Conformations of Complexes Derived from the Interactions of Two Stereoisomeric Bay-Region 5-Methylchrysene Diol Epoxides with DNA

Abstract

The reaction mechanisms of two isomeric bay-region diol epoxides of 5-methylchrysene (trans-1,2-dihydroxy-anti/-3,4-epoxy-1,2,3,4-tetrahydro-5-methylchrysene (DE-I) and trans-7,8-dihydroxy-anti-9,10-epoxy-7,8,9,10-tetrahydro-5-methylchrysene (DE-II) with double-stranded DNA in aqueous solutions were studied utilizing kinetic flow dichroism and fluorescence techniques. As in the case of the previously studied benzo(a)pyrene-7,8-diol-9,10-oxide isomers (BaPDE), both DE-I and DE-II rapidly form intercalation-type complexes (association constants K = 2700 and 1500 M^?1 respectively in a neutral 5mM phosphate solution). The physically bound diol epoxide molecules react on time scales of minutes to form predominantly tetraols; a greater fraction (6±1%) of DE-I than of DE-II (2–3%) molecules react with the DNA to form covalent products. The DE-II isomer is characterized by a greater reactivity than DE-I, and the rates of reaction are markedly accelerated in the presence of DNA in both cases. The linear dichroism spectra of the covalent adducts reveal that the conformations of both types of adducts are similar, with the long axes of the phenanthrenyl chromophores tilted, on the average, at angles of 38-52° with respect to the average orientations of the transition moments (at 260 nm) of the DNA bases. The conformations of the covalently bound DE-I and DE-II molecules resemble those observed in the case of the highly tumorigenic (+) enantiomer of anti-BaPDE. The differences in the biological properties of these and other polycyclic aromatic diol epoxides are discussed in terms of their reactivities with DNA and the conformations of the adducts formed.     

Role of DDAH-1 in lipid peroxidation product-mediated inhibition of endothelial NO generation

Altered nitric oxide (NO) biosynthesis is thought to play a role in the initiation and progression of atherosclerosis and may contribute to increased risk seen in other cardiovascular diseases. It is hypothesized that altered NO bioavailability may result from an increase in endogenous NO synthase (NOS) inhibitors, asymmetric dimethly araginine (ADMA), and N(G)-monomethyl arginine, which are normally metabolized by dimethyarginine dimethylamine hydrolase (DDAH). Lipid hydroperoxides and their degradation products are generated during inflammation and oxidative stress and have been implicated in the pathogenesis of cardiovascular disorders. Here, we show that the lipid hydroperoxide degradation product 4-hydroxy-2-nonenal (4-HNE) causes a dose-dependent decrease in NO generation from bovine aortic endothelial cells, accompanied by a decrease in DDAH enzyme activity. The inhibitory effects of 4-HNE (50 microM) on endothelial NO production were partially reversed with L-Arg supplementation (1 mM). Overexpression of human DDAH-1 along with antioxidant supplementation completely restored endothelial NO production following exposure to 4-HNE (50 microM). These results demonstrate a critical role for the endogenous methylarginines in the pathogenesis of endothelial dysfunction. Because lipid hydroperoxides and their degradation products are known to be involved in atherosclerosis, modulation of DDAH and methylarginines may serve as a novel therapeutic target in the treatment of cardiovascular disorders associated with oxidative stress.     

Predicting the likely response of data‐poor ecosystems to climate change using space‐for‐time substitution across domains

Predicting ecological response to climate change is often limited by a lack of relevant local data from which directly applicable mechanistic models can be developed. This limits predictions to qualitative assessments or simplistic rules of thumb in data‐poor regions, making management of the relevant systems difficult. We demonstrate a method for developing quantitative predictions of ecological response in data‐poor ecosystems based on a space‐for‐time substitution, using distant, well‐studied systems across an inherent climatic gradient to predict ecological response. Changes in biophysical data across the spatial gradient are used to generate quantitative hypotheses of temporal ecological responses that are then tested in a target region. Transferability of predictions among distant locations, the novel outcome of this method, is demonstrated via simple quantitative relationships that identify direct and indirect impacts of climate change on physical, chemical and ecological variables using commonly available data sources. Based on a limited subset of data, these relationships were demonstrably plausible in similar yet distant (>2000 km) ecosystems. Quantitative forecasts of ecological change based on climate‐ecosystem relationships from distant regions provides a basis for research planning and informed management decisions, especially in the many ecosystems for which there are few data. This application of gradient studies across domains – to investigate ecological response to climate change – allows for the quantification of effects on potentially numerous, interacting and complex ecosystem components and how they may vary, especially over long time periods (e.g. decades). These quantitative and integrated long‐term predictions will be of significant value to natural resource practitioners attempting to manage data‐poor ecosystems to prevent or limit the loss of ecological value. The method is likely to be applicable to many ecosystem types, providing a robust scientific basis for estimating likely impacts of future climate change in ecosystems where no such method currently exists.     

