of healthy fat to be had by living in the ocean and consuming algae.

For over 40 years, Crawford has argued that rising rates of mental illness are a result of post–World War II dietary changes, especially the move toward land-sourced food and the medical community’s subsequent support of low-fat diets. He feels that omega-3’s from seafood were critical to humans’ rapid neural march toward higher cognition, and are therefore critical to brain health. “The continued rise in mental illness is an incredibly important threat to mankind and society, and moving away from marine foods is a major contributor,” says Crawford.

University of Sherbrooke physiology professor Stephen Cunnane tends to agree that aquatically sourced nutrients were crucial to human evolution. It’s the importance of coastal living he’s not sure about. He believes hominins would’ve incorporated fish from lakes and rivers into their diet for millions of years. In his view, it wasn’t just omega-3’s that contributed to our big brains, but a cluster of nutrients found in fish: iodine, iron, zinc, copper, and selenium among them. “I think DHA was hugely important to our evolution and brain health, but I don’t think it was a magic bullet all by itself,” he says. “Numerous other nutrients found in fish and shellfish were very probably important too and are now known to be good for the brain.”

Marean agrees. “Accessing the marine food chain could have had a huge impact on fertility, survival, and overall health, including brain health, in part, due to the high return on omega-3 fatty acids and other nutrients.” But, he speculates, before MIS6, hominins would have had access to plenty of brain-healthy terrestrial nutrition, including meat from animals that consumed omega-3-rich plants and grains.

Cunnane agrees with Marean to a degree. He’s confident that higher intelligence evolved gradually over millions of years as mutations inching the cognitive needle forward conferred survival and reproductive advantages — but he maintains that certain advantages like, say, being able to shuck an oyster, allowed an already intelligent brain to thrive.

Foraging marine life in the waters off of Africa likely played an important role in keeping some of our ancestors alive and supported our subsequent propagation throughout the world. By this point, the human brain was already a marvel of consciousness and computing, not too dissimilar to the one we carry around today.

In all likelihood, Pleistocene humans probably got their nutrients and calories wherever they could. If we lived inland, we hunted. Maybe we speared the occasional catfish. We sourced nutrients from fruits, leaves, and nuts. A few times a month, those of us near the coast enjoyed a feast of mussels and oysters. 😊

COMMENT: Hi Dan, Thanks for sharing this entertaining essay; I have two minor comments.
This hypothesis of the ancient African Homo Sapiens populations staying close to the coastline, for regular seafood feasts is exactly the same hypothesis proposed for the Australian aboriginals during times of severe climate and drought. Those people arrived from (current) Indonesia/Papua New Guinea more than ~40 000 years ago, and were believed to have stayed largely along the coastal regions. While some of the population gradually moved inland — where they invented the boomerang for hunting purposes — the major portion of aboriginals remained along the coast and enjoyed frequent “oyster parties.”

Regarding the Eskimo diet; to my knowledge, Greenland Eskimos started eating fish and other small seafood only rather recently. Their traditional diet was whales and other marine mammals. I don’t know how much PUFAs are present in whale meat and whale fat (blubber).
Cheers, M

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Omicron variant largely avoids antibodies produced by present vaccines ??

The SARS-CoV-2 B.1.1.529 (omicron) variant contains 15 mutations in the receptor-binding domain (RBD). How Omicron evades RBD-targeted neutralizing antibodies — requires immediate investigation. Authors [see attached] used high-throughput yeast display screening to determine the profiles of RBD-escaping mutations for 247 human anti-RBD neutralizing antibodies and showed that the neutralizing antibodies can be classified by unsupervised clustering into six epitope groups (A–F) — a grouping that is highly concordant with knowledge-based structural classifications.

Various single mutations of Omicron can impair neutralizing antibodies of different epitope groups: [a] Neutralizing antibodies in groups A–D, the epitopes of which overlap with the ACE2-binding motif, are largely escaped by K417N, G446S, E484A and
Q493R; [b] Antibodies in group E (e.g., S309) and [c] Antibodies in group F (e.g., CR3022), which often exhibit broad sarbecovirus neutralizing activity, are less affected by Omicron, but a subset of neutralizing antibodies are still escaped by
G339D, N440K and S371L. Furthermore, Omicron pseudovirus neutralization showed that neutralizing antibodies that sustained single mutations could also be escaped, owing to multiple synergetic mutations on their epitopes.

