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.     

Validating Landsat-based landscape metrics with fine-grained land cover data

ContextModerate-grained data may not always represent landscape structure in adequate detail which could cause misleading results. Certain metrics have been shown to be predictable with changes in scale; however, no studies have verified such predictions using independent fine-grained data.ObjectivesOur objective was to use independently derived land cover datasets to assess relationships between metrics based on fine- and moderate-grained data for a range of analysis extents. We focus on metrics that previous literature has shown to have predictable relationships across scales.MethodsThe study area was located in eastern Connecticut. We compared a 1 m land cover dataset to a 30 m resampled dataset, derived from the 1 m data, as well as two Landsat-based datasets. We examined 11 metrics which included cover areas and patch metrics. Metrics were analyzed using analysis extents ranging from 100 to 1400 m in radius.ResultsThe resampled data had very strong linear relationships to the 1 m data, from which it was derived, for all metrics regardless of the analysis extent size. Landsat-based data had strong correlations for most cover area metrics but had little or no correlation for patch metrics. Increasing analysis areas improved correlations.ConclusionsRelationships between coarse- and fine-grained data tend to be much weaker when comparing independent land cover datasets. Thus, trends across scales that are found by resampling land cover are likely to be unsuitable for predicting the effects of finer-scale elements in the landscape. Nevertheless, coarser data shows promise in predicting fine-grained for cover area metrics provided the analysis area used is sufficiently large.     

Resolving the Conflicts Between Biodiversity Conservation and Socioeconomic Development in China: Fuzzy Clustering Approach

Resolving the conflicts between biodiversity conservation and socioeconomic development is a global pursuit for the long-run prospects of the human species. Based on Wenchuan County, a typical county in southwestern China, a group of 20 indicators quantifying regional biodiversity and socioeconomic development was established to classify and evaluate the county area spatially. A fuzzy c-means clustering (FCM) algorithm was used as the classification method. Three indices including BD, DL and DR characterizing the value of biodiversity, the level and rate of socioeconomic development of the delineated regions were formulated. The results indicated that Wenchuan County was optimally classified into 4 types of regions (region I to IV). The area percentages of the regions vary widely from 4.3 to 65.7%. The sequences of the regions on biodiversity, socioeconomic development level, and socioeconomic development rate were, respectively, IV > II > III > I, I > III > II > IV and III >I >II >IV. The spatial strategy on coordinating biodiversity conservation and regional development is to develop mainly from the east(I, II, III) and to conserve mainly in the west(IV). Eco-industry, such as eco-tourism and eco-agriculture, need to be emphasized in the process of regional development. The quantitative methods used here may have a wide applicability.     

Ants resort to majority concession to reach democratic consensus in the presence of a persistent minority

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Effects of emergence phenology, taxa tolerances and taxonomic resolution on the use of the Chironomid Pupal Exuvial Technique in river biomonitoring

1. We studied chironomid communities of four rivers in south‐eastern Finland, differing in their water quality, during summer 2004 using the Chironomid Pupal Exuvial Technique, CPET. The aims of the study were to (i) test the adequacy of the generic‐level identification in the CPET method, (ii) define the emergence patterns of chironomid taxa classified as intolerant to organic pollution, (iii) assess the tolerance levels of intolerant chironomids and (iv) identify taxa most indicative of good water quality. 2. Procrustean rotation analysis indicated very strong concordance between the ordinations using either species or genus‐level data, suggesting that generic‐level identification of chironomids is adequate for biomonitoring based on CPET. However, when only a few taxa occur in great numbers, it may be advisable to identify these to the species level, especially if these taxa are important indicators of the impact in question. 3. The detection of a particular species may require accurate timing of sampling, whereas a species‐rich genus might be detected throughout a season. Given that the emergence of chironomid species may vary from year‐to‐year and between sampling sites, community differences detected at the species level may be related to between‐site variation in species’ emergence patterns rather than true differences in species composition. 4. Indicator species analysis (IndVal) showed that the distribution and abundance of intolerant chironomid taxa differed strongly among the studied rivers. Some of the intolerant taxa were restricted to unimpacted conditions, whereas others occurred mainly in impacted rivers. Thus, the indicator status of some genera (e.g. Eukiefferiella, Parametriocnemus, Stempellinella and Tvetenia) needs reassessment.     