ROVER variant caller: read-pair overlap considerate variant-calling software applied to PCR-based massively parallel sequencing datasets

Background

We recently described Hi-Plex, a highly multiplexed PCR-based target-enrichment system for massively parallel sequencing (MPS), which allows the uniform definition of library size so that subsequent paired-end sequencing can achieve complete overlap of read pairs. Variant calling from Hi-Plex-derived datasets can thus rely on the identification of variants appearing in both reads of read-pairs, permitting stringent filtering of sequencing chemistry-induced errors. These principles underly ROVER software (derived from Read Overlap PCR-MPS variant caller), which we have recently used to report the screening for genetic mutations in the breast cancer predisposition gene PALB2. Here, we describe the algorithms underlying ROVER and its usage.

Results

ROVER enables users to quickly and accurately identify genetic variants from PCR-targeted, overlapping paired-end MPS datasets. The open-source availability of the software and threshold tailorability enables broad access for a range of PCR-MPS users.

Methods

ROVER is implemented in Python and runs on all popular POSIX-like operating systems (Linux, OS X). The software accepts a tab-delimited text file listing the coordinates of the target-specific primers used for targeted enrichment based on a specified genome-build. It also accepts aligned sequence files resulting from mapping to the same genome-build. ROVER identifies the amplicon a given read-pair represents and removes the primer sequences by using the mapping co-ordinates and primer co-ordinates. It considers overlapping read-pairs with respect to primer-intervening sequence. Only when a variant is observed in both reads of a read-pair does the signal contribute to a tally of read-pairs containing or not containing the variant. A user-defined threshold informs the minimum number of, and proportion of, read-pairs a variant must be observed in for a ‘call’ to be made. ROVER also reports the depth of coverage across amplicons to facilitate the identification of any regions that may require further screening.

Conclusions

ROVER can facilitate rapid and accurate genetic variant calling for a broad range of PCR-MPS users.     

Inferring the contribution of sexual reproduction,migration and off‐season survival to the temporal maintenance of microbial populations: a case study on the wheat fungal pathogen Puccinia striiformis f.sp. tritici

Understanding the mode of temporal maintenance of plant pathogens is an important domain of microbial ecology research. Due to the inconspicuous nature of microbes, their temporal maintenance cannot be studied directly through tracking individuals and their progeny. Here, we suggest a series of population genetic analyses on molecular marker variation in temporally spaced samples to infer about the relative contribution of sexual reproduction, off‐season survival and migration to the temporal maintenance of pathogen populations. We used the proposed approach to investigate the temporal maintenance of wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici (PST), in the Himalayan region of Pakistan. Multilocus microsatellite genotyping of PST isolates revealed high genotypic diversity and recombinant population structure across all locations, confirming the existence of sexual reproduction in this region. The genotypes were assigned to four genetic groups, revealing a clear differentiation between zones with and without Berberis spp., the alternate host of PST, with an additional subdivision within the Berberis zone. The lack of any differentiation between samples across two sampling years, and the very infrequent resampling of multilocus genotypes over years at a given location was consistent with limited over‐year clonal survival, and a limited genetic drift. The off‐season oversummering population in the Berberis zone, likely to be maintained locally, served as a source of migrants contributing to the temporal maintenance in the non‐Berberis zone. Our study hence demonstrated the contribution of both sexual recombination and off‐season oversummering survival to the temporal maintenance of the pathogen. These new insights into the population biology of PST highlight the general usefulness of the analytical approach proposed.     

