Protein engineering of cytochrome c by semisynthesis: substitutions at Glutamic acid 66

We have used protein semisynthesis to prepare four analogues of horse cytochrome c, in which the glutamic acid residue at position 66 has been removed and replaced by norvaline, glutamine, lysine and, as a methodological control, glutamic acid. This residue is quite strongly conserved in mitochondrial cytochrome c, and forms part of a cluster of acidic residues that occurs in all cytochromes c but whose function is obscure. Comparative studies of the physical and biochemical properties of the analogues have now disclosed two specific roles for Glu66 in the protein. It contributes significantly to the stabilization of the active conformation of the protein, probably by salt bridge formation, and it appears to participate in the redox-state-dependent ATP-binding site of cytochrome c. Our results also support two general views of the role of surface charged residues in cytochrome c, namely that their disposition influences both redox potential, through the electrostatic field felt at the redox centre, and the kinetics of electron transfer, through the dipole moment they generat

Computational and statistical approaches for quantifying the role of multi-scale heterogeneity in Leishmania transmission dynamics

Leishmaniasis, a neglected tropical disease caused by infection with Leishmania parasites, affects millions of people annually across the globe. Leishmania transmission is facilitated by the sand fly vector, thus occurring across a range of climates with notable hotspots in Brazil and India. Its persistence despite ongoing eradication efforts underscores the importance of a complete understanding of the transmission dynamics in a range of environments. Developing this understanding requires tailored tools as the transmission dynamics are affected by heterogeneity at multiple scales, giving rise to a complex web of interactions. At the micro-scale, transmission is influenced by the heterogeneous parasite distributions of the host’s skin as well as the complex parasite life cycle in the sand fly and its link to sand fly biting behaviour. We derive and parameterise a simple model incorporating these factors, finding that their interactions give rise to unexpected transmission opportunities. The communities in which leishmaniasis typically propagates are highly heterogeneous but also ideal candidates for deploying network models. We test analytic estimates for two epidemiologically relevant quantities, the R0 (the average number of secondary infections caused by a single infected individual over their entire duration of infection) and the endemic equilibrium, in the context of heterogeneous networks. Although both prove to be unreliable for these structured communities, they have the potential to improve our understanding of when and where epidemics are likely to occur and be more severe. We also demonstrate the potential of using survival analysis to investigate medium and large-scale dynamics, first by confirming the role of distance in leishmaniasis transmissibility at the community level, and then by highlighting the role of social vulnerability in creating endemic hotspots. We then offer guidance for optimal application of survival analysis to future leishmaniasis research. Finally, these findings are synthesised with the wider literature to identify potential methodological improvements and further avenues of inquiry to further develop our knowledge of leishmaniasis transmission

Optical Band Splitting and Electronic Perturbations of the Heme Chromophore in Cytochrome c at Room Temperature Probed by Visible Electronic Circular Dichroism Spectroscopy

AbstractWe have measured the electronic circular dichroism (ECD) of the ferri- and ferro-states of several natural cytochrome c derivatives (horse heart, chicken, bovine, and yeast) and the Y67F mutant of yeast in the region between 300 and 750nm. Thus, we recorded the ECD of the B- and Q-band region as well as the charge-transfer band at ∼695nm. The B-band region of the ferri-state displays a nearly symmetric couplet at the B0-position that overlaps with a couplet 790cm−1 higher in energy, which we assigned to a vibronic side-band transition. For the ferro-state, the couplet is greatly reduced, but still detectable. The B-band region is dominated by a positive Cotton effect at energies lower than B0 that is attributed to a magnetically allowed iron→heme charge-transfer transition as earlier observed for nitrosyl myoglobin and hemoglobin. The Q-band region of the ferri-state is poorly resolved, but displays a pronounced positive signal at higher wavenumbers. This must result from a magnetically allowed transition, possibly from the methionine ligand to the dxy-hole of Fe3+. For the ferro-state, the spectra resolve the vibronic structure of the Qv-band. A more detailed spectral analysis reveals that the positively biased spectrum can be understood as a superposition of asymmetric couplets of split Q0 and Qv-states. Substantial qualitative and quantitative differences between the respective B-state and Q-state ECD spectra of yeast and horse heart cytochrome c can clearly be attributed to the reduced band splitting in the former, which results from a less heterogeneous internal electric field. Finally, we investigated the charge-transfer band at 695nm in the ferri-state spectrum and found that it is composed of at least three bands, which are assignable to different taxonomic substates. The respective subbands differ somewhat with respect to their Kuhn anisotropy ratio and their intensity ratios are different for horse and yeast cytochrome c. Our data therefore suggests different substate populations for these proteins, which is most likely assignable to a structural heterogeneity of the distal Fe-M80 coordination of the heme chromophore

