Different populations of RNA polymerase II in living mammalian cells

RNA polymerase II is responsible for transcription of most eukaryotic genes, but, despite exhaustive analysis, little is known about how it transcribes natural templates in vivo. We studied polymerase dynamics in living Chinese hamster ovary cells using an established line that expresses the largest (catalytic) subunit of the polymerase (RPB1) tagged with the green fluorescent protein (GFP). Genetic complementation has shown this tagged polymerase to be fully functional. Fluorescence loss in photobleaching (FLIP) reveals the existence of at least three kinetic populations of tagged polymerase: a large rapidly-exchanging population, a small fraction resistant to 5,6-dichloro-1-β-D-ribofuranosylbenzimidazole (DRB) but sensitive to a different inhibitor of transcription (i.e. heat shock), and a third fraction sensitive to both inhibitors. Quantitative immunoblotting shows the largest fraction to be the inactive hypophosphorylated form of the polymerase (i.e. IIA). Results are consistent with the second (DRB-insensitive but heat-shock-sensitive) fraction being bound but not engaged, while the third (sensitive to both DRB and heat shock) is the elongating hyperphosphorylated form (i.e. IIO)

Advective relief of CO2 limitation in microphytobenthos in highly productive sandy sediments

Following field observations of increased photosynthesis at increased rates of sediment flushing in sandy sediments, we conducted a series of laboratory experiments to elucidate the mechanism behind these observations. Column experiments in which water was pumped though sand at rates ranging from 0 to 613 L m−2 d−1 showed that carbon (C) fixation, as measured using carbon‐14 (14C) incorporation, increased from 6.4 to 8.6 mmol m−2 h−1 with increasing rates of flushing. Bottle incubations showed that the addition of inorganic nutrients [ammonium ion (NH4+), inorganic phosphate (HPO4−), silicic acid Si(OH)4] did not stimulate C fixation over short‐term incubations. Microprofiles of pH showed that the pH within the photic zone increased to 8.9, reducing free carbon dioxide (CO2) concentrations to ~0.5 µmol L−1. Further bottle incubations, where pH and total inorganic carbon (TCO2) were manipulated, showed that high pH (9.6) did not affect photosynthesis if free CO2 was present at concentrations of 10 µmol L−1, suggesting a direct effect of low free CO2 concentrations. 14C fixation profiles at a resolution of 100 µm recorded by b‐radiation imaging showed that while the depth specific maximum rates of C fixation were the same under both diffusive and advective (flushed) conditions, the integrated rates of photosynthesis were highest under flushed conditions because of a thickening of the photosynthetic zone. We conclude that advective pore‐water transport can enhance benthic photosynthesis in shallow permeable sand sediments by counteracting CO2 limitation

Quasi-circular Orbits for Spinning Binary Black Holes

Using an effective potential method we examine binary black holes where the individual holes carry spin. We trace out sequences of quasi-circular orbits and locate the innermost stable circular orbit as a function of spin. At large separations, the sequences of quasi-circular orbits match well with post-Newtonian expansions, although a clear signature of the simplifying assumption of conformal flatness is seen. The position of the ISCO is found to be strongly dependent on the magnitude of the spin on each black hole. At close separations of the holes, the effective potential method breaks down. In all cases where an ISCO could be determined, we found that an apparent horizon encompassing both holes forms for separations well inside the ISCO. Nevertheless, we argue that the formation of a common horizon is still associated with the breakdown of the effective potential method.Comment: 13 pages, 10 figures, submitted to PR

Must naive realists be relationalists?

Relationalism maintains that perceptual experience involves, as part of its nature, a distinctive kind of conscious perceptual relation between a subject of experience and an object of experience. Together with the claim that perceptual experience is presentational, relationalism is widely believed to be a core aspect of the naive realist outlook on perception. This is a mistake. I argue that naive realism about perception can be upheld without a commitment to relationalism