Navigational ability in the domestic fowl (Gallus gallus domesticus)

Little is known about the navigational abilities of domestic fowl. The question of how chickens represent and orient in space becomes relevant when they are kept in non-cage systems. Since the sun is known to be the dominant spatial organiser in other diurnal bird species, we started our investigation of the chicken’s spatial abilities by subjecting them to a food-searching task with the sun as the only consistent visual cue. In an additional experiment we tried to rule out the use of auditory cues in finding a food reward.

Eight ISA Brown chicks were housed in outdoor pens. A separate test arena comprised an open-topped, opaque-sided wooden octagon (2 m wide and 1.5 m high). Eight goal boxes with food pots were attached to each of the arena sides; a wooden barrier inside each goal box prevented the birds from seeing the food pot before entering. After habituation we tested during five daily 5 min trials whether the chicks were able to find food in a systematically allocated goal direction. Food residue in every foot pot controlled for the use of olfactory cues and no external landmark cues were visible. Every day each box was unpredictably moved to a randomly assigned side of the arena and the side to face north was also randomly allocated, to prevent the chicks from using cues other than the sun’s position. Circular statistics were used to determine whether birds moved in a non-random direction and if so, if they significantly oriented goalwards. The results showed that seven of the eight birds moved significantly in the goal direction. It seems likely that the chicks used the sun to orient. Due to weather constraints only four chicks received the same treatment on a new location, to rule out the use of auditory cues. Two of these four chicks significantly moved in the goal direction.

The results from our experiments show that domestic chicks use spatial memory to orient towards a hidden goal. Moreover, their orientation is most likely to be based on sun cues opening up the possibility that the sun compass may dominate even in this ancestrally predominantly ground-living forest bird.     

Varying responses of insect herbivores to altered plant chemistry under organic and conventional treatments

The hypothesis that plants supplied with organic fertilizers are better defended against insect herbivores than those supplied with synthetic fertilizers was tested over two field seasons. Organic and synthetic fertilizer treatments at two nitrogen concentrations were supplied to Brassica plants, and their effects on the abundance of herbivore species and plant chemistry were assessed. The organic treatments also differed in fertilizer type: a green manure was used for the low-nitrogen treatment, while the high-nitrogen treatment contained green and animal manures. Two aphid species showed different responses to fertilizers: the Brassica specialist Brevicoryne brassicae was more abundant on organically fertilized plants, while the generalist Myzus persicae had higher populations on synthetically fertilized plants. The diamondback moth Plutella xylostella (a crucifer specialist) was more abundant on synthetically fertilized plants and preferred to oviposit on these plants. Glucosinolate concentrations were up to three times greater on plants grown in the organic treatments, while foliar nitrogen was maximized on plants under the higher of the synthetic fertilizer treatments. The varying response of herbivore species to these strong differences in plant chemistry demonstrates that hypotheses on defence in organically grown crops have over-simplified the response of phytophagous insects.     

Sub-alpine amphibian distributions related to species palatability to non-native salmonids in the Klamath mountains of northern California

