Prediction of protein disorder at the domain level

Intrinsically disordered/unstructured proteins exist in a highly flexible conformational state largely devoid of secondary structural elements and tertiary contacts. Despite their lack of a well defined structure, these proteins often fulfill essential regulatory functions. The intrinsic lack of structure confers functional advantages on these proteins, allowing them to adopt multiple conformations and to bind to different binding partners. The structural flexibility of disordered regions hampers efforts solving structures at high resolution by X-ray crystallography and/or NMR. Removing such proteins/regions from high-throughput structural genomics pipelines would be of significant benefit in terms of cost and success rate. In this paper we outline the theoretical background of structural disorder, and review bioinformatic predictors that can be used to delineate regions most likely to be amenable for structure determination. The primary focus of our review is the interpretation of prediction results in a way that enables segmentation of proteins to separate ordered domains from disordered regions.     

Overpressured layer chromatographic determination of aflatoxin B1, B2, G1 and G2 in red paprika

Determination of aflatoxin B1 and total aflatoxin (B1 + B2 + G1 + G2) in red paprika powder is described using column chromatographic sample clean-up, overpressured layer chromatography (OPLC) separation and fluorescence densitometric evaluation. Two OPLC methods were developed for separation of the four aflatoxins. The detection limit and quantification limit of aflatoxins in red paprika were 0.5 and 1 μg/kg in both methods, respectively. Recovery experiment was carried out with sample containing 1.74 μg/kg aflatoxin B1 and 3.56 μg/kg total aflatoxins measured by European standard HPLC method. Mean recovery amounted to 78.5% (SD 16.1%, n = 5) for aflatoxin B1 and 81.8% (SD 17.1%, n = 5) for total aflatoxins in the case of method 1. It was 105.3% (SD 10.7%, n = 5) for aflatoxin B1 and 97.4% (SD 18.6%, n = 5) for total aflatoxins using the method 2. Despite of that the Hungarian climate is not proper for the toxin production of moulds high aflatoxin B1 contaminated red paprika purchased from the market was found, which may originate from mixing of imported paprika containing very high level toxin with Hungarian one.     

Application of cyclodextrins in environmental bioassays for soil

Based on our former experience on contaminant solubilisation and mobilisation in the process of soil remediation we used cyclodextrins as additives in environmental bioassays, for improving solubility and bioavailability of the contaminant in soil and as a consequence sensitivity of the bioassay. In this article we introduce the findings on the application of RAMEB (randomly methylated ??-cyclodextrin) for testing PCP (pentachlorophenol) in soil, in three bioassays: bacterial luminescence-inhibition test with Vibrio fischeri, protozoon growth inhibition test with Tetrahymena pyriformis, and Ames mutagenicity test. We applied RAMEB which has a high solubilising capacity on many typical soil contaminant and PCP, because contradictory results were published for its toxicity and mutagenicity. The RAMEB-aided Ames test, gave a sudden and expressed increase in the mutagenicity of PCP, however, Ames mutagenicity was negative without cyclodextrin (CD). Based on these results we tried to apply RAMEB for increasing sensitivity of other bioassays, such as acute toxicity tests with different test organisms. According to our results the effect of RAMEB on bioavailability and toxic effect depends not only on the K _ow value (octanol?Cwater partition coefficient) of the chemical substances, but also on the test organism, the water-content of the test-matrix and the applied concentration of RAMEB, as well as its ratio to PCP. We collected all the characteristics of the bioassays applied for PCP and some other contaminants and showed the measured effect data in comparison with each other. We found that in the complex system of soil and soil suspension, used in the bioassays, the interactions between soil solid, water and gaseous phases, as well as between the test organism and RAMEB result in K _ow dependent partition of the contaminant between solid and water phases of soil, RAMEB, and the test organism. The conclusion is that RAMEB undoubtedly has an influence on the fate and behaviour of the contaminant in soil and soil suspensions, and the direction of the RAMEB-induced changes depends on the effective concentration of the RAMEB in the bioassay, the time of contact, the type of test organism, and the characteristics of the RAMEB?Ccontaminant complex. In those cases, when RAMEB increased the effect of a contaminated environmental sample, this CD-induced increase can be considered as a ??realistic worse case?? situation, which can be very useful in risk assessment, resulting in a moderate overestimate in the value of environmental risk.     

