Redox potential of the Rieske iron-sulfur protein: Quantum-chemical and electrostatic study

Quantum-chemical study of structures, energies, and effective partial charge distribution for several models of the Rieske protein redox center is performed in terms of the B3LYP density functional method in combination with the broken symmetry approach using three different atomic basis sets. The structure of the redox complex optimized in vacuum differs markedly from that inside the protein. This means that the protein matrix imposes some stress on the active site resulting in distortion of its structure. The redox potentials calculated for the real active site structure are in a substantially better agreement with the experiment than those calculated for the idealized structure. This shows an important role of the active site distortion in tuning its redox potential. The reference absolute electrode potential of the standard hydrogen electrode is used that accounts for the correction caused by the water surface potential. Electrostatic calculations are performed in the framework of the polarizable solute model. Two dielectric permittivities of the protein are employed: the optical permittivity for calculation of the intraprotein electric field, and the static permittivity for calculation of the dielectric response energy. Only this approach results in a reasonable agreement of the calculated and experimental redox potentials.     

Transmission vs. Diffuse Transmission in Circular Dichroism: What to Choose for Probing Solid‐State Samples?

Recent advances in equipment enabled the collection of solid‐state electronic circular dichroism (ECD) spectra using the commercially available integrating sphere attachment for a regular ECD spectrometer. This accessory was designed to reduce negative factors occurring in solid‐state ECD measurements, and is, thereby, very useful for recording diffuse transmittance CD (DTCD) spectra using the pellet technique. In the present article, the operating principle of the integrating sphere and utility of the DTCD method in recording solid‐state ECD spectra is demonstrated. Based on illustrative examples, i.e., 10‐camphorsulfonic acid ammonium, cholest‐4‐en‐3‐one, (3R,4R,5S)‐oseltamivir, and (S)‐linezolid, ECD solid‐state measurements were performed by means of both transmission and diffusion methods and later compared. Selection of these compounds as models for comparative studies was made in view of their different chromophoric systems and the profound importance in the pharmaceutical industry. During the course of this work the benefits and limitations of the use of integrating sphere are presented. The final conclusion is that more relevant solid‐state spectra can be obtained by means of the DTCD method. Chirality 27:441–448, 2015. © 2015 Wiley Periodicals, Inc.     

Vegetation‐mediated impacts of trends in global radiation on land hydrology: a global sensitivity study

Incident solar radiation has changed in the last 50 years, as an initial dimming trend from 1960 to approximately 1990 was followed by an ongoing brightening period, with concomitant changes in the partitioning between direct and diffuse fractions. Such radiation changes are expected to affect the global water cycle. In this study, we use the Community Land Model (CLM) to perform global offline simulations for the period 1948–2004 and study the effects of solar forcing changes on trends in evapotranspiration and runoff. The modeled components of the hydrologic cycle respond strongly to the imposed radiation changes in several regions, especially in the tropics. Exceptions are regions with soil moisture‐limited evapotranspiration regime, such as the U.S. Great Plains. In Europe and the Eastern US, the imposed 7 W m^?2 solar dimming for 1960–1990 leads to an evapotranspiration reduction of 1.5 W m^?2 or approximately 5% of the mean and an enhancement of runoff by equal percentage. In these regions, the imposed 6 W m^?2 solar brightening leads to a 3 W m^?2 increase of evapotranspiration in 1990–2004, and a runoff reduction of between 7 and 10% of the mean. Additional simulations investigating the impact of higher diffuse radiation fraction during 1960–1990 suggest mostly an increase of evapotranspiration in the tropics of 2.5 W m^?2 (3% of mean) due to increased photosynthesis from shaded leaves, but with smaller opposite effects elsewhere because of lower ground evaporation. The runoff trend resulting from the imposed radiation/aerosols effect is of the same sign and approximate relative magnitude (but larger absolute magnitude) as those calculated, in various studies, for other potential drivers of runoff change such as climate, CO₂, or land use. These results thus strengthen the claim that radiation effects on runoff are not to be neglected. Understanding the impacts of radiation on the water cycle will affect projections of river flow and freshwater availability for human consumption.     

