Cell Type

RNA-mediated gene duplication, fixation, and ecological adaptation

Chromosomal Arrangement of Phosphorelay Genes Couples Sporulation and DNA Replication Excerpt: The simplicity of this coordination mechanism suggests that it may be widely applicable in a variety of gene regulatory and stress-response settings. Reported as: Bacteria use DNA replication to time key decision Excerpt: “Successful sporulation requires two complete copies of the bacterial chromosome, so coordination between the sporulation decision and the completion of DNA replication is very important,” Narula said. “A good analogy might be a semester-long course in…

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“New” epigenetic mechanism for lifelong learning?

Critical Role of Histone Turnover in Neuronal Transcription and Plasticity Reported as: Lifelong learning is made possible by recycling of histones, study says Also reported as: New epigenetic mechanism revealed in brain cells Excerpt: In humans, researchers used a technique called 14C/12C bomb pulse dating to measure turnover. The technique is based on the fact that high levels of radioactive carbon (14C) were released into the atmosphere during the 1950s and 1960s, when open-air nuclear bomb testing occurred following the…

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Amino acid substitutions are not mutations

DNA data explosion lights up the Bronze Age Excerpt: …a mutation linked to thick hair and numerous sweat glands, once thought to have emerged in East Asians, was common in Scandinavians as early as 7,700 years ago — potentially revealing a connection between these groups. My comment: Serious scientists know that what was reported to be a mutation is a nutrient-dependent amino acid substitution linked to expression of a receptor, which is linked to selection of food. Modeling Recent Human…

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Living the life that randomness created? (Sarcasm alert)

The Living Set Mathematical and computational approaches are making strides in understanding how life might have emerged and organized itself from the basic chemistry of early Earth. By Wim Hordijk | June 1, 2015 Excerpt: Put some E. coli in a dish with appropriate nutrients, and after a few days the dish will be teeming with new bacterial offspring. My comment: Put some genetically altered P. fluorescens in a dish and leave them “over-the-weekend” with their missing flagella over-the-weekend. Forget…

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Alternative splicings: epigenetics meets pharmacogenomics

Alternative splicing [is] …a regulated process during gene expression that results in a single gene coding for multiple proteins… [T]he proteins translated from alternatively spliced mRNAs will contain differences in their amino acid sequence and, often, in their biological functions…. See also: Alternative RNA Splicing in Evolution Excerpt: It now appears that alternative splicing is, perhaps, the most critical evolutionary factor determining the differences between human beings and other creatures. See also: From Fertilization to Adult Sexual Behavior Excerpt: Small…

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Epigenetic regulation of aging by glycine and GnRH

Summary:  “…the regulation of two genes involved with the production of glycine, the smallest and simplest amino acid, is partly responsible for some of the characteristics of aging. This indicates that the aging process in the mitochondrion is controlled by epigenetic regulation, not by mutations.” My comment: The broad-based extension of the fact that aging is epigenetically controlled, extends everything known about RNA-mediated cell type differentiation across the life history transitions of all genera. The focus here is on vertebrates,…

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Viruses and the human-like microbiome

Ocean’s microbiome has incredible diversity – and human likeness Excerpt: The microbiome of the world’s biggest ecosystem and one of the smallest appear to function in surprisingly similar ways. The New Scientist article  reports on: Structure and function of the global ocean microbiome Journal article abstract conclusion: …vertical stratification with epipelagic community composition mostly driven by temperature rather than other environmental factors or geography. We identify ocean microbial core functionality and reveal that >73% of its abundance is shared with…

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Informing the biologically uninformed

Please help those who are not biologically uninformed link the latest information from Science Magazine to RNA-mediated cell type differentiation in all genera. For example, see:  Eukaryotic plankton diversity in the sunlit ocean Introduction: The sunlit surface layer of the world’s oceans functions as a giant biogeochemical membrane between the atmosphere and the ocean interior (1). My comment: That fact links the anti-entropic epigenetic effects of the sun’s biological energy from the de novo creation of amino acids to RNA-mediated…

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Batch effect vs epigenetic effects

A reanalysis of mouse ENCODE comparative gene expression data [awaiting peer review] was reported as: Batch Effect Behind Species-Specific Results? Excerpt: genes in the mouse heart were expressed in a pattern more similar to that of other mouse tissues, such as the brain or liver, than the human heart. My comment: If that was an accurate representation of biologically-based cause and effect, it could not be supported by what is currently known about the biophysically constrained chemistry of nutrient-depenent pheromone-controlled…

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Bee-birthed epigenetics and primate cell types

Summary: This is a fantastic video representation of how nutrient-dependent pheromone-controlled RNA-directed DNA methylation links ecological variation to RNA-mediated ecological adaptations via amino acid substitutions in all genera. The Birth of a Bee Excerpt: After the queen bee lays a single egg in a cell of the comb, the worker bees feed the egg for a few days until it hatches into a larva. The larva continues to eat and grow until Day 10. Then, the worker bees cap the…

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