Structural Insights into the Mechanism of Base Excision by MBD4

DNA glycosylases remove damaged or modified nucleobases by cleaving the N-glycosyl bond and the correct nucleotide is restored through subsequent base excision repair. In addition to excising threatening lesions, DNA glycosylases contribute to epigenetic regulation by mediating DNA demethylation and perform other important functions. However, the catalytic mechanism remains poorly defined for many glycosylases, including MBD4 (methyl-CpG binding domain IV), a member of the helix-hairpin-helix (HhH) superfamily. MBD4 excises thymine from G·T mispairs, suppressing mutations caused by deamination of 5-methylcytosine, and it removes uracil and modified uracils (e.g., 5-hydroxymethyluracil) mispaired with guanine. To investigate the mechanism of MBD4 we solved high-resolution structures of enzyme-DNA complexes at three stages of catalysis. Using a non-cleavable substrate analog, 2′-deoxy-pseudouridine, we determined the first structure of an enzyme-substrate complex for wild-type MBD4, which confirms interactions that mediate lesion recognition and suggests that a catalytic Asp, highly conserved in HhH enzymes, binds the putative nucleophilic water molecule and stabilizes the transition state. Observation that mutating the Asp (to Gly) reduces activity by 2700-fold indicates an important role in catalysis, but probably not one as the nucleophile in a double-displacement reaction, as previously suggested. Consistent with direct-displacement hydrolysis, a structure of the enzyme-product complex indicates a reaction leading to inversion of configuration. A structure with DNA containing 1-azadeoxyribose models a potential oxacarbenium-ion intermediate and suggests the Asp could facilitate migration of the electrophile towards the nucleophilic water. Finally, the structures provide detailed snapshots of the HhH motif, informing how these ubiquitous metal-binding elements mediate DNA binding.     

Nutrient responses to the liming of lake Gårdsjön

The acidified lakes Lake Gårdsjön and Lake Stora Hästevatten the reference lake have been monitored since 1979 and 1980 respectively. The lakes are situated in SW Sweden; in an area severly affected by acid deposition. Lake Gårdsjön was limed in spring 1982. This paper analyses changes in nutrient concentrations upon liming of Lake Gårdsjön. The liming of Lake Gårdsjön was followed by a slight increase in ammonium, nitrate, and dissolved organic nitrogen concentrations. A drastic decrease occurred in particulate nitrogen and particulate carbon, whereas dissolved organic carbon increased. Total phosphorus and particulate phosphorus concentrations were similar to pre-limed conditions. The long-term decrease in phosphorus concentration, exhibited by the reference lake, was not identified in Lake Gårdsjön after liming, but total phosphorus concentration was still less than half compared to Lake Gårdsjön in the early 1970's. Additional measures such as phosphorus fertilization, should in certain cases be considered in addition to liming if the goal is to restore lakes to their pre-acidic conditions.     

Preparation of capacitor’s electrode from sunflower seed shell

Series of nanoporous carbons are prepared from sunflower seed shell (SSS) by two different strategies and used as electrode material for electrochemical double-layer capacitor (EDLC). The surface area and pore-structure of the nanoporous carbons are characterized intensively using N₂ adsorption technique. The results show that the pore-structure of the carbons is closely related to activation temperature and dosage of KOH. Electrochemical measurements show that the carbons made by impregnation-activation process have better capacitive behavior and higher capacitance retention ratio at high drain current than the carbons made by carbonization-activation process, which is due to that there are abundant macroscopic pores and less interior micropore surface in the texture of the former. More importantly, the capacitive performances of these carbons are much better than ordered mesoporous carbons and commercial wood-based active carbon, thus highlighting the success of preparing high performance electrode material for EDLC from SSS.     

Aging-related changes in the sensitivity of the system of respiratory control and the intensity of free-radical processes in humans

Results of a comparative study of the sensitivity of the system of respiratory control to increases in the CO₂ concentration and the intensity of free-radical processes in young and elderly subjects are described. It is shown that normal (natural) aging is accompanied by a decrease in the sensitivity of the respiratory system to hypercapnic stimulation and a parallel significant decrease in the activity of catalase in the blood of examined subjects. Mechanisms responsible for the modifications of the sensitivity of the system of respiratory control to hypercapnia are discussed; these shifts can be at least partly related to changes in the intensity of production of free radicals observed in elderly subjects. Neirofiziologiya/Neurophysiology, Vol. 40, No. 1, pp. 53–57, January–February, 2008.     

Regional differences in the carbon isotopic compositions of teak from two monsoonal regimes of India

Inter and intra-annual carbon isotope compositions (δ¹³C) of several annual growth rings of teak trees from two monsoonal regimes from India were studied and compared with the corresponding oxygen isotopic (δ¹⁸O) variations. In teak from both the regimes, amplitudes of intra-annual δ¹³C were ∼2-3 times lower than that observed in δ¹⁸O. Seasonal cycle with lower δ¹³C values at the middle and higher at ring boundaries was observed for teak from central India, dominated by the southwest monsoon. Positive correlations of intra-annual δ¹³C values with the corresponding δ¹⁸O values of the same rings and with relative humidity (RH) of the concurrent period suggest a dominant role of RH in controlling δ¹³C values of teak from central India. Intra-annual δ¹³C variations of teak from southern India, receiving both the southwest and northeast monsoons, revealed an initial decreasing trend followed by an increasing trend before culminating in depleted ¹³C values at the end of the growing season. No correlation was observed between intra-annual δ¹³C and δ¹⁸O variations of teak trees from southern India. Regional differences in the climatology of δ¹³C of atmospheric CO₂ or the lengths of growing season could be likely reasons for differing intra-annual δ¹³C variations of teak from the two climatic regimes.     

Dynamic Light Regulation of Photosynthesis (A Review)

Regulatory reactions providing the photosynthetic apparatus with the ability to respond to variations of irradiance by changes in activities of the light and the dark stages of photosynthesis within a time range of seconds and minutes are considered in the review. At the light stage, such reactions are related to the changes in both distribution of light energy between two photosystems and probability of nonphotochemical dissipation of absorbed quanta in PSI and PSII. These regulatory reactions operate in a negative feedback mode, thus avoiding overreduction of electron transport chain and minimizing the probability of generation of reactive oxygen species. The crucial role in preventing the generation of reactive oxygen species belongs to dynamic regulation of electron transport activity despite the presence of complex system of their detoxification in chloroplasts. In dark reactions of Calvin cycle, the regulatory responses involve a positive feedback principle being related to redox regulation of activities of several enzymes, which is sensitive to the reduction status of PSI acceptor side. The complex of regulatory reactions based on negative and positive feedback principles provides prolonged functioning of a chloroplast and high stability of photosynthetic activity under various light conditions.