The goal of this study was to examine how introduced trout influence the distributions and abundances of a sub‐alpine amphibian assemblage whose members display a variety of different life‐history and defence strategies. Our study was conducted in the sub‐alpine lentic habitats of three wilderness areas that form the core of the Klamath‐Siskiyou Bioregion of northern California, a biodiversity ‘hotspot’ that supports the highest diversity of sub‐alpine, lentic‐breeding amphibians in the western USA. These wilderness areas contain no native fishes, but all have been populated with non‐native trout for recreational fishing. Five of the eight amphibian species that occur in this region were sufficiently common to use in our study; these included one that breeds in both temporary and permanent waters and is palatable to fish (Pacific treefrog, Pseudacris regilla), two that breed primarily in permanent waters and are unpalatable to fish (western toad, Bufo boreas, and rough‐skinned newt, Taricha granulosa), and two that breed primarily in permanent waters and are palatable to fish (Cascades frog, Rana cascadae, and long‐toed salamander, Ambystoma macrodactylum). Based on life histories and predator defence strategies (i.e. palatable or not), we predicted that the three palatable species would likely be negatively correlated with introduced trout, but with P. regilla less impacted because of its use of both temporary and permanent waters. We predicted that B. boreas and T. granulosa would not be significantly correlated with introduced trout due to the lack of any predator/prey interactions between them. We surveyed 728 pond, lake, or wet meadow sites during the summers of 1999–2002, using timed gill‐net sets to measure trout occurrence and relative density, and visual encounter surveys to determine amphibian presence and abundance. We used semiparametric logistic regression models to quantify the effect of trout presence/absence and density on the probability of finding amphibian species in a water body while accounting for variation within and among the various lentic habitats sampled. The distributions of P. regilla, A. macrodactylum and R. cascadae were strongly negatively correlated with trout presence across all three wilderness areas. Ambystoma macrodactylum was 44 times more likely to be found in lakes without fish than in lakes with fish. Rana cascadae and P. regilla were 3.7 and 3.0 times more likely, respectively, to be found in fishless than fish‐containing waters. In contrast, the two unpalatable species were either uncorrelated (T. granulosa) or positively correlated (B. boreas) with fish presence. We found that the relative density of fish (catch per unit effort) was negatively correlated with the combined abundances of the three palatable amphibians, and also with both the length and the condition of the fish themselves. Our results are consistent with a compelling body of evidence that introduced fishes greatly alter the aquatic community structure of mountain lakes, ponds, and wet meadows.     

Identification of the N-linked glycosylation sites of vitamin K-dependent carboxylase and effect of glycosylation on carboxylase function

The vitamin K-dependent carboxylase is an integral membrane protein which is required for the post-translational modification of a variety of vitamin K-dependent proteins. Previous studies have suggested carboxylase is a glycoprotein with N-linked glycosylation sites. In this study, we identify the N-glycosylation sites of carboxylase by mass spectrometric peptide mapping analyses combined with site-directed mutagenesis. Our mass spectrometric results show that the N-linked glycosylation in carboxylase occurs at positions N459, N550, N605, and N627. Eliminating these glycosylation sites by changing asparagine to glutamine caused the mutant carboxylase to migrate faster on SDS-PAGE gels, adding further evidence that these sites are glycosylated. In addition, the mutation studies identified N525, a site that cannot be recovered by mass spectroscopy analysis, as a glycosylation site. Furthermore, the potential glycosylation site at N570 is glycosylated only if all five natural glycosylation sites are simultaneously mutated. Removal of the oligosaccharides by glycosidase from wild-type carboxylase or by elimination of the functional glycosylation sites by site-directed mutagenesis did not affect either the carboxylation or epoxidation activity when the small FLEEL pentapeptide was used as a substrate, suggesting that N-linked glycosylation is not required for the enzymatic function of carboxylase. In contrast, when site N570 and the five natural glycosylation sites were mutated simultaneously, the resulting carboxylase protein was degraded. Our results suggest that N-linked glycosylation is not essential for carboxylase enzymatic activity but is important for protein folding and stability.     

Early life-history processes and their implications for the invasion of the barnacle Balanus glandula

As invasions become increasingly prevalent, it is important to understand how spread may be moderated by environmental conditions. This study considered the effect of location and changing substratum temperature on the early life-history processes of the alien barnacle Balanus glandula and its native comparator, Chthamalus dentatus, along the South African coast. Using settlement plates of different colours, temperature was manipulated to assess settlement, mortality, recruitment and growth of the two species. These variables were tracked over 10 weeks using repeat photography. Unexpectedly, there was no evidence of an effect of temperature on early life-history processes of either species. Settlement by the two barnacles was spatially segregated, with B. glandula occurring only on the West Coast where it is the dominant intertidal barnacle, while C. dentatus settled only on the South Coast, which has only recently been invaded by the alien. Despite this, it was notable that the relative settlement of B. glandula on rock was higher than that of C. dentatus. However, the lack of mortality of the native resulted in comparable levels of recruitment among the species. Nonetheless, the propensity of B. glandula to settle sporadically, coupled with fast growth, suggests that the invader may still possess the ability to become dominant along the newly invaded South Coast. This study highlights that measurements of early life-history parameters may not adequately predict the future range and impacts of alien species unless interpreted within the broader context of the nature of the recipient region and species-specific traits of the invader.