Studies On The Cross Strand Hydrogen Bonds In DNA Double Helices

Abstract

A systematic analysis has been carried out to examine all the stereochemically possible bifurcated hydrogen bonds including those of cross strand type between propeller twisted base pairs in DNA double helices by stereochemical considerations involving base pairs alone and by molecular mechanics studies on dimer and trimer duplexes. The results show that there are limited number of combinations of adjacent base pairs that would facilitate bifurcated cross- strand hydrogen bond (CSH). B-type helices concomitant with negative propeller twist seem to be more favored for the occurrence of CSH than canonical A-type helices because of slide in the latter. The results also demonstrate that helices with appropriate sequences may possess continuous run of these propeller twist driven cross strand hydrogen bonds indicating that they may infact be considered as yet another general structural feature of DNA helices.     

The limitations of ‘inter-racial contact’: stories from young South Africa

This paper argues that, while the demise of apartheid has led to many situations in which South Africans now come into closer contact with one another, this increased ‘contact’ does not amount to greater racial integration. Contact occurs within a context of unequal power relations in which ‘whiteness’ continues to be privileged over ‘blackness’. The result is that white people tend to benefit more from contact with the racial ‘other’ than black people, who often experience this contact as reinforcing their expectations of continued white dominance and privilege. While contact may undermine blatantly racist practices and overt racial conflict, racialized patterns of reasoning continue to exist, often unnoticed and unchallenged. These include the assumption that race is an incontrovertible fact of experience, the privileging of whiteness, the assumption that there exist different (biological) races which evince different forms of social behaviour and that these are essential properties of people rather than being historically or socially contingent.     

Bird attacks on a butterfly with marginal eyespots and the role of prey concealment against the background

Small eyespots on butterflies have long been thought to deflect attacks, and birds are the presumptive drivers selecting for these patterns; however, evidence of this function is still ambiguous. Marginal eyespots typically consist of a UV‐reflective white pupil, surrounded by one black and one yellowish ring. We have recently shown that Cyanistes caeruleus (blue tits) attack such eyespots, but only under low light intensities with accentuated UV levels: the increased salience of the eyespots relative to the rest of the butterfly probably explains this result. Possibly the background against which the butterfly is concealed may deceive birds to make similar errors. We therefore presented speckled wood butterflies decorated with eyespots (or controls without eyespots) to C. caeruleus against two backgrounds: oak and birch bark. Our results show that: (1) eyespots, independent of background, were effective in deflecting attacks; (2) the time elapsed between a bird landing and the attack was interactively dependent on the background and whether the butterfly bore an eyespot; and (3) the speed at which a butterfly was attacked predicted the outcome, with faster birds being more prone to errors than slower birds. This underscores a speed–accuracy trade‐off in the predators, and that background plays a role in the defensive qualities of marginal eyespots. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 109 , 290–297.     

Relative roles of dispersal dynamics and competition in determining the isotopic niche breadth of a wetland fish

1. The niche variation hypothesis predicts that among‐individual variation in niche use will increase in the presence of intraspecific competition and decrease in the presence of interspecific competition. We sought to determine whether the local isotopic niche breadth of fish inhabiting a wetland was best explained by competition for resources and the niche variation hypothesis, by dispersal of individuals from locations with different prey resources or by a combination of the two. We analysed stable isotopes of carbon and nitrogen as indices of feeding niche and compared metrics of within‐site spread to characterise site‐level isotopic niche breadth. We then evaluated the explanatory power of competing models of the direct and indirect effects of several environmental variables spanning gradients of disturbance, competition strength and food availability on among‐individual variation of the eastern mosquitofish (Gambusia holbrooki). 2. The Dispersal model posits that only the direct effect of disturbance (i.e. changes in water level known to induce fish movement) influences among‐individual variation in isotopic niche. The Partitioning model allows for only direct effects of local food availability on among‐individual variation. The Combined model allows for both hypotheses by including the direct effects of disturbance and food availability. 3. A linear regression of the Combined model described more variance than models limited to the variables of either the Dispersal or Partitioning models. Of the independent variables considered, the food availability variable (per cent edible periphyton) explained the most variation in isotopic niche breadth, followed closely by the disturbance variable (days since last drying event). 4. Structural equation modelling provided further evidence that the Combined model was best supported by the data, with the Partitioning and the Dispersal models only modestly less informative. Again, the per cent edible periphyton was the variable with the largest direct effect on niche variability, with other food availability variables and the disturbance variable only slightly less important. Indirect effects of heterospecific and conspecific competitor densities were also important, through their effects on prey density. 5. Our results support the Combined hypotheses, although partitioning mechanisms appear to explain the most diet variation among individuals in the eastern mosquitofish. The results also support some predictions of the niche variation hypothesis, although both conspecific and interspecific competition appeared to increase isotopic niche breadth in contrast to predictions that interspecific competition would decrease it. We think this resulted from high diet overlap of co‐occurring species, most of which consume similar macroinvertebrates.     