In total, >85% of the tested neutralizing antibodies were escaped by Omicron. With regard to neutralizing-antibody-based drugs, the neutralization potency of LY-CoV016, LY-CoV555, REGN10933, REGN10987, AZD1061, AZD8895 and BRII-196 was

greatly undermined by Omicron — whereas VIR-7831 and DXP-604 still functioned at a diminished efficacy. Together, these data suggest that infection with Omicron would result in considerable humoral immune evasion, and that neutralizing antibodies targeting the sarbecovirus-conserved-region will remain most effective. Authors’ state that their results “will advance the development of antibody-based drugs and vaccines against Omicron and future variants.”

This is one paper in the 24 Feb issue of Nature; five more papers on this similar topic are published in sequence [see below]. 😊
DwN
Nature 24 Feb 2022; 602: 657-664
But also see: pp 654-656, 664-670, 671-675, 676-681 & 682-688

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**HGNC Newsletter** Winter 2022

Some of you will find the 2022 Winter HGNC NewsLetter relevant and of interest. 😊
DwN

https://blog.genenames.org/hgnc/2022/02/24/Winter_newsletter_2022
Winter newsletter 2022

Newsletters · 24 Feb 2022
Thanks to our Scientific Advisory Board

We would like to thank all the members of our SAB for attending our (mostly virtual) annual meeting from 27-28th January. We hope that we might be able to host a less virtual version in the future! We were pleased to welcome our new board member, Cecilia Arighi, who works within several different protein information projects, including UniProt, Protein Ontology and BioCreative. While Professor Helen Firth has rotated off the board, we are delighted that she has agreed to remain associated with HGNC as our Clinical Advisor.
Play ‘Genele’ – the gene symbol guessing game

How many of you have tried Genele, the fun gene symbol guessing game made by Dr Andrew Holding? It might just remind you of a popular word guessing game that has taken the world by storm in the last few months ;-). We love Genele so much that we have linked to it from our home page. So take a break for a few minutes daily to guess the gene symbol – go on, you can even use genenames.org to help you out a little!

Progress on the VGNC project

We now have more than ~108,500 genes approved in total for our VGNC project, with 14,019 cat genes, 16,751 chimpanzee genes, 16,856 cattle genes, 15,567 dog genes, 15,704 horse genes, 14,677 Rhesus macaque genes and 13,898 pig genes with approved VGNC symbols. This includes over 6,000 new VGNC genes within the last year! Below is a graph showing our progress with each core species.
Wanted – a new VGNC full stack developer

We are currently advertising for a new full stack developer to work on our VGNC project. The closing date is 10th March, so please notify anybody you know that might be interested in this position!
Update on genes with the ‘stable’ tag

We have 2821 gene symbols tagged as ‘stable’ as of February 23rd 2022, an increase of 209 since our Autumn newsletter. Examples of genes within the new stable set include NHEJ1, the causative gene for Severe combined immunodeficiency with microcephaly growth retardation, and sensitivity to ionizing radiation, NKX6-2, the causative gene for Spastic ataxia 8, autosomal recessive, with hypomyelinating leukodystrophy and KNG1, the causative gene for High molecular weight kininogen deficiency.

In order for a gene to be marked as stable, an HGNC curator manually reviews the gene symbol to check that this is unlikely to ever be changed in future. During the review of the 209 genes that were marked as stable in the last quarter, no gene symbols were changed and the descriptive names of just seven genes were altered. In most cases this was to make the name more functionally informative – For example, the gene name of NUBPL was updated from “nucleotide binding protein like” to “NUBP iron-sulfur cluster assembly factor, mitochondrial”; EPG5 was updated from “ectopic P-granules autophagy protein 5 homolog” to “ectopic P-granules 5 autophagy tethering factor”; CD3E was updated from “CD3e molecule” to “CD3 epsilon subunit of T-cell receptor” and CD3G was updated from “CD3g molecule” to “CD3 gamma subunit of T-cell receptor complex”.
Updates to placeholder symbols

