Theoretical Analysis of the Base Stacking in DNA: Choice of the Force Field and a Comparison with the Oligonucleotide Crystal Structures

Abstract

It follows from previous studies that changes in the base pair vertical separation (BPVS) influence the architecture of DNA much more than any other conformational parameter. This inspired us to compare BPVS in the available oligonucleotide crystal structures with the optimum values provided by nine different empirical potentials employed in the theoretical studies of DNA conformation. This comparison shows that BPVS is reproduced by three fields in all steps of the highly resolved o] i go nucleoli de crystal structures while the remaining six empirical potentials, including AMBER, GROMOS and CHARMM, provide systematic deviations. We further find that the base pairs are poorly stacked (mostly compressed) in some other refined DNA crystal structures. Our analysis indicates that this poor stacking originates from improperly determined positions of the bases. The approach described in the present communication can be used to identify DNA structures which are not accurate enough for studies of the relationships between the base sequence and DNA conformation.     

Exploring the impact of spatial patterns on restoration efforts: promoting self-facilitating feedback mechanisms with an innovative biodegradable seed mussel collector

Transplantations of organisms in aquatic ecosystems play an important role in ecological restoration and commercial practices. However, success rates of these transplantations, especially when ecosystem engineers are involved, are often low. To enhance transplantation success, the promotion of self-facilitation between transplants that mitigate environmental stressors is crucial. Besides, spatial patterns resulting from self-facilitation can enhance ecosystem resilience. Using blue mussels as a model organism, we explored the possibility of increasing transplantation success in a subtidal ecosystem. We used biodegradable structures (“BioShell-SMCs”) to ameliorate self-facilitating feedback mechanisms to overcome environmental stressors in the initial post-transplantation phase, and to increase transplantation success by implementing large-scale spatial configurations, mimicking natural mussel bed patterns. The structures are an innovation of traditional seed mussel collectors (SMCs) used in mussel cultivation. They consist of a biodegradable net based on a compound of aliphatic polyesters, filled with empty cockle shells around a coconut fiber rope. We tested whether different spatial configurations could increase transplantation success of mussel seed: low versus high density labyrinth pattern and banded pattern. The results of this experiment showed high losses (approximately 75%), with no significant variation between configurations. The lack of migration due to unexpected retention of the biodegradable net hindered the initiation of natural aggregations, resulting in increased competition among mussels. Besides, factors such as hydrodynamic dislodgement, burial and interannual variation likely contributed to the observed losses. While the BioShell-SMC has not demonstrated large-scale success, this research contributes to understanding the mechanisms that underlie successful transplantation strategies in aquatic ecosystems.     

Qualitative Risk Assessment of Surface Water Contamination with Cryptosporidium Sp. Oocysts: A Case Study of Three Agricultural Catchments

In recent years there have been a number of waterborne outbreaks of cryptosporidiosis in some major urban centers in Ireland. The Irish Environmental Protection Agency has adapted and modified the qualitative “Scottish Water Directions” to help prevent such outbreaks. When this risk assessment method was applied to three small agricultural river catchments in Ireland, the results suggested an equal risk of water contamination for each catchment. A survey was conducted in each catchment focusing on agricultural activity and surface waters. Fecal samples were collected from 1–8-week-old calves along with associated slurry and dung from beef and dairy farms and water samples were collected monthly at the outlet of the three catchments. Two of the catchments had much higher infection rates among neonatal calves as well as higher oocyst contamination of surface waters than the remaining one. It was concluded that the qualitative risk assessment could be more robust if cognizance was taken of the temporal and epidemiological aspects of cryptosporidiosis in beef and dairy herds.     

Robust Estimates of Divergence Times and Selection with a Poisson Random Field Model: A Case Study of Comparative Phylogeographic Data

Mutation frequencies can be modeled as a Poisson random field (PRF) to estimate speciation times and the degree of selection on newly arisen mutations. This approach provides a quantitative theory for comparing intraspecific polymorphism with interspecific divergence in the presence of selection and can be used to estimate population genetic parameters. Although the original PRF model has been extended to more general biological settings to make statistical inference about selection and divergence among model organisms, it has not been incorporated into phylogeographic studies that focus on estimating population genetic parameters for nonmodel organisms. Here, we modified a recently developed time-dependent PRF model to independently estimate genetic parameters from a nuclear and mitochondrial DNA data set of 22 sister pairs of birds that have diverged across a biogeographic barrier. We found that species that inhabit humid habitats had more recent divergence times and larger effective population sizes than those that inhabit drier habitats, and divergence time estimated from the PRF model were similar to estimates from a coalescent species-tree approach. Selection coefficients were higher in sister pairs that inhabited drier habitats than in those in humid habitats, but overall the mitochondrial DNA was under weak selection. Our study indicates that PRF models are useful for estimating various population genetic parameters and serve as a framework for incorporating estimates of selection into comparative phylogeographic studies.     

Correlation Between Thermal Aggregation and Stability of Lysozyme with Salts Described by Molar Surface Tension Increment: An Exceptional Propensity of Ammonium Salts as Aggregation Suppressor

Protein aggregation is a critical problem for biotechnology and pharmaceutical industries. Despite the fact that soluble proteins have been used for many applications, our understanding of the effect of the solution chemistry on protein aggregation still remains to be elucidated. This paper investigates the process of thermal aggregation of lysozyme in the presence of various types of salts. The simple law was found; the aggregation rate of lysozyme increased with increasing melting temperature of the protein (T _m) governed by chemical characteristics of additional salts. Ammonium salts were, however, ruled out; the aggregation rates of lysozyme in the presence of the ammonium salts were smaller than the ones estimated from T _m. Comparing with sodium salts, ammonium salts increased the solubility of the hydrophobic amino acids, indicating that ammonium salts adsorb the hydrophobic region of proteins, which leads to the decrease in aggregation more effectively than sodium salts. The positive relation between aggregation rate and T _m was described by another factor such as the surface tension of salt solutions. Fourier transform infrared spectral analysis showed that the thermal aggregates were likely to form β-sheet in solutions that give high molar surface tension increment. These results suggest that protein aggregation is attributed to the surface free energy of the solution.     

Achene Wall Anatomy and Surface Sculpturing of Lactuca L. and Related Genera （Compositae： Lactuceae） with Notes on Their Systematic Significance

The achene wail anatomy and surface sculpturing of 14 species representing Lactuca L. and related genera were Investigated to evaluate inter-and Intrageneric relationships. The achene wall anatomy of the studied species can be divided Into two types： winged and ribbed. The winged type is present in Lactuca L., Pterocypsela Shlh, Clcerblta Wallr., Chaetoserls Shlh and Stenoseris Shlh, and is characterized by protruding wings and costae in transverse section. Winged type achene mesocarps are composed of parenchymatous cells and fiber ceils, and the distinct fibrous strands are confined to the costae or wings of the achenes. The ribbed type is present in Notoseris Shih and Paraprenanthes Chang ex Shih, and Is characterized by only having costae In transverse section. Fiber cells are continuous in the costae and intercostae, in surface sculpturing, the ornamentation and the shape of epidermal cells are different among these genera. The results Indicate that L. altalca and L. serrlola should be conspeclfic, and that L. dollchophylla is probably an Intermediate taxon between Lactuca and Chaetoserls. The results also support the separation of Pterocypseia, Paraprenanthes, Notoseris, Chaetoseris and Stenoserls from Lactuca and Clcerblta as independent entitles. Close affinities between Pterocypsela and Lactuca, Paraprenanthes and Notoserls, and Chaetoserls and Stenoserls are also proposed.