Leg impairment magnifies reproductive costs in male Mediterranean fruit flies,Ceratitis capitata

Injuries frequently accumulate with age in nature. Despite the commonality of injury and the resulting impairment, there are limited experimental data for the effects of impairment on life history trade‐offs between reproduction and survival in insects. We tested the effects of artificial injury and the resulting impairment on the reproductive costs and behavior of male medflies, Ceratitis capitata (Wiedemann) (Diptera: Tephritidae). Treatment flies were impaired by amputating tarsomere segments 2–5 from the right foreleg at either eclosion or age 22 days. The effect of impairment and age on the cost of reproduction was tested by varying the timing of female availability among the treatments. Courtship behavior and copulation rates were observed hourly from age 2–5 days to determine the effects of impairment on reproductive behavior. Female access combined with the impairment reduced the life expectancy of males more than the impairment alone, whereas the health effect of amputation was influenced by age. Conversely, the risk of death due to impairment was not influenced by the males' mating status prior to amputation. The males' copulation success was reduced due to impairment, whereas courtship behavior was not affected. Impairment does not reduce the males' impulse to mate, but decreases the females' receptivity to copulation, while also increasing the cost of each successful mating. Overall, minor impairment lowers the reproductive success of males and reduces longevity.     

Amyloplast displacement is necessary for gravisensing in Arabidopsis shoots as revealed by a centrifuge microscope

The starch‐statolith hypothesis proposes that starch‐filled amyloplasts act as statoliths in plant gravisensing, moving in response to the gravity vector and signaling its direction. However, recent studies suggest that amyloplasts show continuous, complex movements in Arabidopsis shoots, contradicting the idea of a so‐called ‘static’ or ‘settled’ statolith. Here, we show that amyloplast movement underlies shoot gravisensing by using a custom‐designed centrifuge microscope in combination with analysis of gravitropic mutants. The centrifuge microscope revealed that sedimentary movements of amyloplasts under hypergravity conditions are linearly correlated with gravitropic curvature in wild‐type stems. We next analyzed the hypergravity response in the shoot gravitropism 2 (sgr2) mutant, which exhibits neither a shoot gravitropic response nor amyloplast sedimentation at 1  g . sgr2 mutants were able to sense and respond to gravity under 30  g conditions, during which the amyloplasts sedimented. These findings are consistent with amyloplast redistribution resulting from gravity‐driven movements triggering shoot gravisensing. To further support this idea, we examined two additional gravitropic mutants, phosphoglucomutase (pgm) and sgr9, which show abnormal amyloplast distribution and reduced gravitropism at 1  g . We found that the correlation between hypergravity‐induced amyloplast sedimentation and gravitropic curvature of these mutants was identical to that of wild‐type plants. These observations suggest that Arabidopsis shoots have a gravisensing mechanism that linearly converts the number of amyloplasts that settle to the ‘bottom’ of the cell into gravitropic signals. Further, the restoration of the gravitropic response by hypergravity in the gravitropic mutants that we tested indicates that these lines probably have a functional gravisensing mechanism that is not triggered at 1  g .     