Purification and characterization of the Danish (skive) variant of mouse liver alcohol dehydrogenase

The partially inbred Danish (Skive) strain of mice exhibits a form of liver alcohol dehydrogenase (ADH) which differs in electrophoretic mobility from that of all other inbred mouse strains thus far examined, e.g., C57BL/10, DBA/2J, and BALB/c. In order to compare the catalytic and molecular properties of the variant and normal enzyme forms, they were purified to homogeneity by ion-exchange and affinity chromatography. Tryptic peptides of reduced and carboxymethylated subunits of the normal and variant ADH forms were mapped by thin-layer two-dimensional electrophoresis and chromatography and by reversed-phase high-performance liquid chromatography. A unique nonapeptide in the Danish mouse liver ADH which did not appear in enzymes from C57BL/10, DBA/2J, or BALB/c mice was identified by both methods. Amino acid sequencing of this peptide revealed that the Arg residue at position 124, as predicted from the cDNA sequence of ADH in DBA/2J mice, has been replaced by Leu in the Danish variant. The Leu for Arg substitution in the variant form appears to account for its decreased cathodic mobility with electrophoresis in starch gels at pH 7.2. The K _m and V _max of ADH from the Danish strain for three primary alcohols and three aldehydes were similar in value to those of ADH from the C57BL/10, DBA/2J, and BALB/c strains. Based on the X-ray structure of horse liver ADH, position 124 is on the solvent-exposed surface of the catalytic domain. The finding that the kinetic constants are similar for the normal and variant forms is consistent with the observation that this residue is not in the active site and that there is no known role for it in the ADH catalytic mechanism.This work was supported by NIAAA Grant AA-04307.     

Ecology and community dynamics of Kubo people in the tropical lowlands of Papua New Guinea

Kubo producer-units (families and independent bachelors) could have been self-sufficient in the production of bananas but chose not to be. Nor did they seek self-sufficiency in the production of any combination of staple carbohydrate foods (bananas, tubers, sago flour) or, in the long term, strive for balance in the exchange of food with other producer-units. Despite the fact that bananas, which provided 50% of people's energy needs, were a delayed-return crop Kubo communities were very unstable. This instability and the failure to choose the option of self-sufficiency were connected and were mediated through intense intracommunity sharing that, ultimately, served to negotiate a concern with sorcery. The people grew bananas in the way they did, not out of environmental necessity, but to accommodate the crop to the needs of sharing and, thereby, facilitate community living.     

4',6-Dichloroflavan (BW683C): Enantiomeric separation by hplc/dad and antirhinovirus activity

Racemic 4',6-dichloroflavan (BW683C), a highly effective inhibitor of rhinovirus serotype 1B in vitro, was resolved by high-performance liquid chromatography on a chiral stationary phase. The enantiomers were separately collected and circular dichroism curves were obtained, in order to determine the absolute configuration of the two enantiomers. The activity of the isomers was studied on human rhinovirus serotype 1B multiplication in HeLa cell cultures, by means of the plaque reduction assay. Both enantiomers were potent inhibitors of virus replication; by comparing the IC₅₀ values, the S form was 3.5 times more effective than the R form.     

Preparative resolution of some 5,5-hydantoin derivatives via formation of diastereoisomeric salts

Several preparative resolutions of 5,5-disubstituted hydantoins have been achieved via fractional crystallization of diastereoisomeric salts. The process can be extended by making use of the difference between the variation of solubilities of the hydantoins and their salts with α-methylbenzylamine as a function of the alkalinity of the medium. Optimization for each resolution procedure involves a refinement of the excess amount of base needed. © 1992 Wiley-Liss, Inc.