Since the last newsletter we have continued to work on updating C#orf symbols where possible. The following symbols were all updated based on data in publications:

C11orf49 -> CSTPP1, centriolar satellite-associated tubulin polyglutamylase complex regulator 1
C7orf26 -> INTS15, integrator complex subunit 15
C9orf116 -> PIERCE1, piercer of microtubule wall 1
C15orf65 -> PIERCE2, piercer of microtubule wall 2
C7orf61 -> SPACDR, sperm acrosome developmental regulator

The nomenclature of the FAM71 family was updated following a consultation with researchers working on these genes. The symbol “GARI” had been published for FAM71F2 but this was not a suitable gene symbol for approval because it is a poor search term and is similar to the approved symbol GAR1. The community agreed upon “GARIN” for “golgi associated RAB2 interactor” as a suitable alternative root symbol for the FAM71 family. For genes where the function of the encoded protein has not been confirmed as a golgi associated RAB2 interactor, the term “family member” was added into the gene name. The updates were as follows:

FAM71F2 -> GARIN1A, golgi associated RAB2 interactor 1A
FAM71F1 -> GARIN1B, golgi associated RAB2 interactor 1B
FAM71D -> GARIN2, golgi associated RAB2 interactor 2
FAM71B -> GARIN3, golgi associated RAB2 interactor 3
FAM71A -> GARIN4, golgi associated RAB2 interactor family member 4
FAM71E1 -> GARIN5A, golgi associated RAB2 interactor 5A
FAM71E2 -> GARIN5B, golgi associated RAB2 interactor family member 5B
FAM71C -> GARIN6, golgi associated RAB2 interactor family member 6

Gene Symbols in the News

We bring news of two gene therapy stories, the first is the successful treatment of sickle cell disease via gene editing of the BCL11A gene to switch adults to making fetal hemoglobin rather than the affected adult hemoglobin that causes the red blood cells to ‘sickle’. The treatment is so successful that patients have not needed hospital visits since. The second is in earlier stages and is the first attempt to treat Tay-Sachs disease, caused by mutation of the HEXA gene. A low dose of treatment was delivered to the brain and spine of two young girls, who are now clinically stable with slowed or no disease progression. Further studies will use higher doses of treatment.

A new as yet unnamed neurodevelopmental disorder has been identified that is caused by mutation of the PAX5 gene. After discovering a mutation in one patient, researchers used GeneMatcher to find another 15 patients with PAX5 mutations who all exhibited similar characteristics of developmental delay, intellectual disability and autism spectrum disorder.

An SNP located within a chemokine receptor cluster that affects expression of CCR1, CCR2, CCR3 and CCR5 has been shown to increase the risk of severe COVID-19 disease but lower the risk of becoming infected with HIV. Interestingly, this SNP was inherited from Neanderthals and rose in frequency over 10,000 years ago, suggesting that this may have been due to selective pressure from a virus infecting humans around this time, such as smallpox.

Finally we bring news of a gene variant identified in dog that is responsible for the small size in breeds such as chihuahua and miniature schnauzers. The mutation is carried on a long non-coding RNA gene that is antisense to the insulin-growth factor-1 protein coding IGF1 gene.
Publications

Braschi B, Omran H, Witman G.B, Pazour, G.J, Pfister, K.K, Bruford, E.A, King, S.M. Consensus nomenclature for dyneins and associated assembly factors. J Cell Biol. 2022 Feb 7;221(2):e202109014. Epub 2022 Jan 10. PMID: 35006274 PMCID: PMC8754002 DOI: 10.1083/jcb.202109014. Please also read the accompanying guest blog post by Dr Stephen M. King Naming Dynein Components and their Cytoplasmic Associated Factors.

Ho M, Thompson B, Fisk JN, Nebert DW, Bruford EA, Vasiliou V, Bunick CG. Update of the keratin gene family: evolution, tissue-specific expression patterns, and relevance to clinical disorders. Hum Genomics. 2022 Jan 6;16(1):1. DOI: 10.1186/s40246-021-00374-9. PMID: 34991727. PMCID: PMC8733776

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The Military-Industrial-Academic-Political-Scientific Complex

The Military-Industrial-Academic-Political-Scientific Complex

J. Scott Turner

January 24, 2022

Sixty-one years ago, just before leaving office, Dwight D. Eisenhower delivered his farewell address. The most remembered and oft-quoted sentence of that address was an admonition:

In the councils of government, we must guard against the acquisition of unwarranted influence, whether sought or unsought, by the military-industrial complex.

