Theoretical and computational analysis of the membrane potential generated by cytochrome c oxidase upon single electron injection into the enzyme

AbstractWe have developed theory and the computational scheme for the analysis of the kinetics of the membrane potential generated by cytochrome c oxidase upon single electron injection into the enzyme. The theory allows one to connect the charge motions inside the enzyme to the membrane potential observed in the experiments by using data from the “dielectric topography” map of the enzyme that we have created. The developed theory is applied for the analysis of the potentiometric data recently reported by the Wikström group [I. Belevich, D.A. Bloch, N. Belevich, M. Wikström and M.I. Verkhovsky, Exploring the proton pump mechanism of cytochrome c oxidase in real time, Proc. Natl. Acad. Sci. U. S. A. 104 (2007) 2685–2690] on the O to E transition in Paracoccus denitrificans oxidase. Our analysis suggests, that the electron transfer to the binuclear center is coupled to a proton transfer (proton loading) to a group just “above” the binuclear center of the enzyme, from which the pumped proton is subsequently expelled by the chemical proton arriving to the binuclear center. The identity of the pump site could not be determined with certainty, but could be localized to the group of residues His326 (His291 in bovine), propionates of heme a3, Arg 473/474, and Trp164. The analysis also suggests that the dielectric distance from the P-side to Fe a is 0.4 or larger. The difficulties and pitfalls of quantitative interpretation of potentiometric data are discussed

Near-Infrared Extinction in The Coalsack Globule 2

We have conducted J, H, and Ks imaging observations for the Coalsack Globule 2 with the SIRIUS infrared camera on the IRSF 1.4 m telescope at SAAO, and determined the color excess ratio, E(J-H)/E(H-Ks). The ratio is determined in the same photometric system as our previous study for the rho Oph and Cha clouds without any color transformation; this enables us to directly compare the near-infrared extinction laws among these regions. The current ratio E(J-H)/E(H-Ks) = 1.91 +- 0.01 for the extinction range 0.5 < E(J-H) <1.8 is significantly larger than the ratios for the rho Oph and Cha clouds (E(J-H)/E(H-Ks) = 1.60-1.69). This ratio corresponds to a large negative index alpha = 2.34 +- 0.01 when the wavelength dependence of extinction is approximated by a power law which might indicate little growth of dust grains, or larger abundance of dielectric non-absorbing components such as silicates, or both in this cloud. We also confirm that the color excess ratio for the Coalsack Globule 2 has a trend of increasing with decreasing optical depth, which is the same trend as the rho Oph and Cha clouds have.Comment: 13 pages, 5 figures, and 2 tables, Ap

Bayesian analysis of the astrobiological implications of life's early emergence on Earth

Life arose on Earth sometime in the first few hundred million years after the young planet had cooled to the point that it could support water-based organisms on its surface. The early emergence of life on Earth has been taken as evidence that the probability of abiogenesis is high, if starting from young-Earth-like conditions. We revisit this argument quantitatively in a Bayesian statistical framework. By constructing a simple model of the probability of abiogenesis, we calculate a Bayesian estimate of its posterior probability, given the data that life emerged fairly early in Earth's history and that, billions of years later, curious creatures noted this fact and considered its implications. We find that, given only this very limited empirical information, the choice of Bayesian prior for the abiogenesis probability parameter has a dominant influence on the computed posterior probability. Although terrestrial life's early emergence provides evidence that life might be common in the Universe if early-Earth-like conditions are, the evidence is inconclusive and indeed is consistent with an arbitrarily low intrinsic probability of abiogenesis for plausible uninformative priors. Finding a single case of life arising independently of our lineage (on Earth, elsewhere in the Solar System, or on an extrasolar planet) would provide much stronger evidence that abiogenesis is not extremely rare in the Universe.Comment: updated acknowledgement

Reciprocal Changes in Factor XIII and Retinal Transglutaminase Expressions in the Fish Retina During Optic Nerve Regeneration

