Influence of proline on the thermostability of the active site and membrane arrangement of transmembrane proteins

Proline residues play a fundamental and subtle role in the dynamics, structure, and function in many membrane proteins. Temperature derivative spectroscopy and differential scanning calorimetry have been used to determine the effect of proline substitution in the structural stability of the active site and transmembrane arrangement of bacteriorhodopsin. We have analyzed the Pro-to-Ala mutation for the helix-embedded prolines Pro⁵⁰, Pro⁹¹, and Pro¹⁸⁶ in the native membrane environment. This information has been complemented with the analysis of the respective crystallographic structures by the FoldX force field. Differential scanning calorimetry allowed us to determine distorted membrane arrangement for P50A and P186A. The protein stability was severely affected for P186A and P91A. In the case of Pro⁹¹, a single point mutation is capable of strongly slowing down the conformational diffusion along the denaturation coordinate, becoming a barrier-free downhill process above 371 K. Temperature derivative spectroscopy, applied for first time to study thermal stability of proteins, has been used to monitor the stability of the active site of bacteriorhodopsin. The mutation of Pro⁹¹ and Pro¹⁸⁶ showed the most striking effects on the retinal binding pocket. These residues are the Pro in closer contact to the active site (activation energies for retinal release of 60.1 and 76.8 kcal/mol, respectively, compared to 115.8 kcal/mol for WT). FoldX analysis of the protein crystal structures indicates that the Pro-to-Ala mutations have both local and long-range effects on the structural stability of residues involved in the architecture of the protein and the active site and in the proton pumping function. Thus, this study provides a complete overview of the substitution effect of helix-embedded prolines in the thermodynamic and dynamic stability of a membrane protein, also related to its structure and function.     

Effects of mixing on methane production during thermophilic anaerobic digestion of manure: lab-scale and pilot-scale studies

The effect of mixing on anaerobic digestion of manure was evaluated in lab-scale and pilot-scale experiments at 55 degrees C. The effect of continuous (control), minimal (mixing for 10 min prior to extraction/feeding) and intermittent mixing (withholding mixing for 2h prior to extraction/feeding) on methane production was investigated in three lab-scale continuously stirred tank reactors. On comparison to continuous mixing, intermittent and minimal mixing strategies improved methane productions by 1.3% and 12.5%, respectively. Pilot-scale studies also supported the lab-scale results with an average 7% increase in biogas yields during intermittent mixing compared to continuous mixing. The effect of mixing intensities (minimal, gentle or vigorous) in batch assays at 55 degrees C showed that when the process was overloaded by high substrate to inoculum ratio (40/60), gentle (35 times per minute) or minimal mixing (10 min mixing before feeding) was advantageous compared to vigorous mixing (110 times per minute). On the other hand, under low substrate to inoculum ratio (10/90), gentle mixing was the best. The study thus indicated that mixing schemes and intensities have some effect on anaerobic digestion of manures.     

A duplex real-time PCR assay for detection of drug-induced mitochondrial DNA depletion in HepG2 cells

Screening of drug-induced mitochondrial DNA (mtDNA) depletion during early preclinical drug development is of major interest. Here we describe the establishment of a novel duplex calibrator-normalized real-time polymerase chain reaction (PCR) assay for rapid and reliable quantification of mtDNA in HepG2 cells. This assay involves quantification of an mtDNA target gene (cytochrome b) relative to a nuclear DNA (nDNA) reference gene (β-actin) in one tube. The assay was evaluated for its precision, linearity, and reproducibility, and reliable detection of mtDNA depletion was demonstrated. Using this novel real-time PCR assay, drug-induced mtDNA depletion could be accurately detected.     

Isolation of the fibrocrystalline body, a structure present in haloarchaeal species, from Halobacterium salinarum

An organized structure, the fibrocrystalline body (FB), has been isolated from the archaeon Halobacterium salinarum. The structure is also present in, and can be isolated from, other extreme halophilic archaea. FB is present in the cytoplasm during the exponential growth and early stationary phases. This structure is affected by vincristine, an antitumoral drug, which targets tubulin. The drug causes fragmentation of the FB, changes in the cell shape, and growth inhibition. Taken together, these results point toward an important role in the life of the cell for this highly organized structure.     

Role of Ca2+ in the metabolism of phenolic compounds in tobacco leaves (Nicotiana tabacum L.)