Testing of divergent patterns of butterfly niche breadth in a peninsula

The butterfly fauna on the Korean peninsula are comprised of both the Palearctic and Oriental species. We hypothesized that the Oriental species (immigrated across the sea) tend to have a wider niche breadth compared with the Palearctic species (immigrated from the continent) since the former migrates long distances across the sea and has to adapt to new environments. We tested this hypothesis using Korean butterfly data on distribution, habitat, food and life history traits. The distribution and ecological traits such as habitat breadth, overwintering stage, and voltinism of the Oriental species were found to be significantly different from the Palearctic species. However, the diet breadth and food plant type were not different. These results partly confirm the peninsula niche breadth hypothesis, which predicted that Oriental species have a broader niche breadth than Palearctic species.     

Plant functional diversity enhances associations of soil fungal diversity with vegetation and soil in the restoration of semiarid sandy grassland

The trait‐based approach shows that plant functional diversity strongly affects ecosystem properties. However, few empirical studies show the relationship between soil fungal diversity and plant functional diversity in natural ecosystems. We investigated soil fungal diversity along a restoration gradient of sandy grassland (mobile dune, semifixed dune, fixed dune, and grassland) in Horqin Sand Land, northern China, using the denaturing gradient gel electrophoresis of 18S rRNA and gene sequencing. We also examined associations of soil fungal diversity with plant functional diversity reflected by the dominant species' traits in community (community‐weighted mean, CWM) and the dispersion of functional trait values (FD_is). We further used the structure equation model (SEM) to evaluate how plant richness, biomass, functional diversity, and soil properties affect soil fungal diversity in sandy grassland restoration. Soil fungal richness in mobile dune and semifixed dune was markedly lower than those of fixed dune and grassland (P < 0.05). Soil fungal richness was positively associated with plant richness, biomass, CWM plant height, and soil gradient aggregated from the principal component analysis, but SEM results showed that plant richness and CWM plant height determined by soil properties were the main factors exerting direct effects. Soil gradient increased fungal richness through indirect effect on vegetation rather than direct effect. The negative indirect effect of FDis on soil fungal richness was through its effect on plant biomass. Our final SEM model based on plant functional diversity explained nearly 70% variances of soil fungal richness. Strong association of soil fungal richness with the dominant species in the community supported the mass ratio hypothesis. Our results clearly highlight the role of plant functional diversity in enhancing associations of soil fungal diversity with community structure and soil properties in sandy grassland ecosystems.     

A mast‐seeding desert shrub regulates population dynamics and behavior of its heteromyid dispersers

Granivorous rodent populations in deserts are primarily regulated through precipitation‐driven resource pulses rather than pulses associated with mast‐seeding, a pattern more common in mesic habitats. We studied heteromyid responses to mast‐seeding in the desert shrub blackbrush (Coleogyne ramosissima), a regionally dominant species in the Mojave–Great Basin Desert transition zone. In a 5‐year study at Arches National Park, Utah, USA, we quantified spatiotemporal variation in seed resources in mast and intermast years in blackbrush‐dominated and mixed desert vegetation and measured responses of Dipodomys ordii (Ord's kangaroo rat) and Perognathus flavescens (plains pocket mouse). In blackbrush‐dominated vegetation, blackbrush seeds comprised >79% of seed production in a mast year, but 0% in the first postmast year. Kangaroo rat abundance in blackbrush‐dominated vegetation was highest in the mast year, declined sharply at the end of the first postmast summer, and then remained at low levels for 3 years. Pocket mouse abundance was not as strongly associated with blackbrush seed production. In mixed desert vegetation, kangaroo rat abundance was higher and more uniform through time. Kangaroo rats excluded the smaller pocket mice from resource‐rich patches including a pipeline disturbance and also moved their home range centers closer to this disturbance in a year of low blackbrush seed production. Home range size for kangaroo rats was unrelated to seed resource density in the mast year, but resource‐poor home ranges were larger (P < 0.001) in the first postmast year, when resources were limiting. Blackbrush seeds are higher in protein and fat but lower in carbohydrates than the more highly preferred seeds of Indian ricegrass (Achnatherum hymenoides) and have similar energy value per unit of handling time. Kangaroo rats cached seeds of these two species in similar spatial configurations, implying that they were equally valued as stored food resources. Blackbrush mast is a key resource regulating populations of kangaroo rats in this ecosystem.