RNA-directed DNA methylation

Energy dependent RNA-mediated immunity (2)

See also: Energy dependent RNA-mediated immunity (1) Neuroscience of Early-Life Learning in C. elegans See also:  Pan-neuronal imaging in roaming Caenorhabditis elegans Reported as: Watching sensory information translate into behavior “We have long been recording behavior in worms, but we and others have concluded that, if you want to get physiologically relevant neural activity patterns, you have to look at neurons inside a behaving animal,” Samuel explained. “Only in that context are all feedback loops intact, where behavioral output modulates…

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Energy-dependent RNA-mediated immunity (1)

Regulatory evolution of innate immunity through co-option of endogenous retroviruses Excerpt: The analysis revealed a primate-specific element that orchestrates the transcriptional response to interferons. Selection can therefore act on selfish genetic elements to generate novel gene networks. Reported as: A copy-and-paste gene regulatory network Excerpt: Chuong et al. provide evidence that concerted processes, involving endogenous retroviruses (ERVs), which are remarkably abundant in mammalian genomes, have contributed to the evolution of the regulatory systems that control the mammalian immune system (6).…

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The toxic river of neo-Darwinian pseudoscience

Mechanistic Basis of Resistance to PCBs in Atlantic Tomcod from the Hudson River Excerpt: Our results indicate that resistance can be due to one structural change in the coding region of a single gene and that evolutionary change in anthropogenically challenged natural populations can be rapid. My comment: Structural changes to the coding region of all genes are nutrient-dependent. This article was published in 2011 and it ignored everything known to serious scientists about the obvious links from non-coding RNAs…

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Science vs semantics

Re-interpreting long-term evolution experiments — Is delayed adaptation an example of historical contingency or a consequence of intermittent selection? Excerpt: “… the series of events used to explain adaptation in the short-transfer LTEE (and in speciation) might need to be revised. The amplification model supported by this article has already be proposed as a means of evolving new genes (1) and has been experimentally shown capable of generating a novel genetic function within as few as 3000 cell generations (11).…

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From angstroms to ecosystems and entropy

Text with these references to follow. The two submissions should be available within the month. I will announce the availability and add the text with links to the citations at that time. From hydrogen-atom transfer in DNA base pairs to ecosystems [1] Evolutionary resurrection of flagellar motility via rewiring of the nitrogen regulation system [2] Ultraviolet Absorption Induces Hydrogen-Atom Transfer in G⋅C Watson–Crick DNA Base Pairs in Solution. [3] Photonic Maxwell’s Demon [4] Common origins of RNA, protein and lipid…

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Bacteria see the light and they adapt (2)

Differential Odour Coding of Isotopomers in the Honeybee Brain Conclusion: In summary, we provided the first neurophysiological evidence of differential neural coding of isotopomers. Also, in light of the recent literature on ODEs, and considering that odour transduction in insects occurs in ≈2 ms24, it seems unlikely that perireceptor events could be responsible for the reported isotope sensitivity. Finally, we performed direct measurements of the vibrational spectra of each odorant, and reported that spectral differences among isotopomers well reflect differences in…

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Soil bacteria, bulls, cows, microRNAs, and mammary glands (2)

See also: Soil bacteria, bulls, cows, microRNAs, and mammary glands For comparison to everything known about how chemotaxis and phototaxis must be linked to supercoiled DNA via the nutrient-dependent pheromone-controlled physiology of reproduction in the context of the microRNA/messenger RNA balance and RNA-mediated cell type differentiation, see: Spectral Tuning of Killer Whale (Orcinus orca) Rhodopsin: Evidence for Positive Selection and Functional Adaptation in a Cetacean Visual Pigment Excerpt: Using codon-based likelihood models, we also found significant evidence for positive selection…

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Soil bacteria, bulls, cows, microRNAs, and mammary glands

What is Life? Excerpt:  Indeed, in the case of higher animals we know the kind of orderliness they feed upon well enough, viz. the extremely well-ordered state of matter in more or less complicated organic compounds, which serve them as foodstuffs. After utilizing it they return it in a very much degraded form -not entirely degraded, however, for plants can still make use of it. (These, of course, have their most power supply of ‘negative entropy’ the sunlight) My comment:…

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Bringing RNA back to epigenetics (20 years later)

Has Contemporary Academia Outgrown the Carl Sagan Effect?  [Subscription required] Excerpt (with my emphasis): [Sean Carroll] offered 13 pieces of advice…: “Do good research; Make an impact in the field; Bring in grant money… Don’t be too well known outside the field; Don’t write a book; Choose your hobbies wisely.” Carroll argued that academics look askance at colleagues that have too high of a public profile. Not out of envy—but because they worry that public scientists care more about their…

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Effects on invertebrate GnRH and affects on primate behavior

Introduction: Energy-dependent changes in hydrogen-atom transfer in DNA base pairs in solution have again been linked to hormone-organized and hormone-activated behaviors by the conserved molecular mechanisms we detailed in the molecular epigenetics section of our 1996 Hormones and Behavior review. The practical application of those details has been reported in the context of this article, published in the New England Journal of Medicine. Effects of Testosterone Treatment in Older Men Daily Diagnosis is emailed each weekday to members of the…

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