Time variations of 222Rn concentration and air exchange rates in a Hungarian cave

A long-term radon concentration monitoring was carried out in the Pál-völgy cave, Budapest, Hungary, for 1.5 years. Our major goal was to determine the time dependence of the radon concentration in the cave to characterise the air exchange and define the most important environmental parameters that influence the radon concentration inside the cave. The radon concentration in the cave air was measured continuously by an AlphaGuard radon monitor, and meteorological parameters outside the cave were collected simultaneously. The air's radon concentration in the cave varied between 104 and 7776 Bq m^?3, the annual average value was 1884±85 Bq m^?3. The summer to winter radon concentration ratio was as high as 21.8. The outside air temperature showed the strongest correlation with the radon concentration in the cave, the correlation coefficient (R) was 0.76.     

Electron irradiation assisted annealing of boron and phosphorus implanted silicon layers

Radíatíon annealing due to a 1.0 MeV election beam of intensity 25 μA/cm² was studied in silicon samples implanted with phosphorus and boron ions and annealed at 350–500°C. A significant annealing enhancement as compared to thermal annealing has been observed in phosphorus-implanted samples. In boron-implanted samples, a fast initial rise of electrical activity is followed by a continuous decrease of carrier concentration. The results are interpreted in terms of two competing processes: electron irradiation induced removal of post-implantation defects and introduction of simple electrically active defects.     

Athermal effects in ion implanted layers

Abstract

Defect structure and electrical characterization of boron and arsenic implanted layers has been investigated for implantation under athermal (light) excitation. This Photon Assisted (PA) implantation owes its specific properties to an additional electric field acting on charged particles including carriers and charged defects. It was shown that in case of n-type silicon this extra field draws charged vacancies and self-interstitials towards each other and, thus, diminishes transient diffusion of boron. This effect resulted in junctions which are about 20% shallower compared to conventionally processed reference wafers. Experiments using light of an Ar-ion laser and white light of a high pressure Xe arc lamp were compared. Some deactivation of carriers in the deeper laying parts of the p-region was always a by-product.     

Löwdin’s bracketing function revisited

A variational principle is formulated for Löwdin’s bracketing function. Setting the bracketing function stationary leads to the eigenvalue equation of the resolvent operator. An Eckart-type inequality is derived for the wavefunction optimized this way. A linearized approximation of the resolvent eigenvalue equation—reminiscent of the simplest coupled electron pair (CEPA0) treatment—is examined. We prove that the asymmetric energy formula of the resulting approximate function is a strict lower bound.     

Differential scanning calorimetry (DSC) of blood serum in chronic obstructive pulmonary disease (COPD)

Chronic obstructive pulmonary disease (COPD) is a major global health challenge with a gloom perspective of being one of the big three cause of death by 2020. No reliable/reproducible biomarker has been identified so far to match the clinically-based staging system (GOLD). Blood samples of 30 subjects divided into 6 groups (no-COPD/-smoker, no-COPD/non-smoker, COPD I, COPD II, COPD III, COPD IV) with 5 patients in each were tested by differential scanning calorimetry. There is a clear 15.4 % difference between the heat flow maxima measured when no-COPD subjects were compared in accordance to their smoking/non-smoking status. Odds ratio of different heat flow in actively smoking COPD patients in stage IV and stage I was 1.61. A reverse tendency is detected in the relevant non-smoking COPD groups. The differences are inconsistent in intermediate stages (COPD II and III). DSC seems to be an applicable and objective method for monitoring nicotine abuse. There is a chance to detect specific typology of thermokinetic patterns in the two extremes of COPD (I vs. IV). Further studies with increased sample size are needed to allow calculations on specificity/sensitivity/positive and negative predictive value of enthalpies and heat flow maximums. The first clinically relevant blood-based COPD marker on the intravascular side of the alveo-capillary screen is demonstrated by our pilot study.     

Diffusion measurement of implanted Sb into Si,using SiO2 encapsulation

Large, asymmetric atomic relaxations have been shown to play a crucial role in the structure and properties of several point defects in oxide materials. Examples include trapped hole centers in alkaline-earth oxides and E1′ and E4′ oxygen-vacancy centers and peroxy-radical defects in silicon dioxide. Schirmer's “bound small polaron” model, applied in particular to the alkaline-earth oxide defects, and model treatments of the E1′ center in SiO2 by Yip, Griscom and Fowler clearly illustrate the important spectroscopic consequences of such atomic relaxations. In fact, such effects had been incorporated in Lüty's classic model of the Type II FA center in alkali halides. Edwards and Fowler have recently applied MNDO and MINDO/3 quantum-chemistry approaches to the E1′, E4′, and peroxy radical defects in SiO2. These calculations generally corroborate suggested models and bear as well on possible creation mechanisms. Large relaxation effects are likely to be important in many other defects in oxide materials.