Articles on Vedanta school of philosophy.

Over 80% of the genes in the E. coli chromosome express fewer than a hundred copies each of their protein products per cell. It is argued here that transcription of these genes is neither constitutive nor regulated by protein factors, but rather, induced by the act of replication. The utility of such replication‐induced (RI) transcription to the temporal regulation of synthesis of determinate quantities of low copy number (LCN) proteins is described. It is suggested that RI transcription may be necessitated, (...) as well as facilitated, by the folding of the bacterial chromosome into a compact nucleoid. Mechanistic aspects of the induction of transcription by replication are discussed with respect to the modulation of transcriptional initiation by negative supercoiling effects, promoter methylation status and derepression. It is shown that RI transcription offers plausible explanations for the constancy of the C period of the E. coli cell cycle and the remarkable conservation of gene order in the chromosomes of enteric bacteria. Some experimental tests of the hypothesis are proposed. (shrink)

Transcription and DNA supercoiling are known to be linked by a cause‐effect relationship that operates in both directions. It is proposed here that this two‐way relationship may be exploited by the E. coli genome to facilitate constitutive transcription of supercoil‐sensitive genes by polymerase batteries made up of uniformly spaced RNA polymerase elongation complexes. Specifically, it is argued that (1) polymerases transcribing DNA in tandem cooperate to relax each other's transcription‐driven positive supercoils; and (2) negative supercoils driven upstream by elongation complexes (...) tend to be ‘harnessed’ and used to cooperatively (and periodically) initiate fresh transcription from promoters. Harnessing of transcription‐driven negative supercoils is thought to be achieved through the erection of protein barriers to the rotational upstream propagation of supercoils from transcription events. The possible relevance of such cooperation amongst polymerases to the activation of transcription by DNA‐binding protein factors is emphasized. Some testable predictions are made and implications are discussed. (shrink)

We propose that hyper‐inflammation (HYPi) is a ‘‘runaway’’ consequence of acute inflammation (ACUi) that arises more easily (and also abates less easily) in those who host a pre‐existing chronic inflammation (CHRi), because (i) most factors involved in generating an ACUi to limit viral proliferation are already present when there is an underlying CHRi, and also because (ii) anti‐inflammatory (AI) mechanisms for the abatement of ACUi (following containment of viral proliferation) are suppressed and desensitized where there is an underlying CHRi, with (...) this causing the ACUi to spiral into a HYPi. Stress, pollution, diet, and gut microbiomes (alterable in weeks through dietary changes) have an intimate and bidirectional cause‐effect relationship with CHRi. We propose that avoidance of CHRi‐promoting foods and adoption of CHRi‐suppressing foods could reduce susceptibility to HYPi, in Covid‐19 and in other viral diseases, such as influenza, which are characterized by episodic and unpredictable HYPi. (shrink)