Restoring Remote Ecosystems

Indirect effects from climate‐driven changes in ecosystems that are remote from direct human activity pose challenges for ecological restoration. Significant and often indirect impacts on alpine ecosystems, the primary ecosystem under consideration in this article, threaten historical‐reference conditions and the viability of some species. The impetus for restoration is similar to projects involving more direct and proximate impacts, but the issues are more complicated in remote ecosystems. Restoration efforts in remote ecosystems might do more harm than good, and the effort required for effective restoration might be greater than easily justified given the shortfall of resources for restoring more heavily impacted ecosystems. The long duration and integration of impacts on remote landscapes pose a distinct set of challenges to restorationists. Intervening in remote ecosystems makes them less remote by definition (they are now affected by human agency). In this article, we examine scientific, technical, and moral issues and offer an initial model for assessing the appropriateness of restoring remote landscapes.     

Diffusely adherent Escherichia coli strains expressing Afa/Dr adhesins (Afa/Dr DAEC): hitherto unrecognized pathogens

Diffusely adherent Escherichia coli (DAEC) strains are currently considered to constitute a putative sixth group of diarrheagenic E. coli. However, on the basis of their diffuse adherence to HEp-2 and HeLa cells, the detection of afa/dra/daa-related operons encoding this adherence phenotype, and the mobilization of decay-accelerating factor, both commensal and pathogenic strains can be classified as Afa/Dr DAEC isolates. Furthermore, strains associated with diarrheal diseases and strains causing extra-intestinal infections can also be identified as Afa/Dr DAEC strains. Although several cell signaling events that occur after epithelial cells have been infected by Afa/Dr DAEC have been reported, the pathophysiological processes that allow intestinal and extra-intestinal infections to develop are not fully understood. This review focuses on the genetic organization of the afa/dra/daa-related operons and on the virulence factors that trigger cellular responses, some of which are deleterious for the host cells. Finally, this review suggests future lines of research that could help to elucidate these questions.     

Eutrophication in Australian Rivers, Reservoirs and Estuaries – A Southern Hemisphere Perspective on the Science and its Implications

Australian science has made rapid advances in the last decade in understanding eutrophication processes in inland waters and estuaries. The freshwater research on which these advances are based was triggered by well-publicised blooms of cyanobacteria during the 1980s and early 1990s, particularly a 1000 km long bloom on the Darling River. In estuaries the study which greatly enhanced our understanding but simultaneously served to stimulate further research into estuarine eutrophication, the Port Phillip Bay Study, was initially designed to address perceived problems of toxicants in the Bay but provided profound insights into drivers for, and ecosystem responses to, eutrophication. Subsequent estuarine research has largely been stimulated by management questions arising from Australia’s increasing coastal development for residential purposes. The research has shown that some of the beliefs extant at the time of the blooms were incorrect. For example, it is now clear that stratification and light penetration, not nutrient availability, are the triggers for blooms in the impounded rivers of southeastern Australia, although nutrient exhaustion limits the biomass of blooms. Again, nitrogen seems to play as important a role as phosphorus does in controlling the biomass of these freshwater blooms. The research has also shown that aspects of eutrophication, such as nutrient transport, are dominated by different processes in different parts of Australia. Many of the biophysical processes involved in eutrophication have now been quantified sufficiently for models to be developed of such processes as sediment-nutrient release, stratification, turbidity and algal growth in both freshwater and estuarine systems. In some cases the models are reliable enough for the knowledge gained in particular waterbodies to be applied elsewhere. Thus, there is now a firm scientific foundation for managers to rely upon when managing algal blooms. Whilst these findings have already been presented to managers and communities throughout Australia, there is still a considerable way to go before they are absorbed into their modus operandi.     