Given the essential role played by phenol metabolism in many resistance responses to different types of stress, the aim of the present work was to determine how different application rates of calcium may influence this metabolic process. Increased calcium in the nutrient solution in which tobacco plants were grown considerably reduced the foliar concentration of phenolic compounds. Calcium clearly exerted a positive influence on the activities of enzymes (phenylalanine ammonia-lyase, polyphenol oxidase and peroxidase) involved in the metabolism of the phenolics. High dosages of calcium (5 mM) promoted more oxidation than synthesis of these compounds, thus explaining the lower concentration of the phenolics.     

The nature of iron released by resident and stimulated mouse peritoneal macrophages

Mouse peritoneal macrophages were allowed to ingest ⁵⁹Fe, ¹²⁵I-labelled transferrin-antitransferrin immune complexes, and the release of ⁵⁹Fe and degraded transferrin was studied. Some iron was released as ferritin, but a major portion was bound by bovine transferrin present in the culture medium, which contained fetal calf serum. If the medium was saturated with iron prior to incubation with the cells, little of the released iron was then bound by transferrin but appeared either as a high molecular weight fraction or, if nitrilotriacetate was present in the medium, some also appeared as a low molecular weight fraction. The release of non-ferritin iron was biphasic, the early, rapid phase being more prolonged with resident cells than with stimulated cells. The rate of release in the late phase did not differ significantly between resident and stimulated cells. Incubation at 0°C completely suppressed the release of degraded transferrin, but iron release continued at about 30% of the rate seen in control cultures at 37°C. A model for the intracellular handling of ingested iron is proposed to take account of the different release patterns of resident and stimulated macrophages.     

Sampling in aerobiology. Differences between traverses along the length of the slide in Hirst sporetraps

Two years of data from four longitudinal traverses along each day's slide prepared from a continuously running Burkard sporetrap have been analyzed statistically. Using the Friedman test, a statistically significant difference was found between the four traverses, with a greater than 7% loss of pollen grains in the two outer traverses in relation to the inner. Four slides were then selected for more detailed analysis, using 18 longitudinal traverses with a 1-mm separation from the upper to the lower edge of the Melinex tape. There was found to be a progressive decline from the centre to the outside, and more than 4% of pollen grains were found outside the typical 14 mm width of the impaction orifice. There was no correlation between pollen grain size and the decline in counts from the centre to the outside. For the complete data set, there was a general rise in the diversity of pollen types with increasing sample counts, but above about 1000 pollen grains per sample there were no more than 27 pollen types found, often even fewer. A discussion is presented of whether four traverses really should be a fixing sample size, or whether it might be better to fix the total pollen count beginning with a traverse in the middle of the slide and ending with a variable number of traverses when that count is reached.     

Environmental analysis of airborne pollen occurrence,pollen source distribution and phenology of <Emphasis Type="Italic">Fraxinus angustifolia</Emphasis>

Narrow-leafed ash (Fraxinus angustifolia) is a common polygamous tree growing on the banks of rivers in the western Mediterranean region. Pollination occurs during winter, and the tree’s pollen is among the most abundant during that season. This work aims to relate the phenology of pollen shedding, source tree distribution, meteorology and airborne pollen occurrence for the species. Aerobiological sampling was conducted in Badajoz (south-western Spain) using a Hirst volumetric sampler over 24 years (1993–2016). Trees were geo-localized in a circle 500 m in diameter surrounding the pollen sampler. During the last two periods, pollination phenology was studied in 10 specimens, five in the surroundings of the pollen station and five 3 km apart, at a frequency of 3–4 days on average. Moreover, a detailed analysis of pollen occurrence was conducted for these two periods. Daily data for the whole period and hourly data over the last 2 years were used, including pollen monitoring and meteorology. A comparison was made between pollen occurrence and source distribution. The main pollen season lasted on average 53 (28–75) days. Average values were less than 10 grains m^?3, except for two periods of 23–24 grains m^?3. Daily data and hourly data correlation with meteorology showed different signs in correlation analysis. Hourly analysis showed that the maximum concentration occurred just after noon. Most pollen was recorded at an average temperature of 9 °C. Analysis of pollen sources and pollen occurrence showed a close relationship between predominant wind directions and tree distribution. Peaks of phenology were not coincident with pollen peaks. No trends in pollination were found. Non-homogeneous distribution of pollen sources for Fraxinus angustifolia provided a suitable tool to demonstrate that wind direction plays a relevant role when aerobiological data are interpreted according to source distribution. A limitation in phenology analysis and aerobiological data was noted in the narrow-leafed ash species.