Perceptions of auditor independence: U.K. evidence

The reality and perception of auditor independence is fundamental to public confidence in financial reporting. A new Independence Standards Board was set up in the U.S. in 1997 and the European Union (EU) is currently seeking to establish a common core of independence principles. The general setting within which audit decisions are made and independence perceptions are formed is evolving rapidly due to competitive and regulatory changes. Policy-makers must work continuously to evaluate the critical threat factors and develop appropriate independence principles. This paper explores the potential of recent regulatory reforms in the United Kingdom (U.K.), many of which are unique to that country, to strengthen the independence framework. Using a questionnaire instrument, U.K. interested parties' perceptions of the influence on auditor independence of a large set of 45 economic and regulatory factors are elicited. Most factors have a significant impact on independence perceptions for all groups (finance directors, audit partners, and financial journalists). The principal threat factors relate to economic dependence and non-audit service provision, while the principal enhancement factors relate to regulatory changes introduced in the early 1990s (the existence of an audit committee, the risk of referral to the Financial Reporting Review Panel and the risk to the audit firm of loss of Registered Auditor status). Exploratory factor analysis reduces the factor set to a smaller number of uncorrelated underlying dimensions

Transient absorption spectroscopy detection of sensitized delayed fluorescence in chiral benzophenone/naphthalene systems

Transient absorption spectroscopy has proven to be a powerful tool to investigate the formation and decay of excited singlet states upon triplet–triplet annihilation, following T–T energy transfer from a selectively excited sensitizer. Thus, upon selective excitation of benzophenone (BZP) by laser flash photolysis (LFP) at λ = 355 nm in the presence of naphthalene (NPT), a negative band centered at 340 nm has been detected, with growth and decay in the microsecond timescale. It has been assigned to the P-type NPT delayed-fluorescence. In the case of chiral BZP/NPT systems, stereodifferentiation has been observed in the kinetics of the involved photophysical processesFinancial support from the MICINN (Grant CTQ2010-14882 and predoctoral fellowship to P. B.) is gratefully acknowledged.Bonancía Roca, P.; Jiménez Molero, MC.; Miranda Alonso, MÁ. (2011). Transient absorption spectroscopy detection of sensitized delayed fluorescence in chiral benzophenone/naphthalene systems. Chemical Physics Letters. 515(1-3):194-196. https://doi.org/10.1016/j.cplett.2011.08.096S1941965151-

Redox evolution of a degassing magma rising to the surface.

Volatiles carried by magmas, either dissolved or exsolved, have a fundamental effect on a variety of geological phenomena, such as magma dynamics1–5 and the composition of the Earth's atmosphere 6. In particular, the redox state of volcanic gases emanating at the Earth's surface is widely believed to mirror that of the magma source, and is thought to have exerted a first-order control on the secular evolution of atmospheric oxygen6,7. Oxygen fugacity (fO2 ) estimated from lava or related gas chemistry, however, may vary by as much as one log unit8–10, and the reason for such differences remains obscure. Here we use a coupled chemical–physical model of conduit flow to show that the redox state evolution of an ascending magma, and thus of its coexisting gas phase, is strongly dependent on both the composition and the amount of gas in the reservoir. Magmas with no sulphur show a systematic fO2 increase during ascent, by as much as 2 log units. Magmas with sulphur show also a change of redox state during ascent, but the direction of change depends on the initial fO2 in the reservoir. Our calculations closely reproduce the H2S/SO2 ratios of volcanic gases observed at convergent settings, yet the difference between fO2 in the reservoir and that at the exit of the volcanic conduit may be as much as 1.5 log units. Thus, the redox state of erupted magmas is not necessarily a good proxy of the redox state of the gases they emit. Our findings may require re-evaluation of models aimed at quantifying the role of magmatic volatiles in geological processes