A study of protein structure changes during hydration by diffuse X-ray scattering: II. Fourier transform analysis of diffuse X-ray scattering data

Radial distribution functions were deduced by Fourier transform analysis of the angular dependences of diffuse X-ray scattering intensities for the following proteins with different hydration degrees: water-soluble α-protein myoglobin, water-soluble (α + β) protein lysozyme, and transmembrane proteins from the photosynthetic reaction centers of purple bacteria Rhodobacter sphaeroides and Blastochlorii (Rhodopseudomonas) viridis. The results of Fourier transform analysis of X-ray scattering intensities give quantitative characteristics of the mechanism underlying the influence of water on the formation of biological macromolecules. On the one hand, water loosens the network of hydrogen bonds, which results in a considerable conformational mobility in the molecules of lysozyme and myoglobin and the reaction centers. On the other hand, water stabilizes and orders the protein globule. A strict correlation was found between the shift of the “first” maximum of the radial distribution function, loosening of the intraglobular hydrogen bonds, increase in the intramolecular mobility, and appearance of pronounced functional activity in macromolecules. The pattern of behavior of the first maximum in the transmembrane proteins of the reaction center was similar to that observed for the water-soluble proteins. However, the first maximum reached the limiting value of 2.9 Å at a considerably lower hydration degree compared with the water-soluble proteins. A quick transition of the protein complex of the reaction center to its native state is due to the fact that the dehydrated conformation of this complex is very close to the native conformation. Comparison of the radial distribution function for water, water-soluble proteins, and transmembrane proteins suggests a quantitative conclusion that water is the least densely packed and ordered system, the water-soluble proteins are more densely packed than water, and the transmembrane proteins are the most densely packed and ordered system.     

A spectrum of novel NPHS1 and NPHS2 gene mutations in pediatric nephrotic syndrome patients from Pakistan

Background

Mutations in the NPHS1 and NPHS2 genes are among the main causes of early-onset and familial steroid resistant nephrotic syndrome respectively. This study was carried out to assess the frequencies of mutations in these two genes in a cohort of Pakistani pediatric NS patients.

Methods

Mutation analysis was carried out by direct sequencing of the NPHS1 and NPHS2 genes in 145 nephrotic syndrome (NS) patients. This cohort included 36 samples of congenital or infantile onset NS cases and 39 samples of familial cases obtained from 30 families.

Results

A total of 7 homozygous (6 novel) mutations were found in the NPHS1 gene and 4 homozygous mutations in the NPHS2 gene. All mutations in the NPHS1 gene were found in the early onset cases. Of these, one patient has a family history of NS. Homozygous p.R229Q mutation in the NPHS2 gene was found in two children with childhood-onset NS.

Conclusions

Our results show a low prevalence of disease causing mutations in the NPHS1 (22% early onset, 5.5% overall) and NPHS2 (3.3% early onset and 3.4% overall) genes in the Pakistani NS children as compared to the European populations. In contrast to the high frequency of the NPHS2 gene mutations reported for familial SRNS in Europe, no mutation was found in the familial Pakistani cases. To our knowledge, this is the first comprehensive screening of the NPHS1 and NPHS2 gene mutations in sporadic and familial NS cases from South Asia.     

Brilliant camouflage: photonic crystals in the diamond weevil, Entimus imperialis

The neotropical diamond weevil, Entimus imperialis, is marked by rows of brilliant spots on the overall black elytra. The spots are concave pits with intricate patterns of structural-coloured scales, consisting of large domains of three-dimensional photonic crystals that have a diamond-type structure. Reflectance spectra measured from individual scale domains perfectly match model spectra, calculated with anatomical data and finite-difference time-domain methods. The reflections of single domains are extremely directional (observed with a point source less than 5°), but the special arrangement of the scales in the concave pits significantly broadens the angular distribution of the reflections. The resulting virtually angle-independent green coloration of the weevil closely approximates the colour of a foliaceous background. While the close-distance colourful shininess of E. imperialis may facilitate intersexual recognition, the diffuse green reflectance of the elytra when seen at long-distance provides cryptic camouflage.