I remember the phrase “military-industrial complex” as a big thing in the sixties. Through that lens, wars were not fought for reasons of compelling national interest, they were fought to enrich defense contractors. It became a convenient trope to the protest culture of the sixties, framing everything from environmental degradation (enriching chemical companies) to public health (enriching pharmaceutical companies) to automobile safety (enriching automobile companies). In all its forms, the innumerable “etc-industrial complexes” were the leavening for protest and political activism, all variations on the same theme: an unseemly and closed relationship of government with favored businesses — and the interests of ordinary people be damned.

Eisenhower had a deeper point, though, sometimes forgotten. It wasn’t just a cabal of military and defense contractors that worried Eisenhower; it was that an emerging “scientific-technological elite,” propped up by burgeoning public spending, would come to dominate, not serve, public policy. The deepening penetration of government funding into the sciences would similarly undermine the value of the sciences. Speaking of the ”technological revolution” then ongoing, Eisenhower wrote:

research has become central . . . more formalized, complex, and costly. A steadily increasing share is conducted for, by, or at the direction of, the Federal government.

. . . the free university, historically the fountainhead of free ideas and scientific discovery, has experienced a revolution in the conduct of research. Partly because of the huge costs involved, a government contract becomes virtually a substitute for intellectual curiosity. . .

The prospect of domination of the nation’s scholars by Federal employment, project allocations, and the power of money is ever present and is gravely to be regarded.

[emphasis mine]

Just one year later, recognizing Eisenhower’s warning of the corrupting influence of growing federal support of research universities, Senator William Fulbright began to speak of the “military-industrial-academic complex.” Fulbright’s concern was primarily over what he regarded as the militarization of academic research, but it’s worth remembering that Eisenhower was warning that the pursuit of federal money would prevail over the curiosity-driven search for knowledge that is the beating heart of the ethos of scientific research.

Shift now to the present day. The “scientific and technological elite” Eisenhower warned about is clearly here, deeply entrenched and wielding enormous power. David Eisenhower, currently a professor in the Annenberg School for Communications, sees the entrenched scientific elite operating in public health authorities’ intervention into civil government. They ostentatiously wear the mask of “science,” but behind that mask lurks a tangled web of collusion between government scientists, non-governmental organizations (NGOs), and foreign governments — all fueled by enormous and unaccountable streams of federal cash.

The technological elites, for their part, have aggrandized such power and influence that they serve as the censorship wing of the scientific elite, and more broadly of the electoral interests of one political party over the other. The enormous federal expenditures for scientific research in the universities that worried Eisenhower in 1961 have continued to grow with nary a blip. In 1961, total federal expenditure for university research was $595 million. Presently, it is more than $50 billion. Among the items we have purchased with that largesse is a stridently politicized and partisan “science” that serves the interests of the “scientific and technological elite” rather than the dispassionate source of knowledge that we, the taxpayers who support the whole edifice, were promised.

The military-industrial complex that so worried Eisenhower has not gone away. Instead, it has morphed into a military-industrial-academic-scientific-political complex that is coming more and more to resemble the corporatism underpinning Italian fascism: a “partnership” of government, industry, and academy that puts its collective interests ahead of individuals. Eisenhower warned that the externalities of federal financial incentives could eventually destroy the ethos of the “solitary inventor, tinkering in his shop.” Despite Eisenhower’s admonition, we continue to hurtle down this highway at ever-increasing speed.

Where is the off-ramp?

Dr. J. Scott Turner is Director of the Diversity in the Sciences Project for the National Association of Scholars.

COMMENT: Thanks Dan,

The Military-Industrial Complex was bad enough, but when research is becoming so colored — by the desire to patent every little trivial discovery — then the collaborative spirit gets lost. No sharing of data, and no real exchange of ideas or problem-solving anymore. This is very sad! ☹

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