[email protected] mammals, fish retinal ganglion cells have the capacity to repair their axons even after optic nerve transection. In the process of fish optic nerve regeneration, a large number of genes have been described as regeneration-associated molecules. Using molecular cloning techniques, we identified two types of cDNA clones belonging to the transglutaminase (TG) family which were upregulation genes; one is cellular factor XIII (cFXIII) and the other is a tissue type TG named retinal transglutaminase (TGR). cFXIII mRNA started to increase in the retinal ganglion cells at 1-2 days, peaked at 5-7 days, and returned to the control level by 20 days post optic nerve injury. In contrast, TGR mRNA started to increase at day 5-10, peaked at day 20, and then gradually decreased by day 40 after nerve injury. To elucidate the molecular involvement of these TGs in optic nerve regeneration, we studied the effects of recombinant TGR protein or overexpression of cFXIII using a retinal explant culture system. cFXIII effectively induced neurite outgrowth only from naïve (intact) retinas. In contrast, the TGR protein significantly enhanced neurite outgrowth only from primed retinas, in which the optic nerve had been crushed 5-7 days previously. These reciprocal expressions of cFXIII and TGR suggest that these two types of TGs are important for the neurite sprouting and axonal elongation processes, respectively, during optic nerve regeneration processes

V1647 Orionis (IRAS 05436-0007) : A New Look at McNeil's Nebula

We present a study of the newly discovered McNeil's nebula in Orion using the JHKs-band simultaneous observations with the near-infrared (NIR) camera SIRIUS on the IRSF 1.4m telescope. The cometary infrared nebula is clearly seen extending toward north and south from the NIR source (V1647 Orionis) that illuminates McNeil's nebula. The compact nebula has an apparent diameter of about 70 arcsec. The nebula is blue (bright in J) and has a cavity structure with two rims extending toward north-east and north-west. The north-east rim is brighter and sharp, while the north-west rim is diffuse. The north-east rim can be traced out to ~ 40 arcsec from the location of the NIR source. In contrast, no cavity structure is seen toward the south, although diffuse nebula is extended out to ~ 20 arcsec. New NIR photometric data show a significant variation in the magnitudes (> 0.15 mag) of the source of McNeil's nebula within a period of one week, that is possibly under the phase of eruptive variables like FUors or EXors.Comment: 13 pages, 5 figures in JPEG format. Accepted for the publication in PASJ Letter

The Distance to the Galactic Center Derived From Infrared Photometry of Bulge Red Clump Stars

On the basis of the near infrared observations of bulge red clump stars near the Galactic center, we have determined the galactocentric distance to be R_0 = 7.52 +- 0.10 (stat) +- 0.35 (sys) kpc. We observed the red clump stars at |l| < 1.0 deg and 0.7 deg < |b| < 1.0 deg with the IRSF 1.4 m telescope and the SIRIUS camera in the H and Ks bands. After extinction and population corrections, we obtained (m - M)_0 = 14.38 +- 0.03 (stat) +- 0.10 (sys). The statistical error is dominated by the uncertainty of the intrinsic local red clump stars' luminosity. The systematic error is estimated to be +- 0.10 including uncertainties in extinction and population correction, zero-point of photometry, and the fitting of the luminosity function of the red clump stars. Our result, R_0 = 7.52 kpc, is in excellent agreement with the distance determined geometrically with the star orbiting the massive black hole in the Galactic center. The recent result based on the spatial distribution of globular clusters is also consistent with our result. In addition, our study exhibits that the distance determination to the Galactic center with the red clump stars, even if the error of the population correction is taken into account, can achieve an uncertainty of about 5%, which is almost the same level as that in recent geometrical determinations.Comment: 14 pages, 4 figures, accepted by Ap

Variabilities of the sea level anomalies in the upstream areas of the Kuroshio Current

The relationship between The Kuroshio velocities and Sea Level Anomalies (SLA) in the upstream areas (between Taiwan and Yonaguni Island) is investigated based on satellite altimetry observation. Mean of the SLA data from 2005-2008 show that in the northeast of Taiwan tends to form strong eddy activity. Furthermore, the type of eddy that forms in the upstream areas is difference every season, cold (warm) eddy more exists in summer (winter). The speed of the Kuroshio in the upstream areas is determined by combination of High- Frequency (HF) radar and Copernicus Marine Environment Monitoring Service (CMEMS) data. These two are exhibited that Kuroshio speed become faster (slower) in summer (winter). High positive correlation of the Kuroshio speed and SLA are found in between Yonaguni and Iriomote Island. When the Kuroshio speed in the middle of HF radar areas (123.375° N) became faster, it coincided with transition of warm eddy to cold eddy in the northeast of Taiwan and vice versa