RNA Directed

From gut bacteria to breast milk and back

Breast milk may alter behaviour of babies Milk contains sugars designed to feed gut bacteria that affect brain Excerpt:  Breast milk contains a lot of sugars that infants can’t digest, but that feed bacteria that live in human intestines. Those bacteria don’t just help digest food, said Hinde. “They can release chemical signals that travel to the infant’s brain and shape neurodevelopment.” Studies in mice and rats show that signals released by bacteria in the gut can affect how sociable and…

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Chance mutations — not natural selection

A Surprise for Evolution in Giant Tree of Life Excerpt (with my emphasis): Each variant adapted to suit a different ecological niche. But Blair Hedges, a biologist at Temple University in Philadelphia, has proposed a provocative alternative: Adaptation had little to do with it. It was simply a matter of chance and time. See also: The Surprising Origins of Evolutionary Complexity July 16, 2013 Excerpt: Some argue that life has a built-in tendency to become more complex over time. Others…

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Viruses in gut microbes

Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells 5/4/15 Excerpt: Extended Data Figure 3 | Generation of H3.3-isoform-specific antibodies. Related to Fig. 1. a, Schematic of amino acid sequence differences for the canonical histones H3.1 and H3.2 versus the histone variant H3.3. H3.3 differs from H3.2 or H3.1 at only 4 or 5 amino acids, positions 31, 87, 89, 90 and 96, as indicated. My comment: The difference in amino acid substitutions can be linked…

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MicroRNAs and the exposome (2)

Odd histone helps suppress jumping genes in stem cells, study says Excerpt 1) Chemical modifications to these histones can change the expression of genes, making them more available for expression or silencing them by compacting the DNA-protein complex. Oddball H3.3 varies from its regular counterpart H3 by only few amino acids. Excerpt 2) The research has implications beyond epigenetics. “This study also hints at a fascinating question in biology: How do cells balance the potential evolutionary benefit of mobile elements,…

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MicroRNAs and the exposome

 MicroRNAs as Potential Signatures of Environmental Exposure or Effect: A Systematic Review Excerpt: Researchers are currently publishing extensive lists of miRNAs that are responsive to environmental exposures and showing their utility as biomarkers of effect. Future research should focus on identifying the molecular mechanism behind miRNA expression changes in response to exposure to determine whether the changes in miRNA expression are merely a symptom of the (patho)physiological processes the organism undergoes after exposure, or whether miRNAs are the drivers responsible…

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Finding odor and taste receptors everywhere

Bitter taste receptor agonists elicit G-protein-dependent negative inotropy in the murine heart was published in October 2014 and reported in May 2015 as: Researchers find bitter taste receptors on human hearts Excerpt: “While the underlying physiology behind this phenomenon remains unclear, this is now a major area of ongoing investigation.” For a historical perspective on this major area of ongoing investigation, see also: From ion channel to organismic phenotype: An example of integrative translational research into cardiac electromechanics (2013) and…

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Linking the origin of birds to dinosaurs

Weird-winged dino sets science world aflutter (w/ Video) Excerpt: “It is definitely an example showing how much experimentation occurred,” said palaeontologist Xu Xing of the Chinese Academy of Sciences in Beijing, who co-authored a study in the journal Nature. “Close to the origin of birds (from dinosaurs)… many lineages tried in a different way to get into the air, but finally only one group succeeded.” My comment:  This example of what is placed into the context of evolutionary experimentation could…

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pH, water, amino acids and protein folding

Solubilities of amino acids in water at various pH values under 298.15 K and Translational tuning optimizes nascent protein folding in cells link what is currently known about the biophysically constrained chemistry of nutrient-dependent RNA-mediated protein folding to cell type differentiation in all genera via conserved molecular mechanisms.  Mutations are linked from perturbed protein folding to pathology. See for example: From “Science Mission” 5/2/15 at 12 pm Water diffusion and neurodegenerative disease linked to Hydration water mobility is enhanced around tau…

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Epigenetics vs the fossil record

Evolution of stem cells traced in study of fossilized rodent teeth Excerpt: “the mechanism that allowed the shift from longer teeth to continuously growing ones… probably linked to a regulatory element of DNA that activates the transcription of a gene or genes.” My comment: Nutrient-dependent pheromone-controlled fixation of RNA-mediated amino acid substitutions links the epigenetic landscape to the physical landscape of DNA in the organized genomes of species from microbes to man via conserved molecular mechanisms of the biophysically constrained…

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An epigenetic mark links algae, worms, and flies

New Epigenetic Mark Found on Metazoan DNA Three studies identify roles for N6-methyladenosine in algae, worms, and flies. By Jenny Rood | April 30, 2015 Excerpt (with my emphasis): “In bacteria, 6mA marks the template strand during DNA replication, enabling a cell to spot errors and regulate the cell cycle. The modification also helps differentiate bacterial DNA from viral genomic material, which lacks methylation.” My comment: The ability of a cell or organism to recognize self vs other differences enables…

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  • What Darwin proved: there’s no such thing as a species
    GENETICS As Animals Mingle, a Baffling Genetic Barrier A short stretch of DNA is challenging what it means to be a species. By: Emily Singer August 5, 2014 Excerpt: “Scientists have dubbed such regions of the genome “islands of speciation.” The persistence of such islands is a phenomenon that has been observed in a variety of […]
  • Randomness and Divine Providence
    A Q&A on randomness and God’s providence …the main goal is to really put together a collection of scholarly studies of these issues: physicists, biologists, […]