Redox control of sulfur degassing in silicic magmas

International audienceExplosive eruptions involve mainly silicic magmas in which sulfur solubility and diffusivity are low. This inhibits sulfur exsolution during magma uprise as compared to more mafic magmas such as basalts. Silicic magmas can nevertheless liberate large quantities of sulfur as shown by the monitoring of SO2 in recent explosive silicic eruptions in arc settings, which invariably have displayed an excess of sulfur relative to that calculated from melt degassing. If this excess sulfur is stored in a fluid phase, it implies a strong preference of sulfur for the fluid over the melt under oxidized conditions, with fluid/melt partition coefficients varying between 50 and 2612, depending on melt composition. Experimentally determined sulfur partition coefficients for a dacite bulk composition confirm this trend and show that in volcanic eruptions displaying excess gaseous sulfur, the magmas were probably fluid-saturated at depth. The experiments show that in more reduced silicic magmas, those coexisting only with pyrrhotite, the partition coefficient decreases dramatically to values around 1, because pyrrhotite locks up nearly all the sulfur of the magma. Reevaluation of the sulfur yields of some major historical eruptions in the light of these results shows that for oxidized magmas, the presence of 1-5 wt % fluid may indeed account for the differences observed between the petrologic estimate of the sulfur yield and that constrained from ice core data. Explosive eruptions of very large magnitude but involving reduced and cool silicic magmas, such as the Toba or the Bishop events, release only minor amounts of sulfur and could have consequently negligible long-term (years to centuries) atmospherical effects. This redox control on sulfur release diminishes as the melt composition becomes less silicic and as temperature increases, because both factors favor more efficient melt sulfur degassing owing to the increased diffusivity of sulfur in silicate melts under such conditions

The Pleistocene cinder cones surrounding Volcán Colima, Mexico re-visited: eruption ages and volumes, oxidation states, and sulfur content

Located at the volcanic front in the western Mexican arc, in the Colima Rift, is the active Volcán Colima, which lies on the southern end of the massive (∼450 km 3 ) Colima-Nevado volcanic complex. Along the margins of this andesitic volcanic complex, is a group of 11 scoria cones and associated lavas, which have been dated by the 40 Ar/ 39 Ar method. Nine scoria cones erupted ∼1.3 km 3 of alkaline magma (basanite, leucite-basanite, minette) between 450 and 60 ka, with >99% between 240 and 60 ka. Two additional cones (both the oldest and calc-alkaline) erupted <0.003 km 3 of basalt (0.5 Ma) and <0.003 km 3 of basaltic andesite (1.2 Ma), respectively. Cone and lava volumes were estimated with the aid of digital elevation models (DEMs). The eruption rate for these scoria cones and their associated lavas over the last 1.2 Myr is ∼1.2 km 3 /Myr, which is more than 400 times smaller than that from the andesitic Colima-Nevado edifice. In addition to these alkaline Colima cones, two other potassic basalts erupted at the volcanic front, but ∼200 km to the ESE (near the historically active Volcán Jorullo), and were dated at 1.06 and 0.10 Ma. These potassic suites reflect the tendency in the west-central Mexican arc for magmas close to the volcanic front to be enriched in K 2 O relative to those farther from the trench.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/47809/1/445_2005_Article_15.pd

Cytomegalovirus Retinitis: The Neglected Disease of the AIDS Pandemic

The authors describe CMV retinitis in resource-poor settings and suggest possibilities for management

A Network Model for Primary Production Highlights Linkages Between Salmonid Populations and Autochthonous Resources

Spatial variation in fish densities across river networks suggests that the influence of food and habitat resources on assemblages varies greatly throughout watersheds. Conceptual models predict that in situ primary production should vary with river characteristics, but the influence of autochthonous resource availability on the capacity for river reaches to support fish is poorly understood. We estimated primary production throughout the South Fork and Middle Fork of the John Day River, Oregon, by measuring diel cycles in dissolved oxygen (DO) during July 2013. Using these data, we (1) evaluated the extent to which juvenile salmonid abundance and resource limitation correlated with areas of high gross primary production (GPP), (2) developed models to predict GPP from both site‐level measurements and remotely sensed data, and (3) made predictions of GPP across the entirety of the Middle Fork John Day River (MFJD) network and assessed the utility of these spatially continuous predictions for describing variation fish densities at broad scales. We produced reliable estimates of GPP at sites where DO loggers were deployed using measurements of solar exposure, water temperature, and conductivity measured at each site, as well as surrogates for these data estimated from remote sensing data sources. Estimates of GPP across fish sampling sites explained, on average, 58–63% of the variation in juvenile salmonid densities during the summer sampling period, and 51–83% during the fall sampling period, while continuous network predictions of GPP explained 44% of the variation in fish densities across 29 km of the MFJD. Further, GPP explained nearly half of the variation in juvenile steelhead dietary resource limitation, as inferred from bioenergetics modeling results. These results comprise a first effort at quantifying variation in autochthonous production across an entire river network and, importantly, provide a much‐needed food‐web context for guiding more effective fish and habitat management